Comprehensive analysis identifies histone 2A ubiquitination as a marker for aging and pan-cancer prognosis
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ABSTRACT:
ORGANISM(S): Mus Musculus
SUBMITTER: 
Feiyang Ji
PROVIDER: PXD035091 | iProX | Tue Jul 05 00:00:00 BST 2022
REPOSITORIES: iProX
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Project description:By simultaneously capturing thousands of ubiquitination sites, mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA) mass spectrometry and neural network-based data processing, specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples the number of quantified ubiquitinated peptides, to 70,000 identifications in single LC-MS runs. At the same time, it significantly improves robustness and quantification precision, thus for the first time enabling large-scale ubiquitinomics screens. We further report a novel strategy for capturing targets of deubiquitinases (DUBs), by simultaneously recording the dynamics of the ubiquitinome and the proteome and at high temporal resolution upon enzyme inhibition. Applying it to the anticancer target USP7, we accurately time ubiquitination and consequent changes in abundance of more than 8,000 proteins, thereby mapping novel putative USP7 targets. We show a strikingly fast modulation of the ubiquitinome when inhibiting USP7 and discover hundreds of ubiquitination sites that are regulated within minutes. Yet only a small fraction of those are degraded, thus dissecting the degradative and non-degradative scope of USP7 action. Mapping the impact of different USP7 inhibitors on the ubiquitinome, we observe substantial overlap of their signatures, but also marked differences. Our method enables for the first time to rapidly profile the mode-of-action of candidate drugs targeting DUBs or ubiquitin ligases at an unprecedented depth.
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Project description:We demonstrated that loss of Histone 2A Ubiquitination and PRC1 activity drives uveal melanoma progression
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Project description:Sustained caloric restriction (CR) extends lifespan in animal models but the mechanism and primary tissue target(s) have not been identified. Gene expression changes with aging and CR were examined in both heart and subcutaneous white adipose tissue (WAT) of F344 male rats using Affymetrix® RAE 230 arrays and validated by qRT-PCR on 18 genes. In heart, age- associated changes but not CR-associated changes in old. In WAT, genes were identified where the aging change is suppressed by CR (candidate markers of healthy aging) and those affected by CR but not normal aging (candidate longevity assurance genes). 10-21% of age-associated genes were regulated in common between tissues. Gene set enrichment analysis (GSEA) revealed coordinate small magnitude changes in ribosomal, proteasomal, and mitochondrial genes with similarities between heart and WAT. Further analysis revealed PPARgamma as a potential upstream regulator of altered gene expression in old CR WAT. These results demonstrate a reduced mRNA response to CR with age in heart relative to WAT. In WAT, we identified candidate CR mimetic targets and candidate markers of healthy aging. These data suggest a role for subcutaneous WAT in the effects of CR and strengthen the role for PPAR signaling in aging and CR while indicating that the effects of CR in heart can occur independent of global changes in mRNA level. Experiment Overall Design: Tissues (n=5-7 animals per group) were obtained from the NIH-NIA aging rodent tissue bank. According to supplier records, animals were housed in a specific pathogen free barrier facility under contract with BioReliance. AL animals were housed 3 per cage and CR animals were housed singly. CR (60% of AL) was initiated at 4 months of age with a switch from the NIH 31 to NIH fortified diet. F344 male rats were sacrificed at 4 months (4AL) or 28 months of age (28AL, 28CR). Animals with gross tumor pathologies were excluded from the study. All animals were euthanized by CO2 asphixiation and tissues were frozen in liquid nitrogen then stored at â80°C. Subcutaneous WAT was collected from the abdominal region. Recorded body weights differed dramatically between the 3 groups (4AL = 253±8 g, 28AL = 382±20 g, 28CR = 288±7 g) and heart weight as a fraction of body weight was not significantly different between the groups (data not shown). The apical ~1/3 of the heart was homogenized for the expression studies. Sections from the cut face were stained with haematoxylin and eosin to confirm expected aging-associated pathology changes.
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Project description:Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial viral co infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and dysregulation of immune responses. Epithelial cells act as the first line of defense and detect pathogens by a high variety of pattern recognition receptors. The post translational modification ubiquitin is involved in almost every cellular process. Moreover, ubiquitination contributes to the regulation of host immune responses, influenza A virus uncoating and transport within host cells. We applied proteomics with a special focus on ubiquitination to assess the impact of single bacterial and viral as well as bacterial viral co-infections on bronchial epithelial cells. We used Tandem Ubiquitin Binding Entities to enrich polyubiquitinated proteins and assess changes in the ubiquitinome. Infecting 16HBE cells with Streptococcus pyogenes led to an increased abundance of proteins related to mitochondrial translation and energy metabolism in proteome and ubiquitinome. In contrast, influenza A virus infection mainly altered the ubiquitinome. Co-infections had no additional impact on protein abundances or affected pathways. Changes in protein abundance and enriched pathways were assigned to imprints of both infecting pathogens.
