1 2987 103 GENETIC EPIDEMIOLOGY IN KIDNEY DISEASE. FAMILIAL AGGREGATION OF CHRONIC KIDNEY DISEASE AND ITS COMPONENT PHENOTYPES-REDUCED GLOMERULAR FILTRATION RATE, PROTEINURIA AND RENAL HISTOLOGIC CHANGES-HAS LONG BEEN RECOGNIZED. RATES OF SEVERE KIDNEY DISEASE ARE ALSO KNOWN TO DIFFER MARKEDLY BETWEEN POPULATIONS BASED ON ANCESTRY. THESE EPIDEMIOLOGIC OBSERVATIONS SUPPORT THE EXISTENCE OF NEPHROPATHY SUSCEPTIBILITY GENES. SEVERAL MOLECULAR GENETIC TECHNOLOGIES ARE NOW AVAILABLE TO IDENTIFY CAUSATIVE LOCI. THE PRESENT ARTICLE SUMMARIZES AVAILABLE STRATEGIES USEFUL FOR IDENTIFYING NEPHROPATHY SUSCEPTIBILITY GENES, INCLUDING CANDIDATE GENE ASSOCIATION, FAMILY-BASED LINKAGE, GENOME-WIDE ASSOCIATION AND ADMIXTURE MAPPING (MAPPING BY ADMIXTURE LINKAGE DISEQUILIBRIUM) APPROACHES. EXAMPLES OF LOCI DETECTED USING THESE TECHNIQUES ARE PROVIDED. EPIGENETIC STUDIES AND FUTURE DIRECTIONS ARE ALSO DISCUSSED. THE IDENTIFICATION OF NEPHROPATHY SUSCEPTIBILITY GENES, COUPLED WITH MODIFIABLE ENVIRONMENTAL TRIGGERS IMPACTING THEIR FUNCTION, IS LIKELY TO IMPROVE RISK PREDICTION AND TRANSFORM CARE. DEVELOPMENT OF NOVEL THERAPIES TO PREVENT PROGRESSION OF KIDNEY DISEASE WILL FOLLOW. 2017 2 2955 34 GENETIC AND EPIGENETIC FACTORS INFLUENCING CHRONIC KIDNEY DISEASE. CHRONIC KIDNEY DISEASE (CKD) HAS BECOME A SERIOUS PUBLIC HEALTH PROBLEM BECAUSE OF ITS ASSOCIATED MORBIDITY, PREMATURE MORTALITY, AND ATTENDANT HEALTHCARE COSTS. THE RISING NUMBER OF PERSONS WITH CKD IS LINKED WITH THE AGING POPULATION STRUCTURE AND AN INCREASED PREVALENCE OF DIABETES, HYPERTENSION, AND OBESITY. THERE IS AN INHERITED RISK ASSOCIATED WITH DEVELOPING CKD, AS EVIDENCED BY FAMILIAL CLUSTERING AND DIFFERING PREVALENCE RATES ACROSS ETHNIC GROUPS. PREVIOUS STUDIES TO DETERMINE THE INHERITED RISK FACTORS FOR CKD RARELY IDENTIFIED GENETIC VARIANTS THAT WERE ROBUSTLY REPLICATED. HOWEVER, IMPROVEMENTS IN GENOTYPING TECHNOLOGIES AND ANALYTIC METHODS ARE NOW HELPING TO IDENTIFY PROMISING GENETIC LOCI AIDED BY INTERNATIONAL COLLABORATION AND MULTICONSORTIA EFFORTS. MORE RECENTLY, EPIGENETIC MODIFICATIONS HAVE BEEN PROPOSED TO PLAY A ROLE IN BOTH THE INHERITED SUSCEPTIBILITY TO CKD AND, IMPORTANTLY, TO EXPLAIN HOW THE ENVIRONMENT DYNAMICALLY INTERACTS WITH THE GENOME TO ALTER AN INDIVIDUAL'S DISEASE RISK. GENOME-WIDE, EPIGENOME-WIDE, AND WHOLE TRANSCRIPTOME STUDIES HAVE BEEN PERFORMED, AND OPTIMAL APPROACHES FOR INTEGRATIVE ANALYSIS ARE BEING DEVELOPED. THIS REVIEW SUMMARIZES RECENT RESEARCH AND THE CURRENT STATUS OF GENETIC AND EPIGENETIC RISK FACTORS INFLUENCING CKD USING POPULATION-BASED INFORMATION. 2014 3 527 37 ASTHMA AND THE MISSING HERITABILITY PROBLEM: NECESSITY FOR MULTIOMICS APPROACHES IN DETERMINING ACCURATE RISK PROFILES. ASTHMA IS RANKED AMONG THE MOST COMMON CHRONIC CONDITIONS AND HAS BECOME A SIGNIFICANT PUBLIC HEALTH ISSUE DUE TO THE RECENT AND RAPID INCREASE IN ITS PREVALENCE. INVESTIGATIONS INTO THE UNDERLYING GENETIC FACTORS PREDICT A HERITABLE COMPONENT FOR ITS INCIDENCE, ESTIMATED BETWEEN 35% AND 90% OF CAUSATION. DESPITE THE APPLICATION OF LARGE-SCALE GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND ADMIXTURE MAPPING APPROACHES, THE PROPORTION OF VARIANTS IDENTIFIED ACCOUNTS FOR LESS THAN 15% OF THE OBSERVED HERITABILITY OF THE DISEASE. THE DISCREPANCY BETWEEN THE PREDICTED HERITABLE COMPONENT OF DISEASE AND THE PROPORTION OF HERITABILITY MAPPED TO THE CURRENTLY IDENTIFIED SUSCEPTIBILITY LOCI HAS BEEN TERMED THE 'MISSING HERITABILITY PROBLEM.' HERE, WE EXAMINE RECENT STUDIES INVOLVING BOTH THE ANALYSIS OF GENETICALLY ENCODED FEATURES THAT CONTRIBUTE TO ASTHMA AND ALSO THE ROLE OF NON-ENCODED HERITABLE CHARACTERISTICS, INCLUDING EPIGENETIC, ENVIRONMENTAL, AND DEVELOPMENTAL ASPECTS OF DISEASE. THE IMPORTANCE