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Scientific Publications by Torsten Nielsen

(this list last updated December 23, 2023)

This page lists my publications currently in print; articles in press, submitted and manuscripts-in-preparation are listed under . Due to copyright restrictions, abstracts are not presented (most are hyperlinked), but a short summary of each paper is included. Bigger font designates papers of special significance to my current projects and plans and/or to clinical practice. Citations and statistics are available on my Google Scholar page.

Nezha S. Benabdallah, Vineet Dalal, R. Wilder Scott, Fady Marcous, Afroditi Sotiriou, Felix K.F. Kommoss, Anastasija Pejkovska, Ludmila Gaspar, Lena Wagner, Francisco J. Sanchez-Rivera, Monica Ta, Shelby Thornton, Torsten O. Nielsen, T. Michael Underhill, Ana Banito. Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability. Nature Structural & Molecular Biology 2023 Nov; 30(11):1640-1652.

Working with our colleague Ana Banito's group at DKFZ Heidelberg and members of our NIH-funded FusONC2 team, we show that the SSX component of the synovial sarcoma fusion oncoprotein binds to chromatin sites that have been marked by Polycomb Repressor Complex 1.1 with the modified histone H2AK119Ub. This is a property of SSX, not requiring SS18, as rare non-SS18 partners (EWS, MN1) for SSX in synovial sarcoma still bind these genomic sites.

Torsten O Nielsen, Samuel CY Leung, Nazia Riaz, Anna M Mulligan, Zuzana Kos, Anita Bane, Timothy J Whelan. Ki67 assessment protocol as an integral biomarker for avoiding radiotherapy in the LUMINA breast cancer trial. Histopathology 2023 Dec; 83(6):903-11.

When clinical trials are published, they present the patient information and the statistical analyses in great detail, but commonly skim through the diagnostic test methodology. The abemaciclib controversy of 2022 was one such consequence -- clinical demand for a biomarker test, but pathologists left with inadequate information for how to deliver it. Anticipating this situation with the LUMINA trial, we proactively wrote up a detailed description of the specific methodology we used. This was published in open access format, available on-line just one week after the primary trial results were published in the New England Journal of Medicine!  field, the LUMINA trial.

Timothy J. Whelan, Sally Smith, Sameer Parpia, Anthony W. Fyles, Anita Bane, Fei-Fei Liu, Eileen Rakovitch, Lynn Chang, Christiaan Stevens, Julie Bowen, Sawyna Provencher, Valerie Théberge, Anne Marie Mulligan, Zuzana Kos, Mohamed A. Akra, K. David Voduc, Tarek Hijal, Ian S. Dayes, Gregory Pond, James R. Wright, Torsten O. Nielsen*, Mark N. Levine. Omitting Radiotherapy after Breast-Conserving Surgery in Luminal A Breast Cancer. New England Journal of Medicine 2023 Aug 17; 389:612-19. *co-senior author

This practice-changing clinical trial represents the culmination of a decade of work. We added Ki67 to existing criteria for low risk breast cancer (ER positive, small, node negative, not high grade, adequate surgery and endocrine therapy). For women with a Luminal A phenotype (Ki67 ≤ 13%), we broke with standard-of-care by omitting adjuvant radiotherapy. Recurrence rates were extremely low -- approximately equal to the rate of breast cancer in the untreated opposite breast -- meaning many women with breast cancer can be safely spared the costs and side effects of radiation.

Nazia Riaz, Tiffany Jean, Timothy J. Whelan, Torsten O. Nielsen. Evolving role of radiotherapy de-escalation in early invasive breast cancer. Cancers 2023 Feb 16;15(4):1260.

This is a timely review of a topic very active in 2023: the capacity to add molecular risk testing to clinical factors, to identify a group of women who will have a very low local recurrence rate if treated with surgery and endocrine therapy (only). Standard of care is to use adjuvant radiotherapy, but this is expensive, inconvenient and has both common short term side effects and a small risk of dangerous long term toxicities. We discuss the concept and the several active trials, presaging our own contribution to the field, the LUMINA trial.

Angela Goytain, Kenneth Tou En Chang, Jian Y. Goh, Torsten O. Nielsen, Tony L. Ng. Diagnosis of fusion associated sarcomas by exon expression imbalance and gene expression. Journal of Molecular Diagnostics 2023 Feb; 25:121-31.

The elegant, inexpensive and quick nanoString-based pansarcoma fusion assay we developed and implemented as our primary sarcoma molecular diagnostic tool doesn't actually cover everything. In particular, the fusion-specific probe strategy we used has trouble for diagnoses with a high variability in exon splice site location or multiple alternative partner genes. We solve this problem with the parallel approach described in this paper, relying on the relative expression of the 5'-most vs. the 3'-most exons in potential partner genes involved in sarcoma fusion oncogenes.

Karama Asleh, Ana Lluch, Angela Goytain, Carlos Barrios, Xue Q. Wang, Laura Torrecillas, Dongxia Gao, Manuel Ruiz Borrego, Samuel Leung, José Bines, Ángel Guerrero, Jose Ángel García Sáenz, Juan Miguel Cejalvo, Jesus Herranz, Roberto Torres, Juan de la Haba-Rodriguez, Henry Gómez, Federico Rojo, Torsten O. Nielsen, Miguel Martin. Triple negative PAM50 non-basal breast cancer subtype predicts benefit from extended adjuvant capecitabine. Clinical Cancer Research 2023 Jan 17; 29(2):389-400.

Karama and I spent many years trying to access materials from triple negative breast cancer trials that would allow us to assess preditors for capecitabine response. Working with the Spanish breast cancer clinical trials group (GEICAM), we were able to apply a custom nanoString-based gene expression panel to 658 tumor specimens, confirming that women with features of the enigmatic mesenchymal subtype (non-basal by PAM50, expressing high levels of a mast cell signature) are the ones gaining the most benefit from adjuvant capecitabine 

Karama Asleh, Nazia Riaz, Torsten O. Nielsen. Heterogeneity of triple negative breast cancer: Current advances in subtyping and treatment implications. Journal of Experimental and Clinical Cancer Research 2022 Sep 1; 41(1):265.

This tour-de-force review article, covering the state-of-the-science of the clinical entity of triple negative breast cancer, arose from combining (1) the presentation I was invited to give to the International Society of Breast Pathology at its 2022 meeting in Los Angeles, entitled "Breast cancer pathology now and in the future: research," with (2) the introductory chapter of Karama Asleh's PhD thesis. It covers a lot of ground, and is worth a read!

Elahe Shenasa, Elisabeth S. Stovgaard, Maj-Brit Jensen, Karama Asleh, Nazia Riaz, Doris Gao, Sam Leung, Bent Ejlertsen, Anne-Vibeke Laenkholm, Torsten O. Nielsen. Neither Tumor-Infiltrating Lymphocytes nor Cytotoxic T Cells Predict Enhanced Benefit from Chemotherapy in the DBCG77B Phase III Clinical Trial. Cancers 2022 Aug 5;14(15):3808.

The DBCG77B clinical trial was a classic study that randomized women with high risk early breast cancer to adjuvant cyclophophamide-based chemotherapy vs. no chemotherapy. This randomization allowed us to assess the predictive value of immune infiltrates for chemotherapy benefit. Despite sound reasons to postulate such a connection, results were negative -- pre-existing immune infiltrates, indicative of immunogenic breast tumors, do not portend improved benefits from cyclophosphamide-based chemotherapy.

Ainiah R. Raquib, Jakob Hofvander, Monica Ta, Torsten O. Nielsen. Expanding the use of an SS18-SSX antibody for molecular assays in synovial sarcoma. Applied Immunohistochemistry and Molecular Morphology 2022 Sep 1; 30(8):531-539.

In my student Ainiah Raquib's first paper, she demonstrates how a recently-available antibody that is specific to the most common fusion junctional epitope of the SS18-SSX oncoprotein can be used on tissue microarrays, in genetically engineered mouse models, for immunefluorescence, proximity ligation assay and chromatin immunoprecipitation.

Mitch Dowsett, Torsten Nielsen, David Rimm, Daniel F. Hayes. Ki67 as a companion diagnostic – good or bad news? Journal of Clinical Oncology 2022 Nov 20; 40(33):3796-3799.

Controversially, the cdk4/6 inhibitor abemaciclib was approved by the FDA for the adjuvant treatment of ER positive breast cancer only in cases where the Ki67 index was 20% or greater. However, Ki67 scoring has high interobserver variability and the visual estimates advocated by the sponsoring drug company are likely to lack analytical validity in clinical practice. We review the rationale behind this approval, highlight readily anticipated problems and suggest potential solutions.

Acs B, Leung SCY, Kidwell KM, Arun I, Augulis R, Badve SS, Bai Y, Bane AL, Bartlett JMS, Bayani J, Bigras G, Blank A, Buikema H, Chang MC, Dietz RL, Dodson A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hartman J, Kos Z, Lænkholm AV, Laurinavicius A, Levenson RM, Mahboubi-Ardakani R, Mastropasqua MG, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Quintayo MA, Rau TT, Reinhard S, Robertson S, Salgado R, Sugie T, van der Vegt B, Viale G, Zabaglo LA, Hayes DF, Dowsett M, Nielsen TO, Rimm DL; International Ki67 in Breast Cancer Working Group of the Breast International Group and North American Breast Cancer Group (BIG-NABCG). Systematically higher Ki67 scores on core biopsy samples compared to corresponding resection specimen in breast cancer: a multi-operator and multi-institutional study. Modern Pathology 2022 Oct;35(10):1362-1369.

The International Ki67 working group completed a large scale study comparing profileration index on core needle vs excision samples. Likely because of the much more consistent and rapid fixation of core needle samples, excisions seem to underestimate the real proliferative index as measured by Ki67 immunohistochemistry by a whopping 5%, and sample types are not interchangeable for assessment. Core biopsies are preferable.

Caitlyn Brashears, Bethany C. Prudner, Richa Rathore, Katharine E. Caldwell, Carina A. Dehner, Jane L. Buchanan, Sara E.S. Lange, Neal Poulin, Jennifer K. Sehn, Jason Roszik, Dirk Spitzer, Kevin B. Jones, Regis J. O'Keefe, Torsten O. Nielsen, Eric B. Taylor, Jason M. Held, William Hawkins, Brian A. Van Tine. Malic enzyme 1 absence in synovial sarcoma shifts antioxidant system dependence and increases sensitivity to ferroptosis induction with ACXT3102. Clinical Cancer Research 2022 Aug 15; 28(16):3573-3589.

In this work, I helped a colleague from Washington University St. Louis with specimens, models and validation work in his group's study of the particular metabolic dependencies in synovial sarcoma and how this creates therapeutic opportunities.

Karama Asleh, Gian L. Negri, Sandra E. Spencer Miko, Shane Colborne, Christopher S. Hughes, Xiu Q. Wang, Doris Gao, C. Blake Gilks, Stephen K.L. Chia, Torsten O. Nielsen, Gregg B. Morin. Proteomic analysis of breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes. Nature Communications 2022 Feb; 13:896.

In this product of several years of work in collaboration with Gregg Morin of BC Cancer, we apply two of his significant new technologies to breast cancer, for the first time. These are the SP3-CTP method for proteomic profiling on formalin-fixed, paraffin-embedded pathology specimens, and IsoDoping methodology that allows accurate quantification of rare but important peptides such as enzymes and transcription factors. Profiling over 300 samples, we are able to recapitulate key RNA classifications (intrinsic subtypes, triple negative subtypes) while identifying their key proteins that could be used as diagnostic biomarkers and therapeutic targets.  

Xue Qi Wang, Angela Goytain, Brendan Dickson, Torsten Owen Nielsen. Advances in sarcoma molecular diagnostics. Genes, Chromosomes and Cancer 2022 Jun; 61(6):332-345.

During the first year of the COVID crisis, when travel was shut down, I gave an all-virtual presentation entitled "Sarcoma molecular diagnostics: the new generation of techniques entering clinical practice" to an international Sarcoma Webinar Series hosted by The Institute for Cancer Research, London UK. This evolved into a review article updating the sarcoma field on how we have moved away from RT-PCR and FISH towards higher throughput techniques based on massive parallel sequencing and nanoString technologies.

Nazia Riaz, Samantha Burugu, Angela S. Cheng, Samuel C.Y Leung, Dongxia Gao, Torsten O Nielsen. Prognostic significance of CSF-1R expression in early invasive breast cancer. Cancers 2021; 13(22):5769   

Nazia Riaz is another trainee I am proud to have helped to the point of leading major breast cancer studies herself. Dr. Riaz is a breast cancer surgeon-scientist who the better part of two years on sabbatical with me (a time when COVID was ravaging the globe and slowing scientific progress). Nazia was very productive on several fronts, including handling the data analysis and writeup of this large study of the expression of a macrophage-associated biomarker in breast cancer that can be targeted by new therapies.

Kristina-Ana Klaric, Nazia Riaz, Karama Asleh, Xiu Qing Wang, Tadros Atalla, Sarah Strickland, Torsten O Nielsen, Zuzana Kos. SOX10 is a highly specific biomarker of basal-like breast cancer. Histopathology 2022 Feb; 80(3):589-97   

My former postdoc / resident trainee Zuzana Kos had quite a bit of success in my lab back in 2013. She went on to a breast cancer fellowship in Toronto, and then a staff pathology position in Ottawa, before eventually working her way back to Vancouver as a breast cancer subspecialist at BC Cancer. This work represents her first stab as a senior author directing trainees of her own, from Ottawa and Vancouver, and shows the value of a biomarker already used for melanoma and sarcoma diagnosis as a breast cancer subtype marker.

Karama Asleh, Dongsheng Tu, Dongxia Gao, Vivien Bramwell, Mark N. Levine, Kathleen I. Pritchard, Lois E. Shepherd, Torsten O Nielsen. Predictive significance of an optimized immunohistochemical panel for basal-like breast cancer: Results from the Canadian Cancer Trials Group CCTG MA.5 and CCTG MA.12 phase III clinical trials. Clinical Cancer Research 2021 Dec; 27: 6570-6579   

This study took quite a while to complete, as it represents a formal prospective-retrospective analysis of two separate Canadian breast cancer clinical trials and the product of a decade of developmental biomarker work that was started by former PhD student Jennifer Won and carried forward by subsequent graduate student Karama Asleh . The goal here was to see the extent to which the simplified basal breast cancer detection panel, using INPP4B and nestin (but agnostic to ER, PR or HER2), is predictive for breast cancer treatment. We find that indeed basal cases so identified do better on CMF than CEF chemotherapy, and do not benefit from tamoxifen.

Karama Asleh, Nazia Riaz, Angela S Cheng, Dongxia Gao, Samuel CY Leung, Meenakshi Anurag, Torsten O Nielsen. Proteomics-derived basal biomarker DNA-PKcs is associated with intrinsic subtype and long-term clinical outcomes in breast cancer. npj Breast Cancer 2021 Sep 9;7(1):114   

Our ongoing quest to characterize and find the best biomarkers for the basal-like subtype of breast cancer, in this case built on recent public data from an international breast cancer proteomics consortium. We took advantage of our access to large, independent series of breast cancers tied to outcome to implicate a DNA repair protein in the biology of basal like cases, anticancer immune responses and poor outcomes, with implications for treatment of this aggressive kind of breast cancer that tends to affect younger women.

Elisabeth S Stovgaard, Karama Asleh, Nazia Riaz, Samuel Leung, Dongxia Gao, Lise B Nielsen, Anne-Vibeke Lænkholm, Eva Balslev, Mai-Britt R Jensen, Dorte Nielsen, Torsten O Nielsen. The immune microenvironment and relation to clinical outcomes in advanced breast cancer patients treated with docetaxel with or without gemcitabine. OncoImmunology 2021 May 11;10(1):1924492   

In this formal prospective-retrospective clinical trial analysis run in collaboration with the Danish Breast Cancer Group, we find that low levels of the T-regulatory lymphocyte biomarker FOXP3 predicts benefit from adding gemcitabine to docetaxel chemotherapy in metastatic breast cancer, albeit only in the hormone receptor-negative subtypes. Elisabeth Stovgaard was supposed to come to Vancouver to do this work as an external rotation for her PhD, but COVID-19 put paid to that plan, unfortunately. But, we worked out the full collaboration over Zoom!

Alvin Qiu, Torsten O. Nielsen. Synovial sarcoma oncogenesis revealed by single cell profiling. Trends in Cancer 2021; 7(6):482-3.  

We were solicited to write a review of a major new paper that described the first extensive published effort to profile gene expression in synovial sarcoma at the single cell level -- and to set those results into the wider context of the field. We describe how researchers at the Broad Institute in Boston identify a core oncogenic program driven by the SS18-SSX oncoprotein, and its implications for biology and treatment.

Shawn C Chafe, Nazia Riaz, Samantha Burugu, Dongxia Gao, Samuel Leung, Anna Lee, Cheng Han Lee, Shoukat Dedhar, Torsten O Nielsen. G-CSF expression in breast cancer and its association with carbonic anhydrase IX and immune checkpoints. Cancers 2021; 13(5):1022

A colleague from BC Cancer, Dr. Shoki Dedhar, initiated this project; he is a world expert in the molecular oncology of hypoxia, cell-cell interactions and cell motility. We provided a large clinical dataset to validate some of the molecular biology he has worked on, and ended up tracking the innate immune biomarkers G-CSF and CD163 and their relation to the tissue hypoxia marker CAIX. Results continue to point to the existence of a good prognosis variant of ER negative breast cancers that is at least partially recognized by multiple players in the host immune system.

Mei-Yin C. Polley, Roberto A. Leon-Ferre, Samuel Leung, Angela Cheng, Dongxia Gao, Jason Sinnwell, Heshan Liu, David W. Hillman, Abraham Eyman-Casey, Judith A. Gilbert, Vivian Negron, Judy C. Boughey, Minetta C. Liu, James N. Ingle, Krishna Kalari, Fergus Couch, Jodi M. Carter, Daniel W. Visscher, Torsten O. Nielsen, Matthew P. Goetz. A clinical calculator to predict disease outcomes in women with triple-negative breast cancer. Breast Cancer Research and Treatment 2021 Feb;185(3):557-566.

While nomograms exist to stratify risk in ER positive breast cancers, tools for triple negative and basal breast cancers are not as well defined. Here we supported colleagues from the Mayo Clinic to validate a tool they developed, using our large British Columbia breast cancer biomarker and clinical database. Doing so required extensive chart reviews so as to be able to add the Neutrophil-to-Lymphocyte Ratio parameter required. This is part of a body of work to identify a group of women with surprisingly low risk disease, who may not need the standard, aggressive treatment for this type of breast cancer.

Torsten O. Nielsen, Samuel C.Y. Leung , David L. Rimm, Andrew Dodson, Balazs Acs, Sunil Badve, Carsten Denkert, Matthew J. Ellis, Susan Fineberg, Margaret Flowers, Hans H. Kreipe, Anne-Vibeke Laenkholm, Hongchao Pan, Frédérique M. Penault-Llorca, Mei-Yin Polley, Roberto Salgado, Ian E. Smith, Tomoharu Sugie, John M.S. Bartlett, Lisa M. McShane, Mitch Dowsett, Daniel F. Hayes. Assessment of Ki67 in Breast Cancer: Updated Recommendations from the International Ki67 in Breast Cancer Working Group. JNCI Journal of the National Cancer Institute 2021; 113(7):808-819. Published correpondance and reply also appears in JNCI.

This "white paper" represents the culmination of 10 years of work by our international group, summarizing our work and our recommendations for the standardization of Ki67 assessment by immunohistochemistry in breast cancer: methodology and clinical applications. Following our group's meeting at The Princeton Club in New York, I took the lead role in organizing our writeup, which is fully open access. Our hope is that this inexpensive, widely available biomarker can help guide optimal breast cancer therapy worldwide!

Jenny Wang, Amy Wang, Anika Hsu, Angela Goytain, Tony L Ng, Torsten O Nielsen. A rapid and cost-effective gene expression assay for the diagnosis of well differentiated and dedifferentiated liposarcomas. Journal of Molecular Diagnostics 2021 Mar;23(3):274-284.

After developing and securing diagnostic accreditation for our pan-sarcoma fusion assay, the main leftover diagnostic need for FISH technology in sarcomas was MDM2 12q amplicon testing, needed for accurate classification of liposarcomas. Here we find a nanoString-based solution, by testing for coordinate overexpression of 20 genes (18 from the 12q13-15 amplicon region), providing an accurate, rapid and inexpensive means for distinguishing lipoma from liposarcoma, and dedifferentiated liposarcoma from undifferentiated pleomorpic sarcoma even on core needle biopsies where the microscope is insufficient to tell apart these tumors, all of which require different management. This article was the subject of a press release!

