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In-depth Profiling and Quantification of the lysine acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

ABSTRACT: This is supplemental data of “ In-depth Profiling and Quantification of the lysine acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer ” project. In this data, we employed an integrated proteomics and acetylomics strategy to characterize of three Huh7 cells (NC1, NC2, NC3) and three SIRT2 overexpression cells (SIRT2-1, SIRT2-2, SIRT2-3) with 4D proteomics technology. Proteomics analysis identified a total of 5052 proteins, of which 4255 proteins were quantified across all samples. A total of 5307 acetylation sites on 2094 proteins were identified.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: jia xu

LAB HEAD: Ruibing Chen

PROVIDER: PXD031636 | Pride | 2022-07-02

REPOSITORIES: pride

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Dataset's files

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			Action	DRS
	ace.xlsx	Xlsx
	ace_NC1.d.zip	Other
	ace_NC2.d.zip	Other
	ace_NC3.d.zip	Other
	ace_SIRT2_1.d.zip	Other

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Publications

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer.

Xu Jia J Guan Xinyu X Jia Xiaodong X Li Hongyan H Chen Ruibing R Lu Yinying Y

Molecular & cellular proteomics : MCP 20220608 8

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adja ...[more]

PMID: 35688384

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In-depth Profiling and Quantification of the Acetylproteome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Project description:In this study, we employed an integrated proteomics and acetyl-proteomics strategy to characterize of 8 tumors and 8 matched normal adjacent tissues (NATs) with 4D proteomics technology. Proteomics analysis identified a total of 6551 proteins, of which 5411 proteins were quantified across all samples. A total of 8789 acetylation sites on 2348 proteins were identified, of which 5112 sites of 1620 proteins contained quantitative information.

2022-07-02 | PXD026729 | Pride

Identification of dASF/SF2 potential mRNA targets

Project description:Deciphering the role of alternative splicing in developmental processes relies on the identification of key genes whose expression is controlled by splicing regulators throughout growth of a whole organism. Targeting expression of five SR proteins in the developing eye of Drosophila allowed us to show that these splicing factors induce various phenotypic alterations concerning eye organogenesis and viability. Although both dASF/SF2 and B52 caused defects in ommatidia structure, only B52 impairs normal photoreceptor axons projection and neurogenesis in visual ganglia. Consistently, microarray analyses revealed that many of the B52 targets are involved in brain organogenesis and we show that their splicing profile is altered both in B52 loss and gain of function. Conversely, a large proportion of dASF/SF2 targets are involved in eye development. This differential effect argues that SR proteins confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions. Keywords: genetic modification Experiment aimed at identifying dASF/SF2 potential mRNA targets in the Drosophila developing eye Control: GMR X GFP-NLS trangenic larvae The 2 IP- GFP cy3 vs ASF cy5 rep.1 and IP- GFP cy5 vs ASF cy3 rep.1 samples correspond to dye-swap experiments. Two replicates (rep1 and rep2) are included.

2007-09-17 | E-GEOD-5857 | biostudies-arrayexpress

Identification of B52 potential mRNA targets

Project description:Deciphering the role of alternative splicing in developmental processes relies on the identification of key genes whose expression is controlled by splicing regulators throughout growth of a whole organism. Targeting expression of five SR proteins in the developing eye of Drosophila allowed us to show that these splicing factors induce various phenotypic alterations concerning eye organogenesis and viability. Although both dASF/SF2 and B52 caused defects in ommatidia structure, only B52 impairs normal photoreceptor axons projection and neurogenesis in visual ganglia. Consistently, microarray analyses revealed that many of the B52 targets are involved in brain organogenesis and we show that their splicing profile is altered both in B52 loss and gain of function. Conversely, a large proportion of dASF/SF2 targets are involved in eye development. This differential effect argues that SR proteins confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions. Keywords: genetic modification Experiment aimed at identifying B52 potential mRNA targets in the Drosophila developing eye Control: GMR X GFP-NLS trangenic larvae The 2 IP- GFP cy3 vs B52 cy5 rep.1 and IP- GFP cy5 vs B52 cy3 rep.1 samples correspond to dye-swap experiments. Two replicates (rep1 and rep2) are included.

2007-09-17 | E-GEOD-5858 | biostudies-arrayexpress

Ubiquitination regulation of streptococcus agalactiae infection in dairy cow mammary epithelial cells

Project description:A total of 5239 proteins were identified in this study, of which 4601 proteins contained quantitative information. If 1.5 times is used as the change threshold and t-test p-value<0.05 as the standard, then among the quantified proteins, the expression of 325 proteins in the T/C comparison group will be up-regulated and the expression of 704 proteins will be down-regulated. Based on the above data, we conducted a systematic bioinformatics analysis of proteins containing quantitative information, including protein annotation, functional classification, functional enrichment, and cluster analysis based on functional enrichment. And combining the above information provides a reference direction for the downstream in-depth research based on proteomics.

