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Kondratyev M, Pesic A, Ketela T, Stickle N, Beswick C, Shalev Z, Marastoni S, Samadian S, Dvorkin-Gheva A, Sayad A, Bashkurov M, Boasquevisque P, Datti A, Pugh TJ, Virtanen C, Moffat J, Grénman RA, Koritzinsky M, Wouters BG. Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer. Commun Biol 2023; 6:538. [PMID: 37202533 DOI: 10.1038/s42003-023-04828-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
During cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of "matched" pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.
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Affiliation(s)
- Maria Kondratyev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
| | - Aleksandra Pesic
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Natalie Stickle
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Christine Beswick
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Zvi Shalev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Stefano Marastoni
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Soroush Samadian
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Anna Dvorkin-Gheva
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Mikhail Bashkurov
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Pedro Boasquevisque
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Alessandro Datti
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Carl Virtanen
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Bradly G Wouters
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
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Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, Fiandalo M, Foti M, Khotskaya Y, Lee J, Peters N, Sweeney S, Abraham J, Brenton JD, Caldas C, Doherty G, Nimmervoll B, Pinilla K, Martin JE, Rueda OM, Sammut SJ, Silva D, Cao K, Heath AP, Li M, Lilly J, MacFarland S, Maris JM, Mason JL, Morgan AM, Resnick A, Welsh M, Zhu Y, Johnson B, Li Y, Sholl L, Beaudoin R, Biswas R, Cerami E, Cushing O, Dand D, Ducar M, Gusev A, Hahn WC, Haigis K, Hassett M, Janeway KA, Jänne P, Jawale A, Johnson J, Kehl KL, Kumari P, Laucks V, Lepisto E, Lindeman N, Lindsay J, Lueders A, Macconaill L, Manam M, Mazor T, Miller D, Newcomb A, Orechia J, Ovalle A, Postle A, Quinn D, Reardon B, Rollins B, Shivdasani P, Tramontano A, Van Allen E, Van Nostrand SC, Bell J, Datto MB, Green M, Hubbard C, McCall SJ, Mettu NB, Strickler JH, Andre F, Besse B, Deloger M, Dogan S, Italiano A, Loriot Y, Ludovic L, Michels S, Scoazec J, Tran-Dien A, Vassal G, Freeman CE, Hsiao SJ, Ingham M, Pang J, Rabadan R, Roman LC, Carvajal R, DuBois R, Arcila ME, Benayed R, Berger MF, Bhuiya M, Brannon AR, Brown S, Chakravarty D, Chu C, de Bruijn I, Galle J, Gao J, Gardos S, Gross B, Kundra R, Kung AL, Ladanyi M, Lavery JA, Li X, Lisman A, Mastrogiacomo B, McCarthy C, Nichols C, Ochoa A, Panageas KS, Philip J, Pillai S, Riely GJ, Rizvi H, Rudolph J, Sawyers CL, Schrag D, Schultz N, Schwartz J, Sheridan R, Solit D, Wang A, Wilson M, Zehir A, Zhang H, Zhao G, Ahmed L, Bedard PL, Bruce JP, Chow H, Cooke S, Del Rossi S, Felicen S, Hakgor S, Jagannathan P, Kamel-Reid S, Krishna G, Leighl N, Lu Z, Nguyen A, Oldfield L, Plagianakos D, Pugh TJ, Rizvi A, Sabatini P, Shah E, Singaravelan N, Siu L, Srivastava G, Stickle N, Stockley T, Tang M, Virtaenen C, Watt S, Yu C, Bernard B, Bifulco C, Cramer JL, Lee S, Piening B, Reynolds S, Slagel J, Tittel P, Urba W, VanCampen J, Weerasinghe R, Acebedo A, Guinney J, Guo X, Hunter-Zinck H, Yu T, Dang K, Anagnostou V, Baras A, Brahmer J, Gocke C, Scharpf RB, Tao J, Velculescu VE, Alexander S, Bailey N, Gold P, Bierkens M, de Graaf J, Hudeček J, Meijer GA, Monkhorst K, Samsom KG, Sanders J, Sonke G, ten Hoeve J, van de Velde T, van den Berg J, Voest E, Steinhardt G, Kadri S, Pankhuri W, Wang P, Segal J, Moung C, Espinosa-Mendez C, Martell HJ, Onodera C, Quintanar Alfaro A, Sweet-Cordero EA, Talevich E, Turski M, Van’t Veer L, Wren A, Aguilar S, Dienstmann R, Mancuso F, Nuciforo P, Tabernero J, Viaplana C, Vivancos A, Anderson I, Chaugai S, Coco J, Fabbri D, Johnson D, Jones L, Li X, Lovly C, Mishra S, Mittendorf K, Wen L, Yang YJ, Ye C, Holt M, LeNoue-Newton ML, Micheel CM, Park BH, Rubinstein SM, Stricker T, Wang L, Warner J, Guan M, Jin G, Liu L, Topaloglu U, Urtis C, Zhang W, D’Eletto M, Hutchison S, Longtine J, Walther Z. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Sci Rep 2022; 12:19055. [PMID: 36351964 PMCID: PMC9646734 DOI: 10.1038/s41598-022-21448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
