Single-cell multi-omics sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation

Int J Oral Sci. 2026 Apr 17;18(1):37. doi: 10.1038/s41368-026-00432-9.

ABSTRACT

Pain is the most common symptom of temporomandibular joint (TMJ) disorders, which present significant clinical challenges due to their complexity and limited treatment options. Our previous study demonstrates that gut microbiome-derived butyrate is critical for the modulation of TMJ pain. In this study, we investigated its underlying mechanisms, and we found that oral administration of tributyrin, a prodrug of butyrate, not only significantly alleviated TMJ pain but also reversed the reduction in histone acetylation in the spinal trigeminal nucleus caudalis (Sp5C) under the TMJ pain condition. Using single-cell multi-omics sequencing, we profiled gene expression and chromatin accessibility in the Sp5C cells at the single-cell resolution. Bioinformatics analysis revealed that TMJ pain disrupted both the expression and chromatin accessibility of Nop14, Matk, Idh3b, Ndst2, and Tomm6 across four cell types in the Sp5C, and these alterations were reversed by tributyrin treatment. Specifically, Nop14 exhibited increased chromatin accessibility at its promoter region under TMJ pain condition, and knockdown of Nop14 in the Sp5C restored histone acetylation and alleviated TMJ pain. Together, our findings reveal cell-type-specific gene regulation that underlies butyrate-mediated epigenetic regulation of TMJ pain, which suggesting that targeting gut microbiome metabolites could develop a non-opioid novel therapy for TMJ disorders.

PMID:41997906 | DOI:10.1038/s41368-026-00432-9