2022-10-13 | PXD028659 | Pride

Acetylomics on rhein treated NLRP3 activated J774A.1 macrophages

Project description:The aim of this project is to observe the effect of 5 μM rhein treatment on the acetylation level of NLRP3 activated macrophages. We primed J774A.1 cells with 100ng/mL LPS for 12 hours followed by 5μM rhein treatment for 30 minutes. Finally, the cells were stimulated with 4 mM ATP for 30 min to trigger the inflammasome assembly. Cell lysates were collected after ATP stimulation by cell scrapers, and acetylomics were performed as described below.

2024-10-17 | PXD044992 | Pride

Deacetylation of Sirt2 regulates PKM2 ubiquitination and its effect on liver glucose metabolism

Project description:In order to explore the effects of SIRT2 on the liver metabolic function of mice under metabolic stress, we constructed SIRT2 knockout mice.

2023-04-08 | GSE229161 | GEO

Sirt2 Inhibition Reprograms T Cell Metabolism to Confer Superior Anti-Tumor Immunity

Project description:Metabolism is a key driver of T cell functions, and the switch from oxidative-phosphorylation to aerobic glycolysis is a hallmark of T cell activation. However, the mechanisms underlying the metabolic switch remain unclear. Here, we report that the Sirtuin-2 (Sirt2) deacetylase protein functions as a metabolic checkpoint that harnesses T cell effector functions and impairs anti-tumor immunity. Specifically, upregulation of Sirt2 expression in human tumor-infiltrating T lymphocytes (TILs) negatively correlates with response to Nivolumab and TIL therapy in non-small cell lung cancer. Mechanistically, Sirt2 suppresses aerobic glycolysis by deacetylating key glycolytic enzymes. Accordingly, Sirt2-deficient T cells manifest increased glycolysis, display enhanced proliferation and effector functions, and have superior anti-tumor activity. Importantly, pharmacologic inhibition of Sirt2 endows human TILs with these superior metabolic fitness and enhanced effector functions. These findings indicate Sirt2 as an actionable target for reprogramming T cell metabolism to augment a broad spectrum of cancer immunotherapies.

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The deacetylase SIRT2 contributes to autoimmune disease pathogenesis by modulating IL-17A and IL-2 transcription

Project description:Aberrant expression of IL-17A together with abated IL-2 production by effector CD4+ T cells contributes to the pathogenesis of systemic lupus erythematosus (SLE). Here we report that Sirtuin 2 (SIRT2), a member of the family of NAD+-dependent histone deacetylases, suppresses IL-2 production by CD4+ T cells while it promotes their differentiation into Th17 cells. Mechanistically, we show that SIRT2 is responsible for the deacetylation of p70S6K and the activation of the mTORC1/HIF-1α/RORγt pathway and the generation of Th17 cells differentiation. Additionally, SIRT2 is responsible for the deacetylation of c-Jun and histones on the Il-2 gene, resulting in decreased IL-2 production. We found that the transcription factor inducible cAMP early repressor (ICER), which is overexpressed in T cells from people with SLE and lupus-prone mice, binds directly to the Sirt2 promoter and promotes its transcription. AK-7, a SIRT2 inhibitor limited the ability of adoptively transferred antigen-specific CD4+ T cells to cause autoimmune encephalomyelitis and disease in the lupus-prone MRL/lpr mice. Finally, CD4+ T cells from SLE patients exhibited increased expression of SIRT2, and pharmacological inhibition of SIRT2 in primary CD4+ T cells from patients with SLE attenuated their ability to differentiate into Th17 cells and promoted IL-2–producing T cells. Collectively, these results suggest that SIRT2-mediated deacetylation is essential for the aberrant expression of IL-17A and IL-2 and that SIRT2 may be a promising molecular target for new therapies for SLE.

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Sirtuin 2 Promotes HCMV Replication by Regulating Cell Cycle Progression

Project description:The host cell cycle is a major target for manipulation by viral pathogens, which often replicate in certain cell cycle stages. The prevalent pathogen human cytomegalovirus (HCMV), for instance, only replicates during G1 and therefore employs diverse mechanisms for regulating cell cycle progression. Here, we demonstrate that the human enzyme sirtuin 2 (SIRT2) is required for HCMV-mediated cell cycle dysregulation. By combining virology assays with mass pectrometry-based proteome, acetylome, and interactome analyses, we have defined a pro-virus function for SIRT2 in regulating the G1 to S phase transition.

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