Noncoding Genomics in Gastric Cancer and the Gastric Precancerous Cascade: Pathogenesis and Biomarkers

Abstract

Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related death, whose patterns vary among geographical regions and ethnicities. It is a multifactorial disease, and its development depends on infection by Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), host genetic factors, and environmental factors. The heterogeneity of the disease has begun to be unraveled by a comprehensive mutational evaluation of primary tumors. The low-abundance of mutations suggests that other mechanisms participate in the evolution of the disease, such as those found through analyses of noncoding genomics. Noncoding genomics includes single nucleotide polymorphisms (SNPs), regulation of gene expression through DNA methylation of promoter sites, miRNAs, other noncoding RNAs in regulatory regions, and other topics. These processes and molecules ultimately control gene expression. Potential biomarkers are appearing from analyses of noncoding genomics. This review focuses on noncoding genomics and potential biomarkers in the context of gastric cancer and the gastric precancerous cascade.

Figure 1

Sequence of lesions produced by Helicobacter pylori infection (cag-positive vacA s1m1 is the most aggressive strain). The precancerous cascade starts with atrophic gastritis, which progresses to intestinal metaplasia, dysplasia, and, finally, gastric cancer.

Figure 2

Higher levels of methylation are observed in gastric mucosae of H. pylori-positive volunteers than in H. pylori-negative volunteers. Methylation levels were measured in the corpus and antrum of 56 H. pylori-negative volunteers and 98 H. pylori-positive volunteers. All the eight CGIs (core region of p16, noncore regions of p16 and THBD; core regions of LOX, HRASLS, FLNc, and HAND1; and p41ARC exonic CGI) showed significantly elevated methylation levels (5.4- to 303-fold) in the H. pylori-positive volunteers. Methylation levels in the corpus were at the same levels as those in the antrum (taken with permission from [61]).

Figure 3

(a) RPRM methylation in tumor and nontumor adjacent mucosa (NTAM) tissues: higher methylation levels in tumor tissues are observed in comparison to NTAM in all six paired GC cases (taken from [63]). (b) Histogram representing the percentage of positive cases for Reprimo and other genes (APC, SHP1, CDH-1, ER, SEMA3B, and 3OST2) in 43 prospectively collected gastric cancer cases and 31 asymptomatic age- and gender-matched controls. Only Reprimo shows significant differences in plasma between gastric cancer and asymptomatic controls (taken with permission from [68]).

Figure 4

Canonical pathway of miRNA biogenesis in human. miRNAs are transcribed by RNA polymerase II (RNAP II) from intergenic, intronic, or polycistronic loci to long primary transcript, called primary miRNA (pri-miRNA), which consists in a stem, a terminal loop, and single-stranded RNA segments at both the 5′- and 3′-UTR sides. Microprocessor complex (Drosha and DGCR8 cofactor) cleaves the stem-loop and releases a small hairpin-shaped RNA, called precursor miRNA (pre-miRNA). Following, pre-miRNA is exported into the cytoplasm by the transport complex formed by protein exportin 5 (EXP5) and GTP-binding nuclear protein RAN-GTP. Subsequently, pre-miRNAs are cleaved by a ternary complex formed by Dicer, TAR RNA Binding Protein (TRBP), and Protein Activator of PKR (PACT), producing small RNA duplexes (miRNA-miRNA ^∗). Next, these are loaded onto an Argonaute protein (AGO) to form an immature RNA-Induced Silencing Complex (RISC) or pre-RISC, in a process mediated for Heat shock cognate 70- (Hsc70-) Heat shock protein (Hsp90) chaperone complex. AGO protein separates the two strands to generate a mature RISC effector. Finally, RISC binds the target mRNA through complementary binding of 6 to 8 base pairs of the miRNA, with a specific sequence of the target resulting in the gene silencing.

Figure 5

Marked increasing expression of miR-221, miR-376c, and miR-744 over time in 20 GC cases during 15-year (1989–2003) follow-up period. Error bars represent 95% CI (taken with permission from [103]).