1 8 114 'OMIC' GENETIC TECHNOLOGIES FOR HERBAL MEDICINES IN PSYCHIATRY. THE FIELD OF GENETICS, WHICH INCLUDES THE USE OF 'OMIC' TECHNOLOGIES, IS AN EVOLVING AREA OF SCIENCE THAT HAS EMERGING APPLICATION IN PHYTOTHERAPY. OMIC STUDIES INCLUDE PHARMACOGENOMICS, PROTEOMICS AND METABOLOMICS. HERBAL MEDICINES, AS MONOTHERAPIES, OR COMPLEX FORMULATIONS SUCH AS TRADITIONAL CHINESE HERBAL PRESCRIPTIONS, MAY BENEFIT FROM OMIC STUDIES, AND THIS NEW FIELD MAY BE TERMED 'HERBOMICS'. APPLYING HERBOMICS IN THE FIELD OF PSYCHIATRY MAY PROVIDE ANSWERS ABOUT WHICH HERBAL INTERVENTIONS MAY BE EFFECTIVE FOR INDIVIDUALS, WHICH GENETIC PROCESSES ARE TRIGGERED, AND THE SUBSEQUENT NEUROCHEMICAL PATHWAYS OF ACTIVITY. THE USE OF PROTEOMIC TECHNOLOGY CAN EXPLORE THE DIFFERING EPIGENETIC EFFECTS ON NEUROCHEMICAL GENE EXPRESSION BETWEEN INDIVIDUAL HERBS, ISOLATED CONSTITUENTS AND COMPLEX FORMULAE. THE POSSIBILITIES OF SIDE EFFECTS OR INSUFFICIENT RESPONSE TO THE HERB CAN ALSO BE ASSESSED VIA PHARMACOGENOMIC ANALYSIS OF POLYMORPHISMS OF CYTOCHROME P450 LIVER ENZYMES OR P-GLYCOPROTEIN. WHILE ANOTHER NOVEL APPLICATION OF OMIC TECHNOLOGY IS FOR THE VALIDATION OF THE CONCEPT OF SYNERGY IN INDIVIDUAL HERBAL EXTRACTS AND PRESCRIPTIVE FORMULATIONS. CHRONIC ADMINISTRATION OF PSYCHOTROPIC HERBAL MEDICINES MAY DISCOVER IMPORTANT EFFECTS ON CHROMATIN REMODELLING VIA MODIFICATION OF HISTONE AND DNA METHYLATION. THIS PAPER FOCUSES ON THE EMERGING FIELD OF HERBOMICS, AND IS TO OUR KNOWLEDGE THE FIRST PUBLICATION TO EXPLORE THIS IN THE AREA OF PSYCHIATRY. 2012 2 6598 30 TWINSUK: THE UK ADULT TWIN REGISTRY UPDATE. TWINSUK IS THE LARGEST COHORT OF COMMUNITY-DWELLING ADULT TWINS IN THE UK. THE REGISTRY COMPRISES OVER 14,000 VOLUNTEER TWINS (14,838 INCLUDING MIXED, SINGLE AND TRIPLETS); IT IS PREDOMINANTLY FEMALE (82%) AND MIDDLE-AGED (MEAN AGE 59). IN ADDITION, OVER 1800 PARENTS AND SIBLINGS OF TWINS ARE REGISTERED VOLUNTEERS. DURING THE LAST 27 YEARS, TWINSUK HAS COLLECTED NUMEROUS QUESTIONNAIRE RESPONSES, PHYSICAL/COGNITIVE MEASURES AND BIOLOGICAL MEASURES ON OVER 8500 SUBJECTS. DATA WERE COLLECTED ALONGSIDE FOUR COMPREHENSIVE PHENOTYPING CLINICAL VISITS TO THE DEPARTMENT OF TWIN RESEARCH AND GENETIC EPIDEMIOLOGY, KING'S COLLEGE LONDON. SUCH COLLECTION METHODS HAVE RESULTED IN VERY DETAILED LONGITUDINAL CLINICAL, BIOCHEMICAL, BEHAVIORAL, DIETARY AND SOCIOECONOMIC COHORT CHARACTERIZATION; IT PROVIDES A MULTIDISCIPLINARY PLATFORM FOR THE STUDY OF COMPLEX DISEASE DURING THE ADULT LIFE COURSE, INCLUDING THE PROCESS OF HEALTHY AGING. THE MAJOR STRENGTH OF TWINSUK IS THE AVAILABILITY OF SEVERAL 'OMIC' TECHNOLOGIES FOR A RANGE OF SAMPLE TYPES FROM PARTICIPANTS, WHICH INCLUDES GENOMEWIDE SCANS OF SINGLE-NUCLEOTIDE VARIANTS, NEXT-GENERATION SEQUENCING, METABOLOMIC PROFILES, MICROBIOMICS, EXOME SEQUENCING, EPIGENETIC MARKERS, GENE EXPRESSION ARRAYS, RNA SEQUENCING AND TELOMERE LENGTH MEASURES. TWINSUK FACILITATES AND ACTIVELY ENCOURAGES SHARING THE 'TWINSUK' RESOURCE WITH THE SCIENTIFIC COMMUNITY - INTERESTED RESEARCHERS MAY REQUEST DATA VIA THE TWINSUK WEBSITE (HTTP://TWINSUK.AC.UK/RESOURCES-FOR-RESEARCHERS/ACCESS-OUR-DATA/) FOR THEIR OWN USE OR FUTURE COLLABORATION WITH THE STUDY TEAM. IN ADDITION, FURTHER COHORT DATA COLLECTION IS PLANNED VIA THE WELLCOME OPEN RESEARCH GATEWAY (HTTPS://WELLCOMEOPENRESEARCH.ORG/GATEWAYS). THE CURRENT ARTICLE PRESENTS AN UP-TO-DATE REPORT ON THE APPLICATION OF TECHNOLOGICAL ADVANCES, NEW STUDY PROCEDURES IN THE COHORT AND FUTURE DIRECTION OF TWINSUK. 