1 1156 173 CONSIDERING THE USE OF THE TERMS STRAIN AND ADAPTATION IN PRION RESEARCH. EVOLUTIONARY BIOLOGISTS AND DISEASE BIOLOGISTS USE THE TERMS STRAIN AND ADAPTATION IN CHRONIC WASTING DISEASE (CWD) RESEARCH IN DIFFERENT WAYS. IN EVOLUTIONARY BIOLOGY, A STRAIN IS A NASCENT GENETIC LINEAGE THAT CAN BE DESCRIBED BY A GENEALOGY, AND A PHYLOGENETIC NOMENCLATURE CONSTRUCTED TO REFLECT THAT GENEALOGY. PRION STRAINS ARE DESCRIBED AS SHOWING DISTINCT HOST RANGE, CLINICAL PRESENTATION, DISEASE PROGRESSION, AND NEUROPATHOLOGICAL AND PRP BIOCHEMICAL PROFILES, AND LACK INFORMATION THAT WOULD PERMIT PHYLOGENETIC RECONSTRUCTION OF THEIR HISTORY. PRION STRAINS ARE ALTERNATIVE PROTEIN CONFORMATIONS, SOMETIMES DERIVED FROM THE SAME GENOTYPE. I SUGGEST REFERRING TO PRION STRAINS AS ECOTYPES, BECAUSE THE VARIANT PHENOTYPIC CONFORMATIONS ("STRAINS") ARE A FUNCTION OF THE INTERACTION BETWEEN PRNP AMINO ACID GENOTYPE AND THE HOST ENVIRONMENT. IN THE CASE OF CWD, A PRION ECOTYPE IN WHITE-TAILED DEER WOULD BE DESCRIBED BY ITS GENOTYPE AND THE HOST IN WHICH IT OCCURS, SUCH AS THE H95 + ECOTYPE. HOWEVER, AN EVOLUTIONARY NOMENCLATURE IS DIFFICULT BECAUSE NOT ALL INDIVIDUALS WITH THE SAME PRNP GENOTYPE SHOW SIGNS OF CWD, THEREFORE CREATING A NOMENCLATURE REFLECTING AND ONE-TO-ONE RELATIONSHIP BETWEEN PRNP GENEALOGY AND CWD PRESENCE IS DIFFICULT. FURTHERMORE, VERY LITTLE INFORMATION EXISTS ON THE PHYLOGENETIC DISTRIBUTION OF CWD ECOTYPES IN WILD DEER POPULATIONS. ADAPTATION HAS A CLEAR MEANING IN EVOLUTIONARY BIOLOGY, THE DIFFERENTIAL SURVIVAL AND REPRODUCTION OF INDIVIDUAL GENOTYPES. IF A NEW PRION ECOTYPE ARISES IN A PARTICULAR HOST AND KILLS MORE HOSTS OR KILLS AT AN EARLIER AGE, IT IS THE ANTITHESIS OF THE EVOLUTIONARY DEFINITION OF ADAPTATION. HOWEVER, PRION STRAINS MIGHT BE TRANSMITTED ACROSS GENERATIONS EPIGENETICALLY, BUT WHETHER THIS REPRESENTS ADAPTATION DEPENDS ON THE FITNESS CONSEQUENCES OF THE STRAIN. PROTEIN PHENOTYPES OF PRNP THAT CAUSE TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHIES (TSES), AND CWD, ARE MALADAPTIVE AND WOULD NOT BE PROPAGATED GENETICALLY OR EPIGENETICALLY VIA A PROCESS CONSISTENT WITH AN EVOLUTIONARY VIEW OF ADAPTATION. I SUGGEST TERMING THE PROCESS OF PRION STRAIN ORIGINATION "PHENOTYPIC TRANSFORMATION", AND ONLY ADAPTATION IF EVIDENCE SHOWS THEY ARE NOT MALADAPTIVE AND PERSIST OVER EVOLUTIONARY TIME PERIODS (E.G., THOUSANDS OF GENERATIONS) AND ACROSS DISTINCT SPECIES BOUNDARIES (VIA INHERITANCE). THUS, PRION BIOLOGISTS USE STRAIN AND ADAPTATION, HISTORICALLY EVOLUTIONARY TERMS, IN QUITE DIFFERENT WAYS. 2021 2 3819 35 INTRINSIC MUTAGENIC PROPERTIES OF 5-CHLOROCYTOSINE: A MECHANISTIC CONNECTION BETWEEN CHRONIC INFLAMMATION AND CANCER. DURING CHRONIC INFLAMMATION, NEUTROPHIL-SECRETED HYPOCHLOROUS ACID CAN DAMAGE NEARBY CELLS INDUCING THE GENOMIC ACCUMULATION OF 5-CHLOROCYTOSINE (5CLC), A KNOWN INFLAMMATION BIOMARKER. ALTHOUGH 5CLC HAS BEEN SHOWN TO PROMOTE EPIGENETIC CHANGES, IT HAS BEEN UNKNOWN HERETOFORE IF 5CLC DIRECTLY PERPETRATES A MUTAGENIC OUTCOME WITHIN THE CELL. THE PRESENT WORK SHOWS THAT 5CLC IS INTRINSICALLY MUTAGENIC, BOTH IN VITRO AND, AT A LEVEL OF A SINGLE MOLECULE PER CELL, IN VIVO. USING BIOCHEMICAL AND GENETIC APPROACHES, WE HAVE QUANTIFIED THE MUTAGENIC AND TOXIC PROPERTIES OF 5CLC, SHOWING THAT THIS LESION CAUSED C-->T TRANSITIONS AT FREQUENCIES RANGING FROM 3-9% DEPENDING ON THE POLYMERASE TRAVERSING THE LESION. X-RAY CRYSTALLOGRAPHIC STUDIES PROVIDED A MOLECULAR BASIS FOR THE MUTAGENICITY OF 5CLC; A SNAPSHOT OF HUMAN POLYMERASE BETA REPLICATING ACROSS A PRIMED 5CLC-CONTAINING TEMPLATE UNCOVERED 5CLC ENGAGED IN A NASCENT BASE PAIR WITH AN INCOMING DATP ANALOG. ACCOMMODATION OF THE CHLORINE SUBSTITUENT IN THE TEMPLATE MAJOR GROOVE ENABLED