1 3625 206 IN VIVO GENOME AND METHYLOME ADAPTATION OF CAG-NEGATIVE HELICOBACTER PYLORI DURING EXPERIMENTAL HUMAN INFECTION. MULTIPLE STUDIES HAVE DEMONSTRATED RAPID BACTERIAL GENOME EVOLUTION DURING CHRONIC INFECTION WITH HELICOBACTER PYLORI IN CONTRAST, LITTLE WAS KNOWN ABOUT GENETIC CHANGES DURING THE FIRST STAGES OF INFECTION, WHEN SELECTIVE PRESSURE IS LIKELY TO BE HIGHEST. USING SINGLE-MOLECULE, REAL-TIME (SMRT) AND ILLUMINA SEQUENCING TECHNOLOGIES, WE ANALYZED GENOME AND METHYLOME EVOLUTION DURING THE FIRST 10 WEEKS OF INFECTION BY COMPARING THE CAG PATHOGENICITY ISLAND (CAGPAI)-NEGATIVE H. PYLORI CHALLENGE STRAIN BCS 100 WITH PAIRS OF H. PYLORI REISOLATES FROM GASTRIC ANTRUM AND CORPUS BIOPSY SPECIMENS OF 10 HUMAN VOLUNTEERS WHO HAD BEEN INFECTED WITH THIS STRAIN AS PART OF A VACCINE TRIAL. MOST GENETIC CHANGES DETECTED IN THE REISOLATES AFFECTED GENES WITH A SURFACE-RELATED ROLE OR A PREDICTED FUNCTION IN PEPTIDE UPTAKE. APART FROM PHENOTYPIC CHANGES OF THE BACTERIAL ENVELOPE, A DUPLICATION OF THE CATALASE GENE WAS OBSERVED IN ONE REISOLATE, WHICH RESULTED IN HIGHER CATALASE ACTIVITY AND IMPROVED SURVIVAL UNDER OXIDATIVE STRESS CONDITIONS. THE METHYLOMES ALSO VARIED IN SOME OF THE REISOLATES, MOSTLY BY ACTIVITY SWITCHING OF PHASE-VARIABLE METHYLTRANSFERASE (MTASE) GENES. THE OBSERVED IN VIVO MUTATION SPECTRUM WAS REMARKABLE FOR A VERY HIGH PROPORTION OF NONSYNONYMOUS MUTATIONS. ALTHOUGH THE DATA SHOWED SUBSTANTIAL WITHIN-STRAIN GENOME DIVERSITY IN THE CHALLENGE STRAIN, MOST ANTRUM AND CORPUS REISOLATES FROM THE SAME VOLUNTEERS WERE HIGHLY SIMILAR TO EACH OTHER, INDICATING THAT THE CHALLENGE INFECTION REPRESENTS A MAJOR SELECTIVE BOTTLENECK SHAPING THE TRANSMITTED POPULATION. OUR FINDINGS SUGGEST RAPID IN VIVO SELECTION OF H. PYLORI DURING EARLY-PHASE INFECTION PROVIDING ADAPTATION TO DIFFERENT INDIVIDUALS BY COMMON MECHANISMS OF GENETIC AND EPIGENETIC ALTERATIONS.IMPORTANCE EXCEPTIONAL GENETIC DIVERSITY AND VARIABILITY ARE HALLMARKS OF HELICOBACTER PYLORI, BUT THE BIOLOGICAL ROLE OF THIS PLASTICITY REMAINS INCOMPLETELY UNDERSTOOD. HERE, WE HAD THE RARE OPPORTUNITY TO INVESTIGATE THE MOLECULAR EVOLUTION DURING THE FIRST WEEKS OF H. PYLORI INFECTION BY COMPARING THE GENOMES AND EPIGENOMES OF H. PYLORI STRAIN BCS 100 USED TO CHALLENGE HUMAN VOLUNTEERS IN A VACCINE TRIAL WITH THOSE OF BACTERIA REISOLATED FROM THE VOLUNTEERS 10 WEEKS AFTER THE CHALLENGE. THE DATA PROVIDE MOLECULAR INSIGHTS INTO THE PROCESS OF ESTABLISHMENT OF THIS HIGHLY VERSATILE PATHOGEN IN 10 DIFFERENT HUMAN INDIVIDUAL HOSTS, SHOWING, FOR EXAMPLE, SELECTION FOR CHANGES IN HOST-INTERACTION MOLECULES AS WELL AS CHANGES IN EPIGENETIC METHYLATION PATTERNS. THE DATA PROVIDE IMPORTANT CLUES TO THE EARLY ADAPTATION OF H. PYLORI TO NEW HOST NICHES AFTER TRANSMISSION, WHICH WE BELIEVE IS VITAL TO UNDERSTAND ITS SUCCESS AS A CHRONIC PATHOGEN AND DEVELOP MORE EFFICIENT TREATMENTS AND VACCINES. 2020 2 5078 39 PHYSIOLOGY AND PATHOPHYSIOLOGY OF MATRIX METALLOPROTEASES. MATRIX METALLOPROTEASES (MMPS) COMPRISE A FAMILY OF ENZYMES THAT CLEAVE PROTEIN SUBSTRATES BASED ON A CONSERVED MECHANISM INVOLVING ACTIVATION OF AN ACTIVE SITE-BOUND WATER MOLECULE BY A ZN(2+) ION. ALTHOUGH THE CATALYTIC DOMAIN OF MMPS IS STRUCTURALLY HIGHLY SIMILAR, THERE ARE MANY DIFFERENCES WITH RESPECT TO SUBSTRATE SPECIFICITY, CELLULAR AND TISSUE LOCALIZATION, MEMBRANE BINDING AND REGULATION THAT MAKE THIS A VERY VERSATILE FAMILY OF ENZYMES WITH A MULTITUDE OF PHYSIOLOGICAL FUNCTIONS, MANY OF WHICH ARE STILL NOT FULLY UNDERSTOOD. ESSENTIALLY, ALL MEMBERS OF THE MMP FAMILY HAVE BEEN LINKED TO DISEASE DEVELOPMENT, NOTABLY TO CANCER METASTASIS, CHRONIC INFLAMMATION AND THE ENSUING TISSUE DAMAGE AS WELL AS TO NEUROLOGICAL DISORDERS. THIS HAS STIMULATED A FLURRY OF STUDIES INTO MMP INHIBITORS AS THERAPEUTIC AGENTS, AS WELL AS INTO MEASURING MMP LEVELS AS DIAGNOSTIC OR PROGNOSTIC MARKERS. AS WITH MOST PROTEIN FAMILIES, DECIPHERING THE FUNCTION(S) OF MMPS IS DIFFICULT, AS THEY CAN MODIFY MANY PROTEINS. WHICH OF THESE REACTIONS ARE PHYSIOLOGICALLY OR PATHOPHYSIOLOGICALLY RELEVANT IS OFTEN NOT CLEAR, ALTHOUGH STUDIES ON KNOCKOUT ANIMALS, HUMAN GENETIC AND EPIGENETIC, AS WELL AS BIOCHEMICAL STUDIES USING NATURAL OR SYNTHETIC INHIBITORS HAVE PROVIDED INSIGHT TO A GREAT EXTENT. IN THIS REVIEW, WE WILL GIVE AN OVERVIEW OF 23 MEMBERS OF THE HUMAN MMP FAMILY AND DESCRIBE FUNCTIONS, LINKAGES TO DISEASE AND STRUCTURAL AND MECHANISTIC FEATURES. MMPS CAN BE GROUPED INTO SOLUBLE (INCLUDING MATRILYSINS) AND MEMBRANE-ANCHORED SPECIES. WE ADHERE TO THE 'MMP NOMENCLATURE' AND PROVIDE THE READER WITH REFERENCE TO THE MANY, OFTEN DIVERSE, NAMES FOR THIS ENZYME FAMILY IN THE INTRODUCTION. 