Mayanne Zhu, Elahe Shenasa, Torsten Nielsen. Sarcomas: immune biomarker expression and checkpoint inhibitor trials. Cancer Treatment Reviews 2020 Dec; 91:102115

During the COVID-19 lockdown first phase, laboratories were shut down. It was a good time to stop and reflect on the state-of-the-science in one's field ... and write review articles! Working as I do on sarcomas and on immuno-oncology biomarkers, and noting the rapid changes in the field and lack of timely reviews, my trainees and I put together this timely synthesis of which sarcoma types show evidence of immunogenicity and what the status is of clinical trials (early signals being seen in alveolar soft part sarcoma, angiosarcoma, dedifferentiated liposarcoma and undifferentiated pleomorphic sarcomas).

Roberto Salgado, Andrew M. Bellizzi, David Rimm, John M.S. Bartlett, Torsten Nielsen, Moch Holger, Anne-Vibeke Laenkholm, Cecily Quinn, Gabor Cserni, Isabela Werneck Cuna, Isabel Alvarado-Cabrero, Ian Cree. How current assay-approval policies are leading to unintended imprecision medicine. Lancet Oncology 2020; 21(11):1399-1401.

Many new anticancer drugs are being produced, targeted to specific genetic changes under the rubric of "precision medicine." These drugs are only effective in molecularly-defined subsets of cancers, and typically are being approved in conjuction with a companion diagnostic test. However, while the drugs themselves are subjected to rigorous data standards in terms of required supporting evidence from clinical trials, companion diagnostics are not being held to anything remotely close to the same level of scrutiny. We describe why and how this needs to change.

Nacev BA, Jones KB, Intlekofer AM, Yu JSE, Allis CD, Tap WD, Ladanyi M, Nielsen TO. The epigenomics of sarcoma. Nature Reviews Cancer 2020 Oct; 20(10):608-623

Together with colleagues from the Memorial Sloan-Kettering Cancer Center in New York, and the Huntsman Cancer Institute in Utah, I review how sarcoma biology is linked to changes in chromatin structure at several levels. These include modifications to DNA methylation, mutations in histones or in the enzymes that modify histone proteins, nucleosome positioning and three-dimensional chromatin structure. We also discuss how new generations of drugs might be able to target these alterations.

Svetlana Bortnik, Basile Tessier-Cloutier, Samuel Leung, Jing Xu, Karama Asleh, Samantha Burugu, Jamie McGrill, Kendall Greening, Fatemeh Derakhshan, Stephen Yip, Tony Ng, Karen Gelmon, Torsten O. Nielsen, Sharon M. Gorski. Differential expression and prognostic relevance of autophagy-related markers ATG4B, GABARAP and LC3B in breast cancer. Breast Cancer Research and Treatment 2020 Oct; 183(3):525-47.

Autophagy is a biological process whereby a cell breaks parts of itself down, a way in which cancer cells can gain energy to survive. Proteins controlling these pathways are potential targets for emerging anticancer therapies, and this study documents how three such autophagy regulators are expressed in breast cancer subtypes, and what this means for patient survival.

Cuige Zhu, Anna Rogers, Karama Asleh, Jennifer Won, Dongxia Gao, Samuel Leung, Shan Li, Kiran R. Vij, Jian Zhu, Jason M. Held, Zhongsheng You, Torsten O. Nielsen, Jieya Shao. Ser784 phosphorylation of VCP is a critical event for DNA damage response and is associated with survival among chemotherapy-treated breast cancer patients. Cell Reports 2020 Jun 9; 31(10): 107745.

The DNA damage response directs, for example, how many conventional chemotherapy agents affect cell fate. In this Open Access paper, we helped a US-based discoverer of one such pathway demonstrate how one such pathway may relate to resistance to chemotherapy.

Hudeček J, Voorwerk L, van Seijen M, Nederlof I, de Maaker M, van den Berg J, van de Vijver KK, Sikorska K, Adams S, Demaria S, Viale G, Nielsen TO, Badve SS, Michiels S, Symmans WF, Sotiriou C, Rimm DL, Hewitt SM, Denkert C, Loibl S, Loi S, Bartlett JMS, Pruneri G, Dillon DA, Cheang MCU, Tutt A, Hall JA, Kos Z, Salgado R, Kok M, Horlings HM; International Immuno-Oncology Biomarker Working Group. Application of a risk-management framework for integration of stromal tumor infiltrating lymphocytes in clinical trials. npj Breast Cancer 2020 May 12; 6:15.

I have a longstanding interest in how to bring scientific measurement of novel biomarkers into clinical trials. This Open Access publication describes how best to do so, in the case of a very test of whether a cancer is likely being recognized by the immune system (and hence direct what types of immunotherapy therapy might best be matched to which biopsied tumors).

Kos Z, Roblin E, Kim RS, Michiels S, Gallas BD, Chen W, van de Vijver KK, Goel S, Adams S, Demaria S, Viale G, Nielsen TO, Badve SS, Symmans WF, Sotiriou C, Rimm DL, Hewitt S, Denkert C, Loibl S, Luen SJ, Bartlett JMS, Savas P, Pruneri G, Dillon DA, Cheang MCU, Tutt A, Hall JA, Kok M, Horlings HM, Madabhushi A, van der Laak J, Ciompi F, Laenkholm AV, Bellolio E, Gruosso T, Fox SB, Araya JC, Floris G, Hudeček J, Voorwerk L, Beck AH, Kerner J, Larsimont D, Declercq S, Van den Eynden G, Pusztai L, Ehinger A, Yang W, AbdulJabbar K, Yuan Y, Singh R, Hiley C, Bakir MA, Lazar AJ, Naber S, Wienert S, Castillo M, Curigliano G, Dieci MV, André F, Swanton C, Reis-Filho J, Sparano J, Balslev E, Chen IC, Stovgaard EIS, Pogue-Geile K, Blenman KRM, Penault-Llorca F, Schnitt S, Lakhani SR, Vincent-Salomon A, Rojo F, Braybrooke JP, Hanna MG, Soler-Monsó MT, Bethmann D, Castaneda CA, Willard-Gallo K, Sharma A, Lien HC, Fineberg S, Thagaard J, Comerma L, Gonzalez-Ericsson P, Brogi E, Loi S, Saltz J, Klaushen F, Cooper L, Amgad M, Moore DA, Salgado R; International Immuno-Oncology Biomarker Working Group. Pitfalls in assessing stromal tumour infiltrating lymphocytes (sTILs) in breast cancer. npj Breast Cancer 2020 May 12;6:17.

My former trainee, Zuzana Kos, is now at BC Cancer, and took the lead on behalf of our international group in this Open Access article that serves to help pathologists successfully interpret the degree of immune response evident in standard breast cancer biopsy and sugical specimens.

Amgad M, Stovgaard ES, Balslev E, Thagaard J, Chen W, Dudgeon S, Sharma A, Kerner JK, Denkert C, Yuan Y, AbdulJabbar K, Wienert S, Savas P, Voorwerk L, Beck AH, Madabhushi A, Hartman J, Sebastian MM, Horlings HM, Hudeček J, Ciompi F, Moore DA, Singh R, Roblin E, Balancin ML, Mathieu MC, Lennerz JK, Kirtani P, Chen IC, Braybrooke JP, Pruneri G, Demaria S, Adams S, Schnitt SJ, Lakhani SR, Rojo F, Comerma L, Badve SS, Khojasteh M, Symmans WF, Sotiriou C, Gonzalez-Ericsson P, Pogue-Geile KL, Kim RS, Rimm DL, Viale G, Hewitt SM, Bartlett JMS, Penault-Llorca F, Goel S, Lien HC, Loibl S, Kos Z, Loi S, Hanna MG, Michiels S, Kok M, Nielsen TO, Lazar AJ, Bago-Horvath Z, Kooreman LFS, van der Laak JAWM, Saltz J, Gallas BD, Kurkure U, Barnes M, Salgado R, Cooper LAD; International Immuno-Oncology Biomarker Working Group. Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. npj Breast Cancer 2020 May 12;6:16.

Despite the apparent clinical value of counting stromal tumor-infiltrating lymphocytes, and the validated methods for visual scoring we have previously presented, this work is tedious and time-consuming. Better might be to using digital image capture and analysis software, although that in itself would require standardization. Many groups are working in this area, and we present some key concepts.

Tomo Osako, Hakwoo Lee, Gulisa Turashvili, Derek Chiu, Steven McKinney, Stacey E. Joosten, Darcy Wilkinson, Torsten O. Nielsen, Wilbert Zwart, Joanne T. Emerman, Connie J. Eaves, Carlos Caldas, Samuel Aparicio. Age-correlated protein and transcript expression in breast cancer and normal breast tissues is dominated by endocrine effects. Nature Cancer 1pages 518532 (2020).

This Open Access article in a new Nature journal does an in-depth analysis of how many important gene transcripts vary with patient age across breast cancers, drawing on over 5000 cases. Perhaps surprisingly, this is my first coauthorship with Connie Eaves, one of Canada’s great cancer researchers and with whose larger lab group I originally worked as a summer student back in 1990, giving me my start in cancer molecular biology!

Mayanne MT Zhu, Samantha Burugu, Dongxia Gao, Jamie Yu, Samuel Leung, Basil A Horst, Torsten O Nielsen. Evaluation of glucocorticoid-induced TNF receptor (GITR) expression in breast cancer and across multiple tumor types. Modern Pathology 2020 Sep;33(9):1753-63.

A very bright medical student on a summer elective with me took over and executed a world-first study of this potential immunotherapy target in breast cancer. Drawing on our large collection of other tissue microarrays, we go on to describe its expression in many other cancer types, both on tumor infiltrating lymphocytes but also in some cases by the malignant cells themselves.

Amanda R. Dancsok, Dongxia Gao, Anna F. Lee, Sonja Eriksson Steigen, Jean-Yves Blay, David M. Thomas, Robert G. Maki, Torsten O. Nielsen* & Elizabeth G. Demicco. Tumor-associated macrophages and macrophage-related immune checkpoint expression in sarcomas. OncoImmunology 2020 9:1, 1747340. *Corresponding author.

As part of Amanda's thesis, and working with the "Immunosarc" consortium funded by the Liddy Shriver Sarcoma Initiative, we surveyed 1242 sarcoma specimens for the expression of macrophage-associated biomarkers in a first-of-its-kind study. Macrophage infiltrates were much more common and sizeable than lymphocytes, and may represent a better therapeutic target for some sarcoma subtypes such as chordoma, angiosarcoma and pleomorphic liposarcoma.

Anne-Vibeke Lænkholm, Maj-Britt Jensen, Jens Ole Eriksen, Anne Roslind, Wesley Buckingham, Sean Ferree, Torsten Nielsen and Bent Ejlertsen. Population-based study of Prosigna-PAM50 and outcome among postmenopausal women with estrogen receptor positive and HER2-negative operable invasive lobular and ductal breast cancer. Clinical Breast Cancer 2020 Aug; 20(4):e423-e432.

In our largest study of lobular breast cancers (N=341), we find they are twice as likely as conventional ductal carcinomas to come out as low risk by Prosigna ROR score. However, outcomes for lobulars are somewhat worse than ductal, even when in same ROR category.

Maj-Britt Jensen, Anne-Vibeke Lænkholm, Eva Balslev, Wesley Buckingham, Sean Ferree, Vesna Glavicic, Jeanette Dupont Jensen, Ann Søegaard Knoop, Henning T. Mouridsen, Dorte Nielsen, Torsten O. Nielsen, and Bent Ejlertsen. The Prosigna 50-gene profile and responsiveness to adjuvant anthracycline-based chemotherapy in high-risk breast cancer patients. npj Breast Cancer 2020 Feb 26; 6:7.

This is a formal prospective-retrospective analysis of the DBCG89D clinical trial, which randomized women with breast cancer to conventional (at the time) CMF adjuvant chemotherapy, versus anthracycline-containing CEF chemotherapy. This was a positive study that helped make anthracyclines standard-of-care, although they confer major toxicities. Here, we apply the Prosigna assay to samples from this trial, and find that it is the HER2E subtype that predicts benefit from anthracyclines, whereas the more common Luminal subtypes gain no significant extra benefit.

Gonzalez-Ericsson PI, Stovgaard ES, Sua LF, Reisenbichler E, Kos Z, Carter JM, Michiels S, Le Quesne J, Nielsen TO, Laenkholm AV, Fox SB, Adam J, Bartlett JM, Rimm DL, Quinn C, Peeters D, Dieci MV, Vincent-Salomon A, Cree I, Hida AI, Balko JM, Haynes HR, Frahm I, Acosta-Haab G, Balancin M, Bellolio E, Yang W, Kirtani P, Sugie T, Ehinger A, Castaneda CA, Kok M, McArthur H, Siziopikou K, Badve S, Fineberg S, Gown A, Viale G, Schnitt SJ, Pruneri G, Penault-Llorca F, Hewitt S, Thompson EA, Allison KH, Symmans WF, Bellizzi AM, Brogi E, Moore DA, Larsimont D, Dillon DA, Lazar A, Lien H, Goetz MP, Broeckx G, El Bairi K, Harbeck N, Cimino-Mathews A, Sotiriou C, Adams S, Liu SW, Loibl S, Chen IC, Lakhani SR, Juco JW, Denkert C, Blackley EF, Demaria S, Leon-Ferre R, Gluz O, Zardavas D, Emancipator K, Ely S, Loi S, Salgado R, Sanders M; International Immuno-Oncology Biomarker Working Group. The path to a better biomarker: application of a risk management framework for the implementation of PD-L1 and TILs as immuno-oncology biomarkers into breast cancer clinical trials and daily practice. Journal of Pathology 2020 Apr; 250(5):667-684.

I am part of a large international breast cancer consortium that promulgates guidelines for biomarker dvelopment, specifically in immuno-oncology. This review article covers research guidelines for the development of Programmed Death-Ligand 1 immunohistochemistry and Tumor Infiltrating Lymphocyte counts as biomarkers.

Karama Asleh, Heather-Anne Brauer, Amy Sulivan, L. Susanna Lauttia, Henrik Lindman, Torsten O. Nielsen, Heikki Joensuu, E. Aubrey Thompson, Saranya Chumsri. Predictive gene expression biomarkers for adjuvant capecitabine benefit in early triple negative breast cancer in the FinXX clinical trial. Clinical Cancer Research 2020 Jun 1; 26(11):2603-2614.

A multinational collaborative group, including UBC, nanoString Technologies, Mayo Clinic (Florida), and the Finnish Breast Cancer group came together for this exploratory analysis applying the new Breast 360 and IO 360 gene expression panels to a trial assessing the benefit of capecitabine chemotherapy in breast cancer. We find that several distinct immune signatures predict which women benefit the most from this aggressive form of cancer systemic treatment.

Meenakshi Anurag, Mayanne Zhu, Chen Huang, Suhas Vasaikar, J Wang, J Hoog, Samantha Burugu, Doris Gao, V Suman, Xiang H Zhang, Bing Zhang, Torsten Nielsen, Matthew J Ellis. Immune checkpoint profiles in luminal B breast cancer (Alliance). JNCI: Journal of the National Cancer Institute 2020 Jul 1; 112(7):737-46.

Endocrine-resistant Luminal B-type breast cancers are a major clinical problem. While in general, luminal breast cancers are not immunogenic, we were able to collaborate with US colleagues (as part of the Alliance clinical trials group) to validate their finding that these cancers often express checkpoints that can be targeted by new classes of immunotherapy drugs. This work highlights the ongoing value of our PAM50 signature, tissue microarray biomarker development program, and network of clinical trial group collaborators ... and earned authorships in a top journal for a summer student and a PhD student from my lab.

Angela S Cheng, Samuel CY Leung, Dongxia Gao, Samantha Burugu, Meenakshi Anurag, Matthew J Ellis, Torsten O Nielsen. Mismatch protein loss in breast cancer: clinicopathological associations in a large British Columbia cohort. Breast Cancer Research and Treatment 2020; 179:3-10

In an exciting development, the FDA approved the checkpoint inhibitor drug pembrolizumab for any cancer, from any site, that is deficient in mismatch repair pathways (and hence produces tumors with high levels of mutant neoantigens). This was the first "tissue-agnostic" cancer drug approval -- part of the paradigm shift underway in cancer diagnostics, from the morphologic to the molecular. However, while MMR deficiency is well characterized in colorectal and endometrial carcinomas, comparatively little was known about breast cancer. Using immunohistochemistry, we place the rate of MMR deficiency in breast cancer at 1.9%, in line with smaller / more expensive genomic sequencing analyses that have been reported by others.

Julie Ho, Thomas Peters, Brendan C Dickson, David Swanson, Anita Fernandez, Aurelie Frova-Seguin, Marie-Anne Valentin, Ursula Schramm, Marc Sultan, Torsten O. Nielsen*, Elizabeth G Demicco. Detection of CSF1 rearrangements deleting the 3'UTR in Tenosynovial Giant Cell Tumors. Genes Chromosomes & Cancer 2020 Feb; 59(2):96-105 *Designated as co-senior author

Some of my earlier studies, collaborating with Rob West and Matt van de Rijn at Stanford, led to the identification of CSF1 gene translocations (linking to a highly active collagen promoter) as a driving event behind tenosynovial giant cell tumors. Excitingly, this led others to develop new treatments for this disease that destroys joints in young people. Here, in collaboration with colleagues at the University of Toronto and at Novartis (who are running a trial of a novel antibody-based drug for tenosynovial giant cell tumor), we identify a different mutational mechanism (deletion of the negative regulator sequence in the tail of the gene) that leads to the same biology and should still be susceptible to CSF1 inhibitor drugs.

Amanda R. Dancsok, Nokitaka Setsu, Dongxia Gao, Jean-Yves Blay, David Thomas, Robert G. Maki, Torsten O. Nielsen*, Elizabeth G. Demicco. Expression of immune checkpoint biomarkers in bone and soft-tissue sarcomas: lymphocyte immunoregulatory checkpoints TIM-3 and LAG-3 are more prevalent than PD-(L)1. Modern Pathology 2019 Dec; 32(12):1772-1785. *Corresponding author

Our ImmunoSarc consortium published this survey of over a thousand sarcomas, defining which subtypes are most infiltrated by lymphocytes from the immune system, and which biomarkers are present that might guide future immuno-therapy approaches with checkpoint inhibitor drugs for this group of cancers. This became a results chapter in my MD/PhD student Amanda Dancsok's thesis

Jamie SE Yu, Shane Colborne, Christopher S Hughes, Gregg B. Morin, Torsten O Nielsen. The FUS-DDIT3 interactome in myxoid liposarcoma. Neoplasia 2019; 21:740-751.

In our lab's first serious foray into proteomics, a technology that identifies and quantifies all the proteins in a cancer sample using mass spectrometry, we provide the world's first delineation of the proteins that interact with the mutant fusion oncoprotein that drives myxoid liposarcoma. The article is open access, available to researchers around the world!

Leung SCY, Nielsen TO, Zabaglo LA, Arun I, Badve SS, Bane AL, Bartlett JMS, Borgquist S, Chang MC, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hugh JC, Kos Z, Laenkholm AV, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Sugie T, van der Vegt B, Viale G, Hayes DF, McShane LM, Dowsett M; International Ki67 in Breast Cancer Working Group of the Breast International Group North American Breast Cancer Group (BIG-NABCG). Analytical validation of a standardized scoring protocol for Ki67 immunohistochemistry on breast cancer excision whole sections: an international multicenter collaboration. Histopathology 2019 Aug;75(2):225-235.

This phase of our international project to standardize interpretation of the Ki67 cell proliferation marker, important in breast cancer, demonstrates how our carefully developed, analytically-valid visual scoring approach previously shown to work on tissue microarrays and core biopsies can in fact also be applied onto whole sections from breast cancer surgical excision specimens.

Nikita Patel, Juehong Wang, Kumiko Shiozawa, Kevin B. Jones, Yanfeng Zhang, Jeremy W. Prokop, George G. Davenport, Naoe T. Nihira, Zhenyue Hao, Derek Wong, Laurel Brandsmeier, Sarah K. Meadows, Arthur V. Sampaio, Ryan Vander Werff, Makoto Endo, Mario R. Capecchi, Kelly M. McNagny, Tak W. Mak, Torsten O. Nielsen, T. Michael Underhill, Richard M. Myers, Tadashi Kondo, Le Su. HDAC2 regulates site-specific acetylation of MDM2 and its ubiquitination signaling in tumor suppression. iScience 2019; 13:43-54.

At long last, my former PhD student Le Su published work based on the last chapter of his thesis, wherein he describes a novel way by which levels of the SS18-SSX oncoprotein in synovial sarcoma are regulated. MULE is an MDM2-regulated E3-ubiquitin ligase which tags the oncoprotein for destruction, a pathway that can be activated by HDAC inhibitor drugs. Open access.

Mengtian Zhu, Amanda R. Dancsok, Torsten O. Nielsen. Indoleamine Dioxygenase Inhibitors: Clinical Rationale & Current Development. Current Oncology Reports 2019; 21: 2-14.