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Affiliation(s)
- Debra Van Egeren
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Systems Biology, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Stem Cell Program, Boston Children’s Hospital, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Khushi Kohli
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Jeremy L. Warner
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
| | - Philippe L. Bedard
- grid.17063.330000 0001 2157 2938Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Gregory Riely
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eva Lepisto
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.429426.f0000 0000 9350 5788Present Address: Multiple Myeloma Research Foundation, Norwalk, CT USA
| | - Deborah Schrag
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michele LeNoue-Newton
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paul Catalano
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Kenneth L. Kehl
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Franziska Michor
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.65499.370000 0001 2106 9910The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XThe Ludwig Center at Harvard, Boston, MA USA
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3
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Toma A, Dos Santos C, Burzyńska B, Góra M, Kiliszek M, Stickle N, Kirsten H, Kosyakovsky L, Wang B, van Diepen S, Epelman S, Szekely Y, Marshall JC, Billia F, Lawler PR. Diversity in the Expressed Genomic Host Response to Myocardial Infarction. Circ Res 2022; 131:106-108. [PMID: 35534922 DOI: 10.1161/circresaha.121.318391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Augustin Toma
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.)
| | - Claudia Dos Santos
- Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.).,Interdepartmental Division of Critical Care Medicine, University of Toronto, Canada. (C.d.S., J.C.M., P.R.L.).,St Michael's Hospital, Toronto, Canada (C.d.S., J.C.M.)
| | - Beata Burzyńska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland (B.B., M.G.)
| | - Monika Góra
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland (B.B., M.G.)
| | - Marek Kiliszek
- Department of Cardiology and Internal Diseases, Military Institute of Medicine, Warsaw, Poland (M.K.)
| | | | - Holger Kirsten
- LIFE - Leipzig Research Center for Civilization Diseases and Institute for Medical Informatics, Statistics and Epidemiology, Universität Leipzig, Germany (H.K.)
| | - Leah Kosyakovsky
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA (L.K.)
| | - Bo Wang
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.)
| | - Sean van Diepen
- Division of Cardiology, Department of Critical Care, Department of Medicine, University of Alberta, Edmonton, Canada (S.v.D.)
| | - Slava Epelman
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.).,Ted Rogers Centre for Heart Research, Toronto, Canada (S.E., F.B., P.R.L.)
| | - Yishay Szekely
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.)
| | - John C Marshall
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Canada. (C.d.S., J.C.M., P.R.L.).,St Michael's Hospital, Toronto, Canada (C.d.S., J.C.M.)
| | - Filio Billia
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.).,Ted Rogers Centre for Heart Research, Toronto, Canada (S.E., F.B., P.R.L.)
| | - Patrick R Lawler
- Peter Munk Cardiac Centre, Toronto General Hospital, Canada (A.T., B.W., S.E., Y.S., F.B., P.R.L.).,Department of Medicine (A.T., C.d.S., B.W., S.E., Y.S., F.B., P.R.L.).,Interdepartmental Division of Critical Care Medicine, University of Toronto, Canada. (C.d.S., J.C.M., P.R.L.).,Ted Rogers Centre for Heart Research, Toronto, Canada (S.E., F.B., P.R.L.)
