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Gerashchenko T, Skitchenko R, Korobeynikova A, Kuanysheva K, Khozyainova A, Vorobiev R, Rodionov E, Miller S, Topolnitsky E, Shefer N, Anisimenko M, Zhuikova L, Vashisth M, Pankova O, Perelmuter V, Rezapova V, Artomov M, Denisov E. Whole-exome sequencing reveals an association of rs112065068 in TGOLN2 gene with distant metastasis of non-small cell lung cancer. Gene 2024; 920:148507. [PMID: 38670394 DOI: 10.1016/j.gene.2024.148507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Early prediction and prevention of recurring illness is critical for improving the survival rates of patients with non-small cell lung cancer (NSCLC). Previously, we demonstrated that the presence of premalignant epithelial changes in the small bronchi distant to the primary tumor is associated with NSCLC progression: isolated basal cell hyperplasia (iBCH) indicates a high risk of distant metastasis, BCH combined with squamous metaplasia (BCHSM) - a high risk of locoregional recurrence. Here, we aimed to identify germline single nucleotide variants (SNVs) and insertions and deletions (InDels) associated with distant metastasis and locoregional recurrence in cases with iBCH and BCHSM using whole-exome sequencing of 172 NSCLC patients. The rs112065068 of the TGOLN2 gene was identified only in iBCH patients and was associated with a high risk of distant metastasis (P < .001) and worse metastasis-free survival (HR = 4.19 (95 %CI 1.97-8.93); P < .001). This variant was validated in a group of 109 NSCLC patients using real-time PCR and Sanger sequencing analyses. To our knowledge, this study is the first to identify a germline variant associated with NSCLC distant metastasis.
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Affiliation(s)
- Tatiana Gerashchenko
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia; Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | | | - Anastasia Korobeynikova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia; Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Kristina Kuanysheva
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Anna Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Rostislav Vorobiev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Evgeny Rodionov
- Department of Thoracic Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Sergey Miller
- Department of Thoracic Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Evgeny Topolnitsky
- Department of Surgery with a Course of Mobilization Training and Disaster Medicine, Siberian State Medical University, Moskovskiy Tract 2, Tomsk 634050, Russia
| | - Nikolay Shefer
- Department of Surgery with a Course of Mobilization Training and Disaster Medicine, Siberian State Medical University, Moskovskiy Tract 2, Tomsk 634050, Russia
| | - Maxim Anisimenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Ac. Lavrentieva Ave. 10, Novosibirsk 630090, Russia
| | - Lilia Zhuikova
- Laboratory of Epidemiology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Mrinal Vashisth
- Tomsk State University, Lenina Ave. 36, Tomsk 634050, Russia
| | - Olga Pankova
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Vladimir Perelmuter
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia
| | - Valeria Rezapova
- ITMO, Kronverksky Pr. 49, Bldg. A, St. Petersburg, 197101, Russia; University Cote D'Azur, Grand Château 28 Avenue de Valrose, Nice 06103, France
| | - Mykyta Artomov
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - Evgeny Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Kooperativny Str. 5, Tomsk 634009, Russia; Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, Moscow 117198, Russia.
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Barnet-Griness O, Gruber SB, Lipkin SM, Shulman K, Haddad R, Galili R, Rennert G. Ataxia telangiectasia-mutated rs56009889 and risk of common cancers. Eur J Cancer Prev 2024:00008469-990000000-00159. [PMID: 39150041 DOI: 10.1097/cej.0000000000000906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
A polymorphic variant in the ataxia telangiectasia-mutated (ATM) gene, rs56009889, was recently associated with an increased risk of lung cancer. We studied the role of this variant in the etiology of other cancers. Data from three population-based case-control studies of colon, breast, and lung cancer were used. Participants in these studies (4517 cases, 3383 controls) underwent a genome-wide association study using 500K Illumina OncoArray. The frequency of the AG/AA genotypes differed between Ashkenazi (4.6%) and Sephardi (0.2%) Jews (P < 0.001). AG/AA frequency was significantly higher in Ashkenazi lung cancer (11.9%) than in controls (2.8%) [adjusted odds ratio (OR) = 5.4]. Females had a higher risk than males (OR = 12.8 versus 3.5). The adjusted OR for colorectal cancer was 1.40 [95% confidence interval (CI) = 1.01-2.0, P = 0.045] and for breast cancer was 1.43 (95% CI = 1.01-2.04, P = 0.046). Never-smokers variant carriers were at higher risk of lung and colon, but not breast, cancer. Cases with the AG/AA genotype had lower mean age at diagnosis, but this difference was significant only for breast cancer (-3.2 years, P = 0.007). No associations were observed with overall survival. Among the breast cancer subjects, the OR for having triple-negative tumors was 0.45 for AG/AA versus GG genotype (95% CI = 0.2-0.9, P = 0.02). We confirm the strong association between ATM rs56009889 and lung cancer risk in Ashkenazi Jews and report a mild association with the risk of breast cancer and colorectal cancer.
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Affiliation(s)
- Ofra Barnet-Griness
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | | | - Steven M Lipkin
- Program in Mendelian Genetics, Weill-Cornell Medicine, New York, New York, USA
| | - Katerina Shulman
- Haifa and Western Galilee District Oncology Service, Clalit Health Services
| | | | | | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
- Faculty of Medicine, Technion-Israel Institute of Technology
- Association for Promotion of Research in Precision Medicine (APRPM) (A.R.), Haifa, Israel
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3
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Laguna JC, Tagliamento M, Lambertini M, Hiznay J, Mezquita L. Tackling Non-Small Cell Lung Cancer in Young Adults: From Risk Factors and Genetic Susceptibility to Lung Cancer Profile and Outcomes. Am Soc Clin Oncol Educ Book 2024; 44:e432488. [PMID: 38788188 DOI: 10.1200/edbk_432488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Lung cancer has traditionally been associated with advanced age; however, its increasing incidence among young adults raises concerning questions regarding its etiology and unique considerations for this population. In contrast to the older population, the onset of lung cancer at younger age may be attributed to a complex interplay of incompletely understood individual susceptibility and prevalent environmental risk factors beyond tobacco smoke exposure, such as radon gas and air pollution, which are widespread globally. Consequently, this leads to distinct clinical and molecular profiles, requiring a tailored approach. Furthermore, a diagnosis of cancer represents a threatening event during the prime years of a young person's life, prompting concern about career development, social aspects, fertility aspirations, and physical independence. This poses significant additional challenges for health care professionals in a field that remains underexplored. This comprehensive review recognizes lung cancer in young adults as a distinct entity, exploring its clinical and molecular characteristics, diverse predisposing factors, and priorities in terms of quality of life, with the aim of providing practical support to oncologists and enhancing our understanding of this under-researched population.