This is a review article we were solicited to write, concerning a set of new immuno-oncology therapies with a mechanism of action distinct from other agents. We cover some of the biology and much of the trial landscape of this emerging class of drugs that can, via metabolic changes, enhance anticancer immune responses.

Karama Asleh, Stina Lyck Carstensen, Charlotte Levin Tykjær Jørgensen, Samantha Burugu, Dongxia Gao, Jennifer R. Won, Maj-Britt Jensen, Eva Balslev, Anne-Vibeke Lænkholm, Dorte L. Nielsen, Bent Ejlertsen, Torsten O. Nielsen. Basal biomarkers Nestin and INPP4B predict gemcitabine benefit in metastatic breast cancer samples from the phase III SBG0102 clinical trial. International Journal of Cancer 2019; 144(10):2578-86.

As my student Jennifer Won showed, the aggressive basal subtype of breast cancer can be identified using two IHC biomarkers (nestin and INPP4B), regardless of ER, PR or HER2 status. As my Danish PhD exchange student Charlotte Jorgensen showed, basal subtype (by PAM50) predicts gemcitabine benefit in metastatic breast cancer. My student Karama Asleh then took the logical step of testing if the inexpensive two marker IHC panel for basal breast cancer could be predictive on its own for gemcitabine benefit, and the answer was yes.

Samantha Burugu, Dongxia Gao, Samuel Leung, Stephen K. Chia, Torsten O. Nielsen. TIM-3 expression in breast cancer. OncoImmunology 2018 Aug 23;7(11):e1502128

Similar to our study of LAG-3, here we assess the expression of the target of an emerging class of new checkpoint inhibitor drugs in a large series of breast cancers, and provide a rationale for combination therapy approaches. Open access.

Balazs Acs, Vasiliki Pelekanou, Yalai Bai, Sandra Martinez-Morilla, Maria Toki, Samuel C. Y. Leung, Torsten O. Nielsen, David L. Rimm. Ki67 Reproducibility using Digital Image Analysis: An Inter-platform and Inter-Operator Study. Laboratory Investigation 2019 Jan;99(1):107-117.

Having seen promising results with initial, non-standardized automated image analysis platforms applied to breast cancer, we tested new "deep learning" / artificial intelligence platforms, including the open access QuPath software system. Results were spectacular in terms of inter-platform analytical reproducibility, and furthermore correlated with patient prognosis, suggesting even early iterations of this techology have both analytical and clinical validity.

Obi L Griffith, Nicholas C Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Luo, Dongsheng Tu, Belinda Yeo, Jason Kunisaki, Christopher A Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J Ainscough, Zachary L Skidmore, Katie Campbell, Runjun Kumar, Catrina Fronick, Lisa Cook, Jacqueline E Snider, Sherri Davies, Shayam M Kavuri, Eric C Chang, Vincent Magrini, David E Larson, Robert S Fulton, Shuzhen Liu, Samuel Leung, David Voduc, Ron Bose, Mitch Dowsett, Richard K Wilson, Torsten O Nielsen, Elaine R Mardis, Matthew J Ellis. The prognostic effects of somatic mutations in pre versus postmenopausal ER-positive breast cancer. Nature Communications 2018 9(1):3476.

This open access study presents panel sequencing results from 83 cancer genes across nearly 1000 breast cancer specimens I sourced from BC Cancer and from the Canadian Cancer Trials Group. In addition to validating the common TP53 and PIK3CA mutation frequency, we provide a great deal of public data about the long tail of uncommon mutations (such as NF1 and DDR1) that characterize luminal breast cancer, with enough cases to assess their prognostic implications.

David L. Rimm, Samuel C.Y. Leung, Lisa M. McShane, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Martin C. Chang, Michelle Dean, Carsten Denkert, Emeka Enwere, Chad Galderisi, Abhi Gholap, Judith C. Hugh, Anagha Jadhav, Elizabeth Kornaga, Arvydas Laurinavicius, Richard Levenson, Joema Lima, Keith Miller, Liron Pantanowitz, Tammy Piper, Jason Ruan, Malini Srinivasan, Shakeel Virk, Ying Wu, Hau Yang, Daniel F. Hayes, Torsten O. Nielsen and Mitch Dowsett. An international multicenter study to evaluate reproducibility of automated scoring methods for assessment of Ki67 in breast cancer. Modern Pathology 2019 Jan;32(1):59-69.

Our international Ki67 team has been systematically and diligently working to standardize pathologists' visual assessment of Ki67, with some success. Automated imaging, however, seems to be much more consistent right off the bat, even without standardization. Here we show that, with minimal other instructions, different platforms and software yield surprisingly consistent Ki67 scores when applied to the same series of breast cancers.

Maj-Britt Jensen, Anne-Vibeke Lænkholm, Torsten O. Nielsen, Jens Ole Eriksen, Wesley Buckingham, Sean Ferree, Bent Ejlertsen. The Prosigna gene expression assay and responsiveness to adjuvant cyclophosphamide-based chemotherapy in premenopausal high-risk breast cancer patients. Breast Cancer Research 2018 July 27;20(1):79.

This study applies the NanoString PAM50 (Prosigna) assay onto the DBCG77B clinical trial which randomized women to cyclophosphamide-based adjuvant chemotherapy, or no chemotherapy. We show that our validated gene expression assay is actually predictive for chemotherapy benefit. Specifically, basal and Luminal B patients are the ones who benefit most from conventional cytotoxic adjuvant chemotherapy, whereas significant benefits were not seen in the other two major subtypes.

Klauschen F, Müller KR, Binder A, Bockmayr M, Hägele M, Seegerer P, Wienert S, Pruneri G, de Maria S, Badve S, Michiels S, Nielsen TO, Adams S, Savas P, Symmans F, Willis S, Gruosso T, Park M, Haibe-Kains B, Gallas B, Thompson AM, Cree I, Sotiriou C, Solinas C, Preusser M, Hewitt SM, Rimm D, Viale G, Loi S, Loibl S, Salgado R, Denkert C; International Immuno-Oncology Biomarker Working Group. Scoring of tumor-infiltrating lymphocytes: From visual estimation to machine learning. Seminars in Cancer Biology 2018; 52:151-7.

I contributed to an international team that produced this white-paper (guideline) review article for how TILs can be assessed by computational image analysis methodologies, describing the major strategies within a special article of Seminars in Cancer Biology devoted to immuno-oncology.

Banito A, Li X, Laporte AN, Roe JS, Sanchez-Vega F, Huang CH, Dancsok A, Hatzi K, Chen CC, Tschaharganeh DF, Chandwani R, Tasdemir N, Jones KB, Capecchi MR, Vakoc CR, Schultz N, Ladanyi M, Nielsen TO, Lowe SW. The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma. Cancer Cell 2018 Mar 12;33(3):527-541

In collaboration with researchers at Memorial Sloan-Kettering Cancer Center in New York (as well as my colleagues in Utah), we identify a new cofactor by which the synovial sarcoma mutant oncoprotein acts, called KDM2B. This partner protects the epigenetic state of underlying genes, locking the cells into an embryonic phenotype of cell growth without proper differentiation. A major advance in our understanding of how the SS18-SSX protein causes synovial sarcoma, this article was the subject of an editorial in Cancer Cell and suggests new potential epigenetic therapy strategies for this disease that most commonly afflicts adolescents and young adults.

Anne-Vibeke Lænkholm, Maj-Britt Jensen, Jens Ole Eriksen, Birgitte Bruun Rasmussen, Ann S. Knoop, Wesley Buckingham, Sean Ferree, Carl Schaper, Torsten O. Nielsen, Taryn Haffner, Torben Kibøl, Maj-Lis Møller Talman, Anne Marie Bak Jylling, Tomasz Piotr Tabor, Bent Ejlertsen. The PAM50 Risk of Recurrence score predicts 10-year distant recurrence in a comprehensive Danish cohort of postmenopausal women allocated to 5 years of endocrine therapy for hormone receptor-positive early breast cancer. Journal of Clinical Oncology 2018 March; 36:735-40.

Working with my Danish colleagues we provide a population-based external clinical validation of the Prosigna (NanoString PAM50) test. When applied to a cohort of virtually all women in Denmark who presented with the most common type of early breast cancer in the early 2000s, Prosigna had a 99.5% technical success rate and identified a group of women with such a low risk type of breast cancer that their survival was excellent for at least 10 years, without requiring chemotherapy, and even if node positive. JCO included a very favourable and supportive editorial in the same issue.

Kenneth TE Chang, Angela Goytain, Tracy Tucker, Aly Karsan, Cheng-Han Lee, Torsten O. Nielsen, Tony L. Ng. Development and Evaluation of a Pan-Sarcoma Fusion Gene Detection Assay Using the NanoString nCounter Platform. Journal of Molecular Diagnostics 2018 Jan; 20(1):63-77

This is an important paper from our group, that arose out of a sabbatical rotation Kenneth Chang (a pediatric pathologist from Singapore) did with me. Angela my senior technologist did much of the leg work and my sarcoma diagnostic colleague Tony Ng helped take forward our study designing a new diagnostic tool for sarcomas based on NanoString technology. This assay is a real winner, replacing cumbersome FISH and RT-PCR assays with a single pan-sarcoma test that is much cheaper and faster than NGS-based sequencing solutions. In fact, the test has "gone live" in Vancouver and is now our lead sarcoma molecular diagnostic assay. We made this paper open access and are happy to share our methods and reagents with the world!

Anne-Vibeke Lænkholm, Maj-Britt Jensen, Jens Ole Eriksen, Wesley Buckingham, Sean Ferree, Torsten O. Nielsen, Bent Ejlertsen. The ability of PAM50 Risk of Recurrence Score to predict 10-year distant recurrence in hormone receptor positive postmenopausal women with special histological subtypes. Acta Oncologica 2018 Jan;57(1):44-50.

This is the third of a series of papers I published in a special issue of Acta Oncologica, describing successes from the Danish Breast Cancer Group's clinical trials and their ongoing value for breast cancer studies. Anne-Vibeke Laenkholm, a colleague from Svendborg with whom I had two excellent family home-exchanges, analyzed our dataset on the large DBCG 99C cohort of women with breast cancer to pull out several rare subtypes of breast cancer (apocrine, medullary, mucinous, papillary, secretory, tubular, neuroendocrine). We were able to show that the Prosigna PAM50 assay worked for those cases, too.

Tinne Laurberg, Trine Tramm, Torsten Nielsen, Jan Alsner, Silje Nord, Simen Myhre, Therese Sørlie, Samuel Leung, Cheng Fan, Charles Perou, Karen Gelmon, J Overgaard, David Voduc, Aleix Prat, Maggie Chon U Cheang. Intrinsic subtypes and benefit from postmastectomy radiotherapy in node-positive premenopausal breast cancer patients who received adjuvant chemotherapy – results from two independent randomized trials. Acta Oncologica 2018 Jan;57(1):38-43.

In this second of a series of papers published in a special issue of Acta Oncologica, describing successes from the Danish Breast Cancer Group's clinical trials and their ongoing value for breast cancer studies, we published the work Tinne Laurberg did during her PhD external rotation with me in Vancouver. This looked at the benefit of axillary radiation therapy in node positive women. Whereas in our LuminA trial we are testing if it is safe to omit breast radiation in low risk primary tumors treated by breast conserving surgery, here we found that even molecularly low risk Luminal A patients benefit from regional adjuvant radiation.

Maj-Britt Jensen, Torsten O. Nielsen, Ann S. Knoop, Anne-Vibeke Lænkholm, Eva Balslev, Bent Ejlertsen. Mortality and recurrence rates among systemically untreated high risk breast cancer patients. Acta Oncologica 2018 Jan;57(1):135-140.

The first of a series of papers published in a special issue of Acta Oncologica, describing successes from the Danish Breast Cancer Group's clinical trials and their ongoing value for breast cancer studies. My previous work on DBCG77B, published in February and the subject of a platform presentation at the San Antonio Breast Cancer Symposium, was repurposed for statistical modeling in an effort to see if any low risk group of women could be identified when tumor size was large, nodes were positive and systemic therapy not given. Answer: no.

Karama Asleh-Aburaya, Jennifer R Won, Dongxia Gao, K David Voduc, Torsten O Nielsen. Nestin expression in breast cancer: association with prognosis and subtype on 3641 cases with long term followup. Breast Cancer Research and Treatment 2018 Feb;168(1):107-115.

My team's past work (Jennifer Won's thesis) identified nestin as one of the best IHC biomarkers of the aggressive basal subtype of breast cancer. Here, we got around to applying it onto our British Columbia "big series" cohort tissue microarrays, and showed its value as a solo marker. It's found in about 10% of breast cancer and identifies a poor prognosis group, importantly including a subset of ER+ breast cancers that might be clinically considered luminal, but appear to carry basal biology.

Dieci MV, Radosevic-Robin N, Fineberg S, van den Eynden G, Ternes N, Penault-Llorca F, Pruneri G, D'Alfonso TM, Demaria S, Castaneda C, Sanchez J, Badve S, Michiels S, Bossuyt V, Rojo F, Singh B, Nielsen T, Viale G, Kim SR, Hewitt S, Wienert S, Loibl S, Rimm D, Symmans F, Denkert C, Adams S, Loi S, Salgado R; International Immuno-Oncology Biomarker Working Group on Breast Cancer. Update on tumor-infiltrating lymphocytes (TILs) in breast cancer, including recommendations to assess TILs in residual disease after neoadjuvant therapy and in carcinoma in situ: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer. Seminars in Cancer Biology 2018; 52:16-25.

To be honest, I didn't contribute much to this article from the IIOBWGBC, beyond a detailed edit of others' work. As part of the core group originally promulgating recommendations for TIL assessment for invasive breast cancer excision specimens, I was involved in meetings and critical discussions on how to port this strategy to the related issues of DCIS and post-neoadjuvant residual disease.

Samantha Burugu, Doris Gao, Samuel Leung, Stephen K. Chia, Torsten Nielsen. LAG-3+ tumor infiltrating lymphocytes in breast cancer: clinical correlates and association with PD-1/PD-L1+ tumors. Annals of Oncology 2017 Dec 1;28(12):2977-2984.

This work, the first detailed description of the expression of the immunooncology target LAG3 in breast cancer, not only secured my student Samantha a podium poster discussion at the San Antonio Breast Cancer Symposium, but also got accepted at an excellent journal. Our data supports strategies to combine emerging LAG3 targeting drugs with PD1/PDL1 inhibitors, due to coexpression of LAG3 and other checkpoints on Tumor Infiltrating Lymphocytes in breast cancers.

Patrick S Tarpey, Sam Behjati, Matthew D Young, Inigo Martincorena, Ludmil B Alexandrov, Sarah J Farndon, Charlotte Guzzo, Claire Hardy, Calli Latimer, Adam P Butler, Jon W Teague, Adam Shlien, P Andrew Futreal, Sohrab Shah, Ali Bashashati, Farzad Jamshidi, Torsten O. Nielsen, David Huntsman, Daniel Baumhoer, Sebastian Brandner, Jay Wunder, Brendan Dickson, Patty Cogswell, Josh Sommer, Joanna J Phillips, M Fernanda Amary, Roberto Tirabosco, Nischalan Pillay, Stephen Yip, Michael R Stratton, Adrienne M Flanagan, Peter J Campbell. The driver landscape of sporadic chordoma. Nature Communications 2017 Oct 12;8(1):890.

My student Farzad and I, under the auspices of the Terry Fox Research Institute forme fruste tumor project led by David Huntsman, contributed to an international effort to understand the biology of chordomas, a dangerous tumor of the spine that emerges from embryological remnants and causes major problems due to its location. We did not find a consistent driver mutation, unfortunately, although our data support abnormal activation of notochordal transcription factors

Tony LH Chu, Marisa Connell, Lixin Zhou, Zhengcheng He, Jennifer R Won, S Mohammed Rahavi, Helen Chen, Pooja Mohan, Oksana Nemirovsky, Abbas Fotovati, Miguel Angel Pujana, Gregor S Reid, Torsten O Nielsen, Nelly Pante, Christopher A Maxwell. Cell cycle-dependent tumor engraftment and migration are enabled by Aurora-A. Molecular Cancer Research 2018;16:16-31

One of the things we do in the GPEC lab is help out basic scientists assess the clinical relevance of their discoveries in cancer biology. In this study, we helped out researchers based at the BC Child & Family Research Institute assess the activation status of Aurora Kinase A in a set of over 3000 breast cancers, linked to clinical outcome. This was a side project for my former PhD student Jennifer Won, which did eventually turn into a paper in a good journal.

Samantha Burugu, Amanda R. Dancsok, Torsten O. Nielsen. Emerging targets in cancer immunotherapy. Seminars in Cancer Biology 2018; 52:39-52.

Immunotherapy was the hottest topic of 2017. My students Samantha and Amanda were doing PhD projects on immune biomarker expression in breast cancer, and sarcomas, respectively. As part of an international consortium of pathologists and oncologists studying immune biomarkers, we were invited to contribute to a special issue of the high impact review journal Seminars in Cancer Biology, on the topic of new targets for new drugs in the field -- such as LAG3, TIM3, VISTA, TIGIT, GITR and several others.

Laporte AN, Poulin NM, Barrott JJ, Wang XQ, Lorzadeh A, Vander Werff R, Jones KB, Underhill TM, Nielsen TO. Death by HDAC inhibition in synovial sarcoma cells. Molecular Cancer Therapeutics 2017 Dec;16(12):2656-2667

In this, the crowning chapter in Aimee Laporte's PhD thesis, we track the detailed transcriptional effects of the use of the effective histone deacetylase inhibitor (quisinostat) in synovial sarcoma, and for the first time undertake a detailed comparison across different types of cancers. We identify activation of cell cycle arrest, differentiation and apoptosis pathways, and confirm these effects are associated with therapeutic benefit in mouse models of synovial sarcoma.

Liu S, Chen B, Burugu S, Leung S, Gao D, Virk S, Kos Z, Parulekar WR, Shepherd L, Gelmon KA, Nielsen TO. Role of cytotoxic tumor-infiltrating lymphocytes in predicting outcomes in metastatic HER2-positive breast cancer: a secondary analysis of a randomized clinical trial. JAMA Oncology 2017 Nov 9;3(11):e172085]

In a formal, prespecified analysis of a randomized clinical trial, we found that the presence of only a low level of infiltrating cytotoxic T cells (measured by CD8) in breast cancer excisions predicted which patients would, when they later developed metastases, respond better to antibody-based anti-HER2 treatment with trastuzumab than to a non-immune-inducing anti-HER2 treatment approach with lapatinib. Results could have wider implications for when antibody-based drugs might have advantages over standard small molecule drugs that have the same target.

Hendry S, Salgado R, ... Nielsen T ... Fox SB. Assessing tumor-infiltrating lymphocytes in solid tumors: a practical review for pathologists and proposal for a standardized method from the international immunooncology biomarkers working group: Part 1: Assessing the host immune response, TILs in invasive breast carcinoma and ductal carcinoma in situ, metastatic tumor deposits and areas for further research. Advances in Anatomical Pathology 2017; 24:235-251

I was part of an international group of pathologists and oncologists, working to provide guidelines on how to standardize the assessment of tumor infiltrating lymphocytes in breast cancer.

de Graaff MA, Malu S, Guardiola I, Kruisselbrink AB, de Jong Y, Corver WE, Gelderblom H, Hwu P, Nielsen TO, Lazar AJ, Somaiah N, Bovée JVMG. High-throughput screening of myxoid liposarcoma cell lines: survivin is essential for tumor growth. Translational Oncology 2017; 10(4):546-554.

Funded by the Liddy Shriver Sarcoma Initiative, our consortium of researchers based in Leiden, Houston and Vancouver applied a high throughput drug screen to the new cell line model we had created, and identified a candidate target for therapy in myxoid liposarcoma.

Chapman JW, Liu S, Leung S, Nielsen TO. Competing Risks of Mortality by PAM50 Intrinsic Subtype of British Columbia Tamoxifen-Treated Cohort of Postmenopausal Patients With Breast Cancer. Clinical Breast Cancer 2017 Jul;17(4):e215-e224

Judy-Anne Chapman, a breast cancer clinical statistician with the Canadian Cancer Trials Group, did this careful statistical re-analysis of the highly detailed patient clinical data that has been captured by the British Columbia Breast Outcomes Unit, in relation to the PAM50 mRNA expression profile and intrinsic molecular subtype. Results confirm that intrinsic molecular subtype is highly associated with patient outcomes, even when all known clinical factors are taken into account.

Laporte AN, Barrott JJ, Yao RJ, Poulin NM, Brodin BA, Jones KB, Underhill TM, Nielsen TO. HDAC and Proteasome Inhibitors Synergize to Activate Pro-Apoptotic Factors in Synovial Sarcoma. PLoS One 2017 Jan;12(1):e0169407

Our work to develop new treatments for synovial sarcoma took an interesting twist, when our unbiassed drug screening efforts kept re-discovering the effectiveness of HDAC inhibitors against this disease. The other top hit was a different class of drugs called proteasome inhibitors. Interestingly, the combination has been tried in patients with multiple myeloma, and shown to be safe and effective. Here we build a strong preclinical case that these drug classes synergize to break up the synovial sarcoma oncoprotein complex and induce apoptosis, providing a rationale for a possible clinical trial approach, repurposing agents that work in haematopoietic disease for the treatment of a sarcoma.

