Advances in epigenetics of gastric cancer

Gastric cancer is a deadly disease and remains the third leading cause of cancer-related death worldwide. The 5-year overall survival rate of patients with early-stage localized gastric cancer is more than 60%, whereas that of patients with distant metastasis is less than 5%. Surgical resection is the best option for early-stage gastric cancer, while chemotherapy is mainly used in the middle and advanced stages of this disease, despite the frequently reported treatment failure due to chemotherapy resistance. Therefore, there is an unmet medical need for identifying new biomarkers for the early diagnosis and proper management of patients, to achieve the best response to treatment. Long non-coding RNAs (lncRNAs) in body fluids have attracted widespread attention as biomarkers for early screening, diagnosis, treatment, prognosis, and responses to drugs due to the high specificity and sensitivity. In the present review, we focus on the clinical potential of lncRNAs as biomarkers in liquid biopsies in the diagnosis and prognosis of gastric cancer. We also comprehensively discuss the roles of lncRNAs and their molecular mechanisms in gastric cancer chemoresistance as well as their potential as therapeutic targets for gastric cancer precision medicine.

e15509 Background: Studies showed that the gene promoter methylation may be the third important mechanisms of gene expression regulation. Abnormal methylation of tumor suppressor gene can be detected in the early stage of tumor, by screening the methylation profile of gastric cancer (GC), it can provide theoretical and experimental evidence for early diagnosis, treatment and prognosis. Methods: Detecte p16, hMLH1 and CDH1 promoter methylation, the p16, hMLH1 and E-cadher expression in GC tissues and its correlation with clinicopathological features and prognosis. Detect methylation of hMLH1 promoter and mRNA expression in GC cell line and normal gastric mucosa cell line. Clone formation assay and Transwell test. Results: The methylation of hMLH1 and CDH1 in GC and adjacent tissues were statistically significant . The methylation of hMLH1 was related to alcohol , CA199 level and Borrman. The methylation of CDH1 was related to the CEA level. The methylation of hMLH1 promoter is related to OS in GC patients. The methylation of p16 and CDH1 was not related to the OS ofGC patients. The GC patients with 0 or 1 gene methylation had a better prognosis than those with 3 or 2 gene methylation. The p16, hMLH1 and E-cadherin protein expression in GC and adjacent tissues were statistically significant. The p16 protein expression was related to tumor size. The hMLH1 protein expression was related to the CA199 level and tumor size. The E-cadherin expression in GC patients with drinking history was lower than ones without drinking history. The p16, hMLH1 and E-cadherin protein expression was not related to the OS of GC patients. There was a negative correlation between hMLH1 gene methylation and its protein expression in GC. The number of clones in the control group and the experimental group were 180 ± 3 and 169 ± 6. The number of cells in the control group and the experimental group were 135 ± 4.08 and 125 ± 4.18. Conclusions: The methylation of multiple genes is associated with the prognosis, which can provide theoretical basis for accurate treatment and prognosis for GC patients.

Gastrointestinal (GI) cancer represent significant health challenges, affecting the digestive system with often subtle symptoms that can delay diagnosis. GI cancers account for a higher global mortality rate than any other cancer, largely due to the limited availability of highly effective treatment options." Due to next-generation sequencing and new preclinical model tools, that we have learned more regarding its pathophysiology and molecular changes. Every molecular subtype has been characterised molecularly and new treatment targets have been found. Furthermore, tumour xenografts and organoids are grown from patients and are increasingly powerful resources for investigating GI patients' genetic evolution, identifying biomarkers, screening drugs, and conducting preclinical evaluations of personalised medicine approaches. Gastrointestinal (GI) cancer research is rapidly evolving, with recent advancements in precision medicine and immunotherapy offering new treatment options. Cuttingedge therapies, such as immune checkpoint inhibitors and targeted therapies like BRAF and HER2 inhibitors, are showing promise in treating specific types of GI cancers. These changes are making it possible for the age of precision medicine to use a mix of clinical, genomebased, and phenotype-based methods to diagnose and treat each GI patient individually. Clinical trials are exploring novel combinations of therapies to enhance survival rates and reduce side effects for patients with GI cancers, including colorectal, gastric, and pancreatic cancers. These developments are reshaping the future of gastrointestinal oncology. The purpose of this review is to study the current state of knowledge about predictive biomarkers, prospective novel targeted treatments, potential causes of conflicting trial outcomes, and the prospects for precision medicine in gastric cancer in the future.

