Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolic Maturation Media Improves Physiological Function of Human iPSC-derived Cardiomyocytes

ABSTRACT: iPSC-derived cardiomyocytes (iPSC-CMs) have enormous potential for the study of human cardiac disorders. However, their physiological immaturity severely limits their utility as a model system and their adoption for drug discovery. In this study, we describe a maturation media (MM) designed to provide oxidative substrates adapted to the metabolic needs of hiPSC-CMs as compared to standard RPMI/B27 media. RNA sequencing was performed to gain insight into the underlying molecular basis for the changes. Compared to baseline (day 21) conditions, three weeks subsequent exposure to MM (day 41) caused a significant differential expression in genes. GO analysis of the MM-differentially upregulated genes were informative, mapping to mitochondrial metabolism. Additionally, multiple Ca2+ cycling/sarcoplasmic reticulum (SR), sarcomeric, and ion channel genes were differentially expressed. These gene expression changes indicated that supplementation with oxidative substrates and subsequent metabolic changes might affect cardiomyocyte electrophysiology, Ca2+ cycling and contractility.

ORGANISM(S): Homo sapiens

PROVIDER: GSE151279 | GEO | 2020/06/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Advanced physiological maturation of iPSC-derived human cardiomyocytes using an algorithm-directed optimization of defined media components

Project description:Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) hold tremendous promise for in vitro modeling to assess native myocardial function and disease mechanisms as well as testing drug safety and efficacy. However, current iPSC-CMs are functionally immature, resembling in vivo CMs of fetal or neonatal developmental states. The use of targeted culture media and organoid formats have been identified as potential high-yield contributors to improve CM maturation. This study presents a novel iPSC-CM maturation medium formulation, designed using a differential evolutionary approach with oxidative capacity as an objective metric for iterative optimization. Relative to gold-standard reference formulations, our approach significantly matured morphology, Ca2+ handling, electrophysiology, and metabolism, which was further validated by multi-omic screening, for cells in either pure or co-cultured microtissue formats. Together, these findings not only provide a reliable workflow for highly functional iPSC-CMs for downstream use, but also demonstrate the power of high-dimensional optimization processes in evoking advanced biological function in vitro.

2022-10-05 | GSE214617 | GEO

Patient-Specific and Genome-Edited Induced Pluripotent Stem Cell-Derived Cardiomyocytes Elucidate Single-Cell Phenotype of Brugada Syndrome

Project description:This study recruited 2 patients with type 1 BrS carrying 2 different sodium voltage-gated channel alpha subunit 5 variants as well as 2 healthy control subjects. We generated iPSCs from their skin fibroblasts by using integration-free Sendai virus. We used directed differentiation to create purified populations of iPSC-CMs. BrS iPSC-CMs showed reductions in inward sodium current density and reduced maximal upstroke velocity of action potential compared with healthy control iPSC-CMs. Furthermore, BrS iPSC-CMs demonstrated increased burden of triggered activity, abnormal calcium (Ca2+) transients, and beating interval variation. Correction of the causative variant by genome editing was performed, and resultant iPSC-CMs showed resolution of triggered activity and abnormal Ca2+ transients. Gene expression profiling of iPSC-CMs showed clustering of BrS compared with control subjects. Furthermore, BrS iPSC-CM gene expression correlated with gene expression from BrS human cardiac tissue gene expression.

