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Spatial Transcriptomics Unravels Palmitoylation and Zonation-Dependent Gene Regulation by AEG-1 in Mouse Liver

ABSTRACT: Spatial Transcriptomics Unravels Palmitoylation and Zonation-Dependent Gene Regulation by AEG-1 in Mouse Liver

PROVIDER: PRJNA1085111 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28254633_1.fastq.gz	Fastqsanger.gz
	SRR28254633_2.fastq.gz	Fastqsanger.gz
	SRR28254634_1.fastq.gz	Fastqsanger.gz
	SRR28254634_2.fastq.gz	Fastqsanger.gz

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Spatial Transcriptomics Unravels Palmitoylation and Zonation-Dependent Gene Regulation by AEG-1 in Mouse Liver

Project description:Obesity-induced metabolic dysfunction-associated steatohepatitis (MASH) leads to hepatocellular carcinoma (HCC). Astrocyte-elevated gene-1/Metadherin (AEG-1/MTDH) plays a key role in promoting MASH and HCC. AEG-1 is palmitoylated at residue cysteine 75 (Cys75) and a knock-in mouse representing mutated Cys75 to serine (AEG-1-C75S) showed activation of MASH- and HCC-promoting gene signature when compared to wild-type littermates (AEG-1-WT). The liver consists of 3 zones, periportal, midlobular and pericentral, and zone-specific dysregulated gene expression impairs metabolic homeostasis in the liver, contributing to MASH and HCC. Here, to elucidate how palmitoylation influences AEG-1-mediated gene regulation in regards to hepatic zonation, we performed spatial transcriptomics (ST) in the livers of AEG-1-WT and AEG-1-C75S littermates.

2024-06-05 | GSE261057 | GEO

Palmitoylation negatively regulates AEG-1 function

Project description:In vitro studies revealed that AEG-1 is palmitoylated at cysteine at a.a. 75 position. In order to check how palmitoylation regulates AEG-1 function in vivo we generated a knockin moue using CRISPR/Cas9 taking in which cysteine 75 was mutated to serine (AEG-1-C75S). Hepatocytes were isolated from AEG-1-WT and AEG-1C75S littermates, total RNA was isolated and RNA-sequencing was performed.

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Palmitoylation negatively regulates AEG-1 function

Project description:Palmitoylation negatively regulates AEG-1 function

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Astrocyte Elevated Gene-1/Metadherin (AEG-1/MTDH) in Myeloid Cells Regulates Metabolic Dysfunction-Associated Steatohepatitis (MASH) [Spatial Transcriptomics]

Project description:Astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) plays an important role in regulating lipid metabolism and inflammation in hepatocytes, and promotes metabolic dysfunction-associated steatohepatitis (MASH). Myeloid cells, such as macrophages, play a key role in regulating inflammation. Here we investigated the role of AEG-1 in myeloid cells in regulating high fat/high sugar diet (HF/HSD)-induced MASH. Both male and female AEG-1MAC mice were significantly protected from MASH development compared to AEG-1fl/fl mice.

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Expression data from AEG-1fl/fl and AEG-1DHEP mice which have conditional hepatocyte-specific knockout of AEG-1 (Astrocyte elevated gene 1)

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Project description:The widespread adoption of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput and lossless method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5,000 proteins from individual HEK293 cell. Applied to murine liver, EasySCP achieved spatially resolved proteomics profiling of hepatocytes zonation, detecting an average of 3,500 proteins per hepatocyte and uncovering zonation patterns for 3,277 out of 5,267 proteins, representing unprecedented depth and coverage in single-cell liver proteomics. Building on 215 conserved zonation markers, we further developed hepatocyte spatial status score (HSS) that enables accurately reconstruct liver zonation across single-cell and spatial multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics.

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AEG-1 silencing induced gene expression alteration in glioma cells

Project description:This experiment is designed to evaluate gene expression alteration following AEG-1 (MTDH) silencing in glioma cells. AEG-1 is found to be a potential regulator through interaction with other transcription factor. We intended to investigate the enriched transcription factor dependent downstream gene sets regulated by AEG-1 form the differential expressed genes we obtained from AEG-1 silencing. Total RNA were extracted from U87MG glioma cells stably silencing AEG-1 and correspondent pSuper Retro vector cells respectively. Passage 5 of the indicated cells after infection and selection were harvested for RNA extraction.

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