1 5990 99 TGF-BETA1 PROMOTES EXPRESSION OF FIBROSIS-RELATED GENES THROUGH THE INDUCTION OF HISTONE VARIANT H3.3 AND HISTONE CHAPERONE HIRA. RENAL FIBROSIS IS A HISTOLOGICAL MANIFESTATION THAT OCCURS IN ALMOST EVERY TYPE OF CHRONIC KIDNEY DISEASE. HISTONE VARIANT H3.3 AND ITS CHAPERONE, HISTONE CELL CYCLE REGULATION DEFECTIVE HOMOLOG A (HIRA), SERVE AS EPIGENETIC MARKS THAT REGULATE TRANSCRIPTIONAL ACTIVITY. IN THIS STUDY, WE ASSESSED THE ROLES OF HISTONE H3.3 AND HIRA IN UNILATERAL URETERAL-OBSTRUCTION (UUO) MICE. IN UUO MICE, THE LEVELS OF HISTONE H3.3 AND HIRA WERE SIGNIFICANTLY UPREGULATED IN THE KIDNEYS. THESE UPREGULATED LEVELS WERE DECREASED BY A TGF-BETA1 NEUTRALIZING ANTIBODY. TGF-BETA1 INDUCED HISTONE H3.3 AND HIRA EXPRESSION IN VITRO VIA A SMAD3-DEPENDENT PATHWAY IN NORMAL RAT KIDNEY (NRK)-52E CELLS. ADDITIONALLY, KNOCKDOWN OF HIRA EXPRESSION DECREASED HISTONE H3.3 EXPRESSION AND FIBROGENESIS IN NRK-52E CELLS AFTER TGF-BETA1 STIMULATION. CHROMATIN IMMUNOPRECIPITATION ANALYSIS REVEALED THAT PROMOTERS OF FIBROSIS-RELATED GENES WERE IMMUNOPRECIPITATED WITH BOTH HISTONE H3.3 AND HIRA IN NRK-52E CELLS. LASTLY, IN HUMAN KIDNEY BIOPSIES FROM PATIENTS DIAGNOSED WITH IGA NEPHROPATHY, HISTONE H3.3 AND HIRA IMMUNOSTAINING CORRELATED POSITIVELY WITH AREAS OF FIBROSIS AND ESTIMATED GLOMERULAR FILTRATION RATE. IN CONCLUSION, TGF-BETA1 INDUCES EXPRESSION OF HISTONE H3.3 AND HIRA, WHICH REGULATES EXPRESSION OF FIBROSIS-RELATED GENES.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
2 4001 44 LOSS OF MEN1 LEADS TO RENAL FIBROSIS AND DECREASES HGF-ADAMTS5 PATHWAY ACTIVITY VIA AN EPIGENETIC MECHANISM. BACKGROUND: RENAL FIBROSIS IS A SERIOUS CONDITION THAT RESULTS IN THE DEVELOPMENT OF CHRONIC KIDNEY DISEASES. THE MEN1 GENE IS AN EPIGENETIC REGULATOR THAT ENCODES THE MENIN PROTEIN AND ITS ROLE IN KIDNEY TISSUE REMAINS UNCLEAR. METHODS: KIDNEY HISTOLOGY WAS EXAMINED ON PARAFFIN SECTIONS STAINED WITH HEMATOXYLIN-EOSIN STAINING. MASSON'S TRICHROME STAINING AND SIRIUS RED STAINING WERE USED TO ANALYZE RENAL FIBROSIS. GENE AND PROTEIN EXPRESSION WERE DETERMINED BY QUANTITATIVE REAL-TIME PCR (QPCR) AND WESTERN BLOT, RESPECTIVELY. IMMUNOHISTOCHEMISTRY STAINING IN THE KIDNEY TISSUES FROM MICE OR PATIENTS WAS USED TO EVALUATE PROTEIN LEVELS. FLOW CYTOMETRY WAS USED TO ANALYZE THE CELL CYCLE DISTRIBUTIONS AND APOPTOSIS. RNA-SEQUENCING WAS PERFORMED FOR DIFFERENTIAL EXPRESSION GENES IN THE KIDNEY TISSUES OF THE MEN1F/F AND MEN1?/? MICE. CHROMATIN IMMUNOPRECIPITATION SEQUENCING (CHIP-SEQ) WAS CARRIED OUT FOR IDENTIFICATION OF MENIN- AND H3K4ME3-ENRICHED REGIONS WITHIN THE WHOLE GENOME IN THE MOUSE KIDNEY TISSUE. CHIP-QPCR ASSAYS WERE PERFORMED FOR OCCUPANCY OF MENIN AND H3K4ME3 AT THE GENE PROMOTER REGIONS. LUCIFERASE REPORTER ASSAY WAS USED TO DETECT THE PROMOTER ACTIVITY. THE EXACERBATED UNILATERAL URETERAL OBSTRUCTION (UUO) MODELS IN THE MEN1F/F AND MEN1?/? MICE WERE USED TO ASSESS THE PHARMACOLOGICAL EFFECTS OF RH-HGF ON RENAL FIBROSIS. RESULTS: THE EXPRESSION OF MEN1 IS REDUCE IN KIDNEY TISSUES OF FIBROTIC MOUSE AND HUMAN DIABETIC PATIENTS AND TREATMENT WITH FIBROTIC FACTOR RESULTS IN THE DOWNREGULATION OF MEN1 EXPRESSION IN RENAL TUBULAR EPITHELIAL CELLS (RTECS). DISRUPTION OF MEN1 IN RTECS LEADS TO HIGH EXPRESSION OF ALPHA-SMA AND COLLAGEN 1, WHEREAS MEN1 OVEREXPRESSION RESTRAINS EPITHELIAL-TO-MESENCHYMAL TRANSITION (EMT) INDUCED BY TGF-BETA TREATMENT. CONDITIONAL