Comprehensive transcriptome profiling identifies distinct gene expression pattern of post‐stroke muscle compared to denervation and disuse muscles in mice

Abstract

Ischemic stroke is a complex cerebral vascular incident resulting in widescale global systemic changes, including a significant loss of skeletal muscle mass and function. Post-stroke muscle atrophy is precipitous, in part a consequence of the simultaneous contribution of motor neuron inactivity, and long-term immobilization (IMM). Middle cerebral artery occlusion (MCAO) is a well-established model serving as an indispensable tool in human ischemic stroke research to study the clinical consequences and develop therapeutic strategies. Due to the intrinsic involvement of innervation deficits and disuse in stroke, MCAO is often compared to experimental models of denervation (DEN; e.g., nerve transection), and IMM (hind-limb immobilization). However, ischemic stroke catalyzes a systemic milieu, whereby DEN and IMM exist only as a standalone piece of the global puzzle affecting muscle. Recently, we uncovered myriad transcriptional alterations in skeletal muscle after 60min MCAO in mice. Although similar transcriptomic analyses have been conducted in skeletal muscle from mice that underwent DEN and IMM, it is unclear whether the molecular origin of post-stroke muscle atrophy is similar to or different from DEN and IMM models. To determine this, we performed a cross-study analysis in skeletal muscle using RNAseq data from MCAO, DEN and IMM models. FASTQ files were ascertained via NCBI (SRP220337) and compared to our published MCAO sequencing data (doi:10.3390/genes11070726) to determine differentially expressed genes (DEG) and gene ontology (GO) enrichment. MCAO exhibited 476 and 603 unique up- and down-regulated DEG, respectively compared to DEN and IMM. Our analysis revealed 19 GO terms exclusive to MCAO. Several unique terms were related to the nervous system (e.g., GO:0050769). 10 GO terms were shared between models, with several related to proteolysis (e.g., GO:0006511). Analysis of shared terms revealed differentially annotated genes within terms. Ubiquitin-dependent catabolic process was enriched in all models, however 13 of the annotated genes were unique to MCAO. Analysis also revealed shared GO terms between MCAO and DEN only, such as heterocycle metabolic process (GO: 0046483) and mitochondrial membrane (GO: 0031966). Although these terms were enriched in both models, the relative genes annotated to these terms varied. For example, heterocycle metabolic process (GO: 0031966) had only 1 annotated gene in common, with 79 genes unique to MCAO annotated to this term. Notably, all genes annotated to this term were up-regulated in MCAO, while conversely down-regulated in DEN. These results are the first to show unique transcriptomic profiles in mouse muscle between MCAO, DEN, and IMM models. These data suggest that stroke-induced muscle atrophy may involve additional contributory factors, potentially due to the systemic nature of stroke. Further research is necessary to better elucidate the potential upstream mechanisms unique to stroke, contributing to post-stroke skeletal muscle atrophy.