Summary: New Drexel University research shows a single protein can reshape gene expression across many pain-related pathways.
Source: Drexel University
Chronic pain is a widespread, disabling and costly public health issue in the United States. It affects more than 100 million Americans, with annual costs estimated at $635 billion, according to an American Pain Society report.
Current treatments for chronic pain—nonsteroidal anti-inflammatory drugs (NSAIDs), opioids, anticonvulsants and antidepressants—provide meaningful relief for only about half of patients. Opioid misuse and overdose have further complicated treatment strategies: prescription opioid deaths have risen sharply since the late 1990s, creating an urgent need for safer, more effective therapies.
Researchers at Drexel University College of Medicine are investigating epigenetic mechanisms that regulate pain with the goal of identifying novel, non-addictive drug targets. Their recent study, published in the journal Epigenetics & Chromatin, demonstrates how a single regulatory protein, methyl-CpG-binding protein 2 (MeCP2), can act as a master controller of gene networks involved in pain modulation.
“By understanding how this pathway operates after nerve injury, we hope to uncover genes that could be targeted by new pain medications that do not carry addiction risk,” said Melissa Manners, PhD, lead author of the study, under the supervision of principal investigator Seena Ajit, PhD, assistant professor at Drexel University College of Medicine.
The team focused on epigenetic regulation—heritable changes in gene activity that occur without alterations to the DNA sequence. Epigenetic mechanisms are increasingly recognized as important contributors to disease, including chronic pain conditions. MeCP2 is an epigenetic regulator that binds to methylated DNA and can activate, repress or remodel chromatin to control gene expression. Mutations in MeCP2 cause Rett syndrome, a neurodevelopmental disorder that, interestingly, is associated with altered pain perception.
Given this connection, the researchers hypothesized that peripheral nerve injury might change how MeCP2 binds across the genome in sensory neurons, thereby altering expression of multiple downstream genes that contribute to neuropathic pain.
The study examined dorsal root ganglia (DRG), clusters of sensory neuron cell bodies that transmit pain and other somatosensory signals to the spinal cord. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), the team mapped MeCP2 binding sites across the mouse genome in DRG tissue four weeks after a spared nerve injury (SNI) model of neuropathic pain.
Key findings included an increase in MeCP2 levels in DRG after nerve injury, and a redistribution of MeCP2 binding from noncoding regions toward transcriptionally active genomic regions, including protein-coding genes and small regulatory RNA loci. Although the overall number of MeCP2 binding sites did not change dramatically after injury, the locations of binding shifted to regions more relevant to gene regulation.
To evaluate functional consequences of this redistribution, the researchers examined one specific locus: mmu-miR-126, a microRNA gene that showed enriched MeCP2 binding following SNI. Increased MeCP2 occupancy at the miR-126 locus was associated with repression of miR-126 expression; this repression did not result from changes in DNA methylation at the locus. Reduced miR-126 led to increased expression of its target genes, Dnmt1 and Vegfa, both in cultured neuronal cells and in the injured DRG. In Mecp2-null mice, these targets were reduced compared with wild-type controls, supporting a role for MeCP2 in activating Dnmt1 and Vegfa expression in this context.
Delivering miR-126 intrathecally after injury lowered Dnmt1 and Vegfa expression in the DRG but did not fully reverse mechanical and thermal hypersensitivity in the nerve-injury model, indicating that MeCP2 controls multiple genes and pathways that together influence pain sensitivity.
Overall, the study provides molecular evidence that changes in genome-wide MeCP2 distribution after peripheral nerve injury can directly and indirectly modulate expression of many genes in sensory neurons. These genome-wide shifts in MeCP2 binding offer a mechanistic framework for how epigenetic regulation contributes to the development and maintenance of neuropathic pain.
Source: Lauren Ingeno, Drexel University College of Medicine
Journal: Epigenetics & Chromatin (study: “Genome-wide redistribution of MeCP2 in dorsal root ganglia after peripheral nerve injury” by Melissa T. Manners, Adam Ertel, Yuzhen Tian and Seena K. Ajit). Published online May 27, 2016. DOI: 10.1186/s13072-016-0073-5
Abstract
Genome-wide redistribution of MeCP2 in dorsal root ganglia after peripheral nerve injury
Background
Methyl-CpG-binding protein 2 (MeCP2) binds methylated cytosines and plays a central role in neuronal development and function by regulating gene expression through activation, repression and chromatin remodeling. Mutations in MeCP2 cause Rett syndrome, which includes altered nociception. MeCP2 expression increases in mouse dorsal root ganglia after peripheral nerve injury, but the functional consequences of that increase were unclear. To identify MeCP2-bound regions in the DRG and determine changes induced by nerve injury, chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed four weeks after spared nerve injury (SNI).
Results
While the total number of MeCP2 binding sites across the genome was similar between SNI and sham controls, SNI induced a redistribution of MeCP2 to transcriptionally relevant regions. Enriched MeCP2 binding at the miR-126 locus after nerve injury repressed miR-126 expression without changing local DNA methylation. Downregulation of miR-126 resulted in upregulation of its targets Dnmt1 and Vegfa in neuronal cells and in the SNI model; these targets were downregulated in Mecp2-null mice, indicating a regulatory role for MeCP2 in activating Dnmt1 and Vegfa. Intrathecal miR-126 delivery reduced Dnmt1 and Vegfa expression in DRG but did not fully reverse injury-induced hypersensitivity.
Conclusions
Changes in the global distribution of MeCP2 can lead to direct and indirect modulation of gene expression in the DRG after peripheral nerve injury. Alterations in MeCP2 genome-wide binding provide a molecular basis for epigenetic mechanisms that contribute to neuropathic pain and identify candidate pathways for future therapeutic exploration.