Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1073215 | ENA |
REPOSITORIES: ENA
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Project description:Adhesive capsulitis (AC) affects 2–5% of the population worldwide. Patients with severe AC fail to regain a complete range of movement and experience years of shoulder pain. Unfortunately, the underlying mechanism of severe AC remains unclear. Here, we performed an integrated transcriptomic and metabolomic data analysis of serum and tissue samples from patients with severe AC, mild AC, and healthy controls. Pathways related to muscle development and myogenesis positively correlated with severe AC progression. Further, we identified an arginine-citrulline gene-compound network that may play a central role in severe AC. Comparing differentially regulated metabolites from tissue and serum, two phospholipids were recognized as potential serum markers for severe AC. In conclusion, this is the first comprehensive integrated -omics study on severe AC and provides insights into genes and compounds of the arginine-citrulline metabolic pathway that may be potential therapeutic targets for treating AC.
2023-05-30 | GSE190023 | GEO
Project description:Integrated transcriptomic and metabolomic analysis reveals arginine-citrulline gene-compound network is critical for severe adhesive capsulitis progression
| PRJNA785604 | ENA
Project description:Citrullination, the deimination of arginine residues into citrulline, has been implicated in the aetiology of several diseases. In multiple sclerosis (MS), citrullination is thought to be a major driver of pathology, through hypercitrullination and destabilization of myelin. As such, inhibition of citrullination has been suggested as a therapeutical strategy for MS. Here we show that citrullination by peptidylarginine deiminase 2 (PADI2) is in contrast required for normal oligodendrocyte differentiation, myelination and motor function. We identify several targets for PADI2, including not only myelin-related proteins, but also several chromatin-associated proteins, implicating PADI2 in epigenetic regulation. Accordingly, we observe that PADI2 inhibition and its knockdown affect chromatin accessibility and prevent the upregulation of genes involved in oligodendrocyte differentiation. Moreover, mice lacking PADI2, display motoric dysfunction and a decreased number of myelinated axons in the corpus callosum. Our study demonstrates that citrullination is required for oligodendrocyte lineage progression and myelination and thus its targeted activation in the oligodendrocyte lineage might be beneficial in the context of remyelination in diseases as MS.
2019-04-23 | GSE115929 | GEO
Project description:Estrogen receptor M-NM-1 (ER), a member of the nuclear hormone receptor superfamily, regulates transcriptional activity by ligand-dependent recruitment of cofactors which, in turn, locally alter chromatin structure. It is generally believed that co-factor activity at target promoters leads to a more open, transcriptionally permissive chromatin structure, however, these mechanisms remain to be fully established. Peptidylarginine deiminases (PADIs) catalyze the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline and this activity has been linked to the gene regulation. Here, we found that PADI2 citrullinate H3 Arginine 26 (H3R26) in vitro and, using a specific H3R26 citrulline (H3Cit26) antibody, we demonstrate that H3Cit26 occurs in vivo following 17M-NM-2-estradiol (E2) stimulation and this unique and pronounced global activation of H3Cit26 is ER-dependent. Using a mammalian-based promoter chromosomal array system, we observed that citrullination at H3R26 is robust and co-localizes with ER at decondensed chromatin loci. Additionally, this histone modification is specifically enriched at ER bound regions of target promoters, forming a permissive chromatin environment for gene transactivation. Interestingly, we have shown in a reciprocal way, that either depletion of PADI2 or inhibition of ER not only dramatically abolished E2-induced activation of H3Cit26 on gene promoters but also affect ER recruitment. Collectively, our results demonstrate that citrullination of H3R26 by PADI2 following estrogen stimulation plays a role in ER target gene activation, likely via decondensation of the local chromatin architecture. Two H3Cit26 ChIP-chip biological replicates under vehicle treatment and two H3Cit26 ChIP-chip biological replicates under E2 stimulation from MCF-7 human breast cancer cells are included.
2012-09-04 | E-GEOD-32599 | biostudies-arrayexpress
Project description:The Nuclesome Remodelling and Deacetylation (NuRD) complex is an epigenetic regulator of gene expression comprising two mutually exclusive ATPase subunits CHD3 or CHD4. Here we show that CHD4 silencing in multiple types of cancer cells de-represses expression of the PADI1 (Protein Arginine Deiminase 1) and PADI3 enzymes that convert arginine to citrulline. Increased PADI1 and PADI3 expression enhances citrullination of three arginines of the key glycolytic regulatory enzyme PKM2 (pyruvate kinase) promoting excessive glycolysis, lowered ATP levels and slowed proliferation. PKM2 citrullination lowers its sensitivity to the allosteric inhibitors Tryptophan and Phenylalanine shifting equilibrium towards the allosteric activator Serine, thereby bypassing the normal physiological regulation of glycolysis by low Serine levels. Our results describe a novel pathway linking epigenetic regulation of PADI1 and PAD3 expression by CHD4 to glycolytic flux and the control of cancer cell growth.