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Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Marco Tagliamento
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genova, Genova, Italy
- Department of Medical Oncology, Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genova, Genova, Italy
- Department of Medical Oncology, Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
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4
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Yu Z, Zhang Z, Liu J, Wu X, Fan X, Pang J, Bao H, Yin J, Wu X, Shao Y, Liu Z, Liu F. Identification of pathogenic germline variants in a large Chinese lung cancer cohort by clinical sequencing. Mol Oncol 2024; 18:1301-1315. [PMID: 37885353 PMCID: PMC11076998 DOI: 10.1002/1878-0261.13548] [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: 06/01/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
Genetic factors play significant roles in the tumorigenicity of lung cancer; however, there is lack of systematic and large-scale characterization of pathogenic germline variants for lung cancer. In this study, germline variants in 146 preselected cancer-susceptibility genes were detected in 17 904 Chinese lung cancer patients by clinical next-generation sequencing. Among 17 904 patients, 1738 patients (9.7%) carried 1840 pathogenic/likely pathogenic (P/LP) variants from 87 cancer-susceptibility genes. SBDS (SBDS ribosome maturation factor) (1.37%), TSHR (thyroid stimulating hormone receptor) (1.20%), BLM (BLM RecQ like helicase) (0.62%), BRCA2 (BRCA2 DNA repair associated) (0.62%), and ATM (ATM serine/threonine kinase) (0.45%) were the top five genes with the highest overall prevalence. The top mutated pathways were all involved in DNA damage repair (DDR). Case-control analysis showed SBDS c.184A>T(p.K62*), TSHR c.1574T>C(p.F525S), BRIP1 (BRCA1 interacting helicase 1) c.1018C>T(p.L340F), and MUTYH (mutY DNA glycosylase) c.55C>T(p.R19*) were significantly associated with increased lung cancer risk (q value < 0.05). P/LP variants in certain genes were associated with early onset of lung cancer. Our study indicates that Chinese lung cancer patients have a higher prevalence of P/LP variants than previously reported. P/LP variants are distributed in multiple pathways and dominated by DNA damage repair-associated pathways. The association between identified P/LP variants and lung cancer risk requires further studies for verification.
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Affiliation(s)
- Zhe Yu
- Department of Respiratory MedicineNingbo NO.2 HospitalChina
| | - Zirui Zhang
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Jun Liu
- Department of ChemotherapyAffiliated Hospital of Nantong UniversityChina
| | | | | | | | - Hua Bao
- Nanjing Geneseeq Technology Inc.China
| | - Jiani Yin
- Nanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Zhengcheng Liu
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Fang Liu
- Senior Department of OncologyThe Fifth Medical Center of PLA General HospitalBeijingChina
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5
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Thu KL, Yoon JY. ATM-the gene at the moment in non-small cell lung cancer. Transl Lung Cancer Res 2024; 13:699-705. [PMID: 38601449 PMCID: PMC11002499 DOI: 10.21037/tlcr-23-853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Affiliation(s)
- Kelsie L. Thu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Keenan Research Centre for Biomedical Sciences, St. Michael’s Hospital of Unity Health Toronto, Toronto, Canada
| | - Ju-Yoon Yoon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine, Division of Pathology, Unity Health Toronto, Toronto, Canada
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6
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Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P. Pan-cancer proteogenomics characterization of tumor immunity. Cell 2024; 187:1255-1277.e27. [PMID: 38359819 PMCID: PMC10988632 DOI: 10.1016/j.cell.2024.01.027] [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: 04/26/2023] [Revised: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024]
Abstract
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Francesca Pia Caruso
- BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua M Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Erol Evangelista
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoyu Song
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Berk Turhan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David A Lewis
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rossana Lazcano Segura
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Maciej Wiznerowicz
- Department of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland
| | - Tania J González-Robles
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Antonio Iavarone
- Department of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Alexey I Nesvizhskii
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcin Cieslik
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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7
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Sorscher S, LoPiccolo J, Heald B, Chen E, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder E, Lee H, Nussbaum RL, Martins R, Esplin ED. Rate of Pathogenic Germline Variants in Patients With Lung Cancer. JCO Precis Oncol 2023; 7:e2300190. [PMID: 37992258 PMCID: PMC10681406 DOI: 10.1200/po.23.00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Germline genetic testing (GGT) is now recommended for all patients diagnosed with ovarian or pancreatic cancer and for a large proportion of patients based solely on a diagnosis of colorectal or breast cancer. However, GGT is not yet recommended for all patients diagnosed with lung cancer (LC), primarily because of a lack of evidence that supports a significant frequency of identifying pathogenic germline variants (PGVs) in these patients. This study characterizes GGT results in a cohort of patients with LC. METHODS We reviewed deidentified data for 7,788 patients with GGT (2015-2022). PGV frequencies were compared to a control cohort of unaffected individuals. GGT results were stratified by genomic ancestry, history of cancer, and PGV clinical actionability per current guidelines. RESULTS Of all patients with LC, 14.9% (1,161/7,788) had PGVs. The rate was similar when restricted to patients with no cancer family history (FH) or personal history (PH) of other cancers (14.3%). PGVs were significantly enriched in BRCA2, ATM, CHEK2, BRCA1, and mismatch repair genes compared with controls. Patients of European (EUR) genomic ancestry had the highest PGV rate (18%) and variants of uncertain significance were significantly higher in patients of non-EUR genomic ancestry. Of the PGVs identified, 61.3% were in DNA damage repair (DDR) genes and 95% were clinically actionable. CONCLUSION This retrospective study shows a LC diagnosis identifies patients with a significant likelihood of having a cancer-predisposing PGV across genomic ancestries. Enrichment of PGVs in DDR genes suggests that these PGVs may contribute to LC cancer predisposition. The frequency of PGVs among patients with LC did not differ significantly according to FH or PH of other cancers.
