1
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Vasudev NS, Scelo G, Glennon KI, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Cartledge J, Soomro N, Adeyoju A, Patel PM, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE. Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma. Clin Cancer Res 2023; 29:1220-1231. [PMID: 36815791 PMCID: PMC10068441 DOI: 10.1158/1078-0432.ccr-22-1936] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/12/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk prediction and inform adjuvant treatment decisions. We explored the role of tumor genomics in this setting, leveraging the largest cohort to date of localized ccRCC tissues subjected to targeted gene sequencing. EXPERIMENTAL DESIGN The somatic mutation status of 12 genes was determined in 943 ccRCC cases from a multinational cohort of patients, and associations to outcomes were examined in a Discovery (n = 469) and Validation (n = 474) framework. RESULTS Tumors containing a von-Hippel Lindau (VHL) mutation alone were associated with significantly improved outcomes in comparison with tumors containing a VHL plus additional mutations. Within the Discovery cohort, those with VHL+0, VHL+1, VHL+2, and VHL+≥3 tumors had disease-free survival (DFS) rates of 90.8%, 80.1%, 68.2%, and 50.7% respectively, at 5 years. This trend was replicated in the Validation cohort. Notably, these genomically defined groups were independent of tumor mutational burden. Amongst patients eligible for adjuvant therapy, those with a VHL+0 tumor (29%) had a 5-year DFS rate of 79.3% and could, therefore, potentially be spared further treatment. Conversely, patients with VHL+2 and VHL+≥3 tumors (32%) had equivalent DFS rates of 45.6% and 35.3%, respectively, and should be prioritized for adjuvant therapy. CONCLUSIONS Genomic characterization of ccRCC identified biologically distinct groups of patients with divergent relapse rates. These groups account for the ∼80% of cases with VHL mutations and could be used to personalize adjuvant treatment discussions with patients as well as inform future adjuvant trial design.
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Affiliation(s)
- Naveen S. Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Ghislaine Scelo
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Kate I. Glennon
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Michelle Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Louis Letourneau
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Robert Eveleigh
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Nazanin Nourbehesht
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Madeleine Arseneault
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Antoine Paccard
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sharon M. Jackson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Behnoush Abedi-Ardekani
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom
| | - Peter J. Selby
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Sebastian Trainor
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Michael Kimuli
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Jon Cartledge
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Naeem Soomro
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Poulam M. Patel
- Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Magdalena B. Wozniak
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Ivana Holcatova
- Charles University in Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | | | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Estelle Chanudet
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - David Zaridze
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Anush Moukeria
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Oxana Shangina
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucuresti, Romania
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Ljiljana Bogdanovic
- Institute of Pathology, School of Medicine Belgrade, University of Belgrade, Belgrade, Serbia
| | - Bozidar Kovacevic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Anne Cambon-Thomsen
- Institut National de la Santé et de la Recherche Médicale (INSERM) and Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | - Guillaume Bourque
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Alvis Brazma
- European Bioinformatics Institute, European Molecular Biology Laboratory, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jörg Tost
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie Francois Jacob, University Paris Saclay, Evry, France
| | - Paul Brennan
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Mark Lathrop
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Yasser Riazalhosseini
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Rosamonde E. Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
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2
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Demko N, Glennon KI, Arseneault M, Lach K, Nishimura T, Tanguay S, Riazalhosseini Y, Brimo F. A Sarcomatoid Renal Cell Carcinoma with Clear Cell Papillary-Like Primary Tumor and Lymph Node Metastasis: A Diagnostic Conundrum. Int J Surg Pathol 2022:10668969221145011. [PMID: 36562104 DOI: 10.1177/10668969221145011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/24/2022]
Abstract
Clear cell papillary renal cell tumor (CCPRCT) is a distinct clinical entity with characteristic pathological features and non-aggressive clinical behavior. Diagnostically challenging cases present when there are immunomorphological findings of CCPRCT associated with heterogeneous morphologies, aggressive histological features, and advanced pathological stages-so-called CCPRCT-like tumors. In this report, we describe a heterogeneous, multifocal renal tumor with immunomorphological characteristics of CCPRCT but with associated aggressive features such as sarcomatoid and necrotic areas, perirenal and sinus fat involvement, and most notably, lymph node metastasis composed entirely of classic CCPRCT morphology and immunophenotype. Immunohistochemical and fluorescence in situ hybridization studies did not support a translocation renal cell carcinoma. Molecular analyses did not identify common mutations or chromosomal abnormalities seen in clear cell renal cell carcinoma or ELOC-mutated renal cell carcinoma. This case highlights that rare renal cell tumors remain difficult to classify and the distinction between CCPRCT and CCPRCT-like tumors remains to be better defined.