2019 3 3285 27 HIDRADENITIS SUPPURATIVA: A PERSPECTIVE ON GENETIC FACTORS INVOLVED IN THE DISEASE. HIDRADENITIS SUPPURATIVA (HS) IS A CHRONIC INFLAMMATORY SKIN DISEASE OF THE PILOSEBACEOUS UNIT, CLINICALLY CONSISTING OF PAINFUL NODULES, ABSCESSES, AND SINUS TRACTS MOSTLY IN, BUT NOT LIMITED TO, INTERTRIGINOUS SKIN AREAS. HS CAN BE DEFINED AS A COMPLEX SKIN DISEASE WITH MULTIFACTORIAL ETIOLOGIES, INCLUDING-AMONG OTHERS-GENETIC, IMMUNOLOGIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS. BASED ON GENETIC HETEROGENEITY AND COMPLEXITY, THREE DIFFERENT FORMS CAN BE RECOGNIZED AND CONSIDERED SEPARATELY AS SPORADIC, FAMILIAL, AND SYNDROMIC. TO DATE, SEVERAL GENETIC VARIANTS ASSOCIATED TO DISEASE SUSCEPTIBILITY, DISEASE-ONSET, AND/OR TREATMENT RESPONSE HAVE BEEN REPORTED; SOME OF THESE RESIDE IN GENES ENCODING THE GAMMA-SECRETASE SUBUNITS WHEREAS OTHERS INVOLVE AUTOINFLAMMATORY AND/OR KERATINIZATION GENES. THE AIM OF THIS PERSPECTIVE WORK IS TO PROVIDE AN OVERVIEW OF THE CONTRIBUTION OF SEVERAL GENETIC STUDIES ENCOMPASSING FAMILY LINKAGE ANALYSES, TARGET CANDIDATE GENE STUDIES, AND -OMIC STUDIES IN THIS FIELD. IN OUR VIEWPOINT, WE DISCUSS THE ROLE OF GENETICS IN HIDRADENITIS SUPPURATIVA CONSIDERING FINDINGS BASED ON SANGER SEQUENCING AS WELL AS THE MORE RECENT NEXT GENERATION SEQUENCING (I.E., EXOME SEQUENCING OR RNA SEQUENCING) WITH THE AIM OF BETTER UNDERSTANDING THE ETIO-PATHOGENESIS OF THE DISEASE AS WELL AS IDENTIFYING NOVEL THERAPEUTIC STRATEGIES. 2022 4 4270 19 MICROBIAL DYSBIOSIS AND THE HOST AIRWAY EPITHELIAL RESPONSE: INSIGHTS INTO HIV-ASSOCIATED COPD USING MULTI'OMICS PROFILING. BACKGROUND: PEOPLE LIVING WITH HIV (PLWH) ARE AT INCREASED RISK OF DEVELOPING CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) INDEPENDENT OF CIGARETTE SMOKING. WE HYPOTHESIZED THAT DYSBIOSIS IN PLWH IS ASSOCIATED WITH EPIGENETIC AND TRANSCRIPTOMIC DISRUPTIONS IN THE AIRWAY EPITHELIUM. METHODS: AIRWAY EPITHELIAL BRUSHINGS WERE COLLECTED FROM 18 COPD + HIV + , 16 COPD - HIV + , 22 COPD + HIV - AND 20 COPD - HIV - SUBJECTS. THE MICROBIOME, METHYLOME, AND TRANSCRIPTOME WERE PROFILED USING 16S SEQUENCING, ILLUMINA INFINIUM METHYLATION EPIC CHIP, AND RNA SEQUENCING, RESPECTIVELY. MULTI 'OMIC INTEGRATION WAS PERFORMED USING DATA INTEGRATION ANALYSIS FOR BIOMARKER DISCOVERY USING LATENT COMPONENTS. A CORRELATION > 0.7 WAS USED TO IDENTIFY KEY INTERACTIONS BETWEEN THE 'OMES. RESULTS: THE COPD + HIV -, COPD -HIV + , AND COPD + HIV + GROUPS HAD REDUCED SHANNON DIVERSITY (P = 0.004, P = 0.023, AND P = 5.5E-06, RESPECTIVELY) COMPARED TO INDIVIDUALS WITH NEITHER COPD NOR HIV, WITH THE COPD + HIV + GROUP DEMONSTRATING THE MOST REDUCED DIVERSITY. MICROBIAL COMMUNITIES WERE SIGNIFICANTLY DIFFERENT BETWEEN THE FOUR GROUPS (P = 0.001). MULTI 'OMIC INTEGRATION IDENTIFIED CORRELATIONS BETWEEN BACTEROIDETES PREVOTELLA, GENES FUZ, FASTKD3, AND ACVR1B, AND EPIGENETIC FEATURES CPG-FUZ AND CPG-PHLDB3. CONCLUSION: PLWH WITH COPD MANIFEST DECREASED DIVERSITY AND ALTERED MICROBIAL COMMUNITIES IN THEIR AIRWAY EPITHELIAL MICROBIOME. THE REDUCTION IN PREVOTELLA IN THIS GROUP WAS LINKED WITH EPIGENETIC AND TRANSCRIPTOMIC DISRUPTIONS IN HOST GENES INCLUDING FUZ, FASTKD3, AND ACVR1B. 2023 5 3863 17 IT'S WHAT AND WHEN YOU EAT: AN OVERVIEW OF TRANSCRIPTIONAL AND EPIGENETIC RESPONSES TO DIETARY PERTURBATIONS IN PANCREATIC ISLETS. OUR EVER-CHANGING MODERN ENVIRONMENT IS A SIGNIFICANT CONTRIBUTOR TO THE INCREASED PREVALENCE OF MANY CHRONIC DISEASES, AND PARTICULARLY, TYPE 2 DIABETES MELLITUS (T2DM). ALTHOUGH THE MODERN ERA HAS USHERED IN NUMEROUS CHANGES TO OUR DAILY LIVING CONDITIONS, CHANGES IN "WHAT" AND "WHEN" WE EAT APPEAR TO DISPROPORTIONATELY FUEL THE RISE OF T2DM. THE PANCREATIC ISLET IS A KEY BIOLOGICAL CONTROLLER OF AN ORGANISM'S GLUCOSE HOMEOSTASIS AND THUS PLAYS AN OUTSIZED ROLE TO COORDINATE THE RESPONSE TO ENVIRONMENTAL FACTORS TO PRESERVE EUGLYCEMIA