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Ye Z, Mo C, Ke H, Yan Q, Chen C, Kochunov P, Hong LE, Mitchell BD, Chen S, Ma T. Meta-Analysis of Transcriptome-Wide Association Studies across 13 Brain Tissues Identified Novel Clusters of Genes Associated with Nicotine Addiction. Genes (Basel) 2021; 13:37. [PMID: 35052378 PMCID: PMC8775257 DOI: 10.3390/genes13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 12/01/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified and reproduced thousands of diseases associated loci, but many of them are not directly interpretable due to the strong linkage disequilibrium among variants. Transcriptome-wide association studies (TWAS) incorporated expression quantitative trait loci (eQTL) cohorts as a reference panel to detect associations with the phenotype at the gene level and have been gaining popularity in recent years. For nicotine addiction, several important susceptible genetic variants were identified by GWAS, but TWAS that detected genes associated with nicotine addiction and unveiled the underlying molecular mechanism were still lacking. In this study, we used eQTL data from the Genotype-Tissue Expression (GTEx) consortium as a reference panel to conduct tissue-specific TWAS on cigarettes per day (CPD) over thirteen brain tissues in two large cohorts: UK Biobank (UKBB; number of participants (N) = 142,202) and the GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN; N = 143,210), then meta-analyzing the results across tissues while considering the heterogeneity across tissues. We identified three major clusters of genes with different meta-patterns across tissues consistent in both cohorts, including homogenous genes associated with CPD in all brain tissues; partially homogeneous genes associated with CPD in cortex, cerebellum, and hippocampus tissues; and, lastly, the tissue-specific genes associated with CPD in only a few specific brain tissues. Downstream enrichment analyses on each gene cluster identified unique biological pathways associated with CPD and provided important biological insights into the regulatory mechanism of nicotine dependence in the brain.
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Affiliation(s)
- Zhenyao Ye
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Chen Mo
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Hongjie Ke
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD 20742, USA;
| | - Qi Yan
- Irving Medical Center, Department of Obstetrics & Gynecology, Columbia University, New York, NY 10032, USA;
| | - Chixiang Chen
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
| | - L. Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Shuo Chen
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (Z.Y.); (C.M.); (P.K.); (L.E.H.)
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD 20742, USA;
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