KNOCKOUT OF MEN1 RESULTED IN CHRONIC RENAL FIBROSIS AND UUO-INDUCED TUBULOINTERSTITIAL FIBROSIS (TIF), WHICH IS ASSOCIATED WITH AN INCREASED INDUCTION OF EMT, G2/M ARREST AND JNK SIGNALING. MECHANISTICALLY, MENIN RECRUITS AND INCREASES H3K4ME3 AT THE PROMOTER REGIONS OF HEPATOCYTE GROWTH FACTOR (HGF) AND A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 5 (ADAMTS5) GENES AND ENHANCES THEIR TRANSCRIPTIONAL ACTIVATION. IN THE UUO MICE MODEL, EXOGENOUS HGF RESTORED THE EXPRESSION OF ADAMTS5 AND AMELIORATED RENAL FIBROSIS INDUCED BY MEN1 DEFICIENCY. CONCLUSIONS: THESE FINDINGS DEMONSTRATE THAT MEN1 IS AN ESSENTIAL ANTIFIBROTIC FACTOR IN RENAL FIBROGENESIS AND COULD BE A POTENTIAL TARGET FOR ANTIFIBROTIC THERAPY.	2022	

3 3128 42 GIPC-REGULATED IGFBP-3 PROMOTES HSC MIGRATION IN VITRO AND PORTAL HYPERTENSION IN VIVO THROUGH A BETA1-INTEGRIN PATHWAY. BACKGROUND & AIMS: TRANSFORMING GROWTH FACTOR (TGF-BETA)-INDUCED ACTIVATION OF QUIESCENT HEPATIC STELLATE CELLS (HSCS) AND THEIR TRANSFORMATION TO MYOFIBROBLASTS IS A KEY EVENT IN LIVER FIBROSIS AND PORTAL HYPERTENSION. GIPC (ALSO REFERRED TO AS SYNECTIN) IS A DOWNSTREAM SIGNAL ACTIVATION MOLECULE OF TGF-BETA AND OTHER RECEPTORS. IN THIS STUDY, WE SOUGHT TO IDENTIFY NOVEL GENES TARGETED BY TGF-BETA AND GIPC AND ELUCIDATE IF AND HOW THEY MAY CONTRIBUTE TO LIVER FIBROSIS. METHODS: WE PERFORMED SEQUENTIAL MESSENGER RNA SEQUENCING ANALYSIS ON TGF-BETA-STIMULATED HSCS AND THEN ON TGF-BETA-STIMULATED HSCS IN THE PRESENCE AND ABSENCE OF GIPC ALSO REFERRED TO AS SYNECTIN (GIPC) KNOCKDOWN. INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN-3 (IGFBP-3) TRANSPORT PROTEIN EMERGED AS A TOP ACTIVATION TARGET OF BOTH TGF-BETA AND GIPC. QUANTITATIVE POLYMERASE CHAIN REACTION, ENZYME-LINKED IMMUNOSORBENT ASSAY, TARGETED CHROMATIN IMMUNOPRECIPITATION, AND WESTERN BLOT ANALYSIS WERE DONE FOR FURTHER CONFIRMATION. RESULTS: IGFBP-3, AN INSULIN GROWTH FACTOR TRANSPORT PROTEIN, EMERGED AS A TOP ACTIVATION TARGET OF BOTH TGF-BETA AND GIPC, WHICH WAS CONFIRMED BY QUANTITATIVE POLYMERASE CHAIN REACTION, ENZYME-LINKED IMMUNOSORBENT ASSAY, AND WESTERN BLOT ANALYSIS. TARGETED CHROMATIN IMMUNOPRECIPITATION SHOWED THAT GIPC INCREASES THE HISTONE 3 LYSINE 27 (H3K27) ACETYLATION ACTIVATING MARK AND CONCURRENTLY DECREASES THE H3K27 INHIBITORY TRIMETHYLATION (H3K27M3) MARK, PROVIDING AN EPIGENETIC CORRELATE TO THE GENE REGULATION CHANGES. IN VIVO, GLOBAL KNOCKOUT OF IGFBP-3 MICE RESULTED IN ATTENUATION OF HSC ACTIVATION MARKERS AND ATTENUATION OF PORTAL PRESSURE IN RESPONSE TO CHRONIC LIVER INJURY MODELS. ANALYSIS OF SERUM LEVELS FROM CIRRHOTIC PATIENTS ALSO SHOWED AN IGFBP-3 INCREASE OF MORE THAN 2-FOLD COMPARED WITH HEALTHY CONTROLS. FINALLY, IN VITRO MECHANISM STUDIES SHOWED THAT IGFBP-3 PROMOTES HSC MIGRATION THROUGH INTEGRIN-DEPENDENT PHOSPHORYLATION OF PROTEIN KINASE B. CONCLUSIONS: TGF-BETA UP-REGULATES IGFBP-3 THROUGH GIPC, LEADING TO INCREASED HSC MIGRATION IN VITRO AND PROMOTES PORTAL HYPERTENSION IN VIVO. THESE STUDIES SUPPORT THE ROLE OF IGFBP-3 AS A POTENTIAL PATHOPHYSIOLOGIC TARGET OR BIOMARKER IN CHRONIC LIVER DISEASE.	2020	
                                                                                                                                                                                                                                                                                        
