Multi-tissue spatial transcriptomics identified simultaneous responses to oxidative stress and apoptosis in parallel with tissue-specific reprogramming in modeled chronic kidney disease-mineral and bone disorder

Abstract Musculoskeletal dysfunction in chronic kidney disease-mineral and bone disorder (CKD-MBD) is associated with morbidity and mortality. Disease alterations in bone and muscle, and among muscle fiber types, have largely been tested by candidate gene analysis in individual tissues. We undertook a multi-tissue spatial transcriptomics (ST) approach to identify and differentiate tissue-specific and -common genomic reprogramming occurring simultaneously in cortical bone, muscle, and marrow during CKD-MBD. Visium ST was used on femur-muscle histological cross sections from male mice with adenine diet-induced CKD-MBD (0.2%; 4 wk), or casein control diet. The spatial sequencing datasets were analyzed for differential gene expression and pathway analyses. Transcriptional changes were validated using qPCR in the contralateral tissues as well as in the original sections. Uniform manifold approximation and projection analyses paired with hallmark transcript mapping distinguished cortical bone and bone marrow, slow vs. fast twitch muscle fiber cell populations, including 3 fast twitch muscle subtypes (IIa, IIx, and IIb). Upregulation of apoptosis and oxidative stress pathways, including genes P4hb, known to induce apoptosis, and S100a9, associated with responses to inflammation, occurred across all CKD-MBD tissues. Specifically in muscle, atrophy-associated genes (Trim63, Fbxo32) were upregulated by 3-4-fold, and a novel 2-5-fold increase was observed in the mRNA encoding the structural gene Nrap in both CKD-MBD fast and slow twitch skeletal muscle. Fiber subtypes manifested specific disturbances, including a slow-twitch increase in Car3 (3-fold), and fast-twitch muscle enrichment of ubiquitin-mediated proteolysis and RUNX1-driven transcriptional pathways. In bone, CKD-MBD differentially increased pre-osteoblast markers Tnc and Mmp13 but markedly decreased Bglap and Col3a1 (96.6%; 95.3%), whereas marrow downregulated heme biosynthetic pathways along with ~90% suppression of histone gene Hist1h1b, supporting wider genomic changes. Unbiased ST identified transcriptional alterations involving pan-tissue oxidative stress and apoptosis caused by CKD-MBD. Tissue-unique phenotypes were also found, potentially providing novel targets for improvement of musculoskeletal function during CKD-MBD.