OF VERTICAL MATERNAL MICROBIOME TRANSFER AND THE INFLUENCE OF MATERNAL IMMUNE FACTORS ON FETAL CONDITIONING IN THE INHERITANCE OF DISEASE ARE ALSO DISCUSSED. IN ORDER TO HIGHLIGHT THE BROAD ARRAY OF BIOLOGICAL INPUTS THAT CONTRIBUTE TO THE SUM OF HERITABLE RISK FACTORS ASSOCIATED WITH ALLERGIC DISEASE INCIDENCE THAT, TOGETHER, CONTRIBUTE TO THE INDUCTION OF A PRO-ATOPIC STATE. CURRENTLY, THERE IS A NEED TO DEVELOP IN-DEPTH MODELS OF ASTHMA RISK FACTORS TO OVERCOME THE LIMITATIONS ENCOUNTERED IN THE INTERPRETATION OF GWAS RESULTS IN ISOLATION, WHICH HAVE RESULTED IN THE MISSING HERITABILITY PROBLEM. HENCE, MULTIOMICS ANALYSES NEED TO BE ESTABLISHED CONSIDERING GENETIC, EPIGENETIC, AND FUNCTIONAL DATA TO CREATE A TRUE SYSTEMS BIOLOGY-BASED APPROACH FOR ANALYZING THE REGULATORY PATHWAYS THAT UNDERLIE THE INHERITANCE OF ASTHMA AND TO DEVELOP ACCURATE RISK PROFILES FOR DISEASE. 2022 4 2982 34 GENETIC CONSIDERATIONS IN PEDIATRIC CHRONIC KIDNEY DISEASE. CHRONIC KIDNEY DISEASE (CKD) IN CHILDREN IS AN IRREVERSIBLE PROCESS THAT, IN SOME CASES, MAY LEAD TO END-STAGE RENAL DISEASE. THE MAJORITY OF CHILDREN WITH CKD HAVE A CONGENITAL DISORDER OF THE KIDNEY OR UROLOGICAL TRACT ARISING FROM BIRTH. THERE IS STRONG EVIDENCE FOR BOTH A GENETIC AND EPIGENETIC COMPONENT TO PROGRESSION OF CKD. UTILIZATION OF GENE-MAPPING STRATEGIES, RANGING FROM GENOME-WIDE ASSOCIATION STUDIES TO SINGLE-NUCLEOTIDE POLYMORPHISM ANALYSIS, SERVES TO IDENTIFY POTENTIAL GENETIC VARIANTS THAT MAY LEND TO DISEASE VARIATION. GENOME-WIDE ASSOCIATION STUDIES EVALUATING POPULATION-BASED DATA HAVE IDENTIFIED DIFFERENT LOCI ASSOCIATED WITH CKD PROGRESSION. ANALYSIS OF SINGLE-NUCLEOTIDE POLYMORPHISMS ON AN INDIVIDUAL LEVEL SUGGESTS THAT SECONDARY SYSTEMIC SEQUELAE OF CKD ARE CLOSELY RELATED TO DYSFUNCTION OF THE CARDIOVASCULAR-INFLAMMATORY AXIS AND MAY LEAD TO ADVANCED CARDIOVASCULAR DISEASE THROUGH ABNORMAL VASCULAR CALCIFICATION AND ACTIVATION OF THE RENIN-ANGIOTENSIN SYSTEM. SIMILARLY, GENETIC VARIANTS AFFECTING CYTOKINE CONTROL, FIBROSIS, AND PARENCHYMAL DEVELOPMENT MAY MODULATE CKD THROUGH DEVELOPMENT AND ACCELERATION OF RENAL INTERSTITIAL FIBROSIS. EPIGENETIC STUDIES EVALUATE MODIFICATION OF THE GENOME THROUGH DNA METHYLATION, HISTONE MODIFICATION, OR RNA INTERFERENCE, WHICH MAY BE DIRECTLY INFLUENCED BY EXTERNAL OR ENVIRONMENTAL FACTORS DIRECTING GENOMIC EXPRESSION. LASTLY, IMPROVED UNDERSTANDING OF THE GENETIC AND EPIGENETIC CONTRIBUTION TO CKD PROGRESSION MAY ALLOW PROVIDERS TO IDENTIFY A POPULATION AT ACCELERATED RISK FOR DISEASE PROGRESSION AND APPLY NOVEL THERAPIES TARGETED AT THE GENETIC MECHANISM OF DISEASE. 2016 5 4743 28 NOVEL INSIGHTS FROM GENETIC AND EPIGENETIC STUDIES IN UNDERSTANDING THE COMPLEX URAEMIC PHENOTYPE. LIKE IN MANY OTHER COMMON COMPLEX DISORDERS, STUDIES OF CHRONIC KIDNEY DISEASE (CKD) CAN NOW MAKE USE OF THE INCREASING KNOWLEDGE OF THE HUMAN GENOME, ITS VARIATIONS AND IMPACT ON DISEASE SUSCEPTIBILITY, INITIATION, PROGRESSION AND COMPLICATIONS. SUCH STUDIES ARE FACILITATED BY NOVEL READILY AVAILABLE HIGH THROUGH-PUT GENOTYPING METHODS AND SOPHISTICATED ANALYTICAL APPROACHES TO SCAN THE GENOME FOR DNA VARIATIONS AND EPIGENETIC MODIFICATIONS. HERE, WE REVIEW SOME OF THE RECENT DISCOVERIES THAT HAVE EMERGED FROM THESE STUDIES AND EXPANDED OUR KNOWLEDGE OF GENETIC RISK LOCI AND EPIGENETIC MARKERS IN CKD PATHOPHYSIOLOGY. OBSTACLES AND PRACTICAL ISSUES IN THIS FIELD ARE DISCUSSED. 