4 1298 31 DECREASED NUCLEAR RECEPTOR ACTIVITY AND EPIGENETIC MODULATION ASSOCIATES WITH DOWN-REGULATION OF HEPATIC DRUG-METABOLIZING ENZYMES IN CHRONIC KIDNEY DISEASE. PATIENTS WITH CHRONIC KIDNEY DISEASE (CKD) REQUIRE MANY MEDICATIONS. CYP2C AND CYP3A DRUG-METABOLIZING ENZYMES PLAY A CRITICAL ROLE IN DETERMINING THE PHARMACOKINETICS OF THE MAJORITY OF PRESCRIBED MEDICATIONS. THESE ENZYMES ARE TRANSCRIPTIONALLY REGULATED BY THE NUCLEAR RECEPTORS PREGNANE X RECEPTOR (PXR) AND HEPATIC NUCLEAR FACTOR 4ALPHA (HNF-4ALPHA). EXPRESSION OF CYP2C AND CYP3A IS DECREASED IN CKD; HOWEVER, THE MECHANISMS BY WHICH THIS OCCURS IS UNKNOWN. WE INDUCED CKD IN RATS BY 5/6 NEPHRECTOMY AND USED CHROMATIN IMMUNOPRECIPITATION (CHIP) TO DETERMINE NUCLEAR RECEPTOR- AND EPIGENETIC ALTERATION-MEDIATED DIFFERENCES IN THE PROMOTER REGION OF THE CYP2C AND CYP3A GENES. RNA POLYMERASE II AND HNF-4ALPHA BINDING WAS DECREASED 76 AND 57% IN THE CYP2C11 PROMOTOR AND 71 AND 77% IN THE CYP3A2 PROMOTER, RESPECTIVELY (P<0.05). CHIP ALSO REVEALED A 57% DECREASE IN PXR BINDING TO THE CYP3A2 PROMOTER IN CKD RATS (P<0.05). THE DECREASE IN PXR AND HNF-4ALPHA BINDING WAS ACCOMPANIED BY DIMINISHED HISTONE 4 ACETYLATION IN THE CYP3A2 PROMOTER (48%) AND HISTONE 3 ACETYLATION IN THE CYP2C11 (77%) AND CYP3A2 (77%) PROMOTER LOCI FOR NUCLEAR RECEPTOR ACTIVATION (P<0.05). THIS STUDY SUGGESTS THAT DECREASED NUCLEAR RECEPTOR BINDING AND HISTONE ACETYLATION MAY CONTRIBUTE TO THE MECHANISM OF DRUG-METABOLIZING ENZYME DOWN-REGULATION AND ALTERED PHARMACOKINETICS IN CKD.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
5 2155 32 EPIGENETIC MECHANISMS AND METABOLIC REPROGRAMMING IN FIBROGENESIS: DUAL TARGETING OF G9A AND DNMT1 FOR THE INHIBITION OF LIVER FIBROSIS. OBJECTIVE: HEPATIC STELLATE CELLS (HSC) TRANSDIFFERENTIATION INTO MYOFIBROBLASTS IS CENTRAL TO FIBROGENESIS. EPIGENETIC MECHANISMS, INCLUDING HISTONE AND DNA METHYLATION, PLAY A KEY ROLE IN THIS PROCESS. CONCERTED ACTION BETWEEN HISTONE AND DNA-MEHYLTRANSFERASES LIKE G9A AND DNMT1 IS A COMMON THEME IN GENE EXPRESSION REGULATION. WE AIMED TO STUDY THE EFFICACY OF CM272, A FIRST-IN-CLASS DUAL AND REVERSIBLE G9A/DNMT1 INHIBITOR, IN HALTING FIBROGENESIS. DESIGN: G9A AND DNMT1 WERE ANALYSED IN CIRRHOTIC HUMAN LIVERS, MOUSE MODELS OF LIVER FIBROSIS AND CULTURED MOUSE HSC. G9A AND DNMT1 EXPRESSION WAS KNOCKED DOWN OR INHIBITED WITH CM272 IN HUMAN HSC (HHSC), AND TRANSCRIPTOMIC RESPONSES TO TRANSFORMING GROWTH FACTOR-BETA1 (TGFBETA1) WERE EXAMINED. GLYCOLYTIC METABOLISM AND MITOCHONDRIAL FUNCTION WERE ANALYSED WITH SEAHORSE-XF TECHNOLOGY. GENE EXPRESSION REGULATION WAS ANALYSED BY CHROMATIN IMMUNOPRECIPITATION AND METHYLATION-SPECIFIC PCR. ANTIFIBROGENIC ACTIVITY AND SAFETY OF CM272 WERE STUDIED IN MOUSE CHRONIC CCL(4) ADMINISTRATION AND BILE DUCT LIGATION (BDL), AND IN HUMAN PRECISION-CUT LIVER SLICES (PCLSS) IN A NEW BIOREACTOR TECHNOLOGY. RESULTS: G9A AND DNMT1 WERE DETECTED IN STROMAL CELLS IN AREAS OF ACTIVE FIBROSIS IN HUMAN AND MOUSE LIVERS. G9A AND DNMT1 EXPRESSION WAS INDUCED DURING MOUSE HSC ACTIVATION, AND TGFBETA1 TRIGGERED THEIR CHROMATIN RECRUITMENT IN HHSC. G9A/DNMT1 KNOCKDOWN AND CM272 INHIBITED TGFBETA1 FIBROGENIC RESPONSES IN HHSC. TGFBETA1-MEDIATED PROFIBROGENIC METABOLIC REPROGRAMMING WAS ABROGATED BY CM272, WHICH RESTORED GLUCONEOGENIC GENE EXPRESSION AND MITOCHONDRIAL FUNCTION THROUGH ON-TARGET EPIGENETIC EFFECTS. CM272 INHIBITED FIBROGENESIS IN MICE AND PCLSS WITHOUT TOXICITY. CONCLUSIONS: DUAL G9A/DNMT1 INHIBITION BY COMPOUNDS LIKE CM272 MAY BE A NOVEL THERAPEUTIC STRATEGY FOR TREATING LIVER FIBROSIS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
