CRISPR/Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE195484 | GEO | 2022/02/26
REPOSITORIES: GEO
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Project description:Although organ hypofunction and immunosuppression are life-threatening features of severe sepsis, the hypofunctioning organs and immune cells usually regain normal functionality if patients survive. We tested the hypothesis that low extracellular pH (pHe) can induce reversible metabolic and functional changes in tissue macrophages. When compared with macrophages cultured at normal pHe, macrophages living in an acidic medium used less glucose and exogenous fatty acid to produce ATP. Lactate, glutamine, and de novo synthesized fatty acids supported ATP production by mitochondria that gained greater mass, maximal oxygen consumption rate, and spare respiratory capacity. The cells transitioned to a M2-like state, with altered immune responses to LPS and slightly decreased phagocytic ability, yet they regained basal energy production, normal mitochondrial function and pro-inflammatory responsiveness when neutral pHe was restored. Low pHe induces changes that support macrophage survival while rendering the cells less pro-inflammatory (more ‘tolerant’) and less able to phagocytose bacteria. Macrophage responses to low interstitial pH may contribute to the reversible organ hypofunction and immunoparalysis noted in many patients with sepsis.
2021-04-15 | GSE164697 | GEO
Project description:Many solid tumors grow slowly, with an average volume doubling time of several months to multiple years. Yet, most studies to date have focused mainly on the short-term fate of cancerous cells upon exposure to acidic pHe (extracellular pH), a common hallmark of tumor microenvironment. Little is known about how solid tumors, such as intractable PDAC originated from pancreatic ductal cells that secrete alkaline fluids, evolve to tolerate and adapt to the sustained and prolonged exposure of acidic pHe stress. We established a series of PDAC tumor cells exposed to prolonged periods of extracellular acidification. These biological materials were further subjected to microarray analysis to detail the genome-wide gene expression profiles and to identify the differential expressed genes related to the long-term adaptation of PDAC tumor cells to the extracellular chronic acidosis stress.
2022-04-20 | GSE180043 | GEO
Project description:This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification. Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. STAT3 associates with the vacuolar H+-ATPase on lysosomal membranes in a coiled coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing and increasing cytosolic and lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild type STAT3 as well as STAT3 mutants unable to activate target genes (Tyr-705-Phe and DNA binding mutant) or to regulate mitochondrial respiration (Ser-727-Ala). Upon cytosolic acidification, phospho-Tyr-705-STAT3 is rapidly dephosphorylated, transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium and to enhance cell survival. These data reveal STAT3 as a regulator of intracellular pH, and vice versa intracellular pH as a regulator of STAT3 localization and activity.
2018-01-03 | GSE108495 | GEO
Project description:Extracellular pH (pHe) is lower in many tumors than in the corresponding normal tissue. Acidic tumor microenvironment has been shown to facilitate epithelial mesenchymal transition (EMT) and tumor metastasis, while the mechanisms underlying tumor acidic microenvironment-induced tumor cell metastasis remain undefined. Here, we aimed to investigate the tumor metastasis and the EMT by acidic microenvironment and to explore their mechanisms and clinical significance in lung cancer. Results showed that acidic pHe remarkably enhanced invasion ability of lung cells accompanying with increased mesenchymal and decreased epithelial markers. Moreover, acidic pHe triggered the inhibition of microRNA-7 (miR-7) expression and activation of TGF-β2/SMAD signaling. Mechanistic studies showed that TGF-β2 is a direct potential target gene of miR-7, and acidity-induced metastasis could be abolished by treatment with a TGFβRI inhibitor, anti-TGF-β2 antibody and miR-7 mimic, respectively. The clinical samples further revealed that miR-7 was decreased in lung tissues and antagonistically correlated with TGF-β2 expression, associating with overall survival and metastasis. In conclusion, our study indicated that acidic pHe showed enhanced invasive potential, and enhanced potential to develop experimental metastases by a novel mechanism involving tumor acidic microenvironment-induced regulation of miR-7/TGF-β2/SMAD axis. Our findings suggest that the possibility that pHe of the primary tumor may be an important prognostic parameter for lung cancer patients merit clinical investigation. Moreover, miR-7 may serve as prognostic molecular marker and a novel therapeutic target for lung cancer.
2022-04-01 | PXD016524 | Pride
Project description:Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low soil pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic or physiological basis of acid tolerance about gene expression under acidic conditions. To identify genes responding to pH stress we studied the transcriptomes of cells grown under different pH conditions. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 minutes at pH 4.5. Transcriptomes were determined by RNA-Seq. From a total of 6289 protein-coding genes, 383 were found to be differentially expressed under acidic conditions versus control, among which 351 were induced and 32 repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, but also enzymes involved in amino acid and carbohydrate metabolism and proton extrusion. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.
2018-05-17 | GSE108074 | GEO
Project description:In order to cause disease, the food- and water-borne pathogen Campylobacter jejuni must face the extreme acidity of the host stomach as well as cope with pH fluctuations in the intestine. In the present study, C. jejuni NCTC 11168 was grown under mild acidic conditions mimicking those encountered in the intestine. The resulting transcriptional profiles revealed how this bacterium fine-tunes gene expression in response to acid stress. This adaptation involves differential expression of respiratory pathways, induction of genes for phosphate transport and repression of energy generation and intermediary metabolism genes. Keywords: acid shock; dose response; transcriptional response to 3 mild-acidic pH growth conditions (pH6.5, pH 6.0 and pH5.0)
2008-01-21 | GSE9920 | GEO
Project description:To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH 2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains. To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ delta cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains
2011-01-10 | GSE24267 | GEO
Project description:Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment. We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation. Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB. Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism. To use RNA-seq to analyze the transcriptome patterns under acid stress
2015-04-16 | E-GEOD-67925 | biostudies-arrayexpress
Project description:Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment. We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation. Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB. Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism.
2015-04-16 | GSE67925 | GEO
Project description:To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH 2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains. To examine the role of a glycosylphosphatidylinositol-linked aspartyl protease, CgYps1, in the regulation of pH homeostasis in Candida glabrata, transcriptional profiling analysis was carried out on wild-type and Cgyps1∆ delta cells grown in YNB medium (pH 5.5) and in YNB medium adjusted to pH2.0. Genes involved in carbohydrate and amino acid metabolism, protein folding and stress response pathways were found to be differentially regulated in response to acidic environment in both the strains Agilent one-color experiment,Organism: Yeast ,Agilent-026378 Genotypic designed Custom Candida glabrata 8x15k , Labeling kit: Agilent Quick-Amp labeling
2011-01-10 | E-GEOD-24267 | biostudies-arrayexpress