1 2124 94 EPIGENETIC IMPLICATION OF GENE-ADJACENT RETROELEMENTS IN HELICOBACTER PYLORI-INFECTED ADULTS. A CHRONIC INFLAMMATORY CONDITION OF GASTRIC MUCOSA CAN FACILITATE THE INFLUX OF NEW STEM CELLS INTO THE STOMACH. EPIGENETIC CODES, SUCH AS DNA METHYLATION, MAY BE RESPONSIBLE FOR THE STABLE MAINTENANCE OF EPIGENETIC PHENOTYPES ESTABLISHED IN THE NEW STOMACH-ADAPTED STEM CELLS. A NUMBER OF HYPOTHESES HAVE BEEN MADE FOR THE ROLE OF CPG-ISLAND METHYLATION, WHICH IS COMMON IN THE HELICOBACTER PYLORI-INFECTED STOMACH. HOWEVER, THEY COULD NOT EXPLAIN THE PLAUSIBLE ROLE OF CPG-ISLAND METHYLATION IN THE RE-ESTABLISHMENT OF EPIGENETIC PHENOTYPES. THESE ISLANDS ARE HIGHLY REPETITIVE SEQUENCES DENSELY METHYLATED THROUGHOUT THE HUMAN GENOME, THE SO-CALLED PARASITIC RETROELEMENTS, WHICH EXPAND A NUMBER OF CDNA COPIES WITH REVERSE TRANSCRIPTASE. THE DENSELY METHYLATED RETROELEMENTS ADJACENT TO THE HOST GENES CAN FORM THE TRANSITIONAL-CPG SITES AROUND GENE-CONTROL REGIONS THAT ARE BARELY METHYLATED. THIS REVIEW FOCUSES ON THE PUTATIVE ROLE OF TRANSITIONAL CPG METHYLATION IN THE ADAPTIVE DIFFERENTIATION OF NEW STEM CELLS IN THE H. PYLORI-INFECTED STOMACH. 2012 2 5767 34 SPECIES-SPECIFIC ROLE OF GENE-ADJACENT RETROELEMENTS IN HUMAN AND MOUSE GASTRIC CARCINOGENESIS. HELICOBACTER PYLORI (HP) INFECTION PROMOTES THE RECRUITMENT OF BONE MARROW STEM CELLS INTO CHRONIC GASTRITIS LESIONS. SOME OF THESE MARROW STEM CELLS CAN DIFFERENTIATE INTO GASTRIC EPITHELIAL CELLS AND NEOPLASTIC CELLS. WE PROPOSE THAT HP-ASSOCIATED METHYLATION COULD STABILIZE TRANS-DIFFERENTIATION OF MARROW-DERIVED STEM CELLS AND THAT AN UNSTABLE METHYLATION STATUS IS ASSOCIATED WITH A RISK OF GASTRIC CANCER. PATHOBIOLOGIC BEHAVIOR OF EXPERIMENTAL MOUSE GASTRIC CANCER IS MILD COMPARED TO INVASIVE AND METASTATIC HUMAN GASTRIC CANCER. DIFFERENCES IN EPIGENETIC STABILIZATION OF ADULT CELL PHENOTYPES BETWEEN HUMANS AND MICE COULD PROVIDE A FOUNDATION TO EXPLORE THE DEVELOPMENT OF INVASIVE AND METASTATIC GASTRIC CANCER. RETROELEMENTS ARE HIGHLY REPETITIVE SEQUENCES THAT PLAY AN ESSENTIAL ROLE IN THE GENERATION OF SPECIES DIVERSITY. IN THIS REVIEW, WE ANALYZED RETROELEMENTS ADJACENT TO HUMAN AND MOUSE HOUSEKEEPING GENES AND PROPOSED A POSSIBLE EPIGENETIC MECHANISM FOR HP-ASSOCIATED CARCINOGENESIS. 2018 3 3220 37 HELICOBACTER PYLORI AND MICRORNAS: RELATION WITH INNATE IMMUNITY AND PROGRESSION OF PRENEOPLASTIC CONDITIONS. THE ACCEPTED PARADIGM FOR INTESTINAL-TYPE GASTRIC CANCER PATHOGENESIS IS A MULTISTEP PROGRESSION FROM CHRONIC GASTRITIS INDUCED BY HELICOBACTER PYLORI (H. PYLORI) TO GASTRIC ATROPHY, INTESTINAL METAPLASIA, DYSPLASIA AND ULTIMATELY GASTRIC CANCER. THE GENETIC AND MOLECULAR MECHANISMS UNDERLYING DISEASE PROGRESSION ARE STILL NOT COMPLETELY UNDERSTOOD AS ONLY A FRACTION OF COLONIZED INDIVIDUALS EVER DEVELOP NEOPLASIA SUGGESTING THAT BACTERIAL, HOST AND ENVIRONMENTAL FACTORS ARE INVOLVED. MICRORNAS ARE NONCODING RNAS THAT MAY INFLUENCE H. PYLORI-RELATED PATHOLOGY THROUGH THE REGULATION OF THE TRANSCRIPTION AND EXPRESSION OF VARIOUS GENES, PLAYING AN IMPORTANT ROLE IN INFLAMMATION, CELL PROLIFERATION, APOPTOSIS AND DIFFERENTIATION. INDEED, H. PYLORI HAVE BEEN SHOWN TO MODIFY MICRORNA EXPRESSION IN THE GASTRIC MUCOSA AND MICRORNAS ARE INVOLVED IN THE IMMUNE HOST RESPONSE TO THE BACTERIA AND IN THE REGULATION OF THE INFLAMMATORY RESPONSE. MICRORNAS HAVE A KEY ROLE IN THE REGULATION OF INFLAMMATORY PATHWAYS AND H. PYLORI MAY INFLUENCE INFLAMMATION-MEDIATED GASTRIC CARCINOGENESIS POSSIBLY THROUGH DNA METHYLATION AND EPIGENETIC SILENCING OF TUMOR SUPPRESSOR MICRORNAS. FURTHERMORE, MICRORNAS INFLUENCED BY H. PYLORI ALSO