2011 3 6703 41 VERSATILE WORKFLOW FOR CELL TYPE-RESOLVED TRANSCRIPTIONAL AND EPIGENETIC PROFILES FROM CRYOPRESERVED HUMAN LUNG. COMPLEXITY OF LUNG MICROENVIRONMENT AND CHANGES IN CELLULAR COMPOSITION DURING DISEASE MAKE IT EXCEPTIONALLY HARD TO UNDERSTAND MOLECULAR MECHANISMS DRIVING DEVELOPMENT OF CHRONIC LUNG DISEASES. ALTHOUGH RECENT ADVANCES IN CELL TYPE-RESOLVED APPROACHES HOLD GREAT PROMISE FOR STUDYING COMPLEX DISEASES, THEIR IMPLEMENTATION RELIES ON LOCAL ACCESS TO FRESH TISSUE, AS TRADITIONAL TISSUE STORAGE METHODS DO NOT ALLOW VIABLE CELL ISOLATION. TO OVERCOME THESE HURDLES, WE DEVELOPED A VERSATILE WORKFLOW THAT ALLOWS STORAGE OF LUNG TISSUE WITH HIGH VIABILITY, PERMITS THOROUGH SAMPLE QUALITY CHECK BEFORE CELL ISOLATION, AND BEFITS SEQUENCING-BASED PROFILING. WE DEMONSTRATE THAT CRYOPRESERVATION ENABLES ISOLATION OF MULTIPLE CELL TYPES FROM BOTH HEALTHY AND DISEASED LUNGS. BASAL CELLS FROM CRYOPRESERVED AIRWAYS RETAIN THEIR DIFFERENTIATION ABILITY, INDICATING THAT CELLULAR IDENTITY IS NOT ALTERED BY CRYOPRESERVATION. IMPORTANTLY, USING RNA SEQUENCING AND EPIC ARRAY, WE SHOW THAT GENE EXPRESSION AND DNA METHYLATION SIGNATURES ARE PRESERVED UPON CRYOPRESERVATION, EMPHASIZING THE SUITABILITY OF OUR WORKFLOW FOR OMICS PROFILING OF LUNG CELLS. MOREOVER, WE OBTAINED HIGH-QUALITY SINGLE-CELL RNA-SEQUENCING DATA OF CELLS FROM CRYOPRESERVED HUMAN LUNGS, DEMONSTRATING THAT CRYOPRESERVATION EMPOWERS SINGLE-CELL APPROACHES. OVERALL, THANKS TO ITS SIMPLICITY, OUR WORKFLOW IS WELL SUITED FOR PROSPECTIVE TISSUE COLLECTION BY ACADEMIC COLLABORATORS AND BIOBANKS, OPENING WORLDWIDE ACCESS TO VIABLE HUMAN TISSUE. 2021 4 6738 31 WHAT'S YOUR CUP OF TEA? THE ROLE OF HERBAL COMPOUNDS IN THE MANAGEMENT OF MULTIPLE SCLEROSIS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC, INFLAMMATORY, NEURODEGENERATIVE DISEASE THAT IS CHARACTERIZED BY A COMPLEX ETIOLOGY. EFFORTS TOWARDS THE MANAGEMENT OF MS HAVE LONG BEEN DIRECTED TOWARDS SYMPTOMATIC RELIEF, AS WELL AS THE USE OF IMMUNE-MODULATORY, DISEASE MODIFYING THERAPIES; HOWEVER, INCONSISTENT TREATMENT RESPONSES STILL PREVAIL, INCREASING THE RISK FOR DISEASE PROGRESSION. WHILE A GREAT DEAL OF RESEARCH ATTEMPTED TO UNRAVEL THE COMPLEXITY OF TREATMENT RESPONSES IN LIGHT OF EPIGENETIC VARIABILITY, PARALLEL EFFORTS IN THE DIRECTION OF ALTERNATIVE MEDICINE MAY BE AS PARAMOUNT. HERBAL COMPOUNDS HAVE LONG BEEN REGARDED AS SAFE AND VERSATILE OPTIONS FOR AIDING IN VARIOUS DISORDERS, INCLUDING NEURODEGENERATIVE CONDITIONS LIKE MS. NUMEROUS STUDIES HAVE TAKEN INTEREST IN A MYRIAD OF HERBAL PLANTS FOR THEIR POTENTIAL BENEFIT IN ALLEVIATING SOME OF THE MOST COMMON MS SYMPTOMS SUCH AS SPASTICITY AND FATIGUE, DELAYING THE PROGRESSION OF THE DISEASE, AS WELL AS INFLUENCING THE OVERALL QUALITY OF LIFE FOR MS PATIENTS. THIS REVIEW AIMS TO PROVIDE A COMPREHENSIVE OVERVIEW OF RECENT CLINICAL STUDIES EXAMINING THE EFFECTS OF VARIOUS HERBAL PLANTS ON DIFFERENT ASPECTS OF MS, IN AN ATTEMPT TO SHED LIGHT ON AN IMPORTANT TOOL FOR AIDING IN THE MANAGEMENT OF THIS COMPLEX AND MULTIFACTORIAL DISEASE. 2023 5 1168 45 CONTRIBUTION OF EPITHELIAL AND GUT MICROBIOME INFLAMMATORY BIOMARKERS TO THE IMPROVEMENT OF COLORECTAL CANCER PATIENTS' STRATIFICATION. IN ORDER TO ENSURE THAT PRIMARY ENDPOINTS OF CLINICAL STUDIES ARE ATTAINED, THE PATIENTS' STRATIFICATION IS AN IMPORTANT ASPECT. SELECTION CRITERIA INCLUDE AGE, GENDER, AND ALSO SPECIFIC BIOMARKERS, SUCH AS INFLAMMATION SCORES. THESE CRITERIA ARE NOT SUFFICIENT TO ACHIEVE A STRAIGHTFORWARD SELECTION, HOWEVER, IN CASE OF MULTIFACTORIAL DISEASES, WITH UNKNOWN OR PARTIALLY IDENTIFIED MECHANISMS, OCCASIONALLY INCLUDING HOST FACTORS, AND THE MICROBIOME. IN THESE CASES, THE EFFICACY OF INTERVENTIONS IS DIFFICULT TO PREDICT, AND AS A RESULT, THE SELECTION OF SUBJECTS IS OFTEN RANDOM. COLORECTAL CANCER (CRC) IS A HIGHLY HETEROGENEOUS DISEASE, WITH VARIABLE CLINICAL FEATURES, OUTCOMES, AND RESPONSE TO THERAPY; THE CRC ONSET AND PROGRESS INVOLVES MULTIPLE SEQUENTIAL STEPS WITH ACCUMULATION OF GENETIC ALTERATIONS, NAMELY, MUTATIONS, GENE AMPLIFICATION, AND EPIGENETIC CHANGES. THE GUT MICROBES, EITHER EUBIOTIC OR