6 3049 35 GENOME-WIDE ANALYSIS REVEALS ZINC TRANSPORTER ZIP9 REGULATED BY DNA METHYLATION PROMOTES RADIATION-INDUCED SKIN FIBROSIS VIA THE TGF-BETA SIGNALING PATHWAY. RADIATION-INDUCED SKIN FIBROSIS IS A DETRIMENTAL AND CHRONIC DISORDER THAT OCCURS AFTER RADIATION EXPOSURE. DNA METHYLATION HAS BEEN CHARACTERIZED AS AN IMPORTANT REGULATORY MECHANISM OF MULTIPLE PATHOLOGICAL PROCESSES. IN THIS STUDY, WE COMPARED THE GENOME-WIDE DNA METHYLATION STATUS IN RADIATION-INDUCED FIBROTIC SKIN AND ADJACENT NORMAL TISSUES OF RATS BY METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING. RADIATION-INDUCED FIBROTIC SKIN SHOWED DIFFERENTIALLY METHYLATED REGIONS ASSOCIATED WITH 3,650 PROTEIN-CODING GENES, 72 MICRORNAS, 5,836 LONG NONCODING RNAS AND 3 PIWI-INTERACTING RNAS. BY INTEGRATING THE MRNA AND METHYLATION PROFILES, THE ZINC TRANSPORTER SLC39A9/ZIP9 WAS INVESTIGATED IN GREATER DETAIL. THE PROTEIN LEVEL OF ZIP9 WAS INCREASED IN IRRADIATED SKIN TISSUES OF HUMANS, MONKEYS, AND RATS, ESPECIALLY IN RADIOGENIC FIBROTIC SKIN TISSUES. RADIATION INDUCED THE DEMETHYLATION OF A CPG DINUCLEOTIDE IN EXON 1 OF ZIP9 THAT RESULTED IN RECRUITMENT OF THE TRANSCRIPTIONAL FACTOR SP1 AND INCREASED ZIP9 EXPRESSION. OVEREXPRESSION OF ZIP9 RESULTED IN ACTIVATION OF THE PROFIBROTIC TRANSFORMING GROWTH FACTOR-BETA SIGNALING PATHWAY THROUGH PROTEIN KINASE B IN HUMAN FIBROBLASTS. IN ADDITION, RADIATION-INDUCED SKIN FIBROSIS WAS ASSOCIATED WITH INCREASED ZINC ACCUMULATION. THE ZINC CHELATOR N,N,N',N'-TETRAKIS(2-PYRIDYLMETHYL)-1,2-ETHYLENEDIAMINE ABROGATED ZIP9-INDUCED ACTIVATION OF THE TRANSFORMING GROWTH FACTOR-BETA SIGNALING PATHWAY AND ATTENUATED RADIATION-INDUCED SKIN FIBROSIS IN A RAT MODEL. IN SUMMARY, OUR FINDINGS ILLUSTRATE EPIGENETIC REGULATION OF ZIP9 AND ITS CRITICAL ROLE IN PROMOTING RADIATION-INDUCED SKIN FIBROSIS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
7 5636 36 SERELAXIN ALLEVIATES CARDIAC FIBROSIS THROUGH INHIBITING ENDOTHELIAL-TO-MESENCHYMAL TRANSITION VIA RXFP1. RATIONALE: CARDIAC FIBROSIS IS AN INTEGRAL CONSTITUENT OF EVERY FORM OF CHRONIC HEART DISEASE, AND PERSISTENCE OF FIBROSIS REDUCES TISSUE COMPLIANCE AND ACCELERATES THE PROGRESSION TO HEART FAILURE. RELAXIN-2 IS A HUMAN HORMONE, WHICH HAS VARIOUS PHYSIOLOGICAL FUNCTIONS SUCH AS MEDIATING RENAL VASODILATION IN PREGNANCY. ITS RECOMBINANT FORM SERELAXIN HAS RECENTLY BEEN TESTED IN CLINICAL TRIALS AS A THERAPY FOR ACUTE HEART FAILURE BUT DID NOT MEET ITS PRIMARY ENDPOINTS. THE AIM OF THIS STUDY IS TO EXAMINE WHETHER SERELAXIN HAS AN ANTI-FIBROTIC EFFECT IN THE HEART AND THEREFORE COULD BE BENEFICIAL IN CHRONIC HEART FAILURE. METHODS: WE UTILIZED TWO DIFFERENT CARDIAC FIBROSIS MOUSE MODELS (ASCENDING AORTIC CONSTRICTION (AAC) AND ANGIOTENSIN II (ATII) ADMINISTRATION VIA OSMOTIC MINIPUMPS) TO ASSESS THE ANTI-FIBROTIC POTENTIAL OF SERELAXIN. HISTOLOGICAL ANALYSIS, IMMUNOFLUORESCENCE STAINING AND MOLECULAR ANALYSIS WERE PERFORMED TO ASSESS THE FIBROSIS LEVEL AND INDICATE ENDOTHELIAL CELLS WHICH ARE UNDERGOING ENDMT. IN VITRO TGFBETA1-INDUCED ENDOTHELIAL-TO-MESENCHYMAL TRANSITION (ENDMT) ASSAYS WERE PERFORMED IN HUMAN CORONARY ARTERY ENDOTHELIAL CELLS AND MOUSE CARDIAC