Pluripotent Stem Cells Research

Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells

The paper uses MINUTE-ChIP to analyze H3K27me3 and H3K4me3 in mouse ESCs under 2i and serum conditions, finding hypermethylation of H3K27me3 and loss of H3K4me3 at bivalent promoters.

Pumilio Proteins Exert Distinct Biological Functions and Multiple Modes of Post-Transcriptional Regulation in Embryonic Stem Cell Pluripotency and Early Embryogenesis

This study identifies distinct roles of Pum1 and Pum2 in ESC pluripotency and embryogenesis, revealing novel post-transcriptional regulatory mechanisms.

Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm

The paper compares the interactome networks of human embryonic stem cell lines with their tissue of origin, finding limited transcriptome overlap but enriched network properties related to transcriptional activity.

A Latent Variable Model for Evaluation of Disparate Ratings of Stem Cell Colonies by Two Experts

This paper develops a statistical model to evaluate differences in pluripotency ratings of stem cell colonies by two experts, identifying shared and distinct features used in their assessments.

CHD8 regulates the balance between proliferation and differentiation of human iPSCs in neural development

This study shows that CHD8 deficiency in human iPSCs increases cell proliferation and delays neural differentiation, potentially contributing to ASD pathophysiology.

In vivo lineage conversion of vertebrate muscle into early endoderm-like cells

This study shows that differentiated zebrafish muscle cells can be reprogrammed into endoderm-like cells in vivo through Sox32 and Oct4 co-expression, challenging previous assumptions about lineage restriction.

Implantation-Competent Blastocyst-Like Structures from Mouse Pluripotent Stem Cells

This study generates implantation-competent blastocyst-like structures (iBCs) from mouse pluripotent stem cells, demonstrating their ability to implant and develop in vivo.

Single Cell Gene Expression Analysis Reveals Human Stem Cell-Derived Graft Composition in a Cell Therapy Model of Parkinson’s Disease

The paper uses scRNA-seq to analyze graft composition in a Parkinson’s disease cell therapy model, revealing differences between human stem cell-derived and fetal tissue grafts.

High-content interrogation of human induced pluripotent stem cell-derived cortical organoid platforms.

This paper develops a standardized workflow for high-content screening of 3D human stem cell cultures using serum-free embryoid bodies to improve phenotypic drug screening efficiency.

CD49f is a novel marker to purify functional human iPSC-derived astrocytes

This study identifies CD49f as a marker to isolate functional human iPSC-derived astrocytes, which can be stimulated to exhibit a neurotoxic phenotype relevant to neurodegenerative diseases.

Context-dependent requirement of H3K9 methyltransferase activity during cellular reprogramming to iPSCs

This study shows that reducing EHMT1/2 activity during reprogramming with ascorbic acid impairs iPSC formation and viability, highlighting the role of H3K9 methylation in reprogramming efficiency.

Cross-species blastocyst chimerism between nonhuman primates using iPSCs

This paper demonstrates that chimpanzee iPSCs can form cross-species chimeras with rhesus macaque embryos, suggesting functional similarity between human and chimpanzee cells.

Rational reprogramming of cellular states by combinatorial perturbation

The paper develops Reprogram-Seq to screen TF cocktails for reprogramming cell states, identifying a 3-TF combination that reprograms MEFs to epicardial-like cells.

ZIC3 controls the transition from naïve to primed pluripotency.

This study identifies ZIC3 as a key regulator of the transition from naïve to primed pluripotency in mouse ESCs by analyzing open chromatin changes and transcriptional networks.

Emergence of a node-like population within an in vitro derived Neural Mesodermal Progenitors (NMPs) population

The paper analyzes in vitro NMPs derived from ESCs and EpiSCs, finding that EpiSC-derived NMPs more closely resemble in vivo NMPs and contain a node-like population maintaining T expression.

Cell cycle dynamics of human pluripotent stem cells primed for differentiation

The paper analyzes cell cycle dynamics in human pluripotent stem cells primed for differentiation using RNA-sequencing and identifies PI3K signaling's role in early differentiation states.

Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells

The paper identifies piRNA expression during cardiac differentiation of human pluripotent stem cells and suggests their potential role in gene regulation during cardiomyocyte development.

Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming

This study investigates how Gata4, Mef2c, and Tbx5 drive cardiac reprogramming by analyzing transcriptomic and epigenomic changes in fibroblasts.

KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control

The paper shows that KLF4 protein stability, regulated by interactions with pluripotency factors, overrides transcriptional control in ES cells, and mutations affecting stability prevent differentiation.

Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells

The paper identifies RNA binding proteins and RNAs interacting with Sox2 in mouse embryonic stem cells, showing coexistence in a ribonucleoprotein complex without evidence of chromatin recruitment regulation.

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

The paper maps multi-omic changes during mouse pluripotency transition, showing phosphoproteome dynamics precede epigenome and transcriptome changes.

Defining reprogramming checkpoints from single-cell analysis of induced pluripotency

This study identifies reprogramming checkpoints in iPSC generation by analyzing single-cell transcriptomes and reveals key gene interactions and regulatory mechanisms.

Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator

The paper uses RNAi screens in isogenic human stem cells to identify SMARCA4 as a differential regulator of stemness and differentiation in hematopoietic and neural stem cells.

G2M splits mouse embryonic stem cells into naïve and formative pluripotency states

The paper identifies two distinct pluripotency states in mouse embryonic stem cells (mESCs) based on G2M phase enrichment, showing naive and formative states marked by Esrrb expression levels.

Chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids.

The paper shows that chemically-defined conditions and signaling molecules can generate primitive endoderm-like cells and support post-implantation-like epiblast development in vitro.

Single cell transcriptome analysis reveals markers of naive and lineage-primed hematopoietic progenitors derived from human pluripotent stem cells.

The paper identifies markers of naive and lineage-primed hematopoietic progenitors from hPSCs using single-cell RNA sequencing and functional assays.

Inter-species differences in response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees

The paper compares hypoxia responses in human and chimpanzee iPSC-derived cardiomyocytes, finding conserved transcriptional responses and species-specific regulatory differences.

DPPA2 and DPPA4 are necessary to establish a totipotent state in mouse embryonic stem cells

This study identifies DPPA2 and DPPA4 as essential for activating Dux and LINE-1 transcription, which is critical for zygotic genome activation in mouse embryos.

Wdr5, Brca1 and Bard1 link the DNA damage response to the mesenchymal-to-epithelial transition during early reprogramming.

The paper identifies Brca1, Bard1, and Wdr5 as factors linking DNA damage response to MET during reprogramming, using siRNA screening and colony morphology analysis.

Single cell expression analysis uncouples transdifferentiation and reprogramming

The paper uses single cell transcriptomics to show that transdifferentiation and reprogramming can be uncoupled in pre-B cells based on their intrinsic plasticity.