THROUGH A DELICATE BALANCE OF ENDOCRINE OUTPUTS. BOTH SUCCESSFUL AND FAILED ADAPTATION TO DYNAMIC ENVIRONMENTAL STIMULI HAS BEEN POSTULATED TO OCCUR DUE TO CHANGES IN THE TRANSCRIPTIONAL AND EPIGENETIC REGULATION OF PATHWAYS ASSOCIATED WITH ISLET SECRETORY FUNCTION AND SURVIVAL. THEREFORE, IN THIS REVIEW WE EXAMINED AND EVALUATED THE CURRENT EVIDENCE ELUCIDATING THE KEY EPIGENETIC MECHANISMS AND TRANSCRIPTIONAL PROGRAMS UNDERLYING THE ISLET'S COORDINATED RESPONSE TO THE INTERACTION BETWEEN THE TIMING AND THE COMPOSITION OF DIETARY NUTRIENTS COMMON TO MODERN LIFESTYLES. WITH THE EXPLOSION OF NEXT GENERATION SEQUENCING, ALONG WITH THE DEVELOPMENT OF NOVEL INFORMATIC AND -OMIC APPROACHES, FUTURE WORK WILL CONTINUE TO UNRAVEL THE ENVIRONMENTAL-EPIGENETIC RELATIONSHIP IN ISLET BIOLOGY WITH THE GOAL OF IDENTIFYING TRANSCRIPTIONAL AND EPIGENETIC TARGETS ASSOCIATED WITH ISLET PERTURBATIONS IN T2DM. 2022 6 5586 28 ROLE OF PERSONALIZED NUTRITION IN CHRONIC-DEGENERATIVE DISEASES. HUMAN NUTRITION IS A BRANCH OF MEDICINE BASED ON FOODS BIOCHEMICAL INTERACTIONS WITH THE HUMAN BODY. THE PHENOTYPIC TRANSITION FROM HEALTH TO DISEASE STATUS CAN BE ATTRIBUTED TO CHANGES IN GENES AND/OR PROTEIN EXPRESSION. FOR THIS REASON, A NEW DISCIPLINE HAS BEEN DEVELOPED CALLED "-OMIC SCIENCE". IN THIS REVIEW, WE ANALYZED THE ROLE OF "-OMICS SCIENCES" (NUTRIGENETICS, NUTRIGENOMICS, PROTEOMICS AND METABOLOMICS) IN THE HEALTH STATUS AND AS POSSIBLE THERAPEUTIC TOOL IN CHRONIC DEGENERATIVE DISEASES. IN PARTICULAR, WE FOCUSED ON THE ROLE OF NUTRIGENETICS AND THE RELATIONSHIP BETWEEN EATING HABITS, CHANGES IN THE DNA SEQUENCE AND THE ONSET OF NUTRITION-RELATED DISEASES. MOREOVER, WE EXAMINED NUTRIGENOMICS AND THE EFFECT OF NUTRIENTS ON GENE EXPRESSION. WE PERUSED THE ROLE OF PROTEOMICS AND METABOLOMICS IN PERSONALIZED NUTRITION. IN THIS SCENARIO, WE ANALYZED ALSO HOW DYSBIOSIS OF GUT MICROBIOTA CAN INFLUENCE THE ONSET AND PROGRESSION OF CHRONIC DEGENERATIVE DISEASES. MOREOVER, NUTRIENTS INFLUENCING AND REGULATING GENE ACTIVITY, BOTH DIRECTLY AND INDIRECTLY, PAVES THE WAY FOR PERSONALIZED NUTRITION THAT PLAYS A KEY ROLE IN THE PREVENTION AND TREATMENT OF CHRONIC DEGENERATIVE DISEASES. 2019 7 6815 20 [EVOLUTIONARY ONTOGENETIC ASPECTS OF PATHOGENETICS OF CHRONIC HUMAN DISEASES]. THIS ARTICLE IS A REVIEW OF SCIENTIFIC PUBLICATIONS, IN WHICH ISSUES OF PATHOGENETICS OF MULTIFACTORIAL DISEASES (MFDS) ARE CONSIDERED FROM THE VIEWPOINT OF EVOLUTION AND ONTOGENY. CONCEPTS EXPLAINING SIGNIFICANCE OF EVOLUTIONARY PROCESSES IN THE FORMATION OF GENETIC ARCHITECTURE OF HUMAN CHRONIC DISEASES ("THRIFTY" GENOMES AND PHENOTYPES, "DRIFTING GENES," DECANALIZATION) ARE ANALYZED. THE ROLES OF NATURAL SELECTION AND GENETIC DRIFT IN THE FORMATION OF HEREDITARY DIVERSITY OF GENES FOR SUSCEPTIBILITY TO MFDS ARE CONSIDERED. THE MODERN CONCEPT OF DISEASE ONTOGENY (SOMATIC MOSAICISM, LOSS OFHETEROZYGOSITY, PARADOMINANT INHERITANCE, EPIGENETIC VARIABILITY) IS DISCUSSED. IT IS DEMONSTRATED THAT THE EVOLUTIONARY AND ONTOGENETIC APPROACHES TO ANALYSIS OF GENIMUC AND OTHER "-OMIC" DATA ARE ESSENTIAL FOR UNDERSTANDING THE BIOLOGY OF DISEASES. 2011 8 4961 26 PATHOGENESIS OF PSORIASIS IN THE "OMIC" ERA. PART II. GENETIC, GENOMIC AND EPIGENETIC CHANGES IN PSORIASIS. PSORIASIS IS A MULTIFACTORIAL DISEASE IN WHICH GENETIC, ENVIRONMENTAL AND EPIGENETIC FACTORS REGULATING GENE EXPRESSION PLAY A KEY ROLE. IN THE "GENOMIC ERA", GENOME-WIDE ASSOCIATION STUDIES TOGETHER WITH TARGET GENOTYPING PLATFORMS PERFORMED IN DIFFERENT ETHNIC POPULATIONS HAVE FOUND MORE THAN 50 GENETIC SUSCEPTIBLE MARKERS ASSOCIATED WITH THE RISK OF PSORIASIS WHICH HAVE BEEN IDENTIFIED SO FAR. UP TILL NOW, THE STRONGEST ASSOCIATION