<div>Abstract<p>Gastric cancer is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvements, the clinical outcome for patients with advanced gastric cancer is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multilevel platform of gastric cancer models, comprising 100 patient-derived xenografts (PDX), primary cell lines, and organoids. Samples were classified according to their histology, microsatellite stability, Epstein–Barr virus status, and molecular profile. This PDX platform is the widest in an academic institution, and it includes all the gastric cancer histologic and molecular types identified by The Cancer Genome Atlas. PDX histopathologic features were consistent with those of patients' primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number gain of tyrosine kinases/<i>KRAS</i> genes, and microsatellite stability status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell–intrinsic microsatellite instability (MSI) signature, which was efficiently exported to gastric cancer, allowing the identification, among microsatellite stable (MSS) patients, of a subset of MSI-like tumors with common molecular aspects and significant better prognosis. In conclusion, we generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel “druggable” targets and optimize therapeutic strategies. Moreover, transcriptomic analysis of gastric cancer PDXs allowed the identification of a cancer cell–intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis.</p>Significance:<p>This study reports a multilevel platform of gastric cancer PDXs and identifies a MSI gastric signature that could contribute to the advancement of precision medicine in gastric cancer.</p></div>

<div>Abstract<p>Gastric cancer is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvements, the clinical outcome for patients with advanced gastric cancer is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multilevel platform of gastric cancer models, comprising 100 patient-derived xenografts (PDX), primary cell lines, and organoids. Samples were classified according to their histology, microsatellite stability, Epstein–Barr virus status, and molecular profile. This PDX platform is the widest in an academic institution, and it includes all the gastric cancer histologic and molecular types identified by The Cancer Genome Atlas. PDX histopathologic features were consistent with those of patients' primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number gain of tyrosine kinases/<i>KRAS</i> genes, and microsatellite stability status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell–intrinsic microsatellite instability (MSI) signature, which was efficiently exported to gastric cancer, allowing the identification, among microsatellite stable (MSS) patients, of a subset of MSI-like tumors with common molecular aspects and significant better prognosis. In conclusion, we generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel “druggable” targets and optimize therapeutic strategies. Moreover, transcriptomic analysis of gastric cancer PDXs allowed the identification of a cancer cell–intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis.</p>Significance:<p>This study reports a multilevel platform of gastric cancer PDXs and identifies a MSI gastric signature that could contribute to the advancement of precision medicine in gastric cancer.</p></div>