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Project description:Changes in mitochondrial bioenergetics in aging T-cells play a key role in the decrease in T-cell function and tumor resistance with aging. The bioactive sphingolipid ceramide, induced by aging stress, is a major player in these changes, as its accumulation at the mitochondrial membranes of both mouse and human aging T-cells induces ceramide-dependent mitophagy, which decreases T-cell viability, cytokine secretion, and anti-tumor activity. Besides lipid signaling, our findings show a general depletion of tricarboxylic acid cycle (TCA) metabolites in aging T-cells, with pools of fumarate, malate, and argininosuccinate significantly decreasing in both mouse and human aging T-cells. In vivo supplementation of fumarate to mouse T-cells seemed to correct some of the functional defects observed in aging, with a protection of T-cell viability, cytokine production, and tumor killing capacity in co-cultures with tumor cells. The fumarate supplementation also led to a decrease in ceramide-dependent mitophagy in the aging T-cells, indicating an interplay between ceramide-dependent mitophagy and fumarate metabolism. Here, the RNAseq data shows a reversal of the genetic signature of aging in T-cells upon supplying fumarate, associated with a significant increase in different metabolic enzymes.
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Project description:The antiapoptotic Bcl-2 family member Bfl-1 is upregulated in many human tumors in which NF-kB is implicated, and contributes significantly to tumor cell survival and chemoresistance. We previously found that NF-kB induces transcription of bfl-1, and that the Bfl-1 protein is also regulated by the ubiquitin-proteasome. However little is known of the role that dysregulation of Bfl-1 turnover plays in cancer. We found that ubiquitination-resistant mutants of Bfl-1 display increased stability and greatly accelerate tumor formation in a mouse model of leukemia/lymphoma. Gene expression profiling revealed that tyrosine kinase Lck is highly upregulated and activated in these tumors compared to the parental cells, as were several genes in the RANK signaling pathway, and leads to activation of the IKK, Akt and Erk signaling pathways, which are key mediators in cancer. Tumor assays with cells coexpressing constitutively active Lck with Bfl-1, or with tumor-derived cells following shRNA-mediated Lck knockdown, unveiled functional cooperation between Bfl-1 and Lck in leukemia/lymphomagenesis. These data demonstrate that ubiquitination is a critical mechanism for regulating Bfl-1 function, and suggest that mutations in bfl-1 or in the signaling pathways that control its ubiquitination may predispose to cancer. Additionally since bfl-1 is upregulated in many human hematopoietic tumors, these data suggest that strategies to promote Bfl-1 ubiquitination may improve therapy in drug-resistant tumors. FL5.12 pro-B cells were stably transfected with Bfl-1DC and p53DD (Parental - P) and injected i.v. into nude mice. The spleens were harvested from three independent mice that developed leukemia/lymphoma (T1, T2, and T3). To identify the changes in gene expression that occurred during tumorigenesis, RNA was isolated from the parental cell line (P) and from three independent splenic tumors (T) and hybridized to Affymetrix Mouse Genome 430A_2.0 arrays. The analysis was performed in duplicate.
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Project description:Changes in mitochondrial bioenergetics in aging T-cells play a key role in the decrease in T-cell function and tumor resistance with aging. The bioactive sphingolipid ceramide, induced by aging stress, is a major player in these changes, as its accumulation at the mitochondrial membranes of both mouse and human aging T-cells induces ceramide-dependent mitophagy, which decreases T-cell viability, cytokine secretion, and anti-tumor activity. Besides lipid signaling, our findings show a general depletion of tricarboxylic acid cycle (TCA) metabolites in aging T-cells, with pools of fumarate, malate, and argininosuccinate significantly decreasing in both mouse and human aging T-cells. In vivo supplementation of fumarate to mouse T-cells seemed to correct some of the functional defects observed in aging, with a protection of T-cell viability, cytokine production, and tumor killing capacity in co-cultures with tumor cells. The fumarate supplementation also led to a decrease in ceramide-dependent mitophagy in the aging T-cells, indicating an interplay between ceramide-dependent mitophagy and fumarate metabolism. Interestingly, T-cells from aging mice with Alzheimer's disease are protected against the aging-induce increase in mitophagy, and their fumarate pools are also protected. Here, the NanoString data shows the changes in metabolic and immune markers in aging T-cells with/out fumarate supplementation, as well as in T-cells from Alzheimer's mice, associated with a significant increase in different metabolic enzymes.
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