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Li B, Jin K, Liu Z, Su X, Xu Z, Liu G, Xu J, Chang Y, Wang Y, Zhu Y, Xu L, Wang Z, Liu H, Zhang W. RAD51 Expression as a Biomarker to Predict Efficacy of Platinum-Based Chemotherapy and PD-L1 Blockade for Muscle-Invasive Bladder Cancer. J Immunother 2024:00002371-990000000-00105. [PMID: 38800996 DOI: 10.1097/cji.0000000000000525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 04/11/2024] [Indexed: 05/29/2024]
Abstract
RAD51, a key recombinase that catalyzes homologous recombination (HR), is commonly overexpressed in multiple cancers. It is curial for DNA damage repair (DDR) to maintain genomic integrity which could further determine the therapeutic response. Herein, we attempt to explore the clinical value of RAD51 in therapeutic guidance in muscle-invasive bladder cancer (MIBC). In this retrospective study, a total of 823 patients with MIBC were included. Zhongshan hospital (ZSHS) cohort (n=134) and The Cancer Genome Atlas-Bladder Cancer (TCGA-BLCA) cohort (n=391) were included for the investigation of chemotherapeutic response. The IMvigor210 cohort (n=298) was utilized to interrogate the predictive efficacy of RAD51 status to programmed cell death ligand-1 (PD-L1) blockade. In addition, the association of RAD51 with genomic instability and tumor immune contexture was investigated. Patients with RAD51 overexpression were more likely to benefit from both platinum-based chemotherapy and immunotherapy rather than RAD51-low patients. The TMB high PD-L1 high RAD51 high subgroup possessed the best clinical benefits from PD-L1 blockade. RAD51-high tumors featured by genomic instability were correlated to highly inflamed and immunogenic contexture with activated immunotherapeutic pathway in MIBC. RAD51 could serve as a prognosticator for treatment response to platinum-based chemotherapy and PD-L1 inhibitor in MIBC patients. Besides, it could also improve the predictive efficacy of TMB and PD-L1.
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Affiliation(s)
- Bingyu Li
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kaifeng Jin
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhaopei Liu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaohe Su
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ziyue Xu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ge Liu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jingtong Xu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuan Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Le Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zewei Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hailong Liu
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
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Hu H, Zhu Y, Pu N, Burkhart RA, Burns W, Laheru D, Zheng L, He J, Goggins MG, Yu J. Association of Germline Variants in Human DNA Damage Repair Genes and Response to Adjuvant Chemotherapy in Resected Pancreatic Ductal Adenocarcinoma. J Am Coll Surg 2020; 231:527-535.e14. [PMID: 32659497 DOI: 10.1016/j.jamcollsurg.2020.06.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/28/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The frequency and significance of the germline variants in DNA damage repair genes still need to be elucidated in patients with sporadic pancreatic ductal adenocarcinoma (PDAC). Our purpose was to determine whether germline variants in DNA damage repair genes were associated with survival of patients with sporadic PDAC. STUDY DESIGN We retrospectively identified 854 patients with sporadic PDAC with germline DNA sequenced in targeted 22 DNA damage repair genes by next-generation sequencing. Outcomes were compared in terms of clinicopathologic features, disease-free survival (DFS), and overall survival (OS). RESULTS Nineteen patients had deleterious mutations; 103 had variant(s) of unknown significance (VUS). Germline DNA damage repair deleterious variant carriers had superior DFS (median, 19.1 months vs 11.9 months, p = 0.012) and OS (median, 29.7 months vs 20.2 months, p = 0.034), as compared with wild-type patients. Germline DNA damage repair VUS variant carriers also had superior DFS when compared with wild-type patients. In subgroup analysis, this improved survival was limited to patients receiving adjuvant chemotherapy, deleterious variant carriers vs wild-type patients DFS (median 36.3 months vs 13.1 months, p = 0.006) and OS (median 43.7 months vs 24.3 months, p = 0.045), VUS variant carriers vs wild-type patients DFS (16.5 months vs 13.1 months, p = 0.007). CONCLUSIONS Having a deleterious variant in a DNA damage repair gene is associated with improved survival after resection and adjuvant chemotherapy for pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Haijie Hu
- Department of Biliary Surgery, West China Hospital of Sichuan University, Sichuan, China; Department of Surgery, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD
| | - Yayun Zhu
- Department of Surgery, Baltimore, MD; Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Ning Pu
- Department of Surgery, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD
| | - Richard A Burkhart
- Department of Surgery, Baltimore, MD; Department Oncology, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - William Burns
- Department of Surgery, Baltimore, MD; Department Oncology, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Daniel Laheru
- Department Pathology, Baltimore, MD; Department Oncology, Baltimore, MD; Department Medicine, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; The Skip Viragh Center for Pancreas Cancer, Baltimore, MD; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, MD
| | - Lei Zheng
- Department of Surgery, Baltimore, MD; Department Oncology, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; The Skip Viragh Center for Pancreas Cancer, Baltimore, MD; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, MD
| | - Jin He
- Department of Surgery, Baltimore, MD; Department Oncology, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Michael G Goggins
- Department Pathology, Baltimore, MD; Department Medicine, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; The Skip Viragh Center for Pancreas Cancer, Baltimore, MD
| | - Jun Yu
- Department of Surgery, Baltimore, MD; The Johns Hopkins University School of Medicine The Pancreatic Cancer Precision Medicine Center of Excellence, Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD.
