Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe

Cellular and Molecular Life Sciences, Journal Year: 2024, Volume and Issue: 81(1)

Published: Sept. 2, 2024

Abstract Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods analysis epigenetic mass-spectrometry chromatin immuno-precipitation, work with fixed cells only. Here we present genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, histone modification associated inactive chromatin. This based on chromodomain MPP8, allows visualization H3K9me3 landscapes single living cells. We used this probe to track induced pluripotent stem (iPSCs) into neurons. Our findings revealed two major waves global reorganization 4-day differentiation, namely first third days, whereas nearly no occurred second fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging Landscapes), which combines probes machine learning approaches, enables classification multiparametric signatures potentially other models.

Language: Английский

---

Transcriptomic comparison between wild-caught and domesticated black tiger shrimp (Penaeus monodon) in early and late-vitellogenic broodstock females

Aquaculture Reports, Journal Year: 2025, Volume and Issue: 41, P. 102675 - 102675

Published: Feb. 13, 2025

Language: Английский

---

Pilot study using a discrete mathematical approach for topological analysis and ssGSEA of gene expression in autosomal recessive polycystic kidney disease

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: May 3, 2025

Autosomal recessive polycystic kidney disease (ARPKD) is a severe genetic disorder characterized by renal cystogenesis and hepatic fibrosis, primarily associated with PKHD1 mutations. While differential expression analysis (DEG) has identified key genes involved in ARPKD, their network-level interactions remain unclear. Recent studies have implicated WNT signaling ARPKD pathogenesis, but topological framework may provide additional insights into gene community structures. This study applied network-based approach integrating single-sample set enrichment (ssGSEA) centrality to investigate communities ARPKD. We three communities: Community 2, centered on IFT22, exhibited stable activation both healthy samples, suggesting its role ciliary function. 5, predominantly activated included linked tissue repair immune regulation. In contrast, 3 was suppressed indicating potential structural instability. Notably, mathematically isolated, limited direct involvement ARPKD-specific transcriptional networks, while the absence of WNT5A, CDH1, FZD10 from defined indicate alterations network associations compared individuals. These findings highlight advantages topology over conventional DEG elucidating pathophysiology. By identifying regulatory hubs, this offers novel mechanisms therapeutic targets.

Language: Английский

---

Mechanisms of intestinal injury in polychaete Perinereis aibuhitensis caused by low-concentration fluorene pollution: Microbiome and metabonomic analyses

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 475, P. 134925 - 134925

Published: June 15, 2024

Language: Английский

---