Epigenetics and Pain. More nurture than nature?


Introduction to epigenetics

It is known that various cellular mechanisms influence inflammation, peripheral sensitization, and pain [1]. Many genes, mutations and single nucleotide polymorphisms (SNPs), and copy number variations (CNVs) of some genes, are implicated in specific chronic pain syndromes [2, 3], but these studies do not fully explain why one patient develops chronic pain following an injury, and another patient does not. In spite of advances in acute pain management, about 50% of patients are known to develop chronic pain following surgeries such as amputation, hernia repair, mastectomy etc. for which one of the key answer is the role of epigenetics [4].

In eukaryotes the genome remains the same throughout all somatic cells in a given organism. Each cell type has specific structures and functions that differ from another. These differences are due to the cell’s unique gene expression patterns that are determined during cellular differentiation. These cell-specific gene expression patterns are known to be affected by an organism’s environment throughout its lifetime which leads to phenotypical changes that have the potential to alter risk of some diseases. On comparison of the DNA sequence to notes in the score of music, epigenetics refers to the subtle or slight degree of difference in meaning, feeling, or tone, or the rhythm that allows the conductor to understand how the notes should be read. Each cell interprets its genetic score in its own way, and therefore the cells play different music.”

pain hyderabad india educationCell-specific gene expression signatures and environment mediated changes in expression patterns can be explained by a complex network of modifications. These modifications are known to affect the DNA, histone proteins and degree of DNA packaging called epigenetic marks. Studies are being carried out to understand these epigenetic modifications in detail. Epigenetics can be defined as the study of heritable modifications in gene expression and phenotype that do not require a change in genetic sequence to manifest their effects (literally meaning “On Top of Genetics”.

Epigenetic modifications include DNA methylation, histone modifications such as histone methylation/ acetylation/ phosphorylation/ SUMOylation, chromatin remodeling and microRNA (miRNA) [5-7]. Even though not all of the above listed epigenetic modifications have demonstrated heritability, they can all alter gene transcription without modification to the underlying genetic sequence. Because these epigenetic patterns can be affected by an organism’s environment, they serve as a bridge between experiences in life and phenotypes. Epigenetic patterns are known to change throughout one’s lifespan, by an environmental exposure or nutritional status. Epigenetic signatures play a role in our appearance [8], behavior, stress response [9, 10], disease susceptibility, and even longevity. The interaction between types of epigenetic modifications in response to environmental factors and vice versa will throw light upon still poorly understood aspects of gene transcription.

pain hyderabad educationA striking example of the power of gene regulation is seen in agouti mice, in which genetically identical twins can look entirely different in both color and size. For example, one mouse may be small and brown, but her twin sister may be obese and yellow. Further analysis showed that the genome of each of these mice is the same, but the gene expression differs. In normal, healthy mice, the agouti genes are kept in the “off” position by the epigenome, by DNA methylation in corresponding regions of DNA, resulting in the DNA’s compaction to prevent transcription. In yellow and/or obese mice, however, the same genes are not methylated; thus, these genes are expressed or “turned on.” Mice whose agouti gene is “on” are also more likely to suffer from diabetes and cancer as adults [8]. The methylation pattern is known to be altered by feeding the mice with mice fed with methyl donors (i.e. Folic acid, Choline, Vitamin B 12 and betaine [11]).

Role of epigenetics and pain

Many laboratory and clinical data support the role of environment on epigenetic modifications that leads to differential gene expression. Available literature highlights the role of epigenetics in chronic pain. Environmental factors are known to alter gene expression and phenotype for painful disorders by inducing epigenetic modifications such as histone acetylation, DNA methylation, and RNA interference. Following injury, expression of transcription factors such as nuclear κB (NF-κB) is increased [12], sodium channels in the injured axon are upregulated [13], μ -opioid receptors in the dorsal root ganglion are downregulated[14, 15], substance P expression is altered [16], and the dorsal horn of the spinal cord is structurally reorganized through axonal sprouting [17]. A patient’s gene expression profile changes rapidly in the post-injury period[18], with over 1,000 genes activated in the dorsal root ganglion alone after nerve injury [19]. The important link between epigenetic regulation and pain is also supported by evidences that show the role of epigenetic control of gene activation in the transition from acute to chronic pain. It is also known that, immunologic response and inflammatory cytokine expression are under epigenetic control [20, 21]. Glucocorticoid receptor (GR) functions, affecting pain sensitivity, inflammation, and the development of autoimmune disease, is modulated by epigenetic mechanism [22-24]. Genes such as glutamic acid decarboxylase 65 (GAD65) that code for pain regulatory enzymes in the central nervous system are known to be hypoacetylated and downregulated in inflammatory and nerve injury pain states [25]. Epigenetic modifications are involved in opioid receptor regulation and function, with implications for endogenous pain modulation systems and pain severity [10, 26].

David J. Clark’s group tested a group of mice for the degree of pain sensitivity in their hind paws. These mice had small surgical incisions made in their hind paws after being anesthetized. These mice were then regularly injected with suberoylanilide hydroxamic acid (SAHA), ( preventing deacetylation promoting gene transcription), or anacardic acid, which prevents acetylation reducing gene transcription. It was shown that regulation of histone acetylation can control pain sensitization after an incision. Specifically, maintaining histone in a relatively deacetylated state reduced hypersensitivity after incision. This study throws light on the epigenetic regulation of a specific gene known as CXCR2 and one of its chemokine ligands (KC). They also found that these epigenetic changes lasted even after the recovery of animals from their incisions, a property that might help explain why some patients suffer from chronic postoperative pain [27].


