Biology subjects

Khanabadi, B.

Publications and source records attributed to Khanabadi, B..

2 recordsLinked to original sources

bioRxiv2023

Integrated bioinformatics and wet-lab analysis revealed prominent inflammatory genes of Extracellular Matrix as prognostic biomarkers in patients with advance IBD requiring early surgery

BackgroundThe number of patients with inflammatory bowel disease (IBD) is increasing worldwide. Due to the fact that at the age of 20 to 30 years, this autoimmune disease is very common; Investigating and identifying prognostic biomarkers in advanced IBD is very important; Because according to the identification of these biomarkers, patients who need early surgery can be nominated and undergo surgery without wasting time and treatment costs. In this study, with the aim of identifying effective biomarkers involved in the inflammatory part of extracellular matrix (ECM) in the early surgery of IBD, separately from Crohns disease and ulcerative colitis. MethodIn this study, we examined 50 patients in both patient groups as well as the normal group. The expression of the nominated genes MASP2, DKC1, HNF4A, and STAT3 was analyzed using quantitative polymerase chain reaction (Q-PCR) and relative quantification was determined using the 2-{Delta}{Delta}Ct method. ROC curve analysis was performed to compare IBD (UC & CD) and normal for the investigated genes. The correlation between adhesion molecule gene expression and immunophenotype was analyzed. Also we comprehensively analyzed the genetic alteration, prognostic value and gene regulatory networks using multiple databases. ResultThe obtained results showed that MASP2 and DKC1 genes were significantly expressed in advanced UC patients, as well as HNF4A and STAT3 in advanced CD patients. ConclusionIt can be stated that the biomarker panel MASP2, DKC1, HNF4A, and STAT3 related to them have a significant prognostic role in the candidates of IBD patients for early surgery. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/570869v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1f1de07org.highwire.dtl.DTLVardef@27db16org.highwire.dtl.DTLVardef@a095f2org.highwire.dtl.DTLVardef@d46c38_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Mixed data analysis detected Endocrine Fibroblast Growth Factors (FGF19, FGF21, and FGF23) as Prognostic and Diagnostic Markers of Colorectal Neoplasia and Carcinoma

BackgroundEndocrine fibroblast growth factors (eFGFs) play important roles in various cellular signaling processes such as development and differentiation. These genes were also found to be significantly related to several cancer. However, little is known about the role of eFGFs in colon neoplasia and colon adenocarcinoma (COAD). MethodsWe performed systematically and comprehensively investigated the gene expression, DNA methylation, prognostic significance, genetic alteration, co-expressed genes, protein-protein interaction, small molecules pathway, and drug interactions of eFGFs based on the TIMER2.0, GEPIA2, UALCAN, OncoDB, cBioPortal, LinkedOmics, STRING, SMPDB, htfTarget, mirTarBase, circBank and DGIdb databases. Ultimately, the correlations of eFGFs expressions between polyp and COAD tissues compared to normal mucosa were validated using qRT-PCR as a cross-sectional part of our study. ResultsThe results indicated that eFGFs are highly expressed in COAD, and abnormal gene expressions may be related to promoter methylation. In this matter, methylation analysis revealed promotor hypermethylation of FGF19 and FGF21. Conversely, FGF23 was shown to have a tendency for promotor hypomethylation. Moreover, hypermethylation of FGF21 and FGF23 and downregulation of FGF23 were found to be detrimental to the survival of COAD patients. KEGG pathway analyses indicated that the co-expressed genes of eFGF family members were mainly related to the regulation of the actin cytoskeleton and, more notably, in Ras signaling, PI3k-Akt signaling, Rap1 signaling, and cancer pathways. Based on qRT-PCR results, FGF21 was significantly overexpressed in the colon polyps compared to normal mucosa. Additionally, RNA expression of FGF21 and FGF23 was markedly elevated in adenomatous polyps as opposed to hyperplastic polyps. ConclusionCollectively, these findings reveal the critical roles of eFGFs in COAD tumorigenesis and suggest eFGF family members as promising prognostic and diagnostic markers for CRC as well as discriminating markers for high-risk from low-risk polyps.

bioinformatics↗