A UNIQUE INTERACTION BETWEEN 5CLC AND THE INCOMING DATP, WHICH WOULD FACILITATE MUTAGENIC LESION BYPASS. THE TYPE OF MUTATION INDUCED BY 5CLC, THE C-->T TRANSITION, HAS BEEN PREVIOUSLY SHOWN TO OCCUR IN SUBSTANTIAL AMOUNTS BOTH IN TISSUES UNDER INFLAMMATORY STRESS AND IN THE GENOMES OF MANY INFLAMMATION-ASSOCIATED CANCERS. IN FACT, MANY SEQUENCE-SPECIFIC MUTATIONAL SIGNATURES UNCOVERED IN SEQUENCED CANCER GENOMES FEATURE C-->T MUTATIONS. THEREFORE, THE MUTAGENIC ABILITY OF 5CLC DOCUMENTED IN THE PRESENT STUDY MAY CONSTITUTE A DIRECT FUNCTIONAL LINK BETWEEN CHRONIC INFLAMMATION AND THE GENETIC CHANGES THAT ENABLE AND PROMOTE MALIGNANT TRANSFORMATION. 2015 3 5852 23 SUBLIMINAL (LATENT) PROCESSING OF PAIN AND ITS EVOLUTION TO CONSCIOUS AWARENESS. BY UNCONSCIOUS OR COVERT PROCESSING OF PAIN WE REFER TO NASCENT INTERACTIONS THAT AFFECT THE EVENTUAL DELIVERANCE OF PAIN AWARENESS. THUS, INTERNAL PROCESSES (VIZ., REPEATED NOCICEPTIVE EVENTS, INFLAMMATORY KINDLING, REORGANIZATION OF BRAIN NETWORKS, GENETIC) OR EXTERNAL PROCESSES (VIZ., ENVIRONMENT, SOCIOECONOMIC LEVELS, MODULATION OF EPIGENETIC STATUS) CONTRIBUTE TO ENHANCING OR INHIBITING THE PRESENTATION OF PAIN AWARENESS. HERE WE PUT FORWARD THE NOTION THAT FOR MANY PATIENTS, ONGOING SUB-CONSCIOUS CHANGES IN BRAIN FUNCTION ARE SIGNIFICANT PLAYERS IN THE EVENTUAL MANIFESTATION OF CHRONIC PAIN. IN THIS REVIEW, WE PROVIDE CLINICAL EXAMPLES OF NASCENT OR WHAT WE TERM PRE-PAIN PROCESSES AND THE NEUROBIOLOGICAL MECHANISMS OF HOW THESE CHANGES MAY CONTRIBUTE TO PAIN, BUT ALSO POTENTIAL OPPORTUNITIES TO DEFINE THE PROCESS FOR EARLY THERAPEUTIC INTERVENTIONS. 2018 4 5525 29 RNA BINDING PROTEINS IN SENESCENCE: A POTENTIAL COMMON LINKER FOR AGE-RELATED DISEASES? AGING REPRESENTS THE MAJOR RISK FACTOR FOR THE ONSET AND/OR PROGRESSION OF VARIOUS DISORDERS INCLUDING NEURODEGENERATIVE DISEASES, METABOLIC DISORDERS, AND BONE-RELATED DEFECTS. AS THE AVERAGE AGE OF THE POPULATION IS PREDICTED TO EXPONENTIALLY INCREASE IN THE COMING YEARS, UNDERSTANDING THE MOLECULAR MECHANISMS UNDERLYING THE DEVELOPMENT OF AGING-RELATED DISEASES AND THE DISCOVERY OF NEW THERAPEUTIC APPROACHES REMAIN PIVOTAL. WELL-REPORTED HALLMARKS OF AGING ARE CELLULAR SENESCENCE, GENOME INSTABILITY, AUTOPHAGY IMPAIRMENT, MITOCHONDRIA DYSFUNCTION, DYSBIOSIS, TELOMERE ATTRITION, METABOLIC DYSREGULATION, EPIGENETIC ALTERATIONS, LOW-GRADE CHRONIC INFLAMMATION, STEM CELL EXHAUSTION, ALTERED CELL-TO-CELL COMMUNICATION AND IMPAIRED PROTEOSTASIS. WITH FEW EXCEPTIONS, HOWEVER, MANY OF THE MOLECULAR PLAYERS IMPLICATED WITHIN THESE PROCESSES AS WELL AS THEIR ROLE IN DISEASE DEVELOPMENT REMAIN LARGELY UNKNOWN. RNA BINDING PROTEINS (RBPS) ARE KNOWN TO REGULATE GENE EXPRESSION BY DICTATING AT POST-TRANSCRIPTIONAL LEVEL THE FATE OF NASCENT TRANSCRIPTS. THEIR ACTIVITY RANGES FROM DIRECTING PRIMARY MRNA MATURATION AND TRAFFICKING TO MODULATION OF TRANSCRIPT STABILITY AND/OR TRANSLATION. ACCUMULATING EVIDENCE HAS SHOWN THAT RBPS ARE EMERGING AS KEY REGULATORS OF AGING AND AGING-RELATED DISEASES, WITH THE POTENTIAL TO BECOME NEW DIAGNOSTIC AND THERAPEUTIC TOOLS TO PREVENT OR DELAY AGING PROCESSES. IN THIS REVIEW, WE SUMMARIZE THE ROLE OF RBPS IN PROMOTING CELLULAR SENESCENCE AND WE HIGHLIGHT THEIR DYSREGULATION IN THE PATHOGENESIS AND PROGRESSION OF THE MAIN AGING-RELATED DISEASES, WITH THE AIM OF ENCOURAGING FURTHER INVESTIGATIONS THAT WILL HELP TO BETTER DISCLOSE THIS NOVEL AND CAPTIVATING MOLECULAR SCENARIO. 