Association of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) with T2DM

Abdulwahab, Rabab Asghar; Allaith, Abdul Ameer A.; Shinwari, Zakia; Alaiya, Ayodele; Giha, Hayder A.

doi:10.1016/j.gene.2019.04.076

Cited by 8 publications

(6 citation statements)

References 38 publications

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“…This study indicated that enriched genes might play important role in PCOS. As previously reported, FOXP3 [446], TIMP4 [447], OAS3 [448], SOCS1 [128], CD74 [129], PLK1 [449], TGFB1 [450], RAPGEF1 [451], SERPINH1 [452], ATF5 [66], GATA6 [133], IGF2BP1 [453], IRX3 [454], FOXC2 [455], SNHG17 [456], TAF1C [457], HHIP (hedgehog interacting protein) [458], POMC (proopiomelanocortin) [459], DOK5 [76], COL1A1 [460], POSTN (periostin) [461], SOD3 [462], ADAMTS13 [463], FABP5 [464], MAPK11 [465], KCTD15 [83], HSPG2 [466], MST1 [467], MGAT2 [468], LGR5 [469], SPINK1 [470], CYP19A1 [471], PLAC8 [90], CD36 [472], AQP5 [473], GIPR (gastric inhibitory polypeptide receptor) [474], ARG1 [475], SORL1 [476], CD4 [477], F11R [478], LEPR (leptin receptor) [479], CDH13 [480], AR (androgen receptor) [481], FOXO1 [102], MALT1 [482], PAM (peptidylglycine alpha-amidating monooxygenase) [483], B2M [484], TCF4 [485], CAV2 [486], HSBP1 [487], COLEC12 [488], ADRA2A [489], SLC38A4 [490], TM6SF2 [491], GLP2R [111], KLB (klotho beta) [492], NFAT5 [493], PON2 [494], ZMAT3 [495], DST (dystonin) [426], MGST3 [496], COQ2 [118], EPHX2 [497], C2 [181] and FAM3C [120] are altered expression in type 2 diabetes mellitus. Previous studies have shown that DRD4 [498], TIMP4 [499], SOCS1 [500], CD74 [501], TGFB1 [502], ACTG2 [503], ISG15 [504], HOXC8 [...…”

Section: Discussionmentioning

confidence: 87%

The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

Vastrad¹,

Vastrad²

2023

Preprint

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Polycystic ovary syndrome (PCOS) is is associated with infertility, obesity, insulin resistance, hyperinsulinemia, type 2 diabetes mellitus, hypertension, cardiovascular problems, neurological and psychological problems and cancer. The specific mechanism of PCOS and its complications remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS and its complications. The next generation squancing (NGS) datset GSE199225 was downloaded from the gene expression omnibus (GEO) database. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the functional enrichment, gene ontology (GO) and REACTOME pathway of the differentially expressed genes. A protein-protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were also constructed for research. The expression of the hub genes was validated using receiver operating characteristic (ROC) curve analysis. We have identified 957 DEGs in total, including 478 up regulated genes and 479 down regulated gene. GO and REACTOME illustrated that DEGs in PCOS were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling and aggregation. Finally, through analyzing the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, we screened hub genes HSPA5, PLK1, RIN3, DBN1, CCDC85B, DISC1, AR, MTUS2, LYN and TCF4 by the Cytoscape software. This study uses a series of bioinformatics technologies to obtain hug genes and key pathways related to PCOS and its complications. These analysis results provide us with novel ideas for finding biomarkers and treatment methods for PCOS and its complications.

