A Multi-Omics Analysis of Bone Morphogenetic Protein 5 (BMP5) mRNA Expression and Clinical Prognostic Outcomes in Different Cancers Using Bioinformatics Approaches

Abstract

Cumulative studies have provided controversial evidence for the prognostic values of bone morphogenetic protein 5 (BMP5) in different types of cancers such as colon, breast, lung, bladder, and ovarian cancer. To address the inconsistent correlation of BMP5 expression with patient survival and molecular function of BMP5 in relation to cancer progression, we performed a systematic study to determine whether BMP5 could be used as a prognostic marker in human cancers. BMP5 expression and prognostic values were assessed using different bioinformatics tools such as ONCOMINE, GENT, TCGA, GEPIA, UALCAN, PrognoScan, PROGgene V2 server, and Kaplan–Meier Plotter. In addition, we used cBioPortal database for the identification and analysis of BMP5 mutations, copy number alterations, altered expression, and protein–protein interaction (PPI). We found that BMP5 is frequently down-regulated in our queried cancer types. Use of prognostic analysis showed negative association of BMP5 down-regulation with four types of cancer except for ovarian cancer. The highest mutation was found in the R321*/Q amino acid of BMP5 corresponding to colorectal and breast cancer whereas the alteration frequency was higher in lung squamous carcinoma datasets (>4%). In PPI analysis, we found 31 protein partners of BMP5, among which 11 showed significant co-expression (p-value < 0.001, log odds ratio > 1). Pathway analysis of differentially co-expressed genes with BMP5 in breast, lung, colon, bladder and ovarian cancers revealed the BMP5-correlated pathways. Collectively, this data-driven study demonstrates the correlation of BMP5 expression with patient survival and identifies the involvement of BMP5 pathways that may serve as targets of a novel biomarker for various types of cancers in human.

Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia

“…CD147, also termed as EMMPRIN or basigin, is a pleiotropic molecule with various effects (Grass & Toole, 2016 ; Iacono et al., 2007 ). Given the emerging use of bioinformatics in biological research (Karim et al., 2020 ; Mehmood et al., 2014 ), it is worth mentioning that, through pathway analyses, CD147 was found to be a significant cell-surface protein contributing to chemoresistance and cell survival in cancer-stem-cell-like cells (Kang et al., 2013 ), and the invasion of various cancers (Li et al., 2015 ; Liang et al., 2016 ; Zheng & Gong, 2017 ). Additionally, it was found to be highly expressed in activated regulatory T lymphocytes, enabling it to be a potential marker for distinguishing cytokine-producing activated T lymphocytes from resting T lymphocytes (Landskron & Taskén, 2013 ; Solstad et al., 2011 ).…”

Suppressor genes as molecular markers of colorectal cancer – a review of the latest reports

“…It is worth emphasising that all previous reports, together with those mentioned above, about the role of BMP5 in CRC have been confirmed in the latest multibioinformatic analysis from 2019 done by Adnan Karim et al According to this report, BMP5 meets the conditions for becoming a new biomarker and a potential therapeutic target for various human cancers, including CRC [48].…”

Computational assessment of MCM2 transcriptional expression and identification of the prognostic biomarker for human breast cancer

“…The mRNA expression levels of MCM2 gene in BC and normal tissue counterparts were evaluated with the Oncomine [ 24 , 25 ], UALCAN ( http://ualcan.path.uab.edu/ ) [ 29 , 30 ], GEPIA2, and HPA ( https://www.proteinatlas.org/ ) databases [ 31 ]. The GEPIA2 database contains data from 1,085 tumors and 291 normal tissues related to BC where the type of cancers can be predicted by the query sample based on the intensity of gene expression.…”

“…The GEPIA2 database contains data from 1,085 tumors and 291 normal tissues related to BC where the type of cancers can be predicted by the query sample based on the intensity of gene expression. The UALCAN is a web-resource to perform in-depth analysis of the cancer transcriptome such as TCGA expression data [ 29 , 30 ]. The UALCAN webserver contains data from 1097 cancers and 114 normal tissues where users can determine the potential biomarkers and validate the potential gene of interest.…”

“…The mRNA expression of the MCM2 gene in BC patients was analyzed based on their clinicopathological characteristics in TCGA datasets with the UALCAN server [ 29 , 30 ]. The analysis was performed by comparing breast cancer tissues with healthy tissues where all the parameters were kept defaults.…”