| Author/Editor | Hauptman, Nina; Jevšinek Skok, Daša; Spasovska, Elena; Boštjančič, Emanuela; Glavač, Damjan | |
| Title | Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer | |
| Type | članek | |
| Vol. and No. | Letnik 12, št. 1 | |
| Publication year | 2019 | |
| Volume | str. 1-17 | |
| ISSN | 1755-8794 - BMC medical genomics | |
| Language | eng | |
| Abstract | Background:Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide and in need ofnovel potential diagnostic biomarkers for early discovery.Methods:We conducted a two-step study. We first employed bioinformatics on data from The Cancer GenomeAtlas to obtain potential biomarkers and then experimentally validated some of them on our clinical samples. Ouraim 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 washypomethylated in 97.3% of samples and down-regulated in all samples, whileFOXD3,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 and84.0% 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. More over, all of these six genes were common in all methylation clusters and mutation statuses of CRCand as such are believed to be an early event in human CRC carcinogenesis and to represent potential CRC biomarkers. | |
| Keywords | kolorektalni rak metilacija eksperimentalna validacija colorectal cancer methylation experimental validation |