WITH THE RISK OF THE DISEASE HAS BEEN PROVED FOR HLA-C*06 GENE. THE MAJORITY OF OTHER PSORIASIS RISK SNPS ARE SITUATED NEAR THE GENES ENCODING MOLECULES INVOLVED IN ADAPTIVE AND INNATE IMMUNITY, AND SKIN BARRIER FUNCTION. MANY CONTEMPORARY STUDIES INDICATE THAT THE EPIGENETIC CHANGES: HISTONE MODIFICATION, PROMOTER METHYLATIONS, LONG NON-CODING AND MICRO-RNA HYPEREXPRESSION ARE CONSIDERED AS FACTORS CONTRIBUTING TO PSORIASIS PATHOGENESIS AS THEY REGULATE ABNORMAL KERATINOCYTE DIFFERENTIATION AND PROLIFERATION, ABERRANT KERATINOCYTES - INFLAMMATORY CELLS COMMUNICATION, NEOANGIOGENESIS AND CHRONIC INFLAMMATION. THE CIRCULATING MIRNAS DETECTED IN THE BLOOD MAY BECOME SPECIFIC MARKERS IN THE DIAGNOSIS, PROGNOSIS AND RESPONSE TO THE TREATMENT OF THE DISEASE. THE INHIBITION OF EXPRESSION IN SELECTED MIRNAS MAY BE A NEW PROMISING THERAPY OPTION FOR PATIENTS WITH PSORIASIS. 2020 9 4893 21 OXIDATIVE STRESS BIOMARKERS IN THE RELATIONSHIP BETWEEN TYPE 2 DIABETES AND AIR POLLUTION. THE INCIDENCE AND PREVALENCE OF TYPE 2 DIABETES HAVE INCREASED IN THE LAST DECADES AND ARE EXPECTED TO FURTHER GROW IN THE COMING YEARS. CHRONIC HYPERGLYCEMIA TRIGGERS FREE RADICAL GENERATION AND CAUSES INCREASED OXIDATIVE STRESS, AFFECTING A NUMBER OF MOLECULAR MECHANISMS AND CELLULAR PATHWAYS, INCLUDING THE GENERATION OF ADVANCED GLYCATION END PRODUCTS, PROINFLAMMATORY AND PROCOAGULANT EFFECTS, INDUCTION OF APOPTOSIS, VASCULAR SMOOTH-MUSCLE CELL PROLIFERATION, ENDOTHELIAL AND MITOCHONDRIAL DYSFUNCTION, REDUCTION OF NITRIC OXIDE RELEASE, AND ACTIVATION OF PROTEIN KINASE C. AMONG TYPE 2 DIABETES DETERMINANTS, MANY DATA HAVE DOCUMENTED THE ADVERSE EFFECTS OF ENVIRONMENTAL FACTORS (E.G., AIR POLLUTANTS) THROUGH MULTIPLE EXPOSURE-INDUCED MECHANISMS (E.G., SYSTEMIC INFLAMMATION AND OXIDATIVE STRESS, HYPERCOAGULABILITY, AND ENDOTHELIAL AND IMMUNE RESPONSES). THEREFORE, HERE WE DISCUSS THE ROLE OF AIR POLLUTION IN OXIDATIVE STRESS-RELATED DAMAGE TO GLYCEMIC METABOLISM HOMEOSTASIS, WITH A PARTICULAR FOCUS ON ITS IMPACT ON HEALTH. IN THIS CONTEXT, THE IMPROVEMENT OF NEW ADVANCED TOOLS (E.G., OMIC TECHNIQUES AND THE STUDY OF EPIGENETIC CHANGES) MAY PROVIDE A SUBSTANTIAL CONTRIBUTION, HELPING IN THE EVALUATION OF THE INDIVIDUAL IN HIS BIOLOGICAL TOTALITY, AND OFFER A COMPREHENSIVE ASSESSMENT OF THE MOLECULAR, CLINICAL, ENVIRONMENTAL, AND EPIDEMIOLOGICAL ASPECTS. 2021 10 1 17 ON DECEMBER 5, 2017, THE NATIONAL ACADEMIES OF SCIENCES, ENGINEERING, AND MEDICINE HOSTED A PUBLIC WORKSHOP TITLED NUTRIGENOMICS AND THE FUTURE OF NUTRITION IN WASHINGTON, DC, TO REVIEW CURRENT KNOWLEDGE IN THE FIELD OF NUTRIGENOMICS AS IT RELATES TO NUTRITION. WORKSHOP PARTICIPANTS EXPLORED THE INFLUENCE OF GENETIC AND EPIGENETIC EXPRESSION ON NUTRITIONAL STATUS AND THE POTENTIAL IMPACT OF PERSONALIZED NUTRITION ON HEALTH MAINTENANCE AND CHRONIC DISEASE PREVENTION. THIS PUBLICATION SUMMARIZES THE PRESENTATIONS AND DISCUSSIONS FROM THE WORKSHOP. 2018 11 4869 20 OSTEOARTHRITIS YEAR IN REVIEW: GENETICS, GENOMICS, EPIGENETICS. OBJECTIVE: IN THIS REVIEW, WE HAVE HIGHLIGHTED ADVANCES IN GENETICS, GENOMICS AND EPIGENETICS IN THE FIELD OF OSTEOARTHRITIS (OA) OVER THE PAST YEAR. METHODS: A LITERATURE SEARCH WAS PERFORMED USING PUBMED AND THE CRITERIA: "OSTEOARTHRITIS" AND ONE OF THE FOLLOWING TERMS "GENETIC(S), GENOMIC(S), EPIGENETIC(S), EPIGENOMIC(S), NONCODING RNA, MICRORNA, LONG NONCODING RNA, LNCRNA, CIRCULAR RNA, RNA SEQUENCING, SINGLE CELL SEQUENCING, OR DNA METHYLATION BETWEEN APRIL 1, 2019 AND APRIL 30, 2020. RESULTS: WE IDENTIFIED 653 UNIQUE PUBLICATIONS, MANY STUDIES SPANNED MULTIPLE SEARCH TERMS. WE SUMMARIZED ADVANCES RELATING TO EVOLUTIONARY GENETICS, PAIN, ETHNICITY SPECIFIC RISK FACTORS, FUNCTIONAL