Scientific publications

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

Mar 13, 2024 | Magazine: EBioMedicine

Ana Patiño-García  1 , Elizabeth Guruceaga  2 , Maria Pilar Andueza  3 , Marimar Ocón  4 , Jafait Junior Fodop Sokoudjou  5 , Nicolás de Villalonga Zornoza  5 , Gorka Alkorta-Aranburu  6 , Ibon Tamayo Uria  2 , Alfonso Gurpide  3 , Carlos Camps  7 , Eloísa Jantus-Lewintre  8 , Maria Navamuel-Andueza  4 , Miguel F Sanmamed  9 , Ignacio Melero  10 , Mohamed Elgendy  11 , Juan Pablo Fusco  12 , Javier J Zulueta  13 , Juan P de-Torres  4 , Gorka Bastarrika  14 , Luis Seijo  15 , Ruben Pio  16 , Luis M Montuenga  17 , Mikel Hernáez  18 , Idoia Ochoa  19 , Jose Luis Perez-Gracia  20

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.

CITATION  EBioMedicine. 2024 Mar 13:102:105048.  doi: 10.1016/j.ebiom.2024.105048