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Kondratyev M, Pesic A, Dvorkin-Sheva A, Ketela T, Stickle N, Aiiles L, Grenman R, Koritzinsky M, Wouters B. Abstract 2311: Identification of therapeutic targets in HNSCC. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
HNSCC is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due in large part to metastatic disease. The underlying biology associated with metastatic disease and poor outcome in HNSCC remains unclear. Importantly, metastatic cells acquire new properties that permit them to invade surrounding tissues and seed metastasis at distant sites. While these acquired properties contribute to aggressiveness of metastatic cancer, they can be exploited to target metastatic cells selectively, sparing toxicity in normal tissues. We used functional genomic technologies to identify new therapeutic targets for advanced disease in HNSCC. These targets were identified by conducting whole genome shRNA screens in matched sets of cell lines derived from primary HNSCC tumors and their respective metastatic sites/recurrences. Since hypoxia is an important attribute of aggressive and therapy resistant subpopulations of HNSCC tumor cells, we also aimed to identify genes that became essential when cells are exposed to hypoxia. To complement the data from the functional screens and to further characterize our cell line collection, we utilized several high through put approaches including mutational analysis, proteomics and gene expression profiling. Moreover, we performed chemical screens using libraries of over 4000 FDA approved drugs with the aim to combine our functional genomic data with the results from the drug screens to discover drug/gene “hit” combinations that would provide a basis for development of novel anti-cancer therapies.While HNSCC derived cell lines represent a valuable tool to study this disease, their biology might not always accurately represent the biology of the tumors they were derived from. Therefore, we looked at the expression of the components of several key pathways that we discovered using the in vitro characterization in a patient material from over HNSCC surgical samples constructed into a TMA. Five of the hits belonged to the Notch signalling pathway and 4 others came from the proteomic analysis as they showed higher levels of surface expression in metastatic cells and/or under hypoxic conditions. Interestingly, higher proportion of patients with late stages of HNSCC belonged to the high Jag2 and Hey1 populations as compared to patients with low stages of HNSCC that mostly expressed low or intermediate levels of these proteins. This data is in line with our observations that Jag2 and Hey1 expression is elevated in cells derived from metastatic sites and is low in cells derived from primary tumors. Proportion of cells with high CD66 and TRAIL proteins was also higher among the late stage tumors suggesting that these biomarkers are of interest for further investigation. We discovered several molecular pathways that are important in metastatic/hypoxic HNSCC. We are investigating our ability to target these pathways using FDA approved drugs in order to achieve durable cures.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Anna Dvorkin-Sheva, Troy Ketela, Natalie Stickle, Laurie Aiiles, Reidar Grenman, Marianne Koritzinsky, Brad Wouters. Identification of therapeutic targets in HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2311.
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Affiliation(s)
| | | | | | - Troy Ketela
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Laurie Aiiles
- 1University Health Network, Toronto, Ontario, Canada
| | | | | | - Brad Wouters
- 1University Health Network, Toronto, Ontario, Canada
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5
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Tone AA, McCuaig JM, Ricker N, Boghosian T, Romagnuolo T, Stickle N, Virtanen C, Zhang T, Kim RH, Ferguson SE, May T, Laframboise S, Armel S, Demsky R, Volenik A, Stuart-McEwan T, Shaw P, Oza A, Kamel-Reid S, Stockley T, Bernardini MQ. The Prevent Ovarian Cancer Program (POCP): Identification of women at risk for ovarian cancer using complementary recruitment approaches. Gynecol Oncol 2021; 162:97-106. [PMID: 33858678 DOI: 10.1016/j.ygyno.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Up to 20% of high-grade serous ovarian carcinomas (HGSOC) are hereditary; however, historical uptake of genetic testing is low. We used a unique combination of approaches to identify women in Ontario, Canada, with a first-degree relative (FDR) who died from HGSOC without prior genetic testing, and offer them multi-gene panel testing. METHODS From May 2015-Sept 2019, genetic counseling and testing was provided to eligible participants. Two recruitment strategies were employed, including self-identification in response to an outreach campaign and direct targeting of FDRs of deceased HGSOC patients treated at our institution. The rate of pathogenic variants (PV) in established/potential ovarian cancer risk genes and the benefits/challenges of each approach were assessed. RESULTS A total of 564 women enrolled in response to our outreach campaign (n = 473) or direct recruitment (n = 91). Mean age at consent was 52 years and 96% did not meet provincial testing criteria. Genetic results were provided to 528 individuals from 458 families. The rate of PVs in ovarian cancer risk genes was highest when FDRs were diagnosed with HGSOC <60 years (9.4% vs. 3.9% ≥ 60y, p = 0.0160). Participants in the outreach vs. direct recruitment cohort had a similar rate of PVs; however, uptake of genetic testing (97% vs. 89%; p = 0.0036) and study completion (95% vs. 87%; p = 0.0062) rates were higher in the former. Eleven participants with pathogenic variants have completed risk-reducing gynecologic surgery, with one stage I HGSOC and two breast cancers identified. CONCLUSION Overall PV rates in this large cohort were lower than expected; however, we provide evidence that genetic testing criteria in Ontario should include individuals with a deceased FDR diagnosed with HGSOC <60 years of age.
