Three Distinct Cell Types Express Extracellular Matrix Proteins In Different Niches During Skeletal Muscle Fibrosis. Mus musculus

Tissue extracellular matrix provides structural support and creates unique niches for resident cells . However, the identities of cells responsible for creating specific ECM niches have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain ECM niches in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I expressing cells in all three cell populations increase proportionally in fibrotic muscle indicating that all cell types participate in the fibrosis process. Furthermore, it is shown that the ECM gene expression profile is not qualitatively altered in fibrotic muscle. This suggests that muscle fibrosis in this model results from an increased number of collagen I expressing cells and not the initiation of a specific fibrotic gene expression program. Finally, in fibrotic muscle, we show that these collagen I expressing cell populations differentially express distinct ECM proteins – fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins and skeletal muscle progenitor cells differentially express genes important for the satellite cell niche. Overall design: RNA sequencing was performed on Illumina HiSeq 2500 (rapid run mode). 2 to 4 biological replicates for each cell type (FAP, SMP and FB) under each condition (DKO and WT) were multiplexed across two lanes (total samples=20). 100 base-paired reads per sample with an average of 22 million reads per sample were obtained. RNA read mapping and the initial quality control was performed using the OSA algorithm (16) to the mouse reference genome version mm10, with Refseq annotation.