Simultaneous Transcriptional Reprogramming in Cortical Bone, Muscle, and Bone Marrow Uncovered by Spatial Transcriptomics in Modeled CKD

Background: Musculoskeletal dysfunction in CKD-MBD is common, causing increased morbidity and mortality; however, the contribution of multi-tissue genetic reprogramming is not understood. Further, the interactions between bone and muscle, and among muscle fiber types have only been tested by candidate gene analysis and in individual tissues. Herein, we tested spatially unique transcriptional reprogramming occurring simultaneously across cortical bone, muscle, and marrow. Methods: Visium spatial transcriptomics (ST) was used on femur-muscle cross sections from male mice with adenine diet-induced CKD (0.2%, 4 wks), or casein control diet. Results: UMAP analyses paired with hallmark transcript mapping distinguished slow and fast twitch muscle fibers, including three fast-twitch subtypes (IIa, IIx, IIb), as well as cortical bone and bone marrow in the same histology sections. Consistent with disease phenotypes, atrophy-associated genes (Trim63, Fbxo32) were upregulated in CKD muscle, 1.76-1.92 and 1.67-1.94 log2-fold, respectively. Interestingly, a novel increase in the structural gene Nrap was detected across CKD fast and slow-twitch muscle (1.24-2.29 log2-fold), whereas fiber subtypes showed specific disturbances, including a slow-twitch muscle increase in Car3 (1.69 log2-fold) and enrichment of ubiquitin-mediated proteolysis and transcriptional regulation by RUNX1 pathways in fast-twitch muscle. In cortical bone, differing effects of CKD on osteoblast gene expression occurred, with increased mRNAs for Tnc/Mmp13 and decreased expression of Bglap and Col3a1 (96.6% and 95.3%). Further, glycolysis pathways were downregulated in CKD cortical bone. Bone marrow showed expected changes with CKD, including enrichment of inflammation and downregulation of heme biosynthetic pathways. Additionally, we found a novel 89.3% decrease in expression of Hist1h1b, contributing to downregulation of chromatin-related pathways. Along with tissue specific changes, we also identified pathways shared across tissues, most notably increased intrinsic apoptosis signaling with CKD. Conclusion: Unbiased ST identified novel effects of CKD concurrently within bone, bone marrow, and specific muscle subtypes associated with tissue-unique and -common musculoskeletal pathologies. Funding: NIDDK Support - NIDDK Support, NIDDK Support