DYSBIOTIC, COULD INFLUENCE THE CRC EVOLUTION THROUGH A COMPLEX AND VERSATILE CROSSTALK WITH THE INTESTINAL AND IMMUNE CELLS, PERMANENTLY CHANGING THE TUMOR MICROENVIRONMENT. THERE HAVE BEEN SIGNIFICANT ADVANCES IN THE DEVELOPMENT OF PERSONALIZED APPROACHES FOR CRC SCREENING, TREATMENT, AND POTENTIAL PREVENTION. ADVANCES IN MOLECULAR TECHNIQUES BRING NEW CRITERIA FOR PATIENTS' STRATIFICATION-MUTATIONAL ANALYSIS AT THE TIME OF DIAGNOSIS TO GUIDE TREATMENT, FOR EXAMPLE. GUT MICROBIOME HAS EMERGED AS THE MAIN TRIGGER OF GUT MUCOSAL HOMEOSTASIS. THIS MAY IMPACT CANCER SUSCEPTIBILITY THROUGH MAINTENANCE OF THE EPITHELIAL/MUCUS BARRIER AND PRODUCTION OF PROTECTIVE METABOLITES, SUCH AS SHORT-CHAIN FATTY ACIDS (SCFAS) VIA INTERACTIONS WITH THE HOSTS' DIET AND METABOLISM. MICROBIOME DYSBIOSIS LEADS TO THE ENRICHMENT OF CANCER-PROMOTING BACTERIAL POPULATIONS, LOSS OF PROTECTIVE POPULATIONS OR MAINTAINING AN INFLAMMATORY CHRONIC STATE, ALL OF WHICH CONTRIBUTE TO THE DEVELOPMENT AND PROGRESSION OF CRC. MEANWHILE, VARIATIONS IN PATIENT RESPONSES TO ANTI-CANCER IMMUNO- AND CHEMOTHERAPIES WERE ALSO LINKED TO INTER-INDIVIDUAL DIFFERENCES IN INTESTINE MICROBIOMES. THE AUTHORS AIM TO HIGHLIGHT THE CONTRIBUTION OF EPITHELIAL AND GUT MICROBIOME INFLAMMATORY BIOMARKERS IN THE IMPROVEMENT OF CRC PATIENTS' STRATIFICATION TOWARDS A PERSONALIZED APPROACH OF EARLY DIAGNOSIS AND TREATMENT. 2021 6 2342 32 EPIGENETIC REGULATION OF MACROPHAGE POLARIZATION AND FUNCTION. MACROPHAGE POLARIZATION REFERS TO DEVELOPMENT OF A SPECIFIC PHENOTYPE IMPORTANT FOR TISSUE HOMEOSTASIS OR HOST DEFENSE IN RESPONSE TO ENVIRONMENTAL CUES. ENVIRONMENTAL FACTORS THAT INDUCE MACROPHAGE POLARIZATION INCLUDE CYTOKINES AND MICROBIAL FACTORS PRODUCED BY PATHOGENS OR COMMENSAL MICROBIOTA. SIGNALING PATHWAYS UTILIZED BY THESE POLARIZING FACTORS HAVE BEEN WELL CHARACTERIZED, BUT IT IS LESS CLEAR HOW SIGNALS ARE CONVERTED INTO COMPLEX AND SUSTAINED PATTERNS OF GENE EXPRESSION, AND HOW MACROPHAGES ARE REPROGRAMMED DURING POLARIZATION TO ALTER THEIR RESPONSES TO SUBSEQUENT ENVIRONMENTAL CHALLENGES. EMERGING EVIDENCE, REVIEWED HERE, SUGGESTS AN IMPORTANT ROLE FOR EPIGENETIC MECHANISMS IN MODULATING AND TRANSMITTING SIGNALS DURING MACROPHAGE POLARIZATION AND REPROGRAMMING. DEEPER UNDERSTANDING OF EPIGENETIC REGULATION OF MACROPHAGE PHENOTYPE WILL ENABLE DEVELOPMENT OF GENE-SPECIFIC THERAPEUTIC APPROACHES TO ENHANCE HOST DEFENSE WHILE PRESERVING TISSUE INTEGRITY AND PREVENTING CHRONIC INFLAMMATORY DISEASES. 2013 7 3550 39 IMMUNOSENESCENCE IN ATHEROSCLEROSIS: A ROLE FOR CHRONIC VIRAL INFECTIONS. IMMUNE SYSTEM IS A VERSATILE AND DYNAMIC BODY ORGAN WHICH OFFERS SURVIVAL AND ENDURANCE OF HUMAN BEINGS IN THEIR HOSTILE LIVING ENVIRONMENT. HOWEVER, SIMILAR TO OTHER CELLS, IMMUNE CELLS ARE HIJACKED BY SENESCENCE. THE AGEING IMMUNE CELLS LOSE THEIR BENEFICIAL FUNCTIONS BUT CONTINUE TO PRODUCE INFLAMMATORY MEDIATORS WHICH DRAW OTHER IMMUNE AND NON-IMMUNE CELLS TO THE SENESCENCE LOOP. IMMUNOSENESCENCE HAS BEEN SHOWN TO BE ASSOCIATED WITH DIFFERENT PATHOLOGICAL CONDITIONS AND DISEASES, AMONG WHICH ATHEROSCLEROSIS HAS RECENTLY COME TO LIGHT. THERE ARE COMMON DRIVERS OF BOTH IMMUNOSENESCENCE AND ATHEROSCLEROSIS; E.G. INFLAMMATION, REACTIVE OXYGEN SPECIES (ROS), CHRONIC VIRAL INFECTIONS, GENOMIC DAMAGE, OXIDIZED-LDL, HYPERTENSION, CIGARETTE SMOKE, HYPERGLYCAEMIA, AND MITOCHONDRIAL FAILURE. CHRONIC VIRAL INFECTIONS INDUCE INFLAMMAGING, SUSTAINED CYTOKINE SIGNALING, ROS GENERATION AND DNA DAMAGE WHICH ARE ASSOCIATED WITH ATHEROGENESIS. ACCUMULATING EVIDENCE SHOWS THAT SEVERAL DNA AND RNA VIRUSES ARE STIMULATORS OF IMMUNOSENESCENCE AND ATHEROSCLEROSIS IN AN INTERRELATED NETWORK. DNA VIRUSES SUCH AS CMV, EBV AND HBV UPREGULATE P16, P21 AND P53 SENESCENCE-ASSOCIATED MOLECULES; INDUCE INFLAMMAGING, METABOLIC REPROGRAMMING OF INFECTED CELLS, REPLICATIVE SENESCENCE AND TELOMERE SHORTENING. RNA VIRUSES SUCH AS HCV AND HIV INDUCE ROS GENERATION, DNA DAMAGE, INDUCTION OF SENESCENCE-ASSOCIATED SECRETORY PHENOTYPE (SASP), METABOLIC REPROGRAMMING OF INFECTED CELLS, G1 CELL CYCLE ARREST, TELOMERE SHORTENING, AS WELL AS EPIGENETIC MODIFICATIONS OF DNA AND HISTONES. THE NEWLY EMERGED SARS-COV-2 VIRUS IS ALSO A POTENT INDUCER OF CYTOKINE STORM AND SASP. THE SPIKE PROTEIN OF SARS-COV-2 PROMOTES SENESCENCE PHENOTYPE IN ENDOTHELIAL CELLS BY AUGMENTING P16, P21, SENESCENCE-ASSOCIATED BETA-GALACTOSIDASE (SA-BETA-GAL) AND ADHESION MOLECULES EXPRESSION. THE IMPACT OF SARS-COV-2 MEGA-INFLAMMATION ON ATHEROGENESIS, HOWEVER, REMAINS TO BE INVESTIGATED. IN THIS REVIEW WE FOCUS ON THE COMMON PROCESSES IN IMMUNOSENESCENCE AND ATHEROGENESIS CAUSED BY CHRONIC VIRAL INFECTIONS AND DISCUSS THE CURRENT KNOWLEDGE ON THIS TOPIC. 