1
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Kim JW, Marsilla J, Kazmierski M, Tkachuk D, Huang SH, Xu W, Cho J, Ringash J, Bratman S, Haibe-Kains B, Hope A. Impact of radiotherapy quality assurance on nasopharyngeal carcinoma: Usage of a novel web-based quality assurance application. Pract Radiat Oncol 2023:S1879-8500(23)00057-7. [PMID: 36948414 DOI: 10.1016/j.prro.2023.03.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
PURPOSE We used a new web application for rapid review of radiotherapy (RT) target volumes to evaluate the relationship between target delineation compliance with the international guidelines and outcomes of definitive RT for nasopharyngeal carcinoma (NPC). MATERIALS AND METHODS The dataset consists of CT simulation scans, RT structures, and clinical data of 354 pathology-confirmed NPC patients treated with intensity-modulated RT between 2005 and 2017. Target volumes were peer-reviewed in RT QA rounds, and target contours were revised, if recommended, before treatment. We imported the contours of intermediate-risk clinical target volumes of the primary tumor (IR-CTVp) of 332 patients into the application. Inclusion of anatomic sites within IR-CTVp was determined in accordance with 2018 International guideline for CTV delineation for NPC and correlated with time to local failure (TTLF) using Cox-regression. RESULTS In the peer-review QA analysis, local and distant control and overall survival (OS) rates were similar between peer-reviewed and non-reviewed cases and between cases with and without target contour changes. In the CTV compliance analysis, with a median follow-up of 5.6 years, 5-year TTLF and OS rates were 93.1% and 85.9% respectively. The most frequently non-guideline compliant anatomic sites were sphenoid sinus (n=69, 20.8%), followed by cavernous sinus (n=38, 19.3%), left and right petrous apices (n=37 and 32, 11.1% and 9.6%), and clivus (n=14, 4.2%). Among 23 patients with a local failure (6.9%), the number of non-compliant cases were 8 for sphenoid sinus, 7 cavernous sinus, 4 left and 3 right petrous apices, and 2 clivus. Cavernous sinus-conforming cases showed higher TTLF in comparison with non-conforming cases (93.6% vs 89.1%, p=0.013). Multivariable analysis confirmed that cavernous sinus non-compliance was prognostic for TTLF. CONCLUSIONS Our application allowed rapid quantitative review of CTVp in a large NPC cohort. While compliance with the international guidelines was high, under-coverage of the cavernous sinus was correlated with TTLF.
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Affiliation(s)
- Jun Won Kim
- Department of Radiation Oncology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Joseph Marsilla
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Michal Kazmierski
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Center/University of Toronto, Toronto, Ontario, Canada
| | - John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Scott Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre/University of Toronto, Toronto, Ontario, Canada.
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2
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Bareche Y, Kelly D, Abbas-Aghababazadeh F, Nakano M, Esfahani PN, Tkachuk D, Mohammad H, Samstein R, Lee CH, Morris LGT, Bedard PL, Haibe-Kains B, Stagg J. Leveraging big data of immune checkpoint blockade response identifies novel potential targets. Ann Oncol 2022; 33:1304-1317. [PMID: 36055464 DOI: 10.1016/j.annonc.2022.08.084] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The development of immune checkpoint blockade (ICB) has changed the way we treat various cancers. While ICB produces durable survival benefits in a number of malignancies, a large proportion of treated patients do not derive clinical benefit. Recent clinical profiling studies have shed light on molecular features and mechanisms that modulate response to ICB. Nevertheless, none of these identified molecular features were investigated in large enough cohorts to be of clinical value. MATERIALS AND METHODS Literature review was carried out to identify relevant studies including clinical dataset of patients treated with ICB [anti-programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1), anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) or the combination] and available sequencing data. Tumor mutational burden (TMB) and 37 previously reported gene expression (GE) signatures were computed with respect to the original publication. Biomarker association with ICB response (IR) and survival (progression-free survival/overall survival) was investigated separately within each study and combined together for meta-analysis. RESULTS We carried out a comparative meta-analysis of genomic and transcriptomic biomarkers of IRs in over 3600 patients across 12 tumor types and implemented an open-source web application (predictIO.ca) for exploration. TMB and 21/37 gene signatures were predictive of IRs across tumor types. We next developed a de novo GE signature (PredictIO) from our pan-cancer analysis and demonstrated its superior predictive value over other biomarkers. To identify novel targets, we computed the T-cell dysfunction score for each gene within PredictIO and their ability to predict dual PD-1/CTLA-4 blockade in mice. Two genes, F2RL1 (encoding protease-activated receptor-2) and RBFOX2 (encoding RNA-binding motif protein 9), were concurrently associated with worse ICB clinical outcomes, T-cell dysfunction in ICB-naive patients and resistance to dual PD-1/CTLA-4 blockade in preclinical models. CONCLUSION Our study highlights the potential of large-scale meta-analyses in identifying novel biomarkers and potential therapeutic targets for cancer immunotherapy.