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Affiliation(s)
- Alicia A Tone
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Ovarian Cancer Canada, Toronto, Canada
| | - Jeanna M McCuaig
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nicole Ricker
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Talin Boghosian
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Tina Romagnuolo
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | - Natalie Stickle
- Bioinformatics and HPC Core, The University Health Network, Toronto, Canada
| | - Carl Virtanen
- Bioinformatics and HPC Core, The University Health Network, Toronto, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada
| | - Raymond H Kim
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada; Medical Oncology, The University Health Network, Toronto, Canada
| | - Sarah E Ferguson
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
| | - Taymaa May
- Gynecologic Oncology, The University Health Network, Toronto, Canada
| | | | - Susan Armel
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Rochelle Demsky
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexandra Volenik
- Familial Cancer Clinic, The University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Patricia Shaw
- Gynecologic Pathology, The University Health Network, Toronto, Canada
| | - Amit Oza
- Medical Oncology, The University Health Network, Toronto, Canada
| | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada; Clinical Laboratory Genetics, The University Health Network, Toronto, Canada
| | - Tracy Stockley
- Advanced Molecular Diagnostics Laboratory, The University Health Network, Toronto, Canada; Clinical Laboratory Genetics, The University Health Network, Toronto, Canada
| | - Marcus Q Bernardini
- Gynecologic Oncology, The University Health Network, Toronto, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada.
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6
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Care M, McCuaig J, Clarke B, Grenier S, Kim RH, Rouzbahman M, Stickle N, Bernardini M, Stockley TL. Tumor and germline next generation sequencing in high grade serous cancer: experience from a large population-based testing program. Mol Oncol 2020; 15:80-90. [PMID: 33030818 PMCID: PMC7782089 DOI: 10.1002/1878-0261.12817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to determine the prevalence of somatic and germline pathogenic variants (PVs) in high‐grade serous cancer (HGSC) and to demonstrate the technical feasibility and effectiveness of a large‐scale, population‐based tumor testing program. It involved a retrospective review of genetic test results in 600 consecutive HGSC tumor samples and a subsequent comparison of germline and tumor results in a subset of 200 individuals. Tumor testing was successful in 95% of samples (570/600) with at least one BRCA1/2 PV identified in 16% (93/570) of cases. Among the 200 paired cases, BRCA1/2 PVs were detected in 38 tumors (19%); 58% were somatic (22/38); and 42% were germline (16/38). There was 100% concordance between germline and tumor test results. This is the largest series of BRCA1/2 testing in HGSC (tumor‐only and paired cohorts), reported to date, and our data show that an effectively designed and validated population‐based tumor testing program can be used to determine both treatment eligibility and hereditary cancer risk.
