ArticleBMC medical genomics2017
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.
Article in BMC medical genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 49 papers, 3 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
49 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.Respiratory research · 2022Pooled it
- Peripheral blood microbial signatures in current and former smokers.Scientific reports · 2021Pooled it
- Integrative genomics identifies new genes associated with severe COPD and emphysema.Respiratory research · 2018Pooled it
- Genomics and response to long-term oxygen therapy in chronic obstructive pulmonary disease.Journal of molecular medicine (Berlin, Germany) · 2018Trial
- Moderate hypoxaemia and cognitive impairment in individuals with cigarette smoke exposure.ERJ open research · 2026Article
- Overlap between COPD genetic association results and transcriptional quantitative trait loci.HGG advances · 2026Article
- Article
- Molecular determinants of lung function decline: a multi-level analysis of gene expression.Respiratory research · 2025Article
- The molecular impact of cigarette smoking resembles aging across tissues.Genome medicine · 2025Article
- RNA splicing: Novel star in pulmonary diseases with a treatment perspective.Acta pharmaceutica Sinica. B · 2025Review
- LungGENIE: the lung gene-expression and network imputation engine.BMC genomics · 2025Article
- Multi-center Korean cohort study based on RNA-sequencing data targeting COPD patients.Scientific data · 2024Article
- Identifying chronic obstructive pulmonary disease from integrative omics and clustering in lung tissue.BMC pulmonary medicine · 2023Article
- Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis.Respiratory research · 2023Article
- Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers.Scientific reports · 2023Article
- Article
- sJIVE: Supervised Joint and Individual Variation Explained.Computational statistics & data analysis · 2022Article
- Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice.Redox biology · 2022Article
- Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models.International journal of molecular sciences · 2022Review
- Learning processes in hierarchical pairs regulate entire gene expression in cells.Scientific reports · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
Abstract
backgroundCigarette smoking is the leading modifiable risk factor for disease and death worldwide. Previous studies quantifying gene-level expression have documented the effect of smoking on mRNA levels. Using RNA sequencing, it is possible to analyze the impact of smoking on complex regulatory phenomena (e.g. alternative splicing, differential isoform usage) leading to a more detailed understanding of the biology underlying smoking-related disease.
methodsWe used whole-blood RNA sequencing to describe gene and exon-level expression differences between 229 current and 286 former smokers in the COPDGene study. We performed differential gene expression and differential exon usage analyses using the voom/limma and DEXseq R packages. Samples from current and former smokers were compared while controlling for age, gender, race, lifetime smoke exposure, cell counts, and technical covariates.
resultsAt an adjusted p-value <0.05, 171 genes were differentially expressed between current and former smokers. Differentially expressed genes included 7 long non-coding RNAs that have not been previously associated with smoking: LINC00599, LINC01362, LINC00824, LINC01624, RP11-563D10.1, RP11-98G13.1, AC004791.2. Secondary analysis of acute smoking (having smoked within 2-h) revealed 5 of the 171 smoking genes demonstrated an acute response above the baseline effect of chronic smoking. Exon-level analyses identified 9 exons from 8 genes with significant differential usage by smoking status, suggesting smoking-induced changes in isoform expression.
conclusionsTranscriptomic changes at the gene and exon levels from whole blood can refine our understanding of the molecular mechanisms underlying the response to smoking.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.