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Affiliation(s)
| | - Jaclyn LoPiccolo
- Hematology/Oncology Division, Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | - Hayan Lee
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Renato Martins
- Hematology, Oncology and Palliative Care Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
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Farinea G, Crespi V, Listì A, Righi L, Bironzo P, Merlini A, Malapelle U, Novello S, Scagliotti GV, Passiglia F. The Role of Germline Mutations in Thoracic Malignancies: Between Myth and Reality. J Thorac Oncol 2023; 18:1146-1164. [PMID: 37331604 DOI: 10.1016/j.jtho.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
Considering the established contribution of environmental factors to the development of thoracic malignancies, the inherited susceptibility of these tumors has rarely been explored. However, the recent introduction of next-generation sequencing-based tumor molecular profiling in the real-word setting enabled us to deeply characterize the genomic background of patients with lung cancer with or without smoking-related history, increasing the likelihood of detecting germline mutations with potential prevention and treatment implications. Pathogenic germline variants have been detected in 2% to 3% of patients with NSCLC undergoing next-generation sequencing analysis, whereas the proportion of germline mutations associated with the development of pleural mesothelioma widely varies across different studies, ranging between 5% and 10%. This review provides an updated summary of emerging evidence about germline mutations in thoracic malignancies, focusing on pathogenetic mechanisms, clinical features, therapeutic implications, and screening recommendations for high-risk individuals.
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Affiliation(s)
- Giovanni Farinea
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Veronica Crespi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Angela Listì
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Alessandra Merlini
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | | | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
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Wang Y, Zhang T, Du H, Yang M, Xie G, Liu T, Deng S, Yuan W, He S, Wu D, Xu Y. Dipeptidase‑2 is a prognostic marker in lung adenocarcinoma that is correlated with its sensitivity to cisplatin. Oncol Rep 2023; 50:161. [PMID: 37449493 PMCID: PMC10360146 DOI: 10.3892/or.2023.8598] [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: 02/17/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023] Open
Abstract
Lung cancer accounts for the highest percentage of cancer morbidity and mortality worldwide, and lung adenocarcinoma (LUAD) is the most prevalent subtype. Although numerous therapies have been developed for lung cancer, patient prognosis is limited by tumor metastasis and more effective treatment targets are urgently required. In the present study, gene expression profiles were extracted from the Gene Expression Omnibus database and mRNA expression data were downloaded from The Cancer Genome Atlas database. In addition, TIMER 2.0 database was used to analyze the expression of genes in normal and multiple tumor tissues. Protein expression was confirmed using the Human Protein Atlas database and LUAD cell lines, sphere formation assay, western blotting, and a xenograft mouse model were used to confirm the bioinformatics analysis. Dipeptidase‑2 (DPEP2) expression was significantly decreased in LUAD and was negatively associated with prognosis. DPEP2 overexpression substantially inhibited epithelial‑mesenchymal transition (EMT) as well as LUAD cell metastasis, and limited the expression of the cancer stem cell transformation markers, CD44 and CD133. In addition, DPEP2 improved LUAD sensitivity to cisplatin by inhibiting EMT; this was verified in vitro and in vivo. These data indicated that DPEP2 upregulates E‑cadherin, thereby regulating cell migration, cancer stem cell transformation, and cisplatin resistance, ultimately affecting the survival of patients with LUAD. Overall, the findings of the present suggest that DPEP2 is important in the development of LUAD and can be used both as a prognostic marker and a target for future therapeutic research.
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Affiliation(s)
- Yuanyi Wang
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Ting Zhang
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Hongfei Du
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Min Yang
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Guangsu Xie
- Clinical Laboratory, Xindu District People's Hospital of Chengdu, Chengdu, Sichuan 610500, P.R. China
| | - Teng Liu
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Shihua Deng
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Wei Yuan
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Shuang He
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Dongming Wu
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Ying Xu
- College of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
- Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
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10
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Yoon JY, Roth JJ, Rushton CA, Morrissette JJD, Nathanson KL, Cohen RB, Rosenbaum JN. Homologous recombination pathway gene variants identified by tumor-only sequencing assays in lung carcinoma patients. Transl Lung Cancer Res 2023; 12:1236-1244. [PMID: 37425424 PMCID: PMC10326790 DOI: 10.21037/tlcr-22-749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/25/2023] [Indexed: 07/11/2023]
Abstract
Background The homologous recombination (HR) repair pathway plays a key role in double-stranded DNA break repair, and germline HR pathway gene variants are associated with increased risk of several cancers, including breast and ovarian cancer. HR deficiency is also a therapeutically targetable phenotype. Methods Somatic (tumour-only) sequencing was performed on 1,109 cases of lung tumors, and the pathological data were reviewed to filter for lung primary carcinomas. Cases were filtered for variants (disease-associated or of uncertain significance) in 14 HR pathway genes, including BRCA1, BRCA2, and ATM. The clinical, pathological and molecular data were reviewed. Results Sixty-one HR pathway gene variants in 56 patients with primary lung cancer were identified. Further filtering by variant allele fraction (VAF) of ≥30% identified 17 HR pathway gene variants in 17 patients. ATM gene variants were most the commonly identified (9/17), including two patients with c.7271T>G (p.V2424G), a variant in the germline that is associated with increased familial cancer risk. Four (4/17) patients had a family history of lung cancer, among which three patients had ATM gene variants suspected to be germline in origin. In three other patients with BRCA1/2 or PALB2 gene variants who had undergone germline testing, the variants were confirmed to be germline; lung cancer was the sentinel cancer in two of these patients with a BRCA1 or PALB2 variant. Conclusions Genomic variants in the HR repair pathway identified in tumor-only sequencing and occurring at higher VAFs (i.e., ≥30%) may suggest a germline origin. Correlating with personal and family history, a subset of these variants is also suggested to be associated with familial cancer risks. Patient age, smoking history and driver mutation status are expected to be a poor screening tool in identifying these patients. Finally, the relative enrichment for ATM variants in our cohort suggests a possible association between ATM mutation and lung cancer risk.