2023 5 2566 24 EPIGENETICS MECHANISMS IN RENAL DEVELOPMENT. APPRECIATION FOR THE ROLE OF EPIGENETIC MODIFICATIONS IN THE DIAGNOSIS AND TREATMENT OF DISEASES IS FAST GAINING ATTENTION. TREATMENT OF CHRONIC KIDNEY DISEASE STEMMING FROM DIABETES OR HYPERTENSION AS WELL AS WILMS TUMOR WILL ALL PROFIT FROM KNOWLEDGE OF THE CHANGES IN THE EPIGENOMIC LANDSCAPES. TO DO SO, IT IS ESSENTIAL TO CHARACTERIZE THE EPIGENOMIC MODIFIERS AND THEIR MODIFICATIONS UNDER NORMAL PHYSIOLOGICAL CONDITIONS. THE TRANSCRIPTION FACTOR PAX2 WAS IDENTIFIED AS A MAJOR EPIGENETIC PLAYER IN THE EARLY SPECIFICATION OF THE KIDNEY. NOTABLY, THE PROGENITORS OF ALL NEPHRONS THAT RESIDE IN THE CAP MESENCHYME DISPLAY A UNIQUE BIVALENT HISTONE SIGNATURE (EXPRESSING REPRESSIVE EPIGENETIC MARKS ALONGSIDE ACTIVATION MARKS) ON LINEAGE-SPECIFIC GENES. THESE CELLS ARE DEEMED POISED FOR DIFFERENTIATION AND COMMITMENT TO THE NEPHROGENIC LINEAGE. IN RESPONSE TO THE APPROPRIATE INDUCING SIGNAL, THESE GENES LOSE THEIR REPRESSIVE HISTONE MARKS, WHICH ALLOW FOR THEIR EXPRESSION IN NASCENT NEPHRON PRECURSORS. SUCH KNOWLEDGE OF THE EPIGENETIC LANDSCAPE AND THE RESULTANT CELL FATE OR BEHAVIOR IN THE DEVELOPING KIDNEY WILL GREATLY IMPROVE THE OVERALL SUCCESS IN DESIGNING REGENERATIVE STRATEGIES AND TISSUE REPROGRAMMING METHODOLOGIES FROM PLURIPOTENT CELLS. 2016 6 1977 21 EPIGENETIC ALTERATIONS IN ACUTE KIDNEY INJURY. ACUTE KIDNEY INJURY (AKI) IS A RISK FACTOR FOR CHRONIC KIDNEY DISEASE AND DEATH. DESPITE PROGRESS MADE IN UNDERSTANDING THE CELLULAR AND MOLECULAR BASIS OF AKI PATHOGENESIS THERE HAS BEEN NO IMPROVEMENT IN THE HIGH MORTALITY RATE FROM THIS DISEASE IN DECADES. EPIGENETICS IS ONE OF THE MOST INTENSIVELY STUDIED FIELDS OF BIOLOGY TODAY AND REPRESENTS A NEW PARADIGM FOR UNDERSTANDING THE PATHOPHYSIOLOGY OF DISEASE. ALTHOUGH EPIGENETICS OF AKI IS A NASCENT FIELD, THE AVAILABLE INFORMATION ALREADY IS PROVIDING COMPELLING EVIDENCE THAT CHROMATIN BIOLOGY PLAYS A CRITICAL ROLE IN THIS DISEASE. IN THIS ARTICLE WE EXPLORE WHAT IS KNOWN ABOUT THE CONTRIBUTION OF EPIGENETIC MECHANISMS TO THE PATHOPHYSIOLOGY OF AKI AND HOW THIS KNOWLEDGE ALREADY IS GUIDING THE DEVELOPMENT OF NEW DIAGNOSTIC TOOLS AND EPIGENETIC THERAPIES. 2013 7 6272 20 THE ORIGIN AND PATHOGENESIS OF ENDOMETRIOSIS. RECENT MOLECULAR GENETIC FINDINGS ON ENDOMETRIOSIS AND NORMAL ENDOMETRIUM SUGGEST A MODIFIED MODEL IN WHICH CIRCULATING EPITHELIAL PROGENITOR OR STEM CELLS INTENDED TO REGENERATE UTERINE ENDOMETRIUM AFTER MENSTRUATION MAY BECOME OVERREACTIVE AND TRAPPED OUTSIDE THE UTERUS. THESE TRAPPED EPITHELIUM-COMMITTED PROGENITOR CELLS FORM NASCENT GLANDS THROUGH CLONAL EXPANSION AND RECRUIT POLYCLONAL STROMAL CELLS, LEADING TO THE ESTABLISHMENT OF DEEP INFILTRATING ENDOMETRIOSIS. ONCE FORMED, THE ECTOPIC TISSUE BECOMES SUBJECT TO IMMUNE SURVEILLANCE, RESULTING IN CHRONIC INFLAMMATION. THE INFLAMMATORY RESPONSE ORCHESTRATED BY NUCLEAR FACTOR-KAPPAB SIGNALING IS EXACERBATED BY ABERRATIONS IN THE ESTROGEN RECEPTOR-BETA AND PROGESTERONE RECEPTOR PATHWAYS, WHICH ARE ALSO AFFECTED BY LOCAL INFLAMMATION, FORMING A DYSREGULATED INFLAMMATION-HORMONAL LOOP. GLANDULAR EPITHELIUM WITHIN ENDOMETRIOTIC TISSUE HARBORS CANCER-ASSOCIATED MUTATIONS THAT ARE FREQUENTLY DETECTED IN ENDOMETRIOSIS-RELATED OVARIAN CANCERS. IN THIS REVIEW, WE SUMMARIZE RECENT ADVANCES THAT HAVE ILLUMINATED THE ORIGIN AND PATHOGENESIS OF ENDOMETRIOSIS AND HAVE PROVIDED NEW AVENUES FOR RESEARCH THAT PROMISE TO IMPROVE THE EARLY DIAGNOSIS AND MANAGEMENT OF ENDOMETRIOSIS. 