INTRODUCTION: Helicobacter pylori (HP) is a type 1 carcinogen for gastric cancer (GC), the second most common cause of cancer-related death worldwide. The limited benefit of HP eradication or nutritional intervention in risk reduction and the dismal prognosis of GC underlie the urgent need for new preventive strategies. We have recently shown that Hp causes aberrant DNA methylation of tumor suppressor genes to promote gastric carcinogenesis (Cheng et al. 2013). However, the functional and mechanistic relationships between aberrant DNA methylation and GC remain elusive. AIMS&METHODS: We investigated the effect of 5-aza-2′-deoxycytidine (5′Aza-dC), a FDA-approved demethylating agent in a murine GC model induced by N-Nitroso-N-methylurea (MNU). Using MethylCap-microarray, quantitative RT-PCR and Western blot, we identified novel DNA methylation-controlled genes in paired GC tumors/adjacent tissues (4), 5′Aza-dC-treated (3) and -untreated (3) normal mucosa samples, followed by pyrosequencing and gene expression validation in human GC samples and cell lines. Gene functions were investigated by cell cycle and colony formation assays. RESULTS: At 52 weeks-post MNU exposure, GC was developed in 8 out of 19 mice. Administration of 5′Aza-dC for 24 weeks significantly reduced GC incidence from 42.1 to 11.1% (2/18 mice; p<0.05). Microarray analysis uncovered 12 significant and recurrent hypermethylated genes exclusive in GCs. However, only growth/differentiation factor 1 (Gdf1), a ligand for transforming growth factor-beta (TGF-β) signaling, had significantly lower mRNA expression in tumors compared to both tumor-adjacent and normal tissues (p<0.05). Notably, 5′Aza-dC treatment reactivated Gdf1 expression to the normal mucosal level. In human GCs, aberrant GDF1 methylation (>1.5-fold increase compared to tumor-adjacent tissues) was observed in 58.3% (14 out of 24) cases, which was accompanied with significant GDF1 down-regulation in both mRNA (p<0.005) and protein levels. Compared with normal mucosa, 7/8 GC cell lines exhibited GDF1 silencing, which could be reactivated by genome demethylation. Ectopic GDF1 expression increased SMAD2/3 phosphorylation and significantly suppressed GC cell proliferation at least partially through G1 phase cell cycle arrest. CONCLUSIONS: Epigenetic silencing of GDF1 may abrogate the growth-inhibitory effects of TGF-β signaling and render selective growth advantage to gastric epithelial cells during carcinogenesis. Our findings demonstrate a causal relationship between DNA methylation and GC development and lend support to demethylating drugs for GC chemoprevention trial. This study was supported by RFCID (08070172) and CUHK Direct Grant. REFERENCE: Cheng AS, et al. Helicobacter pylori causes epigenetic dysregulation of FOXD3 to promote gastric carcinogenesis. Gastroenterology 2013;144:122-33.e9. Citation Format: Wei Qin Yang, May S. M. Li, Wei Kang, Li Han Zeng, Tian Hai Wang, Anthony W. Chan, Enders K. W. Ng, Ka F. To, Francis K. L. Chan, Jun Yu, Michael W.Y. Chan, Joseph J. Y. Sung, Alfred S. L. Cheng. Reactivation of growth/differentiation factor 1 contributes to the chemopreventive effect of 5-aza-2′deoxycytidine in gastric cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1245. doi:10.1158/1538-7445.AM2014-1245

Gastric cancer (GC) is a major cause of cancer-related mortality worldwide. It is often associated with a bad prognosis because of its asymptomatic phenotype until advanced stages, highlighting the need for its prevention and early detection. GC development is preceded by the emergence of gastric preneoplasia lesions (GPNLs), namely atrophic gastritis (AG), intestinal metaplasia (IM), and dysplasia (DYS). GC is currently diagnosed by endoscopy, which is invasive and costly and has limited effectiveness for the detection of GPNLs. Therefore, the discovery of non-invasive biomarkers in liquid biopsies, such as blood samples, in order to identify the presence of gastric preneoplasia and/or cancer lesions at asymptomatic stages is of paramount interest. This comprehensive review provides an overview of recently identified plasma/serum proteins and their diagnostic performance for the prediction of GPNLs and early cancer lesions. Autoantibodies appear to be promising biomarkers for AG, IM and early gastric cancer detection, along with inflammation and immunity-related proteins and antibodies against H. pylori virulence factors. There is a lack of specific protein biomarkers with which to detect DYS. Despite the need for further investigation and validation, some emerging candidates could pave the way for the development of reliable, non-invasive diagnostic tests for the detection and prevention of GC.

Objectives: Gastric cancer is one of the leading causes of morbidity and mortality worldwide. As in other cancers, the development and progression of gastric cancer has been attributed to many factors, including infection with Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), genetic alterations, and epigenetic silencing due to aberrant methylation of tumor suppressor genes. The purpose of this work is to analyze the promoter methylation status of P53 (TP53) and E-cadherin (CDH1) genes and its association with EBV and H. pylori infections in the gastric cancer patients of Grand Casablanca. Methods: In this study, a total of 50 gastric cancer patients were recruited. Methylation in tumor tissues was detected by methylation-specific PCR (MSP), and the clinical relevance was statistically analyzed. Results: Results revealed a methylation of TP53 promoter observed in 36% of gastric carcinoma cases, which was significantly higher than adjacent normal tissue [p?0.0001]. While no methylation of CDH1 promoter was observed. Furthermore, the frequency of TP53 promoter methylation was significantly different with intestinal and diffuse types of gastric cancer [22.3% vs 77.7%; <0.05]. Moreover cases with EBV infection had higher frequencies of TP53 methylation [p<0.05], while no significant correlation between H. pylori and TP53 methylation was observed. Conclusion: Thus; the present data suggest a vital role of epigenetic alteration of TP53 in the causation and development of gastric cancer, especially Epstein-Barr virus-associated gastric cancer in our population. Keywords: Epstein-Barr virus, CDH1, gastric cancer, methylation, TP53, helicobacter pylori