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Affiliation(s)
- Ju-Yoon Yoon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Laboratory Medicine, St. Michael’s Hospital, Toronto, ON, Canada
| | - Jacquelyn J. Roth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chase A. Rushton
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine L. Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roger B. Cohen
- Division of Hematology Oncology, Department of Medicine, Perelman Center for Advanced Medicine, Philadelphia, PA, USA
| | - Jason N. Rosenbaum
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, PA, USA
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11
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Hernandez-Martinez JM, Rosell R, Arrieta O. Somatic and germline ATM variants in non-small-cell lung cancer: Therapeutic implications. Crit Rev Oncol Hematol 2023:104058. [PMID: 37343657 DOI: 10.1016/j.critrevonc.2023.104058] [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: 05/15/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
ATM is an apical kinase of the DNA damage response involved in the repair of DNA double-strand breaks. Germline ATM variants (gATM) have been associated with an increased risk of developing lung adenocarcinoma (LUAD), and approximately 9% of LUAD tumors harbor somatic ATM mutations (sATM). Biallelic carriers of pathogenic gATM exhibit a plethora of immunological abnormalities, but few studies have evaluated the contribution of immune dysfunction to lung cancer susceptibility. Indeed, little is known about the clinicopathological characteristics of lung cancer patients with sATM or gATM alterations. The introduction of targeted therapies and immunotherapies, and the increasing number of clinical trials evaluating treatment combinations, warrants a careful reexamination of the benefits and harms that different therapeutic approaches have had in lung cancer patients with sATM or gATM. This review will discuss the role of ATM in the pathogenesis of lung cancer, highlighting potential therapeutic approaches to manage ATM-deficient lung cancers.
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Affiliation(s)
- Juan-Manuel Hernandez-Martinez
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan); CONACYT-Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Rafael Rosell
- Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain; (4)Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Oscar Arrieta
- Thoracic Oncology Unit and Experimental Oncology Laboratory, Instituto Nacional de Cancerología de México (INCan).
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12
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Bin Y, Ding P, Liu L, Tong F, Dong X. Classification of the immune microenvironment associated with 12 cell death modes and construction of a prognostic model for squamous cell lung cancer. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04789-w. [PMID: 37169931 DOI: 10.1007/s00432-023-04789-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE An increasing number of patients with lung squamous cell carcinoma (LUSC) are benefiting from immunotherapy. However, the individual immune profile of patients who respond to treatment is unclear. Multiple programmed cell death (PCD) patterns play an important role in the proliferation and differentiation of tumor cells, predicting the efficacy of immunotherapy using a risk model for programmed cell death gene combinations LUSC risk model. METHODS Genes associated with 12 types of PCD were analyzed to establish a prognostic model. Risk scores were calculated using PCDG-based expression profiles, and LUSC patients were classified into two groups. Tumor immune microenvironment (TIME) characteristics and immunotherapy responses were compared between the two groups. Finally, staging was predicted using the extreme gradient boosting tree algorithm (eXtreme Gradient Boosting, XGBoost), and an algorithmic model was constructed to predict the prognosis of LUSC patients based on the PCDG risk score. RESULTS A stepwise downscaling of 1256 PCDGs was performed to screen out 16 genes associated with LUSC prognosis to construct a risk model. Immune cell infiltration levels, the immunotherapy response, and prognostic differences were different between these two groups of patients. The classification prediction model based on the XGBoost algorithm and the prognostic model based on the risk score were able to distinguish the risk subtypes and individual prognosis of LUSC patients, respectively. CONCLUSIONS PCD patterns exert a crucial effect on the development of LUSC. An evaluation of different PCD patterns in LUSC improves the understanding of the characteristics of infiltrating immune cells and mutational features of the TIME, distinguishes LUSC patients who might benefit from immunotherapy, and predicts their future survival.
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Affiliation(s)
- Yawen Bin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Peng Ding
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lichao Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fan Tong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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13
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Borja NA, Silva-Smith R, Huang M, Parekh DJ, Sussman D, Tekin M. Atypical ATMs: Broadening the phenotypic spectrum of ATM-associated hereditary cancer. Front Oncol 2023; 13:1068110. [PMID: 36865800 PMCID: PMC9971806 DOI: 10.3389/fonc.2023.1068110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.
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Affiliation(s)
- Nicholas A. Borja
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Rachel Silva-Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Marilyn Huang
- Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Dipen J. Parekh
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Daniel Sussman
- Division of Digestive Health and Liver Diseases, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States,John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States,*Correspondence: Mustafa Tekin,
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14
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H3K27 acetylation activated-CCS regulates autophagy and apoptosis of lung cancer by alleviating oxidative stress. Tissue Cell 2023; 80:101964. [PMID: 36402120 DOI: 10.1016/j.tice.2022.101964] [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: 06/04/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022]
Abstract
Copper chaperone for superoxide dismutase (CCS) is abnormally expressed in various human malignancies. However, the function and mechanism of CCS in lung cancer progression remain unclear. In the current study, CCS protein and mRNA levels were found to be increased in lung adenocarcinoma (LUAD) tissue and cell lines. Patients with higher CCS levels had a poorer prognosis. Decreasing the enrichment of histone H3 Lys27 acetylation (H3K27ac) by A-485 inhibited CCS expression. CCS depletion upregulated reactive oxygen species (ROS) levels, aggravated oxidative stress, inhibited autophagy, inhibited cell survival, and promoted apoptosis. The treatment of antioxidant N-Acetyl-L-cysteine (NAC) rescued these changes induced by CCS depletion. CCS also was found to be related to the immune infiltration of CD8 + T cells and regulatory T cells in LUAD. These data indicated that overexpression of CCS activated by H3K27 acetylation relieved oxidative stress, promoted autophagy, and inhibited apoptosis. CCS may be regarded as a potential therapeutic target for LUAD.