ENDOTHELIAL CELLS (MCECS) AND WERE EXAMINED USING MOLECULAR METHODS. CHROMATIN IMMUNOPRECIPITATION-QPCR ASSAY WAS UTILIZED TO IDENTIFY THE SERELAXIN EFFECT ON CHROMATIN REMODELING IN THE RXFP1 PROMOTER REGION IN MCECS. RESULTS: OUR RESULTS DEMONSTRATE A SIGNIFICANT AND DOSE-DEPENDENT ANTI-FIBROTIC EFFECT OF SERELAXIN IN THE HEART IN BOTH MODELS. WE FURTHER SHOW THAT SERELAXIN MEDIATES THIS EFFECT, AT LEAST IN PART, THROUGH INHIBITION OF ENDMT THROUGH THE ENDOTHELIAL RELAXIN FAMILY PEPTIDE RECEPTOR 1 (RXFP1). WE FURTHER DEMONSTRATE THAT SERELAXIN ADMINISTRATION IS ABLE TO INCREASE ITS OWN RECEPTOR EXPRESSION (RXFP1) THROUGH EPIGENETIC REGULATION IN FORM OF HISTONE MODIFICATIONS BY ATTENUATING TGFBETA-PSMAD2/3 SIGNALING IN ENDOTHELIAL CELLS. CONCLUSIONS: THIS STUDY IS THE FIRST TO IDENTIFY THAT SERELAXIN INCREASES THE EXPRESSION OF ITS OWN RECEPTOR RXFP1 AND THAT THIS MEDIATES THE INHIBITION OF ENDMT AND CARDIAC FIBROSIS, SUGGESTING THAT SERELAXIN MAY HAVE A BENEFICIAL EFFECT AS ANTI-FIBROTIC THERAPY IN CHRONIC HEART FAILURE.	2020	
                                                                                                                                                                                                                                                                                                                   
8 4696 25 NF-KAPPAB REPRESSES RETINOIC ACID RECEPTOR-MEDIATED GPRC5A TRANSACTIVATION IN LUNG EPITHELIAL CELLS TO PROMOTE NEOPLASIA. CHRONIC INFLAMMATION IS ASSOCIATED WITH LUNG TUMORIGENESIS, IN WHICH NF-KAPPAB-MEDIATED EPIGENETIC REGULATION PLAYS A CRITICAL ROLE. LUNG TUMOR SUPPRESSOR G PROTEIN-COUPLED RECEPTOR, FAMILY C, MEMBER 5A (GPRC5A), IS REPRESSED IN MOST NON-SMALL CELL LUNG CANCER (NSCLC); HOWEVER, THE MECHANISMS REMAIN UNCLEAR. HERE, WE SHOW THAT NF-KAPPAB ACTS AS A TRANSCRIPTIONAL REPRESSOR IN SUPPRESSION OF GPRC5A. NF-KAPPAB INDUCED GPRC5A REPRESSION BOTH IN VITRO AND IN VIVO. INTRIGUINGLY, TRANSACTIVATION OF NF-KAPPAB DOWNSTREAM TARGETS WAS NOT REQUIRED, BUT THE TRANSACTIVATION DOMAIN OF RELA/P65 WAS REQUIRED FOR GPRC5A REPRESSION. NF-KAPPAB DID NOT BIND TO ANY POTENTIAL CIS-ELEMENT IN THE GPRC5A PROMOTER. INSTEAD, P65 WAS COMPLEXED WITH RETINOIC ACID RECEPTOR ALPHA/BETA (RARALPHA/BETA) AND RECRUITED TO THE RA RESPONSE ELEMENT SITE AT THE GPRC5A PROMOTER, RESULTING IN DISRUPTED RNA POLYMERASE II COMPLEXING AND SUPPRESSED TRANSCRIPTION. NOTABLY, PHOSPHORYLATION ON SERINE 276 OF P65 WAS REQUIRED FOR INTERACTION WITH RARALPHA/BETA AND REPRESSION OF GPRC5A. MOREOVER, NF-KAPPAB-MEDIATED EPIGENETIC REPRESSION WAS THROUGH SUPPRESSION OF ACETYLATED HISTONE H3K9 (H3K9AC), BUT NOT DNA METHYLATION OF THE CPG ISLANDS, AT THE GPRC5A PROMOTER. CONSISTENTLY, A HISTONE DEACETYLASE INHIBITOR, BUT NOT DNA METHYLATION INHIBITOR, RESTORED GPRC5A EXPRESSION IN NSCLC CELLS. THUS, NF-KAPPAB INDUCES TRANSCRIPTIONAL REPRESSION OF GPRC5A VIA A COMPLEX WITH RARALPHA/BETA AND MEDIATES EPIGENETIC REPRESSION VIA SUPPRESSION OF H3K9AC.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