STUDIES OF GENE VARIANTS, AND INTERACTIONS BETWEEN CODING AND NON-CODING RNAS IN OA PATHOGENESIS. CONCLUSIONS: STUDIES HAVE IDENTIFIED VARIANTS CONTRIBUTING TO OA SUSCEPTIBILITY, CANDIDATE BIOMARKERS FOR DIAGNOSIS AND PROGNOSIS, AS WELL AS PROMISING THERAPEUTIC CANDIDATES. VALIDATION IN MULTIPLE COHORTS, MULTI-OMICS STRATEGIES, AND MACHINE LEARNING AIDED COMPUTATIONAL ANALYSES HAVE ALL CONTRIBUTED TO THE STRENGTH OF PUBLISHED LITERATURE. OPEN ACCESS DATA-SETS, GREATER SAMPLE SIZES TO CAPTURE BROADER POPULATIONS AND UNDERSTANDING DISEASE MECHANISMS BY INVESTIGATING THE INTERACTIONS BETWEEN MULTIPLE TISSUE TYPES WILL FURTHER AID IN PROGRESS TOWARDS UNDERSTANDING AND CURING OA. 2021 12 1290 21 DECODING THE GENETIC AND EPIGENETIC BASIS OF ASTHMA. ASTHMA IS A COMPLEX AND HETEROGENEOUS CHRONIC INFLAMMATORY DISEASE OF THE AIRWAYS. ALONGSIDE ENVIRONMENTAL FACTORS, ASTHMA SUSCEPTIBILITY IS STRONGLY INFLUENCED BY GENETICS. GIVEN ITS HIGH PREVALENCE AND OUR INCOMPLETE UNDERSTANDING OF THE MECHANISMS UNDERLYING DISEASE SUSCEPTIBILITY, ASTHMA IS FREQUENTLY STUDIED IN GENOME-WIDE ASSOCIATION STUDIES (GWAS), WHICH HAVE IDENTIFIED THOUSANDS OF GENETIC VARIANTS ASSOCIATED WITH ASTHMA DEVELOPMENT. VIRTUALLY ALL THESE GENETIC VARIANTS RESIDE IN NON-CODING GENOMIC REGIONS, WHICH HAS OBSCURED THE FUNCTIONAL IMPACT OF ASTHMA-ASSOCIATED VARIANTS AND THEIR TRANSLATION INTO DISEASE-RELEVANT MECHANISMS. RECENT ADVANCES IN GENOMICS TECHNOLOGY AND EPIGENETICS NOW OFFER METHODS TO LINK GENETIC VARIANTS TO GENE REGULATORY ELEMENTS EMBEDDED WITHIN NON-CODING REGIONS, WHICH HAVE STARTED TO UNRAVEL THE MOLECULAR MECHANISMS UNDERLYING THE COMPLEX (EPI)GENETICS OF ASTHMA. HERE, WE PROVIDE AN INTEGRATED OVERVIEW OF (EPI)GENETIC VARIANTS ASSOCIATED WITH ASTHMA, FOCUSING ON EFFORTS TO LINK THESE DISEASE ASSOCIATIONS TO BIOLOGICAL INSIGHT INTO ASTHMA PATHOPHYSIOLOGY USING STATE-OF-THE-ART GENOMICS METHODOLOGY. FINALLY, WE PROVIDE A PERSPECTIVE AS TO HOW DECODING THE GENETIC AND EPIGENETIC BASIS OF ASTHMA HAS THE POTENTIAL TO TRANSFORM CLINICAL MANAGEMENT OF ASTHMA AND TO PREDICT THE RISK OF ASTHMA DEVELOPMENT. 2023 13 6454 31 THIRD JESUS CULEBRAS LECTURE - MOLECULAR BIOLOGY AND CLINICAL NUTRITION; WHERE DO WE STAND AND WHERE DO WE GO? NUTRITION PLAYS A FUNDAMENTAL ROLE IN THE MAINTENANCE OF HEALTH AND THE TREATMENT OF DISEASE, AND SERVES AS THE CROSSROADS FOR MANY DISCIPLINES. BIOCHEMISTRY AND MOLECULAR BIOLOGY REPRESENTS A KEY BRAND OF SCIENCE TO ASCERTAIN THE MECHANISM OF ACTION OF NUTRIENTS AND OTHER FOOD BIOACTIVE COMPOUNDS IN HEALTH AND DISEASE. THE AIM OF THE PRESENT JESUS M. CULEBRAS LECTURE IS TO CONSIDER THE FUTURE OF THE RELATIONSHIPS BETWEEN MOLECULAR BIOLOGY AND CLINICAL NUTRITION AND TO DISCUSS THE USE OF MOLECULAR AND GENETIC TOOLS TO STUDY MOLECULAR RESPONSES TO DIETARY FACTORS AND THE METABOLIC CONSEQUENCES OF FOOD AND TO CONSIDER MAJOR CHALLENGES ON HUMAN NUTRITION SCIENCES IN THE 21(ST) CENTURY. PARTICULAR EMPHASIS IS GIVEN TO THE IDENTIFICATION AND USE OF NOVEL BIOMARKERS IN INFLAMMATORY DISEASES. LIKEWISE, THE IMPORTANCE OF THE HUMAN MICROBIOME AND HOW MICROORGANISMS CAN BE SAFELY UTILIZED IN THE PREVENTION AND MANAGEMENT OF INFECTIOUS AND CHRONIC DISEASES ARE DISCUSSED. MOREOVER, THE KEY ROLE OF NUTRIGENETICS, NUTRIGENOMICS AND EPIGENETICS IN THE NEW ERA OF NUTRITION IS CONSIDERED. NUTRIGENETICS REFERS TO THE ROLE OF DNA SEQUENCE VARIATION IN THE RESPONSES TO NUTRIENTS, WHEREAS NUTRIGENOMICS IS THE STUDY OF THE ROLE OF NUTRIENTS IN GENE EXPRESSION. EPIGENETICS IS THE STUDY OF MITOTICALLY HERITABLE ALTERATIONS IN GENE EXPRESSION POTENTIAL THAT ARE NOT CAUSED BY DNA SEQUENCE ALTERATIONS. IN THE PAST DECADE, IT HAS INCREASINGLY BEEN RECOGNIZED THAT DYSREGULATION OF EPIGENETIC MECHANISMS MAY PLAY AN IMPORTANT ROLE IN HUMAN DISEASE. INDEED, THERE IS INCREASING INTEREST IN EPIGENETIC MECHANISMS UNDERLYING PHENOTYPE MODIFICATION MODULATED BY NUTRIENTS. FURTHER RESEARCH IN THOSE AREAS SHOULD CONTRIBUTE TO EVALUATE FUNCTIONALITY OF SPECIFIC NUTRIENTS AND BIOACTIVE COMPOUNDS IN CLINICAL NUTRITION AND ALLOW PERSONALIZED NUTRITIONAL ADVICE. 