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15
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Esai Selvan M, Onel K, Gnjatic S, Klein RJ, Gümüş ZH. Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics. NPJ Precis Oncol 2023; 7:13. [PMID: 36707626 PMCID: PMC9883433 DOI: 10.1038/s41698-023-00354-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Recent studies show that rare, deleterious variants (RDVs) in certain genes are critical determinants of heritable cancer risk. To more comprehensively understand RDVs, we performed the largest-to-date germline variant calling analysis in a case-control setting for a multi-cancer association study from whole-exome sequencing data of 20,789 participants, split into discovery and validation cohorts. We confirm and extend known associations between cancer risk and germline RDVs in specific gene-sets, including DNA repair (OR = 1.50; p-value = 8.30e-07; 95% CI: 1.28-1.77), cancer predisposition (OR = 1.51; p-value = 4.58e-08; 95% CI: 1.30-1.75), and somatic cancer drivers (OR = 1.46; p-value = 4.04e-06; 95% CI: 1.24-1.72). Furthermore, personal RDV load in these gene-sets associated with increased risk, younger age of onset, increased M1 macrophages in tumor and, increased tumor mutational burden in specific cancers. Our findings can be used towards identifying high-risk individuals, who can then benefit from increased surveillance, earlier screening, and treatments that exploit their tumor characteristics, improving prognosis.
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Affiliation(s)
- Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Rifkin AS, Less EM, Wei J, Shi Z, Zheng SL, Helfand BT, Hulick PJ, Krantz SB, Xu J. Association of Reported Candidate Monogenic Genes With Lung Cancer Risk. Clin Lung Cancer 2023; 24:313-321. [PMID: 36781323 DOI: 10.1016/j.cllc.2023.01.005] [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: 09/07/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 01/28/2023]
Abstract
INTRODUCTION/BACKGROUND Published studies on association of germline monogenic genes and lung cancer risk were inconsistent. Our objective is to assess the validity of reported candidate monogenic genes for their association with lung cancer. MATERIALS AND METHODS A systematic review of published papers prior to August 2022 was performed first to identify all genes where germline mutations were associated with lung cancer risk. We then performed a confirmation study in 2,050 lung cancer cases and 198,553 controls in the UK Biobank (UKB). Germline mutations of these genes were identified from sequencing data and annotated using The American College of Medical Genetics criteria. The robust SKAT-O, a gene-based analysis that properly controls for false positives due to unbalanced case-control ratio, was used for association tests adjusting for age at recruitment, gender, and genetic background. RESULTS The systematic review identified 12 genes that were statistically significantly associated with lung cancer risk in at least one study (P < .05), including ATM, BLM, BRCA2, BRIP1, CHEK2, FANCA, FANCD2, MSH6, PMS1, RAD51C, RAD51D, and TP53. When pathogenic/likely pathogenic mutations were aggregated within each gene, the association was confirmed for ATM (P = 4.47E-4) at the study-wise significance level (P < .0042, Bonferroni correction for 12 tests). Suggestive evidence of association was found for 2 other genes, BRCA2 (P = .007) and TP53 (P = .03). Among these 3 genes, the lung cancer risks range from 1.95 (BRCA2) to 5.28 (TP53). CONCLUSION This study provides statistical evidence for association of previously reported genes and lung cancer risk and has clinical utility for risk assessment and genetic counseling.
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Affiliation(s)
- Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL
| | - Ethan M Less
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL
| | - Siqun Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL; Department of Surgery, NorthShore University HealthSystem, Evanston, IL; University of Chicago Pritzker School of Medicine, Chicago, IL
| | - Peter J Hulick
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL
| | - Seth B Krantz
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL; University of Chicago Pritzker School of Medicine, Chicago, IL
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL; Department of Surgery, NorthShore University HealthSystem, Evanston, IL; University of Chicago Pritzker School of Medicine, Chicago, IL.
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 PMCID: PMC9585683 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately 45 genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of the current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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18
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Sang J, Zhang T, Kim J, Li M, Pesatori AC, Consonni D, Song L, Liu J, Zhao W, Hoang PH, Campbell DS, Feng J, D'Arcy ME, Synnott N, Chen Y, Wu Z, Zhu B, Yang XR, Brown KM, Choi J, Shi J, Landi MT. Rare germline deleterious variants increase susceptibility for lung cancer. Hum Mol Genet 2022; 31:3558-3565. [PMID: 35717579 PMCID: PMC9558843 DOI: 10.1093/hmg/ddac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Although multiple common susceptibility loci for lung cancer (LC) have been identified by genome-wide association studies, they can explain only a small portion of heritability. The etiological contribution of rare deleterious variants (RDVs) to LC risk is not fully characterized and may account for part of the missing heritability. Here, we sequenced the whole exomes of 2777 participants from the Environment and Genetics in Lung cancer Etiology study, a homogenous population including 1461 LC cases and 1316 controls. In single-variant analyses, we identified a new RDV, rs77187983 [EHBP1, odds ratio (OR) = 3.13, 95% confidence interval (CI) = 1.34-7.30, P = 0.008] and replicated two previously reported RDVs, rs11571833 (BRCA2, OR = 2.18; 95% CI = 1.25-3.81, P = 0.006) and rs752672077 (MPZL2, OR = 3.70, 95% CI = 1.04-13.15, P = 0.044). In gene-based analyses, we confirmed BRCA2 (P = 0.007) and ATM (P = 0.014) associations with LC risk and identified TRIB3 (P = 0.009), involved in maintaining genome stability and DNA repair, as a new candidate susceptibility gene. Furthermore, cases were enriched with RDVs in homologous recombination repair [carrier frequency (CF) = 22.9% versus 19.5%, P = 0.017] and Fanconi anemia (CF = 12.5% versus 10.2%, P = 0.036) pathways. Our results were not significant after multiple testing corrections but were enriched in cases versus controls from large scale public biobank resources, including The Cancer Genome Atlas, FinnGen and UK Biobank. Our study identifies novel candidate genes and highlights the importance of RDVs in DNA repair-related genes for LC susceptibility. These findings improve our understanding of LC heritability and may contribute to the development of risk stratification and prevention strategies.
