Identification of MSX1 and DCLK1 as mRNA Biomarkers for Colorectal Cancer Detection Through DNA Methylation Information

Abstract

Colorectal cancer is the second most deadly malignancy in the United States. However, the currently screening options had their limitation. Novel biomarkers for colorectal cancer detections are necessary to reduce the mortality. The clinical information, mRNA expression levels and DNA methylation information of colorectal cancer were downloaded from TCGA. The patients were separated into training group and testing group based on their platforms for DNA methylation. Beta values of DNA methylation from tumor tissues and normal tissues were utilized to figure out the position that were differentially methylated. The expression levels of mRNA of thirteen genes, whose CpG islands were differentially methylated, were extracted from the RNA-Seq results from TCGA. The probabilities whether the mRNA was differentially expressed between tumor and normal samples were calculated using Student's t-test. Logistic regression and decision tree were built for cancer detection and their performances were evaluated by the area under the curve (AUC). Twenty-four genomic locations were differentially methylated, which could be mapped to eleven genes. Nine out of eleven genes had differentially expressed mRNA levels, which were used to build the model for cancer detection. The final detection models consisting of mRNA expression levels of these nine genes had great performances on both training group and testing group. The model that constructed in this study suggested MSX1 and DCLK1 might be used in colorectal cancer detection or as target of cancer therapies. J. Cell. Physiol. 232: 1879-1884, 2017. © 2016 Wiley Periodicals, Inc.

A Combined four-mRNA Signature Associated with Lymphatic Metastasis for Prognosis of Colorectal Cancer

“…With the development of high-throughput sequencing, microarray technology and bioinformatics, more and more biomarkers have been discovered to effectively predict the prognosis of patients with CRC [17]. For example, Ai-Jun Sun et al started bioinformatics data mining from the DNA methylation information in the tcga database and found that MSX1 and DCLK1, which are involved in DNA methylation, may be used as biomarkers for CRC [18]. Zong Z et al found that MSI-2 is highly expressed in CRC tissues.…”

Increased DCLK1 correlates with the malignant status and poor outcome in malignant tumors: a meta-analysis

“…Recently, it has been reported that combination of DCLK1 inhibition with irradiation has a synergistic effect in HNSCC cell lines [ 11 ]. DCLK1 is therefore considered as an attractive and potential therapeutic target in the treatment of malignant tumors [ 30 , 31 ]. Due to the limitations of currently available evidence on the therapeutic effects and molecular biology of DCLK1 in malignant tumors, Further studies are warranted to investigate these in more detail.…”

Biological significance of RNA-seq and single-cell genomic research in woody plants

“…These results would be valuable for functional genomic studies of desert plants under abiotic stresses (Long et al 2014). In another RNAseq study in H. ammodendron, RNA-seq analyses have identified a total of 87,109 unigenes and 3353 of them were differentially expressed in shoots and 4564 of them differentially expressed in in roots (Gao et al 2017).…”

“…Novel biomarkers are important for detection of growth, development, and disease resistance. Single cell RNA-seq is valuable to elucidate cell type composition through identification of transcripts and biomarkers; for example, methylated genomic locations could be used to build the model for disease detection (Sun et al 2017). RNA nextgeneration sequencing could be used to characterize patterns of miRNAs and comprehensive profiling of miRNA transcriptome will provide to be useful for further functional validation and biomarker identification (Gecaj et al 2017).…”