9  669 31 BONE MARROW STROMAL CELL ANTIGEN-1 (CD157) REGULATED BY SPHINGOSINE KINASE 2 MEDIATES KIDNEY FIBROSIS. CHRONIC KIDNEY DISEASE IS A PROGRESSIVE DISEASE THAT MAY LEAD TO END-STAGE RENAL DISEASE. INTERSTITIAL FIBROSIS DEVELOPS AS THE DISEASE PROGRESSES. THERAPIES THAT FOCUS ON FIBROSIS TO DELAY OR REVERSE PROGRESSIVE RENAL FAILURE ARE LIMITED. WE AND OTHERS SHOWED THAT SPHINGOSINE KINASE 2-DEFICIENT MICE (SPHK2 (-/-)) DEVELOP LESS FIBROSIS IN MOUSE MODELS OF KIDNEY FIBROSIS. SPHINGOSINE KINASE2 (SPHK2), ONE OF TWO SPHINGOSINE KINASES THAT PRODUCE SPHINGOSINE 1-PHOSPHATE (S1P), IS PRIMARILY LOCATED IN THE NUCLEUS. S1P PRODUCED BY SPHK2 INHIBITS HISTONE DEACETYLASE (HDAC) AND CHANGES HISTONE ACETYLATION STATUS, WHICH CAN LEAD TO ALTERED TARGET GENE EXPRESSION. WE HYPOTHESIZED THAT SPHK2 EPIGENETICALLY REGULATES DOWNSTREAM GENES TO INDUCE FIBROSIS, AND WE PERFORMED A COMPREHENSIVE ANALYSIS USING THE COMBINATION OF RNA-SEQ AND CHIP-SEQ. BST1/CD157 WAS IDENTIFIED AS A GENE THAT IS REGULATED BY SPHK2 THROUGH A CHANGE IN HISTONE ACETYLATION LEVEL, AND BST1 (-/-) MICE WERE FOUND TO DEVELOP LESS RENAL FIBROSIS AFTER UNILATERAL ISCHEMIA-REPERFUSION INJURY, A MOUSE MODEL OF KIDNEY FIBROSIS. ALTHOUGH BST1 IS A CELL-SURFACE MOLECULE THAT HAS A WIDE VARIETY OF FUNCTIONS THROUGH ITS VARIED ENZYMATIC ACTIVITIES AND DOWNSTREAM INTRACELLULAR SIGNALING PATHWAYS, NO STUDIES ON THE ROLE OF BST1 IN KIDNEY DISEASES HAVE BEEN REPORTED PREVIOUSLY. IN THE CURRENT STUDY, WE DEMONSTRATED THAT BST1 IS A GENE THAT IS REGULATED BY SPHK2 THROUGH EPIGENETIC CHANGE AND IS CRITICAL IN KIDNEY FIBROSIS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
10 3161 30 GRAINYHEAD-LIKE 2 (GRHL2) INHIBITS KERATINOCYTE DIFFERENTIATION THROUGH EPIGENETIC MECHANISM. WE RECENTLY IDENTIFIED GRAINYHEAD-LIKE 2 (GRHL2), A MAMMALIAN HOMOLOG OF GRAINYHEAD IN DROSOPHILA, TO BE A NOVEL TRANSCRIPTION FACTOR THAT REGULATES HTERT GENE EXPRESSION AND ENHANCES PROLIFERATION OF NORMAL HUMAN EPIDERMAL KERATINOCYTES (NHEK). IN THE CURRENT STUDY, WE SHOW THAT GRHL2 IMPAIRS KERATINOCYTE DIFFERENTIATION THROUGH TRANSCRIPTIONAL INHIBITION OF THE GENES CLUSTERED AT THE EPIDERMAL DIFFERENTIATION COMPLEX (EDC), LOCATED AT CHROMOSOME 1Q21. GENE EXPRESSION PROFILING AND SUBSEQUENT IN VITRO ASSAYS REVEALED CONSISTENT DOWNREGULATION OF EDC GENES, FOR EXAMPLE, IVL, KRT1, FLG, LCES, AND SPRRS, IN NHEK EXPRESSING EXOGENOUS GRHL2. IN VIVO BINDING ASSAY BY CHROMATIN IMMUNOPRECIPITATION REVEALED GRHL2 ASSOCIATION AT THE PROMOTER REGIONS OF ITS TARGET GENES, MANY OF WHICH BELONG TO EDC. EXOGENOUS GRHL2 EXPRESSION ALSO INHIBITED RECRUITMENT OF HISTONE DEMETHYLASE JMJD3 TO THE EDC GENE PROMOTERS AND ENHANCED THE LEVEL OF HISTONE 3 LYS 27 TRIMETHYLATION ENRICHMENT AT THESE PROMOTERS. SURVEY OF GRHL2 EXPRESSION IN HUMAN SKIN TISSUES DEMONSTRATED ENHANCED PROTEIN AND MRNA LEVELS IN CHRONIC SKIN LESIONS WITH IMPAIRED KERATINOCYTE DIFFERENTIATION, FOR EXAMPLE, ATOPIC DERMATITIS AND PSORIASIS, COMPARED WITH NORMAL EPIDERMIS. THESE DATA INDICATE THAT GRHL2 IMPAIRS EPIDERMAL DIFFERENTIATION BY INHIBITING EDC GENE EXPRESSION THROUGH EPIGENETIC MECHANISMS AND SUPPORT ITS ROLE IN THE HYPERPROLIFERATIVE SKIN DISEASES.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
11  368 35 AMYLOID BETA-MEDIATED EPIGENETIC ALTERATION OF INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 3 CONTROLS CELL SURVIVAL IN ALZHEIMER'S DISEASE. SWEDISH DOUBLE MUTATION (KM670/671NL) OF AMYLOID PRECURSOR PROTEIN (APP) IS REPORTED TO INCREASE TOXIC AMYLOID BETA (ABETA) PRODUCTION VIA ABERRANT CLEAVAGE AT THE BETA-SECRETASE SITE AND THEREBY CAUSE EARLY-ONSET ALZHEIMER'S DISEASE (AD). HOWEVER, THE UNDERLYING MOLECULAR MECHANISMS LEADING TO AD PATHOGENESIS REMAINS LARGELY UNKNOWN. PREVIOUSLY, OUR