Alternatively Spliced Isoforms of MUC4 and ADAM12 as Biomarkers for Colorectal Cancer Metastasis

Abstract

There is a pertinent need to develop prognostic biomarkers for practicing predictive, preventive and personalized medicine (PPPM) in colorectal cancer metastasis. The analysis of isoform expression data governed by alternative splicing provides a high-resolution picture of mRNAs in a defined condition. This information would not be available by studying gene expression changes alone. Hence, we utilized our prior data from an exon microarray and found ADAM12 and MUC4 to be strong biomarker candidates based on their alternative splicing scores and pattern. In this study, we characterized their isoform expression in a cell line model of metastatic colorectal cancer (SW480 & SW620). These two genes were found to be good prognostic indicators in two cohorts from The Cancer Genome Atlas database. We studied their exon structure using sequence information in the NCBI and ENSEMBL genome databases to amplify and validate six isoforms each for the ADAM12 and MUC4 genes. The differential expression of these isoforms was observed between normal, primary and metastatic colorectal cancer cell lines. RNA-Seq analysis further proved the differential expression of the gene isoforms. The isoforms of MUC4 and ADAM12 were found to change expression levels in response to 5-Fluorouracil (5-FU) treatment in a dose-, time- and cell line-dependent manner. Furthermore, we successfully detected the protein isoforms of ADAM12 and MUC4 in cell lysates, reflecting the differential expression at the protein level. The change in the mRNA and protein expression of MUC4 and ADAM12 in primary and metastatic cells and in response to 5-FU qualifies them to be studied as potential biomarkers. This comprehensive study underscores the importance of studying alternatively spliced isoforms and their potential use as prognostic and/or predictive biomarkers in the PPPM approach towards cancer.

Characterizing and forecasting neoantigens-resulting from MUC mutations in COAD

“…In this study, through comprehensive analyses by TSNAD v2.0 NetMHCpan v4.0, 157 INDELs, 1 TS, and 57 SNVs were identified as potential neoantigens for MUC mutated genes showing high affinity with MHC-I. Interestingly, 94 INDELs were for MUC4, which is consistent with a previous study that found that MUC4 was highly alternative splicing in CRC [ 68 ].…”

Characterizing and Forecasting Neoantigens Resulting from MUC Mutations in COAD

“…Based on analyses with TSNAD v1.0 NetMHCpan v4.0 [26,60,61] MUC4, which is consistent with a previous study that found that MUC4 was highly alternative splicing in CRC [63].…”

Dissecting Crucial Gene Markers Involved in HPV-Associated Oropharyngeal Squamous Cell Carcinoma from RNA-Sequencing Data through Explainable Artificial Intelligence

“…Current methods for diagnosing and monitoring OPSCC remain insufficient; the development of biomarkers can help in early patient diagnosis and monitoring of treatment response, thereby improving the survival rates and lowering the recurrence rates. The development of predictive biomarkers can predict a disease's course and ascertain therapeutics' success [19]. Differential expression analysis scrutinizes gene expression motifs and collocates the molecular processes underlying convoluted illnesses.…”