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Affiliation(s)
- Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela C Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Lei Song
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Monica E D'Arcy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naoise Synnott
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yingxi Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Laitman Y, Nielsen SM, Bernstein-Molho R, Heald B, Hatchell KE, Esplin ED, Friedman E. Cancer risks associated with heterozygous ATM loss of function and missense pathogenic variants based on multigene panel analysis. Breast Cancer Res Treat 2022; 196:355-361. [PMID: 36094610 DOI: 10.1007/s10549-022-06723-z] [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: 06/13/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Cancer risks conferred by germline, heterozygous, ATM pathogenic/likely pathogenic variants (PSVs) are yet to be consistently determined. The current study assessed these risks by analysis of a large dataset of ATM heterozygote loss of function (LOF) and missense PSV carriers tested with a multigene panel (MGP). METHODS De-identified data of all individuals who underwent ATM sequencing as part of MGP between October 2015 and February 2020 were reviewed. In cancer cases, rates for the six most prevalent variants and for all LOF and missense PSV combined were compared with rates of the same PSV in ethnically matched, healthy population controls. Statistical analysis included Chi-square tests and odds ratios calculations. RESULTS For female breast cancer cases, LOF )1794/219,269) and missense (301/219,269) ATM PSVs were seen at higher rates compared to gnomAD non-cancer controls (n = 157/56,001 and n = 27/61,208; p < 0.00001, respectively). Notably, the rate of the c.103C > T variant was higher in controls than in breast cancer cases [p = 0.001; OR 0.31 (95% CI 0.1-0.6)]. For all cancer cases combined, compared with non-cancer population controls, LOF (n = 143) and missense (n = 15) PSVs reported in both datasets were significantly more prevalent in cancer cases [ORLOF 1.7 (95% 1.5-1.9) ORmissense 3.0 (95% CI 2.3-4); p = 0.0001]. CONCLUSION Both LOF and missense heterozygous ATM PSVs are more frequently detected in cases of several cancer types (breast, ovarian, prostate, lung, pancreatic) compared with healthy population controls. However, not all ATM PSVs confer an increased cancer risk (e.g., breast).
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Affiliation(s)
- Yael Laitman
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Rinat Bernstein-Molho
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel.,The Breast Cancer Unit, Oncology Institute, The Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | | | | | - Eitan Friedman
- The Oncogenetics Unit, Institute of Human Genetics, The Sheba Medical Center, Tel-Hashomer, Israel. .,The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel. .,Meirav High-Risk Clinic, Sheba Medical Center, 52621, Tel-Hashomer, Israel.
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20
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Petrackova A, Savara J, Turcsanyi P, Gajdos P, Papajik T, Kriegova E. Rare germline ATM variants of uncertain significance in chronic lymphocytic leukaemia and other cancers. Br J Haematol 2022; 199:371-381. [PMID: 36029002 DOI: 10.1111/bjh.18419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 12/26/2022]
Abstract
Germline pathogenic ATM (ataxia-telangiectasia mutated) variants are associated with the risk of multiple cancers; however, genetic testing reveals a large number of ATM variants of uncertain significance (VUS). Here, we studied germline ATM variants occurring in a real-world cohort of 336 patients with chronic lymphocytic leukaemia (CLL) and public cancer whole-exome/genome-sequencing datasets (445 CLL, 75 mantle cell lymphoma, 216 metastatic breast cancer, 140 lung cancer patients). We found that two-thirds of rare germline ATM variants are pathogenic (18%-50%) or VUS-predicted pathogenic (50%-82%), depending on cancer type and reaching a prevalence of up to 8%, and one-third are VUS-predicted benign. Patients with both pathogenic and VUS-predicted pathogenic variants, all heterozygous, mostly missense, are more predisposed to biallelic ATM inactivation by acquiring deletion (del)11q than patients without these variants, similar to patients with somatic ATM variants. A functional assay of ATM activity in primary CLL cells proved that VUS-predicted pathogenic ATM variants partially reduce ATM activity and concurrent del(11q) leads to complete loss of ATM activity. The rare germline variants were associated with reduced progression-free survival in CLL on novel agents, comparable to somatic ATM or TP53 disruptions. Our results highlight the need to determine the pathogenicity of VUS in clinically relevant genes such as ATM.