2020 8 3393 50 HOST DETERMINANTS OF PRION STRAIN DIVERSITY INDEPENDENT OF PRION PROTEIN GENOTYPE. PHENOTYPIC DIVERSITY IN PRION DISEASES CAN BE SPECIFIED BY PRION STRAINS IN WHICH BIOLOGICAL TRAITS ARE PROPAGATED THROUGH AN EPIGENETIC MECHANISM MEDIATED BY DISTINCT PRP(SC) CONFORMATIONS. WE INVESTIGATED THE ROLE OF HOST-DEPENDENT FACTORS ON PHENOTYPIC DIVERSITY OF CHRONIC WASTING DISEASE (CWD) IN DIFFERENT HOST SPECIES THAT EXPRESS THE SAME PRION PROTEIN GENE (PRNP). TWO CWD STRAINS THAT HAVE DISTINCT BIOLOGICAL, BIOCHEMICAL, AND PATHOLOGICAL FEATURES WERE IDENTIFIED IN TRANSGENIC MICE THAT EXPRESS THE SYRIAN GOLDEN HAMSTER (SGH) PRNP. THE CKY STRAIN OF CWD HAD A SHORTER INCUBATION PERIOD THAN THE WST STRAIN OF CWD, BUT AFTER TRANSMISSION TO SGH, THE INCUBATION PERIOD OF CKY CWD WAS APPROXIMATELY 150 DAYS LONGER THAN WST CWD. LIMITED PROTEINASE K DIGESTION REVEALED STRAIN-SPECIFIC PRP(SC) POLYPEPTIDE PATTERNS THAT WERE MAINTAINED IN BOTH HOSTS, BUT THE SOLUBILITY AND CONFORMATIONAL STABILITY OF PRP(SC) DIFFERED FOR THE CWD STRAINS IN A HOST-DEPENDENT MANNER. WST CWD PRODUCED PRP(SC) AMYLOID PLAQUES IN THE BRAIN OF THE SGH THAT WERE PARTIALLY INSOLUBLE AND STABLE AT A HIGH CONCENTRATION OF PROTEIN DENATURANT. HOWEVER, IN TRANSGENIC MICE, PRP(SC) FROM WST CWD DID NOT ASSEMBLE INTO PLAQUES, WAS HIGHLY SOLUBLE, AND HAD LOW CONFORMATIONAL STABILITY. SIMILAR STUDIES USING THE HY AND DY STRAINS OF TRANSMISSIBLE MINK ENCEPHALOPATHY RESULTED IN MINOR DIFFERENCES IN PRION BIOLOGICAL AND PRP(SC) PROPERTIES BETWEEN TRANSGENIC MICE AND SGH. THESE FINDINGS INDICATE THAT HOST-SPECIFIC PATHWAYS THAT ARE INDEPENDENT OF PRNP CAN ALTER THE PRP(SC) CONFORMATION OF CERTAIN PRION STRAINS, LEADING TO CHANGES IN THE BIOPHYSICAL PROPERTIES OF PRP(SC), NEUROPATHOLOGY, AND CLINICAL PRION DISEASE. IMPORTANCE: PRIONS ARE MISFOLDED PATHOGENIC PROTEINS THAT CAUSE NEURODEGENERATION IN HUMANS AND ANIMALS. TRANSMISSIBLE PRION DISEASES EXHIBIT A SPECTRUM OF DISEASE PHENOTYPES AND THE BASIS OF THIS DIVERSITY IS ENCODED IN THE STRUCTURE OF THE PATHOGENIC PRION PROTEIN AND PROPAGATED BY AN EPIGENETIC MECHANISM. IN THE PRESENT STUDY, WE INVESTIGATED PRION DIVERSITY IN TWO HOSTS SPECIES THAT EXPRESS THE SAME PRION PROTEIN GENE. WHILE PRIOR REPORTS HAVE DEMONSTRATED THAT PRION STRAIN PROPERTIES ARE STABLE UPON INFECTION OF THE SAME HOST SPECIES AND PRION PROTEIN GENOTYPE, OUR FINDINGS INDICATE THAT CERTAIN PRION STRAINS CAN UNDERGO DRAMATIC CHANGES IN BIOLOGICAL PROPERTIES THAT ARE NOT DEPENDENT ON THE PRION PROTEIN. THEREFORE, HOST FACTORS INDEPENDENT OF THE PRION PROTEIN CAN AFFECT PRION DIVERSITY. UNDERSTANDING HOW HOST PATHWAYS CAN MODIFY PRION DISEASE PHENOTYPES MAY PROVIDE CLUES ON HOW TO ALTER PRION FORMATION AND LEAD TO TREATMENTS FOR PRION, AND OTHER, HUMAN NEURODEGENERATIVE DISEASES OF PROTEIN MISFOLDING. 2015 9 2444 28 EPIGENETIC STATES OF NEPHRON PROGENITORS AND EPITHELIAL DIFFERENTIATION. IN MAMMALS, FORMATION OF NEW NEPHRONS ENDS PERINATALLY DUE TO CONSUMPTION OF MESENCHYMAL PROGENITOR CELLS. PREMATURE DEPLETION OF PROGENITORS DUE TO PREMATURITY OR POSTNATAL LOSS OF NEPHRONS DUE TO INJURY CAUSES CHRONIC KIDNEY DISEASE AND HYPERTENSION. INTENSIVE EFFORTS ARE CURRENTLY INVESTED IN DESIGNING REGENERATIVE STRATEGIES TO FORM NEW NEPHRON PROGENITORS FROM PLURIPOTENT CELLS, WHICH UPON FURTHER DIFFERENTIATION PROVIDE A POTENTIAL SOURCE OF NEW NEPHRONS. TO KNOW IF REPROGRAMED RENAL CELLS CAN MAINTAIN THEIR IDENTITY AND FATE REQUIRES KNOWLEDGE OF THE EPIGENETIC STATES OF NATIVE NEPHRON PROGENITORS AND THEIR PROGENY. IN THIS ARTICLE, WE SUMMARIZE CURRENT KNOWLEDGE AND GAPS IN THE EPIGENOMIC LANDSCAPE OF THE DEVELOPING KIDNEY. WE NOW KNOW THAT PAX2/PTIP/H3K4 METHYLTRANSFERASE ACTIVITY PROVIDES THE INITIAL EPIGENETIC SPECIFICATION SIGNAL TO THE METANEPHRIC MESENCHYME. DURING NEPHROGENESIS, THE CAP MESENCHYME HOUSING NEPHRON PROGENITORS IS ENRICHED IN BIVALENT CHROMATIN MARKS; AS TUBULOGENESIS PROCEEDS, THE TUBULAR EPITHELIUM ACQUIRES H3K79ME2. THE LATTER MARK IS UNIQUELY INDUCED DURING EPITHELIAL DIFFERENTIATION. ANALYSIS OF HISTONE LANDSCAPES IN CLONAL METANEPHRIC MESENCHYME CELL LINES AND IN WILMS TUMOR AND NORMAL FETAL KIDNEY HAS REVEALED THAT PROMOTERS OF POISED NEPHROGENESIS GENES CARRY BIVALENT HISTONE SIGNATURES IN PROGENITORS. DIFFERENTIATION OR STIMULATION OF WNT SIGNALING PROMOTES RESOLUTION OF BIVALENCY; THIS DOES NOT OCCUR IN WILMS TUMOR CELLS CONSISTENT WITH THEIR DEVELOPMENTAL ARREST. THE USE OF SMALL CELL NUMBER CHIP-SEQ SHOULD FACILITATE THE CHARACTERIZATION OF THE CHROMATIN LANDSCAPE OF THE METANEPHRIC MESENCHYME AND VARIOUS NEPHRON COMPARTMENTS DURING NEPHROGENESIS. ONLY THEN WE WILL KNOW IF STEM AND SOMATIC CELL REPROGRAMMING INTO KIDNEY PROGENITORS RECAPITULATES NORMAL DEVELOPMENT. 