Proteomic and molecular evidences of Il1rl2, Ric8a, Krt18 and Hsp90b1 modulation during experimental hepatic fibrosis and pomegranate supplementation

Husain, Hadiya; Waseem, Mohammad; Ahmad, Riaz

doi:10.1016/j.ijbiomac.2021.06.091

Cited by 10 publications

(8 citation statements)

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“…MAP1LC3B (Microtubule Associated Protein 1 Light Chain 3 Beta) regulates mitophagy by eliminating mitochondria to basal levels to meet cellular energy demands and prevent excessive ROS production, contributing to the optimization of mitochondrial quantity and quality ( Hayashi et al, 2020 ). HSP90B1 (Heat Shock Protein 90 Beta Family Member 1) is associated with calcium ion binding and unfolded protein binding ( Husain et al, 2021 ). MYC (MYC Proto-Oncogene, BHLH Transcription Factor) is a proto-oncogene and encodes a nuclear phosphoprotein that functions in cell cycle progression, apoptosis, and cell transformation ( Flynn and Hogarty, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Ferroptosis Related Genes in Ischemic and Idiopathic Cardiomyopathy: Screening for Potential Pharmacological Targets

Jiang

Chen

Chao

et al. 2022

Front. Cell Dev. Biol.

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Background: Ferroptosis is a new form of cell death recently discovered that is distinct from apoptosis, necrosis and autophagy. This article is expected to provide a new direction for the treatment of cardiomyopathy in the future by screening potential drug targets associated with ferroptosis.Methods: Differential expression analysis of GSE5406 from the Gene Expression Omnibus (GEO) database was performed using the GEO2R tool. Functional annotation of ferroptosis related genes was also performed. Then we constructed protein-protein interaction networks and identified hub genes using Cytoscape. The candidates for pharmacological compounds targeting the hub genes were screened by cMap.Results: Totally 15 ferroptosis related genes (4 upregulated and 11 downregulated) for ischemic cardiomyopathy and 17 ferroptosis related genes (13 upregulated and 4 downregulated) for idiopathic cardiomyopathy were found. The biological processes involved in these genes mainly include negative regulation of apoptotic process, flavonoid metabolic process, response to drug for ischemic cardiomyopathy and cellular response to fibroblast growth factor stimulus, negative regulation of apoptotic process, and response to drug for idiopathic cardiomyopathy. KEGG results showed that these genes were mainly involved in MAPK signaling pathway for ischemic cardiomyopathy and PI3K-Akt signaling pathway for idiopathic cardiomyopathy. We generated a co-expression network for hub genes and obtained top 10 medications suggested respectively for ischemic/idiopathic cardiomyopathy.Conclusion: Our study reveals the potential role of ferroptosis related genes in ischemic and idiopathic cardiomyopathy through bioinformatics analysis. The hub genes and potential drugs may become novel biomarkers for prognosis and precision treatment in the future.

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Section: Discussionmentioning

confidence: 99%

Ferroptosis Related Genes in Ischemic and Idiopathic Cardiomyopathy: Screening for Potential Pharmacological Targets

Jiang

Chen

Chao

et al. 2022

Front. Cell Dev. Biol.

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“…ATM is mainly found in endothelial and epithelial cells ( 125 , 126 ), FGFR1 in fibroblasts and epithelial cells ( 57 , 58 ), FBXW7 in hepatic stellate mesenchymal, mononuclear and pulmonary epithelial stem cells ( 60 – 62 ), ESR1 in myofibroblasts and epithelial cells ( 63 , 64 ), CCND1 in renal glomerular mesangial and hepatic stellate cells ( 66 , 127 ), HIF1A in renal epithelial cells and cardiac fibroblasts ( 68 , 128 ), CEBPB in hematopoietic and renal epithelial cells ( 70 , 71 ), NAMPT in hepatic stellate and renal glomerular mesangial cells ( 72 , 129 ), IRF1 in renal epithelial cells ( 76 ), SOCS1 in hepatocytes and macrophages ( 78 ), SOCS3 in cardiac fibroblasts ( 90 ), ICAM1 in endothelial cells ( 79 ), ETS1 in hepatic stellate and renal epithelial cells ( 130 , 131 ), IL7R in hepatic stellate cells ( 82 ), MMP1 in fibroblasts ( 83 , 132 ), HNF4A in hepatocytes ( 85 ), CCL2 in fibroblasts ( 86 , 133 ), CASP1 in hepatic endothelial cells ( 87 ) and STAT1 in macrophages ( 88 , 89 ). HSP90B1 , although it has been recently reported to be implicated in fibrosis ( 92 ), the specific cell type expressing it, still, remains undetermined.…”

Section: Discussionmentioning

confidence: 99%

Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?

Dovrolis

Filidou²,

Tarapatzi³

et al. 2022

Front. Immunol.

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IntroductionExtracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis.Methods and resultsIn this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn’s disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively.DiscussionThese findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.

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“…This suggests that KRT‐8 and KRT‐18 are also markers of a healthier NP phenotype. Moreover, studies have revealed that KRT18 is not only a biomarker but also a regulator in many diseases 105,107,108,112 . KRT18, as a multiple‐function RBP, has been involved in various bioprocesses, including cell functions (e.g., cell migration, proliferation, and differentiation) 105–107 .…”

Section: Potential Role Of Rna Binding Proteins In Intervertebral Dis...mentioning

confidence: 99%

“…Moreover, studies have revealed that KRT18 is not only a biomarker but also a regulator in many diseases. 105 , 107 , 108 , 112 KRT18, as a multiple‐function RBP, has been involved in various bioprocesses, including cell functions (e.g., cell migration, proliferation, and differentiation). 105 , 106 , 107 Several studies have demonstrated that KRT‐18 regulates cell proliferation and apoptosis through the PTGR mechanism, and it might be a cellular death biomarker.…”

Section: Potential Role Of Rna Binding Protein S I...mentioning

confidence: 99%

Emerging roles ofRNAbinding proteins in intervertebral disc degeneration and osteoarthritis

Li,

Gao

et al. 2023

Orthopaedic Surgery

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The etiology of intervertebral disc degeneration (IDD) and osteoarthritis (OA) is complex and multifactorial. Both predisposing genes and environmental factors are involved in the pathogenesis of IDD and OA. Moreover, epigenetic modifications affect the development of IDD and OA. Dysregulated phenotypes of nucleus pulposus (NP) cells and OA chondrocytes, including apoptosis, extracellular matrix disruption, inflammation, and angiogenesis, are involved at all developmental stages of IDD and OA. RNA binding proteins (RBPs) have recently been recognized as essential post‐transcriptional regulators of gene expression. RBPs are implicated in many cellular processes, such as proliferation, differentiation, and apoptosis. Recently, several RBPs have been reported to be associated with the pathogenesis of IDD and OA. This review briefly summarizes the current knowledge on the RNA‐regulatory networks controlled by RBPs and their potential roles in the pathogenesis of IDD and OA. These initial findings support the idea that specific modulation of RBPs represents a promising approach for managing IDD and OA.

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Proteomic and molecular evidences of Il1rl2, Ric8a, Krt18 and Hsp90b1 modulation during experimental hepatic fibrosis and pomegranate supplementation

Cited by 10 publications

References 77 publications

Ferroptosis Related Genes in Ischemic and Idiopathic Cardiomyopathy: Screening for Potential Pharmacological Targets

Ferroptosis Related Genes in Ischemic and Idiopathic Cardiomyopathy: Screening for Potential Pharmacological Targets

Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?

Emerging roles ofRNAbinding proteins in intervertebral disc degeneration and osteoarthritis

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