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Affiliation(s)
- Y Bareche
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Institut du Cancer de Montréal, Montreal, Canada
| | - D Kelly
- Princess Margaret Cancer Centre, University Health Network, Division of Medical Oncology and Hematology, Toronto, Canada
| | - F Abbas-Aghababazadeh
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - M Nakano
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - P N Esfahani
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - D Tkachuk
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - H Mohammad
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - R Samstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C-H Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - L G T Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - P L Bedard
- Princess Margaret Cancer Centre, University Health Network, Division of Medical Oncology and Hematology, Toronto, Canada
| | - B Haibe-Kains
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada; Department ofComputer Science, University of Toronto, Toronto, Canada; Department ofOntario Institute for Cancer Research, Toronto, Canada; Department ofVector Institute for Artificial Intelligence, Toronto, Canada; Department ofBiostatistics Division, Dalla Lana School of Public Health, Toronto, Canada.
| | - J Stagg
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Institut du Cancer de Montréal, Montreal, Canada.
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3
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Feizi N, Nair SK, Smirnov P, Beri G, Eeles C, Esfahani PN, Nakano M, Tkachuk D, Mammoliti A, Gorobets E, Mer AS, Lin E, Yu Y, Martin S, Hafner M, Haibe-Kains B. PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. Nucleic Acids Res 2022; 50:D1348-D1357. [PMID: 34850112 PMCID: PMC8728279 DOI: 10.1093/nar/gkab1084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/14/2022] Open
Abstract
Cancer pharmacogenomics studies provide valuable insights into disease progression and associations between genomic features and drug response. PharmacoDB integrates multiple cancer pharmacogenomics datasets profiling approved and investigational drugs across cell lines from diverse tissue types. The web-application enables users to efficiently navigate across datasets, view and compare drug dose-response data for a specific drug-cell line pair. In the new version of PharmacoDB (version 2.0, https://pharmacodb.ca/), we present (i) new datasets such as NCI-60, the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) dataset, as well as updated data from the Genomics of Drug Sensitivity in Cancer (GDSC) and the Genentech Cell Line Screening Initiative (gCSI); (ii) implementation of FAIR data pipelines using ORCESTRA and PharmacoDI; (iii) enhancements to drug-response analysis such as tissue distribution of dose-response metrics and biomarker analysis; and (iv) improved connectivity to drug and cell line databases in the community. The web interface has been rewritten using a modern technology stack to ensure scalability and standardization to accommodate growing pharmacogenomics datasets. PharmacoDB 2.0 is a valuable tool for mining pharmacogenomics datasets, comparing and assessing drug-response phenotypes of cancer models.