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Affiliation(s)
- Melanie Care
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeanna McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, University Health Network, Toronto, Canada.,Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, Canada
| | - Blaise Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Sylvie Grenier
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, University Health Network, Toronto, Canada.,Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Marjan Rouzbahman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Natalie Stickle
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Marcus Bernardini
- Department of Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Canada
| | - Tracy L Stockley
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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Spence T, Stickle N, Yu C, Chow H, Feilotter H, Lo B, McCready E, Sadikovic B, Siu LL, Bedard PL, Stockley TL. Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study. ACTA ACUST UNITED AC 2019; 26:e717-e732. [PMID: 31896942 DOI: 10.3747/co.26.5379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background A pilot inter-laboratory proficiency scheme for 5 Ontario clinical laboratories testing tumour samples for the Ontario-wide Cancer Targeted Nucleic Acid Evaluation (octane) study was undertaken to assess proficiency in the identification and reporting of next-generation sequencing (ngs) test results in solid tumour testing from archival formalin-fixed, paraffin-embedded (ffpe) tissue. Methods One laboratory served as the reference centre and provided samples to 4 participating laboratories. An analyte-based approach was applied: each participating laboratory received 10 ffpe tissue specimens profiled at the reference centre, with tumour site and histology provided. Laboratories performed testing per their standard ngs tumour test protocols. Items returned for assessment included genes and variants that would be typically reported in routine clinical testing and variant call format (vcf) files to allow for assessment of ngs technical quality. Results Two main aspects were assessed:■ Technical quality and accuracy of identification of exonic variants■ Site-specific reporting practicesTechnical assessment included evaluation of exonic variant identification, quality assessment of the vcf files to evaluate base calling, variant allele frequency, and depth of coverage for all exonic variants. Concordance at 100% was observed from all sites in the technical identification of 98 exonic variants across the 10 cases. Variability between laboratories in the choice of variants considered clinically reportable was significant. Of the 38 variants reported as clinically relevant by at least 1 site, only 3 variants were concordantly reported by all participating centres as clinically relevant. Conclusions Although excellent technical concordance for ngs tumour profiling was observed across participating institutions, differences in the reporting of clinically relevant variants were observed, highlighting reporting as a gap where consensus on the part of Ontario laboratories is needed.
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Affiliation(s)
- T Spence
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - N Stickle
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - C Yu
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - H Chow
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - H Feilotter
- Kingston, ON: Molecular Diagnostics, Kingston Health Sciences Centre (Feilotter); Department of Pathology and Molecular Medicine, Queen's University (Feilotter)
| | - B Lo
- Ottawa, ON: Molecular Oncology Diagnostics Laboratory, The Ottawa Hospital (Lo); Department of Pathology and Laboratory Medicine, University of Ottawa (Lo)
| | - E McCready
- Hamilton, ON: Hamilton Health Sciences and St. Joseph's Healthcare (McCready); Department of Pathology and Molecular Medicine, McMaster University (McCready)
| | - B Sadikovic
- London, ON: Pathology and Laboratory Medicine Program, London Health Sciences Centre (Sadikovic); Department of Pathology and Laboratory Medicine, Western University (Sadikovic)
| | - L L Siu
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - P L Bedard
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
| | - T L Stockley
- Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley)
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Kondratyev M, Pesic A, Sayad A, Ketela T, Stickle N, Virtanen C, Moffat J, Ailles L, Koritzinsky M, Wouters B. Abstract 3054: Cell surface targets in head and neck cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
HNSCC is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due in large part to metastatic disease. The underlying biology associated with metastatic disease and poor outcome in HNSCC remains unclear. Importantly, metastatic cells acquire new properties that permit them to invade surrounding tissues and seed metastasis at distant sites. While these acquired properties contribute to aggressiveness of metastatic cancer and interfere with success of therapies, they can also potentially be exploited to target metastatic cells selectively, sparing toxicity in normal tissues. We used functional genomic technologies to identify new potential therapeutic targets for advanced disease in HNSCC. These targets were identified by conducting whole genome shRNA screens in matched sets of cell lines derived from primary tumors and their respective metastatic sites, with the goal of identifying genes that become essential for cell survival only following metastasis. Since hypoxia is an important attribute of aggressive and therapy resistant subpopulations of HNSCC tumor cells, we also aimed to identify genes that became essential when cells are exposed to hypoxia. We are particularly interested in the identification of contextual synthetic lethal oncogenes expressed on the cell surface, as those are easily targetable by therapeutic antibodies. To identify these targets, we performed high-throughput flow cytometry screening that enables evaluation of 370 validated cell surface antibodies. Cell surface targets differentially expressed in metastatic lines included CECAM and CCR6 that were previously reported to be implicated in metastasis and tumor progression as well as Thy1, a known marker of stem cells involved in regulation of cell adhesion. Cell surface targets induced under hypoxic conditions across the cell lines included CA9, an enzyme that is known to regulate pH in hypoxic cells and be associated with tumor progression, as well as CD338, CD264 and CD312, that were previously associated with stemness in a few models of cancer. Interestingly, the described proteins were also found to be differentially essential in the shRNA screens, highlighting their functional importance in tumor progression and hypoxia survival. We are currently investigating the role of these proteins in HNSCC metastasis utilizing our unique collection of matched pairs of HNSCC lines from multiple patients. Moreover, we are utilizing our pipeline of patient derived HNSCC xenografts to test the effect of knocking down the described genes in patient tumors. We are also testing the expression of selected hits in histological sections of patient tumorsthe 400-patient TMA by immunohistochemistry looking for correlation with tumor grade, aggressiveness, levels of hypoxia as well as presence/absence of metastasis in the patient.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Azin Sayad, Troy Ketela, Natalie Stickle, Carl Virtanen, Jason Moffat, Laurie Ailles, Marianne Koritzinsky, Brad Wouters. Cell surface targets in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3054.