TRANSCRIPTOME SEQUENCE ANALYSES REVEALED GLOBAL EXPRESSIONAL MODIFICATIONS OF OVER 600 GENES IN APP-SWEDISH MUTANT-EXPRESSING H4 (H4-SW) CELLS COMPARED TO WILD TYPE H4 CELLS. INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 3 (IGFBP3) IS ONE GENE THAT SHOWED SIGNIFICANTLY DECREASED MRNA EXPRESSION IN H4-SW CELLS. IN THIS STUDY, WE INVESTIGATED THE FUNCTIONAL ROLE OF IGFBP3 IN AD PATHOGENESIS AND ELUCIDATED THE MECHANISMS REGULATING ITS EXPRESSION. WE OBSERVED DECREASED IGFBP3 EXPRESSION IN THE H4-SW CELL LINE AS WELL AS THE HIPPOCAMPUS OF AD MODEL TRANSGENIC MICE. TREATMENT WITH EXOGENOUS IGFBP3 PROTEIN INHIBITED ABETA1-42- INDUCED CELL DEATH AND CASPASE-3 ACTIVITY, WHEREAS SIRNA-MEDIATED SUPPRESSION OF IGFBP3 EXPRESSION INDUCED CELL DEATH AND CASPASE-3 CLEAVAGE. IN PRIMARY HIPPOCAMPAL NEURONS, ADMINISTRATION OF IGFBP3 PROTEIN BLOCKED APOPTOTIC CELL DEATH DUE TO ABETA1-42 TOXICITY. THESE DATA IMPLICATE A PROTECTIVE ROLE FOR IGFBP3 AGAINST ABETA1-42-MEDIATED APOPTOSIS. NEXT, WE INVESTIGATED THE REGULATORY MECHANISMS OF IGFBP3 EXPRESSION IN AD PATHOGENESIS. WE OBSERVED ABNORMAL IGFBP3 HYPERMETHYLATION WITHIN THE PROMOTER CPG ISLAND IN H4-SW CELLS. TREATMENT WITH THE DNA METHYLTRANSFERASE INHIBITOR 5-AZA-2'-DEOXYCYTIDINE RESTORED IGFBP3 EXPRESSION AT BOTH THE MRNA AND PROTEIN LEVELS. CHRONIC EXPOSURE TO ABETA1-42 INDUCED IGFBP3 HYPERMETHYLATION AT CPGS, PARTICULARLY AT LOCI -164 AND -173, AND SUBSEQUENTLY SUPPRESSED IGFBP3 EXPRESSION. THEREFORE, WE DEMONSTRATE THAT EXPRESSION OF ANTI-APOPTOTIC IGFBP3 IS REGULATED BY EPIGENETIC DNA METHYLATION, SUGGESTING A MECHANISM THAT CONTRIBUTES TO AD PATHOGENESIS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
12 3153 36 GLUCOSE-INDUCED EXPRESSION OF THE HOMEOTIC TRANSCRIPTION FACTOR PREP1 IS ASSOCIATED WITH HISTONE POST-TRANSLATIONAL MODIFICATIONS IN SKELETAL MUSCLE. AIMS/HYPOTHESIS: CHRONIC HYPERGLYCAEMIA WORSENS INSULIN RESISTANCE IN INDIVIDUALS WITH TYPE 2 DIABETES. WHETHER THIS EFFECT IS CONTRIBUTED BY EPIGENETIC DYSREGULATION AND WHICH GENES ARE INVOLVED REMAIN UNCLEAR. PREP1 (ALSO KNOWN AS PKNOX1) IS A GENE EXERTING MAJOR EFFECTS ON THE SENSITIVITY OF THE GLUCOSE TRANSPORT MACHINERY TO INSULIN. HERE, WE SHOW THAT DYSREGULATION OF PREP1 EXPRESSION BY HIGH GLUCOSE LEVELS IS ASSOCIATED WITH HISTONE MODIFICATIONS AT ITS 5' REGULATORY REGION. METHODS: WE USED MOUSE AND CELL MODELS TO INVESTIGATE PREP1 TRANSCRIPTIONAL REGULATION BY GLUCOSE. RESULTS: DIFFERENTIATED L6 SKELETAL MUSCLE CELLS WERE GROWN IN THE PRESENCE OF EITHER 5.5 OR 25 MMOL/L GLUCOSE (NORMAL [NG] AND HIGH GLUCOSE [HG], RESPECTIVELY). THE HG EXPOSURE INCREASED NUCLEAR FACTOR KAPPA LIGHT CHAIN ENHANCER OF ACTIVATED B CELLS (NF-KAPPAB) P65 BINDING AND RECRUITMENT OF THE SU(VAR)3-9, ENHANCER-OF-ZESTE, TRITHORAX DOMAIN-CONTAINING LYSINE METHYLTRANSFERASE 7 (SET7) HISTONE METHYLTRANSFERASE AND P300 ACETYLTRANSFERASE TO THE 5' REGION OF PREP1, LEADING TO ENHANCED TRANSCRIPTION. IN ADDITION, CHROMATIN IMMUNOPRECIPITATION ASSAYS REVEALED CONCOMITANTLY INCREASED HISTONE H3 MONO- AND DIMETHYLATION AND ACETYLATION AT LYS4 AND LYS9/14, RESPECTIVELY. SKELETAL MUSCLE TISSUE FROM STREPTOZOTOCIN-TREATED DIABETIC MICE ALSO SHOWED PREP1 OVEREXPRESSION ACCOMPANIED BY SIMILARLY INCREASED RECRUITMENT OF NF-KAPPAB P65 AND HISTONE MODIFICATIONS AT THE 5' REGION OF PREP1. IN THESE SAME MICE, AS WELL AS IN PREP1-OVEREXPRESSING L6 CELLS, PREP1-INDUCED RECRUITMENT OF THE REPRESSOR COMPLEX MYOCYTE ENHANCER FACTOR 2 (MEF2)/HISTONE DEACETYLASE 5 (HDAC5) AT THE GLUT4 PROMOTER WAS ALSO INCREASED, LEADING TO REDUCED GLUT4 EXPRESSION. CONCLUSIONS/INTERPRETATION: THESE STUDIES INDICATE THAT HG EXPOSURE INDUCES NF-KAPPAB RECRUITMENT AND HISTONE MODIFICATION AT THE PREP1 5' REGION, THEREBY ENHANCING THE TRANSCRIPTION OF PREP1 AND REPRESSING THAT OF GLUT4. HISTONE CHANGES AT THE PREP1 GENE MAY CONTRIBUTE TO INSULIN RESISTANCE IN INDIVIDUALS WITH TYPE 2 DIABETES.