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Affiliation(s)
- Anna Petrackova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Jakub Savara
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic.,Department of Computer Science, Faculty of Electrical Engineering and Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Peter Turcsanyi
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Petr Gajdos
- Department of Computer Science, Faculty of Electrical Engineering and Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Tomas Papajik
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Eva Kriegova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
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21
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Mukherjee S, Bandlamudi C, Hellmann MD, Kemel Y, Drill E, Rizvi H, Tkachuk K, Khurram A, Walsh MF, Zauderer MG, Mandelker D, Topka S, Zehir A, Srinivasan P, Selvan ME, Carlo MI, Cadoo KA, Latham A, Hamilton JG, Liu YL, Lipkin SM, Belhadj S, Bond GL, Gümüş ZH, Klein RJ, Ladanyi M, Solit DB, Robson ME, Jones DR, Kris MG, Vijai J, Stadler ZK, Amos CI, Taylor BS, Berger MF, Rudin CM, Offit K. Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:1450-1459. [PMID: 35477182 PMCID: PMC9250622 DOI: 10.1158/1055-9965.epi-21-1287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The genetic factors that modulate risk for developing lung cancer have not been fully defined. Here, we sought to determine the prevalence and clinical significance of germline pathogenic/likely pathogenic variants (PV) in patients with advanced lung cancer. METHODS We studied clinical and tumor characteristics of germline PV in 5,118 patients who underwent prospective genomic profiling using paired tumor-normal tissue samples in 468 cancer genes. RESULTS Germline PV in high/moderate-penetrance genes were observed in 222 (4.3%) patients; of these, 193 patients had PV in DNA damage repair (DDR) pathway genes including BRCA2 (n = 54), CHEK2 (n = 30), and ATM (n = 26) that showed high rate of biallelic inactivation in tumors. BRCA2 heterozygotes with lung adenocarcinoma were more likely to be never smokers and had improved survival compared with noncarriers. Fourteen patients with germline PV in lung cancer predisposing genes (TP53, EGFR, BAP1, and MEN1) were diagnosed at younger age compared with noncarriers, and of tumor suppressors, 75% demonstrated biallelic inactivation in tumors. A significantly higher proportion of germline PV in high/moderate-penetrance genes were detected in high-risk patients who had either a family history of any cancer, multiple primary tumors, or early age at diagnosis compared with unselected patients (10.5% vs. 4.1%; P = 1.7e-04). CONCLUSIONS These data underscore the biological and clinical importance of germline mutations in highly penetrant DDR genes as a risk factor for lung cancer. IMPACT The family members of lung cancer patients harboring PV in cancer predisposing genes should be referred for genetic counseling and may benefit from proactive surveillance.
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Affiliation(s)
| | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Esther Drill
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, United States
| | - Kaitlyn Tkachuk
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Aliya Khurram
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sabine Topka
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Karen A Cadoo
- St. James’s Hospital, Trinity College Dublin, Trinity St. James’s Cancer Institute, Dublin 8, Ireland
| | - Alicia Latham
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Jada G Hamilton
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Ying L Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Sami Belhadj
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Gareth L Bond
- University of Birmingham, Birmingham, United Kingdom
| | - Zeynep H Gümüş
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert J Klein
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Zsofia K Stadler
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | | | - Barry S Taylor
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
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22
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Benusiglio PR, Fallet V, Sanchis-Borja M, Coulet F, Cadranel J. Lung cancer is also a hereditary disease. Eur Respir Rev 2021; 30:210045. [PMID: 34670806 PMCID: PMC9488670 DOI: 10.1183/16000617.0045-2021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Pathogenic genetic variants (formerly called mutations) present in the germline of some individuals are associated with a clinically relevant increased risk of developing lung cancer. These germline pathogenic variants are hereditary and are transmitted in an autosomal dominant fashion. There are two major lung cancer susceptibility syndromes, and both seem to be specifically associated with the adenocarcinoma subtype. Li-Fraumeni syndrome is caused by variants in the TP53 tumour-suppressor gene. Carriers are mainly at risk of early-onset breast cancer, sarcoma, glioma, leukaemia, adrenal cortical carcinoma and lung cancer. EGFR variants, T790M in particular, cause the EGFR susceptibility syndrome. Risk seems limited to lung cancer. Emerging data suggest that variants in ATM, the breast and pancreatic cancer susceptibility gene, also increase lung adenocarcinoma risk. As for inherited lung disease, cancer risk is increased in SFTPA1 and SFTPA2 variant carriers independently of the underlying fibrosis. In this review, we provide criteria warranting the referral of a lung cancer patient to the cancer genetics clinic. Pathogenic variants are first identified in patients with cancer, and then in a subset of their relatives. Lung cancer screening should be offered to asymptomatic carriers, with thoracic magnetic resonance imaging at its core.
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Affiliation(s)
- Patrick R Benusiglio
- UF d'Oncogénétique clinique, Département de Génétique et Institut Universitaire de Cancérologie, DMU BioGeM, GH Pitié-Salpêtrière, AP-HP, Sorbonne Université, Paris, France
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Paris, France
| | - Vincent Fallet
- Service de Pneumologie et Oncologie Thoracique, DMU APPROCHES, Hôpital Tenon, AP-HP, Sorbonne Université, Paris, France
- GRC04 Theranoscan, Sorbonne Université, Paris, France
| | - Mateo Sanchis-Borja
- Service de Pneumologie et Oncologie Thoracique, DMU APPROCHES, Hôpital Tenon, AP-HP, Sorbonne Université, Paris, France
| | - Florence Coulet
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 et SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Paris, France
- UF d'Onco-angiogénétique et génomique des tumeurs solides, Département de Génétique, DMU BioGeM, GH Pitié-Salpêtrière, AP-HP, Sorbonne Université, Paris, France
| | - Jacques Cadranel
- Service de Pneumologie et Oncologie Thoracique, DMU APPROCHES, Hôpital Tenon, AP-HP, Sorbonne Université, Paris, France
- GRC04 Theranoscan, Sorbonne Université, Paris, France
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23
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Bao R, Ng A, Sasaki M, Esai Selvan M, Katti A, Lee H, Huang L, Skol AD, Lavarino C, Salvador H, Klein RJ, Gümüş ZH, Mora J, Onel K. Functional Common and Rare ERBB2 Germline Variants Cooperate in Familial and Sporadic Cancer Susceptibility. Cancer Prev Res (Phila) 2021; 14:441-454. [PMID: 33419763 PMCID: PMC8026518 DOI: 10.1158/1940-6207.capr-20-0094] [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: 02/26/2020] [Revised: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022]
Abstract
We investigated a Spanish and Catalan family in which multiple cancer types tracked across three generations, but for which no genetic etiology had been identified. Whole-exome sequencing of germline DNA from multiple affected family members was performed to identify candidate variants to explain this occurrence of familial cancer. We discovered in all cancer-affected family members a single rare heterozygous germline variant (I654V, rs1801201) in ERBB2/HER2, which is located in a transmembrane glycine zipper motif critical for ERBB2-mediated signaling and in complete linkage disequilibrium (D' = 1) with a common polymorphism (I655V, rs1136201) previously reported in some populations as associated with cancer risk. Because multiple cancer types occurred in this family, we tested both the I654V and the I655V variants for association with cancer across multiple tumor types in 6,371 cases of Northern European ancestry drawn from The Cancer Genome Atlas and 6,647 controls, and found that the rare variant (I654V) was significantly associated with an increased risk for cancer (OR = 1.40; P = 0.021; 95% confidence interval (CI), 1.05-1.89). Functional assays performed in HEK 293T cells revealed that both the I655V single mutant (SM) and the I654V;I655V double mutant (DM) stabilized ERBB2 protein and activated ERBB2 signaling, with the DM activating ERBB2 significantly more than the SM alone. Thus, our results suggest a model whereby heritable genetic variation in the transmembrane domain activating ERBB2 signaling is associated with both sporadic and familial cancer risk, with increased ERBB2 stabilization and activation associated with increased cancer risk. PREVENTION RELEVANCE: By performing whole-exome sequencing on germline DNA from multiple cancer-affected individuals belonging to a family in which multiple cancer types track across three generations, we identified and then characterized functional common and rare variation in ERBB2 associated with both sporadic and familial cancer. Our results suggest that heritable variation activating ERBB2 signaling is associated with risk for multiple cancer types, with increases in signaling correlated with increases in risk, and modified by ancestry or family history.
