1    17 114 5' FLANKING REGION OF VAR GENES NUCLEATE HISTONE MODIFICATION PATTERNS LINKED TO PHENOTYPIC INHERITANCE OF VIRULENCE TRAITS IN MALARIA PARASITES. IN THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM ANTIGENIC VARIATION FACILITATES LONG-TERM CHRONIC INFECTION OF THE HOST. THIS IS ACHIEVED BY SEQUENTIAL EXPRESSION OF A SINGLE MEMBER OF THE 60-MEMBER VAR FAMILY. HERE WE SHOW THAT THE 5' FLANKING REGION NUCLEATES EPIGENETIC EVENTS STRONGLY LINKED TO THE MAINTENANCE OF MONO-ALLELIC VAR GENE EXPRESSION PATTERN DURING PARASITE PROLIFERATION. TRI- AND DIMETHYLATION OF HISTONE H3 LYSINE 4 PEAK IN THE 5' UPSTREAM REGION OF TRANSCRIBED VAR AND DURING THE POISED STATE (NON-TRANSCRIBED PHASE OF VAR GENES DURING THE 48 H ASEXUAL LIFE CYCLE), 'BOOKMARKING' THIS MEMBER FOR RE-ACTIVATION AT THE ONSET OF THE NEXT CYCLE. HISTONE H3 LYSINE 9 TRIMETHYLATION ACTS AS AN ANTAGONIST TO LYSINE 4 METHYLATION TO ESTABLISH STABLY SILENT VAR GENE STATES ALONG THE 5' FLANKING AND CODING REGION. FURTHERMORE, WE SHOW THAT COMPETITION EXISTS BETWEEN H3K9 METHYLATION AND H3K9 ACETYLATION IN THE 5' FLANKING REGION AND THAT THESE MARKS CONTRIBUTE EPIGENETICALLY TO REPRESSING OR ACTIVATING VAR GENE EXPRESSION. OUR WORK POINTS TO A PIVOTAL ROLE OF THE HISTONE METHYL MARK WRITING AND READING MACHINERY IN THE PHENOTYPIC INHERITANCE OF VIRULENCE TRAITS IN THE MALARIA PARASITE.	2007	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
2  1899  29 ENERGY BALANCE MODULATION IMPACTS EPIGENETIC REPROGRAMMING, ERALPHA AND ERBETA EXPRESSION, AND MAMMARY TUMOR DEVELOPMENT IN MMTV-NEU TRANSGENIC MICE. THE ASSOCIATION BETWEEN OBESITY AND BREAST CANCER RISK AND PROGNOSIS IS WELL ESTABLISHED IN ESTROGEN RECEPTOR (ER)-POSITIVE DISEASE BUT LESS CLEAR IN HER2-POSITIVE DISEASE. HERE, WE REPORT PRECLINICAL EVIDENCE SUGGESTING WEIGHT MAINTENANCE THROUGH CALORIE RESTRICTION (CR) MAY LIMIT RISK OF HER2-POSITIVE BREAST CANCER. IN FEMALE MMTV-HER2/NEU TRANSGENIC MICE, WE FOUND THAT ERALPHA AND ERBETA EXPRESSION, MAMMARY TUMORIGENESIS, AND SURVIVAL ARE ENERGY BALANCE DEPENDENT IN ASSOCIATION WITH EPIGENETIC REPROGRAMMING. MICE WERE RANDOMIZED TO RECEIVE A CR, OVERWEIGHT-INDUCING, OR DIET-INDUCED OBESITY REGIMEN (N = 27/GROUP). SUBSETS OF MICE (N = 4/GROUP/TIME POINT) WERE EUTHANIZED AFTER 1, 3, AND 5 MONTHS TO CHARACTERIZE DIET-DEPENDENT METABOLIC, TRANSCRIPTIONAL, AND EPIGENETIC PERTURBATIONS. REMAINING MICE WERE FOLLOWED UP TO 22 MONTHS. RELATIVE TO THE OVERWEIGHT AND DIET-INDUCED OBESITY REGIMENS, CR DECREASED BODY WEIGHT, ADIPOSITY, AND SERUM METABOLIC HORMONES AS EXPECTED AND ALSO ELICITED AN INCREASE IN MAMMARY ERALPHA AND ERBETA EXPRESSION. INCREASED DNA METHYLATION ACCOMPANIED THIS PATTERN, PARTICULARLY AT CPG DINUCLEOTIDES LOCATED WITHIN BINDING OR FLANKING REGIONS FOR THE TRANSCRIPTIONAL REGULATOR CCCTC-BINDING FACTOR OF ESR1 AND ESR2, CONSISTENT WITH SUSTAINED TRANSCRIPTIONAL ACTIVATION OF ERALPHA AND ERBETA. MAMMARY EXPRESSION OF THE DNA METHYLATION ENZYME DNMT1 WAS STABLE IN CR MICE BUT INCREASED OVER TIME IN OVERWEIGHT AND DIET-INDUCED OBESITY MICE, SUGGESTING CR OBVIATES EPIGENETIC ALTERATIONS CONCURRENT WITH CHRONIC EXCESS ENERGY INTAKE. IN THE SURVIVAL STUDY, CR ELICITED A SIGNIFICANT SUPPRESSION IN SPONTANEOUS MAMMARY TUMORIGENESIS. OVERALL, OUR FINDINGS SUGGEST A MECHANISTIC RATIONALE TO PREVENT OR REVERSE EXCESS BODY WEIGHT AS A STRATEGY TO REDUCE HER2-POSITIVE BREAST CANCER RISK. CANCER RES; 77(9); 2500-11. (C)2017 AACR.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
3  3052  25 GENOME-WIDE ASSOCIATION ANALYSIS OF PAIN SEVERITY IN DYSMENORRHEA IDENTIFIES ASSOCIATION AT CHROMOSOME 1P13.2, NEAR THE NERVE GROWTH FACTOR LOCUS. DYSMENORRHEA IS A COMMON CHRONIC PELVIC PAIN SYNDROME AFFECTING WOMEN OF CHILDBEARING POTENTIAL. FAMILY STUDIES SUGGEST THAT GENETIC BACKGROUND INFLUENCES THE SEVERITY OF DYSMENORRHEA, BUT GENETIC PREDISPOSITION AND MOLECULAR MECHANISMS UNDERLYING DYSMENORRHEA ARE NOT UNDERSTOOD. IN THIS STUDY, WE CONDUCT THE FIRST GENOME-WIDE ASSOCIATION STUDY TO IDENTIFY GENETIC FACTORS ASSOCIATED WITH DYSMENORRHEA PAIN SEVERITY. A COHORT OF FEMALES OF EUROPEAN DESCENT (N = 11,891) AGED 18 TO 45 YEARS RATED THEIR AVERAGE DYSMENORRHEA PAIN SEVERITY. WE USED A LINEAR REGRESSION MODEL ADJUSTING FOR AGE AND BODY MASS INDEX, IDENTIFYING ONE GENOME-WIDE SIGNIFICANT (P < 5 X 10) ASSOCIATION (RS7523086, P = 4.1 X 10, EFFECT SIZE 0.1 [95% CONFIDENCE INTERVAL, 0.074-0.126]). THIS SINGLE NUCLEOTIDE POLYMORPHISM IS COLOCALISING WITH NGF, ENCODING NERVE GROWTH FACTOR. THE PRESENCE OF ONE RISK ALLELE CORRESPONDS TO A PREDICTED 0.1-POINT INCREASE IN PAIN INTENSITY ON A 4-POINT ORDINAL PAIN SCALE. THE PUTATIVE EFFECTS ON NGF FUNCTION AND/OR EXPRESSION REMAIN UNKNOWN. HOWEVER, GENETIC VARIATION COLOCALISES WITH ACTIVE EPIGENETIC MARKS IN FAT AND OVARY TISSUES, AND EXPRESSION LEVELS IN AORTA TISSUE OF A NONCODING RNA FLANKING NGF CORRELATE. PARTICIPANTS REPORTING EXTREME DYSMENORRHEA PAIN WERE MORE LIKELY TO REPORT BEING POSITIVE FOR ENDOMETRIOSIS, POLYCYSTIC OVARIAN SYNDROME, DEPRESSION, AND OTHER PSYCHIATRIC DISORDERS. OUR RESULTS INDICATE THAT DYSMENORRHEA PAIN SEVERITY IS PARTLY GENETICALLY DETERMINED. NGF ALREADY HAS AN ESTABLISHED ROLE IN CHRONIC PAIN DISORDERS, AND OUR FINDINGS SUGGEST THAT NGF MAY BE AN IMPORTANT MEDIATOR FOR GYNAECOLOGICAL/PELVIC PAIN IN THE VISCERA.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