2014 6 931 33 CHRONIC KIDNEY DISEASE IN CHILDREN AND THE ROLE OF EPIGENETICS: FUTURE THERAPEUTIC TRAJECTORIES. GLOBAL DIFFERENCES IN THE OBSERVED CAUSES OF CHRONIC KIDNEY DISEASE (CKD) IN CHILDREN ARE WELL DOCUMENTED AND ARE ATTRIBUTED TO DISSIMILARITIES IN CLIME, RACE, HEREDITARY, AND ANCESTRY. THUS, FAMILIAL CLUSTERING AND DISPARITIES IN CKD PREVALENCE RATES ACROSS ETHNIC AND RACIAL GROUPS INDICATE THAT THE PROGRESSION OF RENAL DISEASE HAS A STRONG GENETIC COMPONENT. MAMMALIAN STUDIES HAVE DEMONSTRATED A FEASIBLE NEXUS BETWEEN NUTRITION AND NON-GENETIC EXPOSURE (AROUND THE TIME OF CONCEPTION AND IN EPIGENETIC CHANGES) IN THE EXPRESSION OF MAJOR GENES IDENTIFIED IN RENAL ORGANOGENESIS. THE MAJOR CONSEQUENCE IS A REDUCTION IN THE NUMBER OF NEPHRONS, WITH SUBSEQUENT PREDISPOSITION TO HYPERTENSION AND CKD. IDENTIFYING THESE EPIGENETIC CHANGES IS CRUCIAL (DUE TO THEIR POTENTIALLY REVERSIBLE NATURE), AS THEY MAY SERVE AS FUTURE THERAPEUTIC TARGETS TO PREVENT KIDNEY FIBROSIS AND CKD. DESPITE PROGRESS IN THE FIELD OF EPIGENETICS IN ONCOLOGY, RESEARCH IN OTHER SUBSPECIALTIES OF MEDICINE IS LARGELY EXPERIMENTAL WITH FEW EXISTING STUDIES REGARDING THE CLINICAL IMPLICATION OF EPIGENETICS IN RENAL DISEASE. THERAPEUTIC TRAJECTORIES FOR CKD IN CHILDREN BASED ON THE INFLUENCE OF EPIGENETICS MAY EVENTUALLY REVOLUTIONIZE THE MANAGEMENT OF THIS DISEASE. THE AIM OF THE CURRENT NARRATIVE REVIEW IS TO APPRAISE THE ROLE OF EPIGENETICS IN CKD, AND HIGHLIGHT THE POTENTIAL FUTURE THERAPEUTIC PATHWAYS. 2016 7 3399 29 HOW CAN GENETICS AND EPIGENETICS HELP THE NEPHROLOGIST IMPROVE THE DIAGNOSIS AND TREATMENT OF CHRONIC KIDNEY DISEASE PATIENTS? DISCOVERY OF NOVEL IMPROVED TOOLS FOR DIAGNOSIS, PREVENTION AND THERAPY OF CHRONIC KIDNEY DISEASE (CKD) IS AN IMPORTANT TASK FOR THE NEPHROLOGY COMMUNITY AND IT IS LIKELY THAT SCIENTIFIC BREAKTHROUGHS, TO A LARGE EXTENT, WILL BE BASED ON GENOMICS. THE RAPID GROWTH OF THE NUMBER OF GENOME-WIDE ASSOCIATION STUDIES, MAJOR ADVANCES IN DNA SEQUENCING AND OMICS PROFILING, AND ACCELERATING BIOMEDICAL RESEARCH EFFORTS IN THIS AREA HAVE GREATLY EXPANDED THE KNOWLEDGE BASE NEEDED FOR APPLIED GENOMICS. HOWEVER, TRANSLATING AND IMPLEMENTING GENOTYPE-PHENOTYPE DATA INTO GENE-BASED MEDICINE IN CKD POPULATIONS IS STILL IN AN EARLY PHASE AND WILL REQUIRE CONTINUOUS RESEARCH EFFORTS WITH INTEGRATED APPROACHES AND INTENSIFIED INVESTIGATIONS THAT FOCUS ON THE BIOLOGICAL PATHWAYS, WHICH CAUSATIVELY LINK A GENETIC VARIANT WITH THE DISEASE PHENOTYPE. IN THIS ARTICLE, WE REVIEW SOME CURRENT STRATEGIES TO UNRAVEL THESE TRANSLATIONAL GAPS AS WELL AS PROSPECTS FOR THE IMPLEMENTATION OF GENETIC AND EPIGENETIC METHODS INTO NOVEL CLINICAL PRACTICE. 2014 8 3028 24 GENETICS OF COMPLEX AIRWAY DISEASE. THE PAST 3 YEARS HAVE SEEN HIGHLY SIGNIFICANT GENETIC EFFECTS IDENTIFIED FOR A WIDE VARIETY OF COMMON COMPLEX DISEASES, INCLUDING THE AIRWAY DISORDERS OF ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE. IT APPEARS THAT ONLY A PORTION OF THE GENETICALLY MEDIATED SUSCEPTIBILITY TO COMPLEX DISEASES HAS BEEN IDENTIFIED, AND THERE IS MUCH LEFT TO BE DISCOVERED. THIS REVIEW BRIEFLY DESCRIBES THE RESULTS OF THE GENOME-WIDE ASSOCIATION STUDIES OF ASTHMA AND GIVES AN OVERVIEW OF THE PARALLEL AND INCREASINGLY LARGE-SCALE STUDIES THAT ARE TAKING PLACE WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE. THE FUTURE IMPACT IS DISCUSSED OF TECHNOLOGICAL ADVANCES THAT ALLOW INCREASINGLY LARGE-SCALE GENE EXPRESSION STUDIES, NEXT-GENERATION SEQUENCING, AND GENOME-WIDE TESTING FOR EPIGENETIC EFFECTS. THE USE OF GENETIC TECHNOLOGY TO EXAMINE THE AIRWAY MICROBIOTA THAT INTERACT WITH THE MUCOSA IN HEALTH AND DISEASE IS DESCRIBED. 