2015 10 3927 31 LIVER ABNORMALITIES AFTER ELIMINATION OF HCV INFECTION: PERSISTENT EPIGENETIC AND IMMUNOLOGICAL PERTURBATIONS POST-CURE. CHRONIC HEPATITIS C (CHC) IS A MAJOR CAUSE OF HEPATOCELLULAR CARCINOMA (HCC) WORLDWIDE. WHILE DIRECTLY ACTING ANTIVIRAL (DAA) DRUGS ARE NOW ABLE TO CURE VIRTUALLY ALL HEPATITIS C VIRUS (HCV) INFECTIONS, EVEN IN SUBJECTS WITH ADVANCED LIVER DISEASE, WHAT HAPPENS TO THE LIVER AND PROGRESSION OF THE DISEASE AFTER DAA-INDUCED CURE OF VIREMIA IS ONLY BEGINNING TO EMERGE. SEVERAL LARGE-SCALE CLINICAL STUDIES IN DIFFERENT PATIENT POPULATIONS HAVE SHOWN THAT PATIENTS WITH ADVANCED LIVER DISEASE MAINTAIN A RISK FOR DEVELOPING HCC EVEN WHEN THE ORIGINAL INSTIGATOR, THE VIRUS, IS ELIMINATED BY DAAS. HERE WE REVIEW EMERGING STUDIES DERIVED FROM MULTIPLE, COMPLEMENTARY EXPERIMENTAL SYSTEMS INVOLVING PATIENT LIVER TISSUES, HUMAN LIVER CELL CULTURES, HUMAN LIVER SLICE CULTURES, AND ANIMAL MODELS, SHOWING THAT HCV INFECTION INDUCES EPIGENETIC, SIGNALING, AND GENE EXPRESSION CHANGES IN THE LIVER ASSOCIATED WITH ALTERED HEPATIC INNATE IMMUNITY AND LIVER CANCER RISK. OF CRITICAL IMPORTANCE IS THE FACT THAT THESE VIRUS-INDUCED ABNORMALITIES PERSIST AFTER DAA CURE OF HCV. THESE NASCENT FINDINGS PORTEND THE DISCOVERY OF PATHWAYS INVOLVED IN POST-HCV IMMUNOPATHOGENESIS, WHICH MAY BE CLINICALLY ACTIONABLE TARGETS FOR MORE COMPREHENSIVE CARE OF DAA-CURED INDIVIDUALS. 2021 11 2693 31 EVOLUTION, KIDNEY DEVELOPMENT, AND CHRONIC KIDNEY DISEASE. THERE IS A GLOBAL EPIDEMIC OF CHRONIC KIDNEY DISEASE (CKD) CHARACTERIZED BY A PROGRESSIVE LOSS OF NEPHRONS, ASCRIBED IN LARGE PART TO A RISING INCIDENCE OF HYPERTENSION, METABOLIC SYNDROME, AND TYPE 2 DIABETES MELLITUS. THERE IS A TEN-FOLD VARIATION IN NEPHRON NUMBER AT BIRTH IN THE GENERAL POPULATION, AND A 50% OVERALL DECREASE IN NEPHRON NUMBER IN THE LAST DECADES OF LIFE. THE VICIOUS CYCLE OF NEPHRON LOSS STIMULATING HYPERTROPHY BY REMAINING NEPHRONS AND RESULTING IN GLOMERULOSCLEROSIS HAS BEEN REGARDED AS MALADAPTIVE, AND ONLY PARTIALLY RESPONSIVE TO ANGIOTENSIN INHIBITION. ADVANCES OVER THE PAST CENTURY IN KIDNEY PHYSIOLOGY, GENETICS, AND DEVELOPMENT HAVE ELUCIDATED MANY ASPECTS OF NEPHRON FORMATION, STRUCTURE AND FUNCTION. PARALLEL ADVANCES HAVE BEEN ACHIEVED IN EVOLUTIONARY BIOLOGY, WITH THE EMERGENCE OF EVOLUTIONARY MEDICINE, A DISCIPLINE THAT PROMISES TO PROVIDE NEW INSIGHT INTO THE TREATMENT OF CHRONIC DISEASE. THIS REVIEW PROVIDES A FRAMEWORK FOR UNDERSTANDING THE ORIGINS OF CONTEMPORARY DEVELOPMENTAL NEPHROLOGY, AND RECENT PROGRESS IN EVOLUTIONARY BIOLOGY. THE ESTABLISHMENT OF EVOLUTIONARY DEVELOPMENTAL BIOLOGY (EVO-DEVO), ECOLOGICAL DEVELOPMENTAL BIOLOGY (ECO-DEVO), AND DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE (DOHAD) FOLLOWED THE DISCOVERY OF THE HOX GENE FAMILY, THE RECOGNITION OF THE CONTRIBUTION OF CUMULATIVE ENVIRONMENTAL STRESSORS TO THE CHANGING PHENOTYPE OVER THE LIFE CYCLE, AND MECHANISMS OF EPIGENETIC REGULATION. THE MATURATION OF EVOLUTIONARY MEDICINE HAS CONTRIBUTED TO NEW INVESTIGATIVE APPROACHES TO CARDIOVASCULAR DISEASE, CANCER, AND INFECTIOUS DISEASE, AND PROMISES THE SAME FOR CKD. BY INCORPORATING THESE PRINCIPLES, DEVELOPMENTAL NEPHROLOGY IS IDEALLY POSITIONED TO ANSWER IMPORTANT QUESTIONS REGARDING THE FATE OF NEPHRONS FROM EMBRYO THROUGH SENESCENCE. 