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RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

ABSTRACT: Purpose: Detailed exploration of de novo Fatty Acid Synthesis (DNFA) transcription regulation and clinical relevance in melanomas. This study was designed to achieve the following goals: 1) determine the impact of SREBP1 depletion on gene expression in metastatic melanoma cells; 2) determine the specificity of ASO and other reagents inhibiting SREBF1 mRNA. Method: RNA-Seq was performed after culture with control and various SREBF1-depleting agents, including pooled siRNAs and individual ASOs, in HT-144 cells. Results: using STAR, we mapped about 2 X 4 million pair-end sequence reads per sample to the human genome (build GRCh38.94) and identified around 2 million annotated transcripts per sample.

ORGANISM(S): Homo sapiens

PROVIDER: GSE122707 | GEO | 2018/11/20

REPOSITORIES: GEO

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RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

Project description:RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

| PRJNA506045 | ENA

CREB regulated transcriptional coactivator 2 proteome landscape is plausibly modulated by SREBF1

Project description:CRTC2 is a critical transcription cofactor that induces the glucose homeostatic genes by activating CREB. However, energy homeostasis is maintained by multiple pathways, therefore, it is possible that CRTC2 may interact with other transcription factors, especially under metabolic stress. Thereby, CRTC2 liver-specific knockout mice were created and the global proteome, phosphoproteome and acetylome from liver tissue under the high fat diet conditions were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. As expected, differentially expressed proteins (DEPs) are enriched in metabolic pathways that were subsequently corroborated by animal experiments. The consensus DEPs from these datasets were used as seed proteins to generate a protein-protein interaction (PPI) network using STRING and GeneMANIA identified fatty acid synthase (FASN) as the mutually relevant protein. Additional local-PPI (LPPI) analysis of CRTC2 and FASN with DEPs, SREBF1 was found to be a common mediator. CRTC2/CREB and SREBF1 are transcription factors, DNA-binding motif analysis showed multiple CRTC2/CREB regulated genes also possess SREBF1 binding motifs that unveil the possible induction by CRTC2/SREBF1 complex, which is reinforced by structural analysis. Thus, CRTC2/SREBF1 complex plausibly modulate the transcription of multiple proteins that fine-tune the cellular metabolism under metabolic stress.

2023-10-24 | PXD039817 | Pride

Srebf1-mediated fatty acid metabolism is crucial to sustain sugmented pigmentation SREBF1-mediated metabolic reprogramming through fatty acid metabolism sustains augmented melanogenesis

Project description:Methods: mRNA profiles of B16 mouse melanoma cell line during pigmentation induced by culturing at low density were generated by deep sequencing, in dublicate. Library preparation was done using trueseq 4000 for quencing on Illumina paired end sequencing. The sequence read that passed the quality filter were aligned with GRCm38 as reference genome. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample and identified 18753 transcripts in the pigmenting B16 melanocytes from D3 to D7 using HTSeq tool. R-values from Corelation plot varies from 0.98-0.99 between two replicates for different days.

2022-04-19 | GSE164375 | GEO

Transcriptome analysis of SREBF1 silencing and overexpression in thyroid cancer cells

Project description:Malignant thyroid tumors have altered lipid metabolism. Sterol regulatory element-binding transcription factor 1 (SREBF1), also known as sterol regulatory element-binding protein 1 (SREBP-1), regulates cellular lipid homeostasis. We found that SREBF1 expression is a prognostic factor in patients with thyroid cancer and planned to elucidate its oncogenic mechanisms.

2021-04-13 | GSE171966 | GEO

Caspase-4 mediates SREBP1 activation in macrophages

Project description:We identified caspase-4/S1P/SREBP1 pathway that is activated in LPS-treated macrophages. To analyze the functions of caspase-4 and SREBP1 in gene expression in macrophages, we analyzed the effects of deletions of Casp4 and Srebf1 in bone marrow-derived macrophages by RNA-seq.

