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Patiño-García A, Guruceaga E, Andueza MP, Ocón M, Fodop Sokoudjou JJ, de Villalonga Zornoza N, Alkorta-Aranburu G, Uria IT, Gurpide A, Camps C, Jantus-Lewintre E, Navamuel-Andueza M, Sanmamed MF, Melero I, Elgendy M, Fusco JP, Zulueta JJ, de-Torres JP, Bastarrika G, Seijo L, Pio R, Montuenga LM, Hernáez M, Ochoa I, Perez-Gracia JL. Whole exome sequencing and machine learning germline analysis of individuals presenting with extreme phenotypes of high and low risk of developing tobacco-associated lung adenocarcinoma. EBioMedicine 2024; 102:105048. [PMID: 38484556 PMCID: PMC10955643 DOI: 10.1016/j.ebiom.2024.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Tobacco is the main risk factor for developing lung cancer. Yet, while some heavy smokers develop lung cancer at a young age, other heavy smokers never develop it, even at an advanced age, suggesting a remarkable variability in the individual susceptibility to the carcinogenic effects of tobacco. We characterized the germline profile of subjects presenting these extreme phenotypes with Whole Exome Sequencing (WES) and Machine Learning (ML). METHODS We sequenced germline DNA from heavy smokers who either developed lung adenocarcinoma at an early age (extreme cases) or who did not develop lung cancer at an advanced age (extreme controls), selected from databases including over 6600 subjects. We selected individual coding genetic variants and variant-rich genes showing a significantly different distribution between extreme cases and controls. We validated the results from our discovery cohort, in which we analysed by WES extreme cases and controls presenting similar phenotypes. We developed ML models using both cohorts. FINDINGS Mean age for extreme cases and controls was 50.7 and 79.1 years respectively, and mean tobacco consumption was 34.6 and 62.3 pack-years. We validated 16 individual variants and 33 variant-rich genes. The gene harbouring the most validated variants was HLA-A in extreme controls (4 variants in the discovery cohort, p = 3.46E-07; and 4 in the validation cohort, p = 1.67E-06). We trained ML models using as input the 16 individual variants in the discovery cohort and tested them on the validation cohort, obtaining an accuracy of 76.5% and an AUC-ROC of 83.6%. Functions of validated genes included candidate oncogenes, tumour-suppressors, DNA repair, HLA-mediated antigen presentation and regulation of proliferation, apoptosis, inflammation and immune response. INTERPRETATION Individuals presenting extreme phenotypes of high and low risk of developing tobacco-associated lung adenocarcinoma show different germline profiles. Our strategy may allow the identification of high-risk subjects and the development of new therapeutic approaches. FUNDING See a detailed list of funding bodies in the Acknowledgements section at the end of the manuscript.
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Affiliation(s)
- Ana Patiño-García
- Department of Pediatrics and Clinical Genetics, Clínica Universidad de Navarra (CUN), Cancer Center Clínica Universidad de Navarra (CCUN), Program in Solid Tumors, Center for Applied Medical Research (Cima) and Navarra Institute for Health Research (IdisNA), University of Navarra, Pamplona, Spain
| | - Elizabeth Guruceaga
- Bioinformatics Platform, Cima and IdisNA, University of Navarra, Pamplona, Spain
| | - Maria Pilar Andueza
- Department of Oncology, CUN, CCUN and IdisNA, University of Navarra, Pamplona, Spain
| | - Marimar Ocón
- Pulmonary Department, CUN, CCUN and IdisNA, University of Navarra, Pamplona, Spain
| | | | | | | | - Ibon Tamayo Uria
- Bioinformatics Platform, Cima and IdisNA, University of Navarra, Pamplona, Spain
| | - Alfonso Gurpide
- Department of Oncology, CUN, CCUN and IdisNA, University of Navarra, Pamplona, Spain
| | - Carlos Camps
- Department of Medical Oncology, Hospital General Universitario de Valencia, Unidad Mixta TRIAL (Fundación para la Investigación del Hospital General Universitario de Valencia y Centro de Investigación Príncipe Felipe) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Valencia, Spain
| | - Eloísa Jantus-Lewintre
- Department of Biotechnology, Universitat Politècnica de València, Unidad Mixta TRIAL (Fundación para la Investigación del Hospital General Universitario de Valencia y Centro de Investigación Príncipe Felipe) and CIBERONC, Valencia, Spain
| | | | - Miguel F Sanmamed
- Department of Oncology, CUN, Division of Immunology, Cima, CCUN, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain
| | - Ignacio Melero
- Division of Immunology, Cima and Immunotherapy, CUN, CCUN, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain
| | - Mohamed Elgendy
- Institute for Clinical Chemistry and Laboratory Medicine, Mildred-Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC), University Hospital and Faculty of Medicine, Medical Clinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany. Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Juan Pablo Fusco
- Department of Medical Oncology Hospital La Luz, Quirón, Madrid, Spain
| | - Javier J Zulueta
- Pulmonary, Critical Care, and Sleep Division, Mount Sinai Morningside Hospital, New York, USA
| | - Juan P de-Torres
- Pulmonary Department, CUN, CCUN and IdisNA, University of Navarra, Pamplona, Spain
| | | | - Luis Seijo
- Pulmonary Department, CUN, CCUN and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), University of Navarra, Madrid, Spain
| | - Ruben Pio
- Program in Solid Tumors, Cima -CCUN, Department of Biochemistry and Genetics, School of Science, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain
| | - Luis M Montuenga
- Program in Solid Tumors, Cima, Department of Pathology, Anatomy and Physiology, Schools of Medicine and Sciences, CCUN, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain
| | - Mikel Hernáez
- Computational Biology Program, Cima, Data Science and Artificial Intelligence Institute (DATAI), CCUN, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain
| | - Idoia Ochoa
- Electrical and Electronic Engineering Department, Tecnun, DATAI, University of Navarra, San Sebastian, Spain
| | - Jose Luis Perez-Gracia
- Department of Oncology, CUN, CCUN, IdisNA and CIBERONC, University of Navarra, Pamplona, Spain.
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