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Affiliation(s)
- Nadine Demko
- Department of Anatomical Pathology, 5620McGill University, Montréal, Québec, Canada
| | - Kate I Glennon
- Department of Human Genetics, 5620McGill University, Montréal, Québec, Canada.,McGill Genome Centre, 5620McGill University, Montréal, Québec, Canada
| | - Madeleine Arseneault
- Department of Human Genetics, 5620McGill University, Montréal, Québec, Canada.,McGill Genome Centre, 5620McGill University, Montréal, Québec, Canada
| | - Katherine Lach
- Department of Anatomical Pathology, 5620McGill University, Montréal, Québec, Canada
| | - Tamiko Nishimura
- Department of Human Genetics, 5620McGill University, Montréal, Québec, Canada.,McGill Genome Centre, 5620McGill University, Montréal, Québec, Canada
| | - Simon Tanguay
- Division of Urology, 5620McGill University, Montréal, Québec, Canada
| | - Yasser Riazalhosseini
- Department of Human Genetics, 5620McGill University, Montréal, Québec, Canada.,McGill Genome Centre, 5620McGill University, Montréal, Québec, Canada
| | - Fadi Brimo
- Department of Anatomical Pathology, 5620McGill University, Montréal, Québec, Canada
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Glennon KI, Vasudev NS, Scelo G, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Soomro N, Adeyoju A, Patel P, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE. Abstract LB113: Genomic classification to refine prognosis in clear cell renal cell carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb113] [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
Renal cell carcinomas (RCC) are characterized by their heterogenous clinical outcomes, and due to their indeterminate behavior and the absence of routine biomarkers, it is difficult to identify patients who are at high-risk for relapse after curative nephrectomy. To identify genomic biomarkers for clear cell RCC (ccRCC) risk-stratification we interrogated somatic mutation status of 12 RCC-relevant genes using next-generation sequencing (NGS) in tumor-normal pairs from 943 patients with matched follow up data from the Cancer Genomics of the Kidney (CAGEKID) study. We examined associations between genomically-defined patient groups, explained below, and disease-free as well as RCC-specific survival independently in two cohorts of patients (N=469 for cohort 1; 474 for cohort 2). We used the Kaplan-Meier method with log-rank tests to compare survival functions, and Cox proportional hazards models to stratify for patient stage and age to estimate association of each group with survival. RCC-specific survival was assessed with a competing-risks method to include deaths from other causes. Within these cohorts, 76.4% of patients harbored somatic mutations in VHL, the most common driver gene in ccRCC. The most commonly mutated genes within VHL-mutated tumors were PBRM1 (39.7%), SETD2 (19%), BAP1 (14.3%), and KDM5C (8.3%). Less frequently mutated genes included ATM, COL11A1, DMD, TP53, and TRRAP (~3-5%).Among VHL-driven tumors, we identified a new genomic classifier on the basis of the number of mutations in additional RCC driver genes in the panel examined. Patients were classified based on the presence of mutations only in VHL (VHL+0), those with mutations in VHL and one other driver gene (VHL+1), two other driver genes (VHL+2), and 3 or more other driver genes (VHL≥3). We observed within both cohorts that both the risk of disease recurrence as well as RCC-specific death were associated with an increased number of mutations within this classification. When stratified for patient stage and age, the hazard-ratio for 5-year disease-free survival for VHL≥3 patients was 6.69 (p=0.000212), 4.31 for VHL+2 (p=0.000862), and 2.43 for VHL+1 (p=0.035662), compared to patients with only mutations in VHL. These observations were replicated in the second patient cohort, with hazards ratios of 4.55, 2.49, and 1.40, for VHL≥3, VHL+2, and VHL+1 classified patients respectively, indicating that risk of disease recurrence increases with the number of driver mutations. Notably, tumor mutational burden (TMB) was not significantly different between the aforementioned groups, demonstrating that our classifier is independent of TMB. We created a model based on a set of 12 RCC-relevant genes, which can predict risk of relapse for the ~80% of patients with ccRCC that are VHL-driven. This classification can be defined based on a small panel of genes, making it easily applicable to the clinic, in the context of tumor or liquid biopsy analysis.