Luo J, Liu S, Leung S, Gru AA, Tao Y, Hoog J, Ho J, Davies SR, Allred DC, Salavaggione AL, Snider J, Mardis ER, Nielsen TO, Ellis MJ. An mRNA Gene Expression-Based Signature to Identify FGFR1-Amplified Estrogen Receptor-Positive Breast Tumors. Journal of Molecular Diagnostics 2017 Jan; 19(1):147-161

In a creative application of NanoString technology, the presence of DNA level amplifications in a key oncogene is inferred from coordinate expression changes in a cassette of genes from the same chromosomal locus. This allows rapid, inexpensive and accurate determination of gene amplifications from relatively poor quality, small biopsy specimens in a manner that can easily be multiplexed with other tests into a single assay. It also shows a possible diagnostic route to measure the DNA copy status of other genes based on RNA expression changes.

Dancsok AR, Asleh-Aburaya K, Nielsen TO. Advances in sarcoma diagnostics and treatment. Oncotarget 2017; 8:7068-70930.

In 2016, I was again responsible for reviewing the year's sarcoma literature for an educational presentation to the Canadian Cancer Trials Group, as well as to the Toronto International Sarcoma Symposium. The previous review, Lim et al. in Clinical Cancer Research was good enough that the editors of Oncotarget solicited this sequel, updating the latest basic, translational and clinical research advances in sarcoma.

Nielsen TO, Jensen MB, Burugu S, Gao D, Tykjaer Jorgensen CL, Balslev E, Ejlertsen B. High risk premenopausal Luminal A breast cancer patients derive no benefit from adjuvant cyclophosphamide-based chemotherapy: results from the DBCG77B clinical trial. Clinical Cancer Research 2017 Feb 15;23(4):946-953

This important study matched Canadian expertise in breast cancer molecular subtyping with a classic Danish clinical trial randomizing women with high risk early breast cancer to chemotherapy vs. no chemotherapy arms. In a formal prospective-retrospective study with locked down classifiers, prespecified statistical plan, and independent analysis of biomarker status and patient outcomes, we confirmed our primary hypothesis that the most common subtype of breast cancer, Luminal A, in fact predicts that chemotherapy will have no benefit (in a population otherwise greatly benefiting from adjuvant chemotherapy). This work had its debut as a platform presentation at the general plenary session of the San Antonio Breast Cancer Symposium, coupled with a press conference!

Asleh-Aburaya K, Sheffield BS, Kos Z, Won JR, Wang XQ, Gao D, Wolber R, Gilks CB, Bernard PS, Chia SK, Nielsen TO. Basal biomarkers Nestin and INPP4b accurately identify intrinsic subtype in breast cancers that are weakly positive for estrogen receptor. Histopathology 2017 Jan;70(2):185-194

Some cases of breast cancer show only weak positivity for estrogen receptor, when tested by immunohistochemistry. These patients are generally considered to be ER positive and are therefore given endocrine therapy. However, gene expression profile studies by ourselves and others have revealed that such cases are a grab-bag of different subtypes, many misassigned as falsely-positive for ER due to overly sensitive IHC techniques and interpretation. Sorting this out requires expensive gene expression tests, or immunohistochemical subtype biomarkers that do not rely on estrogen receptor results for classification. Our basal panel based on nestin positivity and INPP4B loss meets these criteria, and here we show that it works to identify cases that molecularly and clinically behave like basal breast cancers despite being classified as ER positive by standard clinical testing.

de Graaff MA, Yu JS, Beird HC, Ingram DR, Nguyen T, Juehui Liu J, Bolshakov S, Szuhai K, Åman P, Torres KE, Lev D, Nielsen TO, Bovée JV, Lazar AJ, Somaiah N. Establishment and characterization of a new human myxoid liposarcoma cell line (DL-221) with the FUS-DDIT3 translocation. Laboratory Investigation 2016 Aug;96(8):885-94

Research into myxoid liposarcoma has been hampered by a lack of available cell line models; the few that are widely available are SV-40 transformed and therefore may not be representative of human disease at least in some important ways. In work funded by the Liddy Shriver Sarcoma Initiative, our team of researchers from MD Anderson, Leiden and British Columbia worked together to develop and characterize a new, spontaneously-immortalized myxoid liposarcoma cell line model that we have made available to researchers worldwide.

Samuel C Y Leung, Torsten O Nielsen, Lila Zabaglo, Indu Arun, Sunil S Badve, Anita L Bane, John M S Bartlett, Signe Borgquist, Martin C Chang, Andrew Dodson, Rebecca A Enos, Susan Fineberg, Cornelia M Focke, Dongxia Gao, Allen M Gown, Dorthe Grabau, Carolina Gutierrez, Judith C Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Ming-Gang Lin, Mauro G Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C Kent Osborne, Frédérique M Penault-Llorca, Tammy Piper, Takashi Sakatani, Roberto Salgado, Jane Starczynski, Giuseppe Viale, Daniel F Hayes, Lisa M McShane & Mitch Dowsett on behalf of the International Ki67 in Breast Cancer Working Group of the Breast International Group and North American Breast Cancer Group. Analytical validation of a standardized scoring protocol for Ki67: phase 3 of an international multicenter collaboration. npj Breast Cancer 2, Article number: 16014 (2016) doi:10.1038/npjbcancer.2016.14. Published online: 18 May 2016.

This paper describes the results of "Phase 3" of our international Ki67 working group project, seeking to standardize an analytically-valid method for Ki67 testing in breast cancer. Having previously shown how computer-based standardization cvian greatly improve visual scoring consistency on tissue microarray cores, we moved on to a study on core biopsies. We were successful in translating these improvements, finding that a method that attempts to globally average the score across representative areas of a core biopsy are even more consistent than methods that base the score on the "hot spot."

Samantha Burugu, Karama Asleh-Aburaya, Torsten O. Nielsen. Immune infiltrates in tumor microenvironment of breast cancer, their detection and their clinical implications. Breast Cancer 2017 Jan; 24(1):3-15

This is a timely review article of a "hot topic" in breast cancer - the role of the immune system and therapeutic options that may therefore apply in at least a subset of cases - the project area that will be a major part of my student Samantha Burugu's thesis project.

Aimée N. Laporte, Jennifer X. Ji, Limin Ma, Torsten O. Nielsen*, Bertha A. Brodin. Disruption of SS18-SSX oncoprotein proximity interactions in synovial sarcoma. Oncotarget, 2016 Jun 7; 7(23):34384-94.

Funded by our CCSRI impact grant, we demonstrate how the new proximity ligation assay technique, developed by Swedish colleagues, can interrogate the functional status of the key oncoprotein driving synovial sarcoma. My student Aimee Laporte applies a drug screen that identifies quisinostat as the most active drug targeting and breaking up these protein-protein interactions driving synovial sarcoma, information that is informing clinical trial plans.

Sheffield BS, Kos Z, Asleh-Aburaya K, Wang X, Leung S, Gao D, Won J, Chow C, Rachamadugu R, Stijleman I, Wolber R, Gilks CB, Myles N, Thomson T, Hayes MM, Bernard PS, Nielsen TO, Chia SKL. Molecular subtype profiling of breast cancers weakly-positive for estrogen receptor. Breast Cancer Research and Treatment 2016 Feb; 155(3):483-90.

Since the breast cancer estrogen receptor testing scandal in Newfoundland, in an effort to avoid false negatives, increasingly sensitive techniques with lower interpretation cutpoints have become widely employed. This has created a new problem - overcall of ER positivity in cases that are actually non-luminal. We show here that this is a very real problem among a set of breast cancers interpreted as "weakly positive" by accredited clinical laboratories, becausePAM50 expression profiling reveals that many are of the more aggressive basal subtype that is insensitive to hormonal therapy.

Liu MC, Pitcher BN, Mardis ER, Davies SR, Friedman PN, Snider JE, Vickery TL, Reed JP, DeSchryver K, Singh B, Gradishar WJ, Perez EA, Martino S, Citron ML, Norton L, Winer EP, Hudis CA, Carey LA, Bernard PS, Nielsen TO, Perou CM, Ellis MJ, and Barry WT. PAM50 gene signatures are prognostic for breast cancer patients treated with adjuvant anthracycline and taxane based chemotherapy in C9741 (Alliance). npj Breast Cancer, Article number: 15023 (2016) doi:10.1038/npjbcancer.2015.23. Published online: 06 January 2016.

In my role on the pathology committee for the Alliance for Clinical Trials in Oncology (formerly CALGB), I performed immunohistochemical subtyping of close to 2000 breast cancers from the C9741 clinical trial testing dose dense vs standard dose intensity adjuvant chemotherapy in breast cancer. We find both by IHC and by PAM50 that intrinsic subtype is prognostic among these node positive, high risk women, but does not predict a benefit from dose dense regimens.

Farzad Jamshidi, Ali Bashashati, Karey Shumansky, Brendan Dickson, Nalan Gogkoz, Jay S. Wunder, Irene L. Andrulis, Alexander Lazar, Sohrab P. Shah, David G. Huntsman, Torsten O. Nielsen. The genomic landscape of epithelioid sarcoma cell lines and tumor specimens. Journal of Pathology 2016 Jan;238(1):63-73. doi: 10.1002/path.4636.

This study is the first applying next generation sequencing to epithelioid sarcoma, an aggressive cancer which unlike most kinds of cancer has a predilection for arising in the distal extremities, of adolescents and young adults. The main finding is that, unlike most cancers of young people, this one has a complex genome with a high mutational load - an ominous finding that will make it more difficult to find targeted therapies that will work.

Karnezis AN, Wang Y, Ramos P, Hendricks WPD, Oliva E, D’Angelo E, Prat J, Nucci MR, Nielsen TO, Chow C, Leung S, Kommoss F, Kommoss S, Da Silva AFL, Ronnett BM, Rabban JT, Bowtell DD, Weissman BE, Trent JM, Gilks CB, Huntsman DG. Dual loss of the SWI/SNF complex ATPases SMARCA4/BRG1 and SMARCA2/BRM is highly sensitive and specific for small cell carcinoma of the ovary, hypercalcemic type. Journal of Pathology 2016 Feb;238(3):389-400.

I contributed to this study by my colleague David Huntsman that looked at the molecular causes of a rare but very aggressive ovarian cancer that afflicts young people, by helping to show its second hit cooperative mutation is of a type we also see in sarcomas (particularly, epithelioid sarcoma).

Jamie Lim, Neal Poulin, Torsten O. Nielsen. New strategies in sarcoma: linking genomic and immunotherapy approaches to molecular subtype. Clinical Cancer Research 2015 Nov 1;21(21):4753-9.

I was solicited to write this review article for a major cancer research journal, following my presentation of the sarcoma "year in review" at the 2015 American Association for Cancer Research meeting in Philadelphia. We describe the latest updates from the previous year's research, and look forward as to what the main strategies are to translate basic science research into better clinical care for sarcomas.

K. David Voduc, Torsten O. Nielsen, Charles M. Perou, J. Chuck Harrell, Cheng Fan, Hagen Kennecke, Andy J. Minn, Vincent L. Cryns, Maggie C. U. Cheang. αB-crystallin expression in breast cancer is associated with brain metastasis. npj Breast Cancer, Article number: 15014 (2015) doi:10.1038/npjbcancer.2015.14. Published online: 21 October 2015.

At long last, our followup to Moyano et al 2006 -- the original description of the biological and clinical role played by the small heat shock protein alpha-basic crystallin in breast cancer -- got its followup published, including new information from the "big series" tissue microarray tieing it to brain metastasis. We decided to suppor the new Nature spinoff open access breast cancer journal with this publication, which garnered some international media attention to boot.

Brett Wallden, James Storhoff, Torsten Nielsen, Naeem Dowidar, Carl Schaper, Sean Ferree, Shuzhen Liu, Samuel Leung, Gary Geiss, Jacqueline Snider, Tammi Vickery, Sherri R. Davies, Elaine R. Mardis, Michael Gnant, Ivana Sestak, Matthew J. Ellis, Charles M. Perou, Philip S. Bernard, Joel S Parker. Development and Verification of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay. BMC Medical Genomics 2015; 8:54.

When you develop a new cancer test, there is a responsibility to post the story and details of how it was developed in a public format, for public scrutiny. Our PAM50-based Prosigna test for breast cancer is FDA, Health Canada and EU approved (among other jurisdictions). This paper describes the development and registry evidence behind the test. Open access.

John M.S. Bartlett, Torsten O. Nielsen, Dongxia Gao, Karen A. Gelmon, Mary Anne Quintayo, Jane Starczynski, L. Han, Margot J. Burnell, Marc N. Levine, Bingshu E. Chen, Lois E. Shepherd, Judy-Anne Chapman on behalf of the NCIC-CTG. TLE3 is not a predictive biomarker for taxane sensitivity in the NCIC CTG MA21 clinical trial. British Journal of Cancer 2015 Sep 1;113(5):722-728

Taxanes are heavy-hitter chemotherapy drugs used in breast cancer - effective but with toxicity. Researchers have been trying to find biomarkers that identify which patients need these drugs and which can be spared, and previous reports suggested a protein called TLE3 could serve just such a purpose. However, when we tested this in a high level-of-evidence, formal prospective-retrospective study, we could not confirm this result, and saw problems with the analytical validity of this marker.

Michael Richard Whitehouse, Makoto Endo, Suzanna Zachara, Torsten O. Nielsen, Nelson V. Greidanus, Bassam A. Masri, Donald S. Garbuz, Clive P. Duncan. Adverse Local Tissue Reactions in Metal-on-Polyethylene THA due to Trunnion Corrosion: What is the Risk of Misdiagnosis? Bone and Joint Journal 2015;97-B:1024-30

Metal-on-metal hip replacements have been associated with pseudotumor development due to chronic hypersensitivity reactions. Consequently, they are rarely used, having been superseded by metal-on-polyethylene engineered components. Nevertheless, we find that the trunnion component where the femoral ball and stem are connected can sometimes release Co-Cr-Mo alloy particles, and induce hypersensitivity reactions, which are important not be mistake for infections.

Fei-Fei Liu, Wei Shi, Susan J. Done, Naomi Miller, Melania Pintilie, David Voduc, Torsten O. Nielsen, Sharon Nofech-Mozes, Martin C. Chang, Timothy J. Whelan, Lorna M. Weir, Ivo A. Olivotto, David R. McCready, Anthony W. Fyles. Identification of a low-risk luminal A breast cancer cohort that may not benefit from breast radiotherapy. Journal of Clinical Oncology 2015 Jun 20;33(18):2035-40.

Adjuvant radiation therapy is standard of care for women undergoing breast conserving surgery for breast cancer. However, this is expensive, difficult on patients, and carries its own side effects. Here we find that those women with the low risk Luminal A molecular subtype, in the context of other favourable factors (small tumors caught early in older women, willing to take antiestrogen therapy), have excellent cure rates even without radiation. The safety of this approach is being tested now in our LuminA prospective trial, based on this work.

Gnant M, Sestak I, Filipits M, Dowsett M, Balic M, Lopez-Knowles E, Greil R, Dubsky P, Stoeger H, Rudas M, Jakesz R, Ferree S, Cowens JW, Nielsen T, Schaper C, Fesl C, Cuzick J. Identifying Clinically Relevant Prognostic Subgroups of Postmenopausal Women with Node-positive Hormone Receptor Positive Early Stage Breast Cancer Treated with Endocrine Therapy: A combined analysis of ABCSG-8 and ATAC using the PAM50 risk of recurrence score and Intrinsic Subtype. Annals of Oncology 2015; 26:1685-91

This combined analysis of a large Austrian and a large UK-based breast cancer clinical trial, assessed with the Prosigna assay I invented with my colleagues, confirms, with level 1 evidence, that our test can identify a large fraction of women whose prognosis is so good they can safely avoid chemotherapy even though their disease has spread to lymph nodes.

Maggie CU Cheang, Miguel Martin, Torsten O Nielsen, Aleix Prat, David Voduc, Alvaro Rodriguez-Lescure, Amparo Ruiz, Stephen Chia, Lois Shepherd, Manuel Ruiz-Borrego, Lourdes Calvo, Emilio Alba, Eva Carrasco, Rosalia Caballero, Dongsheng Tu, Kathleen I Pritchard, Mark N Levine, Vivien H Bramwell, Joel Parker, Philip S. Bernard, Matthew J Ellis, Charles M Perou, Angelo Di Leo and Lisa A Carey. Defining breast cancer intrinsic subtypes by quantitative receptor expression. The Oncologist 2015; 20:474-82

This work comes from the Triple Negative Breast Cancer working group of the North American Breast Cancer Group and the Breast International Group, and was led by my former student Maggie Cheang. We demonstrate that many cases that display weak ER staining, although currently classed as hormone senstive tumors and treated with endocrine agents, are actually basal-like breast cancers - which are much more aggressive, and require chemotherapy not hormonal therapy.

Torsten O. Nielsen and Charles M. Perou. CCR 20th Anniversary Commentary: The development of breast cancer molecular subtyping. Clinical Cancer Research, 2015 Apr 15;21:1779-81

One of my most-cited articles, and indeed one of the most-cited articles in Clinical Cancer Research over its first 20 years of existence, was based on work I did as a resident during the summer I started GPEC on a shoestring budget. Building on Chuck Perou's intrinsic subtype gene expression profiles, I helped develop an immunohistochemical surrogate signature. This was a novel approach at the time, and opened up a wide field of validation and clinical correlation research strategies by others, an approach still relevant today.

Mei-Yin C. Polley, Samuel C. Y. Leung, Dongxia Gao, Mauro G. Mastropasqua, Lila A. Zabaglo, John M.S. Bartlett, Lisa M. McShane, Rebecca A. Enos, Sunil Badve, Anita Bane, Signe Borgquist, Susan Fineberg, Ming-Gang Lin, Allen M. Gown, Dorthe Grabau, Carolina Gutierrez, Judith C. Hugh, Takuya Moriya, Yasuyo Ohi, C. Kent Osborne, Frédérique Penault-Llorca, Jean Perrin, Tammy Piper, Peggy Porter, Takashi Sakatani, Roberto Salgado, Jane Starczynski, Anne-Vibeke Lænkholm, Giuseppe Viale, Mitch Dowsett, Daniel F. Hayes, Torsten O. Nielsen …on behalf of the International Ki67 in Breast Cancer Working Group of the Breast International Group and North American Breast Cancer Group (BIG-NABCG). An international study to increase concordance in Ki67 scoring. Modern Pathology 2015; 28:778-86

This work was the product of a lot of organization, experimental design and international collaboration, which I directed as Phase 2 of our NABCG-BIG project to see if Ki67 scoring in breast cancer can have analytical validity. Using an online calibration tool to train scorers in a common method, we find that very good agreement can be achieved, at least on tissue microarrays. This sets a standard for how to achieve consistent scoring of this important proliferation marker and risk indicator, and points the way towards how to apply this technique to core needle biopsies (the subject of our group's Phase 3 study, led by Mitch Dowsett, Lisa McShane, Dan Hayes and myself.

Jamshidi F, Nielsen TO, Huntsman DG. Cancer Genomics: Why Rare is Valuable. Journal of Molecular Medicine 2015; 93:369–381

My MD/PhD student Farzad took the lead in writing this review article, based on our Terry Fox Research Institute-funded forme fruste tumor analysis project. Certain rare cancers provide consistent, interpretable genomic changes that yield important insights not only into biology and treatment of these cancers that often afflict young people, but also provide technical and biological advances that are relevant to more common forms of the disease.

Quincy S. Chu, Torsten O. Nielsen, Thierry Alcindor, Abha Gupta, Makoto Endo, Angela Goytain, Hao Xu, Shaliendra Verma, Richard Tozer, Meg Knowling, Vivien Bramwell, Jean Powers, Lesley K. Seymour, Elizabeth A. Eisenhauer. A Phase II study of SB939, a novel pan-histone deacetylase inhibitor, in patients with translocation-associated recurrent/metastatic sarcomas –NCIC-CTG IND 200. Annals of Oncology 2015 May;26(5):973-81

This was the first clinical trial that I developed and was able to implement the the Investigational New Drug and the Sarcoma Disease Site committees of the NCIC-Clinical Trials Group, and as such I have shared first authorship status with the lead oncologist for the trial. We saw many cases of stable disease - but unfortunately the drug company supplying the experimental agent had financial problems during the trial and we had to close prematurely, before any definitive conclusions could be drawn! We are working on followup studies.

Nielsen TO, Poulin NM, Ladanyi M. Synovial sarcoma: recent discoveries as a roadmap to new avenues for therapy. Cancer Discovery; 5(2); 124–34.