4  3459  19 HYPOMETHYLATION OF NERVE GROWTH FACTOR (NGF) PROMOTES BINDING OF C/EBPALPHA AND CONTRIBUTES TO INFLAMMATORY HYPERALGESIA IN RATS. BACKGROUND: CHRONIC PAIN USUALLY ACCOMPANIED BY TISSUE DAMAGE AND INFLAMMATION. HOWEVER, THE PATHOGENESIS OF CHRONIC PAIN REMAINS UNCLEAR. METHODS: WE INVESTIGATED THE ROLE OF NERVE GROWTH FACTOR (NGF) IN CHRONIC INFLAMMATORY PAIN INDUCED BY COMPLETE FREUND'S ADJUVANT (CFA), EXPLORED THE METHYLATION STATUS OF CPG ISLANDS IN THE PROMOTER REGION OF THE NGF GENE, AND CLARIFIED THE FUNCTION AND MECHANISM OF C/EBPALPHA-NGF SIGNALING PATHWAY FROM EPIGENETIC PERSPECTIVE IN THE CHRONIC INFLAMMATORY PAIN MODEL. RESULTS: CFA INDUCED SIGNIFICANT HYPERALGESIA AND CONTINUOUS UPREGULATION OF NGF MRNA AND PROTEIN LEVELS IN THE L4-6 DORSAL ROOT GANGLIONS (DRGS) IN RATS. HYPOMETHYLATION OF CPG ISLANDS OCCURRED IN THE NGF GENE PROMOTER REGION AFTER CFA TREATMENT. AT THE SAME TIME, THE MIR-29B EXPRESSION LEVEL WAS SIGNIFICANTLY INCREASED, WHILE THE DNA METHYLTRANSFERASE 3B (DNMT3B) LEVEL REDUCED SIGNIFICANTLY. MOREOVER, CFA TREATMENT PROMOTED BINDING OF C/EBPALPHA TO THE NGF GENE PROMOTER REGION AND C/EBPALPHA SIRNA TREATMENT OBVIOUSLY DECREASED EXPRESSION OF NGF LEVELS AND ALSO ALLEVIATE INFLAMMATORY HYPERALGESIA SIGNIFICANTLY IN RATS. CONCLUSION: COLLECTIVELY, THE RESULTS INDICATED THAT CFA LEADS TO THE UPREGULATION OF MIR-29B LEVEL, WHICH REPRESSES THE EXPRESSION OF DNMT3B, ENHANCES THE DEMETHYLATION OF THE NGF GENE PROMOTER REGION, AND PROMOTES THE BINDING OF C/EBPALPHA WITH THE NGF GENE PROMOTER, THUS RESULTS IN THE UPREGULATION OF NGF GENE EXPRESSION AND MAINTENANCE OF CHRONIC INFLAMMATORY PAIN.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
5  1854  24 ELEVATED SEMINAL PLASMA ESTRADIOL AND EPIGENETIC INACTIVATION OF ESR1 AND ESR2 IS ASSOCIATED WITH CP/CPPS. CHRONIC PROSTATITIS/CHRONIC PELVIC PAIN SYNDROME (CP/CPPS) IS ASSOCIATED WITH URINARY TRACT SYMPTOMS AND HORMONAL IMBALANCES AMONGST OTHERS. THE HETEROGENEOUS CLINICAL PRESENTATION, UNEXPLORED MOLECULAR BACKGROUND AND LACK OF PROSTATE BIOPSIES COMPLICATE THERAPY. HERE, USING LIQUID BIOPSIES, WE PERFORMED A COMPREHENSIVE TRANSLATIONAL STUDY ON MEN DIAGNOSED WITH CP/CPPS TYPE III (N= 50; MEDIAN AGE 39.8, RANGE 23-65) AND AGE-MATCHED CONTROLS (N= 61; MEDIAN AGE 36.8, RANGE 20-69), CONSIDERING BIOCHEMICAL PARAMETERS OF BLOOD AND EJACULATES, AND EPIGENETIC REGULATION OF THE ESTROGEN RECEPTOR GENES (ESR1 AND ESR2) IN LEUKOCYTES ISOLATED FROM BLOOD (SYSTEMIC REGULATION) AND IN SOMATIC CELLS ISOLATED FROM EJACULATES (LOCAL REGULATION). WE FOUND ELEVATED 17BETA-ESTRADIOL (E(2)) LEVELS IN SEMINAL PLASMA, BUT NOT IN BLOOD PLASMA, THAT WAS SIGNIFICANTLY ASSOCIATED WITH CP/CPPS AND IMPAIRED URINARY TRACT SYMPTOMS. IN EJACULATED SOMATIC CELLS OF CP/CPPS PATIENTS WE FOUND THAT ESR1 AND ESR2 WERE BOTH SIGNIFICANTLY HIGHER METHYLATED IN CPG-PROMOTERS AND EXPRESSIONALLY DOWN-REGULATED IN COMPARISON TO CONTROLS. MAST CELLS ARE REPORTED TO CONTRIBUTE TO CP/CPPS AND ARE ESTROGEN RESPONSIVE. CONSISTENT WITH THIS, WE FOUND THAT E(2) -TREATMENT OF HUMAN MAST CELL LINES (HMC-1 AND LAD2) RESULTED IN ALTERED CYTOKINE AND CHEMOKINE EXPRESSION. INTERESTINGLY, IN HMC-1 CELLS, POSSESSING EPIGENETICALLY INACTIVATED ESR1 AND ESR2, E(2) -TREATMENT LED TO A REDUCED TRANSCRIPTION OF A NUMBER OF INFLAMMATORY GENES. OVERALL, THESE DATA SUGGEST THAT ELEVATED LOCAL E(2) LEVELS ASSOCIATE WITH AN EPIGENETIC DOWN-REGULATION OF THE ESTROGEN RECEPTORS AND HAVE A PROMINENT ROLE IN CP/CPPS. INVESTIGATING E(2) LEVELS IN SEMEN COULD THEREFORE SERVE AS A PROMISING BIOMARKER TO SELECT PATIENTS FOR ESTROGEN TARGETED THERAPY.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
6   603  21 BETULINIC ACID INHIBITS ENDOMETRIOSIS THROUGH SUPPRESSION OF ESTROGEN RECEPTOR BETA SIGNALING PATHWAY. ENDOMETRIOSIS IS AN INFLAMMATORY GYNECOLOGICAL DISORDER CHARACTERIZED BY ENDOMETRIAL TISSUE GROWTH LOCATED OUTSIDE OF THE UTERINE CAVITY IN ADDITION TO CHRONIC PELVIC PAIN AND INFERTILITY. IN THIS STUDY, WE AIM TO DEVELOP A POTENTIAL THERAPEUTIC TREATMENT BASED ON THE PATHOGENESIS AND MECHANISM OF ENDOMETRIOSIS. OUR PRELIMINARY DATA SHOWED THAT THE EXPRESSION OF ESTROGEN RECEPTOR BETA (ERBETA) WAS SIGNIFICANTLY INCREASED, WHILE ERALPHA WAS SIGNIFICANTLY DECREASED, IN ENDOMETRIOTIC CELLS COMPARED TO NORMAL ENDOMETRIAL CELLS. FURTHER INVESTIGATION SHOWED THAT BETULINIC ACID (BA) TREATMENT SUPPRESSED ERBETA EXPRESSION THROUGH EPIGENETIC MODIFICATION ON THE ERBETA PROMOTER, WHILE HAD NO EFFECT ON ERALPHA EXPRESSION. IN ADDITION, BA TREATMENT SUPPRESSES ERBETA TARGET GENES, INCLUDING SUPEROXIDE DISMUTASE 2 (SOD2), NUCLEAR RESPIRATORY FACTOR-1 (NRF1), CYCLOOXYGENASE 2 (COX2), AND