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Affiliation(s)
- Nikta Feizi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Sisira Kadambat Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Parinaz Nasr Esfahani
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Minoru Nakano
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Anthony Mammoliti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Evgeniya Gorobets
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eva Lin
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Yihong Yu
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Scott Martin
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Marc Hafner
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
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4
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Ortmann J, Rampášek L, Tai E, Mer AS, Shi R, Stewart EL, Mascaux C, Fares A, Pham NA, Beri G, Eeles C, Tkachuk D, Ho C, Sakashita S, Weiss J, Jiang X, Liu G, Cescon DW, O'Brien CA, Guo S, Tsao MS, Haibe-Kains B, Goldenberg A. Assessing therapy response in patient-derived xenografts. Sci Transl Med 2021; 13:eabf4969. [PMID: 34788078 DOI: 10.1126/scitranslmed.abf4969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Janosch Ortmann
- Département AOTI, Université du Québec à Montréal, Montréal, QC H2X3X2, Canada.,Group for Research in Decision Analysis (GERAD), Montreal, QC H3T1J4, Canada
| | - Ladislav Rampášek
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Elijah Tai
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Ruoshi Shi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Erin L Stewart
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Celine Mascaux
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Pulmonology Department, Hôpitaux Universitaires de Strasbourg, 67200 Strasbourg, France.,Laboratory of Molecular Mechanisms of the Stress Response and Pathologies, INSERM U1113, 3 Avenue Molière, 67200 Strasbourg, France
| | - Aline Fares
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Xiaoqian Jiang
- Crown Bioscience Taicang Inc., No.6 Beijing West Road, Taicang, Jiangsu 215400, P. R. China
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Catherine A O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S1A8, Canada.,Department of Physiology, University of Toronto, Toronto, ON M5G1L7, Canada.,Department of Surgery, Toronto General Hospital, Toronto, ON M5G2C4, Canada
| | - Sheng Guo
- Crown Bioscience Taicang Inc., No.6 Beijing West Road, Taicang, Jiangsu 215400, P. R. China
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Benjamin Haibe-Kains
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON M5G1L7, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Hospital for Sick Children, Toronto, ON M5G1X8, Canada.,CIFAR, Toronto, ON M5G1M1, Canada
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5
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Kim J, Marsilla J, Weiss J, Tkachuk D, Jacinto J, Cho J, Hahn E, Bratman S, Haibe-Kains B, Hope A. OC-0518 Impact of observer knowledge on AI delineation assessments: Bias in clinical acceptability testing. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)06944-9] [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: 10/20/2022]
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6
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Kim JW, Marsilla J, Kazmierski M, Tkachuk D, Haibe-Kains B, Hope A. Abstract PO-051: Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: Quality evaluation of nasopharyngeal carcinoma. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.adi21-po-051] [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
Purpose: We developed Label-It, a new web-application for rapid review of radiotherapy (RT) target volumes, and used it to evaluate the relationship between target delineation compliance to the international guidelines and treatment outcomes of nasopharyngeal carcinoma (NPC) patients undergoing definitive RT. Methods and Materials: Our radiographic image database consists of anonymized simulation CT scans, RT structures, and treatment data of 3,211 head and neck cancer patients treated between July 2005 and August 2017. We used 332 patients treated with intensity-modulated RT for pathologically confirmed NPC as the study cohort and imported intermediate risk clinical target volumes of the primary tumor (IR-CTVp) receiving 56 Gy into Label-It. We determined inclusion of anatomic sites within IR-CTVp in accordance with 2018 International guideline for CTV delineation for NPC and correlated the results with time to local failure (TTLF) using Cox-regression. Results: At a median follow-up of 5.6 years, 5-year TTLF and overall survival rates were 93.1% and 85.9% respectively. The most frequently non-compliant anatomic sites were sphenoid sinus (n = 69, 20.8%), followed by cavernous sinus (n = 38, 11.4%), left and right petrous apices (n = 37 and 32, 11.1% and 9.6%), clivus (n = 14, 4.2%), and right and left foramen rotundum (n = 14 and 12, 4.2% and 3.6%). Among 23 patients with a local failure (6.9%), the number of non-compliant cases were 8 for sphenoid sinus, 7 cavernous sinus, 4 left and 3 right petrous apices, and 2 clivus. In Cox regression analysis, T4 disease (p = 0.003), RT alone (p = 0.007), cavernous sinus non-conformity (p = 0.020) were independent prognostic factors for TTLF. Conclusions: Label-It was an effective tool for rapid review of target volumes in a large patient cohort. Despite a high compliance to the international guidelines, inadequate coverage of cavernous sinus was correlated with decreased TTLF.
