Dynamic chromatin accessibility and transcriptome changes following PDGF-BB treatment of bone-marrow derived mesenchymal stem cells [ATAC-seq]
Mesenchymal stem cells (MSCs) are multipotent stem cells that are under investigation for use in clinical trials because they are capable of self-renewal and differentiating into different cell types under defined conditions. Nonetheless, the therapeutic effects of MSCs have been constrained by low engraftment rates, cell fusion, and cell survival. Various strategies have been explored to improve the therapeutic efficacy of MSCs, with platelet-derived growth factor (PDGF)-BB emerging as a promising candidate. To enhance our comprehension of the impact of PDGF-BB on the gene expression profile and chromosomal accessibility of MSCs, RNA-sequencing and analysis of chromatin accessibility profiles were conducted on three human primary MSCs in culture, both with and without stimulation by PDGF-BB.  Integrative analysis of gene expression and chromatin accessibility demonstrated that PDGF-BB treatment modified the chromatin accessibility landscape, marking regions for activation or repression through the AP-1 family transcription factors TEAD, CEBP, and RUNX2. These changes in AP1 transcription factor expression, in turn, led to cell proliferation and differentiation potential towards osteoblasts, adipocytes, or chondrocytes. The degree of MSC differentiation varies among cells isolated from different donors. The presence of an enrichment of exosome-related genes is also noted among all the differentially expressed genes.  In conclusion, the observed changes in AP1 transcription factor expression not only induced cellular proliferation and differentiation, but also revealed variations in the degree of MSC differentiation based on donor-specific differences. Moreover, the enrichment of exosome-related genes among differentially expressed genes suggests a potential significant role for PDGF-BB in facilitating intercellular communication. Overall design: MSCs: PoieticsTM Normal Human Bone Marrow Derived Mesenchymal Stem Cells (hMSC) are isolated from normal (non-diabetic) adult human bone marrow withdrawn from bilateral punctures of the posterior iliac crests of normal volunteers. Three PoieticsTM hMSC cells, namely 36015, 36461, and 36550, sourced from three distinct donors, were acquired from Lonza. These cells were designated as follows: 1 (batch 18TL 169252 from donor 36015), 2 (batch 18TL 241909 from donor 36461), and 3 (batch 18TL 262066 from donor 36550). The MSC cells were grown in a humidified chamber maintained at 37°C and 5% CO2, utilizing MSCBMTM Basal Media (PT-3238) and MSCGMTM SingleQuots Supplement Kit (PT-4105) obtained from Lonza. Media was changed every three days.  MSCs were cultured in media supplemented with 10 ng/ml PDGF-BB (Invitrogen) for 48 hours as the treated sample, while the control sample was cultivated without PDGF-BB. Control and PDGF-BB treated MSCs were concurrently collected from distinct plates for ATACseq analyses.