Comprehensive comparison of gene expression diversity among a variety of human stem cells

Abstract

Several factors, including tissue origins and culture conditions, affect the gene expression of undifferentiated stem cells. However, understanding the basic identity across different stem cells has not been pursued well despite its importance in stem cell biology. Thus, we aimed to rank the relative importance of multiple factors to gene expression profile among undifferentiated human stem cells by analyzing publicly available RNA-seq datasets. We first conducted batch effect correction to avoid undefined variance in the dataset as possible. Then, we highlighted the relative impact of biological and technical factors among undifferentiated stem cell types: a more influence on tissue origins in induced pluripotent stem cells than in other stem cell types; a stronger impact of culture condition in embryonic stem cells and somatic stem cell types, including mesenchymal stem cells and hematopoietic stem cells. In addition, we found that a characteristic gene module, enriched in histones, exhibits higher expression across different stem cell types that were annotated by specific culture conditions. This tendency was also observed in mouse stem cell RNA-seq data. Our findings would help to obtain general insights into stem cell quality, such as the balance of differentiation potentials that undifferentiated stem cells possess.

Impact of genomic background and developmental state on signaling pathways and response to therapy in glioblastoma patient-derived cells

“…Interestingly, reserve respiratory capacity was higher in untreated HF2303 relative to HF2927 cells, and higher in SDC compared to CSCs (S3_Fig). Replication-dependent histones were highly enriched in HF2303 CSCs, in the absence of enrichment in cell proliferation markers (Fig 7, A in S2 Table ), as previously observed for embryonic and induced pluripotent stem cells [59]. Several nuclear pseudogenes with sequence similarity to mitochondrially encoded 16S rRNA (e.g.…”

Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer

“…Although 10 different H3 genes encode the same H3.1 amino acid sequence, a recent study reported that only the HIST1H3H and HIST1H3D genes were differentially regulated in metastatic breast cancer [ 139 ]. This suggests that at the transcript level, these histone genes may not be functionally redundant [ 140 , 141 ]. HIST3H3 is also upregulated in breast cancer and is positively associated with activated polymorphonuclear neutrophil (PMN)-induced breast cancer metastasis [ 142 ].…”

Advancing diabetes treatment: the role of mesenchymal stem cells in islet transplantation

“…Unlike MSCs, iPSCs and ESCs possess greater pluripotency, enabling the generation of a broader range of cell types. However, this approach is associated with increased ethical concerns for ESCs and increased tumorigenic potential for both iPSCs and ESCs ( 18 , 19 ). Compared to their broader differentiation capabilities, the unique advantages of MSCs in regenerative medicine, particularly in mitigating autoimmune responses in diabetes, are the heightened risks associated with iPSCs and ESCs.…”

“…Moreover, the exploration of MSC-derived exosomes represents an advancement in therapeutic strategies for pancreatic islet transplantation, highlighting a new direction in MSC-based treatments (17). These exosomes, as carriers of regenerative and immunomodulatory factors, present a novel approach to enhancing the microenvironment of transplanted islets, potentially reducing immunological rejection and supporting islet cell survival and function.…”