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Affiliation(s)
| | | | - Azin Sayad
- 1University Health Network, Toronto, Ontario, Canada
| | - Troy Ketela
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Carl Virtanen
- 1University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- 2University of Toronto, Toronto, Ontario, Canada
| | - Laurie Ailles
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Brad Wouters
- 1University Health Network, Toronto, Ontario, Canada
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Tone A, McCuaig J, Virtanen C, Zhang T, Ricker N, Romagnuolo T, Stickle N, Kim R, Stuart-McEwan T, Shaw P, Oza A, Kamel-Reid S, Stockley T, Bernardini M. The prevent ovarian cancer program (POCP): Identification of ovarian cancer-associated mutations in self-referring women from low-risk families. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Sukhai MA, Misyura M, Thomas M, Garg S, Zhang T, Stickle N, Virtanen C, Bedard PL, Siu LL, Smets T, Thijs G, Van Vooren S, Kamel-Reid S, Stockley TL. Somatic Tumor Variant Filtration Strategies to Optimize Tumor-Only Molecular Profiling Using Targeted Next-Generation Sequencing Panels. J Mol Diagn 2019; 21:261-273. [PMID: 30576869 DOI: 10.1016/j.jmoldx.2018.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 02/09/2023] Open
Abstract
A common approach in clinical diagnostic laboratories to variant assessment from tumor molecular profiling is sequencing of genomic DNA extracted from both tumor (somatic) and normal (germline) tissue, with subsequent variant comparison to identify true somatic variants with potential impact on patient treatment or prognosis. However, challenges exist in paired tumor-normal testing, including increased cost of dual sample testing and identification of germline cancer predisposing variants. Alternatively, somatic variants can be identified by in silico tumor-only variant filtration precluding the need for matched normal testing. The barrier to tumor-only variant filtration is defining a reliable approach, with high sensitivity and specificity to identify somatic variants. In this study, we used retrospective data sets from paired tumor-normal samples tested on small (48 gene) and large (555 gene) targeted next-generation sequencing panels, to model algorithms for tumor-only variants classification. The optimal algorithm required an ordinal filtering approach using information from variant population databases (1000 Genomes Phase 3, ESP6500, ExAC), clinical mutation databases (ClinVar), and information on recurring clinically relevant somatic variants. Overall the tumor-only variant filtration strategy described in this study can define clinically relevant somatic variants from tumor-only analysis with sensitivity of 97% to 99% and specificity of 87% to 94%, and with significant potential utility for clinical laboratories implementing tumor-only molecular profiling.