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Wood LD, Yurgelun MB, Goggins MG. Genetics of Familial and Sporadic Pancreatic Cancer. Gastroenterology 2019; 156:2041-2055. [PMID: 30660730 DOI: 10.1053/j.gastro.2018.12.039] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/14/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022]
Abstract
In the previous decade, comprehensive genomic analyses have yielded important insights about the genetic alterations that underlie pancreatic tumorigenesis. Whole-exome and whole-genome sequencing of pancreatic ductal adenocarcinomas have confirmed the critical driver genes altered in the majority of pancreatic cancers, as well as identified numerous less frequently altered driver genes, and have delineated cancer subgroups with unique biological and clinical features. It is now appreciated that pancreatic susceptibility gene alterations are often identified in patients with pancreatic cancer without family histories suggestive of a familial cancer syndrome, prompting recent efforts to expand gene testing to all patients with pancreatic cancer. Studies of pancreatic cancer precursor lesions have begun to elucidate the evolutionary history of pancreatic tumorigenesis and to help us understand the utility of biomarkers for early detection and targets to develop new therapeutic strategies. In this review, we discuss the results of comprehensive genomic characterization of pancreatic ductal adenocarcinoma and its precursor lesions, and we highlight translational applications in early detection and therapy.
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Affiliation(s)
- Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Yurgelun MB, Chittenden AB, Morales-Oyarvide V, Rubinson DA, Dunne RF, Kozak MM, Qian ZR, Welch MW, Brais LK, Da Silva A, Bui JL, Yuan C, Li T, Li W, Masuda A, Gu M, Bullock AJ, Chang DT, Clancy TE, Linehan DC, Findeis-Hosey JJ, Doyle LA, Thorner AR, Ducar MD, Wollison BM, Khalaf N, Perez K, Syngal S, Aguirre AJ, Hahn WC, Meyerson ML, Fuchs CS, Ogino S, Hornick JL, Hezel AF, Koong AC, Nowak JA, Wolpin BM. Germline cancer susceptibility gene variants, somatic second hits, and survival outcomes in patients with resected pancreatic cancer. Genet Med 2019; 21:213-223. [PMID: 29961768 PMCID: PMC6666401 DOI: 10.1038/s41436-018-0009-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/20/2018] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Germline variants in double-strand DNA damage repair (dsDDR) genes (e.g., BRCA1/2) predispose to pancreatic adenocarcinoma (PDAC) and may predict sensitivity to platinum-based chemotherapy and poly(ADP) ribose polymerase (PARP) inhibitors. We sought to determine the prevalence and significance of germline cancer susceptibility gene variants in PDAC with paired somatic and survival analyses. METHODS Using a customized next-generation sequencing panel, germline/somatic DNA was analyzed from 289 patients with resected PDAC ascertained without preselection for high-risk features (e.g., young age, personal/family history). All identified variants were assessed for pathogenicity. Outcomes were analyzed using multivariable-adjusted Cox proportional hazards regression. RESULTS We found that 28/289 (9.7%; 95% confidence interval [CI] 6.5-13.7%) patients carried pathogenic/likely pathogenic germline variants, including 21 (7.3%) dsDDR gene variants (3 BRCA1, 4 BRCA2, 14 other dsDDR genes [ATM, BRIP1, CHEK2, NBN, PALB2, RAD50, RAD51C]), 3 Lynch syndrome, and 4 other genes (APC p.I1307K, CDKN2A, TP53). Somatic sequencing and immunohistochemistry identified second hits in the tumor in 12/27 (44.4%) patients with germline variants (1 failed sequencing). Compared with noncarriers, patients with germline dsDDR gene variants had superior overall survival (hazard ratio [HR] 0.54; 95% CI 0.30-0.99; P = 0.05). CONCLUSION Nearly 10% of PDAC patients harbor germline variants, although the majority lack somatic second hits, the therapeutic significance of which warrants further study.
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Affiliation(s)
- Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA.
| | - Anu B Chittenden
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Vicente Morales-Oyarvide
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Douglas A Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Richard F Dunne
- Department of Medicine, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Margaret M Kozak
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marisa W Welch
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Annacarolina Da Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin L Bui
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tingting Li
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wanwan Li
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Atsuhiro Masuda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mancang Gu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrea J Bullock
- Department of Medicine, Division of Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Daniel T Chang
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - Thomas E Clancy
- Department of Surgery, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David C Linehan
- Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Leona A Doyle
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron R Thorner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew D Ducar
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bruce M Wollison
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Natalia Khalaf
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Kimberly Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Sapna Syngal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aram F Hezel
- Department of Medicine, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Albert C Koong
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan A Nowak
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
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