2017-01-12 | GSE93530 | GEO

R14del RNA-seq

Project description:Arrhythmogenic cardiomyopathy (ACM) is characterized by life-threatening ventricular arrhythmias and sudden cardiac death and affects hundreds of thousands of patients worldwide. The deletion of Arginine 14 (p.R14del) in the phospholamban (PLN) gene has been implicated in the pathogenesis of ACM. PLN is a key regulator of sarcoplasmic reticulum (SR) Ca2+ cycling and cardiac contractility. Despite global gene and protein expression studies, the molecular mechanisms of PLN-R14del ACM pathogenesis remain unclear. Using a humanized PLN-R14del mouse model and human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), we investigated the transcriptome-wide mRNA splicing changes associated with the R14del mutation. We identified >200 significant alternative splicing (AS) events and distinct AS profiles were observed in the right (RV) and left (LV) ventricles in PLN- R14del compared to WT mouse hearts. Enrichment analysis of the AS events showed that the most affected biological process was associated with “cardiac cell action potential”, specifically in the RV. We found that splicing of 2 key genes, Trpm4andCamk2d, which encode proteins regulating calcium homeostasis in the heart, were altered in PLN-R14del mouse hearts and human iPSC-CMs. Bioinformatical analysis pointed to the tissue-specific splicing factors Srrm4 and Nova1 as likely upstream regulators of the observed splicing changes in the PLN-R14del cardiomyocytes. Our findings suggest that aberrant splicing may affect Ca2+- homeostasis in the heart, contributing to the increased risk of arrythmogenesis in PLN- R14del ACM.

2022-11-22 | GSE217921 | GEO

Isolation and long-term expansion of murine epidermal stem-like cells

Project description:Epidermis is the most outer layer of the skin and serves as a physical barrier protecting the internal tissues from mechanical and environmental insults. Its constant renewing and regeneration capacity are sustained by the basal keratinocytes, which, through proliferation and differentiation, supply diverse cell types for homeostasis maintenance and injury repair. A major challenge in epidermal research is the difficulty to culture murine keratinocytes. Here we tested murine keratinocyte culture conditions and developed cell lines using low-Ca2+ (0.06 mM) keratinocyte serum-free medium (KSFM-Ca2+) without feeder cells. Cells derived in this condition could be subcultured for >70 passages. These cells displayed basal epithelial cell morphology and expressed keratin (KRT) 14, but lacked the epithelial-characteristic intercellular junctions. After adaptation to the Defined-KSFM (DKSFM) media containing 0.15 mM Ca2+, these cells formed tight- and adherens-junctions and exhibited increased Krt1/10 expression while retaining subculture capacity. Global gene expression studies showed that cells derived in KSFM-Ca2+ media had enriched expression of stem/proliferation markers and that cells adapted in DKSFM media had gene expression signatures of epithelial progenitors. Correspondingly, the KSFM-Ca2+-derived cells had a remarkable capacity of clonal growth, whereas DKSFM-adapted cells could differentiate to suprabasal subtypes in 3D cultures. The generation of stem-like murine keratinocyte lines and the conversion of these cells to epithelial progenitors capable of terminal differentiation provide useful in vitro tools for skin research.

2021-03-23 | GSE167437 | GEO

Comparative gene expression analyses reveal distinct molecular signature between differentially reprogrammed cardiomyocytes

Project description:Cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) or directly reprogrammed from non-myocytes (induced cardiomyocytes, iCMs) are promising sources for heart regeneration or disease modeling. However, the similarities and differences between iPSC-CM and iCM are still unknown. Here we performed transcriptome analyses of beating iPSC-CMs and iCMs generated from cardiac fibroblasts (CFs) of the same origin. Although both iPSC-CMs and iCMs establish CM-like molecular features globally, iPSC-CMs exhibit a relatively hyperdynamic epigenetic status while iCMs exhibit maturation status that more resemble adult CMs. Based on gene expression of metabolic enzymes, iPSC-CMs primarily employ glycolysis while iCMs utilize fatty acid oxidation as the main pathway. Importantly, iPSC-CMs and iCMs exhibit different cell cycle status, alteration of which influenced their maturation. Therefore, our study provides a foundation for understanding the pros and cons of different reprogramming approaches.

2017-09-26 | GSE99814 | GEO

Rhesus iPSC-CMs response to anoxia, comparing with human iPSC-CMs

Project description:Rhesus iPSC-CMs response to anoxia, comparing with human iPSC-CMs

| PRJNA428243 | ENA

Calpain Cleavage of Junctophilin-2 generates a Spectrum of Calcium-dependent Cleavage Products and DNA-rich NT1-Fragment Domains in Cardiomyocytes - PRM Dataset

