New Generation of Clinical Epigenetics Analysis and Diagnosis for Precision Medicine

Abstract

Following the application of epigenetic and epigenomics research into tumor diseases, cardiovascular disease, diabetes, hereditary diseases, and rare diseases, in vitro diagnostics (IVD) epigenetic and epigenomics are increasingly employed for those patients. Here, we review a clinical sampling of epigenetics and epigenomics from patients. We then present procedures, including the detection procedure of clinical epigenetic approaches from clinical samples, clinical epigenomic methods applied to those samples, the small cell number of epigenetics, and epigenomics. Finally, we present the current IVD of epigenetics and epigenomics used for clinical analysis and diagnosis, along with the development of approaches. To improve clinical study and diagnosis, we also introduce clinical research and clinical applications to develop a more comprehensive strategy to maximize the sensitivity and specificity of the epigenetics and epigenomics analysis and diagnosis.

Keywords: epigenetics; epigenomics; in vitro diagnostics (IVD); single-cell diagnosis.

Figure 1

(A) DNA methylation. Methylation of cytosine is a covalent modification of DNA, in which hydrogen H5 of cytosine is replaced by a methyl group under DNA methyltransferase (DNMT). In mammals, 60–90% of all CpGs are methylated. The pattern of methylation controls protein binding to target sites on DNA, affecting changes in gene expression and in chromatin organization, often silencing genes, which physiologically orchestrates processes like differentiation and pathologically leads to cancer. (B) Histone post-transcriptional modification. Histones H2A, H2B, H3, and H4 are formed as the core histones with some long ‘tails’ located on one end for enzyme modifications, including methylation, acetylation, phosphorylation, and ubiquitination to adjust the regulatory proteins. The most well-understandable amino acids in histone in tumor diseases are H3K4Me3 and H3K36Me3 (activity, red color) and H3K9me2/3 and H3K27me3 (repressor, green color). K = lysine and R = arginine. (C) lncRNA modification.

Figure 2

Clinical epigenetic and epigenome analysis. Process from sampling performance, epigenome and epigenome application for DNA hypermethylation, histone modification, and lncRNA for clinical epigenetic and epigenomic analysis and diagnosis. Pink means sampling and abnormal epigenetic changes, which will be discussed in detail in the manual.

Figure 3

Hypermethylation detection technique. All technologies to detect DNA methylation are classified: Local specific genes which have been successfully employed in both research lab and clinical fields; Genomic regions and global measurement at a genome-wide scale based on sequencing technology and microarray, which have been successfully used in both research and clinical fields; Global measures of DNA methylation, which are often applied for research lab or clinical lab with equipment; and DNMT assay.

Figure 4

Abnormal histone detection technique. First step is sampling, including cell level and tissue level. Second step is the ChIP process, including crossing-binding, cell lysis, Ab-binding, and DNA purification. Third is the detection step, including ChIP PCR, ChIP-chip, and ChIP-seq.

Figure 5

Abnormal lncRNA detection technique. (A) Specific lncRNA detection by either real-time PCR, (B) lncRNA FISH, (C) genomic detection by microarray, and (D) next-generation RNA sequencing.

Figure 6

Abnormal histone confirmation technique. After abnormal histone modification is discovered, two kinds of confirmation assays for abnormal histone modification have been used in clinical patients: abnormal acetylation histone modification and abnormal histone methylation modification.