I rarely write reviews, but when asked to do so by a major journal, on a topic very important to me and my research, I was willing to step up to the plate and review a series of recent advances in synovial sarcoma (concerning the function of the fusion oncoprotein encoded by its driver mutation, alterations in epigenetic regulation of gene expression, role of the Wnt pathway, the relative value of mouse and cell models, and consequent possible therapeutic strategies).

Shuzhen Liu, Judy-Anne W. Chapman, Margot J. Burnell, Mark N Levine, Kathleen I. Pritchard, Timothy J Whelan, Hope S. Rugo, Kathy S. Albain, Edith A. Perez, Shakeel Virk, Garrett Barry, Dongxia Gao, Patti O’Brien, Lois E. Shepherd, Torsten O. Nielsen, Karen A. Gelmon. Prognostic and predictive investigation of PAM50 intrinsic subtypes in the NCIC CTG MA.21 phase III chemotherapy trial. Breast Cancer Research and Treatment 2015; 149: 439-448

I am the corresponding author on this study where we applied NanoString PAM50 technology to a large North American clinical trial randomizing women with high risk early breast cancer to one of three different chemotherapy regimens. We found that intrinsic subtypes remain prognostic among these higher risk, aggressively-treated women, but do not predict the best choice among 2nd and 3rd generation chemotherapy options, which may reflect that drugs differing more by pharmacokinetic and toxicity profiles than by mechanisms of action cannot have the relevant differences extracted from the tumor's gene expression profile.

Makoto Endo, Marieke A. de Graaff, Davis R. Ingram, Jamie Lim, Dina C. Lev, Neeta Somaiah, Judith V.M.G. Bovée, Alexander J. Lazar, Torsten O. Nielsen. NY-ESO-1 expression in mesenchymal tumors. Modern Pathology 2015; 28:587-95

This collaboration among sarcoma researchers from Japan, the Netherlands, Texas and Canada, a product of our Liddy Shriver Sarcoma Initiative international collaborative grant, is the world's largest study of the expression of a tumor antigen in sarcomas - an antigen that can be targeted by new immunotherapies being assessed in clinical trials.

Liu S, Foulkes WD, Leung S, Gao D, Lau S, Kos Z, Nielsen TO. Prognostic significance of FOXP3+ tumor infiltrating lymphocytes in breast cancer depends on estrogen receptor and human epidermal growth factor receptor-2 expression status and concurrent cytotoxic T-cell infiltration. Breast Cancer Research 2014 Sept;16(5):432

We put our "big series" cohort back to work again to assess biomarkers associated with the exciting field of anticancer immune responses, which may tie in to developing immunotherapy agents. Although FOXP3 labels regulatory/suppressor T-cells, we find their presence is indicative of an active immune response associated with a good prognosis, although as in our other studies we find that immune responses matter in non-luminal (basal and HER2) subtypes, but imply little in more common luminal (ER positive) forms of the disease.

Salgado R, Denkert C, Demaria S, Sirtaine N, Klauschen F, Pruneri G, Wienert S, Van den Eynden G, Baehne FL, Penault-Llorca F, Perez EA, Thompson EA, Symmans WF, Richardson AL, Brock J, Criscitiello C, Bailey H, Ignatiadis M, Floris G, Sparano J, Kos Z, Nielsen T, Rimm DL, Allison KH, Reis-Filho JS, Loibl S, Sotiriou C, Viale G, Badve S, Adams S, Willard-Gallo K, Loi S. Harmonization of the evaluation of tumor infiltrating lymphocytes (TILs) in breast cancer: recommendations by an international TILs-working group 2014. Annals of Oncology 2015; 26:259-71

Immune response markers may be both prognostic (in non-luminal breast cancers), and even more importantly predictive for new (but expensive) immunotherapy approaches. The simplest biomarker is microscopic assessment of tumor infiltrating lymphocytes, but standard approaches to scoring are needed if studies are to be comparable, and allow the research community to make sense of the burgeoning literature in the area and work toward true clinical utility. My experience leading the Ki67 international consortium, as well as recent publications in the immune biomarker field, led to an invitation for me to contribute to this consensus paper.

Ali HR, Provenzano E, Dawson SJ, Blows FM, Liu B, Shah M, Earl HM, Poole CJ, Hiller L, Dunn JA, Bowden SJ, Twelves C, Bartlett JM, Mahmoud SM, Rakha E, Ellis IO, Liu S, Gao D, Nielsen TO, Pharoah PD, Caldas C. Association of T-cell infiltration with breast cancer survival in 12,483 patients. Annals of Oncology 2014 Aug; 25(8):1536-43

Our previous work on CD8 positive tumor infiltrating lymphocytes in breast cancer was the largest single published dataset on the subject, and featured prominently among the studies that went into this meta-analysis. We demonstrate convincingly that cytotoxic T-cell infiltrates in primary breast cancer specimens are associated with improved prognosis, but only among ER negative (basal) and/or HER2 positive cases.

Jamshidi F, Pleasance E, Li Y, Shen Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao Y, Schein JE, Moore RA, Rassekh R, Huntsman DG, Knowling M, Lim H, Renouf DJ, Jones SJ, Marra MA, Nielsen TO, Laskin J, Yip S. Diagnostic value of next-generation sequencing in an unsual sphenoid tumor. The Oncologist 2014 June;19(6):623-30

The Personalized Oncology Group initiative is our institution's first attempt to bring next generation sequencing into clinical care. One of the first cases where this approach clearly had an impact was in the reassignment of the diagnosis of an aggressive tumor originally thought to be an unusual carcinoma, but which was identified to fall into the class of SMARCB1 deleted tumors usually presenting in younger patients.

Nielsen T, Wallden B, Schaper C, Ferree S, Liu S, Gao D, Barry G, Dowidar N, Maysuria M, Storhoff J. Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens. BMC Cancer 2014 Mar 13;14:177

This work represents the multisite formal technical proof of the analytical validity the Prosigna test, data that lead to its September 2013 FDA and April 2014 Health Canada approvals!

Filipits M, Nielsen TO, Rudas M, Greil R, Stöger H, Jakesz R, Bago-Horvath Z, Dietze O, Regitnig P, Gruber-Rossipal C, Müller-Holzner E, Singer CF, Mlineritsch B, Dubsky P, Bauernhofer T, Hubalek M, Knauer M, Trapl H, Fesl C, Schaper C, Ferree S, Liu S, Cowens JW, Gnant M; Austrian Breast and Colorectal Cancer Study Group. The PAM50 risk-of-recurrence score predicts risk for late distant recurrence after endocrine therapy in postmenopausal women with endocrine-responsive early breast cancer. Clinical Cancer Research 2014 Mar 1;20(5):1298-1305

There are important clinical implications to this secondary analysis of the ABCSG8 trial, which came out into print very shortly after the original Gnant et al. paper. We show that PAM50 remains prognostic beyond five years, and can identify an ulta-low risk group with minimal recurrences even after fifteen years. This result suggests these women – a substantial fraction of the study cohort – will not need extended endocrine therapy.

Charlotte Levin Tykjær Jørgensen, Torsten O. Nielsen, Karsten D. Bjerre, Suzanne Liu, Brett Wallden, Eva Balslev, Dorte L. Nielsen, Bent Ejlertsen. PAM50 breast cancer intrinsic subtypes and effect of gemcitabine in advanced breast cancer patients. Acta Oncologica 2014; 53:776-87

This collaboration between my lab and the Danish Breast Cancer Group was catalyzed by Charlotte’s four month visit to Vancouver, as part of her PhD. In a formal prospective-retrospective analysis of a randomized clinical trial, using the Nanostring version of the PAM50 test, her hypothesis that basal breast cancers would show the greatest sensitivity to gemcitabine chemotherapy held up! Metastatic patients survived longer. This work also led to a patent application for Charlotte and our team.

Gnant M, Filipits M, Greil R, Stoeger H, Rudas M, Bago-Horvath Z, Mlineritsch B, Kwasny W, Knauer M, Singer C, Jakesz R, Dubsky P, Fitzal F, Bartsch R, Steger G, Balic M, Ressler S, Cowens JW, Storhoff J, Ferree S, Schaper C, Liu S, Fesl C, Nielsen TO; on behalf of the Austrian Breast and Colorectal Cancer Study Group. Predicting distant recurrence in receptor-positive breast cancer patients with limited clinicopathological risk: using the PAM50 Risk of Recurrence score in 1478 postmenopausal patients of the ABCSG-8 trial treated with adjuvant endocrine therapy alone. Annals of Oncology 2014 Feb;25(2):339-45

I am especially proud of this paper, which contains the key data needed by the US Food & Drug Adminstration as a registry study to gain approval for the PAM50 test as a medical diagnostic we can deliver to patients! Over 1500 Austrian patients had to be re-consented for the use of their tissues, and I directed very meticulous work to apply the PAM50 subtyping and risk profiling test to their breast cancer specimens. We used the first clinical-grade Nanostring nCounter device -- the prototype version of the Prosigna test that became commecially available in late 2013. We were able to identify a large group of women who have breast cancers with a very low biological and clinical risk, with >95% long term survival even in the absence of chemotherapy.

Endo M, Su L, Nielsen TO. Activating transcription factor 2 in mesenchymal tumors. Human Pathology 2014 Feb;45(2):276-84.

Working with my pathology / orthopaedic surgery fellow from Kyushu, we confirm Le Su's finding of high level ATF2 expression in synovial sarcoma, and go on further to show that its expression is relatively common among the group of translocation-associated sarcomas.

Brandon S Sheffield and Torsten O Nielsen. Myxoid liposarcoma in a 91-year-old patient. Molecular Cytogenetics 2013;6(1):50.

Working with a bright and keen pathology resident, we produced a case report supported by detailed molecular diagnostic work, setting a new record for the oldest patient with a documented myxoid liposarcoma (which usually afflicts young adults). The article is open access.

Mei-Yin C. Polley; Samuel C. Y. Leung; Lisa M. McShane; Dongxia Gao; Judith C. Hugh; Mauro G. Mastropasqua; Giuseppe Viale; Lila A. Zabaglo; Frederique Penault-Llorca; John M.S. Bartlett; Allen M. Gown; W. Fraser Symmans; Tammy Piper; Erika Mehl; Rebecca A. Enos; Daniel F. Hayes; Mitch Dowsett; Torsten O. Nielsen; on behalf of the International Ki67 in Breast Cancer Working Group of the Breast International Group and North American Breast Cancer Group. An international Ki67 reproducibility study. JNCI Journal of the National Cancer Institute 2013 Dec 18;105(24):1897-1906

I was charged with leading a large group of pathologists from North America and Europe in an assessment of whether Ki67 immunohistochemistry, widely used for breast cancer prognosis and in neoadjuvant treatment predictive testing, has sufficient analytical validity to the point where it can be used with true clinical utility. The answer, unfortunately, turned out to be no -- at least not when labs simply used their own expert best practices. Scoring methodology was too different between labs. Ki67 cannot be used for clinical decision-making unless the scoring and decision cutpoints have been internally validated in detail. As a result of this study, I directed an even larger project in standardized Ki67 scoring, which was presented at the 2013 San Antonio Breast Cancer Symposium and will likely be published in 2014.

Chapman JA, Nielsen TO, Ellis MJ, Bernard P, Chia S, Gelmon KA, Pritchard KI, Le Maitre A, Goss PE, Shepherd LE, Bramwell VHC. Effect of continuous statistically standardized measures of estrogen and progesterone receptors on disease-free survival in NCIC CTG MA.12. Breast Cancer Research 2013;15(4):R71.

Clinical biostatistician Judy-Anne Chapman, a member of the NCIC-CTG breast correlative sciences group I co-chair, was able to use the data we generated (and published as Chia et al.) on the MA.12 clinical trial, with its rich set of ER and PR measurements by immunohistochemistry and PCR, to develop a statistically-standardized method of quantitative hormone receptor assessment. This provides more information than cutpoint-based methods.

Won JR, Gao D, Chow C, Cheng J, Lau SY, Ellis MJ, Perou CM, Bernard PS, Nielsen TO. A survey of immunohistochemical biomarkers for basal-like breast cancer against a gene expression gold standard. Modern Pathology 2013 Nov;26(11):1438-50

We spent a few years reviewing all the literature that had built on biomarkers for basal breast cancer since our seminal 2004 publication, and then optimizing IHC tests that could be applied to our tissue microarray series. We find that nestin expression and loss of INPP4B are the best biomarkers for this aggressive type of breast cancer, although no single biomarker is both highly sensitive and specific.

Prat A, Cheang MC, Martín M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined Luminal A breast cancer. Journal of Clinical Oncology 2013; 31:203-9.

With my colleagues at UNC-Chapel Hill, we make what might be our last attempt to improve and optimize the composition of the immunohistochemical definition of low risk, luminal A breast cancers. Progesterone receptor, a breast cancer that is routinely measured in diagnostic settings, helps identify the lowest risk group when it is expressed in >20% of cells in a large series of training and test set cohorts and clinical trial specimens.

Isphording A, Ali RH, Irving J, Goytain A, Nelnyk N, Hoang LN, Gilks CB, Huntsman DG, Nielsen TO, Nucci MR, Lee CH. YWHAE-FAM22 endometrial stromal sarcoma: diagnosis by reverse transcription-polymerase chain reaction in formalin-fixed, paraffin embedded tumor. Human Pathology 2013; 44:837-43.

Having identified a causative translocation for a subset of high grade, aggressive endometrial stromal sarcomas, we detail the methodology that can be applied on tissue from standard formalin-fixed, paraffin-embedded tissue blocks by which this translocation event can be reliably detected for clinical diagnosis.

Bastien RR, Rodríguez-Lescure Á, Ebbert MT, Prat A, Munárriz B, Rowe L, Miller P, Ruiz-Borrego M, Anderson D, Lyons B, Álvarez I, Dowell T, Wall D, Seguí MÁ, Barley L, Boucher KM, Alba E, Pappas L, Davis CA, Aranda I, Fauron C, Stijleman IJ, Palacios J, Antón A, Carrasco E, Caballero R, Ellis MJ, Nielsen TO, Perou CM, Astill M, Bernard PS, Martín M. PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. BMC Medical Genomics 2012 Oct 4;5:44.

This study, with my collaborators in Spain and Utah, compares the results of PAM50 testing by qRT-PCR with qRT-PCR and IHC testing for the three most critcal biomarkers in breast cancer: estrogen receptor, progesterone receptor, and HER2. We find that the PAM50 panel has greater prognostic capacity, on clinical trial specimens. Published in an open access journal, with the article quickly becoming noted has "highly accessed."

Lee CH, Ali RH, Rouzbahman M, Marino-Enriquez A, Zhu M, Guo X, Brunner AL, Chiang S, Leung S, Nelnyk N, Huntsman DG, Blake Gilks C, Nielsen TO, Dal Cin P, van de Rijn M, Oliva E, Fletcher JA, Nucci MR. Cyclin D1 as a diagnostic immunomarker for endometrial stromal sarcoma with YWHAE-FAM22 rearrangement. American Journal of Surgical Pathology 2012 Oct;36(10):1562-70.

Having recently discovered a novel translocation pathognomonic of a group of high grade endometrial stromal sarcomas which cannot reliably be recognized purely by histology, with my GPEC team I assist my colleague Cheng Han Lee is the development of immunohistochemical biomarkers that can be run in standard hospital laboratories, allowing identification of these more aggressive tumors for those without access to specialty molecular diagnostics.

Endo M, Nielsen TO. Pazopanib for metastatic soft-tissue sarcoma. Lancet 2012 Sep 1;380(9844):801

My fellow (from Fukuoka, Japan) and I ask the authors of a major sarcoma clinical trial paper to add detail about the histological subtypes responding to this receptor tyrosine kinase inhibitor, as the lack of such information has really confused and held back the field of sarcoma oncology. They reply with additional details which help the sarcoma community interpret where this drug may be most valuable.

Wishart GC, Bajdik CD, Dicks E, Provenzano E, Schmidt MK, Sherman M, Greenberg DC, Green A, Gelmon K, Kosma VM, Olson JC, Beckmann MW, Winqvist R, Cross SS, Severi G, Huntsman D, Pylkäs K, Ellis I, Nielsen TO, Giles G, Blomqvist C, Fasching PA, Couch FJ, Rakha E, Foulkes WD, Blows FM, Bégin LR, van't Veer LJ, Southey M, Nevanlinna H, Mannermaa A, Cox A, Cheang M, Baglietto L, Caldas C, Garcia-Closas M, Pharoah PD. PREDICT Plus: a population-based validation of a prognostic model for early breast cancer that includes HER2. British Journal of Cancer 2012 Aug 21;107(5):800-7

We provided a large dataset for external validation of an advanced prognostic model of breast cancer outcomes, which improves on tools like Adjuvant! by adding infomration on HER2 status.

Stephen K. Chia, Vivien Bramwell-Wesley, Dongsheng Tu, Lois Shepherd, Shan Jiang, Tammi Vickery, Elaine Mardis, Samuel Leung, Karen Ung, Kathleen Pritchard, Joel S. Parker, Phillip S. Bernard, Charles M. Perou, Matthew J. Ellis, Torsten O. Nielsen. A 50 gene intrinsic subtype classifier for prognosis and prediction of benefit to adjuvant tamoxifen. Clinical Cancer Research 2012 Aug 15;18(16):4465-72.

This paper was the product of a lot of work by a lot of people over a long time: a formal prospective-retrospective study on a Canadian breast cancer clinical trial (randomizing women to tamoxifen, after chemotherapy). We show that our new PAM50 molecular assay for breast cancer subtype does a better job than standard clinical tests (including multiple types of estrogen receptor testing) at predicting which patients benefit from tamoxifen.

Kevin B. Jones, Le Su, Huifeng Jin, Carol Lenz, R. Lor Randall, T. Michael Underhill, Torsten O. Nielsen, Sunil Sharma, Mario R. Capecchi. SS18-SSX2 and the mitochondrial apoptosis pathway in mouse and human synovial sarcomas. Oncogene 2013; 32:2365-71.

This is my first publication where I am a coauthor on a paper on which the senior author is a Nobel Laureate! Mario Capecchi is the winner of the 2007 Nobel Prize in Medicine for his work developing transgenic mouse models and his life story is a fascinating one. In this paper, we provided models and did some molecular biology on the Mcl-1 gene in synovial sarcoma, supporting work by Jones/Capecchi in Utah showing a new anticancer drug (designed to restore programmed cell death pathways) is particularly active in this disease in preclinical models.

Garrett Barry and Torsten O. Nielsen. A Review of the Genetics, Molecular Biology, Existing and Experimental Treatment for Clear Cell Sarcoma of Soft Tissue. Electronic Sarcoma Update Newsletter, June 2012, Volume 9, Number 3.

This is a review article my student Garrett and I put together for the patients and professional audience of the Liddy Shriver Sarcoma Initiative's newsletter, an excellent resource for learning about a complex field. Shortly after its publication, it was translated for publication in Chinese!

Won JR, Gao D, Grant D, Cupples J, Rahemtulla A, Wolber R, Nielsen TO, Gilks CB. Variable performance of commercial epidermal growth factor receptor antibodies in detection of basal-like breast cancer. Histopathology 2012 Sep;61(3):518-9

My graduate student Jennifer helped coordinate a provincial immunohistochemistry quality control study, and highlights challenges in the clinical delivery of accurate EGFR immunohistochemistry as a biomarker for the aggressive basal-like subtype of breast cancer.

Aleix Prat, Joel S Parker, Cheng Fan, Maggie Chon U Cheang, Lance D Miller, Jonas Bergh, Stephen K Chia, Philip S Bernard, Torsten O Nielsen, Matthew J Ellis, Lisa A Carey, Charles M. Perou. Concordance among gene-expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen. Annals of Oncology 2012 Nov;23(11):2866-73

In this publication, we highlight the general overlap among various genomic predictors of breast cancer outcome that are in different stages of commercial development. All are able to identify a low risk group of ER positive cancers that may have a very good prognosis even without chemotherapy.

Karamchandani JR, Nielsen TO, van de Rijn M, West RB. Sox10 and S100 in the diagnosis of soft tissue neoplasms. Applied Immunohistochemistry and Molecular Morphology 2012 Oct;20(5):445-50

I help out my former mentor Matt van de Rijn and his residents and colleagues from Stanford, by providing tissue microarrays to complete the largest survey to date of expression of the transcription factor Sox10 in sarcomas and related tumors.

Su L, Sampaio AV, Jones KB, Pacheco M, Goytain A, Lin S, Poulin N, Yi L, Rossi FM, Kast J, Capecchi MR, Underhill TM, Nielsen TO. Deconstruction of the SS18-SSX Fusion Oncoprotein Complex: Insights into Disease Etiology and Therapeutics. Cancer Cell 2012 Mar 20;21(3):333-47

I'm really proud of this paper, a tour de force in molecular biology, published in the world's top cancer journal, with a Nobel Laureate as a coauthor! Basically we figure out how the synovial sarcoma oncogene causes cancer: by linking Activating Transcription Factor 2 to the opposite function of gene repression, via the TLE corepressor we had earlier discovered to be a diagnostic marker of synovial sarcoma. This was published in the open access 10th anniversary edition of Cancer Cell, with an accompanying commentary on its significance.

