Global DNA 5hmC and CK195hmC+ Contents: A Promising Biomarker for Predicting Prognosis in Small Hepatocellular Carcinoma

Abstract

Background: 5-Hydroxymethylcytosine (5hmC) with dynamic existence possesses multiple regulatory functions. Whereas, 5hmC’s impact on small hepatocellular carcinoma (SHCC) remains unclear. The present work focused on characterizing 5hmC content within SHCC and assessing the possibility of using global genomic 5hmC level as the predicative factor of clinical outcome. Methods: This study applied ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) in measuring 5mC, 5fC and 5hmC contents. In addition, immunohistochemistry (IHC) was adopted to measure CK19 and 5hmC contents. Results: Research showed 5mC, 5hmC, and 5fC contents from global genomics of SHCC reduced extensively compared with healthy samples (p < 0.001). Moreover, SHCC was associated with lymph node metastasis (LNM). Greater 5mC and 5hmC levels were observed in non-metastasis group compared with the metastasis group (p < 0.001). Correlation analysis between the HBV DNA level and 5mC, 5fC and 5hmC levels exhibited that HBV DNA was associated with 5mC, 5hmC, and 5fC content reduction, which was verified in the cytological experiments. Moreover, 5hmC content had a negative correlation with the expression level of CK19 in SHCC. The decrease in 5hmC and CK19 containing 5hmC positive cell (called CK195hmC+) should be ascribed to the bad prognosis among SHCC patients. Conclusions: The contents of 5hmC and CK195hmC+ of genomic DNA might be adopted for predicting SHCC survival as an important biomarker.

Methylation in cornea and corneal diseases: a systematic review

“…This results in a chemical modification where methyl groups are covalently bonded to the cytosine residues [ 37 ]. Different types of DNA methylation include 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), N6-methyladenine and others [ 38 , 39 ], with 5mC being the most common type, and its DNA methylation status is influenced by specific regulatory molecules.…”

5hmC Immunohistochemistry: A Predictor of TERT Promoter Mutational Status in Follicular Thyroid Carcinoma?

“…The antibody was previously validated for use in IHC and in thyroid carcinoma. [15][16][17] 5hmC IHC (Clone 4D9) Following de-paraffinization and rehydration of FFPE sections, heat-induced antigen retrieval was performed using a decloaking chamber (Biocare Medical, Pleasant Hill, CA) set for 5 min at 110C in citrate buffer pH 6 (article C-9999, Sigma-Aldrich, St. Louis, MO). For quenching of endogenous peroxidase, a 30-min incubation in 0.15% hydrogen peroxidase was performed at room temperature, followed by a 30-min blocking step using 1% bovine serum albumin (article A-4503, Sigma-Aldrich, MA).…”

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

“…When we looked at the physiological functions of the TET proteins and their mechanisms of regulation of DNA methylation and transcription, out of the three TET genes TET1 and TET2, expression levels were shown to be low in hepatocellular carcinoma (HCC) tissues [ 303 , 304 ]. Studies have also revealed that global genomic 5hmC levels are down-regulated in HCC tissues and cell lines [ 305 , 306 ]. For designing early detection and therapeutic strategies, 5hmC signatures found in HCC tissues and in circulating cell-free DNA are important [ 305 ].…”