HAVE BEEN FOUND TO BE INVOLVED IN CELL CYCLE REGULATION, APOPTOSIS AND EPITHELIAL-MESENCHYMAL TRANSITION. ALTOGETHER, MICRORNAS SEEM TO HAVE AN IMPORTANT ROLE IN THE PROGRESSION FROM GASTRITIS TO PRENEOPLASTIC CONDITIONS AND NEOPLASTIC LESIONS AND SINCE EACH MICRORNA CAN CONTROL THE EXPRESSION OF HUNDREDS TO THOUSANDS OF GENES, KNOWLEDGE OF MICRORNAS TARGET GENES AND THEIR FUNCTIONS ARE OF PARAMOUNT IMPORTANCE. IN THIS ARTICLE WE PRESENT A COMPREHENSIVE REVIEW ABOUT THE ROLE OF MICRORNAS IN H. PYLORI GASTRIC CARCINOGENESIS, IDENTIFYING THE MICRORNAS DOWNREGULATED AND UPREGULATED IN THE INFECTION AND CLARIFYING THEIR BIOLOGICAL ROLE IN THE LINK BETWEEN IMMUNE HOST RESPONSE, INFLAMMATION, DNA METHYLATION AND GASTRIC CARCINOGENESIS. 2015 4 4994 26 PERFORMANCE OF DNA METHYLATION ON THE MOLECULAR PATHOGENESIS OF HELICOBACTER PYLORI IN GASTRIC CANCER; TARGETED THERAPY APPROACH. GASTRIC CANCER (GC) IS A SIGNIFICANT CAUSE OF CANCER MORTALITY WHICH HAS LED TO FOCUSED EXPLORATION OF THE PATHOLOGY OF GC. THE ADVENT OF GENOME-WIDE ANALYSIS METHODS HAS MADE IT POSSIBLE TO UNCOVER GENETIC AND EPIGENETIC FLUCTUATION SUCH AS ABNORMAL DNA METHYLATION IN GENE PROMOTER REGIONS THAT IS EXPECTED TO PLAY A KEY ROLE IN GC. THE STUDY OF GASTRIC MALIGNANCIES REQUIRES AN ETIOLOGICAL PERSPECTIVE, AND HELICOBACTER PYLORI (H. PYLORI) WAS IDENTIFIED TO PLAY A ROLE IN GC. H. PYLORI INFECTION CAUSES CHRONIC INFLAMMATION OF THE GASTRIC EPITHELIUM CAUSING ABNORMAL POLYCLONAL METHYLATION, WHICH MIGHT RAISE THE RISK OF GC. IN THE LAST TWO DECADES, VARIOUS PATHOGENIC FACTORS BY WHICH H. PYLORI INFECTION CAUSES GC HAVE BEEN DISCOVERED. ABNORMAL DNA METHYLATION IS TRIGGERED IN SEVERAL GENES, RENDERING THEM INACTIVE. IN GC, METHYLATION PATTERNS ARE LINKED TO CERTAIN SUBTYPES INCLUDING MICROSATELLITE INSTABILITY. MULTIPLE CANCER-RELATED PROCESSES ARE MORE USUALLY CHANGED BY ABNORMAL DNA METHYLATION THAN THROUGH MUTATIONS, ACCORDING TO CURRENT GENERAL AND COMBINED INVESTIGATIONS. FURTHERMORE, THE AMOUNT OF ACQUIRED ABNORMAL DNA METHYLATION IS HEAVILY LINKED TO THE CHANCES OF DEVELOPING GC. THEREFORE, WE INVESTIGATED ABNORMAL DNA METHYLATION IN GC AND THE LINK BETWEEN METHYLATION AND H. PYLORI INFECTION. 2022 5 4114 32 MECHANISMS FOR THE INDUCTION OF GASTRIC CANCER BY HELICOBACTER PYLORI INFECTION: ABERRANT DNA METHYLATION PATHWAY. MULTIPLE PATHOGENIC MECHANISMS BY WHICH HELICOBACTER PYLORI INFECTION INDUCES GASTRIC CANCER HAVE BEEN ESTABLISHED IN THE LAST TWO DECADES. IN PARTICULAR, ABERRANT DNA METHYLATION IS INDUCED IN MULTIPLE DRIVER GENES, WHICH INACTIVATES THEM. METHYLATION PROFILES IN GASTRIC CANCER ARE ASSOCIATED WITH SPECIFIC SUBTYPES, SUCH AS MICROSATELLITE INSTABILITY. RECENT COMPREHENSIVE AND INTEGRATED ANALYSES SHOWED THAT MANY CANCER-RELATED PATHWAYS ARE MORE FREQUENTLY ALTERED BY ABERRANT DNA METHYLATION THAN BY MUTATIONS. ABERRANT DNA METHYLATION CAN EVEN BE PRESENT IN NONCANCEROUS GASTRIC MUCOSAE, PRODUCING AN "EPIGENETIC FIELD FOR CANCERIZATION." MECHANISTICALLY, H. PYLORI-INDUCED CHRONIC INFLAMMATION, BUT NOT H. PYLORI ITSELF, PLAYS A DIRECT ROLE IN THE INDUCTION OF ABERRANT DNA METHYLATION. THE EXPRESSION OF THREE INFLAMMATION-RELATED GENES, IL1B, NOS2, AND TNF, IS HIGHLY ASSOCIATED WITH THE INDUCTION OF ABERRANT DNA METHYLATION. IMPORTANTLY, THE DEGREE OF ACCUMULATED ABERRANT DNA METHYLATION IS STRONGLY CORRELATED WITH GASTRIC CANCER RISK. A RECENT MULTICENTER PROSPECTIVE COHORT STUDY DEMONSTRATED THE UTILITY OF EPIGENETIC CANCER RISK DIAGNOSIS FOR METACHRONOUS GASTRIC CANCER. SUPPRESSION OF ABERRANT DNA METHYLATION BY A DEMETHYLATING AGENT WAS SHOWN TO INHIBIT GASTRIC CANCER DEVELOPMENT IN AN ANIMAL MODEL. INDUCTION OF ABERRANT DNA METHYLATION IS THE MAJOR PATHWAY BY WHICH H. PYLORI INFECTION INDUCES GASTRIC CANCER, AND THIS CAN BE UTILIZED FOR TRANSLATIONAL OPPORTUNITIES. 