MATRIX METALLOPROTEINASE-1 (MMP1), SUBSEQUENTLY INCREASING OXIDATIVE STRESS, TRIGGERING MITOCHONDRIAL DYSFUNCTION, DECREASING ELEVATED PROINFLAMMATORY CYTOKINES, AND EVENTUALLY SUPPRESSING ENDOMETRIOTIC CELL PROLIFERATION, MIMICKING THE EFFECT OF ERBETA KNOCKDOWN. ON THE OTHER HAND, GAIN OF ERBETA BY LENTIVIRUS INFECTION IN NORMAL ENDOMETRIAL CELLS RESULTED IN INCREASED CELL PROLIFERATION AND PROINFLAMMATORY CYTOKINE RELEASE, WHILE BA TREATMENT DIMINISHED THIS EFFECT THROUGH ERBETA SUPPRESSION WITH SUBSEQUENT OXIDATIVE STRESS AND APOPTOSIS. OUR RESULTS INDICATE THAT ERBETA MAY BE A MAJOR DRIVING FORCE FOR THE DEVELOPMENT OF ENDOMETRIOSIS, WHILE BA INHIBITS ENDOMETRIOSIS THROUGH SPECIFIC SUPPRESSION OF THE ERBETA SIGNALING PATHWAY. THIS STUDY PROVIDES A NOVEL THERAPEUTIC STRATEGY FOR ENDOMETRIOSIS TREATMENT THROUGH BA-MEDIATED ERBETA SUPPRESSION.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
7  1219  38 CRISPR/CAS9 GENOME EDITING REVEALS THAT THE INTRON IS NOT ESSENTIAL FOR VAR2CSA GENE ACTIVATION OR SILENCING IN PLASMODIUM FALCIPARUM. PLASMODIUM FALCIPARUM RELIES ON MONOALLELIC EXPRESSION OF 1 OF 60 VAR VIRULENCE GENES FOR ANTIGENIC VARIATION AND HOST IMMUNE EVASION. EACH VAR GENE CONTAINS A CONSERVED INTRON WHICH HAS BEEN IMPLICATED IN PREVIOUS STUDIES IN BOTH ACTIVATION AND REPRESSION OF TRANSCRIPTION VIA SEVERAL EPIGENETIC MECHANISMS, INCLUDING INTERACTION WITH THE VAR PROMOTER, PRODUCTION OF LONG NONCODING RNAS (LNCRNAS), AND LOCALIZATION TO REPRESSIVE PERINUCLEAR SITES. HOWEVER, FUNCTIONAL STUDIES HAVE RELIED PRIMARILY ON ARTIFICIAL EXPRESSION CONSTRUCTS. USING THE RECENTLY DEVELOPED P. FALCIPARUM CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS (CRISPR)/CAS9 SYSTEM, WE DIRECTLY DELETED THE VAR2CSA P. FALCIPARUM 3D7_1200600 (PF3D7_1200600) ENDOGENOUS INTRON, RESULTING IN AN INTRONLESS VAR GENE IN A NATURAL, MARKER-FREE CHROMOSOMAL CONTEXT. DELETION OF THE VAR2CSA INTRON RESULTED IN AN UPREGULATION OF TRANSCRIPTION OF THE VAR2CSA GENE IN RING-STAGE PARASITES AND SUBSEQUENT EXPRESSION OF THE PFEMP1 PROTEIN IN LATE-STAGE PARASITES. INTRON DELETION DID NOT AFFECT THE NORMAL TEMPORAL REGULATION AND SUBSEQUENT TRANSCRIPTIONAL SILENCING OF THE VAR GENE IN TROPHOZOITES BUT DID RESULT IN INCREASED RATES OF VAR GENE SWITCHING IN SOME MUTANT CLONES. TRANSCRIPTIONAL REPRESSION OF THE INTRONLESS VAR2CSA GENE COULD BE ACHIEVED VIA LONG-TERM CULTURE OR PANNING WITH THE CD36 RECEPTOR, AFTER WHICH REACTIVATION WAS POSSIBLE WITH CHONDROITIN SULFATE A (CSA) PANNING. THESE DATA SUGGEST THAT THE VAR2CSA INTRON IS NOT REQUIRED FOR SILENCING OR ACTIVATION IN RING-STAGE PARASITES BUT POINT TO A SUBTLE ROLE IN REGULATION OF SWITCHING WITHIN THE VAR GENE FAMILY.IMPORTANCEPLASMODIUM FALCIPARUM IS THE MOST VIRULENT SPECIES OF MALARIA PARASITE, CAUSING HIGH RATES OF MORBIDITY AND MORTALITY IN THOSE INFECTED. CHRONIC INFECTION DEPENDS ON AN IMMUNE EVASION MECHANISM TERMED ANTIGENIC VARIATION, WHICH IN TURN RELIES ON MONOALLELIC EXPRESSION OF 1 OF ~60 VAR GENES. UNDERSTANDING ANTIGENIC VARIATION AND THE TRANSCRIPTIONAL REGULATION OF MONOALLELIC EXPRESSION IS IMPORTANT FOR DEVELOPING DRUGS AND/OR VACCINES. THE VAR GENE FAMILY ENCODES THE ANTIGENIC SURFACE PROTEINS THAT DECORATE INFECTED ERYTHROCYTES. UNTIL RECENTLY, STUDYING THE UNDERLYING GENETIC ELEMENTS THAT REGULATE MONOALLELIC EXPRESSION IN P. FALCIPARUM WAS DIFFICULT, AND MOST STUDIES RELIED ON ARTIFICIAL SYSTEMS SUCH AS EPISOMAL REPORTER GENES. OUR STUDY WAS THE FIRST TO USE CRISPR/CAS9 GENOME EDITING FOR THE FUNCTIONAL STUDY OF AN IMPORTANT, CONSERVED GENETIC ELEMENT OF VAR GENES-THE INTRON-IN AN ENDOGENOUS, EPISOME-FREE MANNER. OUR FINDINGS SHED LIGHT ON THE ROLE OF THE VAR GENE INTRON IN TRANSCRIPTIONAL REGULATION OF MONOALLELIC EXPRESSION.	2017	

8   129  44 A UNIQUE VIRULENCE GENE OCCUPIES A PRINCIPAL POSITION IN IMMUNE EVASION BY THE MALARIA PARASITE PLASMODIUM FALCIPARUM. MUTUALLY EXCLUSIVE GENE EXPRESSION, WHEREBY ONLY ONE MEMBER OF A MULTI-GENE FAMILY IS SELECTED FOR ACTIVATION, IS USED BY THE MALARIA PARASITE PLASMODIUM FALCIPARUM TO ESCAPE THE HUMAN IMMUNE SYSTEM AND PERPETUATE LONG-TERM, CHRONIC INFECTIONS. A FAMILY OF GENES CALLED VAR ENCODES THE CHIEF ANTIGENIC AND VIRULENCE DETERMINANT OF P. FALCIPARUM MALARIA. VAR GENES ARE TRANSCRIBED IN A MUTUALLY EXCLUSIVE MANNER, WITH SWITCHING BETWEEN ACTIVE GENES RESULTING IN ANTIGENIC VARIATION. WHILE RECENT WORK HAS SHED CONSIDERABLE LIGHT ON THE EPIGENETIC BASIS FOR VAR GENE ACTIVATION AND SILENCING, HOW SWITCHING IS CONTROLLED REMAINS A MYSTERY. IN PARTICULAR, SWITCHING SEEMS NOT TO BE RANDOM, BUT INSTEAD APPEARS TO BE COORDINATED TO RESULT IN TIMELY ACTIVATION OF INDIVIDUAL GENES LEADING TO SEQUENTIAL WAVES OF ANTIGENICALLY DISTINCT PARASITE POPULATIONS. THE MOLECULAR BASIS FOR THIS APPARENT COORDINATION IS UNKNOWN. HERE WE SHOW THAT VAR2CSA, AN UNUSUAL AND HIGHLY CONSERVED VAR GENE, OCCUPIES A UNIQUE POSITION WITHIN THE VAR GENE SWITCHING HIERARCHY. INDUCTION OF SWITCHING THROUGH THE DESTABILIZATION OF VAR SPECIFIC CHROMATIN USING BOTH GENETIC