Citation Format: Jun Won Kim, Joseph Marsilla, Michal Kazmierski, Denis Tkachuk, Benjamin Haibe-Kains, Andrew Hope. Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: Quality evaluation of nasopharyngeal carcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-051.
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Affiliation(s)
- Jun Won Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Joseph Marsilla
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michal Kazmierski
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Andrew Hope
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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7
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Seo H, Tkachuk D, Ho C, Mammoliti A, Rezaie A, Madani Tonekaboni S, Haibe-Kains B. SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. Nucleic Acids Res 2020; 48:W494-W501. [PMID: 32442307 PMCID: PMC7319572 DOI: 10.1093/nar/gkaa421] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 12/18/2022] Open
Abstract
Drug-combination data portals have recently been introduced to mine huge amounts of pharmacological data with the aim of improving current chemotherapy strategies. However, these portals have only been investigated for isolated datasets, and molecular profiles of cancer cell lines are lacking. Here we developed a cloud-based pharmacogenomics portal called SYNERGxDB (http://SYNERGxDB.ca/) that integrates multiple high-throughput drug-combination studies with molecular and pharmacological profiles of a large panel of cancer cell lines. This portal enables the identification of synergistic drug combinations through harmonization and unified computational analysis. We integrated nine of the largest drug combination datasets from both academic groups and pharmaceutical companies, resulting in 22 507 unique drug combinations (1977 unique compounds) screened against 151 cancer cell lines. This data compendium includes metabolomics, gene expression, copy number and mutation profiles of the cancer cell lines. In addition, SYNERGxDB provides analytical tools to discover effective therapeutic combinations and predictive biomarkers across cancer, including specific types. Combining molecular and pharmacological profiles, we systematically explored the large space of univariate predictors of drug synergism. SYNERGxDB constitutes a comprehensive resource that opens new avenues of research for exploring the mechanism of action for drug synergy with the potential of identifying new treatment strategies for cancer patients.
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Affiliation(s)
- Heewon Seo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
| | - Anthony Mammoliti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aria Rezaie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
| | - Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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8
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Nair SK, Eeles C, Ho C, Beri G, Yoo E, Tkachuk D, Tang A, Nijrabi P, Smirnov P, Seo H, Jennen D, Haibe-Kains B. ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. Nucleic Acids Res 2020; 48:W455-W462. [PMID: 32421831 PMCID: PMC7319553 DOI: 10.1093/nar/gkaa390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 11/12/2022] Open
Abstract
In the past few decades, major initiatives have been launched around the world to address chemical safety testing. These efforts aim to innovate and improve the efficacy of existing methods with the long-term goal of developing new risk assessment paradigms. The transcriptomic and toxicological profiling of mammalian cells has resulted in the creation of multiple toxicogenomic datasets and corresponding tools for analysis. To enable easy access and analysis of these valuable toxicogenomic data, we have developed ToxicoDB (toxicodb.ca), a free and open cloud-based platform integrating data from large in vitro toxicogenomic studies, including gene expression profiles of primary human and rat hepatocytes treated with 231 potential toxicants. To efficiently mine these complex toxicogenomic data, ToxicoDB provides users with harmonized chemical annotations, time- and dose-dependent plots of compounds across datasets, as well as the toxicity-related pathway analysis. The data in ToxicoDB have been generated using our open-source R package, ToxicoGx (github.com/bhklab/ToxicoGx). Altogether, ToxicoDB provides a streamlined process for mining highly organized, curated, and accessible toxicogenomic data that can be ultimately applied to preclinical toxicity studies and further our understanding of adverse outcomes.