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Affiliation(s)
- Mahadeo A Sukhai
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Maksym Misyura
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mariam Thomas
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Swati Garg
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natalie Stickle
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Carl Virtanen
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe L Bedard
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tina Smets
- Aglient Technologies, Santa Clara, California
| | - Gert Thijs
- Aglient Technologies, Santa Clara, California
| | | | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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11
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Kondratyev M, Pesic A, Ketela T, Sayad A, Marastoni S, Mofat J, Virtanen C, Stickle N, Grenman R, Wouters B. Abstract 407: Novel targets in metastatic HNSCC. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Head and neck carcinoma (HNSCC) is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due in large part to metastatic disease. The underlying biology associated with metastatic disease and poor outcome in HNSCC remains unclear. Importantly, metastatic cells acquire new properties that permit them to invade surrounding tissues and seed metastasis at distant sites. While these acquired properties contribute to aggressiveness of metastatic cancer and interfere with success of therapies, they can also potentially be exploited to target metastatic cells selectively, sparing toxicity in normal tissues. The idea behind this selective targeting is based on discovering molecular pathways that became essential in metastatic cells, and then exploiting this vulnerability through targeted agents. We used functional genomic technologies to identify new potential therapeutic targets for advanced disease in HNSCC. These targets were identified by conducting whole genome shRNA screens in matched sets of cell lines derived from primary tumors and their respective metastatic sites, with the goal of identifying genes that become essential for cell survival only following metastasis. Since hypoxia is an important attribute of aggressive and therapy resistant subpopulations of HNSCC tumor cells, we also aimed to identify genes that became essential when cells are exposed to hypoxia. To complement the functional screens data, we performed targeted sequencing of the most commonly altered genes in HNSCC as reported by the TCGA profiled gene expression in the HNSCC cell lines cultured under normoxia and hypoxia using Illumina microarrays. These analyses led to the discovery of genes that are differentially essential in metastatic cells as well as in cells exposed to hypoxic conditions. Utilizing CRISPR technology, we assembled a library of guide RNAs targeting the discovered hits and are currently validating the top identified genes using both in vitro and in vivo systems. To validate hits that are essential in metastatic cells in vivo, we engineered selected “matched” pairs of HNSCC cell lines to express CAS9 protein upon induction with doxycycline. The cells are then transduced with the library of guides and injected subcutaneously into mice; tumors from control and doxycycline treated animals are compared. The difference in genes that are essential for growth of tumors seeded by primary tumor derived and metastasis derived HNSCC cell lines is then assessed in a quantitative manner.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Troy Ketela, Azin Sayad, Stephano Marastoni, Jason Mofat, Carl Virtanen, Natalie Stickle, Reider Grenman, Brad Wouters. Novel targets in metastatic HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 407.
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Affiliation(s)
| | | | - Troy Ketela
- 1University Health Network, Toronto, Ontario, Canada
| | - Azin Sayad
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Jason Mofat
- 2University of Toronto, Toronto, Ontario, Canada
| | - Carl Virtanen
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Reider Grenman
- 3Turku University and Turku University Hospital, Turku, Finland
| | - Brad Wouters
- 1University Health Network, Toronto, Ontario, Canada
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Cybulska P, Stewart JM, Sayad A, Virtanen C, Shaw PA, Clarke B, Stickle N, Bernardini MQ, Neel BG. A Genomically Characterized Collection of High-Grade Serous Ovarian Cancer Xenografts for Preclinical Testing. The American Journal of Pathology 2018; 188:1120-1131. [DOI: 10.1016/j.ajpath.2018.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 12/06/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
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13
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Lobo N, Gedye C, Brown KR, Paterson J, Stickle N, Moffat J, Jewett MA, Ailles LE. Abstract B09: Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Patients with clear cell renal cell carcinoma (ccRCC) have few therapeutic options, as ccRCC is unresponsive to chemotherapy and is highly resistant to radiation. Recently targeted therapies have extended progression-free survival, but responses are variable and no significant overall survival benefit has been achieved. Commercial ccRCC cell lines are often used as model systems to develop novel therapeutic approaches, but these do not accurately recapitulate primary ccRCC tumors at the genomic and transcriptional levels. Furthermore, ccRCC exhibits significant intertumor genetic heterogeneity, and the limited cell lines available fail to represent this aspect of ccRCC. Our objective was to generate accurate preclinical in vitro models of ccRCC using tumor tissues from ccRCC patients.