AND CHEMICAL METHODS REPEATEDLY LED TO THE RAPID AND EXCLUSIVE ACTIVATION OF VAR2CSA. ADDITIONAL EXPERIMENTS DEMONSTRATED THAT THESE REPRESENT "TRUE" SWITCHING EVENTS AND NOT SIMPLY DE-SILENCING OF THE VAR2CSA PROMOTER, AND THAT ACTIVATION IS LIMITED TO THE UNIQUE LOCUS ON CHROMOSOME 12. COMBINED WITH TRANSLATIONAL REPRESSION OF VAR2CSA TRANSCRIPTS, FREQUENT "DEFAULT" SWITCHING TO THIS LOCUS AND DETECTION OF VAR2CSA UNTRANSLATED TRANSCRIPTS IN NON-PREGNANT INDIVIDUALS, THESE DATA SUGGEST THAT VAR2CSA COULD PLAY A CENTRAL ROLE IN COORDINATING SWITCHING, FULFILLING A PREDICTION MADE BY MATHEMATICAL MODELS DERIVED FROM POPULATION SWITCHING PATTERNS. THESE STUDIES PROVIDE THE FIRST INSIGHTS INTO THE MECHANISMS BY WHICH VAR GENE SWITCHING IS COORDINATED AS WELL AS AN EXAMPLE OF HOW A PHARMACOLOGICAL AGENT CAN DISRUPT ANTIGENIC VARIATION IN PLASMODIUM FALCIPARUM.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
9  3206  26 HDAC9 IS AN EPIGENETIC REPRESSOR OF KIDNEY ANGIOTENSINOGEN ESTABLISHING A SEX DIFFERENCE. BACKGROUND: SEXUAL DIFFERENCE HAS BEEN SHOWN IN THE PATHOGENESIS OF CHRONIC KIDNEY DISEASE INDUCED BY HYPERTENSION. FEMALES ARE PROTECTED FROM HYPERTENSION AND RELATED END-ORGAN DAMAGE. AUGMENTATION OF RENAL PROXIMAL TUBULAR ANGIOTENSINOGEN (AGT) EXPRESSION CAN PROMOTE INTRARENAL ANGIOTENSIN FORMATION AND THE DEVELOPMENT OF ASSOCIATED HYPERTENSION AND KIDNEY INJURY. FEMALE RODENTS EXHIBIT LOWER INTRARENAL AGT LEVELS THAN MALES UNDER NORMAL CONDITIONS, SUGGESTING THAT THE SUPPRESSED INTRARENAL AGT PRODUCTION BY PROGRAMMED MECHANISMS IN FEMALES MAY PROVIDE PROTECTION FROM THESE DISEASES. THIS STUDY WAS PERFORMED TO EXAMINE WHETHER EPIGENETIC MECHANISMS SERVE AS REPRESSORS OF AGT. METHODS: MALE AND FEMALE SPRAGUE DAWLEY RATS WERE USED TO INVESTIGATE SEX DIFFERENCES OF SYSTEMIC, HEPATIC, AND INTRARENAL AGT LEVELS. ALL HISTONE DEACETYLASE (HDAC) MRNA LEVELS IN THE KIDNEYS WERE DETERMINED USING A PCR ARRAY. HDAC9 PROTEIN EXPRESSION IN THE KIDNEYS AND CULTURED RENAL PROXIMAL TUBULAR CELLS (PTC) WAS ANALYZED BY WESTERN BLOT ANALYSIS AND IMMUNOHISTOCHEMISTRY. THE EFFECTS OF HDAC9 ON AGT EXPRESSION WERE EVALUATED BY USING AN INHIBITOR AND SIRNA. CHIP ASSAY WAS PERFORMED TO INVESTIGATE THE INTERACTION BETWEEN THE AGT PROMOTER AND HDAC9. RESULTS: PLASMA AND LIVER AGT LEVELS DID NOT SHOW DIFFERENCES BETWEEN MALE AND FEMALE SPRAGUE-DAWLEY RATS. IN CONTRAST, FEMALES EXHIBITED LOWER AGT LEVELS THAN MALES IN THE RENAL CORTEX AND URINE. IN THE ABSENCE OF SUPPLEMENTED SEX HORMONES, PRIMARY CULTURED RENAL CORTICAL CELLS ISOLATED FROM FEMALE RATS SUSTAINED LOWER AGT LEVELS THAN THOSE FROM MALES, SUGGESTING THAT THE KIDNEYS HAVE A UNIQUE MECHANISM OF AGT REGULATION CONTROLLED BY EPIGENETIC FACTORS RATHER THAN SEX HORMONES. HDAC9 MRNA AND PROTEIN LEVELS WERE HIGHER IN THE RENAL CORTEX OF FEMALE RATS VERSUS MALE RATS (7.09 +/- 0.88, RATIO TO MALE) WHILE OTHER HDACS DID NOT EXHIBIT A SEX DIFFERENCE. HDAC9 EXPRESSION WAS LOCALIZED IN PTC WHICH ARE THE PRIMARY SOURCE OF INTRARENAL AGT. IMPORTANTLY, HDAC9 KNOCKDOWN AUGMENTED AGT MRNA (1.92 +/- 0.35-FOLD) AND PROTEIN (2.25 +/- 0.50-FOLD) LEVELS, SIMILAR TO AN HDAC9 INHIBITOR. FURTHERMORE, AN INTERACTION BETWEEN HDAC9 AND A DISTAL 5' FLANKING REGION OF AGT VIA A HISTONE COMPLEX CONTAINING H3 AND H4 WAS DEMONSTRATED. CONCLUSIONS: THESE RESULTS INDICATE THAT HDAC9 IS A NOVEL SUPPRESSING FACTOR INVOLVED IN AGT REGULATION IN PTC, LEADING TO LOW LEVELS OF INTRARENAL AGT IN FEMALES. THESE FINDINGS WILL HELP TO DELINEATE MECHANISMS UNDERLYING SEX DIFFERENCES IN THE DEVELOPMENT OF HYPERTENSION AND RENIN-ANGIOTENSIN SYSTEM (RAS) ASSOCIATED KIDNEY INJURY.	2017	
                                                                                                                                     
10  3473  27 IDENTIFICATION OF A NOVEL, METHYLATION-DEPENDENT, RUNX2 REGULATORY REGION ASSOCIATED WITH OSTEOARTHRITIS RISK. OSTEOARTHRITIS (OA) IS A COMMON, MULTIFACTORIAL AND POLYGENIC SKELETAL DISEASE THAT, IN ITS SEVEREST FORM, REQUIRES JOINT REPLACEMENT SURGERY TO RESTORE MOBILITY AND TO RELIEVE CHRONIC PAIN. USING TISSUES FROM THE ARTICULATING JOINTS OF 260 PATIENTS WITH OA AND A RANGE OF IN VITRO EXPERIMENTS, INCLUDING CRISPR-CAS9, WE HAVE CHARACTERIZED AN INTERGENIC REGULATORY ELEMENT. HERE, GENOTYPE AT AN OA RISK LOCUS CORRELATES WITH DIFFERENTIAL DNA METHYLATION, WITH ALTERED GENE EXPRESSION OF BOTH A TRANSCRIPTIONAL REGULATOR (RUNX2), AND A CHROMATIN REMODELLING PROTEIN (SUPT3H). RUNX2 IS A STRONG CANDIDATE FOR OA SUSCEPTIBILITY, WITH ITS ENCODED PROTEIN BEING ESSENTIAL FOR SKELETOGENESIS AND HEALTHY JOINT FUNCTION. THE OA RISK LOCUS INCLUDES SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) LOCATED WITHIN AND FLANKING THE DIFFERENTIALLY METHYLATED REGION (DMR). THE OA ASSOCIATION SNP, RS10948172, DEMONSTRATES PARTICULARLY STRONG CORRELATION WITH METHYLATION, AND TWO INTERGENIC SNPS FALLING WITHIN THE DMR (RS62435998 AND RS62435999) DEMONSTRATE GENETIC AND EPIGENETIC EFFECTS ON THE REGULATORY ACTIVITY OF THIS REGION. WE THEREFORE POSIT THAT THE OA SIGNAL MEDIATES ITS EFFECT BY MODULATING THE METHYLATION OF THE REGULATORY ELEMENT, WHICH THEN IMPACTS ON GENE EXPRESSION, WITH RUNX2 BEING THE PRINCIPAL TARGET. OUR STUDY HIGHLIGHTS THE INTERPLAY BETWEEN DNA METHYLATION, OA GENETIC RISK AND THE DOWNSTREAM REGULATION OF GENES CRITICAL TO NORMAL JOINT FUNCTION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