2022 8 2617 47 EPIGENOME TARGETING BY PROBIOTIC METABOLITES. BACKGROUND: THE INTESTINAL MICROBIOTA PLAYS AN IMPORTANT ROLE IN IMMUNE DEVELOPMENT AND HOMEOSTASIS. A DISTURBED MICROBIOTA DURING EARLY INFANCY IS ASSOCIATED WITH AN INCREASED RISK OF DEVELOPING INFLAMMATORY AND ALLERGIC DISEASES LATER IN LIFE. THE MECHANISMS UNDERLYING THESE EFFECTS ARE POORLY UNDERSTOOD BUT ARE LIKELY TO INVOLVE ALTERATIONS IN MICROBIAL PRODUCTION OF FERMENTATION-DERIVED METABOLITES, WHICH HAVE POTENT IMMUNE MODULATING PROPERTIES AND ARE REQUIRED FOR MAINTENANCE OF HEALTHY MUCOSAL IMMUNE RESPONSES. PROBIOTICS ARE BENEFICIAL BACTERIA THAT HAVE THE CAPACITY TO ALTER THE COMPOSITION OF BACTERIAL SPECIES IN THE INTESTINE THAT CAN IN TURN INFLUENCE THE PRODUCTION OF FERMENTATION-DERIVED METABOLITES. PRINCIPAL AMONG THESE METABOLITES ARE THE SHORT-CHAIN FATTY ACIDS BUTYRATE AND ACETATE THAT HAVE POTENT ANTI-INFLAMMATORY ACTIVITIES IMPORTANT IN REGULATING IMMUNE FUNCTION AT THE INTESTINAL MUCOSAL SURFACE. THEREFORE STRATEGIES AIMED AT RESTORING THE MICROBIOTA PROFILE MAY BE EFFECTIVE IN THE PREVENTION OR TREATMENT OF ALLERGIC AND INFLAMMATORY DISEASES. PRESENTATION OF THE HYPOTHESIS: PROBIOTIC BACTERIA HAVE DIVERSE EFFECTS INCLUDING ALTERING MICROBIOTA COMPOSITION, REGULATING EPITHELIAL CELL BARRIER FUNCTION AND MODULATING OF IMMUNE RESPONSES. THE PRECISE MOLECULAR MECHANISMS MEDIATING THESE PROBIOTIC EFFECTS ARE NOT WELL UNDERSTOOD. SHORT-CHAIN FATTY ACIDS SUCH AS BUTYRATE ARE A CLASS OF HISTONE DEACETYLASE INHIBITORS IMPORTANT IN THE EPIGENETIC CONTROL OF HOST CELL RESPONSES. IT IS HYPOTHESIZED THAT THE BIOLOGICAL FUNCTION OF PROBIOTICS MAY BE A RESULT OF EPIGENETIC MODIFICATIONS THAT MAY EXPLAIN THE WIDE RANGE OF EFFECTS OBSERVED. STUDIES DELINEATING THE EFFECTS OF PROBIOTICS ON SHORT-CHAIN FATTY ACID PRODUCTION AND THE EPIGENETIC ACTIONS OF SHORT-CHAIN FATTY ACIDS WILL ASSIST IN UNDERSTANDING THE ASSOCIATION BETWEEN MICROBIOTA AND ALLERGIC OR AUTOIMMUNE DISORDERS. TESTING THE HYPOTHESIS: WE PROPOSE THAT TREATMENT WITH SPECIFIC PROBIOTIC BACTERIA UNDER IN VIVO CONDITIONS WOULD OFFER THE IDEAL CONDITIONS TO EXAMINE THE MICROBIOLOGICAL, IMMUNOLOGICAL AND EPIGENETIC MECHANISMS OF ACTION. ADVANCES IN EPIGENETIC TECHNOLOGY NOW ALLOW INVESTIGATORS TO BETTER UNDERSTAND THE COMPLEX BIOLOGICAL PROPERTIES OF PROBIOTICS AND THEIR METABOLITES. IMPLICATIONS OF THE HYPOTHESIS: DETERMINING THE PRECISE MECHANISMS OF PROBIOTIC ACTION WILL LEAD TO MORE SPECIFIC AND EFFICACIOUS THERAPEUTIC STRATEGIES IN THE PREVENTION OR TREATMENT OF CHRONIC INFLAMMATORY CONDITIONS. 2010 9 6883 29 [RESOLUTION OF INFLAMMATION--PHARMACOLOGICAL ASPECTS]. INFLAMMATION IS A FUNDAMENTAL BIOLOGIC PROCESS EVOLUTIONALLY PRESERVED BY A GERM LINE CODE. THE INTERPLAY OF THE EPIGENETIC WITH THE ENVIRONMENT DIRECTS THE CODE TO TEMPORALLY DISTINCT INFLAMMATORY RESPONSES, WHICH CAN BE ACUTE OR CHRONIC. THE AIM OF THIS STUDY IS TO PRESENT NEW ASPECTS REGARDING THE RESOLUTION OF INFLAMMATION. ACUTE INFLAMMATION NORMALLY RESOLVES BY MECHANISMS STILL SOMEWHAT ELUSIVE. CURRENT EVIDENCE SUGGESTS THAT AN ACTIVE COORDINATED PROGRAM INITIATED THE FIRST FEW HOURS AFTER THE INFLAMMATORY RESPONSE BEGINS AND ITS FAILURE LEAD TO CHRONIC INFLAMMATION. THIS PROCESS IS ESSENTIAL FOR APPROPRIATE HOST RESPONSES, TISSUE PROTECTION AND THE RETURN TO HOMEOSTASIS. PROSTAGLANDINS AND LEUKOTRIENES ARE LIPID MEDIATORS THAT PLAY IMPORTANT ROLES IN HOST DEFENSE AND ACUTE INFLAMMATION. GRANULOCYTES PROMOTE THE SWITCH OF ARACHIDONIC ACID-DERIVED PROSTAGLANDINS AND LEUKOTRIENES TO LIPOXINS, ACTIVE ANTIINFLAMMATORY AND PRO-RESOLUTION MEDIATORS. THE APOPTOSIS OF THE NEUTROPHILS COINCIDES WITH THE BIOSYNTHESIS OF RESOLVINS AND PROTECTINS FROM OMEGA-3 POLYUNSATURATED FATTY ACIDS AND RELEASES ANTI-INFLAMMATORY AND REPARATIVE CYTOKINES. THIS INFORMATION COULD LEAD TO NEW TREATMENTS FOR INFLAMMATORY DISEASES. 