Integrative single-cell RNA-seq and ATAC-seq analysis of the evolutionary trajectory features of adipose-derived stem cells induced into astrocytes

Abstract

This study employs single-cell RNA sequencing (scRNA-seq) and assay for transposase-accessible chromatin with high-throughput sequencing technologies (scATAC-seq) to perform joint sequencing on cells at various time points during the induction of adipose-derived stem cells (ADSCs) into astrocytes. We applied bioinformatics approaches to investigate the differentiation trajectories of ADSCs during their induced differentiation into astrocytes. Pseudotemporal analysis was used to infer differentiation trajectories. Additionally, we assessed chromatin accessibility patterns during the differentiation process. Key transcription factors driving the differentiation of ADSCs into astrocytes were identified using motif and footprint methods. Our analysis revealed significant shifts in gene expression during the induction process, with astrocyte-related genes upregulated and stem cell-related genes downregulated. ADSCs first differentiated into neural stem cell-like cells with high plasticity, which further matured into astrocytes via two distinct pathways. Marked changes in chromatin accessibility were observed during ADSC-induced differentiation, affecting transcription regulation and cell function. Transcription factors analysis identified NFIA/B/C/X and CEBPA/B/D as key regulators in ADSCs differentiation into astrocytes. We observed a correlation between chromatin accessibility and gene expression, with ADSCs exhibiting broad chromatin accessibility prior to lineage commitment, where chromatin opening precedes transcription initiation. In summary, we found that ADSCs first enter a neural stem cell-like state before differentiating into astrocytes. ADSCs also display extensive chromatin accessibility prior to astrocyte differentiation, although transcription has not yet been initiated. These findings offer a theoretical framework for understanding the molecular mechanisms underlying this process.

Keywords: adipose‐derived stem cells; astrocyte; induced differentiation in vitro; pseudotime trajectory; scATAC‐seq; scRNA‐seq.