11  2091  34 EPIGENETIC DYSREGULATION OF VIRULENCE GENE EXPRESSION IN SEVERE PLASMODIUM FALCIPARUM MALARIA. CHRONIC INFECTIONS WITH THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM DEPEND ON ANTIGENIC VARIATION. P. FALCIPARUM ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1), THE MAJOR ERYTHROCYTE SURFACE ANTIGEN MEDIATING PARASITE SEQUESTRATION IN THE MICROVASCULATURE, IS ENCODED IN PARASITES BY A HIGHLY DIVERSE FAMILY OF VAR GENES. ANTIGENIC SWITCHING IS MEDIATED BY CLONAL VARIATION IN VAR EXPRESSION, AND RECENT IN VITRO STUDIES HAVE DEMONSTRATED A ROLE FOR EPIGENETIC PROCESSES IN VAR REGULATION. EXPRESSION OF PARTICULAR PFEMP1 VARIANTS MAY RESULT IN PARASITE ENRICHMENT IN DIFFERENT TISSUES, A FACTOR IN THE DEVELOPMENT OF SEVERE DISEASE. HERE, WE STUDY IN VIVO HUMAN INFECTIONS AND PROVIDE EVIDENCE THAT INFECTION-INDUCED STRESS RESPONSES IN THE HOST CAN MODIFY PFEMP1 EXPRESSION VIA THE PERTURBATION OF EPIGENETIC MECHANISMS. OUR WORK SUGGESTS THAT SEVERE DISEASE MAY NOT BE THE DIRECT RESULT OF AN ADAPTIVE VIRULENCE STRATEGY TO MAXIMIZE PARASITE SURVIVAL BUT THAT IT MAY INDICATE A LOSS OF CONTROL OF THE CAREFULLY REGULATED PROCESS OF ANTIGENIC SWITCHING THAT MAINTAINS CHRONIC INFECTIONS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
12  2300  25 EPIGENETIC REGULATION OF BDNF EXPRESSION IN THE PRIMARY SENSORY NEURONS AFTER PERIPHERAL NERVE INJURY: IMPLICATIONS IN THE DEVELOPMENT OF NEUROPATHIC PAIN. BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) IS KNOWN TO BE UP-REGULATED IN THE DORSAL ROOT GANGLION (DRG) AFTER PERIPHERAL NERVE INJURY, AND TO CONTRIBUTE TO NEUROPATHIC PAIN. HERE, WE FOUND THAT THERMAL HYPERALGESIA AND MECHANICAL ALLODYNIA AT DAY 7 POST-INJURY WERE INHIBITED ONLY WHEN ANTI-BDNF ANTIBODY WAS INTRATHECALLY ADMINISTRATED AT DAY 2 POST-INJURY. CONSISTENT WITH BEHAVIORAL RESULTS, WESTERN BLOT ANALYSIS SHOWED THAT THE EXPRESSION LEVELS OF BDNF PROTEIN IN THE SPINAL DORSAL HORN WERE MARKEDLY INDUCED DURING EARLY STAGE POST-INJURY. MOREOVER, THE MAXIMAL INCREASE IN BDNF MRNA EXPRESSION IN THE DRG WAS OBSERVED AT DAY 1 POST-INJURY, AND SIGNIFICANTLY ELEVATED LEVELS WERE SUSTAINED FOR AT LEAST 14 DAYS. FOUR OF FIVE BDNF MRNA TRANSCRIPTS WERE UP-REGULATED AFTER NERVE INJURY, AND THE MOST INDUCIBLE TRANSCRIPT WAS EXON I. USING A CHROMATIN IMMUNOPRECIPITATION (CHIP) ASSAY, WE FOUND THAT NERVE INJURY PROMOTES HISTONE H3 AND H4 ACETYLATION, TRANSCRIPTIONALLY ACTIVE MODIFICATIONS, AT BDNF PROMOTER I AT DAY 1 POST-INJURY, AND THE LEVELS OF HISTONE ACETYLATION REMAIN ELEVATED FOR AT LEAST 7 DAYS. TAKEN TOGETHER, OUR FINDINGS SUGGEST THAT AN INITIAL INCREASE IN BDNF EXON I EXPRESSION CONTROLLED BY EPIGENETIC MECHANISMS MIGHT HAVE A CRUCIAL ROLE IN THE DEVELOPMENT OF NEUROPATHIC PAIN.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
13   919  21 CHRONIC HYPOXIA DURING GESTATION CAUSES EPIGENETIC REPRESSION OF THE ESTROGEN RECEPTOR-ALPHA GENE IN OVINE UTERINE ARTERIES VIA HEIGHTENED PROMOTER METHYLATION. ESTROGEN RECEPTOR-ALPHA (ERALPHA) PLAYS A KEY ROLE IN THE ADAPTATION OF INCREASED UTERINE BLOOD FLOW IN PREGNANCY. CHRONIC HYPOXIA IS A COMMON STRESS TO MATERNAL CARDIOVASCULAR HOMEOSTASIS AND CAUSES INCREASED RISK OF PREECLAMPSIA. STUDIES IN PREGNANT SHEEP DEMONSTRATED THAT HYPOXIA DURING GESTATION DOWNREGULATED ERALPHA GENE EXPRESSION IN UTERINE ARTERIES. THE PRESENT STUDY TESTED THE HYPOTHESIS THAT HYPOXIA CAUSES EPIGENETIC REPRESSION OF THE ERALPHA GENE IN UTERINE ARTERIES VIA HEIGHTENED PROMOTER METHYLATION. OVINE ERALPHA PROMOTER OF 2035 BP SPANNING FROM -2000 TO +35 OF THE TRANSCRIPTION START SITE WAS CLONED. NO ESTROGEN OR HYPOXIA-INDUCIBLE FACTOR RESPONSE ELEMENTS WERE FOUND AT THE PROMOTER. TWO TRANSCRIPTION FACTOR BINDING SITES, USF(-15) AND SP1(-520), CONTAINING CPG DINUCLEOTIDES WERE IDENTIFIED, WHICH HAD SIGNIFICANT EFFECTS ON THE PROMOTER ACTIVITY. THE USF ELEMENT BINDS TRANSCRIPTION FACTORS USF1 AND USF2, AND THE SP1 ELEMENT BINDS SP1, AS WELL AS ERALPHA THROUGH SP1. DELETION OF THE SP1 SITE ABROGATED 17BETA-ESTRADIOL-INDUCED INCREASE IN THE PROMOTER ACTIVITY. IN NORMOXIC CONTROL SHEEP, CPG METHYLATION AT THE SP1 BUT NOT THE USF SITE WAS SIGNIFICANTLY DECREASED IN UTERINE ARTERIES OF PREGNANT AS COMPARED WITH NONPREGNANT ANIMALS. IN PREGNANT SHEEP EXPOSED TO LONG-TERM HIGH-ALTITUDE HYPOXIA, CPG METHYLATION AT BOTH SP1 AND USF SITES IN UTERINE ARTERIES WAS SIGNIFICANTLY INCREASED. METHYLATION INHIBITED TRANSCRIPTION FACTOR BINDING AND THE PROMOTER ACTIVITY. THE RESULTS PROVIDE EVIDENCE OF HYPOXIA CAUSING HEIGHTENED PROMOTER METHYLATION AND RESULTANT ERALPHA GENE REPRESSION IN UTERINE ARTERIES AND SUGGEST NEW INSIGHTS OF MOLECULAR MECHANISMS LINKING GESTATIONAL HYPOXIA TO ABERRANT UTEROPLACENTAL CIRCULATION AND INCREASED RISK OF PREECLAMPSIA.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
