Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis
Authors: Bai Zilong , Bartelo Nicholas , Aslam Maryam , Murphy Elisabeth A. , Hale Caryn R. , Blachere Nathalie E. , Parveen Salina , Spolaore Edoardo , DiCarlo Edward , Gravallese Ellen M. , Smith Melanie H. ,   Accelerating Medicines Partnership RA/SLE Network, Frank Mayu O. , Jiang Caroline S. , Zhang Haotan , Pyrgaki Christina , Lewis Myles J. , Sikandar Shafaq , Pitzalis Costantino , Lesnak Joseph B. , Mazhar Khadijah , Price Theodore J. , Malfait Anne-Marie , Miller Rachel E. , Zhang Fan , Goodman Susan , Darnell Robert B. , Wang Fei , Orange Dana E. , Albrecht Jennifer , Anolik Jennifer H. , Apruzzese William , Boyce Brendan F. , Boyle David L. , Brenner Michael B. , Bridges S. Louis , Buckley Christopher D. , Buckner Jane H. , Bykerk Vivian P. , Dolan James , Donlin Laura T. , Filer Andrew , Firestein Gary S. , Fonseka Chamith Y. , Gregersen Peter K. , Guthridge Joel M. , Gutierrez-Arcelus Maria , Holers V. Michael , Hughes Laura B. , Ivashkiv Lionel B. , James Eddie A. , James Judith A. , Jonsson A. Helena , Kelly Stephen , Lederer James A. , Lee Yvonne C. , Mandelin Arthur M. , McGeachy Mandy J. , Mears Joseph R. , Meednu Nida , Moreland Larry , Perlman Harris , Rangel-Moreno Javier , Rao Deepak A. , Raychaudhuri Soumya , Ritchlin Christopher , Robinson William H. , Rohani-Pichavant Mina , Seifert Jennifer , Slowikowski Kamil , Tabechian Darren , Utz Paul J. , Watts Gerald F. M. , Wei Kevin 
Published: April 2024

It has been presumed that rheumatoid arthritis (RA) joint pain is related to inflammation in the synovium; however, recent studies reveal that pain scores in patients do not correlate with synovial inflammation. We developed a machine-learning approach (graph-based gene expression module identification or GbGMI) to identify an 815-gene expression module associated with pain in synovial biopsy samples from patients with established RA who had limited synovial inflammation at arthroplasty. We then validated this finding in an independent cohort of synovial biopsy samples from patients who had early untreated RA with little inflammation. Single-cell RNA sequencing analyses indicated that most of these 815 genes were most robustly expressed by lining layer synovial fibroblasts. Receptor-ligand interaction analysis predicted cross-talk between human lining layer fibroblasts and human dorsal root ganglion neurons expressing calcitonin gene–related peptide (CGRP
+
). Both RA synovial fibroblast culture supernatant and netrin-4, which is abundantly expressed by lining fibroblasts and was within the GbGMI-identified pain-associated gene module, increased the branching of pain-sensitive murine CGRP
+
dorsal root ganglion neurons in vitro. Imaging of solvent-cleared synovial tissue with little inflammation from humans with RA revealed CGRP
+
pain-sensing neurons encasing blood vessels growing into synovial hypertrophic papilla. Together, these findings support a model whereby synovial lining fibroblasts express genes associated with pain that enhance the growth of pain-sensing neurons into regions of synovial hypertrophy in RA.