2017 6 2853 20 FROM HELICOBACTER PYLORI INFECTION TO GASTRIC CANCER: CURRENT EVIDENCE ON THE IMMUNE RESPONSE. GASTRIC CANCER (GC) IS THE RESULT OF A MULTIFACTORIAL PROCESS WHOSE MAIN COMPONENTS ARE INFECTION BY HELICOBACTER PYLORI (H. PYLORI), BACTERIAL VIRULENCE FACTORS, HOST IMMUNE RESPONSE AND ENVIRONMENTAL FACTORS. THE DEVELOPMENT OF THE NEOPLASTIC MICROENVIRONMENT ALSO DEPENDS ON GENETIC AND EPIGENETIC CHANGES IN ONCOGENES AND TUMOR SUPPRESSOR GENES, WHICH RESULTS IN DEREGULATION OF CELL SIGNALING PATHWAYS AND APOPTOSIS PROCESS. THIS REVIEW SUMMARIZES THE MAIN ASPECTS OF THE PATHOGENESIS OF GC AND THE IMMUNE RESPONSE INVOLVED IN CHRONIC INFLAMMATION GENERATED BY H. PYLORI. 2022 7 1544 31 DNA METHYLATION IN HUMAN GASTRIC EPITHELIAL CELLS DEFINES REGIONAL IDENTITY WITHOUT RESTRICTING LINEAGE PLASTICITY. BACKGROUND: EPIGENETIC MODIFICATIONS IN MAMMALIAN DNA ARE COMMONLY MANIFESTED BY DNA METHYLATION. IN THE STOMACH, ALTERED DNA METHYLATION PATTERNS HAVE BEEN OBSERVED FOLLOWING CHRONIC HELICOBACTER PYLORI INFECTIONS AND IN GASTRIC CANCER. IN THE CONTEXT OF EPIGENETIC REGULATION, THE REGIONAL NATURE OF THE STOMACH HAS BEEN RARELY CONSIDERED IN DETAIL. RESULTS: HERE, WE ESTABLISH GASTRIC MUCOSA DERIVED PRIMARY CELL CULTURES AS A RELIABLE SOURCE OF NATIVE HUMAN EPITHELIUM. WE DESCRIBE THE DNA METHYLATION LANDSCAPE ACROSS THE PHENOTYPICALLY DIFFERENT REGIONS OF THE HEALTHY HUMAN STOMACH, I.E., ANTRUM, CORPUS, FUNDUS TOGETHER WITH THE CORRESPONDING TRANSCRIPTOMES. WE SHOW THAT STABLE REGIONAL DNA METHYLATION DIFFERENCES TRANSLATE TO A LIMITED EXTENT INTO REGULATION OF THE TRANSCRIPTOMIC PHENOTYPE, INDICATING A LARGELY PERMISSIVE EPIGENETIC REGULATION. WE IDENTIFY A SMALL NUMBER OF TRANSCRIPTION FACTORS WITH NOVEL REGION-SPECIFIC ACTIVITY AND LIKELY EPIGENETIC IMPACT IN THE STOMACH, INCLUDING GATA4, IRX5, IRX2, PDX1 AND CDX2. DETAILED ANALYSIS OF THE WNT PATHWAY REVEALS DIFFERENTIAL REGULATION ALONG THE CRANIOCAUDAL AXIS, WHICH INVOLVES NON-CANONICAL WNT SIGNALING IN DETERMINING CELL FATE IN THE PROXIMAL STOMACH. BY EXTENDING OUR ANALYSIS TO PRE-NEOPLASTIC LESIONS AND GASTRIC CANCERS, WE CONCLUDE THAT EPIGENETIC DYSREGULATION CHARACTERIZES INTESTINAL METAPLASIA AS A FOUNDING BASIS FOR FUNCTIONAL CHANGES IN GASTRIC CANCER. WE PRESENT INSIGHTS INTO THE DYNAMICS OF DNA METHYLATION ACROSS ANATOMICAL REGIONS OF THE HEALTHY STOMACH AND PATTERNS OF ITS CHANGE IN DISEASE. FINALLY, OUR STUDY PROVIDES A WELL-DEFINED RESOURCE OF REGIONAL STOMACH TRANSCRIPTION AND EPIGENETICS. 2022 8 2852 24 FROM GASTRIC INFLAMMATION TO GASTRIC CANCER. THE MAJORITY OF GASTRIC ADENOCARCINOMAS ARE RELATED TO CHRONIC INFLAMMATION INDUCED BY HELICOBACTER PYLORI INFECTION. FOR INTESTINAL-TYPE GASTRIC CANCER, A MULTISTEP PROCESS OF MUCOSAL ALTERATIONS LEADING FROM GASTRITIS VIA GLANDULAR ATROPHY, INTESTINAL METAPLASIA AND DYSPLASIA TO INVASIVE CARCINOMA IS WELL RECOGNIZED. ONGOING CLINICAL STUDIES FOCUS ON A 'POINT OF NO RETURN'. IT IS DEFINED AS A SITUATION WHEN CERTAIN ALTERATIONS ARE NO LONGER REVERSIBLE BY H. PYLORI ERADICATION AND PROGRESSION TO GASTRIC CANCER MAY CONTINUE. H. PYLORI AFFECTS THE MUCOSAL AS WELL AS THE SYSTEMIC IMMUNE RESPONSE BY SECRETION OF CYTOKINES AND THE RECRUITMENT OF DISTINCT INFLAMMATORY CELLS. THE IMMUNE RESPONSE IS CHARACTERIZED BY A BALANCE BETWEEN A TH1-DOMINATED RESPONSE AND THE RECRUITMENT OF ANTIGEN-SPECIFIC REGULATORY T CELLS THAT ALLOW THE BACTERIA TO PERSIST IN HUMAN GASTRIC MUCOSA. BESIDES IMMUNE-MEDIATED EFFECTS, H. PYLORI INDUCES CELLULAR ALTERATIONS AS WELL AS GENETIC ALTERATIONS IN GENES THAT ARE ESSENTIAL FOR THE EPIGENETIC INTEGRITY AND MUCOSAL HOMEOSTASIS. THESE GENETIC ALTERATIONS DURING GASTRIC CANCER DEVELOPMENT ARE IN FOCUS OF INTENSIVE RESEARCH AND SHOULD ULTIMATELY ALLOW THE IDENTIFICATION OF RISK FACTORS INVOLVED IN GASTRIC CARCINOGENESIS. THE DETECTION OF INDIVIDUALS AT HIGH RISK FOR GASTRIC CANCER WOULD HELP TO DESIGN APPROPRIATE STRATEGIES FOR PREVENTION AND SURVEILLANCE. 