2023-01-09 | GSE208374 | GEO

Role of SREBP1 in macrophages during muscle regeneration

Project description:The purpose of this study is to investigate how SREBP1a in macrophages regulates cellular function during muscle regeneration process after injury. We report that the systemic deletion of Srebf1, encoding SREBP1, and macrophage-specific deletion of Srebf1a, encoding SREBP1a, delays the resolution of inflammation, and impairs skeletal muscle regeneration after injury. Srebf1 deficiency impairs mitochondrial function of macrophages and suppresses the accumulation of reparative macrophages to the injured site.

2023-12-17 | GSE232394 | GEO

Transcriptomic analysis of active form of Srebf1-overexpressed fibroblasts in bleomycin-induced lung fibrosis

Project description:Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play central roles in PF, their key regulatory molecules remain unclear. We performed transcriptome analysis of lung fibroblasts from bleomycin- and silica-treated murine lungs and identified 55 hub transcription factors highly connected to gene modules differentially expressed in PF. To elucidate whether fibroblast-specific intervention against the hub transcription factor Srebf1 modulates pathogenic activation of lung fibroblasts in vivo, we intratracheally-transferred active form of Srebf1-overexpressed fibroblasts into bleomycin-treated lungs and performed global transcriptome analysis.

2019-01-30 | GSE110533 | GEO

SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma [4C]

Project description:To determine whether a TP63/KLF5-regulated super-enhancer region can impact SREBF1 transcription, circularized chromosome conformation capture (4C) assays were performed. 4C assays identified complex, extensive interactions between the SREBF1 promoter and the super-enhancer region Moreover, these DNA-DNA contacts were strictly confined within the super-enhancer region, highlighting the specificity of chromatin interactions

2021-06-26 | GSE178923 | GEO

Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing nucleobase modification

Project description:Antisense oligonucleotide (ASO) has the potential to induce hybridization-dependent effects by inadvertent binding of ASOs to RNA with sequences similar to that of the target RNA. In the present study, we examined the effects of the nucleobase derivatives introduced into the gapmer ASOs on gene expression. We performed microarray analysis using NMuLi cells (mouse liver-derived cells) treated with LNA gapmer ASO containing nucleobase modification.

2022-07-12 | GSE197166 | GEO

Epigenetic Control of Androgen Production by Histone H2A Lys130 acetylation

Project description:The biosynthesis of androgen from cholesterol in testis is well understood, however, how cancer cells gauge dwindling androgen to dexterously initiate its de novo synthesis remained elusive. We uncovered that sterol regulatory element-binding protein 1 (SREBP1) and its switch to hitherto unknown dual-phosphorylated form (pY673/951-SREBP1), acts as an androgen sensor. Androgen deficiency promoted SREBP1 dual-phosphorylation, causing its dissociation from androgen receptor (AR) in its androgen-unbound state, followed by nuclear translocation. SREBP1 recruited KAT2A/GCN5 and deposited novel epigenetic marks, histone H2A Lys130-acetylation (H2A-K130ac) in SREBF1, reigniting de novo lipogenesis & steroidogenesis. Tumor-derived androgen retained SREBP1 in cytosol, promoting T cell exhaustion, reflected in elevated PD-1 and Tim3. Reversal of H2A-K130ac or pY-SREBP1 sensitized castration-resistant prostate cancer (CRPC) resistant to androgen synthesis inhibitor, Abiraterone. Further, nuclear SREBP1 and H2A-K130ac levels were significantly increased and directly correlated with late stage prostate cancer patients. Global lipidomics analysis revealed a distinct lipid signature in androgen-deprived CRPCs, resembling the lipid profile of prostate cancers of African-American (AA) men. Overall, self-perpetuating pY-SREBP1/H2A-K130ac signaling explains sex bias in cancers and reveal a novel therapeutic vulnerability wherein synchronous inhibition of GCN5 and Tyr-kinases could overcome drug-resistant disease, benefiting AA men with aggressive prostate cancer.

2023-05-02 | GSE206856 | GEO

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