Next Generation RNA Sequencing Analysis of AMPK Wild Type, AMPKα-KO and AMPKα1-2A U2OS cell Transcriptomes
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ABSTRACT:
PROVIDER: PRJNA579161 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10336239_1.fastq.gz | Fastqsanger.gz | |||
| SRR10336239_2.fastq.gz | Fastqsanger.gz | |||
| SRR10336240_1.fastq.gz | Fastqsanger.gz | |||
| SRR10336240_2.fastq.gz | Fastqsanger.gz | |||
| SRR10336241_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are to compare NGS-derived U2OS transcriptome profiling (RNA-seq) To get insight into the downstream signaling of AMPK and to evaluate protocols for optimal high-throughput data analysis Methods: RNA was extracted by using the Direct-zol™ RNA Miniprep Plus Kit (Zymo Research) and evaluated the purity and concentration of the RNA by ultraviolet spectroscopy (NanoDrop). RNA integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer. RNA sequencing libraries were constructed using 1000 ng of total RNA from each sample and the TruSeqV2 kit from Illumina following manufacturer’s protocol. Illumina NextSeq sequencing and NGS data acquisition were conducted at the UNMC Genomics Core Facility. The libraries were subjected to 75 bp paired-end high-output sequencing using a NextSeq500 sequencer to generate approximately 33.3 to 41.6 million reads per sample. Fastq files were generated using the bc12fastq software, version 1.8.4 and provided to the UNMC Bioinformatics Core facility for further analysis. The original fastq format reads were trimmed and filtered using the fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30). The trimmed fastq files were processed by our facility’s newly developed standard pipeline utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels. TPM values were used for comparison results (student’s t-test) for all the available genes. The Benjamini-Hochberg (BH) adjusted p values were also provided to adjust for multiple testing-caused false discovery rate (FDR) with significant level of adjusted p value of ≤ 0.05. Comparative analysis of parental U2OS (control) vs. AMPKα-KO and control vs. AMPKα1-2A was performed using Ingenuity Pathway Analysis (IPA) to examine canonical pathways similarly altered in each to designate effects due to dysregulation of CDK1 phosphosites. Results: Comparative analysis of parental U2OS (control) vs. AMPKα-KO and control vs. AMPKα1-2A was performed using Ingenuity Pathway Analysis (IPA) to examine canonical pathways similarly altered in each to designate effects due to dysregulation of CDK1 phosphosites. Canonical pathways influencing actin dynamics such as actin cytoskeleton signaling, ILK signaling, and regulation of actin-based motility by Rho were predicted to be significantly activated. The expression of a multitude of genes involved in promoting cellular movement and migration were increased and several inhibitors of cell movement were diminished in AMPKα-KO and α1-2A cells compared to controls. By examining alterations of downstream gene expression, upstream analysis pinpointed numerous possible upstream regulators. Most of the highestscoring upstream effectors were analogously modulated between AMPKα-KO and α1-2A compared to controls, indicating that loss of phosphorylation of AMPK by CDK1 is comparable to AMPK knockout for alterations seen in these particular pathways. We previously detected stark reduction of p-Histone H3 (S10) in both the AMPKα-KO and α1-2A cells, which led to speculate that this was possibly due to either phosphatase dysregulation leading to hyperdephosphorylation, or perturbation of kinase signaling leading to inadequate phosphorylation of Histone H3. Interestingly, there were eight significantly up- or down-regulated phosphatases found to be changed mutually between the AMPKα-KO and α1-2A cells compared to controls. Furthermore, between the two treatments, the expression levels of ten kinases and two mitosis-associated kinases significantly changed compared to controls. Conclusions: Our study represents the first detailed analysis of AMPK Wild Type, AMPKα-KO and AMPKα1-2A U2OS cell Transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that that CDK1 regulates AMPK control of mitotic entry and progression. It remains to be determined which signaling networks or processes CDK1-phosphorylated AMPK utilizes to drive these events.