2019-11-03 | GSE134848 | GEO
Project description:The Nuclesome Remodelling and Deacetylation (NuRD) complex is an epigenetic regulator of gene expression comprising two mutually exclusive ATPase subunits CHD3 or CHD4. Here we show that CHD4 silencing in multiple types of cancer cells de-represses expression of the PADI1 (Protein Arginine Deiminase 1) and PADI3 enzymes that convert arginine to citrulline. Increased PADI1 and PADI3 expression enhances citrullination of three arginines of the key glycolytic regulatory enzyme PKM2 (pyruvate kinase) promoting excessive glycolysis, lowered ATP levels and slowed proliferation. PKM2 citrullination lowers its sensitivity to the allosteric inhibitors Tryptophan and Phenylalanine shifting equilibrium towards the allosteric activator Serine, thereby bypassing the normal physiological regulation of glycolysis by low Serine levels. Our results describe a novel pathway linking epigenetic regulation of PADI1 and PAD3 expression by CHD4 to glycolytic flux and the control of cancer cell growth.
2019-11-03 | GSE134849 | GEO
Project description:Peptidylarginine deiminase (PADI) 2 catalyzes the posttranslational conversion of peptidyl-arginine to peptidyl-citrulline, a process called citrullination. However, the exact function of PADI2 in bone development and bone homeostasis remains unknown. In this study, we found that Padi2 deficiency lead to loss of bone mass and cleidocranial dysplasia (CCD)-like phenotype with delayed calvarial ossification and clavicular hypoplasia due to impaired osteoblast differentiation. Mechanistically, Padi2 depletion drastically reduced RUNX2 protein level and PADI2 stabilized RUNX2 from ubiquitin-proteasomal degradation. Furthermore, we identified a new modification at RUNX2, citrullination of arginine and its conversion to citrulline by PADI2. PADI2 citrullinates RUNX2 via a direct physical interaction and the citrullination sites at RUNX2 by PADI2 were identified by high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Interestingly, in mouse RUNX2 isoform 1 (528 a.a), loss of R381, a citrullination site by PADI2, drastically reduced RUNX2 protein levels, indicating that the citrullination of RUNX2 by PADI2 is required for the maintenance of RUNX2 protein stability. Collectively, our study demonstrates that PADI2-mediated citrullination play key roles in bone formation and bone homeostasis. Also, CCD may result from functional defects of RUNX2 by Padi2 deficiency. These insights into the role of PADI2 in postnatal bone formation and homeostasis and CCD pathogenesis may assist in the development of new therapies for bone diseases including CCD.
2023-10-24 | PXD040179 | Pride
Project description:Citrullination is the conversion of arginine-to-citrulline by protein arginine deiminases (PADs), whose dysregulation is implicated in the pathogenesis of various types of cancers and autoimmune diseases. Consistent with the ability of human cytomegalovirus (HCMV) to induce post-translational modifications of cellular proteins to gain a survival advantage, we show that HCMV infection of primary human fibroblasts triggers PAD-mediated citrullination of several host proteins, and that this activity promotes viral fitness. Citrullinome analysis reveals significant changes in deimination levels of both cellular and viral proteins, with interferon (IFN)-inducible protein IFIT1 being the most heavily deiminated one. As genetic depletion of IFIT1 strongly enhances HCMV growth, and in vitro IFIT1 citrullination impairs its ability to bind to 5’-pppRNA, we propose that viral-induced IFIT1 citrullination is a novel mechanism of HCMV evasion from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection.
2021-07-20 | PXD025803 | Pride
Project description:Citrullination is the conversion of arginine-to-citrulline by protein arginine deiminases (PADs), whose dysregulation is implicated in the pathogenesis of various types of cancers and autoimmune diseases. Consistent with the ability of human cytomegalovirus (HCMV) to induce post-translational modifications of cellular proteins to gain a survival advantage, we show that HCMV infection of primary human fibroblasts triggers PAD-mediated citrullination of several host proteins, and that this activity promotes viral fitness. Citrullinome analysis reveals significant changes in deimination levels of both cellular and viral proteins, with interferon (IFN)-inducible protein IFIT1 being the most heavily deiminated one. As genetic depletion of IFIT1 strongly enhances HCMV growth, and in vitro IFIT1 citrullination impairs its ability to bind to 5’-pppRNA, we propose that viral-induced IFIT1 citrullination is a novel mechanism of HCMV evasion from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection.
2021-07-20 | PXD025818 | Pride
Project description:Estrogen receptor α (ER), a member of the nuclear hormone receptor superfamily, regulates transcriptional activity by ligand-dependent recruitment of cofactors which, in turn, locally alter chromatin structure. It is generally believed that co-factor activity at target promoters leads to a more open, transcriptionally permissive chromatin structure, however, these mechanisms remain to be fully established. Peptidylarginine deiminases (PADIs) catalyze the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline and this activity has been linked to the gene regulation. Here, we found that PADI2 citrullinate H3 Arginine 26 (H3R26) in vitro and, using a specific H3R26 citrulline (H3Cit26) antibody, we demonstrate that H3Cit26 occurs in vivo following 17β-estradiol (E2) stimulation and this unique and pronounced global activation of H3Cit26 is ER-dependent. Using a mammalian-based promoter chromosomal array system, we observed that citrullination at H3R26 is robust and co-localizes with ER at decondensed chromatin loci. Additionally, this histone modification is specifically enriched at ER bound regions of target promoters, forming a permissive chromatin environment for gene transactivation. Interestingly, we have shown in a reciprocal way, that either depletion of PADI2 or inhibition of ER not only dramatically abolished E2-induced activation of H3Cit26 on gene promoters but also affect ER recruitment. Collectively, our results demonstrate that citrullination of H3R26 by PADI2 following estrogen stimulation plays a role in ER target gene activation, likely via decondensation of the local chromatin architecture.
2012-09-04 | GSE32599 | GEO