14  1218  46 CRISPR INTERFERENCE OF A CLONALLY VARIANT GC-RICH NONCODING RNA FAMILY LEADS TO GENERAL REPRESSION OF VAR GENES IN PLASMODIUM FALCIPARUM. THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM USES MUTUALLY EXCLUSIVE EXPRESSION OF THE PFEMP1-ENCODING VAR GENE FAMILY TO EVADE THE HOST IMMUNE SYSTEM. DESPITE PROGRESS IN THE MOLECULAR UNDERSTANDING OF THE DEFAULT SILENCING MECHANISM, THE ACTIVATION MECHANISM OF THE UNIQUELY EXPRESSED VAR MEMBER REMAINS ELUSIVE. A GC-RICH NONCODING RNA (NCRNA) GENE FAMILY HAS COEVOLVED WITH PLASMODIUM SPECIES THAT EXPRESS VAR GENES. HERE, WE SHOW THAT THIS NCRNA FAMILY IS TRANSCRIBED IN A CLONALLY VARIANT MANNER, WITH PREDOMINANT TRANSCRIPTION OF A SINGLE MEMBER OCCURRING WHEN THE NCRNA IS LOCATED ADJACENT TO AND UPSTREAM OF AN ACTIVE VAR GENE. WE DEVELOPED A SPECIFIC CRISPR INTERFERENCE (CRISPRI) STRATEGY THAT ALLOWED FOR THE TRANSCRIPTIONAL REPRESSION OF ALL GC-RICH MEMBERS. A LACK OF GC-RICH NCRNA TRANSCRIPTION LED TO THE DOWNREGULATION OF THE ENTIRE VAR GENE FAMILY IN RING-STAGE PARASITES. STRIKINGLY, IN MATURE BLOOD-STAGE PARASITES, THE GC-RICH NCRNA CRISPRI AFFECTED THE TRANSCRIPTION PATTERNS OF OTHER CLONALLY VARIANT GENE FAMILIES, INCLUDING THE DOWNREGULATION OF ALL PFMC-2TM MEMBERS. WE PROVIDE EVIDENCE FOR THE KEY ROLE OF GC-RICH NCRNA TRANSCRIPTION IN VAR GENE ACTIVATION AND DISCOVERED A MOLECULAR LINK BETWEEN THE TRANSCRIPTIONAL CONTROL OF VARIOUS CLONALLY VARIANT MULTIGENE FAMILIES INVOLVED IN PARASITE VIRULENCE. THIS WORK OPENS NEW AVENUES FOR ELUCIDATING THE MOLECULAR PROCESSES THAT CONTROL IMMUNE EVASION AND PATHOGENESIS IN P. FALCIPARUMIMPORTANCEPLASMODIUM FALCIPARUM IS THE DEADLIEST MALARIA PARASITE SPECIES, ACCOUNTING FOR THE VAST MAJORITY OF DISEASE CASES AND DEATHS. THE VIRULENCE OF THIS PARASITE IS RELIANT UPON THE MUTUALLY EXCLUSIVE EXPRESSION OF CYTOADHERENCE PROTEINS ENCODED BY THE 60-MEMBER VAR GENE FAMILY. ANTIGENIC VARIATION OF THIS MULTIGENE FAMILY SERVES AS AN IMMUNE EVASION MECHANISM, ULTIMATELY LEADING TO CHRONIC INFECTION AND PATHOGENESIS. UNDERSTANDING THE REGULATION MECHANISM OF ANTIGENIC VARIATION IS KEY TO DEVELOPING NEW THERAPEUTIC AND CONTROL STRATEGIES. OUR STUDY UNCOVERS A NOVEL LAYER IN THE EPIGENETIC REGULATION OF TRANSCRIPTION OF THIS FAMILY OF VIRULENCE GENES BY MEANS OF A MULTIGENE-TARGETING CRISPR INTERFERENCE APPROACH.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
15  5657  21 SEX-DEPENDENT PRONOCICEPTIVE ROLE OF SPINAL ALPHA(5) -GABA(A) RECEPTOR AND ITS EPIGENETIC REGULATION IN NEUROPATHIC RODENTS. EXTRASYNAPTIC ALPHA(5) -SUBUNIT CONTAINING GABA(A) (ALPHA(5) -GABA(A) ) RECEPTORS PARTICIPATE IN CHRONIC PAIN. PREVIOUSLY, WE REPORTED A SEX DIFFERENCE IN THE ACTION OF ALPHA(5) -GABA(A) RECEPTORS IN DYSFUNCTIONAL PAIN. HOWEVER, THE UNDERLYING MECHANISMS REMAIN UNKNOWN. THE AIM OF THIS STUDY WAS TO EXAMINE THIS SEXUAL DIMORPHISM IN NEUROPATHIC RODENTS AND THE MECHANISMS INVOLVED. FEMALE AND MALE WISTAR RATS OR ICR MICE WERE SUBJECTED TO NERVE INJURY FOLLOWED BY ALPHA(5) -GABA(A) RECEPTOR INVERSE AGONIST INTRATHECAL ADMINISTRATION, L-655,708. THE DRUG PRODUCED AN ANTIALLODYNIC EFFECT IN NERVE-INJURED FEMALE RATS AND MICE, AND A LOWER EFFECT IN MALES. WE HYPOTHESIZED THAT CHANGES IN ALPHA(5) -GABA(A) RECEPTOR, PROBABLY INFLUENCED BY HORMONAL AND EPIGENETIC STATUS, MIGHT UNDERLIE THIS SEX DIFFERENCE. THUS, WE PERFORMED QPCR AND WESTERN BLOT. NERVE INJURY INCREASED ALPHA(5) -GABA(A) MRNA AND PROTEIN IN FEMALE DORSAL ROOT GANGLIA (DRG) AND DECREASED THEM IN DRG AND SPINAL CORD OF MALES. TO INVESTIGATE THE HORMONAL INFLUENCE OVER ALPHA(5) -GABA(A) RECEPTOR ACTIONS, WE PERFORMED NERVE INJURY TO OVARIECTOMIZED RATS AND RECONSTITUTED THEM WITH 17BETA-ESTRADIOL (E2). OVARIECTOMY ABROGATED L-655,708 ANTIALLODYNIC EFFECT AND E2 RESTORED IT. OVARIECTOMY DECREASED ALPHA(5) -GABA(A) RECEPTOR AND ESTROGEN RECEPTOR ALPHA PROTEIN IN DRG OF NEUROPATHIC FEMALE RATS, WHILE E2 ENHANCED THEM. SINCE DNA METHYLATION MIGHT CONTRIBUTE TO ALPHA(5) -GABA(A) RECEPTOR DOWN-REGULATION IN MALES, WE EXAMINED CPG ISLAND DNA METHYLATION OF ALPHA(5) -GABA(A) RECEPTOR CODING GENE THROUGH PYROSEQUENCING. NERVE INJURY INCREASED METHYLATION IN MALE, BUT NOT FEMALE RATS. PHARMACOLOGICAL INHIBITION OF DNA METHYLTRANSFERASES INCREASED ALPHA(5) -GABA(A) RECEPTOR AND ENABLED L-655,708 ANTINOCICEPTIVE EFFECT IN MALE RATS. THESE RESULTS SUGGEST THAT ALPHA(5) -GABA(A) RECEPTOR IS A SUITABLE TARGET TO TREAT CHRONIC PAIN IN FEMALES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