2013 14 1588 26 DNA METHYLATION PROFILING IMPLICATES EXPOSURE TO PCBS IN THE PATHOGENESIS OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA. OBJECTIVES: TO CHARACTERIZE THE IMPACT OF PCB EXPOSURE ON DNA METHYLATION IN PERIPHERAL BLOOD LEUCOCYTES AND TO EVALUATE THE CORRESPONDING CHANGES IN RELATION TO POSSIBLE HEALTH EFFECTS, WITH A FOCUS ON B-CELL LYMPHOMA. METHODS: WE CONDUCTED AN EPIGENOME-WIDE ASSOCIATION STUDY ON 611 ADULTS FREE OF DIAGNOSED DISEASE, LIVING IN ITALY AND SWEDEN, IN WHOM WE ALSO MEASURED PLASMA CONCENTRATIONS OF 6 PCB CONGENERS, DDE AND HEXACHLOROBENZENE. RESULTS: WE IDENTIFIED 650 CPG SITES WHOSE METHYLATION CORRELATES STRONGLY (FDR < 0.01) WITH PLASMA CONCENTRATIONS OF AT LEAST ONE PCB CONGENER. STRONGER EFFECTS WERE OBSERVED IN MALES AND IN SWEDEN. THIS EPIGENETIC EXPOSURE PROFILE SHOWS EXTENSIVE AND HIGHLY STATISTICALLY SIGNIFICANT OVERLAPS WITH PUBLISHED PROFILES ASSOCIATED WITH THE RISK OF FUTURE B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) AS WELL AS WITH CLINICAL CLL (38 AND 28 CPG SITES, RESPECTIVELY). FOR ALL THESE SITES, THE METHYLATION CHANGES WERE IN THE SAME DIRECTION FOR INCREASING EXPOSURE AND FOR HIGHER DISEASE RISK OR CLINICAL DISEASE STATUS, SUGGESTING AN ETIOLOGICAL LINK BETWEEN EXPOSURE AND CLL. MEDIATION ANALYSIS REINFORCED THE SUGGESTION OF A CAUSAL LINK BETWEEN EXPOSURE, CHANGES IN DNA METHYLATION AND DISEASE. DISEASE CONNECTIVITY ANALYSIS IDENTIFIED MULTIPLE ADDITIONAL DISEASES ASSOCIATED WITH DIFFERENTIALLY METHYLATED GENES, INCLUDING MELANOMA FOR WHICH AN ETIOLOGICAL LINK WITH PCB EXPOSURE IS ESTABLISHED, AS WELL AS DEVELOPMENTAL AND NEUROLOGICAL DISEASES FOR WHICH THERE IS CORRESPONDING EPIDEMIOLOGICAL EVIDENCE. DIFFERENTIALLY METHYLATED GENES INCLUDE MANY HOMEOBOX GENES, SUGGESTING THAT PCBS TARGET STEM CELLS. FURTHERMORE, NUMEROUS POLYCOMB PROTEIN TARGET GENES WERE HYPERMETHYLATED WITH INCREASING EXPOSURE, AN EFFECT KNOWN TO CONSTITUTE AN EARLY MARKER OF CARCINOGENESIS. CONCLUSIONS: THIS STUDY PROVIDES MECHANISTIC EVIDENCE IN SUPPORT OF A LINK BETWEEN EXPOSURE TO PCBS AND THE ETIOLOGY OF CLL AND UNDERLINES THE UTILITY OF OMIC PROFILING IN THE EVALUATION OF THE POTENTIAL TOXICITY OF ENVIRONMENTAL CHEMICALS. 2019 15 6048 23 THE CONCEPTS OF ASTHMA ENDOTYPES AND PHENOTYPES TO GUIDE CURRENT AND NOVEL TREATMENT STRATEGIES. ASTHMA, A COMMON, NON-COMMUNICABLE CHRONIC DISEASE AFFECTS OVER 300 MILLION INDIVIDUALS WORLDWIDE. THE WESTERN WORLD LIFESTYLE IS CLAIMED TO BE RESPONSIBLE FOR THIS HIGH AND INCREASING PREVALENCE. ASTHMA HAS BEEN DEFINED AS A SYNDROME WITH VARIOUS PHENOTYPES AND ENDOTYPES, ALLERGIC ASTHMA AND TYPE 2 ASTHMA BEING THE MOST FREQUENT. A GREAT INCREASE IN PREVALENCE OF ALLERGIC DISEASES HAS NECESSITATED INTENSIVE INVESTIGATIONS BOTH FOR UNDERSTANDING THE UNDERLYING MECHANISMS AND FOR THE DEVELOPMENT OF NOVEL THERAPY OPTIONS WITH LONG-TERM EFFICACY AND LIMITED SIDE-EFFECTS. ALLERGIC PATIENTS DEMONSTRATE UNIQUE PRESENTATIONS WITH VARIABLE VISIBLE CHARACTERISTICS AND DISEASE OUTCOMES DEPENDING ON DIFFERENT MOLECULAR MECHANISMS, RELATED TO INFLUENCE OF GENES AND EPIGENETIC CONTROL BY MICRO- AND MACRO-ENVIRONMENT. AREAS COVERED: THIS ARTICLE REVIEWS THE DEFINITION OF ASTHMA PHENOTYPES AND POSSIBLE ENDOTYPES, ADVANCES IN ALLERGY-IMMUNOLOGY FIELD AND CONTEMPORARY