2011 9 4389 28 MODELING EPIGENETIC MODIFICATIONS IN RENAL DEVELOPMENT AND DISEASE WITH ORGANOIDS AND GENOME EDITING. UNDERSTANDING EPIGENETIC MECHANISMS IS CRUCIAL TO OUR COMPREHENSION OF GENE REGULATION IN DEVELOPMENT AND DISEASE. IN THE PAST DECADES, DIFFERENT STUDIES HAVE SHOWN THE ROLE OF EPIGENETIC MODIFICATIONS AND MODIFIERS IN RENAL DISEASE, ESPECIALLY DURING ITS PROGRESSION TOWARDS CHRONIC AND END-STAGE RENAL DISEASE. THUS, THE IDENTIFICATION OF GENETIC VARIATION ASSOCIATED WITH CHRONIC KIDNEY DISEASE HAS RESULTED IN BETTER CLINICAL MANAGEMENT OF PATIENTS. DESPITE THE IMPORTANCE OF THESE FINDINGS, THE TRANSLATION OF GENOTYPE-PHENOTYPE DATA INTO GENE-BASED MEDICINE IN CHRONIC KIDNEY DISEASE POPULATIONS STILL LACKS FAITHFUL CELLULAR OR ANIMAL MODELS THAT RECAPITULATE THE KEY ASPECTS OF THE HUMAN KIDNEY. THE LATEST ADVANCES IN THE FIELD OF STEM CELLS HAVE SHOWN THAT IT IS POSSIBLE TO EMULATE KIDNEY DEVELOPMENT AND FUNCTION WITH ORGANOIDS DERIVED FROM HUMAN PLURIPOTENT STEM CELLS. THESE HAVE SUCCESSFULLY RECAPITULATED NOT ONLY KIDNEY DIFFERENTIATION, BUT ALSO THE SPECIFIC PHENOTYPICAL TRAITS RELATED TO KIDNEY FUNCTION. THE COMBINATION OF THIS METHODOLOGY WITH CRISPR/CAS9 GENOME EDITING HAS ALREADY HELPED RESEARCHERS TO MODEL DIFFERENT GENETIC KIDNEY DISORDERS. NOWADAYS, CRISPR/CAS9-BASED APPROACHES ALSO ALLOW EPIGENETIC MODIFICATIONS, AND THUS REPRESENT AN UNPRECEDENTED TOOL FOR THE SCREENING OF GENETIC VARIANTS, EPIGENETIC MODIFICATIONS OR EVEN CHANGES IN CHROMATIN STRUCTURE THAT ARE ALTERED IN RENAL DISEASE. IN THIS REVIEW, WE DISCUSS THESE TECHNICAL ADVANCES IN KIDNEY MODELING, AND OFFER AN OVERVIEW OF THE ROLE OF EPIGENETIC REGULATION IN KIDNEY DEVELOPMENT AND DISEASE. 2018 10 6162 27 THE GENETICS OF DIABETIC NEPHROPATHY. UP TO 40% OF PATIENTS WITH TYPE 1 AND TYPE 2 DIABETES WILL DEVELOP DIABETIC NEPHROPATHY (DN), RESULTING IN CHRONIC KIDNEY DISEASE AND POTENTIAL ORGAN FAILURE. THERE IS EVIDENCE FOR A HERITABLE GENETIC SUSCEPTIBILITY TO DN, BUT DESPITE INTENSIVE RESEARCH EFFORTS THE CAUSATIVE GENES REMAIN ELUSIVE. RECENTLY, GENOME-WIDE ASSOCIATION STUDIES HAVE DISCOVERED SEVERAL NOVEL GENETIC VARIANTS ASSOCIATED WITH DN. THE IDENTIFICATION OF SUCH VARIANTS MAY POTENTIALLY ALLOW FOR EARLY IDENTIFICATION OF AT RISK PATIENTS. HERE WE REVIEW THE CURRENT UNDERSTANDING OF THE KEY MOLECULAR MECHANISMS AND GENETIC ARCHITECTURE OF DN, AND DISCUSS THE MERITS OF EMPLOYING AN INTEGRATIVE APPROACH TO INCORPORATE DATASETS FROM MULTIPLE SOURCES (GENETICS, TRANSCRIPTOMICS, EPIGENETIC, PROTEOMIC) IN ORDER TO FULLY ELUCIDATE THE GENETIC ELEMENTS CONTRIBUTING TO THIS SERIOUS COMPLICATION OF DIABETES. 2013 11 2651 27 EPIGENOMICS AND TRANSCRIPTOMICS IN THE PREDICTION AND DIAGNOSIS OF CHILDHOOD ASTHMA: ARE WE THERE YET? ASTHMA IS THE MOST COMMON NON-COMMUNICABLE CHRONIC DISEASE OF CHILDHOOD. DESPITE ITS HIGH PREVALENCE, TO DATE WE LACK METHODS THAT ARE BOTH EFFICIENT AND ACCURATE IN DIAGNOSING ASTHMA. MOST TRADITIONAL APPROACHES HAVE BEEN BASED ON GARNERING CLINICAL EVIDENCE, SUCH AS RISK FACTORS AND EXPOSURES. GIVEN THE HIGH HERITABILITY OF ASTHMA, MORE RECENT APPROACHES HAVE LOOKED AT GENETIC POLYMORPHISMS AS POTENTIAL "RISK FACTORS." HOWEVER, GENETIC VARIANTS EXPLAIN ONLY A SMALL PROPORTION OF ASTHMA RISK, AND HAVE BEEN LESS THAN OPTIMAL AT PREDICTING RISK FOR INDIVIDUAL SUBJECTS. EPIGENOMIC STUDIES OFFER SIGNIFICANT ADVANTAGES OVER PREVIOUS APPROACHES. EPIGENETIC REGULATION IS HIGHLY TISSUE-SPECIFIC, AND CAN INDUCE BOTH SHORT- AND LONG-TERM CHANGES IN GENE EXPRESSION. SUCH CHANGES CAN START IN UTERO, CAN VARY THROUGHOUT THE LIFE SPAN, AND IN SOME INSTANCES CAN BE PASSED ON FROM ONE GENERATION TO ANOTHER. MOST IMPORTANTLY, THE EPIGENOME CAN BE MODIFIED BY ENVIRONMENTAL FACTORS AND EXPOSURES, AND THUS EPIGENETIC AND TRANSCRIPTOMIC PROFILING MAY YIELD THE MOST ACCURATE RISK ESTIMATES FOR A GIVEN PATIENT BY INCORPORATING ENVIRONMENTAL (AND TREATMENT) EFFECTS THROUGHOUT THE LIFESPAN. HERE WE WILL REVIEW THE MOST RECENT ADVANCES IN THE USE OF EPIGENETIC AND TRANSCRIPTOMIC ANALYSIS FOR THE EARLY DIAGNOSIS OF ASTHMA AND ATOPY, AS WELL AS CHALLENGES AND FUTURE DIRECTIONS IN THE FIELD AS IT MOVES FORWARD. WE WILL PARTICULARLY FOCUS ON DNA METHYLATION, THE MOST STUDIED MECHANISM OF EPIGENETIC REGULATION. 