16   352  24 ALTERED GENE EXPRESSION OF VEGF, IGFS AND H19 LNCRNA AND EPIGENETIC PROFILE OF H19-DMR REGION IN ENDOMETRIAL TISSUES OF WOMEN WITH ENDOMETRIOSIS. BACKGROUND: ENDOMETRIOSIS, AS CHRONIC ESTROGEN-DEPENDENT DISEASE, IS DEFINED BY THE PRESENCE OF ENDOMETRIAL-LIKE TISSUE OUTSIDE THE UTERUS. PROLIFERATION OF ENDOMETRIAL TISSUE AND NEOANGIOGENESIS ARE CRITICAL FACTORS IN DEVELOPMENT OF ENDOMETRIOSIS. HENCE, VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF) AS WELL AS INSULIN-LIKE GROWTH FACTOR 1 AND 2 (IGF1, 2) MAY BE INVOLVED AS INDUCERS OF CELLULAR PROLIFERATION OR NEOANGIOGENESIS. IMPRINTED LONG NONCODING RNA H19 (LNCRNA H19) HAS BEEN SUGGESTED TO BE INVOLVED IN PATHOGENESIS OF ENDOMETRIOSIS VIA REGULATION OF CELLULAR PROLIFERATION AND DIFFERENTIATION. EPIGENETIC ABERRATIONS APPEAR TO PLAY AN IMPORTANT ROLE IN ITS PATHOGENESIS. THE PRESENT STUDY WAS DESIGNED TO ELUCIDATE VEGF, IGF1, IGF2 AND H19 LNCRNA GENES EXPRESSION AND EPIGENETIC ALTERATIONS OF DIFFERENTIALLY METHYLATED REGION (DMR) OF H19 (H19-DMR) REGULATORY REGION IN ENDOMETRIAL TISSUES OF PATIENTS WITH ENDOMETRIOSIS, IN COMPARISON WITH CONTROL WOMEN. METHODS: IN THIS CASE-CONTROL STUDY, 24 WOMEN WITH AND WITHOUT ENDOMETRIOSIS WERE STUDIED FOR THE RELATIVE EXPRESSION OF VEGF, IGF1, IGF2 AND H19 LNCRNA GENES USING REAL-TIME POLYMERASE CHAIN REACTION (PCR) TECHNIQUE. OCCUPANCY OF THE MECP2 ON DMR REGION OF H19 GENE WAS ASSESSED USING CHROMATIN IMMUNOPRECIPITATION (CHIP), FOLLOWED BY REAL-TIME PCR. RESULTS: GENES EXPRESSION PROFILE OF H19, IGF1 AND IGF2 WAS DECREASED IN EUTOPIC AND ECTOPIC ENDOMETRIAL TISSUES OF ENDOMETRIOSIS GROUP, COMPARED TO THE CONTROL TISSUES. DECREASED EXPRESSION OF H19 IN ECTOPIC SAMPLES WAS SIGNIFICANT IN COMPARISON WITH THE CONTROLS (P < 0.05). GENE EXPRESSION OF VEGF WAS INCREASED IN EUTOPIC TISSUES OF ENDOMETRIOSIS GROUP, COMPARED TO CONTROL GROUP. WHEREAS ITS EXPRESSION LEVEL WAS LOWER IN ECTOPIC LESIONS VERSUS EUTOPIC AND CONTROL ENDOMETRIAL SAMPLES. CHIP ANALYSIS REVEALED SIGNIFICANT AND NEARLY SIGNIFICANT HYPOMETHYLATION OF H19-DMR REGION II IN EUTOPIC AND ECTOPIC SAMPLES, COMPARED TO THE CONTROL GROUP RESPECTIVELY. THIS EPIGENETIC CHANGE WAS ALIGNED WITH EXPRESSION OF IGF2. WHILE METHYLATION OF H19-DMR REGION I WAS NOT SIGNIFICANTLY DIFFERENT BETWEEN THE EUTOPIC, ECTOPIC AND CONTROL ENDOMETRIAL SAMPLES. CONCLUSION: THESE DATA SHOWED THAT VEGF, IGF1, IGF2 AND H19 LNCRNA GENES EXPRESSION AND EPIGENETIC ALTERATIONS OF H19 LNCRNA HAVE DYNAMIC ROLE IN THE PATHOGENESIS OF ENDOMETRIOSIS, SPECIFICALLY IN THE WAY THAT HYPOMETHYLATION OF H19-DMR REGION II CAN BE INVOLVED IN IGF2 DYSREGULATION IN ENDOMETRIOSIS.	2022	
                                                                                                                                                                                                                      
17  6179  41 THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM CAN SENSE ENVIRONMENTAL CHANGES AND RESPOND BY ANTIGENIC SWITCHING. THE PRIMARY ANTIGENIC AND VIRULENCE DETERMINANT OF THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM IS A VARIANT SURFACE PROTEIN CALLED PFEMP1. DIFFERENT FORMS OF PFEMP1 ARE ENCODED BY A MULTICOPY GENE FAMILY CALLED VAR, AND SWITCHING BETWEEN ACTIVE GENES ENABLES THE PARASITES TO EVADE THE ANTIBODY RESPONSE OF THEIR HUMAN HOSTS. VAR GENE SWITCHING IS KEY FOR THE MAINTENANCE OF CHRONIC INFECTIONS; HOWEVER, WHAT CONTROLS SWITCHING IS UNKNOWN, ALTHOUGH IT HAS BEEN SUGGESTED TO OCCUR AT A CONSTANT FREQUENCY WITH LITTLE OR NO ENVIRONMENTAL INFLUENCE. VAR GENE TRANSCRIPTION IS CONTROLLED EPIGENETICALLY THROUGH THE ACTIVITY OF HISTONE METHYLTRANSFERASES (HMTS). STUDIES IN MODEL SYSTEMS HAVE SHOWN THAT METABOLISM AND EPIGENETIC CONTROL OF GENE EXPRESSION ARE LINKED THROUGH THE AVAILABILITY OF INTRACELLULAR S-ADENOSYLMETHIONINE (SAM), THE PRINCIPAL METHYL DONOR IN BIOLOGICAL METHYLATION MODIFICATIONS, WHICH CAN FLUCTUATE BASED ON NUTRIENT AVAILABILITY. TO DETERMINE WHETHER ENVIRONMENTAL CONDITIONS AND CHANGES IN METABOLISM CAN INFLUENCE VAR GENE EXPRESSION, P. FALCIPARUM WAS CULTURED IN MEDIA WITH ALTERED CONCENTRATIONS OF NUTRIENTS INVOLVED IN SAM METABOLISM. WE FOUND THAT CONDITIONS THAT INFLUENCE LIPID METABOLISM INDUCE VAR GENE SWITCHING, INDICATING THAT PARASITES CAN RESPOND TO CHANGES IN THEIR ENVIRONMENT BY ALTERING VAR GENE EXPRESSION PATTERNS. GENETIC MODIFICATIONS THAT DIRECTLY MODIFIED EXPRESSION OF THE ENZYMES THAT CONTROL SAM LEVELS SIMILARLY LED TO PROFOUND CHANGES IN VAR GENE EXPRESSION, CONFIRMING THAT CHANGES IN SAM AVAILABILITY MODULATE VAR GENE SWITCHING. THESE OBSERVATIONS DIRECTLY CHALLENGE THE PARADIGM THAT ANTIGENIC VARIATION IN P. FALCIPARUM FOLLOWS AN INTRINSIC, PROGRAMED SWITCHING RATE, WHICH OPERATES INDEPENDENTLY OF ANY EXTERNAL STIMULI.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