The presence of JC virus in gastric carcinomas correlates with patient's age, intestinal histological type and aberrant methylation of tumor suppressor genes

Cancers arise from genetic and epigenetic abnormalities that affect oncogenes and tumor suppressor genes, compounded by gene mutations. The N6-methyladenosine (m6A) RNA modification, regulated by methylation regulators, has been implicated in tumor proliferation, differentiation, tumorigenesis, invasion, and metastasis. However, the role of m6A modification patterns in the tumor microenvironment of gastric cancer (GC) remains poorly understood. In this study, we analyzed m6A modification patterns in 267 GC samples utilizing 31 m6A regulators. Using consensus clustering, we identified two unique subgroups of GC. Patients with GC were segregated into high- and low-infiltration cohorts to evaluate the infiltration proportions of the five prognostically significant immune cell types. Leveraging the differential genes in GC, we identified a "green" module via Weighted Gene Co-expression Network Analysis. A risk prediction model was established using the LASSO regression method. The "green" module was connected to both the m6A RNA methylation cluster and immune infiltration patterns. Based on "Module Membership" and "Gene Significance", 37 hub genes were identified, and a risk prediction model incorporating nine hub genes was established. Furthermore, methylated RNA immunoprecipitation and RNA Immunoprecipitation assays revealed that YTHDF1 elevated the expression of DNMT3B, which synergistically promoted the initiation and development of GC. We elucidated the molecular mechanism underlying the regulation of DNMT3B by YTHDF1 and explored the crosstalk between m6A and 5mC modification. m6A RNA methylation regulators are instrumental in malignant progression and the dynamics of tumor microenvironment infiltration of GC. Assessing m6A modification patterns and tumor microenvironment infiltration characteristics in patients with GC holds promise as a valuable prognostic biomarker.

With the increasing application of nanoparticles (NPs) in medical and consumer applications, it is necessary to ensure their safety. As m6A (N6-methyladenosine) RNA modification is one of the most prevalent RNA modifications involved in many diseases and essential biological processes, the relationship between nanoparticles and m6A RNA modification for the modulation of these events has attracted substantial research interest. However, there is limited knowledge regarding the relationship between nanoparticles and m6A RNA modification, but evidence is beginning to emerge. Therefore, a summary of these aspects from current research on nanoparticle-induced m6A RNA modification is timely and significant. In this review, we highlight the roles of m6A RNA modification in the bioimpacts of nanoparticles and thus elaborate on the mechanisms of nanoparticle-induced m6A RNA modification. We also summarize the dynamic regulation and biofunctions of m6A RNA modification. Moreover, we emphasize recent advances in the application perspective of nanoparticle-induced m6A RNA modification in medication and toxicity of nanoparticles to provide a potential method to facilitate the design of nanoparticles by deliberately tuning m6A RNA modification.

Gastric cancer is an aggressive disease with survival remaining poor in the advanced setting. More than a decade after the first targeted treatment was approved, still only HER2, MSI and PDL-1 status have reached everyday practice in terms of guiding treatment options for these patients. However, various new targets and novel treatments have recently been investigated and have shown promise in improving survival outcomes. In this review, we will summarise previous and currently ongoing studies on predictive biomarkers, possible new targeted treatments, potential reasons for conflicting trial results and hope for the future of precision medicine in gastric cancer.

