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Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [RNA-seq]

ABSTRACT: Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [RNA-seq]

PROVIDER: PRJNA1227540 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32472924_1.fastq.gz	Fastqsanger.gz
	SRR32472924_2.fastq.gz	Fastqsanger.gz
	SRR32472925_1.fastq.gz	Fastqsanger.gz
	SRR32472925_2.fastq.gz	Fastqsanger.gz
	SRR32472926_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [scRNA-seq]

Project description:Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [scRNA-seq]

| PRJNA1224788 | ENA

Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [scRNA-seq]

Project description:Human induced pluripotent stem cells (hiPSCs) hold significant potential for advancing our understanding of heart development. Differentiating hiPSCs into cardiac cells allows for modeling early cardiac developmental processes and exploring key signaling pathways. However, variations in differentiation efficiency and poor reproducibility of hiPSC-derived cardiomyocytes (hiPSC-CMs) production have remained a challenge. Here, we report a unique metabolic method to promote hiPSC-CM differentiation that involves marked suppression of the mitochondrial oxidative phosphorylation from the mesendoderm to the cardiac mesoderm, which is regulated by PHGDH, a rate-limiting enzyme in the serine synthesis pathway (SSP). Mechanistically, the analysis of scRNA-seq revealed that SSP inhibition promotes CM lineage differentiation by disrupting the cardiopharyngeal mesoderm lineage differentiation. Our findings show that SSP can regulate cardiac differentiation and have implications in elucidating the potential mechanisms of heart development and pathogenesis of heart disease.

2025-05-24 | GSE289789 | GEO

Serine synthesis pathway regulates cardiac differentiation from human pluripotent stem cells [RNA-seq]

Project description:Differences of metabolism-related gene expression profiles in human pluripotent stem cells (hPSCs) and hPSC-derived cardiomyocytes (hPSC-CMs) were analyzed and successfully identified.

2025-05-24 | GSE290355 | GEO

PHGDH Arginine Methylation by PRMT1 Promotes Serine Synthesis and Represents a Therapeutic Vulnerability in Hepatocellular Carcinoma

Project description:Serine synthesis is crucial for tumor growth and survival, but its regulatory mechanism in cancer remains elusive. Here, using integrative metabolomics and transcriptomics analyses, we show a heterogeneity between metabolite and transcript profiles. Specifically, the level of serine in HCC tissues is increased, whereas the expression of phosphoglycerate dehydrogenase (PHGDH), the first rate-limiting enzyme in serine biosynthesis pathway, is dramatically downregulated. Interestingly, the increased serine level is obtained by enhanced PHGDH catalytic activity due to protein arginine methyltransferase 1 (PRMT1)-mediated methylation of PHGDH at arginine 236. PRMT1-mediated PHGDH methylation and activation potentiates serine synthesis, ameliorates oxidative stress, and promotes HCC growth in vitro and in vivo. FBXO7, an E3 ubiquitin ligase which is downregulated in human HCC tissues, ubiquitinates and downregulates PRMT1 to suppress PHGDH methylation and serine synthesis, leading to the inhibition of HCC cell growth. Furthermore, PRMT1-mediated PHGDH methylation correlates with PHGDH hyperactivation and serine accumulation in human HCC tissues, and is predictive of poor prognosis of HCC patients. Notably, blocking PHGDH methylation with a TAT-tagged non-methylated peptide inhibits serine synthesis and restrains HCC growth, both in an HCC patient-derived xenograft (PDX) model and subcutaneous HCC cell-derived xenograft model. Overall, our findings reveal a novel regulatory mechanism of PHGDH activity and serine synthesis, and suggest PHGDH methylation as a potential therapeutic vulnerability in HCC.