2019 12 3095 38 GENOMIC APPROACHES IN THE SEARCH FOR MOLECULAR BIOMARKERS IN CHRONIC KIDNEY DISEASE. BACKGROUND: CHRONIC KIDNEY DISEASE (CKD) IS RECOGNISED AS A GLOBAL PUBLIC HEALTH PROBLEM, MORE PREVALENT IN OLDER PERSONS AND ASSOCIATED WITH MULTIPLE CO-MORBIDITIES. DIABETES MELLITUS AND HYPERTENSION ARE COMMON AETIOLOGIES FOR CKD, BUT IGA GLOMERULONEPHRITIS, MEMBRANOUS GLOMERULONEPHRITIS, LUPUS NEPHRITIS AND AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE ARE ALSO COMMON CAUSES OF CKD. MAIN BODY: CONVENTIONAL BIOMARKERS FOR CKD INVOLVING THE USE OF ESTIMATED GLOMERULAR FILTRATION RATE (EGFR) DERIVED FROM FOUR VARIABLES (SERUM CREATININE, AGE, GENDER AND ETHNICITY) ARE RECOMMENDED BY CLINICAL GUIDELINES FOR THE EVALUATION, CLASSIFICATION, AND STRATIFICATION OF CKD. HOWEVER, THESE CLINICAL BIOMARKERS PRESENT SOME LIMITATIONS, ESPECIALLY FOR EARLY STAGES OF CKD, ELDERLY INDIVIDUALS, EXTREME BODY MASS INDEX VALUES (SERUM CREATININE), OR ARE INFLUENCED BY INFLAMMATION, STEROID TREATMENT AND THYROID DYSFUNCTION (SERUM CYSTATIN C). THERE IS THEREFORE A NEED TO IDENTIFY ADDITIONAL NON-INVASIVE BIOMARKERS THAT ARE USEFUL IN CLINICAL PRACTICE TO HELP IMPROVE CKD DIAGNOSIS, INFORM PROGNOSIS AND GUIDE THERAPEUTIC MANAGEMENT. CONCLUSION: CKD IS A MULTIFACTORIAL DISEASE WITH ASSOCIATED GENETIC AND ENVIRONMENTAL RISK FACTORS. HENCE, MANY STUDIES HAVE EMPLOYED GENETIC, EPIGENETIC AND TRANSCRIPTOMIC APPROACHES TO IDENTIFY BIOMARKERS FOR KIDNEY DISEASE. IN THIS REVIEW, WE HAVE SUMMARISED THE MOST IMPORTANT STUDIES IN HUMANS INVESTIGATING GENOMIC BIOMARKERS FOR CKD IN THE LAST DECADE. SEVERAL GENES, INCLUDING UMOD, SHROOM3 AND ELMO1 HAVE BEEN STRONGLY ASSOCIATED WITH RENAL DISEASES, AND SOME OF THEIR TRAITS, SUCH AS EGFR AND SERUM CREATININE. THE ROLE OF EPIGENETIC AND TRANSCRIPTOMIC BIOMARKERS IN CKD AND RELATED DISEASES IS STILL UNCLEAR. THE COMBINATION OF MULTIPLE BIOMARKERS INTO CLASSIFIERS, INCLUDING GENOMIC, AND/OR EPIGENOMIC, MAY GIVE A MORE COMPLETE PICTURE OF KIDNEY DISEASES. 2018 13 1170 40 CONTRIBUTION OF GENETICS AND EPIGENETICS TO PROGRESSION OF KIDNEY FIBROSIS. CHRONIC KIDNEY DISEASE (CKD) WHICH CAN LEAD TO END-STAGE RENAL FAILURE REMAINS A PRINCIPAL CHALLENGE IN NEPHROLOGY. WHILE MECHANISTIC STUDIES PROVIDED EXTENSIVE INSIGHTS INTO THE COMMON PATHWAYS OF FIBROGENESIS WHICH UNDERLIE THE PROGRESSION OF CKD, THESE PRE-CLINICAL STUDIES FAIL TO FULLY EXPLAIN THE VASTLY DIFFERENT PROGRESSION SLOPES OF INDIVIDUAL PATIENTS. RECENT STUDIES PROVIDE EVIDENCE THAT GENETIC POLYMORPHISMS AND EPIGENETIC VARIATIONS DETERMINE THE INDIVIDUAL SUSCEPTIBILITY OF PATIENTS TO DEVELOP CHRONIC PROGRESSIVE KIDNEY DISEASE. HERE, WE REVIEW RECENT INSIGHTS THAT WERE PROVIDED BY GENOME-WIDE ASSOCIATION STUDIES (GWASS), GENE-LINKAGE STUDIES AND EPIGENOME ANALYSIS. THE PROGRESSION OF CKD TOWARDS END-STAGE RENAL FAILURE REMAINS A PRINCIPAL UNSOLVED PROBLEM IN NEPHROLOGY AS EFFECTIVE THERAPIES AND PREDICTIVE TESTS ARE STILL NOT AVAILABLE [ 1, 2]. CHRONIC PROGRESSIVE KIDNEY DISEASE IS CAUSED BY A WIDE RANGE OF DISEASES, WITH DIABETES MELLITUS, HYPERTENSION AND PRIMARY GLOMERULOPATHIES BEING THE MOST COMMON CAUSES IN THE WESTERN WORLD [ 3]. INFECTIONS, PHYSICAL OBSTRUCTION, INTERSTITIAL NEPHRITIDES AND GENETIC CYSTIC KIDNEY DISEASES ARE ALSO COMMON CAUSES OF END-STAGE RENAL DISEASE (ESRD) [ 3]. REGARDLESS OF THE PRIMARY UNDERLYING DISEASE, CHRONICALLY INJURED KIDNEYS ARE HISTOMORPHOLOGICALLY CHARACTERIZED BY TUBULOINTERSTITIAL FIBROSIS [ 1]. IN FACT, THE EXTENT OF TUBULOINTERSTITIAL FIBROSIS IS THE BEST PREDICTOR FOR KIDNEY SURVIVAL, IRRESPECTIVE OF THE UNDERLYING DISEASE. FOR