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Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

Type: Transcriptome Analysis
Archiver: European Genome-phenome Archive (EGA)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000333	RNA-seq data from nasal and bronchial tissues in 649 subjects, many with lung cancer. Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to lifestyle risk in the form of cigarette smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, often many years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk are unclear. CT screening of current and former smokers has been shown to reduce lung cancer mortality by up to 26%. To examine whether clinical risk stratification can be improved upon by the addition of genetic data, and to explore the mechanisms of the persisting risk in former smokers, we have analyzed transcriptomic data from accessible airway tissues of 487 subjects. We developed a model to assess smoking associated gene expression changes and their reversibility after smoking is stopped, in both healthy subjects and clinic patients. We find persistent smoking associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune and interferon related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. Our results provide initial evidence for germline-mediated personalised smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.	Illumina HiSeq 2500 Illumina HiSeq 4000	649

Publications	Citations
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk. de Biase MS, Massip F, Wei TT, Giorgi FM, Stark R, Stone A, Gladwell A, O'Reilly M, Schütte D, de Santiago I, Meyer KB, Markowetz F, Ponder BAJ, Rintoul RC, Schwarz RF. Genome Med 16: 2024 54	10
Alterations to the bronchial gene-expression effects of tobacco smoking in people living with HIV. Lee M, Olson A, Pickering RT, Ieong MH, Kivett D, Roche S, Xiao X, Liu G, Asundi A, Lin NH, Lenburg ME. J Acquir Immune Defic Syndr 101: 2026 671-679	0
Statistical knockoffs improve biomarker discovery from transcriptomic data. Cartier J, Lagoas J, Ayadi Y, Fermanian A, Azencott CA, Massip F. Brief Bioinform 27: 2026 bbag148	0