2022-07-11 | GSE207435 | GEO

Phosphoglycerate mutase regulates Treg differentiation through control of serine synthesis and one-carbon metabolism

Project description:The differentiation and suppressive functions of regulatory CD4 T cells (Tregs) are supported by a broad array of metabolic changes, providing potential therapeutic targets for immune modulation. In this study, we focused on the regulatory role of glycolytic enzymes in Tregs and identified phosphoglycerate mutase (PGAM) as being differentially overexpressed in Tregs and associated with a highly suppressive phenotype. Pharmacologic or genetic inhibition of PGAM reduced Treg differentiation and suppressive function while reciprocally inducing markers of a pro-inflammatory, T helper 17 (Th17)-like state. The regulatory role of PGAM was dependent on the contribution of 3-phosphoglycerate (3PG), the PGAM substrate, to de novo serine synthesis. Blocking de novo serine synthesis from 3PG reversed the effect of PGAM inhibition on Treg polarization, while exogenous serine directly inhibited Treg polarization. Addi-tionally, altering serine levels in vivo with a serine/glycine-free diet increased peripheral Tregs and at-tenuated autoimmunity in a murine model of multiple sclerosis. Mechanistically, we found that serine limits Treg polarization by contributing to one-carbon metabolism and methylation of Treg-associated genes. Inhibiting one-carbon metabolism increased Treg polarization and suppressive function both in vitro and in vivo in a murine model of autoimmune colitis. Our study identifies a novel physiologic role for PGAM and highlights the metabolic interconnectivity between glycolysis, serine synthesis, one-car-bon metabolism, and epigenetic regulation of Treg differentiation and suppressive function

2025-06-06 | GSE269846 | GEO

PHGDH Arginine Methylation by PRMT1 Promotes Serine Synthesis and HCC Growth

Project description:Serine synthesis is crucial for tumor growth and survival, but its regulatory mechanism in cancer remains elusive. Phosphoglycerate dehydrogenase (PHGDH) is the first rate-limiting enzyme in serine biosynthesis pathway. Here, we analyzed immunoprecipitated PHGDH from human HEK293T cells by liquid chromatography tandem mass spectrometry (LC-MS/MS), and identified the potential interacting proteins of PHGDH.

2022-07-29 | PXD035287 |

FBXO7 Ubiquitinates PRMT1 to Suppress Serine Synthesis and Tumor Growth in HCC

Project description:Cancer cells are often addicted to de novo serine synthesis to support their survival and rapid proliferation. However, how serine synthesis is regulated in cancer is not well understood. Our recent report demonstrated that protein arginine methyltransferase 1 (PRMT1) is upregulated in hepatocellular carcinoma (HCC) and methylates phosphoglycerate dehydrogenase (PHGDH, the first and rate-limiting enzyme in serine synthesis) at arginine 236, thereby activating PHGDH and promoting serine synthesis. Nevertheless, the mechanisms underlying upregulation of PRMT1 and regulation of PRMT1-PHGDH axis in HCC remain unknown. Here, using label-free quantitative proteomics analysis, we identified the potential interacting proteins of PRMT1.

2024-02-01 | PXD049069 |

Mutant p53 regulates serine-glycine synthesis and essential amino acids intake

Project description:Mutant p53 regulates serine-glycine synthesis and essential amino acids intake

| PRJNA885512 | ENA

Gene Regulation by ATF3 in response to serine deprivation

Project description:The goal of this study is to identify genes that are regulated by activiating transcription factor (ATF3) in the cellular response to serine deprivation. Serine biosynthesis is crucial for cancer cells to proliferate and survival under serine-limiting conditions. We found that ATF3 expression induced by serine deprivation supports cancer cell growth. This RNA-seq study is thus designed to understand how ATF3 regulates serine biosynthesis in cells. The results indicate that ATF3 regulates the genes involved in the serine synthesis pathway.

2021-11-09 | GSE164850 | GEO

Hotspot mutations induce metabolic reprogramming and vulnerability to serine deprivation

Project description:Cancer-associated mutations in the spliceosome gene create a neomorphic protein that produces aberrant mRNA splicing in hundreds of genes, but the ensuing biologic and therapeutic consequences of this missplicing are not well understood. Here we provide evidence that aberrant splicing by mutant alters the transcriptome, proteome, and metabolome of human cells, leading to missplicing-associated downregulation of metabolic genes, decreased mitochondrial respiration, and suppression of the serine synthesis pathway. We also find that mutant induces vulnerability to deprivation of the nonessential amino acid serine, which is mediated by missplicing-associated downregulation of the serine synthesis pathway enzyme PHGDH. This vulnerability is manifest both in vitro and in vivo, as dietary restriction of serine and glycine in mice is able to inhibit the growth ofMUT xenografts. These findings describe a novel role for mutations in altered energy metabolism, and they offer a new therapeutic strategy againstMUT cancers.

2019-12-31 | GSE134475 | GEO

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