ccRCC primary single cell suspensions were cultured in fetal bovine serum (FBS)-containing media or defined serum-free media (DFSM). The apparent efficiency of primary cell culture establishment was high in both culture conditions, but genotyping by single nucleotide polymorphism (SNP) arrays revealed that the majority of cultures in FBS (6 of 8), and all of the cultures in DFSM (8 of 8), contained normal, not cancer cells. To distinguish cancer vs. normal cells in subsequent experiments, we sequenced the von Hippel Lindau (VHL) gene, which is mutated in a large percentage of patients, in a cohort of samples for which cryopreserved viable single cell suspensions were available. Once patients with sequence-detectable mutations were identified, the cells were thawed and cultured as before. Established cultures were then sequenced for the patient-specific VHL mutations. Once again, the majority of cultures in FBS (1 of 7), and all of the cultures in DSFM (7 of 7) contained VHL-wild type cells. The loss of VHL leads to accumulation of hypoxia-inducible factor (HIF) and expression of HIF target genes. Therefore, in an attempt to select for VHL-mutant cancer cells, we used fluorescence activated cell sorting (FACS) to isolate cells expressing Carbonic Anhydrase IX (CA9), a cell surface HIF target. Isolated CA9+ cells were cultured in FBS-containing media, and upon genotyping, we found that VHL-mutant ccRCC cell cultures were established with an efficiency of ~85%. Parallel cultures of bulk single cell suspensions in serum-free conditions again selected for growth of normal (VHL-wild type) cells. The normal cells were verified to be renal proximal tubule epithelial cells based on their expression of renal proximal tubule markers Aquaporin-1 and Alkaline Phosphatase. Transcriptional profiling of ccRCC and matched normal cell cultures identified up- and down-regulated networks in ccRCC and comparison to The Cancer Genome Atlas confirmed the clinical validity of our cell cultures. The ability to establish patient-derived cultures of ccRCC cells and matched normal kidney epithelial cells from almost every patient provides a resource for future development of novel therapies and personalized medicine for ccRCC patients.
Citation Format: Nazleen Lobo, Craig Gedye, Kevin R. Brown, Joshua Paterson, Natalie Stickle, Jason Moffat, Michael A.S. Jewett, Laurie E. Ailles. Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B09.
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Affiliation(s)
| | - Craig Gedye
- 2School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, Nsw, Australia,
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Javadi M, Hofstätter E, Stickle N, Beattie BK, Jaster R, Carter-Su C, Barber DL. The SH2B1 adaptor protein associates with a proximal region of the erythropoietin receptor. J Biol Chem 2012; 287:26223-34. [PMID: 22669948 DOI: 10.1074/jbc.m112.382721] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gene targeting experiments have shown that the cytokine erythropoietin (EPO), its cognate erythropoietin receptor (EPO-R), and associated Janus tyrosine kinase, JAK2, are all essential for erythropoiesis. Structural-functional and murine knock-in experiments have suggested that EPO-R Tyr-343 is important in EPO-mediated mitogenesis. Although Stat5 binds to EPO-R phosphotyrosine 343, the initial Stat5-deficient mice did not have profound erythroid abnormalities suggesting that additional Src homology 2 (SH2) domain-containing effectors may bind to EPO-R Tyr-343 and couple to downstream signaling pathways. We have utilized cloning of ligand target (COLT) screening to demonstrate that EPO-R Tyr(P)-343 and Tyr(P)-401 bind to the SH2 domain-containing adaptor protein SH2B1β. Immunoprecipitation and in vitro mixing experiments reveal that EPO-R binds to SH2B1 in an SH2 domain-dependent manner and that the sequence that confers SH2B1 binding to the EPO-R is pYXXL. Previous studies have shown that SH2B1 binds directly to JAK2, but we show that in hematopoietic cells, SH2B1β preferentially associates with the EPO-R. SH2B1 is capable of constitutive association with EPO-R, which is necessary for its optimal SH2-dependent recruitment to EPO-R-Tyr(P)-343/Tyr(P)-401. We also demonstrate that SH2B1 is responsive to EPO stimulation and becomes phosphorylated, most likely on serines/threonines, in an EPO dose- and time-dependent manner. In the absence of SH2B1, we observe enhanced activation of signaling pathways downstream of the EPO-R, indicating that SH2B1 is a negative regulator of EPO signaling.
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Affiliation(s)
- Mojib Javadi
- Ontario Cancer Institute, Campbell Family Cancer Research Institute, Toronto, Ontario M5G 2M9, Canada
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Stickle N, Iscove NN, Virtanen C, Barbara M, Modi C, Di Berardino T, Greenblatt E, Brown T, Winegarden N. RNA Amplification Strategies: Toward Single‐Cell Sensitivity. Genomics 2010. [DOI: 10.1002/9780470711675.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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