2010 9 1540 29 DNA METHYLATION IN GASTRIC CANCER, RELATED TO HELICOBACTER PYLORI AND EPSTEIN-BARR VIRUS. GASTRIC CANCER IS A LEADING CAUSE OF CANCER DEATH WORLDWIDE, AND SIGNIFICANT EFFORT HAS BEEN FOCUSED ON CLARIFYING THE PATHOLOGY OF GASTRIC CANCER. IN PARTICULAR, THE DEVELOPMENT OF GENOME-WIDE ANALYSIS TOOLS HAS ENABLED THE DETECTION OF GENETIC AND EPIGENETIC ALTERATIONS IN GASTRIC CANCER; FOR EXAMPLE, ABERRANT DNA METHYLATION IN GENE PROMOTER REGIONS IS THOUGHT TO PLAY A CRUCIAL ROLE IN GASTRIC CARCINOGENESIS. THE ETIOLOGICAL VIEWPOINT IS ALSO ESSENTIAL FOR THE STUDY OF GASTRIC CANCERS, AND TWO DISTINCT PATHOGENS, HELICOBACTER PYLORI (H. PYLORI) AND EPSTEIN-BARR VIRUS (EBV), ARE KNOWN TO PARTICIPATE IN GASTRIC CARCINOGENESIS. CHRONIC INFLAMMATION OF THE GASTRIC EPITHELIUM DUE TO H. PYLORI INFECTION INDUCES ABERRANT POLYCLONAL METHYLATION THAT MAY LEAD TO AN INCREASED RISK OF GASTRIC CANCER. IN ADDITION, EBV INFECTION IS KNOWN TO CAUSE EXTENSIVE METHYLATION, AND EBV-POSITIVE GASTRIC CANCERS DISPLAY A HIGH METHYLATION EPIGENOTYPE, IN WHICH ABERRANT METHYLATION EXTENDS TO NOT ONLY POLYCOMB REPRESSIVE COMPLEX (PRC)-TARGET GENES IN EMBRYONIC STEM CELLS BUT ALSO NON-PRC-TARGET GENES. HERE, WE REVIEW ABERRANT DNA METHYLATION IN GASTRIC CANCER AND THE ASSOCIATION BETWEEN METHYLATION AND INFECTION WITH H. PYLORI AND EBV. 2014 10 1912 31 ENVIRONMENT, DIET AND CPG ISLAND METHYLATION: EPIGENETIC SIGNALS IN GASTROINTESTINAL NEOPLASIA. THE EPITHELIAL SURFACES OF THE MAMMALIAN ALIMENTARY TRACT ARE CHARACTERISED BY VERY HIGH RATES OF CELL PROLIFERATION AND DNA SYNTHESIS, AND IN HUMANS THEY ARE HIGHLY SUSCEPTIBLE TO CANCER. THE ROLE OF SOMATIC MUTATIONS AS DRIVERS OF CARCINOGENESIS IN THE ALIMENTARY TRACT IS WELL ESTABLISHED, BUT THE IMPORTANCE OF GENE SILENCING BY EPIGENETIC MECHANISMS IS INCREASINGLY RECOGNISED. METHYLATION OF CPG ISLANDS IS AN IMPORTANT COMPONENT OF THE EPIGENETIC CODE THAT REGULATES GENE EXPRESSION DURING DEVELOPMENT AND NORMAL CELLULAR DIFFERENTIATION, AND A NUMBER OF GENES ARE WELL KNOWN TO BECOME ABNORMALLY METHYLATED DURING THE DEVELOPMENT OF TUMOURS OF THE OESOPHAGUS, STOMACH AND COLORECTUM. ABERRANT PATTERNS OF DNA METHYLATION DEVELOP AS A RESULT OF PATHOLOGICAL PROCESSES SUCH AS CHRONIC INFLAMMATION, AND IN RESPONSE TO VARIOUS DIETARY FACTORS, INCLUDING IMBALANCES IN THE SUPPLY OF METHYL DONORS, PARTICULARLY FOLATES, AND EXPOSURE TO DNA METHYLTRANSFERASE INHIBITORS, WHICH INCLUDE POLYPHENOLS AND POSSIBLY ISOTHIOCYANATES FROM PLANT FOODS. HOWEVER THE IMPORTANCE OF THESE ENVIRONMENTAL INTERACTIONS IN HUMAN HEALTH AND DISEASE REMAINS TO BE ESTABLISHED. RECENT MOVES TO MODIFY THE EXPOSURE OF HUMAN POPULATIONS TO FOLATE, BY MANDATORY SUPPLEMENTATION OF CEREAL FOODS, EMPHASISE THE IMPORTANCE OF UNDERSTANDING THE SUSCEPTIBILITY OF THE HUMAN EPIGENOME TO DIETARY AND OTHER ENVIRONMENTAL EFFECTS. 