Citation Format: Kate I. Glennon, Naveen S. Vasudev, Ghislaine Scelo, Michelle Wilson, Louis Letourneau, Robert Eveleigh, Nazanin Nourbehesht, Madeleine Arseneault, Antoine Paccard, Lars Egevad, Juris Viksna, Edgars Celms, Sharon M. Jackson, Behnoush Abedi-Ardekani, Anne Y. Warren, Peter J. Selby, Sebastian Trainor, Michael Kimuli, Naeem Soomro, Adebanji Adeyoju, Poulam Patel, Magdalena B. Wozniak, Ivana Holcatova, Antonin Brisuda, Vladimir Janout, Estelle Chanudet, David Zaridze, Anush Moukeria, Oxana Shangina, Lenka Foretova, Marie Navratilova, Dana Mates, Viorel Jinga, Ljiljana Bogdanovic, Bozidar Kovacevic, Anne Cambon-Thomsen, Guillaume Bourque, Alvis Brazma, Jörg Tost, Paul Brennan, Mark Lathrop, Yasser Riazalhosseini, Rosamonde E. Banks. Genomic classification to refine prognosis in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB113.
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Affiliation(s)
| | - Naveen S. Vasudev
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Ghislaine Scelo
- 3Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Michelle Wilson
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | | | | | | | | | | | - Lars Egevad
- 4Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juris Viksna
- 5Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Edgars Celms
- 5Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sharon M. Jackson
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Behnoush Abedi-Ardekani
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Anne Y. Warren
- 7Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Peter J. Selby
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Sebastian Trainor
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Michael Kimuli
- 8Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, St James’s University Hospital, Leeds, United Kingdom
| | - Naeem Soomro
- 9Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Poulam Patel
- 11Divison of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Magdalena B. Wozniak
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Ivana Holcatova
- 12Charles University in Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | | | - Vladimir Janout
- 14Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Estelle Chanudet
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - David Zaridze
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Anush Moukeria
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Oxana Shangina
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Lenka Foretova
- 16Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- 16Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dana Mates
- 17National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- 18Carol Davila University of Medicine and Pharmacy, Burghele Clinical Hospital, Bucharest, Romania
| | - Ljiljana Bogdanovic
- 19Institute of Pathology, School of Medicine Belgrade, University of Belgrade, Belgrade
| | - Bozidar Kovacevic
- 20Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade
| | - Anne Cambon-Thomsen
- 21Institut National de la Santé et de la Recherche Médicale (INSERM) and Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | | | - Alvis Brazma
- 22European Bioinformatics Institute, European Molecular Biology Laboratory, EMBL- EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jörg Tost
- 23Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie Francois Jacob, University Paris Saclay, Evry, France
| | - Paul Brennan
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Mark Lathrop
- 1McGill University Genome Centre, Montreal, Quebec, Canada
| | | | - Rosamonde E. Banks
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
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4
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Daniel P, Meehan B, Sabri S, Jamali F, Sarkaria JN, Choi DS, Garnier D, Kitange G, Glennon KI, Paccard A, Karamchandani J, Riazalhosseini Y, Rak J, Abdulkarim B. Detection of Temozolomide-Induced Hypermutation and Response to PD-1 Checkpoint Inhibitor In Recurrent Glioblastoma. Neurooncol Adv 2022; 4:vdac076. [PMID: 35795471 PMCID: PMC9252128 DOI: 10.1093/noajnl/vdac076] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Indexed: 11/16/2022] Open
Abstract
Background Despite aggressive upfront treatment in glioblastoma (GBM), recurrence remains inevitable for most patients. Accumulating evidence has identified hypermutation induced by temozolomide (TMZ) as an emerging subtype of recurrent GBM. However, its biological and therapeutic significance has yet to be described. Methods We combined GBM patient and derive GBM stem cells (GSCs) from tumors following TMZ to explore response of hypermutant and non-hypermutant emergent phenotypes and explore the immune relevance of hypermutant and non-hypermutant states in vivo. Results Hypermutation emerges as one of two possible mutational subtypes following TMZ treatment in vivo and demonstrates distinct phenotypic features compared to non-hypermutant recurrent GBM. Hypermutant tumors elicited robust immune rejection in subcutaneous contexts which was accompanied by increased immune cell infiltration. In contrast, immune rejection of hypermutant tumors were stunted in orthotopic settings where we observe limited immune infiltration. Use of anti-PD-1 immunotherapy showed that immunosuppression in orthotopic contexts was independent from the PD-1/PD-L1 axis. Finally, we demonstrate that mutational burden can be estimated from DNA contained in extracellular vesicles (EVs). Conclusion Hypermutation post-TMZ are phenotypically distinct from non-hypermutant GBM and requires personalization for appropriate treatment. The brain microenvironment may be immunosuppressive and exploration of the mechanisms behind this may be key to improving immunotherapy response in this subtype of recurrent GBM.