2011 10 5469 29 RESOLUTION OF INFLAMMATION AS A NOVEL CHEMOPREVENTIVE STRATEGY. ACUTE INFLAMMATION, A PHYSIOLOGIC RESPONSE TO PROTECT CELLS FROM MICROBIAL INFECTION AND OTHER NOXIOUS STIMULI, IS AUTOMATICALLY TERMINATED BY ENDOGENOUS ANTI-INFLAMMATORY AND PRO-RESOLVING MEDIATORS TO RESTORE HOMEOSTATIC CONDITIONS. HOWEVER, IF TIMELY RESOLUTION OF INFLAMMATION IS FAILED, INFLAMMATION PERSISTS AND CAN PROGRESS TO A CHRONIC INFLAMMATION WHICH HAS LONG BEEN THOUGHT AS A PREDISPOSING FACTOR TO CARCINOGENESIS. EXCESSIVE AND PATHOLOGIC INFLAMMATION CAUSES DNA DAMAGE, GENOMIC INSTABILITY, EPIGENETIC DYSREGULATION, AND ALTERATION OF INTRACELLULAR SIGNALING, ALL OF WHICH ARE INVOLVED IN NEOPLASTIC TRANSFORMATION. TO PREVENT CHRONIC INFLAMMATION AND RESULTING INFLAMMATION-PROMOTED CANCER DEVELOPMENT, UNDERSTANDING THE PROCESS THAT RESOLVES INFLAMMATION IS ESSENTIAL. RESOLUTION OF INFLAMMATION IS AN ACTIVE COORDINATED PROCESS REGULATED BY DISTINCT ANTI-INFLAMMATORY AND PRO-RESOLVING ENDOGENOUS LIPID MEDIATORS, SUCH AS RESOLVINS AND LIPOXINS. THE ROLE OF PRO-INFLAMMATORY SIGNALING IN CARCINOGENESIS HAS BECOME MORE AND MORE EVIDENT AND WELL CHARACTERIZED, BUT THE POTENTIAL ROLE OF PRO-RESOLVING MEDIATORS IN CANCER PREVENTION REMAINS STILL ELUSIVE. IN SEARCHING FOR AN EFFICACIOUS WAY TO PREVENT CHRONIC INFLAMMATION-ASSOCIATED CANCER, THE PRO-RESOLVING SIGNAL TRANSDUCTION PATHWAYS AND THEIR REGULATORS SHOULD BE UNRAVELED. 2013 11 4422 41 MOLECULAR AND GENETIC INFLAMMATION NETWORKS IN MAJOR HUMAN DISEASES. IT HAS BEEN WELL-RECOGNIZED THAT INFLAMMATION ALONGSIDE TISSUE REPAIR AND DAMAGE MAINTAINING TISSUE HOMEOSTASIS DETERMINES THE INITIATION AND PROGRESSION OF COMPLEX DISEASES. ALBEIT WITH THE ACCOMPLISHMENT OF HAVING CAPTURED THE MOST CRITICAL INFLAMMATION-INVOLVED MOLECULES, GENETIC SUSCEPTIBILITIES, EPIGENETIC FACTORS, AND ENVIRONMENTAL FACTORS, OUR SCHEMATA ON THE ROLE OF INFLAMMATION IN COMPLEX DISEASES REMAIN LARGELY PATCHY, IN PART DUE TO THE SUCCESS OF REDUCTIONISM IN TERMS OF RESEARCH METHODOLOGY PER SE. OMICS DATA ALONGSIDE THE ADVANCES IN DATA INTEGRATION TECHNOLOGIES HAVE ENABLED RECONSTRUCTION OF MOLECULAR AND GENETIC INFLAMMATION NETWORKS WHICH SHED LIGHT ON THE UNDERLYING PATHOPHYSIOLOGY OF COMPLEX DISEASES OR CLINICAL CONDITIONS. GIVEN THE PROVEN BENEFICIAL ROLE OF ANTI-INFLAMMATION IN CORONARY HEART DISEASE AS WELL AS OTHER COMPLEX DISEASES AND IMMUNOTHERAPY AS A REVOLUTIONARY TRANSITION IN ONCOLOGY, IT BECOMES TIMELY TO REVIEW OUR CURRENT UNDERSTANDING OF THE MOLECULAR AND GENETIC INFLAMMATION NETWORKS UNDERLYING MAJOR HUMAN DISEASES. IN THIS REVIEW, WE FIRST BRIEFLY DISCUSS THE COMPLEXITY OF INFECTIOUS DISEASES AND THEN HIGHLIGHT RECENTLY UNCOVERED MOLECULAR AND GENETIC INFLAMMATION NETWORKS IN OTHER MAJOR HUMAN DISEASES INCLUDING OBESITY, TYPE II DIABETES, CORONARY HEART DISEASE, LATE ONSET ALZHEIMER'S DISEASE, PARKINSON'S DISEASE, AND SPORADIC CANCER. THE COMMONALITY AND SPECIFICITY OF THESE MOLECULAR NETWORKS ARE ADDRESSED IN THE CONTEXT OF GENETICS BASED ON GENOME-WIDE ASSOCIATION STUDY (GWAS). THE DOUBLE-SWORD ROLE OF INFLAMMATION, SUCH AS HOW THE ABERRANT TYPE 1 AND/OR TYPE 2 IMMUNITY LEADS TO CHRONIC AND SEVERE CLINICAL CONDITIONS, REMAINS OPEN IN TERMS OF THE INFLAMMASOME AND THE CORE INFLAMMATOME NETWORK FEATURES. INCREASINGLY AVAILABLE LARGE OMICS AND CLINICAL DATA IN TANDEM WITH SYSTEMS BIOLOGY APPROACHES HAVE OFFERED AN EXCITING YET CHALLENGING OPPORTUNITY TOWARD RECONSTRUCTION OF MORE COMPREHENSIVE AND DYNAMIC MOLECULAR AND GENETIC INFLAMMATION NETWORKS, WHICH HOLD GREAT PROMISE IN TRANSITING NETWORK SNAPSHOTS TO VIDEO-STYLE MULTI-SCALE INTERPLAYS OF DISEASE MECHANISMS, IN TURN LEADING TO EFFECTIVE CLINICAL INTERVENTION. 2016 12 6169 35 THE GUT MICROBIOTA AND HEALTHY AGING: A MINI-REVIEW. THE GUT MICROBIOTA SHOWS A WIDE INTER-INDIVIDUAL VARIATION, BUT ITS WITHIN-INDIVIDUAL VARIATION IS RELATIVELY STABLE OVER TIME. A FUNCTIONAL CORE MICROBIOME, PROVIDED BY ABUNDANT BACTERIAL TAXA, SEEMS TO BE COMMON TO VARIOUS HUMAN HOSTS REGARDLESS OF THEIR GENDER, GEOGRAPHIC LOCATION, AND AGE. WITH ADVANCING CHRONOLOGICAL AGE, THE GUT MICROBIOTA BECOMES MORE DIVERSE AND VARIABLE. HOWEVER, WHEN MEASURES OF BIOLOGICAL AGE ARE USED WITH ADJUSTMENT FOR CHRONOLOGICAL AGE, OVERALL RICHNESS DECREASES, WHILE A CERTAIN GROUP OF BACTERIA ASSOCIATED WITH FRAILTY INCREASES. THIS HIGHLIGHTS THE IMPORTANCE OF CONSIDERING BIOLOGICAL OR FUNCTIONAL MEASURES OF AGING. STUDIES USING MODEL ORGANISMS INDICATE THAT AGE-RELATED GUT DYSBIOSIS MAY CONTRIBUTE TO UNHEALTHY AGING AND REDUCED LONGEVITY. THE GUT MICROBIOME DEPENDS ON THE HOST NUTRIENT SIGNALING PATHWAYS FOR ITS BENEFICIAL EFFECTS ON HOST HEALTH AND LIFESPAN, AND GUT DYSBIOSIS DISRUPTING THE INTERDEPENDENCE MAY DIMINISH THE BENEFICIAL EFFECTS OR EVEN HAVE REVERSE EFFECTS. GUT DYSBIOSIS CAN TRIGGER THE INNATE IMMUNE RESPONSE AND CHRONIC LOW-GRADE INFLAMMATION, LEADING TO MANY AGE-RELATED DEGENERATIVE PATHOLOGIES AND UNHEALTHY AGING. THE GUT MICROBIOTA COMMUNICATES WITH THE HOST THROUGH VARIOUS BIOMOLECULES, NUTRIENT SIGNALING-INDEPENDENT PATHWAYS, AND EPIGENETIC MECHANISMS. DISTURBANCE OF THESE COMMUNICATIONS BY AGE-RELATED GUT DYSBIOSIS CAN AFFECT THE HOST HEALTH AND LIFESPAN. THIS MAY EXPLAIN THE IMPACT OF THE GUT MICROBIOME ON HEALTH AND AGING. 