2008 11 6841 30 [MECHANISMS OF H. PYLORI INFECTION-INDUCED GASTRIC CARCINOGENESIS]. MANY EPIDEMIOLOGICAL STUDIES HAVE DEMONSTRATED A STRONG ASSOCIATION BETWEEN H. PYLORI (HELICOBACTER PYLORI) INFECTION AND HUMAN GASTRIC CANCER DEVELOPMENT. THE PRECISE MECHANISMS ACCOUNTING FOR GASTRIC CANCER DEVELOPMENT INDUCED BY H. PYLORI INFECTION ARE STILL NOT COMPLETELY UNDERSTOOD. HOWEVER, IT SHOULD BE REASONABLE TO ASSUME THAT THERE ARE TWO DISTINCT MOLECULAR PATHWAYS FOR GASTRIC CARCINOGENESIS BY H. PYLORI INFECTION; THE DIRECT ACTION OF THE BACTERIA ITSELF ON GASTRIC EPITHELIAL CELLS, AND THE ACCUMULATION OF GENETIC CHANGES CAUSED BY PROLONGED BACTERIAL INFECTION AND CHRONIC INFLAMMATION. AS A DIRECT ACTION OF H. PYLORI, BACTERIAL PROTEINS SUCH AS CAGA COULD BE DELIVERED INTO GASTRIC EPITHELIAL CELLS VIA THE TYPE IV SECRETION APPARATUS AND MODIFY THE HOST CELL FUNCTIONS RELATED TO CELL PROLIFERATION. IN ADDITION TO THE DIRECT BACTERIAL ACTION, H. PYLORI INFECTION AND THE RESULTANT INFLAMMATORY RESPONSE CAUSE VARIOUS GENETIC AND EPIGENETIC CHANGES IN TUMOR-RELATED GENES OF THE GASTRIC EPITHELIAL CELLS. NOTABLY, EXPRESSION OF AID (ACTIVATION-INDUCED CYTIDINE DEAMINASE), A DNA EDITING ENZYME THAT UNDERGOES SOMATIC HYPERMUTATION ON HUMAN GENES, IS INDUCED IN RESPONSE TO H. PYLORI INFECTION AND PROINFLAMMATORY CYTOKINE STIMULATION IN HUMAN GASTRIC EPITHELIAL CELLS. AS A RESULT, THE ACCUMULATION OF GENETIC ALTERATIONS WOULD PERSIST UNTIL THE CLINICAL STAGE OF ATROPHIC GASTRITIS AND EVENTUALLY TRIGGER THE MALIGNANT TRANSFORMATION OF GASTRIC CELLS. 2010 12 2994 26 GENETIC PATHOGENESIS OF INFLAMMATION-ASSOCIATED CANCERS IN DIGESTIVE ORGANS. EPIDEMIOLOGICAL, CLINICAL, AND BIOLOGICAL STUDIES CONVINCINGLY DEMONSTRATE THAT CHRONIC INFLAMMATION PREDISPOSES TO THE DEVELOPMENT OF HUMAN CANCERS. IN DIGESTIVE ORGANS, INFLAMMATION-ASSOCIATED CANCERS INCLUDE COLITIS-ASSOCIATED COLORECTAL CANCERS, HELICOBACTER PYLORI-ASSOCIATED GASTRIC CANCER, AS WELL AS BARRETT'S ESOPHAGUS AND ESOPHAGEAL ADENOCARCINOMA ASSOCIATED WITH CHRONIC DUODENOGASTRIC-ESOPHAGEAL REFLUX. CANCER IS A GENOMIC DISEASE, AND STEPWISE ACCUMULATION OF GENETIC AND EPIGENETIC ALTERATIONS OF TUMOR-RELATED GENES LEADS TO THE DEVELOPMENT OF TUMOR CELLS. RECENT GENOME ANALYSES SHOW THAT GENETIC ALTERATIONS, WHICH ARE EVOKED BY INFLAMMATION, ARE LATENTLY ACCUMULATED IN INFLAMED EPITHELIAL CELLS OF DIGESTIVE ORGANS. PRODUCTION OF REACTIVE OXYGEN AND ABERRANT EXPRESSION OF ACTIVATION-INDUCED CYTIDINE DEAMINASE, A NUCLEOTIDE-EDITING ENZYME, COULD BE INDUCED IN INFLAMED GASTROINTESTINAL EPITHELIAL CELLS AND PLAY A ROLE AS A GENOMIC MODULATOR OF INFLAMMATION-ASSOCIATED CARCINOGENESIS. UNDERSTANDING THE MOLECULAR LINKAGE BETWEEN INFLAMMATION AND GENETIC ALTERATIONS WILL OPEN UP A NEW FIELD OF TUMOR BIOLOGY AND PROVIDE A NOVEL STRATEGY FOR THE PREVENTION OF INFLAMMATION-ASSOCIATED TUMORIGENESIS. 2021 13 3233 27 HELICOBACTER, INFLAMMATION, AND GASTRIC CANCER. HELICOBACTER PYLORI INFECTION LEADS TO LONG-LASTING CHRONIC INFLAMMATION AND REPRESENTS THE MOST COMMON RISK FACTOR UNDERLYING GASTRIC CANCER. RECENTLY, NEW INSIGHTS INTO THE MECHANISMS THROUGH WHICH H. PYLORI AND MUCOSAL INFLAMMATION LEAD TO CANCER DEVELOPMENT HAVE EMERGED. H. PYLORI VIRULENCE FACTORS, IN PARTICULAR SPECIFIC CAGA GENOTYPES, REPRESENT MAIN FACTORS IN GASTRIC CANCER, INDUCING ALTERED INTRACELLULAR SIGNALING IN EPITHELIAL CELLS. THE CHRONIC NATURE OF H. PYLORI INFECTION APPEARS TO RELATE TO THE VACA VIRULENCE FACTOR AND TH17/TREG MECHANISMS. A ROLE OF H. PYLORI INFECTION IN EPIGENETIC AND MICRORNA DEREGULATION HAS BEEN SHOWN. MUTATION OF THE EPITHELIAL CELL GENOME, A HALLMARK OF CANCER, WAS DEMONSTRATED TO ACCUMULATE IN H. PYLORI INFECTED STOMACH PARTLY DUE TO INADEQUATE DNA REPAIR. GASTRIC STEM CELLS WERE SHOWN TO BE TARGETS OF OXIDATIVE INJURY IN THE HELICOBACTER-INFLAMMATORY MILIEU. RECENT ADVANCES EMPHASIZING THE CONTRIBUTION OF BACTERIAL FACTORS, INFLAMMATORY MEDIATORS, AND THE HOST EPITHELIAL RESPONSE IN GASTRIC CARCINOGENESIS ARE REVIEWED. 