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Kim P, Kumar H, Yang C, Luo R, Liu J, Zhou X. Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ. Brief Bioinform 2023; 24:bbad314. [PMID: 37635381 PMCID: PMC10516359 DOI: 10.1093/bib/bbad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/10/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to infer the high chance of genomic breakpoint regions. For this, we utilized the high feature importance score area calculated from our recently developed fusion BP prediction model, FusionAI and identified 151 K microhomologies among ~24 K fusion BPs in 20 K fusion genes. From our multiple bioinformatics studies, we found a relationship between sequence homologies and the immune system. This in-silico study will provide novel knowledge on the sequence homologies around the coded structural variants.
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Affiliation(s)
- Pora Kim
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Himansu Kumar
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chengyuan Yang
- School of Public Health Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruihan Luo
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiajia Liu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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2
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Xiang X, Kang J, Jiang J, Zhang Y, Zhang Y, Li L, Peng X. A novel DNA damage repair-related gene signature predicting survival, immune infiltration and drug sensitivity in cervical cancer based on single cell sequencing. Front Immunol 2023; 14:1198391. [PMID: 37449209 PMCID: PMC10337997 DOI: 10.3389/fimmu.2023.1198391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Background Aberrant DNA damage repair (DDR) is one of the hallmarks of tumors, and therapeutic approaches targeting this feature are gaining increasing attention. This study aims to develop a signature of DDR-related genes to evaluate the prognosis of cervical cancer (CC). Methods Differentially expressed genes were identified between high and low DDR groups of cells from the single-cell RNA sequencing dataset GSE168652 based on DDR scores. Using the ssGSEA and WGCNA methods, DDR-related differentially expressed genes were identified from different patients within the TCGA-CESC cohort. Using Cox analysis and LASSO regression analysis, a DDR-related gene signature was constructed based on the intersection of two groups of differentially expressed genes and DDR-related genes from WGCNA, and validated in GSE52903. Immune cell infiltration analysis, mutation analysis, survival analysis, drug sensitivity analysis, etc., were performed in different groups which were established based on the DDR gene signature scoring. A key gene affecting prognosis was selected and validated through biological experiments such as wound healing, migration, invasion, and comet assays. Results A novel DDR-related signature was constructed and the nomogram results showed this signature performed better in predicting prognosis than other clinical features for CC. The high DDR group exhibited poorer prognosis, weaker immune cell infiltration in the immune microenvironment, lower expression of immune checkpoint-related genes, lower gene mutation frequencies and more sensitivity to drugs such as BI.2536, Bleomycin and etc. ITGB1, ZC3H13, and TOMM20 were expressed at higher levels in CaSki and HeLa cells compared to ECT1 cells. Compared with the native CaSki and HeLa cells, the proliferation, migration, invasion and DDR capabilities of CaSki and HeLa cell lines with ITGB1 suppressed expression were significantly decreased. Conclusion The 7 DDR-related gene signature was an independent and powerful prognostic biomarker that might effectively evaluate the prognosis of CC and provide supplementary information for a more personalized evaluation and precision therapy. ITGB1 was a potential candidate gene that may affect the DDR capacity of CC cells, and its mechanism of action was worth further in-depth study.
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Affiliation(s)
- Xiaoqing Xiang
- Department of Internal Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Jiawen Kang
- Department of Internal Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Jingwen Jiang
- Department of Internal Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Yaning Zhang
- The High School Attached to Hunan Normal University, Changsha, China
| | - Yong Zhang
- Department of Internal Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
| | - Lesai Li
- Department of Gynecologic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xiaoning Peng
- Department of Internal Medicine, Medical College of Hunan Normal University, Changsha, Hunan, China
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3
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Li Y, Wang X, Hou X, Ma X. Could Inhibiting the DNA Damage Repair Checkpoint Rescue Immune-Checkpoint-Inhibitor-Resistant Endometrial Cancer? J Clin Med 2023; 12:jcm12083014. [PMID: 37109350 PMCID: PMC10144486 DOI: 10.3390/jcm12083014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Endometrial cancer (EC) is increasingly undermining female health worldwide, with poor survival rates for advanced or recurrent/metastatic diseases. The application of immune checkpoint inhibitors (ICIs) has opened a window of opportunity for patients with first-line therapy failure. However, there is a subset of patients with endometrial cancer who remain insensitive to immunotherapy alone. Therefore, it is necessary to develop new therapeutic agents and further explore reliable combinational strategies to optimize the efficacy of immunotherapy. DNA damage repair (DDR) inhibitors as novel targeted drugs are able to generate genomic toxicity and induce cell death in solid tumors, including EC. Recently, growing evidence has demonstrated the DDR pathway modulates innate and adaptive immunity in tumors. In this review, we concentrate on the exploration of the intrinsic correlation between DDR pathways, especially the ATM-CHK2-P53 pathway and the ATR-CHK1-WEE1 pathway, and oncologic immune response, as well as the feasibility of adding DDR inhibitors to ICIs for the treatment of patients with advanced or recurrent/metastatic EC. We hope that this review will offer some beneficial references to the investigation of immunotherapy and provide a reasonable basis for "double-checkpoint inhibition" in EC.