2018 13 4332 36 MICRORNAS: IMPORTANT MODULATORS OF OXLDL-MEDIATED SIGNALING IN ATHEROSCLEROSIS. OXIDIZED LOW-DENSITY LIPOPROTEIN (OXLDL) IS KNOWN TO BE A MAJOR RISK FACTOR FOR THE INITIATION AND DEVELOPMENT OF ATHEROSCLEROSIS. IT CAN ELICIT AN ARRAY OF ATHEROGENIC RESPONSES IN MULTIPLE TYPES OF CELLS RESIDING IN THE ARTERIAL WALL, SUCH AS ENDOTHELIAL CELLS (ECS), MACROPHAGES, DENDRITIC CELLS (DCS), AND VASCULAR SMOOTH MUSCLE CELLS (VSMCS). ALTHOUGH THEY HAVE BEEN STUDIED FOR MANY YEARS, THE DETAILED MECHANISMS MODULATING OXLDL-INDUCED INFLAMMATION HAVE NOT BEEN FULLY ELUCIDATED. EPIGENETIC MECHANISMS CONSIST OF DNA METHYLATION, HISTONE POST-TRANSLATIONAL MODIFICATIONS (PTMS), AND MICRORNA (MIRNA) ALTERATIONS. RECENTLY, EPIGENETIC FACTORS, ESPECIALLY MIRNAS, HAVE EMERGED AS NOVEL COMPONENTS OF THE GENE EXPRESSION REGULATING OXLDL-TRIGGERED SIGNAL TRANSDUCTION. IN ADDITION TO THEIR REGULATORY ROLES IN SIGNALING MOLECULES, INCREASING EVIDENCE SUGGESTS THAT THE DIFFERENT GENETIC STABILITY AND CROSS-TALK REGULATION AMONG THESE EPIGENETIC FACTORS MAY BE PARTICULARLY IMPORTANT TO THE SUSTAINED INFLAMMATION INITIATED BY TEMPORAL OXLDL STIMULATION. THEREFORE, IN THIS REVIEW, WE PRIMARILY FOCUSED ON THE FUNCTIONAL ROLE OF MIRNAS, AS WELL AS OTHER EPIGENETIC FACTORS, ON MODULATING OXLDL-INDUCED SIGNAL TRANSDUCTION IN DIFFERENT VASCULAR CELLS, WITH A SPECIAL EMPHASIS ON THE CROSSTALK INTERACTIONS BETWEEN MIRNAS AND OTHER EPIGENETIC PLAYERS THAT HELP TRANSLATE TRANSIENT ENVIRONMENT INSULTS INTO CHRONIC INFLAMMATION. MOREOVER, WE EXTENSIVELY DISCUSSED THE POTENTIAL APPLICABILITY OF MIRNAS AS DISEASE BIOMARKERS AND THERAPEUTIC TARGETS IN DIAGNOSING AND TREATING ATHEROSCLEROSIS. 2013 14 1712 40 DYSFUNCTIONAL VASCULAR ENDOTHELIUM AS A DRIVER OF ATHEROSCLEROSIS: EMERGING INSIGHTS INTO PATHOGENESIS AND TREATMENT. ATHEROSCLEROSIS, THE CHRONIC ACCUMULATION OF CHOLESTEROL-RICH PLAQUE WITHIN ARTERIES, IS ASSOCIATED WITH A BROAD SPECTRUM OF CARDIOVASCULAR DISEASES INCLUDING MYOCARDIAL INFARCTION, AORTIC ANEURYSM, PERIPHERAL VASCULAR DISEASE, AND STROKE. ATHEROSCLEROTIC CARDIOVASCULAR DISEASE REMAINS A LEADING CAUSE OF MORTALITY IN HIGH-INCOME COUNTRIES AND RECENT YEARS HAVE WITNESSED A NOTABLE INCREASE IN PREVALENCE WITHIN LOW- AND MIDDLE-INCOME REGIONS OF THE WORLD. CONSIDERING THIS PROMINENT AND EVOLVING GLOBAL BURDEN, THERE IS A NEED TO IDENTIFY THE CELLULAR MECHANISMS THAT UNDERLIE THE PATHOGENESIS OF ATHEROSCLEROSIS TO DISCOVER NOVEL THERAPEUTIC TARGETS FOR PREVENTING OR MITIGATING ITS CLINICAL SEQUELAE. DESPITE DECADES OF RESEARCH, WE STILL DO NOT FULLY UNDERSTAND THE COMPLEX CELL-CELL INTERACTIONS THAT DRIVE ATHEROSCLEROSIS, BUT NEW INVESTIGATIVE APPROACHES ARE RAPIDLY SHEDDING LIGHT ON THESE ESSENTIAL MECHANISMS. THE VASCULAR ENDOTHELIUM RESIDES AT THE INTERFACE OF SYSTEMIC CIRCULATION AND THE UNDERLYING VESSEL WALL AND PLAYS AN ESSENTIAL ROLE IN GOVERNING PATHOPHYSIOLOGICAL PROCESSES DURING ATHEROGENESIS. IN THIS REVIEW, WE PRESENT EMERGING EVIDENCE THAT IMPLICATES THE ACTIVATED ENDOTHELIUM AS A DRIVER OF ATHEROSCLEROSIS BY DIRECTING SITE-SPECIFICITY OF PLAQUE FORMATION AND BY PROMOTING PLAQUE DEVELOPMENT THROUGH INTRACELLULAR PROCESSES, WHICH REGULATE ENDOTHELIAL CELL PROLIFERATION AND TURNOVER, METABOLISM, PERMEABILITY, AND PLASTICITY. MOREOVER, WE HIGHLIGHT NOVEL MECHANISMS OF INTERCELLULAR COMMUNICATION BY WHICH ENDOTHELIAL CELLS MODULATE THE ACTIVITY OF KEY VASCULAR CELL POPULATIONS INVOLVED IN ATHEROGENESIS, AND DISCUSS HOW ENDOTHELIAL CELLS CONTRIBUTE TO RESOLUTION BIOLOGY - A PROCESS THAT IS DYSREGULATED IN ADVANCED PLAQUES. FINALLY, WE DESCRIBE IMPORTANT FUTURE DIRECTIONS FOR PRECLINICAL ATHEROSCLEROSIS RESEARCH, INCLUDING EPIGENETIC AND TARGETED THERAPIES, TO LIMIT THE PROGRESSION OF ATHEROSCLEROSIS IN AT-RISK OR AFFECTED PATIENTS. 