Gastric cancer is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvements, the clinical outcome for patients with advanced gastric cancer is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multilevel platform of gastric cancer models, comprising 100 patient-derived xenografts (PDX), primary cell lines, and organoids. Samples were classified according to their histology, microsatellite stability, Epstein-Barr virus status, and molecular profile. This PDX platform is the widest in an academic institution, and it includes all the gastric cancer histologic and molecular types identified by The Cancer Genome Atlas. PDX histopathologic features were consistent with those of patients' primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number gain of tyrosine kinases/KRAS genes, and microsatellite stability status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell-intrinsic microsatellite instability (MSI) signature, which was efficiently exported to gastric cancer, allowing the identification, among microsatellite stable (MSS) patients, of a subset of MSI-like tumors with common molecular aspects and significant better prognosis. In conclusion, we generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel "druggable" targets and optimize therapeutic strategies. Moreover, transcriptomic analysis of gastric cancer PDXs allowed the identification of a cancer cell-intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis. SIGNIFICANCE: This study reports a multilevel platform of gastric cancer PDXs and identifies a MSI gastric signature that could contribute to the advancement of precision medicine in gastric cancer.

MicroRNAs (miRNAs) have been highlighted as non-invasive clinical biomarkers in liquid biopsy. This study aimed to investigate the clinical significance of circulating tumor suppressors, precursor-miR-488 (pre-miR-488) and miR-488-5p, in the blood of patients with gastric cancer (GC). The expression levels of pre-miR-488 and miR-488-5p in tumor tissues and blood were measured using RT-qPCR, and the clinicopathological and prognostic significance of their expression was assessed in patients with GC. Next, pathway analysis of miR-488-5p expression in GC tissues was performed by gene set enrichment analysis (GSEA) using the TCGA dataset. Finally, pre-miR-488 in exosomes from the plasma of GC patients was analyzed using RT-qPCR. Both pre-miR-488 and miR-488-5p were down-regulated in tumor tissues, whereas their expression in the blood was significantly higher in patients with GC than in healthy controls. Low expression of pre-miR-488 or miR-488-5p in the blood was associated with poor prognosis in patients with GC. Furthermore, low pre-miR-488 expression in the blood was an independent poor prognostic factor for overall survival. miR-488-5p expression tended to be negatively correlated with the expression of gene sets involved in epithelial-mesenchymal transition and hypoxia. pre-miR-488 was detected in exosomes isolated from the plasma of patients with GC. Circulating pre-miR-488 and miR-488-5p expression in the blood may serve as novel prognostic biomarkers for patients with GC, predicting clinical outcomes and guiding therapeutic strategies.

BackgroundIntertumoral heterogeneity represents a significant hurdle to identifying optimized targeted therapies in gastric cancer (GC). To realize precision medicine for GC patients, an actionable gene alteration-based molecular classification that directly associates GCs with targeted therapies is needed.MethodsA total of 207 Japanese patients with GC were included in this study. Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were obtained from surgical or biopsy specimens and were subjected to DNA extraction. We generated comprehensive genomic profiling data using a 435-gene panel including 69 actionable genes paired with US Food and Drug Administration-approved targeted therapies, and the evaluation of Epstein-Barr virus (EBV) infection and microsatellite instability (MSI) status.ResultsComprehensive genomic sequencing detected at least one alteration of 435 cancer-related genes in 194 GCs (93.7%) and of 69 actionable genes in 141 GCs (68.1%). We classified the 207 GCs into four The Cancer Genome Atlas (TCGA) subtypes using the genomic profiling data; EBV (N = 9), MSI (N = 17), chromosomal instability (N = 119), and genomically stable subtype (N = 62). Actionable gene alterations were not specific and were widely observed throughout all TCGA subtypes. To discover a novel classification which more precisely selects candidates for targeted therapies, 207 GCs were classified using hypermutated phenotype and the mutation profile of 69 actionable genes. We identified a hypermutated group (N = 32), while the others (N = 175) were sub-divided into six clusters including five with actionable gene alterations: ERBB2 (N = 25), CDKN2A, and CDKN2B (N = 10), KRAS (N = 10), BRCA2 (N = 9), and ATM cluster (N = 12). The clinical utility of this classification was demonstrated by a case of unresectable GC with a remarkable response to anti-HER2 therapy in the ERBB2 cluster.ConclusionsThis actionable gene-based classification creates a framework for further studies for realizing precision medicine in GC.