Background & Aims

DNA methylation is an important epigenetic regulator of gene expression in response to environmental stimuli. Analgesic drugs are used to relieve pain in conditions such as low back pain by their acute effects on neurological or inflammatory pathways, but they may also have longer lasting effects via alteration of the methylation status of genes in these pathways. Differential DNA methylation has been observed following exposure to opioids,[1] non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen,[2] and other medications. Understanding the long-term effects of drug exposure on methylation and RNA expression may help elucidate the actions and undesirable side effects of analgesic therapeutics.[3] We have performed a genome-wide scan for differentially methylated regions (DMRs) in a clinical population taking a variety of analgesics in order to identify genes regulated by these drugs.

Methods

Data on drug exposure was collected as part of the Quebec Pain Registry (QPR) between 2008 and 2014.[4] Registry participants reported baseline analgesic medication use, including acetaminophen, NSAIDs, gabapentinoids, opioids, and antidepressants. The discovery cohort included participants with chronic low back pain (cLBP, n=235). A second independent cohort, also drawn from QPR participants but with a clinical diagnosis of a neuropathic pain disorder (NP, n=205), was also created for purposes of replication and extension of findings from the discovery cohort. DNA extracted from saliva was assessed using the Illumina MethylationEPIC platform, which quantifies methylation at over 850,000 CpG sites across the genome. We constructed linear regression models using the minfi package[5] in R to identify association between exposure to each drug and methylation status, adjusted for age, sex, enrollment site, baseline pain, and other potentially confounding variables.

Results

Regions of differential methylation were observed for each analgesic drug. We enforced a genome-wide correction to maintain a family-wise error rate of <0.2 as well as a minimum effect size of 5% change in methylation. In the LBP cohort, a significant DMR was found for exposure to gabapentinoids on chromosome 17 near the ALOX12 gene (p=3.9x10-4); this region was also significantly associated with NSAID use (p=1.3x10-4). A second region on chromosome 14 was also associated with NSAID exposure. In the NP cohort, gabapentinoid exposure was associated with a region on chromosome 3 near the THOC7 and ATXN7 genes (p=1.4x10-4), and a separate region on chromosome 16 near the MT1E gene (p=3.6x10-5). A region on chromosome 11 near the TRIM6 gene was associated with NSAID use (p=8.3x10-5).

Conclusions

We identified several genes with potential impact on pain and analgesia that were differentially methylated following exposure to gabapentinoids and NSAIDs. In particular, ALOX12, MT1E, and THOC7 all mediate inflammation through NF-?B pathways, among other mechanisms. The influence of analgesic drug exposure on the transcriptional activity of these genes may provide better understanding of the long-term effects of these drugs.

References

1. Lee M, Joehanes R, McCartney DL, Kho M, Hüls A, Wyss AB, Liu C, Walker RM, R Kardia SL, Wingo TS, Burkholder A, Ma J, Campbell A, Wingo AP, Huan T, Sikdar S, Keshawarz A, Bennett DA, Smith JA, Evans KL, Levy D, London SJ. Opioid medication use and blood DNA methylation: epigenome-wide association meta-analysis. Epigenomics. 2022 Dec;14(23):1479-1492.
2. Marra PS, Nishizawa Y, Yamanashi T, Sullivan EJ, Comp KR, Crutchley KJ, Wahba NE, Shibata K, Nishiguchi T, Yamanishi K, Noiseux NO, Karam MD, Shinozaki G. NSAIDs use history: impact on the genome-wide DNA methylation profile and possible mechanisms of action. Clin Exp Med. 2023 Nov;23(7):3509-3516.
3. Niederberger E, Resch E, Parnham MJ, Geisslinger G. Drugging the pain epigenome. Nat Rev Neurol. 2017 Jul;13(7):434-447.
4. Choinière M, Ware MA, Pagé MG, Lacasse A, Lanctôt H, Beaudet N, Boulanger A, Bourgault P, Cloutier C, Coupal L, De Koninck Y, Dion D, Dolbec P, Germain L, Martin V, Sarret P, Shir Y, Taillefer MC, Tousignant B, Trépanier A, Truchon R. Development and Implementation of a Registry of Patients Attending Multidisciplinary Pain Treatment Clinics: The Quebec Pain Registry. Pain Res Manag. 2017;2017:8123812.
5. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014 May 15;30(10):1363-9.

Presenting Author

Shad Smith

Poster Authors

Shad Smith

PhD

Duke University Medical Center

Lead Author

Xiang Ao

McGill University

Lead Author

Yuntong Sun BS

Duke University

Lead Author

Luda Diatchenko

McGill University

Lead Author

Topics

  • Genetics