2019 12 5966 31 TERMINAL ADDITION IN A CELLULAR WORLD. RECENT ADVANCES IN OUR UNDERSTANDING OF EVOLUTIONARY DEVELOPMENT PERMIT A REFRAMED APPRAISAL OF TERMINAL ADDITION AS A CONTINUOUS HISTORICAL PROCESS OF CELLULAR-ENVIRONMENTAL COMPLEMENTARITY. WITHIN THIS FRAME OF REFERENCE, EVOLUTIONARY TERMINAL ADDITIONS CAN BE IDENTIFIED AS ENVIRONMENTAL INDUCTION OF EPISODIC ADJUSTMENTS TO CELL-CELL SIGNALING PATTERNS THAT YIELD THE CELLULAR-MOLECULAR PATHWAYS THAT LEAD TO DIFFERING DEVELOPMENTAL FORMS. PHENOTYPES DERIVE, THEREBY, THROUGH CELLULAR MUTUALISTIC/COMPETITIVE NICHE CONSTRUCTIONS IN RECIPROCATING RESPONSIVENESS TO ENVIRONMENTAL STRESSES AND EPIGENETIC IMPACTS. IN SUCH TERMS, TERMINAL ADDITION FLOWS ACCORDING TO A LOGIC OF CELLULAR NEEDS CONFRONTING ENVIRONMENTAL CHALLENGES OVER SPACE-TIME. A RECONCILIATION OF EVOLUTIONARY DEVELOPMENT AND TERMINAL ADDITION CAN BE ACHIEVED THROUGH A COMBINED FOCUS ON CELL-CELL SIGNALING, MOLECULAR PHYLOGENIES AND A BROADER UNDERSTANDING OF EPIGENETIC PHENOMENA AMONG EUKARYOTIC ORGANISMS. WHEN UNDERSTOOD IN THIS MANNER, TERMINAL ADDITION HAS AN IMPORTANT ROLE IN EVOLUTIONARY DEVELOPMENT, AND CHRONIC DISEASE MIGHT BE CONSIDERED AS A FORM OF 'REVERSE EVOLUTION' OF THE SELF-SAME PROCESSES. 2018 13 4513 21 MULTI-OMIC APPROACHES TO ACUTE KIDNEY INJURY AND REPAIR. THE KIDNEY HAS A REMARKABLE REGENERATIVE CAPACITY. IN RESPONSE TO ISCHEMIC OR TOXIC INJURY, PROXIMAL TUBULE CELLS CAN PROLIFERATE TO REBUILD DAMAGED TUBULES AND RESTORE KIDNEY FUNCTION. HOWEVER, SEVERE ACUTE KIDNEY INJURY (AKI) OR RECURRENT AKI EVENTS CAN LEAD TO MALADAPTIVE REPAIR AND DISEASE PROGRESSION FROM AKI TO CHRONIC KIDNEY DISEASE (CKD). THE APPLICATION OF SINGLE CELL TECHNOLOGIES HAS IDENTIFIED INJURED PROXIMAL TUBULE CELL STATES WEEKS AFTER AKI, DISTINGUISHED BY A PRO-INFLAMMATORY SENESCENT MOLECULAR SIGNATURE. EPIGENETIC STUDIES HIGHLIGHTED DYNAMIC CHANGES IN THE CHROMATIN LANDSCAPE OF THE KIDNEY FOLLOWING AKI AND DESCRIBED KEY TRANSCRIPTION FACTORS LINKED TO THE AKI RESPONSE. THE INTEGRATION OF MULTI-OMIC TECHNOLOGIES OPENS NEW POSSIBILITIES TO IMPROVE OUR UNDERSTANDING OF AKI AND THE DRIVING FORCES BEHIND THE AKI-TO-CKD TRANSITION, WITH THE ULTIMATE GOAL OF DESIGNING TAILORED DIAGNOSTIC AND THERAPEUTIC STRATEGIES TO IMPROVE AKI OUTCOMES AND PREVENT KIDNEY DISEASE PROGRESSION. 2021 14 5951 21 TARGETING THE RENIN-ANGIOTENSIN-ALDOSTERONE SYSTEM TO PREVENT HYPERTENSION AND KIDNEY DISEASE OF DEVELOPMENTAL ORIGINS. THE RENIN-ANGIOTENSIN-ALDOSTERONE SYSTEM (RAAS) IS IMPLICATED IN HYPERTENSION AND KIDNEY DISEASE. THE DEVELOPING KIDNEY CAN BE PROGRAMMED BY VARIOUS EARLY-LIFE INSULTS BY SO-CALLED RENAL PROGRAMMING, RESULTING IN HYPERTENSION AND KIDNEY DISEASE IN ADULTHOOD. THIS THEORY IS KNOWN AS DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE (DOHAD). CONVERSELY, EARLY RAAS-BASED INTERVENTIONS COULD REVERSE PROGRAM PROCESSES TO PREVENT A DISEASE FROM OCCURRING BY SO-CALLED REPROGRAMMING. IN THE CURRENT REVIEW, WE MAINLY SUMMARIZE (1) THE CURRENT KNOWLEDGE ON THE RAAS IMPLICATED IN RENAL PROGRAMMING; (2) CURRENT EVIDENCE SUPPORTING THE CONNECTIONS BETWEEN THE ABERRANT RAAS AND OTHER MECHANISMS BEHIND RENAL PROGRAMMING, SUCH AS OXIDATIVE STRESS, NITRIC OXIDE DEFICIENCY, EPIGENETIC REGULATION, AND GUT MICROBIOTA DYSBIOSIS; AND (3) AN OVERVIEW OF HOW RAAS-BASED REPROGRAMMING INTERVENTIONS MAY PREVENT HYPERTENSION AND KIDNEY DISEASE OF DEVELOPMENTAL ORIGINS. TO ACCELERATE THE TRANSITION OF RAAS-BASED INTERVENTIONS FOR PREVENTION OF HYPERTENSION AND KIDNEY DISEASE, AN EXTENDED COMPREHENSION OF THE RAAS IMPLICATED IN RENAL PROGRAMMING IS NEEDED, AS WELL AS A GREATER FOCUS ON FURTHER CLINICAL TRANSLATION. 