THIS REASON, FIBROSIS IS CONSIDERED THE COMMON PATHWAY OF CHRONIC PROGRESSIVE KIDNEY DISEASE [ 1]. FIBROGENESIS IS A PATHOLOGICAL SCARRING PROCESS WHICH INVOLVES ACCUMULATION OF ACTIVATED FIBROBLASTS, EXCESSIVE DEPOSITION OF EXTRACELLULAR MATRIX, FAILED REGENERATION OF TUBULAR EPITHELIUM, MICROVASCULAR RAREFACTION AND (MOSTLY STERILE) INFLAMMATION [ 4]. FIBROGENESIS DEPENDS ON A COMPLEX INTERACTION OF THE INVOLVED CELL TYPES WHICH IS ORCHESTRATED BY AN EXTENSIVE NETWORK OF GROWTH FACTORS AND SIGNALLING PATHWAYS (WHICH ARE REVIEWED EXTENSIVELY ELSEWHERE) [ 1]. IN VIEW OF THE DETAILED MECHANISTIC KNOWLEDGE OF THE PATHWAYS THAT ORCHESTRATE RENAL FIBROGENESIS, IT IS PUZZLING WHY PROGRESSION RATES OF CKD DIFFER DRAMATICALLY AMONG PATIENTS WITH IDENTICAL UNDERLYING DISEASES [ 1, 2]. THE FIBROTIC PATHWAYS ARE KNOWN, BUT THE SWITCHES THAT CONTROL THEIR INTENSITIES AND WHICH DETERMINE THE SPEED AT WHICH FIBROSIS MOVES ALONG THE PROGRESSION SLOPE ARE NOT YET UNDERSTOOD [ 1, 2]. THE CONCEPT THAT GENETIC POLYMORPHISMS ARE THE BASIS FOR INDIVIDUAL PROGRESSION RATES OF CKD IS AN OBVIOUS AND ATTRACTIVE ONE. DISTINCT SUSCEPTIBILITIES OF DIFFERENT MOUSE AND RAT STRAINS TO EXPERIMENTAL CKD ARE A STRONG TESTAMENT OF THE IMPACT OF GENETIC VARIATIONS ON RENAL FIBROGENESIS. IDENTIFICATION OF THE UNDERLYING GENETIC POLYMORPHISMS AND MECHANISTIC PROOF OF THEIR INVOLVEMENT IN THE PROGRESSION OF CKD, HOWEVER, IS AN ONGOING CHALLENGE. THERE ARE TWO BASIC APPROACHES: ONE STRATEGY IS TO PERFORM UNBIASED SCREENING TO IDENTIFY GENES WHICH ARE ASSOCIATED WITH CHRONIC PROGRESSIVE KIDNEY DISEASE AND TO THEN PROVE THEIR MECHANISTIC RELEVANCE IN EXPERIMENTAL STUDIES ('GENOTYPE TO PHENOTYPE APPROACH'). THE SECOND STRATEGY IS TO SELECTIVELY ANALYSE POLYMORPHISMS OF GENES WHICH HAVE BEEN IDENTIFIED IN MECHANISTIC STUDIES AS DRIVERS OF RENAL FIBROGENESIS WITH REGARD TO THEIR ASSOCIATION WITH CKD (PHENOTYPE TO GENOTYPE APPROACH). THE PUZZLING OBSERVATION, HOWEVER, IS THAT GENETIC ANALYSIS AND MECHANISTIC STUDIES SO FAR RARELY COMPLEMENT EACH OTHER. THE CURRENT STATE OF AFFAIRS IS REVIEWED IN MORE DETAIL BELOW. 2014 14 396 26 AN UPDATE ON EPIGENETICS AND CHILDHOOD RESPIRATORY DISEASES. EPIGENETIC MECHANISMS, DEFINED AS CHANGES IN PHENOTYPE OR GENE EXPRESSION CAUSED BY MECHANISMS OTHER THAN CHANGES IN THE UNDERLYING DNA SEQUENCE, HAVE BEEN PROPOSED TO CONSTITUTE A LINK BETWEEN GENETIC AND ENVIRONMENTAL FACTORS THAT AFFECT COMPLEX DISEASES. RECENT STUDIES SHOW THAT DNA METHYLATION, ONE OF THE KEY EPIGENETIC MECHANISMS, IS ALTERED IN CHILDREN EXPOSED TO AIR POLLUTANTS AND ENVIRONMENTAL TOBACCO SMOKE EARLY IN LIFE. SEVERAL CANDIDATE GENE STUDIES ON EPIGENETICS HAVE BEEN PUBLISHED TO DATE, BUT IT IS ONLY RECENTLY THAT GLOBAL METHYLATION ANALYSES HAVE BEEN PERFORMED FOR RESPIRATORY DISORDERS SUCH AS ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE. HOWEVER, LARGE-SCALE STUDIES WITH ADEQUATE POWER ARE YET TO BE PRESENTED IN CHILDREN, AND IMPLICATIONS FOR CLINICAL USE REMAIN TO BE EVALUATED. IN THIS REVIEW, WE SUMMARIZE THE RECENT ADVANCES IN EPIGENETICS AND RESPIRATORY DISORDERS IN CHILDREN, WITH A MAIN FOCUS ON METHODOLOGICAL CHALLENGES AND ANALYSES RELATED TO PHENOTYPE AND EXPOSURE USING GLOBAL METHYLATION APPROACHES. 2014 15 97 23 A PRIMER ON THE EPIGENETICS OF KIDNEY FIBROSIS. DESPITE EXTENSIVE KNOWLEDGE OF THE VARIOUS MOLECULAR PATHWAYS THAT CONTRIBUTE TO TUBULOINTERSTITIAL FIBROSIS, IT REMAINS AN UNSOLVED QUESTION WHY THE PROGRESSION RATE OF CHRONIC KIDNEY DISEASE VARIES SUBSTANTIALLY FROM PATIENT TO PATIENT, EVEN AMONG PATIENTS WITH COMMON UNDERLYING NEPHROPATHIES AND COMORBIDITIES. POSSIBLE EXPLANATIONS FOR DIFFERENT SUSCEPTIBILITIES OF INDIVIDUAL PATIENTS TO DEVELOP END-STAGE RENAL FAILURE INCLUDE GENETIC OR EPIGENETIC VARIATIONS, WHICH MODIFY HOW INDIVIDUAL PATIENTS RESPOND TO KIDNEY INJURY. HERE WE REVIEW PRINCIPLES OF EPIGENETIC MECHANISMS IN CONTEXT OF CHRONIC KIDNEY DISEASE AND DISCUSS HOW SUCH INSIGHTS MAY BE UTILIZED FOR FUTURE THERAPEUTIC STRATEGIES AND MAY LEAD TO NOVEL DIAGNOSTIC TOOLS IN THE FUTURE. 