Researchers at the Virginia Commonwealth University School of Pharmacy have identified specific sets of genetic variants that are significantly associated with cigarette addiction. Pinpointing these genetic variants could eventually assist in identifying the biological mechanism behind nicotine addiction and in generating novel drug therapy targets to help people break their addiction to nicotine.
The study, “Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses,” was published in August as an advanced online publication in the Oxford University Press journal Nicotine & Tobacco Research.
“We dug deeper into genes known to be associated with smoking,” said Shaunna L. Clark, Ph.D., research assistant professor, Center for Biomarker Research and Precision Medicine, VCU School of Pharmacy. Previous large-scale, genomewide association studies have identified three genes that are related to cigarette addiction, but the VCU-led study is the first to identify specific sets of genetic variants that might be responsible.
Researchers at the CBRPM sequenced the three genes and their adjacent regions to get a complete catalog of all the genetic variation that could be contributing to addiction. Sequencing the entire gene allowed Clark and her colleagues to examine variants that other studies had not addressed, such as rare variants not commonly found in the population and regulatory variants that can increase or decrease gene expression.
“We found that the tendency toward nicotine addiction is likely caused by many variants, each with a small effect,” Clark said. “Thus, multiple variants within the same gene are related to smoking.”
Funding: The study was supported by the National Institutes of Health (R01 DA024413, R01 MH045268, R01 MH068521, R25 DA026119, K01 AA021266 and K01 MH093731). Researchers from Duke University Medical Center and the University of North Carolina at Chapel Hill contributed to the study.
Source: Anne Dreyfuss – Virginia Commonwealth University
Image Source: The image is in the public domain
Original Research: Abstract for “Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses,” by Shaunna L. Clark, Joseph L. McClay, Daniel E. Adkins, Karolina A. Aberg, Gaurav Kumar, Sri Nerella, Linying Xie, Ann L. Collins, James J. Crowley, Corey R. Quakenbush, Christopher E. Hillard, Guimin Gao, Andrey A. Shabalin, Roseann E. Peterson, William E. Copeland, Judy L. Silberg, Hermine Maes, Patrick F. Sullivan, Elizabeth J. Costello, and Edwin J. van den Oord in Nicotine and Tobacco Research. Published online August 17 2015 doi:10.1093/ntr/ntv166
Abstract
Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses,
Introduction: Genome-wide association study meta-analyses have robustly implicated three loci that affect susceptibility for smoking: CHRNA5\CHRNA3\CHRNB4, CHRNB3\CHRNA6 and EGLN2\CYP2A6. Functional follow-up studies of these loci are needed to provide insight into biological mechanisms. However, these efforts have been hampered by a lack of knowledge about the specific causal variant(s) involved. In this study, we prioritized variants in terms of the likelihood they account for the reported associations.
Methods: We employed targeted capture of the CHRNA5\CHRNA3\CHRNB4, CHRNB3\CHRNA6, and EGLN2\CYP2A6 loci and flanking regions followed by next-generation deep sequencing (mean coverage 78×) to capture genomic variation in 363 individuals. We performed single locus tests to determine if any single variant accounts for the association, and examined if sets of (rare) variants that overlapped with biologically meaningful annotations account for the associations.
Results: In total, we investigated 963 variants, of which 71.1% were rare (minor allele frequency < 0.01), 6.02% were insertion/deletions, and 51.7% were catalogued in dbSNP141. The single variant results showed that no variant fully accounts for the association in any region. In the variant set results, CHRNB4 accounts for most of the signal with significant sets consisting of directly damaging variants. CHRNA6 explains most of the signal in the CHRNB3\CHRNA6 locus with significant sets indicating a regulatory role for CHRNA6. Significant sets in CYP2A6 involved directly damaging variants while the significant variant sets suggested a regulatory role for EGLN2.
Conclusions: We found that multiple variants implicating multiple processes explain the signal. Some variants can be prioritized for functional follow-up.
“Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses,” by Shaunna L. Clark, Joseph L. McClay, Daniel E. Adkins, Karolina A. Aberg, Gaurav Kumar, Sri Nerella, Linying Xie, Ann L. Collins, James J. Crowley, Corey R. Quakenbush, Christopher E. Hillard, Guimin Gao, Andrey A. Shabalin, Roseann E. Peterson, William E. Copeland, Judy L. Silberg, Hermine Maes, Patrick F. Sullivan, Elizabeth J. Costello, and Edwin J. van den Oord in Nicotine and Tobacco Research. Published online August 17 2015 doi:10.1093/ntr/ntv166