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Affiliation(s)
- Sisira Kadambat Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Esther Yoo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Amy Tang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Parwaiz Nijrabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Heewon Seo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School of Oncology and Development Biology, Maastricht University, Maastricht, The Netherlands
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.,Ontario Institute for Cancer Research, Toronto, ON M5G 1L7, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G 1L7, Canada
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9
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Vooijs M, Yu LC, Tkachuk D, Pinkel D, Johnson D, Gray JW. Libraries for each human chromosome, constructed from sorter-enriched chromosomes by using linker-adaptor PCR. Am J Hum Genet 1993; 52:586-97. [PMID: 8447324 PMCID: PMC1682175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We describe here the production of complex libraries enriched in sequences from each human chromosome type, starting with only a few thousand sorter-purified chromosomes. In this procedure, DNA is extracted from the sorted chromosomes, digested to completion by using the frequently cutting restriction endonuclease Sau3A1, and ligated, on each end, to an adaptor oligonucleotide. These fragments are then amplified using PCR with a sequence homologous to the adaptor oligonucleotide as a primer. We have used this procedure to produce PCR libraries for each of the 24 human chromosomes. These libraries were characterized by gel electrophoresis and found to be composed of a continuum of sequences ranging in size from a few hundred to approximately 1,000 bp. The libraries, when used as probes for fluorescence in situ hybridization, stained the target chromosomes more or less continuously, even after PCR amplification for more than 200 cycles. These libraries are useful as hybridization probes to facilitate molecular cytogenetic studies and as sources of probes either for identification of polymorphic short tandemly repeated sequences or for development of sequence-tagged sites.
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Affiliation(s)
- M Vooijs
- Department of Laboratory Medicine, University of California, San Francisco 94143-0808
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Gray J, Pinkel D, Kallioniemi A, Kallioniemi O, Kuo WL, Sakamoto M, Tkachuk D, Waldman F, Weier U. 2 Molecular cytogenetic analysis of chromosome aberrations. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0165-4608(92)90172-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Gray JW, Kuo WL, Liang J, Pinkel D, van den Engh G, Trask B, Tkachuk D, Waldman F, Westbrook C. Analytical approaches to detection and characterization of disease-linked chromosome aberrations. Bone Marrow Transplant 1990; 6 Suppl 1:14-9. [PMID: 2202466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Flow karyotyping and FISH with chromosome specific or disease-locus-specific probes are powerful adjuncts to conventional cytogenetic analysis. Flow karyotyping is well suited to quantitative analysis of DNA content changes that occur during structural rearrangement. FISH with probes for repeated sequences allows ready detection of aneuploidy in interphase cells. FISH with whole chromosome composite probes to metaphase spreads facilitates detection of subtle structural changes and allows detection of structural aberrations that occur at frequencies as low as 10(-3). FISH with locus-specific probes facilitates diagnosis of specific genetic diseases, allows phenotype-genotype correlation on a cell-by-cell basis and may be developed into a sensitive method for detection of residual disease.
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Affiliation(s)
- J W Gray
- Lawrence Livermore National Laboratory, CA
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Griesser H, Tkachuk D, Reis MD, Mak TW. Gene rearrangements and translocations in lymphoproliferative diseases. Blood 1989; 73:1402-15. [PMID: 2653455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- H Griesser
- Ontario Cancer Institute, Toronto, Canada
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Takihara Y, Tkachuk D, Michalopoulos E, Champagne E, Reimann J, Minden M, Mak TW. Sequence and organization of the diversity, joining, and constant region genes of the human T-cell delta-chain locus. Proc Natl Acad Sci U S A 1988; 85:6097-101. [PMID: 3413078 PMCID: PMC281912 DOI: 10.1073/pnas.85.16.6097] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this paper we describe the genomic organization and sequence of the human T-cell receptor delta-chain diversity, joining, and constant genes. There is one delta-chain constant region gene (C delta) located approximately equal to 85 kilobases (kb) upstream of the alpha-chain constant region. The delta-chain constant region consists of four exons, whose organization is very similar to that of the C alpha exons, suggesting that C alpha and C delta may have arisen from a gene duplication event. The first exon encodes most of the extracellular constant domain, the second encodes a hinge-like region, and the third encodes the entire transmembrane segment and intracytoplasmic portion, whereas the last exon contains exclusively 3' untranslated sequences. Three joining segments, J delta 1, J delta 2, and J delta 3, are found approximately equal to 12, approximately equal to 5.7, and approximately equal to 3.4 kb upstream of the first exon of C delta. Two functional diversity gene segments, D delta 1 and D delta 2, which can be productively translated in all three reading frames, are found 1 and 9.6 kb upstream of J delta 1. The presence of two D delta with such potential for diversity may offset the limited repertoire of the J delta and V delta genes. The spacer distribution in the recombinational signals flanking D delta and J delta segments allows recombination with V alpha gene segments; however, examination of delta-chain messages does not indicate that this is the case, suggesting that the delta chain uses unique variable gene segments and raising the question as to the reasons for this phenomenon.