2012 16 5376 36 RECENT DEVELOPMENTS IN EPIGENETICS OF ACUTE AND CHRONIC KIDNEY DISEASES. THE GROWING EPIDEMIC OF OBESITY AND DIABETES, THE AGING POPULATION AS WELL AS PREVALENCE OF DRUG ABUSE HAS LED TO SIGNIFICANT INCREASES IN THE RATES OF THE CLOSELY ASSOCIATED ACUTE AND CHRONIC KIDNEY DISEASES, INCLUDING DIABETIC NEPHROPATHY. FURTHERMORE, EVIDENCE SHOWS THAT PARENTAL BEHAVIOR AND DIET CAN AFFECT THE PHENOTYPE OF SUBSEQUENT GENERATIONS VIA EPIGENETIC TRANSMISSION MECHANISMS. THESE DATA SUGGEST A STRONG INFLUENCE OF THE ENVIRONMENT ON DISEASE SUSCEPTIBILITY AND THAT, APART FROM GENETIC SUSCEPTIBILITY, EPIGENETIC MECHANISMS NEED TO BE EVALUATED TO GAIN CRITICAL NEW INFORMATION ABOUT KIDNEY DISEASES. EPIGENETICS IS THE STUDY OF PROCESSES THAT CONTROL GENE EXPRESSION AND PHENOTYPE WITHOUT ALTERATIONS IN THE UNDERLYING DNA SEQUENCE. EPIGENETIC MODIFICATIONS, INCLUDING CYTOSINE DNA METHYLATION AND COVALENT POST-TRANSLATIONAL MODIFICATIONS OF HISTONES IN CHROMATIN, ARE PART OF THE EPIGENOME, THE INTERFACE BETWEEN THE STABLE GENOME AND THE VARIABLE ENVIRONMENT. THIS DYNAMIC EPIGENETIC LAYER RESPONDS TO EXTERNAL ENVIRONMENTAL CUES TO INFLUENCE THE EXPRESSION OF GENES ASSOCIATED WITH DISEASE STATES. THE FIELD OF EPIGENETICS HAS SEEN REMARKABLE GROWTH IN THE PAST FEW YEARS WITH SIGNIFICANT ADVANCES IN BASIC BIOLOGY, CONTRIBUTIONS TO HUMAN DISEASE, AS WELL AS EPIGENOMICS TECHNOLOGIES. FURTHER UNDERSTANDING OF HOW THE RENAL CELL EPIGENOME IS ALTERED BY METABOLIC AND OTHER STIMULI CAN YIELD NOVEL NEW INSIGHTS INTO THE PATHOGENESIS OF KIDNEY DISEASES. IN THIS REVIEW, WE HAVE DISCUSSED THE CURRENT KNOWLEDGE ON THE ROLE OF EPIGENETIC MECHANISMS (PRIMARILY DNAME AND HISTONE MODIFICATIONS) IN ACUTE AND CHRONIC KIDNEY DISEASES, AND THEIR TRANSLATIONAL POTENTIAL TO IDENTIFY MUCH NEEDED NEW THERAPIES. 2015 17 2107 26 EPIGENETIC FACTORS IN SCHIZOPHRENIA: MECHANISMS AND EXPERIMENTAL APPROACHES. SCHIZOPHRENIA IS A CHRONIC MENTAL DISORDER THAT IS STILL POORLY UNDERSTOOD DESPITE DECADES OF STUDY. MANY FACTORS HAVE BEEN FOUND TO CONTRIBUTE TO THE PATHOGENESIS, INCLUDING NEURODEVELOPMENTAL DISTURBANCE, GENETIC RISK, AND ENVIRONMENTAL INSULT, BUT NO SINGLE ROOT CAUSE HAS EMERGED. WHILE EVIDENCE FROM TWIN STUDIES SUGGESTS A STRONG HERITABLE COMPONENT, FEW INDIVIDUAL LOCI HAVE BEEN IDENTIFIED IN GENOMEWIDE SCREENS, SUGGESTING A ROLE FOR EPIGENETIC EFFECTS. RATHER, LARGE NUMBERS OF WEAKLY ACTING LOCI MAY CUMULATIVELY INCREASE DISEASE RISK, INCLUDING SEVERAL MAPPING TO EPIGENETIC PATHWAYS. IN THIS REVIEW, WE DISCUSS MECHANISMS OF EPIGENETIC REGULATION AND EVIDENCE FOR AN EPIGENETIC CONTRIBUTION TO DISEASE PHENOTYPE. WE FURTHER DESCRIBE THE RANGE OF EXPERIMENTAL TOOLS CURRENTLY AVAILABLE TO STUDY EPIGENETIC EFFECTS ASSOCIATED WITH THE DISEASE. 2019 18 2154 31 EPIGENETIC MECHANISMS AND KIDNEY DISEASES. IN RECENT YEARS, MOLECULAR RESEARCH HAS BROUGHT TO LIGHT A SERIES OF MECHANISMS INVOLVED IN THE REGULATION OF GENE FUNCTION WITHOUT ALTERING THE DNA SEQUENCE. THESE MECHANISMS ARE DESCRIBED WITH THE TERM "EPIGENETICS" AND INCLUDE MODIFICATIONS IN THE STRUCTURE OF THE HUMAN GENOME, LEADING TO HERITABLE AND POTENTIALLY REVERSIBLE CHANGES IN GENE EXPRESSION. THERE IS NOW INCREASING EVIDENCE SUGGESTING THAT SEVERAL CHARACTERISTIC FEATURES OF CHRONIC KIDNEY DISEASE SUCH AS HYPERHOMOCYSTEINEMIA, SUBCLINICAL INFLAMMATION, INCREASED OXIDATIVE STRESS AND OTHERS MAY AFFECT THE HUMAN EPIGENOME. IN ADDITION, ANIMAL