Project description:Calpains are calcium (Ca2+) activated neutral proteases that are involved in several essential signaling pathways. One Calpain-specific proteolytic target is Junctophilin-2 (JP2), an important structural protein of Ca2+ release units required for the excitation-contraction coupling in cardiomyocytes. While downregulation of JP2 by Calpain cleavage in mouse models of heart failure has been reported previously, the precise molecular identity of the Calpain cleavage sites and the (patho-) physiological roles of the JP2 proteolytic products remain controversial. We systematically analyzed the JP2 cleavage fragments as function of Calpain-1 versus Calpain-2 proteolytic activities, revealing that both Calpain isoforms preferentially cleave mouse JP2 at R565, but subsequently also at three additional secondary Calpain cleavage sites. We identified the Calpain-specific primary cleavage products not only in mouse but also in human iPSC-derived cardiomyocytes (hiPSC-CMs). Knockout of RyR2 in hiPSC-CMs destabilized JP2 resulting in an increase of the Calpain-specifc cleavage fragments. The primary N-terminal cleavage product (NT1) accumulated in the nucleus of mouse and human cardiomyocytes in a Ca2+ dependent manner, closely associated with DNA-rich chromosomal regions, where NT1 is proposed to function as a cardioprotective transcriptional regulator in heart failure. Taken together, our data suggest that stabilizing NT1 by preventing secondary cleavage events by Calpain and other proteases could be an important therapeutic target for future studies.

2022-08-12 | PXD031424 | Pride

Calpain Cleavage of Junctophilin-2 generates a Spectrum of Calcium-dependent Cleavage Products and DNA-rich NT1-Fragment Domains in Cardiomyocytes

Project description:Calpains are calcium (Ca2+) activated neutral proteases that are involved in several essential signaling pathways. One Calpain-specific proteolytic target is Junctophilin-2 (JP2), an important structural protein of Ca2+ release units required for the excitation-contraction coupling in cardiomyocytes. While downregulation of JP2 by Calpain cleavage in mouse models of heart failure has been reported previously, the precise molecular identity of the Calpain cleavage sites and the (patho-) physiological roles of the JP2 proteolytic products remain controversial. We systematically analyzed the JP2 cleavage fragments as function of Calpain-1 versus Calpain-2 proteolytic activities, revealing that both Calpain isoforms preferentially cleave mouse JP2 at R565 but subsequently also at three additional secondary Calpain cleavage sites. We identified the Calpain-specific primary cleavage products not only in mouse but also in human iPSC-derived cardiomyocytes (hiPSC-CMs). Knockout of RyR2 in hiPSC-CMs destabilized JP2 resulting in an increase of the Calpain-specifc cleavage fragments. The primary N-terminal cleavage product (NT1) accumulated in the nucleus of mouse and human cardiomyocytes in a Ca2+ dependent manner, closely associated with DNA-rich chromosomal regions, where NT1 is proposed to function as a cardioprotective transcriptional regulator in heart failure. Taken together, our data suggest that stabilizing NT1 by preventing secondary cleavage events by Calpain and other proteases could be an important therapeutic target for future studies.

2022-08-12 | PXD031321 | Pride

Evaluation and mechanism study of cardiotoxicity caused by antipsychotics using human-induced pluripotent stem cell-derived cardiomyocytes

Project description:In this study, a comprehensive evaluation model for studying the cardiac toxicity of antipsychotic drugs was established by using iPSC-CMs. Six antipsychotic drugs, including aripiprazole, risperidone, quetiapine, haloperidol, clozapine, and olanzapine, all induced concentration-dependent QT prolongation in iPSC-CMs upon acute administration, and high concentrations of these drugs caused disorganized sarcomere arrangement in iPSC-CMs.

2024-01-01 | GSE248368 | GEO

Global gene expression analysis of green spotted puffer fish gills in response to environmental calcium changes

Project description:This study aims to understand the molecular adaptation mechanisms of fish gills to environmental Ca2+ changes. Using SuperSAGE, we compared the gene expression profiles of T. nigroviridis gills transferred from natural brackish water (10 ppt salinity,2.9 mM Ca2+) to artificial brackish water with control (2.9 mM), low (0.01 mM) or high (10 mM) Ca2+ concentrations for 2 or 12h.

2011-01-03 | GSE19854 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data