PERSONALIZED THERAPY OPTIONS FOR ASTHMA. EXPERT COMMENTARY: BETTER UNDERSTANDING OF THE COMPLEX IMMUNE NETWORK OF ALLERGIC INFLAMMATION AND KEY PLAYERS OF IMMUNITY IS CONTINUOUSLY BEING PROVIDED FOR CLARIFICATION OF ASTHMA SUB-TYPES. SUCCESSFUL THERAPY OF ASTHMA REQUIRES BETTER DEFINITION OF UNDERLYING PATHOGENESIS, WHICH SEQUENTIALLY COULD END UP WITH 'CUSTOM-TAILORED' INDIVIDUALIZED, EVIDENCE-BASED AND MORE PRECISE THERAPY OPTIONS; A NEW ERA TERMED AS 'PRECISION MEDICINE'. ENDOTYPE, PHENOTYPE, THERATYPE AND BIOMARKER TERMS ARISE AS MAJOR KEYWORDS IN PRECISION/PERSONALIZED MEDICINE. 2018 16 6678 32 USING GENETIC BURDEN SCORES FOR GENE-BY-METHYLATION INTERACTION ANALYSIS ON METABOLIC SYNDROME IN AFRICAN AMERICANS. WITH THE RAPID ADVANCEMENT OF OMICS-BASED RESEARCH, PARTICULARLY BIG DATA SUCH AS GENOME- AND EPIGENOME-WIDE ASSOCIATION STUDIES THAT INCLUDE EXTENSIVE ENVIRONMENTAL AND CLINICAL VARIABLES, DATA ANALYTICS HAVE BECOME INCREASINGLY COMPLEX. RESEARCHERS FACE SIGNIFICANT CHALLENGES REGARDING HOW TO ANALYZE MULTIFACTORIAL DATA AND MAKE USE OF THE FINDINGS FOR CLINICAL TRANSLATION. THE PURPOSE OF THIS ARTICLE IS TO PROVIDE A SCIENTIFIC EXEMPLAR FOR USE OF GENETIC BURDEN SCORES AS A DATA ANALYSIS METHOD FOR STUDIES WITH BOTH GENOTYPE AND DNA METHYLATION DATA IN WHICH THE GOAL IS TO EVALUATE ASSOCIATIONS WITH CHRONIC CONDITIONS SUCH AS METABOLIC SYNDROME (METS). THIS STUDY INCLUDED 739 AFRICAN AMERICAN MEN AND WOMEN FROM THE GENETIC EPIDEMIOLOGY NETWORK OF ARTERIOPATHY STUDY WHO MET DIAGNOSTIC CRITERIA FOR METS AND HAD AVAILABLE GENETIC AND EPIGENETIC DATA. GENETIC BURDEN SCORES FOR EVALUATED GENES WERE NOT SIGNIFICANT AFTER MULTIPLE TESTING CORRECTIONS, BUT DNA METHYLATION AT 2 CPG SITES (DIHYDROOROTATE DEHYDROGENASE CG22381196 PFDR = .014; CTNNA3 CG00132141 PFDR = .043) WAS SIGNIFICANTLY ASSOCIATED WITH METS AFTER CONTROLLING FOR MULTIPLE COMPARISONS. INTERACTIONS BETWEEN THE MARGINALLY SIGNIFICANT CPG SITES AND BURDEN SCORES, HOWEVER, WERE NOT SIGNIFICANT. MORE WORK IS REQUIRED IN THIS AREA TO IDENTIFY INTERMEDIATE BIOLOGICAL PATHWAYS INFLUENCED BY ENVIRONMENTAL, GENETIC, AND EPIGENETIC VARIATION THAT MAY EXPLAIN THE HIGH PREVALENCE OF METS AMONG AFRICAN AMERICANS. THIS STUDY DOES SERVE, HOWEVER, AS AN EXAMPLE OF THE USE OF THE GENETIC BURDEN SCORE AS AN ALTERNATIVE DATA ANALYSIS APPROACH FOR COMPLEX STUDIES INVOLVING THE ANALYSIS OF GENETIC AND EPIGENETIC DATA SIMULTANEOUSLY. 2019 17 2553 23 EPIGENETICS IN PSORIASIS: PERSPECTIVE OF DNA METHYLATION. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE CHARACTERIZED BY EXCESSIVE PROLIFERATION OF KERATINOCYTES (KCS). ONSET OF PSORIASIS IS RELATED TO GENETIC, IMMUNE AND ENVIRONMENTAL FACTORS. THE ENVIRONMENT CAN INTERACT WITH THE GENOME THROUGH EPIGENETIC MODIFICATIONS, INCLUDING DNA METHYLATION, AND THIS MODIFICATION IS INVOLVED IN THE PATHOGENESIS OF PSORIASIS. IN ADDITION TO A SKIN DISEASE, PSORIASIS IS ALSO CONSIDERED A SYSTEMIC DISEASE. WE REVIEWED THE CURRENT LITERATURE OF PSORIATIC DNA METHYLATION FOR STUDIES FROM SEVERAL ASPECTS ON THE DNA METHYLATION DISTRIBUTION PATTERNS IN DIFFERENT TISSUES/CELLS, SINGLE-NUCLEOTIDE POLYMORPHISMS, AND CANDIDATE DISEASE GENES AND IDENTIFIED TARGET GENES REGULATED BY DNA METHYLATION THAT HAVE BEEN DIRECTLY/INDIRECTLY VALIDATED. THIS REVIEW CONTRIBUTES TO A COMPREHENSIVE UNDERSTANDING OF THE IMPORTANT A ROLE THAT DNA METHYLATION PLAYS IN PSORIASIS FROM A HOLISTIC PERSPECTIVE AND WILL PROMOTE THE IMPLEMENTATION OF DNA METHYLATION IN DIAGNOSTIC AND THERAPEUTIC STRATEGIES FOR PSORIATIC PATIENTS. 