Liu S, Lachapelle J, Leung S, Gao D, Foulkes WD, Nielsen TO. CD8+ lymphocyte infiltration is an independent favorable prognostic indicator in basal-like breast cancer. Breast Cancer Research 2012 Mar 15;14(2):R48.

This is quite simply one of the world's largest studies into the prognostic significance of immune infiltrates in cancer, in this case cytotoxic T-lymphocytes. Their presence could reflect either a beneficial attack by the body onto cancer cells, or a means by which the cancer cells co-opt immune cells to help them spread. The literature had given confusing results. We were able to show that it is only the basal breast cancers that are associated with a good prognosis if there is an immune response -- not a consistent association in other subtypes of breast cancer.

Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd L, Levine MN, Pritchard KI, Davies SR, Stijleman IJ, Davis C, Ebbert M, Parker JS, Ellis MJ, Bernard PS, Perou CM, Nielsen TO. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clinical Cancer Research 2012 Apr 15;18:2402-12.

This is one of my first published, formal "prospective-retrospective" clinical trial studies, under the auspices of the NCIC-CTG Breast Cancer Correlative Sciences committee. Using the PAM50 assay for breast cancer intrisic subtype, we demonstrate that almost all the added benefit from substituting in (toxic) anthracycline chemotherapy is conferred to patients with both clinically HER2 positive and PAM50 HER2 subtype tumors. Interesting, the basal group had a trend to the opposite finding, doing better on an older CMF chemotherapy regimen.

Pernille B Hertel, Dongsheng Tu, Bent Ejlertsen, Maj-Britt Jensen, Eva Balslev, Shan Jiang, Frances P O’Malley, Kathleen I Pritchard, Lois E Shepherd, Annette Bartels, Nils Brünner, Torsten O Nielsen. TIMP-1 in combination with HER2 and TOP2A for prediction of benefit from adjuvant anthracyclines in high risk breast cancer patients. Breast Cancer Research and Treatment 2012 Feb; 132:225-34.

A major step in proving the clinical validity of a cancer test is confirmation on a second series, and in particular a high level of evidence can be achieved if two similar randomized clinical trials can be brought to bear on the same question and give the same answer. My Danish colleagues had previously developed a predictor of which women will benefit from anthracyclines (an aggressive type of breast cancer chemotherapy). I was able to arrange a collaboration between the major clinical trial groups in Denmark and Canada to confirm this finding (developed on Danish trial DBCG89D) on the independent Canadian trial MA.5. This work is forming the basis for ongoing collaborations between our two groups.

Andrew H Beck, Ankur R Sangoi, Samuel Leung, Robert J Marinelli, Torsten O Nielsen, Marc van de Vijver, Robert B West, Matt van de Rijn, Daphne Koller. Unbiased data-driven analysis of breast cancer cell morphological features uncovers stromal structure as significant prognostic factor. Science Translational Medicine 2011 Nov 9;3(108):108ra113

This work describes an algorithm developed by my colleagues at Stanford University for the computerized analysis of digitized breast cancer pathology images. We provide a critical validation series that proved this technique is able to identify features associated with subsequent patient survival. A novel finding is the major contribution of features of the breast cancer stroma, as opposed to the cancer cells themselves.

Pacheco M, Nielsen TO. Histone deacetylase 1 and 2 in mesenchymal tumors. Modern Pathology 2012 Feb;25(2):222-30.

In support of the IND.200 clinical trial, we gathered together large numbers of sarcomas in a series of tissue microarrays, and optimized immunohistochemical biomarker tests for the major enzymes targeted by the drug under study (SB939, a histone deacetylase inhibitor). We were able to show consistent, high level expression of HDAC2 in fusion transcription-factor associated mesenchymal tumors.

Mitch Dowsett, Torsten O Nielsen, Roger A’Hern, John Bartlett, R Charles Coombes, Jack Cuzick, Matthew Ellis, Lynn Henry, Tracy Lively, Lisa McShane, Soon Paik, Ljudmila Prudkin, Meredith Regan, Janine Salter, Christos Sotiriou, Ian Smith, Giuseppe Viale, Jo Anne Zujewski, Daniel F Hayes. Ki67 in breast cancer: recommendations from the International Ki67 in Breast Cancer Working Group. JNCI Journal of the National Cancer Institute 2011 November 16;103(22):1656-64.

I was invited to present to an international working group on technical aspects of Ki67 testing, at a meeting in London which evolved into this white paper on best practices for Ki67 measurement, interpretation and clinical use. Although this work represents an important synthesis of two decades of work, it is clear there are many unanswered questions about scoring systems and interobserver consistency. As a result, I am directing a follow-up project with my international colleagues, to define additional best practices for clinical validity.

H. Raza Ali, Sarah-Jane Dawson, Fiona M Blows, Elena Provenzano, Samuel Leung, Torsten Nielsen, Paul D Pharoah, Carlos Caldas. A Ki67/BCL2 index based on immunohistochemistry is highly prognostic in ER positive breast cancer. Journal of Pathology 2012 Jan;226(1):97-107

This work represents a multiinstitutional collaborative effort. Our British colleagues trained a prognostic classifier based on simple immunohistochemistry for the proliferation marker Ki67 and the antiapoptotic protein BCL2. We provided a large independent validation set of over 3000 breast cancer samples, that provided the critical proof of the value of this survival predictor among estrogen receptor expressing breast cancers.

Huwait H, Meneghetti A, Nielsen TO. Kaposi sarcoma of the adrenal gland resembling epithelioid angiosarcoma. Sarcoma 2011; 2011:898257.

My first clinical fellow, Hassan Huwait, worked with me to put together this report that expands the spectrum of histological and clinical presentations of Kaposi sarcoma, and virally-induced vascular neoplasm.

Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young TL, Jones SJ, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. Journal of Pathology 2011 Sep;225(1):12-8.

Whose research career can be considered complete without a study on blind dwarves from Newfoundland? Next generation sequencing gives us a chance to identify new genetic abnormalities underlying rare syndromes, as demonstrated elegantly in this study describing the genotype and phenotype induced by specific hereditary mutations in GNPTG, associated with mucolipidosis.

Lee AF, Yip S, Smith AC, Hayes MM, Nielsen TO, O'Connell JX. Low-grade fibromyxoid sarcoma of the perineum with heterotopic ossification: case report and review of the literature. Human Pathology 2011 Nov;42:1804-9.

An elegant molecular FISH confirmation, by our resident Anna Lee, confirms that low grade fibromyxoid sarcomas can ossify, producing a deceptive appearance on imaging studies and core biopsy.

Rimm DL, Nielsen TO, Jewell SD, Rohrer DC, Broadwater G, Waldman F, Mitchell KA, Singh B, Tsongalis GJ, Frankel WL, Magliocco AM, Lara JF, Hsi ED, Bleiweiss IJ, Badve SS, Chen B, Ravdin PM, Schilsky RL, Thor A, Berry DA; Cancer and Leukemia Group B Pathology Committee. Cancer and Leukemia Group B Pathology Committee guidelines for tissue microarray construction representing multicenter prospective clinical trial tissues. Journal of Clinical Oncology 2011 Jun 1;29(16):2282-90.

I played a major part in the formulation of these guidelines for tissue microarray construction and analysis on clinical trials, drawing on my experience at GPEC and my roles on the CALGB Pathology and NCICCTG Correlative Science executive committees.

McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Computational Biology 2011 May;7(5):e1001138.

In this paper we describe a mathematical algorithmic approach to identifying translocations representing transcribed fusion genes from the immense backdrop of next generation sequencing data, in this case from whole transcriptome shotgun sequencing of many kinds of tumor specimens, including sarcomas. In doing so, we also identify a novel RREB1-TFE3 fusion transcription factor oncogene in a sarcoma from a young adult.

Mehta RJ, Jain RK, Leung S, Choo J, Nielsen T, Huntsman D, Nakshatri H, Badve S. FOXA1 is an independent prognostic marker for ER-positive breast cancer. Breast Cancer Research and Treatment 2012 Feb;131(3):881-90.

Using our 4000-case British Columbia tissue microarray series, we validate FOXA1 as one of those rare good prognostic factors in breast cancer - associated with a low risk subset of estrogen receptor positive tumors.

Nielsen TO. Discovery research to clinical trial: A ten year journey. Clinical and Investigative Medicine 2010 Dec 1;33:E342.

I was privileged to be named the 2010 Joe Doupe Young Investigator Award winner, by the Canadian Society for Clinical Investigation. This article elaborates on my award speech, describing the path I took from resident, through basic science discovery work, setting up my own lab and testing hypotheses in vitro, building evidence and eventually initiating a clinical trial (NCIC-CTG IND.200) for sarcoma patients based on my research.

Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clinical Cancer Research 2010 Nov 1; 16:5222-32.

In this work we apply the new PAM50 gene expression assay to a large collection of paraffin blocks linked to detailed clinical and outcome data. We demonstrate the capacity of this assay to identify the molecular subtype of breast cancer, and its superiority over the best clinical and immunohistochemical models for predicting the outcome of women in the common scenario of hormone-receptor positive breast cancer treated with endocrine therapy.

Cheng H, Clarkson PW, Gao D, Pacheco M, Wang Y, Nielsen TO. Therapeutic antibodies targeting CSF1 impede macrophage recruitment in a xenograft model of tenosynovial giant cell tumor. Sarcoma 2010;2010:174528.

This work, funded by the Sarcoma Foundation of America and the Cancer Research Society, describes the world's first model of tenosynovial giant cell tumor suitable for testing of experimental therapeutics, and demonstrates the effectiveness of antibodies against human CSF1 against this disease. Published in an open access journal.

Kennecke H, Yerushalmi R, Woods R, Cheang MC, Voduc D, Speers CH, Nielsen TO, Gelmon K. Metastatic behavior of breast cancer subtypes. Journal of Clinical Oncology Jul 10;28(20):3271-7.

After an extensive effort to carefully annotate all the information about metastatic site and spread in our British Columbia Breast Cancer Outcomes Unit database, we were able to link intrinsic subtype to patterns of metastatic spread, finding for example that luminal cancers spread preferentially to bone, and basal tumors to lung.

Su L, Cheng H, Sampaio AV, Nielsen TO, Underhill TM. EGR1 reactivation by histone deacetylase inhibitors promotes synovial sarcoma cell death through the PTEN tumor suppressor. Oncogene 2010 Jul;29:4352-61.

This molecular tour-de-force by my student Le Su makes the link connecting the synovial sarcoma oncogene to abnormally low expression of the critical PTEN tumor suppressor gene, an advance in understanding the molecular oncogenesis of this disease which has implications for possible therapies with investigational new drugs.

Pacheco M, Horsman DE, Hayes MM, Clarkson PW, Huwait H, Nielsen TO. Small blue round cell tumor of the interosseous membrane bearing a t(2;22)(q34;q12)/EWS-CREB1 translocation: a case report. Molecular Cytogenetics 2010 Jul;3:12.

This open access case report describes an extremely interesting and deceptive case of clear cell sarcoma.

Blows FM, Driver KE, Schmidt MK, Broeks A, van Leeuwen FE, Wesseling J, Cheang MC, Gelmon K, Nielsen TO, Blomqvist C, Heikkilä P, Heikkinen T, Nevanlinna H, Akslen LA, Bégin LR, Foulkes WD, Couch FJ, Wang X, Cafourek V, Olson JE, Baglietto L, Giles GG, Severi G, McLean CA, Southey MC, Rakha E, Green AR, Ellis IO, Sherman ME, Lissowska J, Anderson WF, Cox A, Cross SS, Reed MW, Provenzano E, Dawson SJ, Dunning AM, Humphreys M, Easton DF, García-Closas M, Caldas C, Pharoah PD, Huntsman D. Subtyping of breast cancer by immunohistochemistry to investigate a relationship between subtype and short and long term survival: a collaborative analysis of data for 10,159 cases from 12 studies. PLoS Medicine 2010 May 25;7(5):e1000279.

We were the largest single contributor to this open access meta-analysis of the immunohistochemical subtyping of breast cancer, which confirmed our findings on the prognostic significance of the Luminal A, Luminal B, HER2-associated and basal breast cancer subtypes.

Nielsen TO, West RB. Translating gene expression into clinical care: sarcomas as a paradigm. Journal of Clinical Oncology 2010 Apr 1;28(10):1796-805.

This work discusses the basic philosophy of the sarcoma research programs we are undertaking at UBC and at Stanford, in the context of our current knowledge and work that is going on world-wide. The editor of JCO solicited this review from me, following my presentation at Harvard Medical School in spring of 2009, and I wrote it with my close colleague Rob West from Stanford.

Voduc KD, Cheang MC, Tyldesley S, Gelmon K, Nielsen TO, Kennecke H. Breast cancer subtypes and the risk of local and regional relapse. Journal of Clinical Oncology 2010 Apr 1;28(10):1684-91

Using our large British Columbia tissue microarray series and our established immunohistochemical panel for breast cancer intrinsic subtyping, we show that the non-Luminal A types of breast cancer are associated with increased risk of both local recurrence and regional lymph node relapse, not only post-lumpectomy, but also post-mastectomy.

Jagdis A, Rubin BP, Tubbs RR, Pacheco M, Nielsen TO. Prospective evaluation of TLE1 as a diagnostic immunohistochemical marker in synovial sarcoma. American Journal of Surgical Pathology 2009 Dec;33(12):1743-51.

Having previously identified TLE1 as a specific and sensitive marker of synovial sarcoma by gene expression and tissue microarray analyses, for the next two year, all incoming cases at the BC Cancer Agency and the Cleveland Clinic where synovial sarcoma was considered in the differential diagnosis were prospectively evaluated for TLE1, keratin, EMA and bcl2 immunostains against a molecular translocation test gold standard. The result: 92% positive predictive value and 100% negative predictive value in a real-life diagnostic situation, cementing its role as the best immunostain for this diagnosis, and obviating the need for more expensive molecular testing in many cases. We believe this will be practice changing.

Subramanian S, Thayanithy V, West RB, Lee CH, Beck AH, Zhu S, Downs-Kelly E, Montgomery K, Goldblum JR, Hogendoorn PC, Corless CL, Oliveira AM, Dry SM, Nielsen TO, Rubin BP, Fletcher JA, Fletcher CD, van de Rijn M. Genome-wide transcriptome analyses reveal p53 inactivation mediated loss of miR-34a expression in malignant peripheral nerve sheath tumours. Journal of Pathology 2010 Jan; 220(1):58-70.

The result of a multi-institution consortium to study the expression profile of malignant peripheral nerve sheath tumors, funded by the US Department of Defense, we were able to link repression of p53 and specific micro-RNA pathways to malignant progression from benign neurofibromas to malignant tumors.

Steigen SE, Schaeffer DF, West RB, Nielsen TO. Expression of insulin-like growth factor 2 in mesenchymal neoplasms. Modern Pathology 2009 Jul;22(7):914-21.

IGF2 is a critical signalling molecule in growth and development, and has been co-opted by many cancers. New drugs targeting this pathway are becoming available. In this study, we use a large series of tissue microarrays from Canada, the USA and Norway to make a comprehensive survey of IGF2 expression in benign and malignant bone and soft tissue tumors. The highest expression was found in solitary fibrous tumors and synovial sarcomas.

Cheang MCU, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. JNCI Journal of the National Cancer Institute 2009 May 20;101(10):736-50.

In this paper from our Strategic Partnering to Evaluate Cancer Signatures consortium, with work spearheaded by our GPEC group, we are able to define a cutpoint for the proliferation index which allows the best distinction between indolent luminal A and aggressive luminal B breast cancers to be made by a cheap immunohistochemistry test. This work is published in an on-line format, freely accessible world-wide.

Cheng H, Dodge J, Mehl E, Liu S, Poulin N, van de Rijn M, Nielsen TO. Validation of immature adipogenic status and identification of prognostic biomarkers in myxoid liposarcoma using tissue microarrays. Human Pathology 2009 Sep;40(9):1244-51.

In this work funded from our CIHR grant, we use gene expression profiling data to identify biomarkers in myxoid/round cell liposarcoma, a deceptively aggressive cancer for which no truly effective systemic therapy is available. Using tissue microarrays linked to outcome, we implicate the IGF and RET oncogenic pathways as prognostically important in this disease.

Espinosa I, Beck AH, Lee CH, Zhu S, Montgomery KD, Marinelli RJ, Ganjoo KN, Nielsen TO, Gilks CB, West RB, van de Rijn M. Coordinate expression of colony-stimulating factor-1 and colony-stimulating factor-1-related proteins is associated with poor prognosis in gynecological and nongynecological leiomyosarcoma. American Journal of Pathology 2009 Jun;174(6):2347-2356.

Our star resident research trainee Chenghan Lee did an elective at Stanford, bringing ideas and specimens from Vancouver to help validate the group's previous finding that macrophage signatures are prognostic in leiomyosarcoma, and extend this to show that this occurs via CSF1 production and signaling by tumor cells, recruiting the macrophages that contribute to aggressive disease features.

Liu S, Chia SK, Mehl E, Leung S, Rajput A, Cheang MC, Nielsen TO. Progesterone receptor is a significant factor associated with clinical outcomes and effect of adjuvant tamoxifen therapy in breast cancer patients. Breast Cancer Research and Treatment 2010 Jan;119(1):53-61.

The value of progesterone receptor testing in breast cancer is controversial. After working our way through many of the commercial antibodies, we were able to show that a new rabbit monoclonal, 1E2, works well on our 4000 case tissue microarray series of British Columbia breast cancers. Furthermore, progesterone receptor testing does recognize a small fraction (4%) of cases which could be missed if estrogen receptor testing was used alone, and adds significant additional prognostic information across treatment groups and in multivariate analyses.

Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS. Supervised risk predictor of breast cancer based on intrinsic subtypes. Journal of Clinical Oncology 2009 Mar 10;27(8):1160-7.

This paper demonstrates the culmination of a lot of our work in the Strategic Partnering to Evaluation Cancer Signatures Program. We define and validate a 50 gene classifier panel that accurately subtypes breast cancers into their major intrinsic subtypes. This panel is prognostic and predictive, and can be assayed by qRT-PCR on standard formalin-fixed, paraffin-embedded laboratory specimens.

Hugh J, Hanson J, Cheang MC, Nielsen TO, Perou CM, Dumontet C, Reed J, Krajewska M, Treilleux I, Rupin M, Magherini E, Mackey J, Martin M, Vogel C. Breast cancer subtypes and response to docetaxel in node-positive breast cancer: use of an immunohistochemical definition in the BCIRG 001 trial. Journal of Clinical Oncology 2009 Mar 10;27(8):1168-76.

Our surrogate immunohistochemical panel for breast cancer intrinsic subtyping was applied to this major international breast cancer trial, and reveals that our classification is predictive of response to docetaxel chemotherapy (which benefits women with all major subtypes except Luminal A breast cancers).

Nguyen A, Su L, Campbell B, Poulin NM, Nielsen TO. Synergism of heat shock protein 90 and histone deacetylase inhibitors in synovial sarcoma. Sarcoma 2009;2009:794901.

Anne Nguyen's MSc thesis culminated in this open-access paper, where we demonstrate that Hsp90 and HDAC inhibitors have synergistic activity against synovial sarcoma in vitro. Morever, this synergism is likely mediated by the Nf-kappa-B pathway, inhibitors of which we also demonstrate (for the first time) to be active against synovial sarcoma.

Adamiak A, Lee CH, Nielsen TO, Webber D, O'Connell JX. Duodenal epithelioid gastrointestinal stromal tumor with prominent granular cell features. Human Pathology 2009 Apr;40(4):599-602.

In this case report, we expand the spectrum of histological appearances for gastrointestinal stromal tumors, proving the diagnosis with DNA sequencing for activating receptor tyrosine kinase mutations.

Voduc D, Nielsen TO. Basal and triple-negative breast cancers: impact on clinical decision-making and novel therapeutic options. Clinical Breast Cancer 2008 Dec;8 Suppl 4:S171-8

Dave Voduc and I were asked to write this review article, and we accepted as there have been several other review articles out there on basal breast cancer, some from people with little real experience in how to interpret the diagnostic aspects of this very aggressive form of breast cancer.

Chia S, Norris B, Speers C, Cheang M, Gilks B, Gown AM, Huntsman D, Olivotto IA, Nielsen TO, Gelmon K. Human epidermal growth factor receptor 2 overexpression as a prognostic factor in a large tissue microarray series of node-negative breast cancers. Journal of Clinical Oncology 2008 Dec 10;26(35):5697-704.

