Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer

Abstract

Background Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide and in need of novel potential diagnostic biomarkers for early discovery. Methods We conducted a two-step study. We first employed bioinformatics on data from The Cancer Genome Atlas to obtain potential biomarkers and then experimentally validated some of them on our clinical samples. Our aim was to find a methylation alteration common to all clusters, with the potential of becoming a diagnostic biomarker in CRC. Results Unsupervised clustering of methylation data resulted in four clusters, none of which had a known common genetic or epigenetic event, such as mutations or methylation. The intersect among clusters and regulatory regions resulted in 590 aberrantly methylated probes, belonging to 198 differentially expressed genes. After performing pathway and functional analysis on differentially expressed genes, we selected six genes: CEP55 , FOXD3 , FOXF2 , GNAO1 , GRIA4 and KCNA5 , for further experimental validation on our own clinical samples. In silico analysis demonstrated that CEP55 was hypomethylated in 98.7% and up-regulated in 95.0% of samples. Genes FOXD3 , FOXF2 , GNAO1 , GRIA4 and KCNA5 were hypermethylated in 97.9, 81.1, 80.3, 98.4 and 94.0%, and down-regulated in 98.3, 98.9, 98.1, 98.1 and 98.6% of samples, respectively. Our experimental data show CEP55 was hypomethylated in 97.3% of samples and down-regulated in all samples, while FOXD3 , FOXF2 , GNAO1 , GRIA4 and KCNA5 were hypermethylated in 100.0, 90.2, 100.0, 99.1 and 100.0%, and down-regulated in 68.0, 76.0, 96.0, 95.2 and 84.0% of samples, respectively. Results of in silico and our experimental analyses showed that more than 97% of samples had at least four methylation markers altered. Conclusions Using bioinformatics followed by experimental validation, we identified a set of six genes that were differentially expressed in CRC compared to normal mucosa and whose expression seems to be methylation dependent. Moreover, all of these six genes were common in all methylation clusters and mutation statuses of CRC and as such are believed to be an early event in human CRC carcinogenesis and to represent potential CRC biomarkers. Electronic supplementary material The online version of this article (10.1186/s12920-019-0501-z) contains supplementary material, which is available to authorized users.

FOXF2 acts as a crucial molecule in tumours and embryonic development

“…CRC is one of the leading causes of cancer deaths worldwide 52 , and FOXF2 predominantly plays an anticancer role in CRC. A study by Hauptman et al showed that the FOXF2 gene was hypermethylated in 81.1% of CRC samples and was downregulated in 98.9% of the samples 26 . In addition, Chen, Zhang et al 27,28 .…”

“…Therefore, regulating the expression level of FOXF2 is an ideal treatment for tumours. Specifically, decreased FOXF2 expression is a marker of poor prognosis in grade II of TNBC 72 , NSCLC 20 , CRC 26 , ESCC 68 , GC 33 . Inhibitors of miR-200, miR-301, miR-182, miR-130, and miR-519 can be used to treat tumours.…”

“…Multiple studies have shown that FOXF2 can have roles in breast cancer 18,19 , lung cancer [20][21][22] , hepatocellular carcinoma (HCC) [23][24][25] , colorectal cancer (CRC) [26][27][28][29] , prostate cancer (PC) [30][31][32] , gastric cancer (GC) 33 , ovarian cancer (OC) 34 , rhabdomyosarcoma (RMS) in mice 35 and other tumours (Table 1). However, FOXF2 can both promote and inhibit proliferation, invasion and metastasis in tumours, depending on the type or subtype of the tumour.…”

Colorectal Cancer Early Detection in Stool Samples Tracing CpG Islands Methylation Alterations Affecting Gene Expression

“…Although knockdown of GRIA4 has been associated with dysregulation of genes involved in invasion and metastasis [15], its functional role in cancer is not fully elucidated. Interestingly, GRIA4-associated CGI has been found hypermethylated in CRC and adenomas [3,4,16].…”

The value of CEP55 gene as a diagnostic biomarker and independent prognostic factor in LUAD and LUSC

“…Related clinical studies have shown that CEP55 can be used as a diagnostic and prognostic marker for several cancers. For example, Nina Hauptman et al [13] found that CEP55 is a potential biomarker for colorectal cancer through bioinformatics methods and clinical studies; Yang Jia et al [14] found that in esophageal squamous cell carcinoma (ESCC), CEP55 overexpression is associated with poor prognosis in patients with locally advanced ESCC. Overexpression of CEP55 was significantly associated with a reduction in overall survival after surgery.…”