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Section: Discussionmentioning

confidence: 87%

The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

Vastrad¹,

Vastrad²

2023

Preprint

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“…Te upregulation of the 2 connective tissue (CT) proteins, fbronectin and vitronectin in men, is not unexpected since men and women have diferent musculoskeletal system properties [46]. Te sex diference in the levels of both PPs was not reported before; however, both proteins were shown to be upregulated in T2DM [6,47]. Te diferences in CT proteins between the 2 sexes have clinical implications; e.g., the incidence of anterior cruciate ligament injury is almost 10 times higher in women compared with men performing the same activity [48], an observation that supports our fndings.…”

Section: Discussionmentioning

confidence: 89%

“…Of the limitations of this study is the small sample size, and lack of validations of the LC-MS/MS results with other methods, although results were previously validated by testing 3 PPs including fbronectin in 80 plasma samples by ELISA [47].…”

Section: Discussionmentioning

confidence: 97%

Sex-Biased Expression of Genes Allocated in the Autosomal Chromosomes: Blood LC-MS/MS Protein Profiling in Healthy Subjects

Giha

Abdulwahab

Abbas³

et al. 2023

Genetics Research

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Background. Sex and gender have a large impact in human health and disease prediction. According to genomic/genetics, men differ from women by a limited number of genes in Y chromosome, while the phenotypes of the 2 sexes differ markedly. Methods. In this study, serum samples from six healthy Bahraini men and women were analyzed by liquid chromatography–mass spectrometry (LC-MS/MS). Bioinformatics databases and tools were used for protein/peptide (PPs) identification and gene localization. The PPs that differed significantly ( p < 0.05, ANOVA) in abundance with a fold change (FC) of ≥1.5 were identified. Results. Revealed 20 PPs, 11 were upregulated in women with very high FC (up to 8 folds), and 9 were upregulated in men but with much lower FC. The PPs are encoded by genes located in autosomal chromosomes, indicative of sex-biased gene expression. The only PP related to sex, the sex hormone-binding globulin, was upregulated in women. The remaining PPs were involved in immunity, lipid metabolism, gene expression, connective tissue, and others, with some overlap in function. Conclusions. The upregulated PPs in men or women are mostly reflecting the functon or risk/protection provided by the PPs to the specific sex, e.g., Apo-B100 of LDLC. Finally, the basis of sex-biased gene expression and sex phenotypic differences needs further investigation.

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“…Of the noticeable upregulated PPs in men, the 2 connective tissue (CT) proteins, bronectin and vitronectin, the sex-differences in the levels of both PPs was not reported before. However, both proteins were noticed to be upregulated in T2DM [6,44]. Furthermore, men and women differ in musculoskeletal system in which CT proteins are major component [45].…”

Section: Discussionmentioning

confidence: 96%

Sex-Biased Expression of Genes Allocated in the Autosomal Chromosomes: Lc-ms/ms Protein Profiling in Healthy Subjects

Giha¹,

Abdulwahab²,

Abbas³

et al. 2021

Preprint

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Sex and gender has large impact in human health and disease prediction. Men differ from women by a limited number of genes in Y chromosome while their phenotypes differ markedly. In this study, serum samples from healthy Bahraini men and women were analyzed by LC-MS/MS. Bioinformatics databases were used for proteins/peptides (PPs) identification and their gene localization. Results revealed that, the PPs which differed significantly (p<0.05 ANOVA) in abundance with fold change (FC) of ³1.5, were twenty, 11 were up-regulated in women (up to 8-folds), and 9 were up-regulated in men but with much lower FC, however, all PPs are encoded by genes located in autosomal chromosomes, indicative of sex-biased gene expression. The only PP related to sex, the sex hormone-binding globulin, was up-regulated in women. The remaining PPs were involved in immunity (6), lipid metabolism (5), gene expression (3) connective tissue (3), and others. The identified PPs were discussed within their physiological and pathological context, in relation to sex e.g. Apo-B100 (pathological cholesterol) was unregulated in men while the inflammatory/immunity related PPs, including Alpha-1-acid glycoproteins, were up-regulated in women. Finally, we propose proteomic as an ideal complementary tool for study of the molecular basis of the sex-biased gene expression.

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Association of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) with T2DM

Cited by 8 publications

References 38 publications

The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

The Identification of Key Genes and Biological Pathways in Polycystic Ovary Syndrome and its Complications by Next Generation Squancing (NGS) and Bioinformatics Analysis

Sex-Biased Expression of Genes Allocated in the Autosomal Chromosomes: Blood LC-MS/MS Protein Profiling in Healthy Subjects

Sex-Biased Expression of Genes Allocated in the Autosomal Chromosomes: Lc-ms/ms Protein Profiling in Healthy Subjects

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