2019-10-24 | GSE139293 | GEO
Project description:Proopiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus (ARC) play a critical role in energy homeostasis. 5’-adenosine monophosphate-activated protein kinase (AMPK) is a serine/threonine kinase, which acts as a main energy sensor in the cell. The heterotrimeric AMPK results from the combination of a catalytic α subunit (α1, α2) with two regulatory subunits, β (β1, β2) and γ (γ1, γ2 and γ3). Hypothalamic AMPK plays a key role in the control of energy balance, but current evidence shows that the precise combination of its heterotrimeric components determines its physiological action. This makes necessary the study of the role of the different subunits in a cell-specific manner. Our findings show that AMPKα1 ablation in POMC neurons has a protective effect over diet-induced obesity because of increased thermogenesis in brown adipose tissue (BAT). At the molecular level, deletion of AMPKα1 in POMC neurons disrupts the ARC phosphoproteome and is associated with an ameliorated endoplasmic reticulum (ER) stress. These findings highlight the complex function of the different AMPK subunits in the hypothalamic regulation of energy balance.
2026-06-30 | PXD068034 | Pride
Project description:In non-small cell lung cancer the role of AMPKα is controversial and its contribution to lung carcinogenesis is not well-defined. To shed light on the molecular mechanisms through which AMPKα could be involved in lung tumorigenesis, we analysed by RNA-sequencing the whole transcriptome upon AMPKα1, AMPKα2 or AMPKα1/α2 knockdown (KD). Furthermore, it remains largely unknown whether long non-coding RNAs (lncRNAs) are involved in the regulation of AMPKα-mediated pathways. Therefore, we examined the lncRNA expression profile and searched for lncRNAs differentially expressed in the same conditions (AMPKα1, AMPKα2 or AMPKα1/α2 KD versus control) in H1299 cells.
2021-05-26 | GSE165843 | GEO
Project description:Metabolic reprogramming controls protective or pathogenic Th17 cell responses; still, the precise molecular pathways that drive distinct immunometabolic states remain elusive. Here, we demonstrate that non-pathogenic Th17 cells induced by the immunoregulatory cytokine activin- A display reduced aerobic glycolysis and increased oxidative phosphorylation (OXPHOS). Notably, signaling through the adenosine A 2A receptor (A 2A R)/AMP-activated protein kinase (AMPK) axis in response to activin-A, boosts OXPHOS and reprograms pathogenic Th17 cells towards non-pathogenic states. Epigenetic studies revealed that pathogenic Th17 cells express highly the CBP/P300 binding protein (PCAF) which facilitates the acetylation of histone 3 at lysine 9 (H3K9ac) at genes related to the mammalian target of rapamycin complex 1 (mTORC1), glycolysis and Th17 pathogenicity programs. Instead, activin-A-treated Th17 cells display an AMPK-mediated suppression of PCAF activity and aerobic metabolism while, accumulate H3K9ac in gene loci related to OXPHOS. Collectively, we uncover A 2A R-AMPK as a central metabolic checkpoint that epigenetically regulates Th17 pathogenicity.
2025-09-27 | GSE284714 | GEO
Project description:Tendon healing is limited by the minimal intrinsic regenerative capacity of the tissue, resulting in the formation of fibrovascular scar tissue rather than functional regeneration. Macrophage immunometabolism governs the balance between inflammation and repair; however, its effects on tendon regeneration are poorly understood. In this study, we investigated the differential activation of macrophage AMP-activated protein kinase (AMPK) and its phenotypic alterations in neonatal and adult tendon injury models. Using myeloid-specific AMPKα1 knockout (LysM-Cre; Ampkα1fl/fl) mice, we found that macrophage AMPKα1 deficiency impairs tendon regeneration and repair capacity, leading to compromised proliferation, migration, and differentiation functions of tendon stem/progenitor cells (TSPCs). Mechanistically, AMPKα1-deficient macrophages exhibited increased TNF-α production, which promoted the expression of Fructose-bisphosphatase 2 (FBP2) in a PI3K/AKT-dependent manner. In addition, knockdown of Fbp2 rescued mitochondrial dysfunction in TSPCs and facilitated tissue repair and regeneration. Collectively, these findings underscore the immunometabolism mechanism linking macrophage AMPKα1 activity to stem cell injury responses via a TNF-α–FBP2 axis and provide potential therapeutic targets for regulating stem cells.