This work represents some of the output from our very active collaboration among the Genetic Pathology Evaluation Centre, the Breast Cancer Outcomes Unit of the BC Cancer Agency, and PhenoPath laboratories. We are able to define the frequency of HER2 overexpression in a large population of early (node negative) breast cancers as 10% - somewhat lower than previous estimates - and show the adverse natural history among a historically-important cohort of patients who did not receive adjuvant systemic therapy.

So AI, Levitt RJ, Eigl B, Fazli L, Muramaki M, Leung S, Cheang MC, Nielsen TO, Gleave M, Pollak M. Insulin-like growth factor binding protein-2 is a novel therapeutic target associated with breast cancer. Clinical Cancer Research 2008 Nov 1;14(21):6944-54.

Working with our close collaborators from the Prostate Centre, who have developed antisense oligonucleotide therapies targeting IGFBP2, we show that this protein is highly expressed in the majority of breast cancers, but not in benign tumors of the breast. This finding suggests that their new antisense drug OGX-225 might have activity against a broad spectrum of breast tumors, affecting a growth pathway co-opted by many cancers.

Habibi G, Leung S, Law JH, Gelmon K, Masoudi H, Turbin D, Pollak M, Nielsen TO, Huntsman D, Dunn SE. Redefining prognostic factors for breast cancer: YB-1 is a stronger predictor of relapse and disease-specific survival than estrogen receptor or HER-2 across all tumor subtypes. Breast Cancer Research 2008 Oct 16;10(5):R86.

The oncogene YB-1, a transcriptional regulator of both the EGFR and HER2 breast cancer oncogenes, is associated with poor patient survival, regardless of biological subtype, in our 4000-case British Columbia breast cancer tissue microarray series.

Arnes JB, Bégin LR, Stefansson IM, Brunet JS, Nielsen TO, Foulkes WD, Akslen LA. Expression of EGFR in relation to BRCA1 status, basal-like markers and prognosis in breast cancer. Journal of Clinical Pathology 2009 Feb;62(2):139-46.

In this paper I contributed data and ideas for a multinational collaborative study confirming the association of the epidermal growth factor receptor oncogene with basal-like breast cancers, particularly those in patients with hereditary BRCA1 forms of aggressive breast cancer.

Heffernan EJ, Lefaivre K, Munk PL, Nielsen TO, Masri BA. Ossifying lipoma of the thigh. British Journal of Radiology 2008 Aug;81(968):e207-10.

This one is just a case report that the radiologists put my name on and published without asking me first. Please never do that to me!

Voduc D, Nielsen TO, Cheang MC, Foulkes WD. The combination of high cyclin E and Skp2 expression in breast cancer is associated with a poor prognosis and the basal phenotype. Human Pathology 2008 Oct;39(10):1431-7.

We assess, on breast cancer tissue microarrays, the cyclin E - p27Kip1 - Skp2 axis, regulating cell cycle control, and find that by immunohistochemistry it is the two oncogenes which are associated with the aggressive basal-like subtype of breast cancer, and with adverse patient outcomes.

Lubieniecka JM, de Bruijn DR, Su L, van Dijk AH, Subramanian S, van de Rijn M, Poulin N, van Kessel AG, Nielsen TO. Histone deacetylase inhibitors reverse SS18-SSX-mediated polycomb silencing of the tumor suppressor early growth response 1 in synovial sarcoma. Cancer Research 2008 Jun 1;68(11):4303-10.

In this work, we identify EGR1 as a gene abnormally suppressed in synovial sarcoma, and go on to demonstate that the key oncogene that drives this cancer directly suppresses EGR1 by recruiting Polycomb proteins to its promoter and methylating its histones. Furthermore, new drugs directly reverse this process, restoring tumor suppressor activity in synovial sarcoma cells. This work is novel in demonstrating one of the first direct targets of the SS18-SSX oncoprotein, its mechanism of action via abnormal epigenetic suppression, and an experimental therapy to reverse this process.

Liu S, Cheng H, Kwan W, Lubieniecka JM, Nielsen TO. Histone deacetylase inhibitors induce growth arrest, apoptosis, and differentiation in clear cell sarcoma models. Molecular Cancer Therapeutics 2008 Jun;7(6):1751-61.

Using two recently-developed investigational new drugs, we show consistent sensitivity of translocation-associated sarcoma cell lines to histone deacetylase inhibitors, including against clear cell sarcoma (for which no effective systemic therapy is currently available).

Crabb SJ, Cheang MC, Leung S, Immonen T, Nielsen TO, Huntsman D, Bajdik CD, Chia SK. Basal breast cancer molecular subtype predicts for lower incidence of axillary lymph node metastases in primary breast cancer. Clinical Breast Cancer 2008 Jun;8(3):249-56.

By applying our surrogate immunopanel definition of basal breast cancer and linking to detailed information about clinical course from the BC Cancer Agency's Breast Cancer Outcomes Unit, we confirm that the aggressive basal-like subtype of breast cancer has a propensity to spread and kill without first involving lymph nodes.

Lee CH, Espinosa I, Jensen KC, Subramanian S, Zhu SX, Varma S, Montgomery KD, Nielsen TO, van de Rijn M, West RB. Gene expression profiling identifies p63 as a diagnostic marker for giant cell tumor of the bone. Modern Pathology 2008 May;21(5):531-9

Chenghan Lee, a graduate of the UBC MD/PhD program, followed in my footsteps to do a resident research elective in Matt van de Rijn's lab. Among the fruits of his labour there was this study using gene and tissue microarrays to analyze giant cell tumor of bone. You can find a .pdf of the article here.

Voduc D, Kenney C, Nielsen TO. Tissue microarrays in clinical oncology. Seminars in Radiation Oncology 2008 Apr;18(2):89-97.

This review article, aimed at clinicians, describes tissue microarray technology, its advantages and disadvantages, and how it can be used to accelerate translation of new research into clinically-useful tests.

Cheang MC, Voduc D, Bajdik C, Leung S, McKinney S, Chia SK, Perou CM, Nielsen TO. Basal-like breast cancer defined by five biomarkers has superior prognostic value than triple-negative phenotype. Clinical Cancer Research 2008 Mar 1;14(5):1368-76.

We demonstrate, on a large population-based tissue microarray series, that almost all the additional risk of the clinically important "triple negative" type of breast cancer is conferred by the subset of "core basal" tumors that express positive markers (EGFR and cytokeratin 5) of basal breast cancer. Furthermore, anthracycline-treated patients may also do relatively poorly if they have this phenotype, which can easily be identified in clinical labs.

Lee CH, Espinosa I, Vrijaldenhoven S, Subramanian S, Montgomery KD, Zhu S, Marinelli RJ, Peterse JL, Poulin N, Nielsen TO, West RB, Gilks CB, van de Rijn M. Prognostic significance of macrophage infiltration in leiomyosarcomas. Clinical Cancer Research 2008 Mar 1;14(5):1423-30.

Macrophage infiltrates in cancer have been linked with aggressive tumor behaviour. Here we identify a macrophage gene expression signature in a subset of leiomyosarcomas, which is not seen in other sarcomas. With tissue microarrays linked to patient outcome, we confirm this finding in larger numbers of patients and show for the first time that such infiltrates portend poor outcomes in soft tissue (but not uterine) leiomyosarcomas.

Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC, Corless CL, Fire AZ, van de Rijn M. MicroRNA expression signature of human sarcomas. Oncogene 2008 Mar 27;27(14):2015-26

Working with Nobel Laureate Andrew Fire, we present the first large microarray study of microRNA expression in human sarcomas

Voduc D, Cheang M, Nielsen T. GATA-3 expression in breast cancer has a strong association with estrogen receptor but lacks independent prognostic value. Cancer Epidemiology, Biomarkers and Prevention 2008 Feb;17(2):365-73

Working with my fellow Dave Voduc and PhD student Maggie Cheang, we use our 4000-case breast cancer tissue microarray to investigate the clinical value of GATA-3, a transcription factor associated with the good prognosis, estrogen receptor positive, Luminal A form of breast cancer.

Espinosa I, Lee CH, Kim MK, Rouse BT, Subramanian S, Montgomery K, Varma S, Corless CL, Heinrich MC, Smith KS, Wang Z, Rubin B, Nielsen TO, Seitz RS, Ross DT, West RB, Cleary ML, van de Rijn M. A novel monoclonal antibody against DOG1 is a sensitive and specific marker for gastrointestinal stromal tumors. American Journal of Surgical Pathology 2008 Feb;32(2):210-218

In continuing followup of our groundbreaking study of sarcoma expression profiling, we develop a diagnostic monoclonal antibody that can be more widely available than our previous polyclonal. DOG1 (aka TMEM16A) is an excellent, sensitive and specific marker for GI stromal tumors, which we are already using diagnostically at Stanford and UBC. It has particular value for kit negative cases.

Cheang MC, van de Rijn M, Nielsen TO. Gene expression profiling of breast cancer. Annual Reviews of Pathology 2008;3:67-97.

My student Maggie and I wrote this critical review of the application of gene expression technology to the study of breast cancer, for the February 2008 issue of Annual Reviews of Pathology: Mechanisms of Disease. If you are interested to read it, direct downloads can be found at the following site: http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.pathmechdis.3.121806.151505

Steigen SE, Straume B, Turbin D, Chan AK, Leung S, Nielsen TO, Lindal S. Clinicopathologic factors and nuclear morphometry as independent prognosticators in KIT-positive gastrointestinal stromal tumors. Journal of Histochemistry and Cytochemistry 2008 Feb;56(2):139-45.

Once our GI stromal tumor tissue array was built, Sonja and I quickly engaged in other studies, including using our BLISS automated image analysis platform to perform a comprehensive study into the value of nuclear morphometry in GI stromal tumors against a gold standard of patient natural history

Jensen KC, Turbin DA, Leung S, Miller MA, Johnson K, Norris B, Hastie T, McKinney S, Nielsen TO, Huntsman DG, Gilks CB, West RB. New cutpoints to identify increased HER2 copy number: analysis of a large, population-based cohort with long-term follow-up. Breast Cancer Research and Treatment 2008 Dec;112(3):453-9

The results of FISH analysis for HER2 on our large breast cancer tissue microarray series took a great deal of time and effort to obtain, but is of value for several studies. Here, we perform comprehensive cutpoint analysis and find that the current requirement for an amplification ratio of >2.2 for a case to be considered positive for HER2 is probably too stringent

Steigen SE, Bjerkehagen B, Haugland HK, Nordrum IS, Løberg EM, Isaksen V, Eide TJ, Nielsen TO. Diagnostic and prognostic markers for gastrointestinal stromal tumors in Norway. Modern Pathology 2008 Jan;21(1):46-53.

Sonja, my sabbatical fellow from the University of Northern Norway, spent a year with me during which time we built, stained and scored a series of GI stromal tumors representing almost the full population of Norway in the two decades preceding the Gleevec era. In our first publication using this material, we describe the series and how established biomarkers map to patient outcome

Heffernan EJ, Alkubaidan FO, Nielsen TO, Munk PL. The imaging appearances of metallosis. Skeletal Radiology 2008 Jan;37(1):59-62

Working with my radiology colleagues in the provincial musculoskeletal tumor group, we identify an extreme case of metallosis resulting from breakdown of a failed joint prosthesis, and present the imaging and pathologic findings

Rakha EA, Tan DS, Foulkes WD, Ellis IO, Tutt A, Nielsen TO, Reis-Filho JS. Are triple negative tumours and basal-like breast cancer synonymous? Breast Cancer Research 2007 Nov 13; 9:404

Marc van de Vijver's group published a study claiming that gene expression analysis revealed ER/PR/HER2 triple negative breast cancers to have Basal expression profiles. Along with other Canadian and British researchers, we had serious concerns with the supporting date presented and the extent of the conclusions that were drawn. It is clear from our own and others' research that there are in fact many "triple negative" cases that behave better than basal tumors, and that there are basal tumors which are positive for at least one of the clinical markers, so these terms can hardly be considered synonymous (despite the conveniences that would create)

Turbin DA, Leung S, Cheang MC, Kennecke HA, Montgomery KD, McKinney S, Treaba DO, Boyd N, Goldstein LC, Badve S, Gown AM, van de Rijn M, Nielsen TO, Gilks CB, Huntsman DG. Automated quantitative analysis of estrogen receptor expression in breast carcinoma does not differ from expert pathologist scoring: a tissue microarray study of 3,484 cases. Breast Cancer Research and Treatment 2008 Aug;110(3):417-26.

The first grant I ever secured as an independent investigator was for automated digital imaging equipment for tissue microarrays, and five years later we published a massive study on its value in breast cancer. To settle the question of who is right, the machine or the human, we compared results to the gold standard of patient outcome. The bottom line is basically a tie: for nuclear immunostains, automated image analysis with appropriately sophisticated software is equal to expert visual analysis, at least in the example of breast cancer estrogen receptor expression

Stratford AL, Habibi G, Astanehe A, Jiang H, Hu K, Park E, Shadeo A, Buys TP, Lam W, Pugh T, Marra M, Nielsen TO, Klinge U, Mertens PR, Aparicio S, Dunn SE. Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy. Breast Cancer Research 2007;9(5):R61.

In a combined basic and translational study with my friend and colleague Sandi Dunn, we link the important YB-1 transcription factor to the aggressive Basal subtype of breast cancer, explaining its high rate of expression of epidermal growth factor receptor, a possible therapeutic target

Ng TL, O'Sullivan MJ, Pallen CJ, Hayes M, Clarkson PW, Winstanley M, Sorensen PH, Nielsen TO, Horsman DE. Ewing Sarcoma with Novel Translocation t(2;16) Producing an In-Frame Fusion of FUS and FEV. Journal of Molecular Diagnostics 2007 Sep;9(4):459-63.

A case I diagnosed as Ewing sarcoma and sent for cytogenetics is found to contain a novel translocation, fusing the unusual alternate 5' partner FUS with the rare Fifth Ewing Variant 3' partner. The result is a fusion oncogene never before described, which would have been missed by standard PCR and FISH diagnostic strategies.

Badve S, Turbin D, Thorat MA, Morimiya A, Nielsen TO, Perou CM, Dunn S, Huntsman DG, Nakshatri H. FOXA1 expression in breast cancer--correlation with luminal subtype A and survival. Clinical Cancer Research 2007 Aug 1;13(15 Pt 1):4415-21

This GPEC collaborative study links FOXA1, an estrogen receptor-associated transcription factor, to the good prognosis Luminal A subtype of breast cancer

Tischkowitz M, Brunet JS, Begin LR, Huntsman DG, Cheang MC, Akslen LA, Nielsen TO, Foulkes WD. Use of immunohistochemical markers can refine prognosis in triple negative breast cancer. BMC Cancer 2007 Jul 24;7(1):134

In collaboration with Will Foulkes' group at McGill, we show that both triple negative and five biomarker methods for surrogate identification of the basal -like phenotype of breast cancer hold up across different institutions. Adding EGFR and CK5/6 positive markers of the basal phenotype identifies a group with particularly high risk over both short and long terms after diagnosis

Wunder JS, Nielsen TO, Maki RG, O'Sullivan B, Alman BA. Opportunities for improving the therapeutic ratio for patients with sarcoma. Lancet Oncology 8:513-24 (2007).

This review article summarizes the state of the art in molecular pathology, local treatment by surgery and radiation, and conventional, targeted and investigational systemic therapy for sarcomas. I contributed the molecular biology and pathology sections as well as discussions on Hsp90 and histone deacetylase inhibitors. Unfortunately, the journal mislabeled the diagnoses in Figure 2 - don't worry, I can tell the difference between MFH and DSRCT!

Cupp JS, Miller MA, Montgomery KD, Nielsen TO, O'Connell JX, Huntsman D, van de Rijn M, Gilks CB, West RB. Translocation and expression of CSF1 in pigmented villonodular synovitis, tenosynovial giant cell tumor, rheumatoid arthritis and other reactive synovitides. American Journal of Surgical Pathology 31:970-6 (2007).

In this followup to our 2006 PNAS article, we show that CSF1-activating translocations can be identified in about 60% of cases of tenosynovial giant cell tumor. However, the remaining cases still show high expression of CSF1, suggesting that this is, indeed, the common biological driver of this tumor, although the mechanism of activation is not always a translocation splicing this gene to a highly active promoter.

Terry J, Saito T, Subramanian S, Ruttan C, Antonescu CR, Goldblum JR, Downs-Kelly E, Corless CL, Rubin BP, van de Rijn M, Ladanyi M, Nielsen TO. TLE1 as a diagnostic immunohistochemical marker for synovial sarcoma emerging from gene expression profiling studies. American Journal of Surgical Pathology 31:240-6 (2007).

Multiple independent gene expression profiling studies of synovial sarcoma, including those from our own group and from Dr. Ladanyi's group at Memorial Sloan-Kettering, find the human groucho homolog TLE1 (a transcriptional repressor of differentiation) to be dramatically overexpressed in synovial sarcoma. We show that antibodies recognizing TLE1 are excellent nuclear biomarkers of this disease that work on clinical material with extremely high senstivity and diagnostic specificity. Primary images are available here.

Cheang MC, Treabo DO, Speers CH, Olivotto IA, Bajdik CD, Chia SK, Goldstein LC, Gelmon KA, Huntsman D, Gilks CB, Nielsen TO, Gown AM. Immunohistochemical detection using the new rabbit monoclonal antibody SP1 of estrogen receptor in breast cancer is superior to mouse monoclonal antibody 1D5 in predicting survival. Journal of Clinical Oncology 24:5637-44 (2006).

With the incredible tool of a 4631-case population-based breast cancer tissue array series with long-term followup, a collaboration between the Genetic Pathology Evaluation Centre and the BCCA Breast Cancer Outcomes Unit, we are validating many exciting new biomarkers in breast cancer, with a particular focus on those identified by expression profiling studies. The first manuscript to come from this work shows the value of a new generation of diagnostic antibodies, which are superior for prognostication and prediction of tamoxifen response in breast cancer. Primary images are available here.

Yehiely F, Moyano JV, Evans JR, Nielsen TO, Cryns VL. Deconstructing the molecular portrait of basal-like breast cancer. Trends in Molecular Medicine 12:537-44 (2006).

In this review article, we discuss the aggressive basal-like subtype of breast cancer, which tends to afflict premenopausal women, is prone to early systemic spread, and for which we currently lack effective targeted therapeutics.

Ring BZ, Seitz RS, Beck R, Shasteen WJ, Tarr SM, Cheang MC, Yoder BJ, Budd GT, Nielsen TO, Hicks DG, Estopinal NC, Ross DT. Novel prognostic immunohistochemical biomarker panel for estrogen receptor-positive breast cancer. Journal of Clinical Oncology 24:3039-47 (2006).

Including standard as well as novel antibodies, a classification and regression tree (CART) strategy and independent tissue microarray series from Alabama, Ohio and British Columbia for validation, we helped develop an immunohistochemical panel that can assess likely patient outcomes for women with estrogen receptor positive breast cancer.

Nielsen TO. Microarray analysis of sarcomas. Advances in Anatomic Pathology 13:166-73 (2006).

In this review article, I summarize the technologies used for microarray analysis of cancer, their advantages and limitations, and the results to date derived from applying these strategies to human primary sarcoma specimens.

Carey LA, Perou CM, Livasy CA, Dressler LG, Cowan D, Conway K, Karaca G, Troester MA, Tse CK, Edmiston S, Deming SL, Geradts J, Cheang MC, Nielsen TO, Moorman PG, Earp HS, Millikan RC. Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA (Journal of the American Medical Association) 295:2492-502 (2006).

Using the surrogate immunohistochemical panel we developed, this study shows that premenopausal African-American women get the more aggressive basal-like subtype of breast cancer at a frequency 2 - 3 times higher than in caucasians or in postmenopausal women of any race. This finding suggests that the poor outcomes seen in this group of women are not simply the product of differences in health care access or socioeconomic status, but rather have a major underlying biological explanation.

Callaghy GM, Pharoah PD, Pinder SE, Hsu FD, Nielsen TO, Ragaz J, Ellis IO, Huntsman D, Caldas C. Bcl-2 is a prognostic marker in breast cancer independent of Nottingham Prognostic Index (NPI). Clinical Cancer Research 12:2468-75 (2006).

Resolving a bit of a controversy in the literature, the anti-apoptotic oncoprotein Bcl-2 is confirmed to be a positive prognostic factor among breast carcinomas. Furthermore, its value holds up not only in our original British Columbia tissue microarray series, but also in an entirely independent series of over 1000 breast cancers from England, and its value holds up in a formal multivariate analysis against standard, validated clinicopathologic prognostic factors for breast cancer.

West RB, Rubin BP, Miller MA, Subramanian S, Kaygusuz G, Montgomery K, Zhu S, Marinelli RJ, De Luca A, Downs-Kelly E, Goldblum JR, Corless CL, Brown PO, Gilks CB, Nielsen TO, Huntsman D, van de Rijn M. A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells. PNAS Proceedings of the National Academy of Sciences of the United States of America 103:690-5 (2006).