2013 14 2033 28 EPIGENETIC CHANGES IN SOLID AND HEMATOPOIETIC TUMORS. THERE ARE THREE CONNECTED MOLECULAR MECHANISMS OF EPIGENETIC CELLULAR MEMORY IN MAMMALIAN CELLS: DNA METHYLATION, HISTONE MODIFICATIONS, AND RNA INTERFERENCE. THE FIRST TWO HAVE NOW BEEN FIRMLY LINKED TO NEOPLASTIC TRANSFORMATION. HYPERMETHYLATION OF CPG-RICH PROMOTERS TRIGGERS LOCAL HISTONE CODE MODIFICATIONS RESULTING IN A CELLULAR CAMOUFLAGE MECHANISM THAT SEQUESTERS GENE PROMOTERS AWAY FROM TRANSCRIPTION FACTORS AND RESULTS IN STABLE SILENCING. THIS NORMALLY RESTRICTED MECHANISM IS UBIQUITOUSLY USED IN CANCER TO SILENCE HUNDREDS OF GENES, AMONG WHICH SOME CRITICALLY CONTRIBUTE TO THE NEOPLASTIC PHENOTYPE. VIRTUALLY EVERY PATHWAY IMPORTANT TO CANCER FORMATION IS AFFECTED BY THIS PROCESS. METHYLATION PROFILING OF HUMAN CANCERS REVEALS TISSUE-SPECIFIC EPIGENETIC SIGNATURES, AS WELL AS TUMOR-SPECIFIC SIGNATURES, REFLECTING IN PARTICULAR THE PRESENCE OF EPIGENETIC INSTABILITY IN A SUBSET OF CANCERS AFFECTED BY THE CPG ISLAND METHYLATOR PHENOTYPE. GENERALLY, METHYLATION PATTERNS CAN BE TRACED TO A TISSUE-SPECIFIC, PROLIFERATION-DEPENDENT ACCUMULATION OF ABERRANT PROMOTER METHYLATION IN AGING TISSUES, A PROCESS THAT CAN BE ACCELERATED BY CHRONIC INFLAMMATION AND LESS WELL-DEFINED MECHANISMS INCLUDING, POSSIBLY, DIET AND GENETIC PREDISPOSITION. THE EPIGENETIC MACHINERY CAN ALSO BE ALTERED IN CANCER BY SPECIFIC LESIONS IN EPIGENETIC EFFECTOR GENES, OR BY ABERRANT RECRUITMENT OF THESE GENES BY MUTANT TRANSCRIPTION FACTORS AND COACTIVATORS. EPIGENETIC PATTERNS ARE PROVING CLINICALLY USEFUL IN HUMAN ONCOLOGY VIA RISK ASSESSMENT, EARLY DETECTION, AND PROGNOSTIC CLASSIFICATION. PHARMACOLOGIC MANIPULATION OF THESE PATTERNS-EPIGENETIC THERAPY-IS ALSO POISED TO CHANGE THE WAY WE TREAT CANCER IN THE CLINIC. 2005 15 1799 28 EFFECT OF HELICOBACTER PYLORI INFECTION ON THE COMPOSITION OF GASTRIC MICROBIOTA IN THE DEVELOPMENT OF GASTRIC CANCER. BACKGROUND: GASTRIC CANCER IS ONE OF THE MOST COMMON CANCER TYPES WORLDWIDE. IN CHINA, GASTRIC CANCER HAS BECOME ONE OF THE MAJOR THREATS FOR PUBLIC HEALTH, RANKING SECOND ON INCIDENCE AND THIRD ON CAUSE OF CANCER DEATH. DESPITE THE COMMON RISK FACTORS THAT PROMOTE THE DEVELOPMENT OF GASTRIC CANCER, THE HUGE QUANTITY OF MICROORGANISM COLONIES WITHIN THE GASTROINTESTINAL TRACT, PARTICULARLY HELICOBACTER PYLORI INFECTION, DEMONSTRATES A CORRELATION WITH CHRONIC INFLAMMATION AND GASTRIC CARCINOGENESIS, AS EPIDEMIOLOGICAL STUDIES HAVE DETERMINED THAT H. PYLORI INFECTION CONFERS APPROXIMATELY 75% OF THE ATTRIBUTABLE RISK FOR GASTRIC CANCER. SUMMARY: THE CURRENT ARTICLE DRAWS AN OVERVIEW ON THE CORRELATION BETWEEN THE MICROBIOTA, INFLAMMATION AND GASTRIC TUMORIGENESIS. H. PYLORI INFECTION HAS BEEN IDENTIFIED AS THE MAIN RISK FACTOR AS IT TRIGGERS EPITHELIAL BARRIER DISRUPTION, SURVIVAL SIGNALING AS WELL AS GENETIC/EPIGENETIC MODULATION. APART FROM H. PYLORI, THE EXISTENCE OF A DIVERSE AND COMPLEX COMPOSITION OF MICROBIOTA IN THE STOMACH HAS BEEN IDENTIFIED, WHICH SUPPORTS A ROLE OF MICROBIOTA IN THE DEVELOPMENT OF GASTRIC CANCER. MOREOVER, METAGENOMICS STUDIES FOCUSED ON THE COMPOSITION AND FUNCTION OF THE MICROBIOTA HAVE ASSOCIATED MICROBIOTA WITH GASTRIC METABOLIC DISEASES AND EVEN TUMORIGENESIS. APART FROM THE GASTRIC MICROBIOTA, INFLAMMATION IS ANOTHER IDENTIFIED CONTRIBUTOR TO CANCER DEVELOPMENT AS WELL. KEY MESSAGE: THOUGH H. PYLORI INFECTION AND THE NON-H. PYLORI MICROBIOTA PLAY A ROLE IN GASTRIC CANCER, THE PROPERTIES OF GASTRIC MICROBIOTA AND MECHANISMS BY WHICH THEY PARTICIPATE IN THE GENESIS OF GASTRIC CANCER ARE STILL NOT CLEARLY DEPICTED. MOREOVER, IT REMAINS TO BE UNDERSTOOD HOW THE PRESENCE OF MICROBIOTA ALONG WITH H. PYLORI INFECTION AFFECTS THE PROGRESS FROM GASTRIC DISEASE TO CANCER. PRACTICAL IMPLICATIONS: THIS ARTICLE SUMMARIZED A CLUE OF THE CURRENT STUDIES ON MICROBIOTA, H. PYLORI INFECTION AND THE PROGRESSION FROM GASTRIC DISEASE TO CANCER. 