2021 18 2919 24 GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS DEFINING LIPID-RELATED TRAITS. PURPOSE OF REVIEW: STEPS TOWARDS REDUCING CHRONIC DISEASE PROGRESSION ARE CONTINUOUSLY BEING TAKEN THROUGH THE FORM OF GENOMIC RESEARCH. STUDIES OVER THE LAST YEAR HAVE HIGHLIGHTED MORE AND MORE POLYMORPHISMS, PATHWAYS AND INTERACTIONS RESPONSIBLE FOR METABOLIC DISORDERS SUCH AS CARDIOVASCULAR DISEASE, OBESITY AND DYSLIPIDEMIA. RECENT FINDINGS: MANY OF THESE CHRONIC ILLNESSES CAN BE PARTIALLY BLAMED BY ALTERED LIPID METABOLISM, COMBINED WITH INDIVIDUAL GENETIC COMPONENTS. CRITICAL EVALUATION AND COMPARISON OF THESE RECENT STUDIES IS ESSENTIAL IN ORDER TO COMPREHEND THE RESULTS, CONCLUSIONS AND FUTURE PROSPECTS IN THE FIELD OF GENOMICS AS A WHOLE. RECENT LITERATURE ELUCIDATES SIGNIFICANT GENE--DIET AND GENE--ENVIRONMENT INTERACTIONS RESULTING IN ALTERED LIPID METABOLISM, INFLAMMATION AND OTHER METABOLIC IMBALANCES LEADING TO CARDIOVASCULAR DISEASE AND OBESITY. SUMMARY: EPIGENETIC AND EPISTATIC INTERACTIONS ARE NOW BECOMING MORE SIGNIFICANTLY ASSOCIATED WITH SUCH DISORDERS, AS GENOMIC RESEARCH DIGS DEEPER INTO THE COMPLEX NATURE OF GENETIC INDIVIDUALITY AND HERITABILITY. THE VAST ARRAY OF DATA COLLECTED FROM GENOME-WIDE ASSOCIATION STUDIES MUST NOW BE EMPOWERED AND EXPLORED THROUGH MORE COMPLEX INTERACTION STUDIES, USING STANDARDIZED METHODS AND LARGER SAMPLE SIZES. IN DOING SO THE ETIOLOGY OF CHRONIC DISEASE PROGRESSION WILL BE FURTHER UNDERSTOOD. 2011 19 4517 21 MULTI-OMICS FACTOR ANALYSIS-A FRAMEWORK FOR UNSUPERVISED INTEGRATION OF MULTI-OMICS DATA SETS. MULTI-OMICS STUDIES PROMISE THE IMPROVED CHARACTERIZATION OF BIOLOGICAL PROCESSES ACROSS MOLECULAR LAYERS. HOWEVER, METHODS FOR THE UNSUPERVISED INTEGRATION OF THE RESULTING HETEROGENEOUS DATA SETS ARE LACKING. WE PRESENT MULTI-OMICS FACTOR ANALYSIS (MOFA), A COMPUTATIONAL METHOD FOR DISCOVERING THE PRINCIPAL SOURCES OF VARIATION IN MULTI-OMICS DATA SETS. MOFA INFERS A SET OF (HIDDEN) FACTORS THAT CAPTURE BIOLOGICAL AND TECHNICAL SOURCES OF VARIABILITY. IT DISENTANGLES AXES OF HETEROGENEITY THAT ARE SHARED ACROSS MULTIPLE MODALITIES AND THOSE SPECIFIC TO INDIVIDUAL DATA MODALITIES. THE LEARNT FACTORS ENABLE A VARIETY OF DOWNSTREAM ANALYSES, INCLUDING IDENTIFICATION OF SAMPLE SUBGROUPS, DATA IMPUTATION AND THE DETECTION OF OUTLIER SAMPLES. WE APPLIED MOFA TO A COHORT OF 200 PATIENT SAMPLES OF CHRONIC LYMPHOCYTIC LEUKAEMIA, PROFILED FOR SOMATIC MUTATIONS, RNA EXPRESSION, DNA METHYLATION AND EX VIVO DRUG RESPONSES. MOFA IDENTIFIED MAJOR DIMENSIONS OF DISEASE HETEROGENEITY, INCLUDING IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE REGION STATUS, TRISOMY OF CHROMOSOME 12 AND PREVIOUSLY UNDERAPPRECIATED DRIVERS, SUCH AS RESPONSE TO OXIDATIVE STRESS. IN A SECOND APPLICATION, WE USED MOFA TO ANALYSE SINGLE-CELL MULTI-OMICS DATA, IDENTIFYING COORDINATED TRANSCRIPTIONAL AND EPIGENETIC CHANGES ALONG CELL DIFFERENTIATION. 2018 20 6858 20 [NUTRIGENOMICS, OBESITY AND PUBLIC HEALTH]. FUNCTIONAL GENOMICS WILL CHANGE KNOWLEDGE AND PRACTICE IN CLINICAL NUTRITION IN THE FORTHCOMING YEARS. THE POSSIBILITY OF PERFORMING AN INDIVIDUAL'S GENETIC PROFILE (GENETIC VARIATIONS AND EPIGENETIC MODIFICATIONS) AS WELL AS THE ABILITY OF ITS INTEGRATION IN A COMPLEX NETWORK OF METABOLIC INTERACTIONS REPRESENTS A HUGE CHALLENGE IN HUMAN NUTRITION. THE INFLUENCE OF NUTRIGENOMICS IN TERMS OF PREVENTION AND TREATMENT OF CHRONIC DISEASES, SUCH AS OBESITY, TYPE 2 DIABETES AND CARDIOVASCULAR DISEASE IN A POPULATION LEVEL REMAINS UNDETERMINED FOR THE MOMENT. THE OPPORTUNITY OF NUTRITIONAL INTERVENTION IN CRITICAL STAGES OF DEVELOPMENT AND THE CHANCE OF CHANGING GENETIC SUSCEPTIBILITY TO DISEASES THROUGH DIET IN A PUBLIC HEALTH BASIS SHOULD LEAD THE FUTURE OF NUTRIGENOMICS BEYOND THE MERE DESIGN OF "PERSONALIZED" FUNCTIONAL FOOD OR DIETS. 2007