2021 15 372 28 AN EMERGING EPIDEMIC OF NONCOMMUNICABLE DISEASES IN DEVELOPING POPULATIONS DUE TO A TRIPLE EVOLUTIONARY MISMATCH. WITH THEIR TRANSITION FROM ADVERSE TO AFFLUENT ENVIRONMENTS, DEVELOPING POPULATIONS EXPERIENCE A RAPID INCREASE IN THE NUMBER OF INDIVIDUALS WITH NONCOMMUNICABLE DISEASES. HERE, WE EMPHASIZE THAT DEVELOPING POPULATIONS ARE MORE SUSCEPTIBLE THAN WESTERN POPULATIONS TO ACQUIRE THESE CHRONIC DISEASES, BECAUSE THEIR GENETIC, CULTURAL, AND EPIGENETIC CHARACTERISTICS DO NOT MATCH WITH THE EAGERLY AWAITED AFFLUENT ENVIRONMENTS. IN REGARD TO THIS, THERE IS AN URGENT NEED FOR PUBLIC HEALTH ORGANIZATIONS TO REORGANIZE CURRENT ENVIRONMENTS IN DEVELOPING POPULATIONS SO AS TO FIT THEIR INHERITED CHARACTERISTICS. UNFORTUNATELY, THIS NEED IS NEGLECTED AS AN ESSENTIAL PART OF THE SUSTAINABLE DEVELOPMENT GOALS THAT FORM THE CORE OF THE UNITED NATIONS' POST-2015 DEVELOPMENT AGENDA. ONLY THROUGH GLOBAL COLLABORATIVE EFFORTS CAN THE ENVIRONMENTS IN DEVELOPING POPULATIONS BE REORGANIZED AND, THEREBY, THE EMERGING EPIDEMIC OF NONCOMMUNICABLE DISEASES BE STALLED. 2016 16 82 33 A NON-GENETIC BASIS FOR CANCER PROGRESSION AND METASTASIS: SELF-ORGANIZING ATTRACTORS IN CELL REGULATORY NETWORKS. IT IS COMMONLY ASSUMED THAT SOMATIC EVOLUTION DRIVES THE MULTI-STEP PROCESS THAT PRODUCES METASTATIC CANCER. BUT IT IS DIFFICULT TO RECONCILE THE INEXORABLE PROGRESSION TOWARDS METASTASIS IN VIRTUALLY ALL CARCINOMAS AND THE ASSOCIATED COMPLEX CHANGE OF CANCER CELL PHENOTYPE, CHARACTERIZED BY AN EPITHELIAL-TO-MESENCHYMAL TRANSITION, WITH THE RANDOM NATURE OF GENE MUTATIONS. GIVEN THEIR IRREVERSIBLE NATURE, IT IS ALSO DIFFICULT TO EXPLAIN WHY CERTAIN METASTATIC CARCINOMAS CAN REFORM NORMAL TISSUE BOUNDARIES AND REMAIN DORMANT FOR YEARS AT DISTANT SITES. HERE WE PROPOSE AN ENCOMPASSING CONCEPTUAL FRAMEWORK BASED ON SYSTEM-LEVEL DYNAMICS OF GENE REGULATORY NETWORKS THAT MAY HELP RECONCILE THESE INCONSISTENCIES. THE CONCEPTS OF GENE EXPRESSION STATE SPACE AND ATTRACTORS ARE INTRODUCED WHICH PROVIDE A MATHEMATICAL AND MOLECULAR BASIS FOR AN "EPIGENETIC LANDSCAPE". WE THEN DESCRIBE HOW CANCER CELLS ARE TRAPPED IN "EMBRYONIC ATTRACTORS" BECAUSE OF DISTORTIONS OF THIS LANDSCAPE CAUSED BY MUTATIONAL REWIRING OF THE REGULATORY NETWORK. THE IMPLICATIONS OF THIS CONCEPT FOR A NEW INTEGRATIVE UNDERSTANDING OF TUMOR FORMATION AND METASTATIC PROGRESSION ARE DISCUSSED. THIS FORMAL FRAMEWORK OF CANCER PROGRESSION UNITES MAINSTREAM GENETIC DETERMINISM WITH ALTERNATIVE IDEAS THAT EMPHASIZE NON-GENETIC INFLUENCES, INCLUDING CHRONIC GROWTH STIMULATION,EXTRACELLULAR MATRIX REMODELING, ALTERATION OF CELL MECHANICS AND DISRUPTION OF TISSUE ARCHITECTURE. 2006 17 5736 15 SMOKE-INDUCED CHANGES TO THE EPIGENOME PROVIDE FERTILE GROUND FOR ONCOGENIC MUTATION. HOW GENETIC AND EPIGENETIC EVENTS SYNERGIZE TO GENERATE THE ONCOGENIC STATE IS NOT WELL UNDERSTOOD. IN THIS ISSUE OF CANCER CELL, VAZ ET AL. PROVIDE COMPELLING EVIDENCE THAT EXPOSURE TO CHRONIC CIGARETTE SMOKE CAUSES PROGRESSIVE EPIGENETIC ALTERATIONS THAT PRIME FOR KEY GENETIC EVENTS TO DRIVE THE DEVELOPMENT OF LUNG CANCER. 2017 18 6350 34 THE ROLE OF EPIGENOMICS IN AQUATIC TOXICOLOGY. OVER THE PAST DECADE, THE FIELD OF MOLECULAR BIOLOGY HAS RAPIDLY INCORPORATED EPIGENETIC STUDIES TO EVALUATE ORGANISM-ENVIRONMENT INTERACTIONS THAT CAN RESULT IN CHRONIC EFFECTS. SUCH RESPONSES ARISE FROM EARLY LIFE STAGE STRESS, THE UTILIZATION OF GENETIC INFORMATION OVER AN INDIVIDUAL'S LIFE TIME, AND TRANSGENERATIONAL INHERITANCE. KNOWLEDGE OF EPIGENETIC MECHANISMS PROVIDES THE POTENTIAL FOR A COMPREHENSIVE EVALUATION OF MULTIGENERATIONAL AND HERITABLE EFFECTS FROM ENVIRONMENTAL STRESSORS, SUCH AS CONTAMINANTS. FOCUSED STUDIES HAVE PROVIDED A GREATER UNDERSTANDING OF HOW MANY RESPONSES TO ENVIRONMENTAL STRESSORS ARE DRIVEN BY EPIGENETIC MODIFIERS. WE DISCUSS THE PROMISE OF EPIGENETICS AND SUGGEST FUTURE RESEARCH DIRECTIONS WITHIN THE FIELD OF AQUATIC TOXICOLOGY, WITH A PARTICULAR FOCUS ON THE POTENTIAL FOR IDENTIFYING KEY HERITABLE MARKS WITH CONSEQUENTIAL IMPACTS AT THE ORGANISM AND POPULATION LEVELS. ENVIRON TOXICOL CHEM 2017;36:2565-2573. (C) 2017 SETAC. 