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Affiliation(s)
- Paul Daniel
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | - Brian Meehan
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | - Siham Sabri
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | - Fatemeh Jamali
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | | | - Dong-sic Choi
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | - Delphine Garnier
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | | | | | | | - Jason Karamchandani
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | | | - Janusz Rak
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
| | - Bassam Abdulkarim
- McGill University, Research Institute of the McGill University Health Centre (Research Institute-MUHC), Montreal, Canada
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5
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Glennon KI, Maralani M, Abdian N, Paccard A, Montermini L, Nam AJ, Arseneault M, Staffa A, Jandaghi P, Meehan B, Brimo F, Tanguay S, Rak J, Riazalhosseini Y. Rational Development of Liquid Biopsy Analysis in Renal Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225825. [PMID: 34830979 PMCID: PMC8616270 DOI: 10.3390/cancers13225825] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Among patients affected by renal cell carcinoma (RCC), the most common type of kidney cancer, it remains difficult to identify those who are at high risk for relapse or metastasis. This is in part due to the absence of reliable clinical biomarkers and robust methods to capture them. The aim of our study was to develop an improved assay to capture prognostic genomic biomarkers in circulating tumor DNA (ctDNA) in RCC. For this purpose, we first established a next generation sequencing (NGS) assay, targeting genes that are tailored for RCC and that are largely excluded from commercially available assays. Next, we showed the reliable performance of this assay to detect prognostic gene mutations in tumor DNA isolated from plasma, and from extracellular vesicles. Thus, our study provides a resource to facilitate ctDNA analysis for precision medicine in RCC. Abstract Renal cell carcinoma (RCC) is known for its variable clinical behavior and outcome, including heterogeneity in developing relapse or metastasis. Recent data highlighted the potential of somatic mutations as promising biomarkers for risk stratification in RCC. Likewise, the analysis of circulating tumor DNA (ctDNA) for such informative somatic mutations (liquid biopsy) is considered an important advance for precision oncology in RCC, allowing to monitor molecular disease evolution in real time. However, our knowledge about the utility of ctDNA analysis in RCC is limited, in part due to the lack of RCC-appropriate assays for ctDNA analysis. Here, by interrogating different blood compartments in xenograft models, we identified plasma cell-free (cf) DNA and extracellular vesicles (ev) DNA enriched for RCC-associated ctDNA. Additionally, we developed sensitive targeted sequencing and bioinformatics workflows capable of detecting somatic mutations in RCC-relevant genes with allele frequencies ≥ 0.5%. Applying this assay to patient-matched tumor and liquid biopsies, we captured tumor mutations in cf- and ev-DNA fractions isolated from the blood, highlighting the potentials of both fractions for ctDNA analysis. Overall, our study presents an RCC-appropriate sequencing assay and workflow for ctDNA analysis and provides a proof of principle as to the feasibility of detecting tumor-specific mutations in liquid biopsy in RCC patients.
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Affiliation(s)
- Kate I. Glennon
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
| | - Mahafarin Maralani
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Narges Abdian
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Antoine Paccard
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Laura Montermini
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Alice Jisoo Nam
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Madeleine Arseneault
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Alfredo Staffa
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
| | - Pouria Jandaghi
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
| | - Brian Meehan
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Fadi Brimo
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada;
| | - Simon Tanguay
- Division of Urology, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Janusz Rak
- The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (N.A.); (L.M.); (B.M.); (J.R.)
| | - Yasser Riazalhosseini
- McGill Genome Centre, McGill University, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada; (K.I.G.); (M.M.); (A.P.); (A.J.N.); (M.A.); (A.S.); (P.J.)
- Department of Human Genetics, McGill University, 1205 Doctor Penfield Avenue, Montreal, QC H3A 1B1, Canada
- Correspondence:
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