Noninvasive early detection of colorectal cancer by hypermethylation of the LINC00473 promoter in plasma cell-free DNA

Abstract

Background Current noninvasive assays have limitations in the early detection of colorectal cancer. We evaluated the clinical utility of promoter methylation of the long noncoding RNA LINC00473 as a noninvasive biomarker to detect colorectal cancer and associated precancerous lesions. Methods We evaluated the epigenetic regulation of LINC00473 through promoter hypermethylation in colorectal cancer cell lines using bisulfite genomic sequencing and expression analyses. DNA methylation of LINC00473 was analyzed in primary colorectal tumors using 450K arrays and RNA-seq from The Cancer Genome Atlas (TCGA). Tissue-based findings were validated in several independent cohorts of colorectal cancer and advanced colorectal polyp patients by pyrosequencing. We explored the clinical utility of LINC00473 methylation for the early detection of colorectal cancer in plasma cell-free DNA by quantitative methylation-specific PCR and droplet digital PCR. Results LINC00473 showed transcriptionally silencing due to promoter hypermethylation in colorectal cancer cell lines and primary tumors. Methylation of the LINC00473 promoter accurately detected primary colorectal tumors in two independent clinical cohorts, with areas under the receiver operating characteristic curves (AUCs) of 0.94 and 0.89. This biomarker also identified advanced colorectal polyps from two other tissue-based clinical cohorts with high diagnostic accuracy (AUCs of 0.99 and 0.78). Finally, methylation analysis of the LINC00473 promoter in plasma cell-free DNA accurately identified patients with colorectal cancer and advanced colorectal polyps (AUCs of 0.88 and 0.84, respectively), which was confirmed in an independent cohort of patients. Conclusions Hypermethylation of the LINC00473 promoter is a new promising biomarker for noninvasive early detection of colorectal cancer and related precancerous lesions.

Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

“…Since the first immortalized cell line (HeLa) was established 25 , human cancer-derived cell lines have been demonstrated to be fundamental models used in laboratories for many years to understand the biology of cancer and pursue clinical applications 21 , 26 , 27 . Recent findings based on the characterization of hundreds of cell lines with omics technologies reinforced the concept of cell line usefulness in medical research 28 .…”

DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma

“…Other reports demonstrated that LINC00473 is downstream of the fusion oncoprotein CRTC1-MAML2 in mucoepidermoid carcinoma, and that the deletion of CRTC2/3 leads to decreased levels of LINC00473 [ 48 , 64 ]. In contrast, LINC00473 was discovered to be transcriptionally silenced due to promoter hypermethylation in colorectal cancer and was suppressed in osteosarcoma cells by the direct binding of ZBTB7A (encoding Pokemon) to the LINC00473 promoter [ 50 , 65 ].…”

Cancer-associated fibroblasts drive colorectal cancer cell progression through exosomal miR-20a-5p-mediated targeting of PTEN and stimulating interleukin-6 production

“…Additionally, the discovery of novel therapeutic targets is of utmost importance for enhancing the treatment of CRC. There is also a pressing need for non-invasive diagnostic tools to reduce the mortality rates associated with CRC [ 33 , 34 ].…”