Aberrant promoter methylation of PPP1R3C and EFHD1 in plasma of colorectal cancer patients

Abstract

Aberrant DNA methylation is a common epigenetic alteration involved in colorectal cancer (CRC). In our previous study, we performed methylated DNA immunoprecipitation-on-chip analysis combined with gene re-expression analysis by 5-aza-2′-deoxycytidine treatment, to identify methylation genes in CRC genome widely. Among these genes, 12 genes showed aberrant hypermethylation frequently in >75% of 149 CRC samples but did not in normal samples. In this study, we aim to find out any of these methylation genes to be utilized for CRC detection using plasma DNA samples. Primers for methylation-specific PCR and pyrosequencing were designed for seven of the 12 genes. Among them, PPP1R3C and EFHD1 were rarely hypermethylated in peripheral blood cells, but frequently hypermethylated in 24 CRC tissue samples and their corresponding plasma samples. In plasma samples, PPP1R3C was methylated in 81% (97/120) of CRC patients, but only in 19% (18/96) of noncancer patients (P = 6 × 10−20, Fisher's exact test). In combined analysis with EFHD1, both genes were methylated in 53% (64/120) of CRC patients, but only in 4% (4/96) of noncancer patients (P = 2 × 10−16), giving high specificity of 96%. At least one of the two genes was methylated in 90% (108/120) of CRC patients, and 36% (35/96) of control patients, giving high sensitivity of 90%. Compared with low sensitivity of carcinoembryonic antigen (17% at stage I, 40% at stage II) and CA19-9 (0% at stage I, 13% at stage II) for early-stage CRCs, sensitivity of aberrant methylation was significantly higher: PPP1R3C methylation at 92% (11/12) for stage I and 77% (23/30) for stage II, and methylation of at least one gene at 100% (12/12) for stage I and 87% (26/30) for stage II. PPP1R3C methylation or its combined use of EFHD1 methylation was highly positive in CRC plasma samples, and they might be useful in detection of CRC, especially for early-stage CRCs.

Storkhead box 2 and melanoma inhibitory activity promote oral squamous cell carcinoma progression

“…Smith et al previously reported that in cDNA microarray analysis STOX2 expression is associated with prognosis in colon cancer, and our results are largely consistent with their findings [ 31 ]. Conversely, CpG island hypermethylation of STOX2 promoter region reportedly reduces STOX2 expression in colon adenoma and adenocarcinoma [ 32 , 33 ]. However, methylation of STOX2 was not observed in OSCC cells (data not shown).…”

DNA methylation markers detected in blood, stool, urine, and tissue in colorectal cancer: a systematic review of paired samples

“…EFHD1 (EF-hand domain family member D1) encodes a calcium-binding protein involved in mitosis, synaptic transmission, and cytoskeletal rearrangement [ 67 ]. In the present systematic review, methylation of EFHD1 had 79% sensitivity and 22% specificity for CRC in plasma [ 32 ]. When combined with the analysis of PPP1R3C methylation, sensitivity was 53% and specificity reached 96% [ 32 ].…”

“…In the present systematic review, methylation of EFHD1 had 79% sensitivity and 22% specificity for CRC in plasma [ 32 ]. When combined with the analysis of PPP1R3C methylation, sensitivity was 53% and specificity reached 96% [ 32 ]. No patients with adenoma were included in this study.…”

Analysis of phosphatases in ER-negative breast cancers identifies DUSP4 as a critical regulator of growth and invasion

“…In this study, we demonstrated that several other phosphatases (PPP1R3C, INPP4B, FBP1, PTPRT, MTMR9, and CANT1) are underexpressed in ER-negative compared to those in ER-positive breast cancers. The PPP1R3C gene is hypermethylated in colorectal cancer (CRC) [ 47 ], and is a candidate tumor suppressor gene in melanoma and is inactivated through promoter methylation [ 48 ]. Gewinner et al have shown that INPP4B regulates the PI3 K pathway and that its gene is located in a region frequently deleted in both breast cancer cell lines and high-grade breast tumors [ 49 – 51 ].…”