2017 19 461 39 ARCHITECTS OF PITUITARY TUMOUR GROWTH. THE PITUITARY IS A MASTER GLAND RESPONSIBLE FOR THE MODULATION OF CRITICAL ENDOCRINE FUNCTIONS. PITUITARY NEUROENDOCRINE TUMOURS (PITNETS) DISPLAY A CONSIDERABLE PREVALENCE OF 1/1106, FREQUENTLY OBSERVED AS BENIGN SOLID TUMOURS. PITNETS STILL REPRESENT A CAUSE OF IMPORTANT MORBIDITY, DUE TO HORMONAL SYSTEMIC DEREGULATION, WITH SURGICAL, RADIOLOGICAL OR CHRONIC TREATMENT REQUIRED FOR ILLNESS MANAGEMENT. THE APPARENT SCARCENESS, UNCOMMON BEHAVIOUR AND MOLECULAR FEATURES OF PITNETS HAVE RESULTED IN A RELATIVELY SLOW PROGRESS IN DEPICTING THEIR PATHOGENESIS. AN APPROPRIATE INTERPRETATION OF DIFFERENT PHENOTYPES OR CELLULAR OUTCOMES DURING TUMOUR GROWTH IS DESIRABLE, SINCE HISTOPATHOLOGICAL CHARACTERIZATION STILL REMAINS THE MAIN OPTION FOR PROGNOSIS ELUCIDATION. IMPROVED KNOWLEDGE OBTAINED IN RECENT DECADES ABOUT PITUITARY TUMORIGENESIS HAS REVEALED THAT THIS PROCESS INVOLVES SEVERAL CELLULAR ROUTES IN ADDITION TO PROLIFERATION AND DEATH, WITH ITS MODULATION DEPENDING ON MANY SIGNALLING PATHWAYS RATHER THAN BEING THE RESULT OF ABNORMALITIES OF A UNIQUE PROLIFERATION PATHWAY, AS SOMETIMES PRESENTED. PITNETS CAN DISPLAY INTRINSIC HETEROGENEITY AND CELL SUBPOPULATIONS WITH DIVERSE BIOLOGICAL, GENETIC AND EPIGENETIC PARTICULARITIES, INCLUDING TUMORIGENIC POTENTIAL. HENCE, TO OBTAIN A BETTER UNDERSTANDING OF PITNET GROWTH NEW APPROACHES ARE REQUIRED AND THE SYSTEMATIZATION OF THE AVAILABLE DATA, WITH THE ROLE OF CELL DEATH PROGRAMS, AUTOPHAGY, STEM CELLS, CELLULAR SENESCENCE, MITOCHONDRIAL FUNCTION, METABOLIC REPROGRAMMING STILL BEING EMERGING FIELDS IN PITUITARY RESEARCH. WE ENVISAGE THAT THROUGH THE COMBINATION OF MOLECULAR, GENETIC AND EPIGENETIC DATA, TOGETHER WITH THE IMPROVED MORPHOLOGICAL, BIOCHEMICAL, PHYSIOLOGICAL AND METABOLICALLY KNOWLEDGE ON PITUITARY NEOPLASTIC POTENTIAL ACCUMULATED IN RECENT DECADES, TUMOUR CLASSIFICATION SCHEMES WILL BECOME MORE ACCURATE REGARDING TUMOUR ORIGIN, BEHAVIOUR AND PLAUSIBLE CLINICAL RESULTS. 2022 20 1366 23 DEVELOPMENTAL ORIGINS OF CHRONIC KIDNEY DISEASE: SHOULD WE FOCUS ON EARLY LIFE? CHRONIC KIDNEY DISEASE (CKD) IS BECOMING A GLOBAL BURDEN, DESPITE RECENT ADVANCES IN MANAGEMENT. CKD CAN BEGIN IN EARLY LIFE BY SO-CALLED "DEVELOPMENTAL PROGRAMMING" OR "DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE" (DOHAD). EARLY-LIFE INSULTS CAUSE STRUCTURAL AND FUNCTIONAL CHANGES IN THE DEVELOPING KIDNEY, WHICH IS CALLED RENAL PROGRAMMING. EPIDEMIOLOGICAL AND EXPERIMENTAL EVIDENCE SUPPORTS THE PROPOSITION THAT EARLY-LIFE ADVERSE EVENTS LEAD TO RENAL PROGRAMMING AND MAKE SUBJECTS VULNERABLE TO DEVELOPING CKD AND ITS COMORBIDITIES IN LATER LIFE. IN ADDITION TO LOW NEPHRON ENDOWMENT, SEVERAL MECHANISMS HAVE BEEN PROPOSED FOR RENAL PROGRAMMING. THE DOHAD CONCEPT OPENS A NEW WINDOW TO OFFSET THE PROGRAMMING PROCESS IN EARLY LIFE TO PREVENT THE DEVELOPMENT OF ADULT KIDNEY DISEASE, NAMELY REPROGRAMMING. HERE, WE REVIEW THE KEY THEMES ON THE DEVELOPMENTAL ORIGINS OF CKD. WE HAVE PARTICULARLY FOCUSED ON THE FOLLOWING AREAS: EVIDENCE FROM HUMAN STUDIES SUPPORT FETAL PROGRAMMING OF KIDNEY DISEASE; INSIGHT FROM ANIMAL MODELS OF RENAL PROGRAMMING; HYPOTHETICAL MECHANISMS OF RENAL PROGRAMMING; ALTERATIONS OF RENAL TRANSCRIPTOME IN RESPONSE TO EARLY-LIFE INSULTS; AND THE APPLICATION OF REPROGRAMMING INTERVENTIONS TO PREVENT THE PROGRAMMING OF KIDNEY DISEASE. 2017