2015 16 2122 29 EPIGENETIC IMPACT OF INFECTION ON CARCINOGENESIS: MECHANISMS AND APPLICATIONS. VIRAL AND BACTERIAL INFECTIONS ARE INVOLVED IN THE DEVELOPMENT OF HUMAN CANCERS, SUCH AS LIVER, NASOPHARYNGEAL, CERVICAL, HEAD AND NECK, AND GASTRIC CANCERS. ABERRANT DNA METHYLATION IS FREQUENTLY PRESENT IN THESE CANCERS, AND SOME OF THE ABERRANTLY METHYLATED GENES ARE CAUSALLY INVOLVED IN CANCER DEVELOPMENT AND PROGRESSION. NOTABLY, ABERRANT DNA METHYLATION CAN BE PRESENT EVEN IN NON-CANCEROUS OR PRECANCEROUS TISSUES, AND ITS LEVELS CORRELATE WITH THE RISK OF CANCER DEVELOPMENT, PRODUCING A SO-CALLED 'EPIGENETIC FIELD FOR CANCERIZATION'. MECHANISTICALLY, MOST VIRAL OR BACTERIAL INFECTIONS INDUCE DNA METHYLATION INDIRECTLY VIA CHRONIC INFLAMMATION, BUT RECENT STUDIES HAVE INDICATED THAT SOME VIRUSES HAVE DIRECT EFFECTS ON THE EPIGENETIC MACHINERY OF HOST CELLS. FROM A TRANSLATIONAL VIEWPOINT, A RECENT MULTICENTER PROSPECTIVE COHORT STUDY DEMONSTRATED THAT ASSESSMENT OF THE EXTENT OF ALTERATIONS IN DNA METHYLATION IN NON-CANCEROUS TISSUES CAN BE USED TO PREDICT CANCER RISK. FURTHERMORE, SUPPRESSION OF ABERRANT DNA METHYLATION WAS SHOWN TO BE A USEFUL STRATEGY FOR CANCER PREVENTION IN AN ANIMAL MODEL. HERE, WE REVIEW THE INVOLVEMENT OF ABERRANT DNA METHYLATION IN VARIOUS TYPES OF INFECTION-ASSOCIATED CANCERS, ALONG WITH INDIVIDUAL INDUCTION MECHANISMS, AND WE DISCUSS THE APPLICATION OF THESE FINDINGS FOR CANCER PREVENTION, DIAGNOSIS, AND THERAPY. 2016 17 2483 25 EPIGENETIC VARIATION AND HUMAN DISEASE. CYTOSINE GUANINE DINUCLEOTIDE (CPG) ISLAND METHYLATION IS A KNOWN MECHANISM OF EPIGENETIC INHERITANCE IN POSTMEIOTIC CELLS. THROUGH ASSOCIATED CHROMATIN CHANGES AND SILENCING, SUCH EPIGENETIC STATES CAN INFLUENCE CELLULAR PHYSIOLOGY AND AFFECT DISEASE RISK AND SEVERITY. OUR STUDIES OF CPG ISLAND METHYLATION IN NORMAL COLORECTAL MUCOSA REVEALED PROGRESSIVE AGE-RELATED INCREASES AT MULTIPLE GENE LOCI, SUGGESTING GENOME-WIDE MOLECULAR ALTERATIONS WITH POTENTIAL TO SILENCE GENE EXPRESSION. HOWEVER, THERE WAS CONSIDERABLE VARIATION IN THE DEGREE OF METHYLATION AMONG INDIVIDUALS OF COMPARABLE AGES. SUCH VARIATION COULD BE RELATED TO GENETIC FACTORS, LIFESTYLE, OR ENVIRONMENTAL EXPOSURES. STUDIES IN ULCERATIVE COLITIS AND HEPATOCELLULAR CIRRHOSIS AND NEOPLASIA REVEALED THAT CHRONIC INFLAMMATORY STATES ARE ACCOMPANIED BY MARKED INCREASES IN CPG ISLAND METHYLATION IN NORMAL-APPEARING TISSUES, CONFIRMING THE HYPOTHESIS THAT PROINFLAMMATORY EXPOSURES COULD ACCOUNT FOR PART OF THE EPIGENETIC VARIATION IN HUMAN POPULATIONS. PRELIMINARY DATA ALSO SUGGEST POTENTIAL INFLUENCES OF LIFESTYLE AND EXPOSURE FACTORS ON CPG ISLAND METHYLATION. IT IS SUGGESTED THAT EPIGENETIC VARIATION RELATED TO AGING, LIFESTYLE, EXPOSURES AND POSSIBLY GENETIC FACTORS, IS ONE OF THE MODULATORS OF ACQUIRED, AGE-RELATED HUMAN DISEASES, INCLUDING NEOPLASIA. 