RNA-seq Analysis of bone marrow mesenchymal stromal cells from DPBS-treated vs FAP inhibitor-treated mice

Purpose: The goal of this study is to compare the transcriptomic differences between bone marrow mesenchymal stromal cells (BMSCs) from DPBS-treated mice and FAP inhibitor (FAPi)-treated mice, in order to find out the differentially expressed genes and pathways underlying the bone phenotypes after FAPi treatment. Methods: The mRNA profiles of BMSCs from DPBS treated mice (n=3) and FAPi treated mice (n=4) were generated by deep sequencing on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads. The sequence reads that passed quality filters were analyzed by STAR and HTSeq. Raw gene counts for each gene was determined by UMI numbers. Results: Using an optimized data analysis workflow, we mapped more than 40 million sequence reads per sample to the mouse genome (mm10) and identified about 9 million raw counts (removing the duplicates by UMIs from Read2) in the BMSCs of DPBS treated mice and FAPi treated mice with HTSeq. Approximately 3% of the genes showed differential expression between BMSCs from DPBS treated mice and FAPi treated mice (fold change > 2.0 or < -2.0 and p value <0.05). Conclusions: Our study revealed the molecular mechanisms underlying the bone-forming activity of FAPi in BMSCs after in vivo administration. Overall design: FAP ihibitor treated (n=4, 500 ug/kg daily intraperitoneal injection for 35 days). DPBS-treated mice (n=3, DPBS injected daily intraperitoneal injection for 35 days). Bone marrow cells were digested and sorted for BMSCs.