2026-02-18 | GSE314597 | GEO
Project description:Background Worldwide, gastric cancer is the fourth most common malignancy and the most common cancer in East Asia. Development of targeted therapies for this disease has focused on a few known oncogenes but has had limited effects. Objective To determine oncogenic mechanisms and novel therapeutic targets specific for gastric cancer by identifying commonly dys-regulated genes from the tumors of both Asian-Pacific and Caucasian patients. Design We generated transcriptomic profiles of 22 Caucasian gastric cancer tumors and their matched non-cancerous samples, and performed an integrative analysis across different gastric cancer gene expression datasets. We examined the inhibition of commonly overexpressed oncogenes and their constituent signaling pathways by RNAi and/or pharmacologic inhibition. Results We found that HNF4α upregulation was a key signaling event in gastric tumors from both Caucasian and Asian patients, and HNF4α antagonism was antineoplastic. Perturbation experiments in GC tumor cell lines and xenograft models further demonstrated that HNF4α is downregulated by AMPKα signaling and the AMPK agonist metformin; blockade of HNF4α activity resulted in cyclin downregulation, cell cycle arrest, and tumor growth inhibition. HNF4α also regulated WNT signaling through its target gene WNT5A, a potential prognostic marker of diffuse type gastric tumors. Conclusions Our results indicate that HNF4α is a targetable oncoprotein in gastric cancer, is regulated by AMPK signaling through AMPKα, and resides upstream of WNT signaling. HNF4α may regulate “metabolic switch” characteristic of a general malignant phenotype and its target WNT5A has potential prognostic values. The AMPKα-HNF4α-WNT5A signaling cascade represents a potentially targetable pathway for drug development. Integrative analysis of Caucasian and Asian-Pacific gastric tumor expression datasets (including newly generated transcriptomic profiling of 22 tumors in this study) revealed a relatively small common sets of highly overexpressed genes.
2014-11-15 | E-GEOD-63288 | biostudies-arrayexpress
Project description:BHLHE40 is a basic helix-loop-helix transcription factor that is involved in multiple cell activities including differentiation, cell cycle, and epithelial-to-mesenchymal transition. While there is growing evidence to support the functions of BHLHE40 in energy metabolism, little is known about the mechanism. In this study, we found that BHLHE40 expression was downregulated in cases of endometrial cancer of higher grade and advanced disease. Knockdown of BHLHE40 in endometrial cancer cells resulted in suppressed oxygen consumption and enhanced extracellular acidification. Suppressed pyruvate dehydrogenase (PDH) activity and enhanced lactated dehydrogenase (LDH) activity was observed in the knockdown cells. Knockdown of BHLHE40 also led to dephosphorylation of AMPKα Thr172 and enhanced phosphorylation of PDHA1 Ser293 and LDHA Tyr10. These results suggested that BHLHE40 modulates PDH and LDH activity by regulating the phosphorylation status of PDHA1 and LDHA. We found that BHLHE40 enhanced AMPKα phosphorylation by directly suppressing the transcription of an AMPKα-specific phosphatase, PPM1F. Our immunohistochemical study showed that the expression of BHLHE40, PPM1F, and phosphorylated AMPKα correlated with the prognosis of endometrial cancer patients. Because AMPK is a central regulator of energy metabolism in cancer cells, targeting the BHLHE40‒PPM1F‒AMPK axis may represent a strategy to control cancer development.