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Affiliation(s)
- Yinuo Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Hou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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4
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Spagnuolo A, Gridelli C. The Role of Immunotherapy in the First-Line Treatment of Elderly Advanced Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15082319. [PMID: 37190247 DOI: 10.3390/cancers15082319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/20/2023] [Accepted: 04/01/2023] [Indexed: 05/17/2023] Open
Abstract
Immune checkpoint inhibitors have changed the history of NSCLC treatment by becoming, alone or in combination with platinum-based chemotherapy, a mainstay of first-line therapy for advanced NSCLC. This increasingly dictates the identification of predictive biomarkers of response that can guide patient selection, in order to rationalize and personalize therapies, particularly in elderly patients. Immunotherapy in these patients raises questions of efficacy and tolerability related to aging, which is accompanied by a progressive decline in various body functions. Physical, biological and psychological changes contribute to individual validity status and, preferably, 'fit' patients are generally enrolled in clinical trials. In elderly patients, especially frail and complex patients with more than one chronic disease, data are poor and specific prospective studies are needed. This review reports the main available results on the use of immune checkpoint inhibitors in older patients with advanced NSCLC, in terms of efficacy and toxicity, and aims to highlight the need to better predict which patients might benefit from immunotherapy agents by probing knowledge and integrating information on immune system changes and age-related physiopathological modifications.
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Affiliation(s)
- Alessia Spagnuolo
- Division of Medical Oncology, 'S. G. Moscati' Hospital, 83100 Avellino, Italy
| | - Cesare Gridelli
- Division of Medical Oncology, 'S. G. Moscati' Hospital, 83100 Avellino, Italy
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5
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Yuan H, Qing T, Zhu S, Yang X, Wu W, Xu K, Chen H, Jiang Y, Zhu C, Yuan Z, Zhang T, Jin L, Suo C, Lu M, Chen X, Ye W. The effects of altered DNA damage repair genes on mutational processes and immune cell infiltration in esophageal squamous cell carcinoma. Cancer Med 2023; 12:10077-10090. [PMID: 36708047 PMCID: PMC10166979 DOI: 10.1002/cam4.5663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/01/2023] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. METHODS Whole-exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor-infiltrating immune cells. Ninety-six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. RESULTS A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency-related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. CONCLUSION This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers.
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Affiliation(s)
- Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Breast Medical Oncology, School of Medicine, Yale University, Connecticut, New Haven, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaorong Yang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Weicheng Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Kelin Xu
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Hui Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Yanfeng Jiang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Chengkai Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Tiejun Zhang
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Chen Suo
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Ming Lu
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Yiwu Research Institute of Fudan University, Yiwu, China
| | - Weimin Ye
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
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6
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Shi C, Qin K, Lin A, Jiang A, Cheng Q, Liu Z, Zhang J, Luo P. The role of DNA damage repair (DDR) system in response to immune checkpoint inhibitor (ICI) therapy. J Exp Clin Cancer Res 2022; 41:268. [PMID: 36071479 PMCID: PMC9450390 DOI: 10.1186/s13046-022-02469-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
As our understanding of the mechanisms of cancer treatment has increased, a growing number of studies demonstrate pathways through which DNA damage repair (DDR) affects the immune system. At the same time, the varied response of patients to immune checkpoint blockade (ICB) therapy has prompted the discovery of various predictive biomarkers and the study of combination therapy. Here, our investigation explores the interactions involved in combination therapy, accompanied by a review that summarizes currently identified and promising predictors of response to immune checkpoint inhibitors (ICIs) that are useful for classifying oncology patients. In addition, this work, which discusses immunogenicity and several components of the tumor immune microenvironment, serves to illustrate the mechanism by which higher response rates and improved efficacy of DDR inhibitors (DDRi) in combination with ICIs are achieved.
