In silico analysis of single‐cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators

Abstract

Spermatogonial stem cells (SSCs), which are at the basis of spermatogenesis process, are valuable cells with different applications in biotechnology and regenerative medicine. Understanding the molecular basis of SSC self-renewal and differentiation at various developmental stages of the male organism is crucial to find key factors in the SSCs fate and function. Therefore, this study was aimed to use single-cell RNA-sequencing dataset analysis for identification of differentially expressed genes (DEGs) and their regulators in 3 and 7 days old mouse-derived single SSCs (mSSCs). Results showed 68 upregulated and 203 downregulated genes in 7 days old mouse-derived SSCs compared to 3 days old mSSCs, which were associated with 1493 and 3077 biological processes, respectively. It also found that DAZL, FKBP6, PAIP2, DDX4, H3F3B, TEX15, XRN2, MAEL, and SOD1 are important factors with the higher gene expression pattern, which may be pivotal for mSSCs fate and function during development of germ cells. Moreover, NR3C1, RXRA, NCOA, ESR1, PML, ATF2, BMI1, POU5F1, and CHD1 were the main central regulators for the upregulated DEGs, while HNF1A, C/EBPα, and NFATC1 were the master regulators for the downregulated DEGs. In this regard, two significant protein complexes were found in the protein-protein interactions network for the upregulated DEGs regulators. Furthermore, 24 protein kinases detected upstream of the main central regulators of DEGs. In conclusion, this study presents DEGs and their transcriptional regulators that are crucial for inducing and regulating SSCs commitment during development, and for developing efficient protocols to identify and isolate SSCs for different applications.

Combinatorial immune and stress response, cytoskeleton and signal transduction effects of graphene and triphenyl phosphate (TPP) in mussel Mytilus galloprovincialis

“…3). Sisakhtnezhad et al indicated that FkBP6 was associated with the self-renewal and maintenance of spermatogonial stem cells (SSCs), which played a key role in the process of spermatogenesis [50]. Therefore, graphene + TPP could induce reproductive toxicity by affecting the expression of FKBP6.…”

Cytoplasmatic Localization of Six1 in Male Testis and Spermatogonial Stem Cells

“…With the development of bulk RNA sequencing and single cell RNA-sequencing (scRNA-Seq) technology, it is possible to explore gene expression profile of different organs and different cells in one organ (10)(11)(12). The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases show the significant upregulation of Six1 in 13 cancer samples when compared with testicular germ cell tumor (TGCT) (13).…”

“…Specifically, mSSCs derived from mice aged 3 or 7 years old were analyzed to identify differentially expressed genes using the scRNA-Seq database. This analysis helped to identify core factors that are involved in germ cell development (10,11).…”