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RNA-seq on human muscle progenitor cells cultured with (1000 uM) or without serine and glycine

ABSTRACT: To determine the transcriptional response to serine and glycine deprivation in human muscle progenitor cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE161357 | GEO | 2020/11/13

REPOSITORIES: GEO

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RNA-seq on human muscle progenitor cells cultured with (1000 uM) or without serine and glycine

Project description:RNA-seq on human muscle progenitor cells cultured with (1000 uM) or without serine and glycine

| PRJNA677950 | ENA

Expression data of peritoneal macrophages from Wild-type mouse cultured in control or serine/glycine-depleted medium.

Project description:Activation of signaling pathways downstream of Toll-like receptor 4 upregulate expression of genes related to serine metabolism. We cultured peritoneal macrophages in control or serine/glycine-depleted medium for 24 hr, stimulated them with LPS (10 ng/ml) for 6 or 12 hr, and collected them to compare the gene expression. Microarray analysis revealed that serine/glycine-depletion in peritoneal macrophages upregulates gene expression of enzymes for serine biosynthesis.

2021-03-31 | GSE156325 | GEO

Exogenous and endogenous serine modulate polarization of tumor-associated macrophages to influence development of nasopharyngeal carcinoma

Project description:To investigate the global gene expression pattern in response to removal of exogenous serine/glycine from the medium, RNA-seq was performed using C666-1 cells cultured in CM or -SG medium for 24 h. The volcano plot exhibited 60 up-regulated and 123 down-regulated genes in C666-1 cells subjected to exogenous serine/glycine deprivation.

2024-04-09 | GSE263382 | GEO

RNA seq of MLL-ENL transformed cells under serine/glycine starvation including a starvation resistant clone

Project description:Primary hematopoietic cells were transformed by retrovirally transduced MLL-ENL. The resulting cell population was either cultured in full medium or under starvation conditions without serine and glycine. In addition a spontaneously arising ser/gly starvation resistant clone was included in this experiment. Nascent RNA was isolated by labeling cells for 1h with 4-thio-uridine and subsequent biotinylation of labeled RNA followed by streptavidin chromatography as described in Garcia-Cuellar et al. CellReports S22111247(16)30259-5.

2021-06-21 | E-MTAB-8738 | biostudies-arrayexpress

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

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.

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Expression data from brain tissue of Rattus norvegicus treated with D-Serine

Project description:d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. Affymetrix microarray technology was used to determine differential gene expression resulting from D-Serine exposure. Keywords: Dose course Male Fisher 344 rats aged 11-12 weeks were treated with various doses (0, 5, 20, 50, 200 and 500 mg/kg) of d-serine and terminally sacrificed 96 hours post-exposure. An approximate 30mg-section of the forebrain was processed for total RNA isolation.

2008-03-08 | E-GEOD-10748 | biostudies-arrayexpress

Raw data for manuscript : "Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD"

Project description:Metabolic dysfunction-associated steatotic liver disease (MASLD) affects one third of the global population. Understanding metabolic pathways involved can provide insights into disease progression and treatment. Untargeted metabolomics of livers from mice with early-stage steatosis uncovered decreased methylated metabolites, suggesting altered one-carbon metabolism. The levels of glycine, a central component of one-carbon metabolism, were lower in mice with hepatic steatosis, consistent with clinical evidence. Stable-isotope tracing demonstrated that increased serine synthesis from glycine via reverse serine hydroxymethyltransferase (SHMT) is the underlying cause for decreased glycine in steatotic livers. Consequently, limited glycine availability in steatotic livers impaired glutathione synthesis under acetaminophen-induced oxidative stress, enhancing acute hepatotoxicity. Glycine supplementation or hepatocyte-specific ablation of the mitochondrial SHMT2 isoform in mice with hepatic steatosis mitigated acetaminophen-induced hepatotoxicity by supporting de novo glutathione synthesis. Thus, early metabolic changes in MASLD that limit glycine availability sensitize mice to xenobiotics even at the reversible stage of this disease.

2023-12-12 | MSV000093653 | MassIVE

Glycine decarboxylase is a metabolic oncogene critical for tumor initiating cells and tumorigenesis in lung cancer

Project description:New approaches to cancer therapies could benefit from a better understanding of the molecular determinants critical to tumor initiating cells (TICs). Here we show that the metabolic enzyme glycine decarboxylase (GLDC) is critical for TICs in non-small cell lung cancer (NSCLC). From a broad range of primary NSCLC tumors, we isolated CD166+ lung TICs that consistently initiated tumorigenesis in NOD/SCID Il2rγ-/- mice. Lung TICs express high levels of the oncogenic stem cell factor LIN28B and the metabolic enzyme GLDC. Over-expression of GLDC and other glycine/serine metabolism enzymes, but not catalytically inactive GLDC, promotes cellular transformation and tumorigenesis. Metabolomic analysis found that GLDC induces dramatic changes in glycolysis and glycine/serine metabolism, leading to changes in pyrimidine metabolism to regulate cancer cell proliferation. Clinically, GLDC over-expression, observed in multiple cancer types, predicts poorer survival in lung cancer patients. Our findings establish a novel link between glycine metabolism and tumorigenesis, and provide novel targets for advancing anti-cancer therapy. Total RNA obtained from tumor sphere compared to CD166+ and CD166- selected cells of xenograft, primary tumor and normal donors

2011-10-25 | E-GEOD-33198 | biostudies-arrayexpress

Expression data from brain tissue of Rattus norvegicus treated with D-Serine

2008-03-08 | GSE10748 | GEO

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