2023-09-04 | GSE241941 | GEO
Project description:Purpose: Mutations in STK11 (LKB1) occur in 17% of lung adenocarcinoma (LUAD) and drive a suppressive (cold) tumor immune microenvironment (TME) and resistance to immunotherapy. The mechanisms underpin the establishment and maintenance of a cold TME in LKB1 mutant LUAD remain poorly understood and the identification of downstream effectors is critical to inform therapeutic strategies to invigorate antitumor immunity. In this study, we investigated the association between inactivation of AMPK, one of the downstream substrates of LKB1, and immune evasion in human LUAD as well as the causal role of AMPK on TME in genetically engineered mouse model (GEMM) of LUAD. Experimental Design: We modeled AMPK inactivation in vivo using GEMM by deleting both AMPKα1 (Prkaa1) and AMPKα2 (Prkaa2) in KrasG12D-driven LUAD (KAA). Furthermore, we investigated the impact of AMPK inactivation on immune cell infiltration and global gene-expression programs of murine LUAD. Gene expression signature from AMPK-deficient murine LUAD was further compared to that of Lkb1 deficient murineLUAD as well as human LUAD with either LKB1 mutation or attenuated AMPK phosphorylation. Results: Inactivation of both AMPKα1 and AMPKα2 accelerates KrasG12D-driven LUAD. AMPK-deficient tumors are characterized with reduced infiltration of CD8+/CD4+ T cells and gene signatures associated with compromised immune microenvironment, which resembles LKB1-deficient murine and human LUAD (KL) as well as LKB1-wildtype LUAD with reduced AMPK phosphorylation. Attenuation of the MHC Class 1 component ß2 microglobulin (ß2M) was identified as a shared feature in KL and KAA murine LUAD as well as in human LUAD with either LKB1 mutations or reduced AMPK phosphorylation. Furthermore, reactivation of AMPK by expression of constitutive active form of AMPKα1 leads to restoration of ß2M level in LKB1 mutant LUAD cells. Conclusions: The results identify attenuation of the LKB1 substrate AMPK as an important mechanism for decreased MHC Class 1 expression and immune evasion in LKB1 mutant LUAD. Translational relevance: LKB1 loss-of-function mutations rank as the third most common genetic alterations found in lung adenocarcinoma and associated with immune evasion. In the current study, on the basis of GEMM of LUAD we established the causal relationship between inactivation of the LKB1 substrate AMPK and immune evasion. Furthermore we find that the status of AMPK phosphorylation is more sensitive than LKB1 mutation in predicting impaired tumor immune microenvironment and likely also for the resistance to immunotherapy. The results also suggest that restoration of AMPK activity could increase the number of patients benefiting from immunotherapy.
2022-01-26 | GSE175479 | GEO
Project description:Existing controversy regarding the importance of AMP-activated protein kinase (AMPK) in fatty acid (FA) oxidation in skeletal muscle with contraction/exercise may to some extent pertain to redundant AMPKα1 signaling. Using a mouse model lacking both AMPKα1 and -α2 in skeletal muscle specifically (mdKO) we hypothesized that FA utilization would be impaired in skeletal muscle. Calorimetric analysis showed a similar respiratory exchange ratio (RER) of AMPKα WT and mdKO mice when fed normal chow, a high fat diet or with prolonged fasting. Though, in vivo treadmill exercise at the same relative intensity induced a higher RER in mdKO mice compared to WT (WT=0.81; mdKO=0.87; p<0.01) indicating a decreased utilization of FA. Ex vivo incubation of soleus muscle revealed that basal and contraction-induced FA oxidation was impaired in mdKO mice, suggesting that the increased RER during in vivo running exercise originated from decreased skeletal muscle FA oxidation. A decreased muscle protein expression of CD36 and FABPpm (by 17-40%) together with abolishment of TBC1D1 Ser237 phosphorylation in mdKO mice, may result in lower FA transport capacity and FA transport protein translocation to sarcolemma, respectively. In summary this study shows that the catalytically active AMPKα subunits are required for normal stimulation of FA utilization during exercise and contractions.
2015-09-30 | GSE61904 | GEO
Project description:Myofibroblasts (MFs) are crucial components of the fibrotic remodeling after myocardial infarction (MI). We have previously demonstrated the centrality of AMPKα1 in post-MI remodeling. Here, we investigate the effects of MF-specific deletion of AMPKα1 on left ventricular (LV) adaptation following MI, and the underlying molecular mechanisms. Importantly, MF-restricted AMPKα1 conditional knockout (cKO) hearts exhibit exacerbated post-MI adverse LV remodeling and are characterized by exaggerated fibrotic response, compared to wild-type (WT) hearts. Myofibroblast proliferation significantly increases in cKO infarcted hearts, coincident with a significant reduction of Connexin 43 (Cx43) expression in MFs. Mechanistically, lack of AMPKα1 in MFs enhances miR-125b expression, which, in turn, downregulates Cx43. Collectively, our data demonstrate a cardinal role for MF-AMPKα1 in cardiac remodeling, as its lineage-specific inactivation accentuates fibrosis and LV dilatation following MI. The deleterious effects of MF-specific AMPKα1 deletion are mediated via Cx43, and its post-transcriptional regulation by miR-125b.
2020-03-25 | GSE147470 | GEO