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Affiliation(s)
- Y Takihara
- Ontario Cancer Institute, University of Toronto, ON
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Griesser H, Champagne E, Tkachuk D, Takihara Y, Lalande M, Baillie E, Minden M, Mak TW. The human T cell receptor alpha-delta locus: a physical map of the variable, joining and constant region genes. Eur J Immunol 1988; 18:641-4. [PMID: 2835248 DOI: 10.1002/eji.1830180424] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this study a physical macro-restriction map of the entire human alpha locus that spans about 1000 kilobase pairs and includes the V alpha, J alpha and C alpha genes is presented. Evidence is provided that gene duplications were involved in the increase of genomic diversity of V alpha genes. In addition, we show a detailed map of a 40-kb region located approximately 100 kg upstream of the human C alpha gene. Direct evidence is provided to support that the human alpha chain locus, like the murine, also contains another T cell constant region gene in the alpha chain locus, the human delta chain gene. In addition, two J segments and one D segment have been identified. Using these genomic probes, we show that several T cell lines, including those known to express the surface gamma/delta heterodimer, have rearranged this region. The design of two separate centers of rearrangement within one locus that are involved in rearrangement events at different times, and the presence of high number of J segments in this region, may render the locus highly vulnerable to chromosomal translocation during T cell development.
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Affiliation(s)
- H Griesser
- Ontario Cancer Institute, Toronto, Canada
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Takihara Y, Champagne E, Griesser H, Kimura N, Tkachuk D, Reimann J, Okada A, Alt FW, Chess L, Minden M. Sequence and organization of the human T cell delta chain gene. Eur J Immunol 1988; 18:283-7. [PMID: 2965024 DOI: 10.1002/eji.1830180216] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A novel human T cell receptor (TcR) gene, located 85 kbp upstream to the C alpha coding regions, was isolated using human genomic clones to identify cDNA homologous to messages encoded by this region. The deduced protein sequence of this gene is highly homologous to that of the newly identified constant region found in the murine TcR alpha chain locus. This gene undergoes rearrangements and is expressed at the RNA level in human thymocytes, peripheral T cells and several leukemic T cell lines which have been shown to express the surface gamma-delta heterodimer, suggesting that this gene encodes the human T cell delta chain.
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Affiliation(s)
- Y Takihara
- Ontario Cancer Institute, University of Toronto, Canada
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Abstract
In an extensive analysis, using a range of restriction endonucleases, HinfI and TaqI were found to differentiate satellites I, II and III & IV. Satellite I is resistant to digestion by TaqI, but is cleaved by HinfI to yield three major fragments of approximate size 770, 850 and 950bp, associated in a single length of DNA. The 770bp fragment contains recognition sites for a number of other enzymes, whereas the 850 and 950bp fragments are "silent" by restriction enzyme analysis. Satellite II is digested by HinfI into a large number of very small (10-80bp) fragments, many of which also contain TaqI sites. A proportion of the HinfI sites in satellite II have the sequence 5'GA(GC)TC. The HinfI digestion products of satellites III and IV form a complete ladder, stretching from 15bp or less to more than 250bp, with adjacent multimers separated by an increment of 5bp. The ladder fragments do not contain TaqI sites and all HinfI sites have the sequence 5'GA(AT)TC. Three fragments from the HinfI ladder of satellite III have been sequenced, and all consist of a tandemly repeated 5bp sequence, 5'TTCCA, with a non-repeated, G+C rich sequence, 9bp in length, at the 3' end.
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