Following up on gene expression profiling results and in situ hybridization validation studies, we have identified a novel translocation, involving the CSF1 gene that causes the development of tenosynovial giant cell tumors and the related condition known as pigmented villonodular synovitis. A fascinating finding is that only a small fraction of the tumor cells are neoplastic, bearing the translocation; the bulk of the tumor is comprised of benign macrophages induced by the high CSF1 levels.

Moyano JV, Evans JR, Chen F, Lu M, Werner ME, Yehiely F, Diaz LK, Turbin D, Karaca G, Wiley E, Nielsen TO, Perou CM, Cryns VL. alphaB-Crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer. Journal of Clinical Investigation 116:261-70 (2006).

Our colleague Vince Cryns, from Northwestern University, characterized an important inhibitor of breast cell apoptosis and differentiation, and proven that it is oncogenic in vitro and in mouse models. We provided clinical validation in breast cancer tissue microarrays of its approximate frequency in the population and of its association with poor prognosis and with the basal-like immunophenotype, and present primary image data on-line. The article was highlighted by an editorial and commentaries in concurrent issues of Nature and Nature Reviews Cancer.

Turbin DA, Cheang MC, Bajdik CD, Gelmon KA, Yorida E, De Luca A, Nielsen TO, Huntsman DG, Gilks CB. MDM2 protein expression is a negative prognostic marker in breast carcinoma. Modern Pathology 19:69-74 (2006).

Using large training and validation breast cancer tissue microarrays, we demonstrate that expression of the oncoprotein MDM2 (an inhibitor of the p53 gene, the "guardian of the genome" whose function is vital in preventing malignancy) is a negative prognostic factor in breast cancer, independent of standard clinical and pathological risk factors. This paper presents the primary image data on-line.

Lubieniecka JM, Nielsen TO. cDNA microarray-based translational research in soft tissue sarcoma. Journal of Surgical Oncology 92:267-71 (2005).

This was an invited minireview, based in part on presentations I had given to the Alberta Cancer Board and the Canadian Association of Pathologists, that summarizes recent advances in gene expression profiling of adult soft tissue sarcomas, and how those findings can be used to develop new targeted therapies for sarcomas.

Liu CL, Montgomery KD, Natkunam Y, West RB, Nielsen TO, Cheang MC, Turbin DA, Marinelli RJ, van de Rijn M, Higgins JP. TMA-Combiner, a simple software tool to permit analysis of replicate cores on tissue microarrays. Modern Pathology 18:1641-8 (2005).

Our group did beta-testing and developmental work to assist our colleagues at Stanford University to develop simple programs (Excel macros) that can quickly organize large matrices of tissue microarray data. This paper describes and demonstrates how data from multiple samples of the same tumor, and multiple scores of the same sample, can be quickly and efficiently consolidated to accelerate data analysis.

Terry J, Lubieniecka JM, Kwan W, Liu S, Nielsen TO. Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin prevents synovial sarcoma proliferation via apoptosis in in vitro models. Clinical Cancer Research 11:5631-8 (2005).

We show that although several specific receptor tyrosine kinases are inactive against synovial sarcoma cell line models, 17AAG, an inhibitor of multiple receptor tyrosine kinases and mutant oncoproteins, is highly effective at inducing apoptotic cell death in monolayer and spheroid growth models, at clinically-achievable concentrations. It is hoped that such findings may provide justification for a clinical trial, as effective systemic agents in this disease are currently unavailable.

Prentice LM, Shadeo A, Lestou VS, Miller MA, Deleeuw RJ, Makretsov N, Turbin D, Brown LA, Macpherson N, Yorida E, Cheang MC, Bentley J, Chia S, Nielsen TO, Gilks CB, Lam W, Huntsman DG. NRG1 gene rearrangements in clinical breast cancer: identification of an adjacent novel amplicon associated with poor prognosis. Oncogene 24:7281-9 (2005).

An amplicon on chromosome 8p, near the neuregulin (NRG1) gene, has been implicated by previous work in breast cancer. Using fluorescent in situ hybridization probes on our breast cancer tissue microarrays, we show in fact that the most common site of amplfication is immediately centromeric to NRG1, with the as-yet-poorly-characterized SPFH2 gene the stronger candidate oncogene, associated with poor prognosis in breast cancer.

Subramanian S, West RB, Marinelli RJ, Nielsen TO, Rubin BP, Goldblum JR, Patel RM, Zhu S, Montgomery K, Ng TL, Corless CL, Heinrich MC, van de Rijn M. The gene expression profile of extraskeletal myxoid chondrosarcoma. Journal of Pathology 206:433-44 (2005).

This paper is the first publication of the gene expression profile for extraskeletal myxoid chondrosarcoma, a malignant tumor of the limbs. Consistent with findings from other translocation-associated sarcomas, we find a very distinctive expression signature which highlights some potential therapeutic targets.

Terry J, Barry TS, Hsu FD, Horsman D, Huntsman DG, Gown AM, Nielsen TO. Fluorescence in situ hybridization for the detection of t(X;18)(p11.2;q11.2) in a synovial sarcoma tissue microarray. Diagnostic Molecular Pathology 14:77-82 (2005).

We demonstrate that an SYT break-apart flourescent in-situ hybridization strategy for the detection of the translocation characteristic of synovial sarcoma is sensitive and specific on archival, formalin-fixed paraffin-embedded standard diagnostic material, even in the technically-demanding tissue microarray format, and therefore represents a readily applicable diagnostic strategy.

West RB, Nuyten DS, Subramanian S, Nielsen TO, Corless CL, Rubin BP, Montgomery K, Zhu S, Patel R, Hernandez-Boussard T, Goldblum JR, Brown PO, van de Vijver M, van de Rijn M. Determination of stromal signatures in breast carcinoma. PLoS Biology 3:e187 (2005).

The expression profiles of two non-malignant soft tissue tumors, namely desmoid-type fibromatosis and solitary fibrous tumor, are presented in detail. A fascinating surprise finding is that these same gene expression signatures are expressed in the stroma of breast cancers, and those breast cancers with the solitary fibrous tumor (epithelial support phenotype) signature have a very much worse prognosis than those with the fibromatosis (scar-like reaction phenotype) signature.

Wiseman SM, Makretsov N, Nielsen TO, Gilks B, Yorida E, Cheang M, Turbin D, Huntsman DG. Co-expression of the Type 1 growth factor receptor family members HER1, HER2 and HER3 has a synergistic negative prognostic effect on breast cancer survival. Cancer 103:1770-7 (2005).

Using tissue microarrays, we assessed by immunohistochemistry the expression of human epidermal growth factor receptor family members HER1, HER2, HER3 and HER4 and conclude that co-expression of any two of the first three is associated with especially poor prognosis.

Ng TL, Gown AM, Barry TS, Cheang MCU, Chan AKW, Turbin DA, Hsu FD, West RB, Nielsen TO. Nuclear beta-catenin expression in bone and soft tissue tumors. Modern Pathology 18:68-74 (2005).

Immunohistochemical analysis of four tissue microarrays representing over 500 cases of a broad variety of mesenchymal neoplasms shows that nuclear expression of beta-catenin, a transcription factor activated by Wnt signalling, is largely confined to just four tumor types. A novel digital image database is used to make primary data accessible to all readers.

Subramanian S, West RB, Corless CL, Ou W, Rubin BP, Chu KM, Leung SY, Yuen ST, Zhu S, Hernandez-Boussard T, Montgomery K, Nielsen TO, Patel RM, Goldblum JR, Heinrich MC, Fletcher JA, van de Rijn M. Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations have distinct gene expression profiles. Oncogene 14:7780-90 (2004).

Gastrointestinal stromal tumors are shown to have distinct expression profiles, depending on whether their fundamental oncogenic mutation is in KIT exon 9, exon 11, or in PDGFRA, and this finding is validated on tissue microarrays, with implications for treatment.

Makretsov NA, Huntsman DG, Nielsen TO, Yorida E, Peacock M, Cheang MCU, Dunn SE, Hayes M, van de Rijn M, Bajdik C, and Gilks CB. Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast cancer. Clinical Cancer Research 10:6143-58 (2004).

Several dozen immunohistochemical markers were applied to serial sections of the same breast cancer tissue microarray. Hierarchical clustering analysis is shown to be capable of determining relationships among markers and tumors, and determining a limited panel of immunostains which are tightly linked to patient outcomes.

Nielsen TO, Hsu FD, Jensen K, Cheang M, Karaca G, Hernandez-Boussard T, Cowan D, Dressler L, Livasy C, Akslen LA, Ragaz J, Gown AM, Gilks CB, van de Rijn M, Perou CM. Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clinical Cancer Research 10:5367-74 (2004).

Using breast cancer tissue microarrays, we confirm the existence of the basal-type poor prognostic subgroup of breast cancer, and demonstrate its association, in many cases, with expression of the epidermal growth factor receptor, a finding with potential therapeutic implications. This paper has been particularly influential, garnering several hundred citations.

West RB, Harvell J, Linn SC, Liu CL, Prapong W, Montgomery K, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Brown PO, van de Rijn M. Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans. American Journal of Surgical Pathology 28:1063-9 (2004).

Following up on DFSP gene expression profiling results published in Am J Pathol (Dec 2003), apolipoprotein D was identified as a specific and sensitive immunomarker for this tumor. Its value in a clinical context is here shown using tissue microarrays.

West RB, Corless CL, Chen X, Rubin BP, Subramanian S, Montgomery K, Zhu S, Ball CA, Nielsen TO, Patel R, Goldblum JR, Brown PO, Heinrich MC, van de Rijn M. The novel marker, DOG1, is expressed ubiquitously in GI Stromal Tumors irrespective of KIT or PDGFRA mutation status. American Journal of Pathology 165:107-13 (2004).

Following up on the expression profiling results we published in Lancet in 2002, we identified an uncharacterized cDNA (FLJ10261), now christened DOG1 (for Discovered On GIST-1). Here we show, using sarcoma tissue microarrays, that an mRNA in situ hybridization probe, as well as a custom polyclonal antibody, created based on the cDNA spot sequence, specifically and sensitively mark gastrointestinal stromal tumors. Tumors with variant PDGF-alpha (as opposed to c-kit) activating mutations are successfully identified using this marker, which otherwise might be mis-diagnosed and inappropriately treated.

Nielsen TO, Andrews HN, Cheang M, Kucab JE, Hsu FD, Ragaz J, Gilks CB, Makretsov N, Bajdik CD, Brookes C, Neckers LM, Evdokimova V, Huntsman DG, Dunn SE: Co-expression of the insulin-like growth factor-1 receptor (IGF-1R) and urokinase plasminogen activator (uPA) in breast cancer is associated with poor survival: Potential for intervention with 17-allylamino geldanamycin (17AAG). Cancer Research 64:286-91 (2004).

The novel compound 17AAG blocks IGF1r-mediated signalling via the AKT pathway, preventing activation of urokinase plasminogen activator, a major effector of tumor invasion. Using tissue arrays representing over 900 cases of breast carcinoma, IGF1 receptor expression correlates with uPA, and with poor patient outcome, highlighting the potential therapeutic role of 17AAG.

Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M: Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. American Journal of Pathology 163:2383-95 (2003).

Results of gene expression profiling and array-CGH on the unusual skin tumor known as DFSP are consistent with its known translocation between chromosomes 17 and 22, and reveals a distinct set of genes which are both amplified and overexpressed

Hughes-Davies L, Huntsman D, Ruas M, Fuks F, Bye J, Chin SF, Milner J, Brown LA, Hsu F, Gilks B, Nielsen T, Schulzer M, Chia S, Ragaz J, Cahn A, Linger L, Ozdag H, Cattaneo E, Jordanova ES, Schuuring E, Yu DS, Venkitaraman A, Ponder B, Doherty A, Aparicio S, Bentley D, Theillet C, Ponting CP, Caldas C, Kouzarides T: EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell 115: 523-525 (November 26, 2003)

Initial identification, cloning and characterization of a gene (EMSY) on chromosome 11 which encodes a protein which epigenetically inactivates the BRCA2 hereditary breast and ovarian cancer gene product. EMSY is amplified in many sporadic cases of breast and ovarian cancer, and this is associated with poor prognosis. This finding helps provide an answer to the elusive question why BRCA mutations are seen in hereditary, but not the more common sporadic, types of breast cancer.
For the month after its publication, this was the most frequently accessed article at Cell!

Nielsen, T.O., Hsu, F.D., O'Connell, J.X., Gilks, C.B., Sorensen, P.H.B., Linn, S.C., West, R.B., Liu, C.L., Botstein, D., Brown, P.O., and van de Rijn, M.: Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. American Journal of Pathology 163:1449-56 (2003).

A tissue microarray containing 46 cases of synovial sarcoma and 29 cases of other soft tissue tumors in its differential diagnosis is built and used to validate protein expression of two markers previously identified by cDNA microarray expression profiling. Heirarchical clustering is performed to organize immunohistochemical results, and possible therapeutic implications are discussed.

Price, G.B., Allarakhia, M., Cossons, N., Nielsen, T., Diaz-Perez, M., Friedlander, P., Tao, L., and Zannis-Hadjopoulos, M.: Identification of a cis-element that determines autonomous DNA replication in eukaryotic cells. Journal of Biological Chemistry 278:19649-59 (2003).

A consensus 36 bp human replication origin DNA sequence, derived from multiple origin assay methods, is shown to drive autonomous replication in vitro and to be present at replication origin sites in human and other animal cells.

Hsu, F.D., Nielsen, T.O., Alkushi, A., Dupuis, B., Huntsman, D., Liu, C.L., van de Rijn, M., and Gilks, C.B.: Multiple tumor tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemisty. Modern Pathology 15:1374-80 (2002).

23 standard immunohistochemical markers are tested on a tissue microarray containing over 350 examples of human tumors, and this method is found to have rapid utility for quality control evaluation of immunohistochemical staining methodologies for quality control purposes.

Crnogorac-Jurcevic, T., Nielsen, T.O., and Lemoine, N.: RT-PCR from laser captured microdissected material. Methods in Molecular Biology, vol. 193. Totawa, New Jersey: Humana Press Inc. Chapter 15, pp197-204 (2002).

A methodological paper describing the preparation of histologic slides for laser capture microdissection, the dissection procedure itself, and the isolation of RNA of sufficient quality for RT-PCR analysis from laser-captured material.

Crnogorac-Jurcevic, T., Efthimiou, E., Nielsen, T., Loader, J., Terris, B., Stamp, G., Keating, S., Baron, A., Scarpa, A. and Lemoine, N.R.: Expression profiling of microdissected pancreatic adenocarcinomas. Oncogene 21:4587-4594 (2002).

The differential gene expression patterns between normal pancreatic ducts and pancreatic adenocarcinoma are analyzed using a custom-built cDNA expression microarray and laser-capture microdissected target RNA.

Nielsen, T.O., West, R.B., Linn, S.C., Alter, O., Tibshirani, R., Knowling, M.A., O’Connell, J.X., Zhu, S., Fero, M., Sherlock, G., Pollack, J.R., Brown, P.O., Botstein, D., and van de Rijn, M.: Molecular portraits of soft tissue tumors. The Lancet 359:1301-1307 (2002).

In collaboration with the group at Stanford University who developed cDNA expression microarray technology, this paper profiles 46 soft tissue tumors and highlights gene clusters that can be used to distinguish tumor types, while also identifying many potential novel markers of synovial sarcomas, GI stromal tumors, leiomyosarcomas and peripheral nerve sheath tumors. Singular Value Decompostion is employed to permit combination of data from two types of spotted microarrays.

Nielsen, T.O., Séjean, G., and Onerheim, R.M.: Paraganglioma of the tongue. Archives of Pathology and Laboratory Medicine 124:877-879 (2000).

An unusual case of paraganglioma, arising at the base of the tongue, is presented along with its immunohistochemical characterization. No parasympathetic ganglia are known to exist in the tongue, and this neuroendocrine tumor has never been described in this location before.

Nielsen, T.O., Cossons, N., Zannis-Hadjopoulos, M. and Price, G.B.: Circular YAC vectors containing short mammalian origin sequences are maintained under selection as HeLa episomes. Journal of Cellular Biochemistry 76:674-685 (2000).

Human replication origin sequences cloned into a YAC vector are demonstrated to replicate autonomously in human cells. Such constructs have the potential to act as a foundation for the construction of human transfection vectors, or a defined human artificial chromosome.

Nielsen, T.O.: Guidelines for legalized euthanasia in Canada: a proposal. Annals of the Royal College of Physicians and Surgeons of Canada 31:314-318 (1998) [published letters/comments appear in the February 1999 issue, 32:8-10 and 43-45, and in the April 1999 issue, 32:176].

The strongest arguments for legalizing euthanasia (liberty and mercy) must be balanced against legitimate fears of slippery slopes to involuntary euthanasia, erosion of palliative care, and the creation of a "duty to die." This essay spells out a detailed proposal for reconciling these concerns, involving the creation of an ethics committee to oversee legalized euthanasia in specific individual cases.

Cossons, N., Nielsen, T.O., Dini, C., Tomilin, N., Young, D.B., Riabowol, K.T., Rattner, J.B., Johnston, R.N., Zannis-Hadjopoulos, M. and Price, G.B.: Circular YAC vectors containing a small mammalian origin sequence can associate with the nuclear matrix. Journal of Cellular Biochemistry 67:439-450 (1997).

Origin sequences cloned into yeast artificial chromosome vectors, as part of a project to build fully defined human artificial chromosomes, are demonstrated to associate with the nuclear matrix, a property considered necessary for proper replication origin and chromosomal function.

Tao, L., Nielsen, T., Friedlander, P., Zannis-Hadjopoulos, M. and Price, G.B.: Differential DNA replication origin activities in human normal skin fibroblast and HeLa cell lines. Journal of Molecular Biology 273:509-518 (1997).

Using a powerful, simplified version of the nascent strand PCR method for origin mapping, several autonomously replicating sequences (including examples from the anti-cruciform / mass screening experiments described in my first publication) are proven to function as in vivo chromosomal replication origins, utilized differently in normal versus transformed cell lines.

Nielsen, T.O.: Human germline gene therapy. McGill Journal of Medicine 3:126-132 (1997). [PDF full text version].

This essay reviews the ethical arguments for and against germline manipulations of human embryos. The technical aspects of the procedure are discussed, as well as the medical indications for germline gene therapy. The paper concludes that the technology will always be impractical and has essentially no medical uses.

Sinnett, D., Woolf E, Xie, W., Glatt, K., Kirkness, E.F., Nielsen, T.O., Zannis-Hadjopoulos, M., Price, G.B. and Lalande, M.: Identification of a putative DNA replication origin in the gamma-aminobutyric acid receptor subunit beta-3 and alpha-5 gene cluster on chromosome 15q11q13, a region associated with allele-specific replication timing. Gene 173:171-177 (1996).

A putative replication origin is identified, by sequence characteristics and an in vitro replication assay, in an imprinted chromosomal region associated with Prader-Willi and Angelman syndromes.

Ruiz, M.T., Pearson, C.E., Nielsen, T., Price, G.B. and Zannis-Hadjopoulos, M.: Co-fractionation of HeLa cell replication proteins with ors-binding activity. Journal of Cellular Biochemistry 58:221-236 (1995).

Protein fractions are purified from human cells; those binding to an origin-containing fragment are shown to permit initiation of DNA replication in an in vitro replication system.

Zannis-Hadjopoulos, M., Nielsen, T.O., Todd, A. and Price, G.B.: Autonomous replication in vivo and in vitro of clones spanning the region of the DHFR origin of bidirectional replication (ori-beta). Gene 151:273-277 (1994).

For the first time, autonomous replication activity is demonstated in fragments derived from the well-characterized DNA replication origin located 3' to the hamster dihydrofolate-reductase gene.

Nielsen, T.O., Piatyszek, M.A., Shay, J.W., Pearson, C.E., Zannis-Hadjopoulos, M. and Price, G.B.: Autonomous replication activity of a human mitochondrial DNA sequence inserted into genomic DNA. International Journal of Oncology 5:1003-1008 (1994).

Fragments of mitochondrial DNA are released upon autolytic degradation of this organelle. The cytochrome oxidase subunit 3 mitochondrial gene has inserted into the c-myc genomic locus in a human cell line (HeLaTG), and interestingly is shown, in this work, to possess autonomous replication activity.

Nielsen, T., Bell, D., Lamoureux, C., Zannis-Hadjopoulos, M. and Price, G.B.: A reproducible method for identification of human genomic DNA autonomously replicating sequences. Molecular and General Genetics 242:280-288 (1994).

Large numbers of putative human DNA replication origins are purified from genomic DNA on the basis of affinity for an anti-cruciform antibody (directed against a DNA secondary structure), followed by mass screening of clones for autonomous replication activity.

Reprints available from: torsten@[nospam]mail.ubc.ca

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