2021 15 2320 37 EPIGENETIC REGULATION OF GENE EXPRESSION AND M2 MACROPHAGE POLARIZATION AS NEW POTENTIAL OMEGA-3 POLYUNSATURATED FATTY ACID TARGETS IN COLON INFLAMMATION AND CANCER. INTRODUCTION: IT HAS BECOME INCREASINGLY CLEAR THAT DIETARY HABITS MAY AFFECT THE RISK/PROGRESSION OF CHRONIC DISEASES WITH A PATHOGENIC INFLAMMATORY COMPONENT, SUCH AS COLORECTAL CANCER. CONSIDERABLE ATTENTION HAS BEEN DIRECTED TOWARD THE ABILITY OF NUTRITIONAL AGENTS TO TARGET KEY MOLECULAR PATHWAYS INVOLVED IN THESE INFLAMMATORY-RELATED DISEASES. AREAS COVERED: OMEGA-3 POLYUNSATURATED FATTY ACIDS (PUFA) AND THEIR OXIDATIVE METABOLITES HAVE ATTRACTED CONSIDERABLE INTEREST AS POSSIBLE ANTI-INFLAMMATORY AND ANTI-CANCER AGENTS, ESPECIALLY IN AREAS SUCH AS THE LARGE BOWEL, WHERE THE INFLUENCE OF ORALLY INTRODUCED SUBSTANCES IS HIGH AND TUMORS SHOW DERANGED PUFA PATTERNS. ON THIS BASIS, WE HAVE ANALYZED PRE-CLINICAL FINDINGS THAT HAVE RECENTLY REVEALED NEW INSIGHT INTO THE MOLECULAR PATHWAYS TARGETED BY OMEGA-3 PUFA. EXPERT OPINION: THE FINDINGS ANALYZED HEREIN DEMONSTRATE THAT OMEGA-3 PUFA MAY EXERT BENEFICIAL EFFECTS BY TARGETING THE EPIGENETIC REGULATION OF GENE EXPRESSION AND ALTERING M2 MACROPHAGE POLARIZATION DURING THE INFLAMMATORY RESPONSE. THESE MECHANISMS NEED TO BE BETTER EXPLORED IN THE LARGE BOWEL, AND FURTHER STUDIES COULD BETTER CLARIFY THEIR ROLE AND THE POTENTIAL OF DIETARY INTERVENTIONS WITH OMEGA-3 PUFA IN THE LARGE BOWEL. THE EPIGENOMIC MECHANISM IS DISCUSSED IN VIEW OF THE POTENTIAL OF OMEGA-3 PUFA TO ENHANCE THE EFFICACY OF OTHER AGENTS USED IN THE THERAPY OF COLORECTAL CANCER. 2016 16 3964 40 LONG NONCODING RNAS IN LUNG CANCER. DESPITE GREAT PROGRESS IN RESEARCH AND TREATMENT OPTIONS, LUNG CANCER REMAINS THE LEADING CAUSE OF CANCER-RELATED DEATHS WORLDWIDE. ONCOGENIC DRIVER MUTATIONS IN PROTEIN-ENCODING GENES WERE DEFINED AND ALLOW FOR PERSONALIZED THERAPIES BASED ON GENETIC DIAGNOSES. NONETHELESS, DIAGNOSIS OF LUNG CANCER MOSTLY OCCURS AT LATE STAGES, AND CHRONIC TREATMENT IS FOLLOWED BY A FAST ONSET OF CHEMORESISTANCE. HENCE, THERE IS AN URGENT NEED FOR RELIABLE BIOMARKERS AND ALTERNATIVE TREATMENT OPTIONS. WITH THE ERA OF WHOLE GENOME AND TRANSCRIPTOME SEQUENCING TECHNOLOGIES, LONG NONCODING RNAS EMERGED AS A NOVEL CLASS OF VERSATILE, FUNCTIONAL RNA MOLECULES. ALTHOUGH FOR MOST OF THEM THE MECHANISM OF ACTION REMAINS TO BE DEFINED, ACCUMULATING EVIDENCE CONFIRMS THEIR INVOLVEMENT IN VARIOUS ASPECTS OF LUNG TUMORIGENESIS. THEY ARE FUNCTIONAL ON THE EPIGENETIC, TRANSCRIPTIONAL, AND POSTTRANSCRIPTIONAL LEVEL AND ARE REGULATORS OF PATHOPHYSIOLOGICAL KEY PATHWAYS INCLUDING CELL GROWTH, APOPTOSIS, AND METASTASIS. LONG NONCODING RNAS ARE GAINING INCREASING ATTENTION AS POTENTIAL BIOMARKERS AND A NOVEL CLASS OF DRUGGABLE MOLECULES. IT HAS BECOME CLEAR THAT WE ARE ONLY BEGINNING TO UNDERSTAND THE COMPLEXITY OF TUMORIGENIC PROCESSES. THE CLINICAL INTEGRATION OF LONG NONCODING RNAS IN TERMS OF PROGNOSTIC AND PREDICTIVE BIOMARKER SIGNATURES AND ADDITIONAL CANCER TARGETS COULD PROVIDE A CHANCE TO INCREASE THE THERAPEUTIC BENEFIT. HERE, WE REVIEW THE CURRENT KNOWLEDGE ABOUT THE EXPRESSION, REGULATION, BIOLOGICAL FUNCTION, AND CLINICAL RELEVANCE OF LONG NONCODING RNAS IN LUNG CANCER. 2016 17 6376 35 THE ROLE OF NEUTROPHILS IN TRAINED IMMUNITY. THE PRINCIPLE OF TRAINED IMMUNITY REPRESENTS INNATE IMMUNE MEMORY DUE TO SUSTAINED, MAINLY EPIGENETIC, CHANGES TRIGGERED BY ENDOGENOUS OR EXOGENOUS STIMULI IN BONE MARROW (BM) PROGENITORS (CENTRAL TRAINED IMMUNITY) AND THEIR INNATE IMMUNE CELL PROGENY, THEREBY TRIGGERING ELEVATED RESPONSIVENESS AGAINST SECONDARY STIMULI. BM PROGENITORS CAN RESPOND TO MICROBIAL AND STERILE SIGNALS, THEREBY POSSIBLY ACQUIRING TRAINED IMMUNITY-MEDIATED LONG-LASTING ALTERATIONS THAT MAY SHAPE THE FATE AND FUNCTION OF THEIR PROGENY, FOR EXAMPLE, NEUTROPHILS. NEUTROPHILS, THE MOST ABUNDANT INNATE IMMUNE CELL POPULATION, ARE PRODUCED IN THE BM FROM COMMITTED PROGENITOR CELLS IN A PROCESS DESIGNATED GRANULOPOIESIS. NEUTROPHILS ARE THE FIRST RESPONDERS AGAINST INFECTIOUS OR INFLAMMATORY CHALLENGES AND HAVE VERSATILE FUNCTIONS IN IMMUNITY. TOGETHER WITH OTHER INNATE IMMUNE CELLS, NEUTROPHILS ARE EFFECTORS OF PERIPHERAL TRAINED IMMUNITY. HOWEVER, GIVEN THE SHORT LIFETIME OF NEUTROPHILS, THEIR ABILITY TO ACQUIRE IMMUNOLOGICAL MEMORY MAY LIE IN THE CENTRAL TRAINING OF THEIR BM PROGENITORS RESULTING IN GENERATION OF REPROGRAMMED, THAT IS, "TRAINED", NEUTROPHILS. ALTHOUGH TRAINED IMMUNITY MAY HAVE BENEFICIAL EFFECTS IN INFECTION OR CANCER, IT MAY ALSO MEDIATE DETRIMENTAL OUTCOMES IN CHRONIC INFLAMMATION. HERE, WE REVIEW THE EMERGING RESEARCH AREA OF TRAINED IMMUNITY WITH A PARTICULAR EMPHASIS ON THE ROLE OF NEUTROPHILS AND GRANULOPOIESIS. 