2002 18 3221 22 HELICOBACTER PYLORI AND THE MOLECULAR PATHOGENESIS OF INTESTINAL-TYPE GASTRIC CARCINOMA. GASTRIC CARCINOMA IS AN INFLAMMATION-RELATED CANCER CAUSED BY LONG-TERM INFECTION WITH THE HUMAN BACTERIAL PATHOGEN, HELICOBACTER PYLORI. THE PATTERN OF ACUTE-ON-CHRONIC INFLAMMATION CAUSES PROGRESSIVE MUCOSAL DAMAGE WHICH MAY RESULT IN ATROPHY WITH METAPLASTIC EPITHELIA AND EVENTUALLY GASTRIC CANCER. RECENTLY, IT HAS BEEN RECOGNIZED THAT H. PYLORI CAN ALSO CAUSE GENETIC INSTABILITY SUCH AS DOUBLE-STRANDED DNA BREAKS AND CAN PRODUCE GENE ACTIVATION AND SILENCING VIA EPIGENETIC PATHWAYS. AS GENETIC INSTABILITY IS THE HALLMARK OF CANCER, WE HIGHLIGHT RECENT PROGRESS IN UNDERSTANDING THE GASTRIC CARCINOGENESIS IN RELATION TO H. PYLORI-RELATED INFLAMMATION, H. PYLORI-INDUCED DOUBLE-STRANDED DNA BREAKAGE AND ABERRANT GENE EXPRESSION AS WELL AS THE MECHANISMS AND ROLE OF H. PYLORI-ASSOCIATED EPIGENETIC CHANGE IN GENE EXPRESSION. 2014 19 2894 26 GASTRIC CANCER AS A STEM-CELL DISEASE: DATA AND HYPOTHESES. THE MAIN FUNCTION OF GASTRIC STEM CELLS IS TO MAINTAIN THE INTEGRITY OF THE GASTROINTESTINAL EPITHELIUM AND REPLENISH ALL THE MATURE CELL LINEAGES. IN ORDER TO ACCOMPLISH THIS, GASTRIC STEM CELLS PROLIFERATE AND SELF-RENEW, GIVING RISE TO TRANSIENT AMPLIFYING CELLS WHICH REPLACE THE CONSTANTLY RENEWING EPITHELIUM, ESPECIALLY AFTER INJURY INDUCED BY LONG-TERM INFLAMMATION. GASTRIC CANCER (GC) REMAINS THE FOURTH MOST COMMON CANCER AND THE SECOND LEADING CAUSE OF DEATH FOR CANCER IN THE WORLD. THE MOST ACCEPTED MODEL OF GASTRIC CARCINOGENESIS PROVIDES A MULTIFACTORIAL AND MULTISTEP PATHOGENESIS, INVOLVING A NUMBER OF INITIATORS AND OTHER CONTINUATOR AGENTS. HELICOBACTER PYLORI INFECTION IS RECOGNIZED AS A NECESSARY BUT INSUFFICIENT CAUSE OF GC. RECENT ADVANCES IN GASTRIC STEM CELL BIOLOGY POINT OUT TO TWO HYPOTHESES. IN THE FIRST, IT IS POSTULATED THAT RESIDENT STEM CELLS MAY, IN A CHRONICALLY INFLAMED ENVIRONMENT, AS IN THE CASE OF HELICOBACTER PYLORI-INDUCED GASTRITIS, ACCUMULATE OVER TIME A SERIES OF GENETIC AND EPIGENETIC CHANGES THAT LEAD TO THE EMERGENCE OF GC STEM CELLS. ALTERNATIVELY, THE SETTING OF CHRONIC INFLAMMATORY STRESS MAY LEAD TO LOSS OF THE INDIGENOUS GASTRIC STEM CELLS FROM THEIR NICHES, FOLLOWED BY RECRUITMENT AND ENGRAFTMENT OF BONE MARROW DERIVED STEM CELLS (BMDCS) INTO THE GASTRIC EPITHELIUM. IN THE MOUSE MODEL, INCREASING EVIDENCE SUPPORTS THE HYPOTHESIS THAT BMDCS ARE IMPORTANT CELLULAR SOURCE OF HELICOBACTER-INDUCED GC. THIS REVIEW HIGHLIGHTS DATA AND HYPOTHESES ABOUT GC AS A MODEL OF STEM-CELL DISEASE. 2014 20 5548 30 ROLE OF EPIGENETIC REPROGRAMMING OF HOST GENES IN BACTERIAL PATHOGENESIS. THE GENOMES ARE REGULARLY TARGETED BY EPIGENETIC REGULATORY MECHANISMS (DNA METHYLATION, HISTONE MODIFICATIONS, BINDING OF REGULATORY PROTEINS) IN INFECTED CELLS. IN ADDITION, PROTEINS ENCODED BY MICROBIAL GENOMES MAY DISTURB THE ACTION OF A SET OF CELLULAR PROMOTERS BY INTERACTING WITH THE SAME EPI-REGULATORY MACHINERY. THE OUTCOME OF THIS MAY RESULT IN EPIGENETIC DYSREGULATION AND SUBSEQUENT CELLULAR DYSFUNCTIONS THAT MAY MANIFEST IN OR CONTRIBUTE TO THE DEVELOPMENT OF PATHOLOGICAL CHANGES. HOW EPIGENETIC METHYLATION DECORATIONS ON DNA AND HISTONES ARE STARTED AND ESTABLISHED REMAINS LARGELY UNKNOWN. THE INHERITED NATURE OF THESE PROCESSES IN REGULATION OF GENES SUGGESTS THAT THEY COULD PLAY KEY ROLES IN CHRONIC DISEASES ASSOCIATED WITH MICROBIAL PERSISTENCE; THEY MIGHT ALSO EXPLAIN SO-CALLED HIT-AND-RUN PHENOMENA IN INFECTIOUS DISEASE PATHOGENESIS. MICROBES INFECTING MAMMALS MAY CAUSE DISEASES BY CAUSING HYPER-METHYLATION OF KEY CELLULAR PROMOTERS AT CPG DI-NUCLEOTIDES AND MAY INDUCE PATHOLOGICAL CHANGES BY EPIGENETIC REPROGRAMMING OF HOST CELLS THEY ARE INTERACTING WITH ELUCIDATION OF THE EPIGENETIC CONSEQUENCES OF MICROBE-HOST INTERACTIONS MAY HAVE IMPORTANT THERAPEUTIC IMPLICATIONS BECAUSE EPIGENETIC PROCESSES CAN BE REVERTED AND ELIMINATION OF MICROBES INDUCING PATHO-EPIGENETIC CHANGES MAY PREVENT DISEASE DEVELOPMENT. 2013