18  3372  30 HISTONE MODIFICATIONS OF THE CRHR1 GENE IN A RAT MODEL OF DEPRESSION FOLLOWING CHRONIC STRESS. MULTIPLE LINES OF EVIDENCE SUGGEST A LINK BETWEEN DEPRESSION AND CHANGES IN HYPOTHALAMIC-PITUITARY-ADRENAL (HPA)-AXIS HORMONE DYNAMICS, INCLUDING ALTERED REGULATION OF THE CORTICOTROPHIN-RELEASING HORMONE (CRH) AND ITS MAIN RECEPTOR, CORTICOTROPHIN-RELEASING HORMONE RECEPTOR 1 (CRHR1). HOWEVER, THE PRECISE MOLECULAR MECHANISMS UNDERLYING DEPRESSION REMAIN POORLY UNDERSTOOD. IN THIS STUDY, WE EMPLOYED A MODEL OF DEPRESSION IN RATS BY SUBJECTING ANIMALS TO 21 DAYS OF CHRONIC UNPREDICTABLE MILD STRESS (CUMS). REAL-TIME PCR AND WESTERN BLOTTING WERE USED TO STUDY THE MRNA AND PROTEIN EXPRESSION LEVELS OF CRHR1 IN THE HYPOTHALAMUS. IN ADDITION, CHROMATIN IMMUNOPRECIPITATION ASSAYS WERE USED TO DETECT HISTONE METHYLATION AT THE CRHR1 GENE PROMOTER; THE LEVELS OF HISTONE H3 TRIMETHYLATION AT LYSINES 4 (H3K4) AND 9 (H3K9) REFLECT ACTIVE TRANSCRIPTION AND TRANSCRIPTIONAL REPRESSION, RESPECTIVELY. RATS EXPOSED TO CUMS EXHIBITED SIGNIFICANT REDUCTION IN LOCOMOTION AND SUCROSE PREFERENCE. THESE BEHAVIORAL ALTERATIONS WERE ASSOCIATED WITH ELEVATED EXPRESSION LEVELS OF CRHR1 MRNA AND PROTEIN IN THE HYPOTHALAMUS OF RATS IN THE CUMS GROUP. WE ALSO FOUND THAT THE LEVELS OF H3K9 TRIMETHYLATION AT THE CRHR1 GENE PROMOTER IN THE CUMS GROUP WERE SIGNIFICANTLY LOWER THAN THOSE IN THE CONTROL GROUP, WHEREAS H3K4 TRIMETHYLATION LEVELS WERE THE SAME FOR BOTH GROUPS. TAKEN TOGETHER, OUR FINDINGS SUGGEST THAT THE INCREASE IN CRHR1 EXPRESSION IN THE HYPOTHALAMUS OF STRESSED RATS CORRELATES WITH A DECREASE IN THE REPRESSIVE CHROMATIN STATE CAUSED BY REDUCED H3K9 TRIMETHYLATION LEVELS. THESE DATA ARE THE FIRST IN VIVO EVIDENCE OF A ROLE FOR CHROMATIN MODIFICATIONS IN THE REGULATION OF CRHR1 GENE EXPRESSION IN THE HYPOTHALAMUS, AND MAY PROVIDE NOVEL INSIGHT INTO THERAPEUTIC APPROACHES TO TREAT DEPRESSION.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
19  5096  38 PLASMODIUM FALCIPARUM SET2 DOMAIN IS ALLOSTERICALLY REGULATED BY ITS PHD-LIKE DOMAIN TO METHYLATE AT H3K36. THE ANTIGENIC VARIATION IS AN ESSENTIAL MECHANISM EMPLOYED BY THE MALARIA PARASITE TO ESTABLISH A CHRONIC INFECTION IN HUMANS. THREE MAJOR VIRULENT PROTEINS EMP1, RIFINS, AND STEVOR HAVE BEEN IMPLICATED IN CONTRIBUTING TO THE ANTIGENIC VARIATION PROCESS AND ARE ENCODED BY MULTIGENE FAMILIES IN PLASMODIUM SPP. THE KEY VIRULENCE FACTOR PFEMP1 IS ENCODED BY VAR GENES, AND IT EXHIBITS A MUTUALLY EXCLUSIVE TRANSCRIPTIONAL SWITCHING BETWEEN VAR GENES, ENSURING AN INDIVIDUAL PARASITE ONLY TRANSCRIBES A SINGLE VAR GENE AT A TIME. EXPRESSION OF VAR GENES IS TIGHTLY REGULATED BY TWO HISTONE EPIGENETIC METHYLATION MARKS H3K36ME3 AND H3K9ME3, OF WHICH THE H3K36ME3 MARK IS HIGHLY ENRICHED ON TRANSCRIPTION START SITES (TSSS) OF SUPPRESSED VAR GENES IN P. FALCIPARUM. HOWEVER, THE MECHANISMS OF H3K36ME3 MARK PROPAGATION ON ALL THE 59 VAR GENES OF P. FALCIPARUM ARE NOT KNOWN. HERE, WE HAVE IDENTIFIED A PHD (PLANT HOMEODOMAIN-LIKE DOMAIN) LIKE DOMAIN PRESENT WITHIN THE PFSET2 PROTEIN THAT SPECIFICALLY BINDS TO THE H3K36ME2 MARK, AN INTERMEDIATE PRODUCT OF THE H3K36ME3 MARK FORMATION ON THE NUCLEOSOME. SURPRISINGLY, WE HAVE FOUND THAT PHD - H3K36ME2 INTERACTION LEADS TO STIMULATION OF SET2 DOMAIN ACTIVITY ON THE NUCLEOSOME SUBSTRATES. THE ALLOSTERIC STIMULATION OF THE PFSET2 DOMAIN BY PHD-LIKE DOMAIN PRESENT WITHIN THE SAME PROTEIN SUGGESTS A NOVEL MECHANISM OF H3K36ME3 MARK PROPAGATION ON VAR GENES OF P. FALCIPARUM. THIS STUDY PROPOSES ALLOSTERIC REGULATION OF PFSET2 PROTEIN BY H3K36ME2 MARK AS AN ESSENTIAL MECHANISM OF VAR GENES SUPPRESSION TO ENSURE SUCCESSFUL ANTIGENIC VARIATION BY THE MALARIA PARASITE.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
20  5651  24 SEX DIFFERENCES IN THE EPIGENETIC REGULATION OF CHRONIC VISCERAL PAIN FOLLOWING UNPREDICTABLE EARLY LIFE STRESS. BACKGROUND: WE PREVIOUSLY REPORTED THAT EARLY LIFE STRESS (ELS) DYSREGULATED GLUCOCORTICOID RECEPTOR (GR) AND CORTICOTROPHIN-RELEASING HORMONE (CRH) EXPRESSION IN THE CENTRAL NUCLEUS OF THE AMYGDALA (CEA). EPIGENETIC MODIFICATIONS SERVE AS MEMORIES OF ADVERSE EVENTS THAT OCCURRED DURING EARLY LIFE. THEREFORE, WE HYPOTHESIZED THAT EPIGENETIC MECHANISMS ALTER GR AND CRH EXPRESSION IN THE CEA AND UNDERLIE CHRONIC VISCERAL PAIN AFTER ELS. METHODS: NEONATAL RATS WERE EXPOSED TO UNPREDICTABLE, PREDICTABLE ELS, OR ODOR ONLY (NO STRESS CONTROL) FROM POSTNATAL DAYS 8 TO 12. IN ADULTHOOD, VISCERAL SENSITIVITY WAS ASSESSED OR THE CEA WAS ISOLATED FOR WESTERN BLOT OR CHIP-QPCR TO STUDY HISTONE MODIFICATIONS AT THE GR AND CRH PROMOTERS. FEMALE ADULT RATS UNDERWENT STEREOTAXIC IMPLANTATION OF INDWELLING CANNULAS FOR MICROINJECTIONS OF GARCINOL (HAT INHIBITOR) INTO THE CEA. AFTER 7 DAYS OF MICROINJECTIONS, VISCERAL SENSITIVITY WAS ASSESSED OR THE CEA WAS ISOLATED FOR CHIP-QPCR ASSAYS. RESULTS: UNPREDICTABLE ELS INCREASED VISCERAL SENSITIVITY IN ADULT FEMALE RATS, BUT NOT IN MALE COUNTERPARTS. ELS INCREASED HISTONE 3 LYSINE 9 (H3K9) ACETYLATION IN THE CEA AND H3K9 ACETYLATION LEVELS AT THE GR PROMOTER IN THE CEA OF ADULT FEMALE RATS. AFTER UNPREDICTABLE ELS, H3K9 ACETYLATION WAS INCREASED AND GR BINDING WAS DECREASED AT THE CRH PROMOTER. ADMINISTRATION OF GARCINOL IN THE CEA OF ADULT FEMALES, THAT UNDERWENT UNPREDICTABLE ELS, NORMALIZED H3K9 ACETYLATION AND RESTORED GR BINDING AT THE CRH PROMOTER. CONCLUSION: DYSREGULATED HISTONE ACETYLATION AND GR BINDING AT THE CRH PROMOTER IN THE CEA ARE AN IMPORTANT MECHANISM FOR "MEMORIZING" ELS EVENTS MEDIATING VISCERAL PAIN IN ADULTHOOD.	2020