2023 18 3596 37 IMPLICATIONS OF SPHINGOLIPIDS ON AGING AND AGE-RELATED DISEASES. AGING IS A PROCESS LEADING TO A PROGRESSIVE LOSS OF PHYSIOLOGICAL INTEGRITY AND HOMEOSTASIS, AND A PRIMARY RISK FACTOR FOR MANY LATE-ONSET CHRONIC DISEASES. THE MECHANISMS UNDERLYING AGING HAVE LONG PIQUED THE CURIOSITY OF SCIENTISTS. HOWEVER, THE IDEA THAT AGING IS A BIOLOGICAL PROCESS SUSCEPTIBLE TO GENETIC MANIPULATION WAS NOT WELL ESTABLISHED UNTIL THE DISCOVERY THAT THE INHIBITION OF INSULIN/IGF-1 SIGNALING EXTENDED THE LIFESPAN OF C. ELEGANS. ALTHOUGH AGING IS A COMPLEX MULTISYSTEM PROCESS, LOPEZ-OTIN ET AL. DESCRIBED AGING IN REFERENCE TO NINE HALLMARKS OF AGING. THESE NINE HALLMARKS INCLUDE: GENOMIC INSTABILITY, TELOMERE ATTRITION, EPIGENETIC ALTERATIONS, LOSS OF PROTEOSTASIS, DEREGULATED NUTRIENT SENSING, MITOCHONDRIAL DYSFUNCTION, CELLULAR SENESCENCE, STEM CELL EXHAUSTION, AND ALTERED INTERCELLULAR COMMUNICATION. DUE TO RECENT ADVANCES IN LIPIDOMIC, INVESTIGATION INTO THE ROLE OF LIPIDS IN BIOLOGICAL AGING HAS INTENSIFIED, PARTICULARLY THE ROLE OF SPHINGOLIPIDS (SL). SLS ARE A DIVERSE GROUP OF LIPIDS ORIGINATING FROM THE ENDOPLASMIC RETICULUM (ER) AND CAN BE MODIFIED TO CREATE A VASTLY DIVERSE GROUP OF BIOACTIVE METABOLITES THAT REGULATE ALMOST EVERY MAJOR CELLULAR PROCESS, INCLUDING CELL CYCLE REGULATION, SENESCENCE, PROLIFERATION, AND APOPTOSIS. ALTHOUGH SL BIOLOGY REACHES ALL NINE HALLMARKS OF AGING, ITS CONTRIBUTION TO EACH HALLMARK IS DISPROPORTIONATE. IN THIS REVIEW, WE WILL DISCUSS IN DETAIL THE MAJOR CONTRIBUTIONS OF SLS TO THE HALLMARKS OF AGING AND AGE-RELATED DISEASES WHILE ALSO SUMMARIZING THE IMPORTANCE OF THEIR OTHER MINOR BUT INTEGRAL CONTRIBUTIONS. 2021 19 6591 28 TUMOR-ASSOCIATED MACROPHAGES AS A PARADIGM OF MACROPHAGE PLASTICITY, DIVERSITY, AND POLARIZATION: LESSONS AND OPEN QUESTIONS. MACROPHAGES ARE PRESENT IN ALL BODY COMPARTMENTS, INCLUDING CANCEROUS TISSUES, AND THEIR FUNCTIONS ARE PROFOUNDLY AFFECTED BY SIGNALS FROM THE MICROENVIRONMENT UNDER HOMEOSTATIC AND PATHOLOGICAL CONDITIONS. TUMOR-ASSOCIATED MACROPHAGES ARE A MAJOR CELLULAR COMPONENT OF CANCER-RELATED INFLAMMATION AND HAVE SERVED AS A PARADIGM FOR THE PLASTICITY AND FUNCTIONAL POLARIZATION OF MONONUCLEAR PHAGOCYTES. TUMOR-ASSOCIATED MACROPHAGES CAN EXERT DUAL INFLUENCE OF CANCER DEPENDING ON THE ACTIVATION STATE, WITH CLASSICALLY ACTIVATED (M1) AND ALTERNATIVELY ACTIVATED (M2) CELLS GENERALLY EXERTING ANTITUMORAL AND PROTUMORAL FUNCTIONS, RESPECTIVELY. THESE ARE EXTREMES IN A CONTINUUM OF POLARIZATION STATES IN A UNIVERSE OF DIVERSITY. TUMOR-ASSOCIATED MACROPHAGES AFFECT VIRTUALLY ALL ASPECTS OF TUMOR TISSUES, INCLUDING STEM CELLS, METABOLISM, ANGIOGENESIS, INVASION, AND METASTASIS. PROGRESS HAS BEEN MADE IN DEFINING SIGNALING MOLECULES, TRANSCRIPTION FACTORS, EPIGENETIC CHANGES, AND REPERTOIRE OF MICRORNAS UNDERLYING MACROPHAGE POLARIZATION. PRECLINICAL AND EARLY CLINICAL DATA SUGGEST THAT MACROPHAGES MAY SERVE AS TOOLS FOR THE DEVELOPMENT OF INNOVATIVE DIAGNOSTIC AND THERAPEUTIC STRATEGIES IN CANCER AND CHRONIC NONRESOLVING INFLAMMATORY DISEASES. 2013 20 2897 26 GASTRIC TUMOR MICROENVIRONMENT. A COMPELLING BODY OF EVIDENCE HAS DEMONSTRATED THAT GASTRIC CANCER HAS A VERY PARTICULAR TUMOR MICROENVIRONMENT, A SIGNATURE VERY SUITABLE TO PROMOTE TUMOR PROGRESSION AND METASTASIS. RECENT INVESTIGATIONS HAVE PROVIDED NEW INSIGHTS INTO THE MULTIPLE MOLECULAR MECHANISMS, DEFINED BY GENETIC AND EPIGENETIC MECHANISMS, SUPPORTING A VERY ACTIVE CROSS TALK BETWEEN THE COMPONENTS OF THE TUMOR MICROENVIRONMENT AND THUS DEFINING THE FATE OF TUMOR PROGRESSION. IN THIS REVIEW, WE INTEND TO HIGHLIGHT THE ROLE OF VERY ACTIVE CONTRIBUTORS AT GASTRIC CANCER TME, PARTICULARLY CANCER-ASSOCIATED FIBROBLASTS, BONE MARROW-DERIVED CELLS, TUMOR-ASSOCIATED MACROPHAGES, AND TUMOR-INFILTRATING NEUTROPHILS, ALL OF THEM SURROUNDED BY AN OVERTIME CHANGING EXTRACELLULAR MATRIX. IN ADDITION, THE VERY ACTIVE CROSS TALK BETWEEN THE COMPONENTS OF THE TUMOR MICROENVIRONMENT, DEFINED BY GENETIC AND EPIGENETIC MECHANISMS, THUS DEFINING THE FATE OF TUMOR PROGRESSION, IS ALSO REVIEWED. 2020