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7
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Choucair K, Naqash AR, Nebhan CA, Nipp R, Johnson DB, Saeed A. Immune Checkpoint Inhibitors: The Unexplored Landscape of Geriatric Oncology. Oncologist 2022; 27:778-789. [PMID: 35781739 PMCID: PMC9438919 DOI: 10.1093/oncolo/oyac119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer is classically considered a disease of aging, with over half of all new cancer diagnoses occurring in patients over the age of 65 years. Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet the participation of older adults with cancer in ICI trials has been suboptimal, particularly at the extremes of age. Despite significant improvement in treatment response and an improved toxicity profile when compared with conventional cytotoxic chemotherapies, many cancers develop resistance to ICIs, and these drugs are not free of toxicities. This becomes particularly important in the setting of older adults with cancer, who are generally frailer and harbor more comorbidities than do their younger counterparts. Immunosenescence, a concept involving age-related changes in immune function, may also play a role in differential responses to ICI treatment in older patients. Data on ICI treatment response in older adult with cancers remains inconclusive, with multiple studies revealing conflicting results. The molecular mechanisms underlying response to ICIs in older cancer patients are poorly understood, and predictors of response that can delineate responders from non-responders remain to be elucidated. In this review, we explore the unique geriatric oncology population by analyzing existing retrospective datasets, and we also sought to highlight potential cellular, inflammatory, and molecular changes associated with aging as potential biomarkers for response to ICIs.
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Affiliation(s)
- Khalil Choucair
- University of Kansas School of Medicine-Wichita, Department of Internal Medicine, Wichita, KS, USA
| | - Abdul Rafeh Naqash
- The University of Oklahoma College of Medicine, Department of Internal Medicine, Division of Hematology/Oncology; Stephenson Cancer Center, Oklahoma City, OK, USA
| | - Caroline A Nebhan
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology/Oncology, Nashville, TN, USA
| | - Ryan Nipp
- The University of Oklahoma College of Medicine, Department of Internal Medicine, Division of Hematology/Oncology; Stephenson Cancer Center, Oklahoma City, Oklahoma, USA
| | - Douglas B Johnson
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology/Oncology, Nashville, Tennessee, USA
| | - Anwaar Saeed
- Kansas University Cancer Center, Department of Medicine, Division of Medical Oncology, Kansas City, KS, USA
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8
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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9
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Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
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Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
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10
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Feng W, Lin A, Sun L, Wei T, Ying H, Zhang J, Luo P, Zhu W. Activation of the chemokine receptor 3 pathway leads to a better response to immune checkpoint inhibitors in patients with metastatic urothelial carcinoma. Cancer Cell Int 2022; 22:186. [PMID: 35562800 PMCID: PMC9107140 DOI: 10.1186/s12935-022-02604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have made important breakthrough in anti-tumor therapy, however, no single biomarker can accurately predict their efficacy. Studies have found that tumor microenvironment is a key factor for determining the response to ICI therapy. Cytokine receptor 3 (C-X-C Motif Chemokine Receptor 3, CXCR3) pathway has been reported to play an important role in the migration, activation, and response of immune cells. We analyzed survival data, genomics, and clinical data from patients with metastatic urothelial carcinoma (mUC) who received ICI treatment to explore the relationship between CXCR3 pathway activation and the effectiveness of ICIs. The Cancer Genome Atlas Bladder Urothelial Carcinoma cohort and six other cohorts receiving ICI treatment were used for mechanism exploration and validation. In the ICI cohort, we performed univariate and multivariate COX analyses and discovered that patients in the CXCR3-high group were more sensitive to ICI treatment. A Kaplan–Meier analysis demonstrated that patients in the high CXCR3-high group had a better prognosis than those in the CXCR3-low group (P = 0.0001, Hazard Ratio = 0.56; 95% CI 0.42−0.75). CIBERSORT analysis found that mUC patients in the CXCR3-high group had higher levels of activated CD8+ T cells, M1 macrophages, and activated NK cells and less regulatory T cell (Treg) infiltration. Immunogenicity analysis showed the CXCR3-high group had higher tumor neoantigen burden (TNB). Our study suggests that CXCR3 pathway activation may be a novel predictive biomarker for the effectiveness of immunotherapy in mUC patients.
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Affiliation(s)
- Wenqin Feng
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Le Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Haoxuan Ying
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
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