STUDIES HAVE SUGGESTED A POSSIBLE LINK BETWEEN NUTRITION AND ENVIRONMENTAL EXPOSURE DURING THE PERICONCEPTIONAL PERIOD AND EPIGENETIC CHANGES IN THE EXPRESSION OF MAJOR GENES IMPLICATED IN KIDNEY ORGANOGENESIS; THESE CHANGES RESULT IN A DIMINISHED NUMBER OF NEPHRONS IN THE DEVELOPING KIDNEY, WHICH PREDISPOSES TO AN INCREASED RISK FOR HYPERTENSION AND CHRONIC KIDNEY DISEASE IN FUTURE LIFE. THE UNDERSTANDING OF THE ROLE OF EPIGENETIC PHENOMENA IN THE PATHOGENESIS OF CHRONIC KIDNEY DISEASE OPENS NEW AVENUES FOR FUTURE THERAPEUTIC STRATEGIES, THROUGH THE DEVELOPMENT OF PHARMACEUTICAL AGENTS THAT TARGET DIRECTLY WITH THE CHANGES IN THE HUMAN EPIGENOME. SUCH EPIGENETIC DRUGS ARE ALREADY IN CLINICAL USE FOR THE TREATMENT OF CANCER AS WELL AS UNDER INVESTIGATION FOR THE USE IN OTHER DISEASES. THIS REVIEW WILL SUMMARIZE THE EXISTING DATA ON THE LINK BETWEEN EPIGENETIC MECHANISMS AND CHRONIC UREMIC MILIEU, AS WELL AS THE PROMISING RESULTS OF ONGOING RESEARCH IN THE FIELD OF EPIGENETIC DRUGS THAT COULD REPRESENT ADDITIONAL OPTIONS IN OUR THERAPEUTIC ARMAMENTARIUM FOR PATIENTS WITH CHRONIC KIDNEY DISEASE. 2011 19 2570 22 EPIGENETICS OF CHRONIC INFLAMMATORY DISEASES. CHRONIC, NONCOMMUNICABLE, AND INFLAMMATION-ASSOCIATED DISEASES REMAIN THE LARGEST CAUSE OF MORBIDITY AND MORTALITY GLOBALLY AND WITHIN THE UNITED STATES. THIS IS MAINLY DUE TO OUR LIMITED UNDERSTANDING OF THE MOLECULAR MECHANISMS THAT UNDERLIE THESE COMPLEX PATHOLOGIES. THE AVAILABLE EVIDENCE INDICATES THAT STUDIES OF EPIGENETICS (TRADITIONALLY DEFINED AS THE HERITABLE CHANGES TO GENE EXPRESSION THAT ARE INDEPENDENT OF CHANGES TO DNA) ARE SIGNIFICANTLY ADVANCING OUR KNOWLEDGE OF THESE INFLAMMATORY CONDITIONS. THIS REVIEW WILL FOCUS ON EPIGENETIC STUDIES OF THREE DISEASES, THAT ARE AMONG THE MOST BURDENSOME GLOBALLY: CARDIOVASCULAR DISEASE, THE NUMBER ONE CAUSE OF DEATHS WORLDWIDE, TYPE 2 DIABETES AND, ALZHEIMER'S DISEASE. THE CURRENT STATUS OF EPIGENETIC RESEARCH, INCLUDING THE ABILITY TO PREDICT DISEASE RISK, AND KEY PATHOPHYSIOLOGICAL DEFECTS ARE DISCUSSED. THE SIGNIFICANCE OF DEFINING THE CONTRIBUTION OF EPIGENETIC DEFECTS TO NONRESOLVING INFLAMMATION AND AGING, EACH ASSOCIATED WITH THESE DISEASES, IS HIGHLIGHTED, AS THESE ARE LIKELY TO PROVIDE NEW INSIGHTS INTO INFLAMMATORY DISEASE PATHOGENESIS. 2019 20 462 29 ARE ALTERATIONS IN DNA METHYLATION RELATED TO CKD DEVELOPMENT? THE MODIFICATIONS IN GENOMIC DNA METHYLATION ARE INVOLVED IN THE REGULATION OF NORMAL AND PATHOLOGICAL CELLULAR PROCESSES. THE EPIGENETIC REGULATION STIMULATES BIOLOGICAL PLASTICITY AS AN ADAPTIVE RESPONSE TO VARIATIONS IN ENVIRONMENTAL FACTORS. THE ROLE OF EPIGENETIC CHANGES IS VITAL FOR THE DEVELOPMENT OF SOME DISEASES, INCLUDING ATHEROGENESIS, CANCERS, AND CHRONIC KIDNEY DISEASE (CKD). THE RESULTS OF STUDIES PRESENTED IN THIS REVIEW HAVE SUGGESTED THAT ALTERED DNA METHYLATION CAN MODULATE THE EXPRESSION OF PRO-INFLAMMATORY AND PRO-FIBROTIC GENES, AS WELL THOSE ESSENTIAL FOR KIDNEY DEVELOPMENT AND FUNCTION, THUS STIMULATING RENAL DISEASE PROGRESSION. ABNORMALLY INCREASED HOMOCYSTEINE, HYPOXIA, AND INFLAMMATION HAVE BEEN SUGGESTED TO ALTER EPIGENETIC REGULATION OF GENE EXPRESSION IN CKD. STUDIES OF RENAL SAMPLES HAVE DEMONSTRATED THE RELATIONSHIP BETWEEN VARIATIONS IN DNA METHYLATION AND FIBROSIS AND VARIATIONS IN ESTIMATED GLOMERULAR FILTRATION RATE (EGFR) IN HUMAN CKD. THE UNRAVELLING OF THE GENETIC-EPIGENETIC PROFILE WOULD ENHANCE OUR UNDERSTANDING OF PROCESSES UNDERLYING THE DEVELOPMENT OF CKD. THE UNDERSTANDING OF MULTIFACETED RELATIONSHIP BETWEEN DNA METHYLATION, GENES EXPRESSION, AND DISEASE DEVELOPMENT AND PROGRESSION COULD IMPROVE THE ABILITY TO IDENTIFY INDIVIDUALS AT RISK OF CKD AND ENABLE THE CHOICE OF APPROPRIATE DISEASE MANAGEMENT. 2022