Though fascinating information is available from study of specific genes, there is a need to focus on groups or systems of many genes simultaneously, and role of epigenetics in controlling these genes/ systems which could give us clues to greater breakthroughs in pain control and other areas of medicine. Epigenetic analysis would be helpful in identifying mechanisms critical to the development of chronic pain after injury, and may provide new pathways and target mechanisms for future drug development and individualized medicine.


1. Basbaum, A.I., et al., Cellular and molecular mechanisms of pain. Cell, 2009. 139(2): p. 267-84.

2. Zubieta, J.K., et al., COMT val158met genotype affects mu-opioid neurotransmitter responses to a pain stressor. Science, 2003. 299(5610): p. 1240-3.

3.  Yuan, R., et al., Two novel SCN9A gene heterozygous mutations may cause partial deletion of pain perception. Pain Med, 2011. 12(10): p. 1510-4.

4. Kehlet, H., T.S. Jensen, and C.J. Woolf, Persistent postsurgical pain: risk factors and prevention. Lancet, 2006. 367(9522): p. 1618-25.

5. Buchheit, T., T. Van de Ven, and A. Shaw, Epigenetics and the transition from acute to chronic pain. Pain Med, 2012. 13(11): p. 1474-90.

6. Crow, M., F. Denk, and S.B. McMahon, Genes and epigenetic processes as prospective pain targets. Genome Med, 2013. 5(2): p. 12.

7. Stielow, C., et al., SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes. Nucleic Acids Res, 2013.

8. Duhl, D.M., et al., Neomorphic agouti mutations in obese yellow mice. Nat Genet, 1994. 8(1): p. 59-65.

9. Weaver, I.C., et al., Epigenetic programming by maternal behavior. Nat Neurosci, 2004. 7(8): p. 847-54.

10. Comb, M. and H.M. Goodman, CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2. Nucleic Acids Res, 1990. 18(13): p. 3975-82.

11. Waterland, R.A. and R.L. Jirtle, Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol, 2003. 23(15): p. 5293-300.

12. Ma, W. and M.A. Bisby, Increased activation of nuclear factor kappa B in rat lumbar dorsal root ganglion neurons following partial sciatic nerve injuries. Brain Res, 1998. 797(2): p. 243-54.

13. Jin, X. and R.W.t. Gereau, Acute p38-mediated modulation of tetrodotoxin-resistant sodium channels in mouse sensory neurons by tumor necrosis factor-alpha. J Neurosci, 2006. 26(1): p. 246-55.

14. Li, Z., et al., Chronic arthritis down-regulates peripheral mu-opioid receptor expression with concomitant loss of endomorphin 1 antinociception. Arthritis Rheum, 2005. 52(10): p. 3210-9.

15. Porreca, F., et al., Spinal opioid mu receptor expression in lumbar spinal cord of rats following nerve injury. Brain Res, 1998. 795(1-2): p. 197-203.

16. Ma, W. and M.A. Bisby, Partial and complete sciatic nerve injuries induce similar increases of neuropeptide Y and vasoactive intestinal peptide immunoreactivities in primary sensory neurons and their central projections. Neuroscience, 1998. 86(4): p. 1217-34.

17. Okamoto, M., et al., Functional reorganization of sensory pathways in the rat spinal dorsal horn following peripheral nerve injury. J Physiol, 2001. 532(Pt 1): p. 241-50.

18. Lee, Y.S., et al., Genetically mediated interindividual variation in analgesic responses to cyclooxygenase inhibitory drugs. Clin Pharmacol Ther, 2006. 79(5): p. 407-18.

19. Hammer, P., et al., mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Genome Res, 2010. 20(6): p. 847-60.

20. Hashimoto, K., et al., DNA demethylation at specific CpG sites in the IL1B promoter in response to inflammatory cytokines in human articular chondrocytes. Arthritis Rheum, 2009. 60(11): p. 3303-13.

21. Su, R.C., et al., Epigenetic regulation of established human type 1 versus type 2 cytokine responses. J Allergy Clin Immunol, 2008. 121(1): p. 57-63 e3.

22. Schlaghecke, R., et al., Glucocorticoid receptors in rheumatoid arthritis. Arthritis Rheum, 1992. 35(7): p. 740-4.

23. Geiss, A., N. Rohleder, and F. Anton, Evidence for an association between an enhanced reactivity of interleukin-6 levels and reduced glucocorticoid sensitivity in patients with fibromyalgia. Psychoneuroendocrinology, 2011. 37(5): p. 671-84.

24. Turner, J.D., et al., Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms. Nucleic Acids Res, 2008. 36(22): p. 7207-18.

25. Zhang, Z., et al., Epigenetic suppression of GAD65 expression mediates persistent pain. Nat Med, 2011. 17(11): p. 1448-55.

26. Nielsen, D.A., et al., Increased OPRM1 DNA methylation in lymphocytes of methadone-maintained former heroin addicts. 2009. 34(4): p. 867-73.

27. Sun, Y., et al., Epigenetic regulation of spinal CXCR2 signaling in incisional hypersensitivity in mice. Anesthesiology, 2013. 119(5): p. 1198-208.


Dr. Krishnan Sivaraman

Post author

PhD (Centre for Cellular and Molecular Biology)

There are 4 Comments

  1. Posted by madhur Reply

    Brilliant Dr Krishnan, thanks a lot for upgrading our knowledge on the fascinating science of “epigenetics”.

  2. Dr Palanisamy Vijayanand
    Posted by Dr Palanisamy Vijayanand Reply

    Very well written Dr. Krishnan. Hope it will go on to fill in the blanks in our understanding of pain.

  3. Posted by Swami Prakash Reply

    Dear Dr. Krishnan,

    Analogy of note and music was interesting. Well written, throughly enjoyed reading. Thank you for sharing.


  4. Posted by Satheesh Reply

    Even a commerce grad like me could understand. Kudos, Dr.Krishnan.

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