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Affiliation(s)
- Riyue Bao
- Hillman Cancer Center, UPMC, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anita Ng
- The Feinstein Institute for Medical Research, Manhasset, New York
| | - Mark Sasaki
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
| | - Myvizhi Esai Selvan
- The Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Alyna Katti
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
| | - Hyesan Lee
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
| | - Lei Huang
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew D Skol
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
| | - Cinzia Lavarino
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - Hector Salvador
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - Robert J Klein
- The Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Zeynep H Gümüş
- The Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Jaume Mora
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Barcelona, Spain
| | - Kenan Onel
- The Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
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24
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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25
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Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI. Rare deleterious germline variants and risk of lung cancer. NPJ Precis Oncol 2021; 5:12. [PMID: 33594163 PMCID: PMC7887261 DOI: 10.1038/s41698-021-00146-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.
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Grants
- R01 CA060691 NCI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01 CA084354 NCI NIH HHS
- R01 HL110883 NHLBI NIH HHS
- U01 CA076293 NCI NIH HHS
- R01 CA080127 NCI NIH HHS
- R01 CA141769 NCI NIH HHS
- P30 ES006096 NIEHS NIH HHS
- P50 CA090578 NCI NIH HHS
- P30 CA022453 NCI NIH HHS
- S10 RR024574 NCRR NIH HHS
- HHSN261201300011C NCI NIH HHS
- R01 CA134682 NCI NIH HHS
- R01 CA134433 NCI NIH HHS
- R01 HL113264 NHLBI NIH HHS
- R01 HL082487 NHLBI NIH HHS
- R01 CA250905 NCI NIH HHS
- U19 CA148127 NCI NIH HHS
- P20 GM103534 NIGMS NIH HHS
- R01 CA092824 NCI NIH HHS
- R01 CA087895 NCI NIH HHS
- U01 HL089897 NHLBI NIH HHS
- K07 CA181480 NCI NIH HHS
- HHSN268201100011I NHLBI NIH HHS
- HHSN268201100011C NHLBI NIH HHS
- R01 CA127219 NCI NIH HHS
- R01 CA074386 NCI NIH HHS
- P30 CA023108 NCI NIH HHS
- U01 HL089856 NHLBI NIH HHS
- P30 ES030285 NIEHS NIH HHS
- P30 CA125123 NCI NIH HHS
- DP1 AG072751 NIA NIH HHS
- U01 CA243483 NCI NIH HHS
- HHSN268200782096C NHLBI NIH HHS
- HHSN268201200007C NHLBI NIH HHS
- N01HG65404 NHGRI NIH HHS
- R35 GM122598 NIGMS NIH HHS
- U01 CA209414 NCI NIH HHS
- R03 CA077118 NCI NIH HHS
- 001 World Health Organization
- DP1 CA174424 NCI NIH HHS
- This work was supported by grants from the National Institutes of Health (R01CA127219, R01CA141769, R01CA060691, R01CA87895, R01CA80127, R01CA84354, R01CA134682, R01CA134433, R01CA074386, R01CA092824, R01CA250905, R01HL113264, R01HL082487, R01HL110883, R03CA77118, P20GM103534, P30CA125123, P30CA023108, P30CA022453, P30ES006096, P50CA090578, U01CA243483, U01HL089856, U01HL089897, U01CA76293, U19CA148127, U01CA209414, K07CA181480, N01-HG-65404, HHSN268200782096C, HHSN261201300011I, HHSN268201100011, HHSN268201 200007C, DP1-CA174424, DP1-AG072751, CA125123, RR024574, Intramural Research Program of the National Human Genome Research Institute (JEB-W), and Herrick Foundation. Dr. Amos is an Established Research Scholar of the Cancer Prevention Research Institute of Texas (RR170048). We also want to acknowledge the Cytometry and Cell Sorting Core support by the Cancer Prevention and Research Institute of Texas Core Facility (RP180672). At Toronto, the study is supported by The Canadian Cancer Society Research Institute (# 020214) to R. H., Ontario Institute for Cancer Research to R. H, and the Alan Brown Chair to G. L. and Lusi Wong Programs at the Princess Margaret Hospital Foundation. The Liverpool Lung Project is supported by Roy Castle Lung Cancer Foundation.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Claudio W Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Christine M Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Scottsdale, AZ, USA
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | - John K Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
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