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                  
13 5863 28 SUPPRESSION OF ALLERGIC ASTHMA BY LOSS OF FUNCTION OF MIZ1-MEDIATED TH1 SKEWING. ASTHMA IS THE MOST PREVALENT CHRONIC RESPIRATORY DISEASE WORLDWIDE. THERE IS CURRENTLY NO CURE, AND IT REMAINS AN IMPORTANT CAUSE OF MORBIDITY AND MORTALITY. HERE WE REPORT THAT LUNG-SPECIFIC LOSS OF FUNCTION OF THE TRANSCRIPTION FACTOR MIZ1 (C-MYC-INTERACTING ZINC FINGER PROTEIN-1) UPREGULATES THE PRO-T-HELPER CELL TYPE 1 CYTOKINE IL-12. UPREGULATION OF IL-12 IN TURN STIMULATES A TH1 RESPONSE, THEREBY COUNTERACTING T-HELPER CELL TYPE 2 RESPONSE AND PREVENTING THE ALLERGIC RESPONSE IN MOUSE MODELS OF HOUSE DUST MITE- AND OVA (OVALBUMIN)-INDUCED ASTHMA. USING TRANSGENIC MICE EXPRESSING CRE UNDER A CELL-SPECIFIC PROMOTER, WE DEMONSTRATE THAT MIZ1 ACTS IN LUNG EPITHELIAL CELLS AND DENDRITIC CELLS IN ASTHMA. CHROMATIN IMMUNOPRECIPITATION COUPLED WITH HIGH-THROUGHPUT DNA SEQUENCING OR QUANTITATIVE PCR REVEALS THE BINDING OF MIZ1 ON THE IL12 PROMOTER INDICATING DIRECT REPRESSION OF IL-12 BY MIZ1. IN ADDITION, HDAC1 (HISTONE DEACETYLASE 1) IS RECRUITED TO THE IL12 PROMOTER IN A MIZ1-DEPDENENT MANNER, SUGGESTING EPIGENETIC REPRESSION OF IL12 BY MIZ1. FURTHERMORE, MIZ1 IS UPREGULATED IN THE LUNGS OF ASTHMATIC MICE. OUR DATA TOGETHER SUGGEST THAT MIZ1 IS UPREGULATED DURING ASTHMA, WHICH IN TURN PROMOTES ASTHMA PATHOGENESIS BY PREVENTING TH1 SKEWING THROUGH THE TRANSCRIPTIONAL REPRESSION OF IL-12.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
14 5601 25 RORALPHA IS CRUCIAL FOR ATTENUATED INFLAMMATORY RESPONSE TO MAINTAIN INTESTINAL HOMEOSTASIS. RETINOIC ACID-RELATED ORPHAN RECEPTOR ALPHA (RORALPHA) FUNCTIONS AS A TRANSCRIPTION FACTOR FOR VARIOUS BIOLOGICAL PROCESSES, INCLUDING CIRCADIAN RHYTHM, CANCER, AND METABOLISM. HERE, WE GENERATE INTESTINAL EPITHELIAL CELL (IEC)-SPECIFIC RORALPHA-DEFICIENT (RORALPHA(DELTAIEC)) MICE AND FIND THAT RORALPHA IS CRUCIAL FOR MAINTAINING INTESTINAL HOMEOSTASIS BY ATTENUATING NUCLEAR FACTOR KAPPAB (NF-KAPPAB) TRANSCRIPTIONAL ACTIVITY. RORALPHA(DELTAIEC) MICE EXHIBIT EXCESSIVE INTESTINAL INFLAMMATION AND HIGHLY ACTIVATED INFLAMMATORY RESPONSES IN THE DEXTRAN SULFATE SODIUM (DSS) MOUSE COLITIS MODEL. TRANSCRIPTOME ANALYSIS REVEALS THAT DELETION OF RORALPHA LEADS TO UP-REGULATION OF NF-KAPPAB TARGET GENES IN IECS. CHROMATIN IMMUNOPRECIPITATION ANALYSIS REVEALS CORECRUITMENT OF RORALPHA AND HISTONE DEACETYLASE 3 (HDAC3) ON NF-KAPPAB TARGET PROMOTERS AND SUBSEQUENT DISMISSAL OF CREB BINDING PROTEIN (CBP) AND BROMODOMAIN-CONTAINING PROTEIN 4 (BRD4) FOR TRANSCRIPTIONAL REPRESSION. TOGETHER, WE DEMONSTRATE THAT RORALPHA/HDAC3-MEDIATED ATTENUATION OF NF-KAPPAB SIGNALING CONTROLS THE BALANCE OF INFLAMMATORY RESPONSES, AND THERAPEUTIC STRATEGIES TARGETING THIS EPIGENETIC REGULATION COULD BE BENEFICIAL TO THE TREATMENT OF CHRONIC INFLAMMATORY DISEASES, INCLUDING INFLAMMATORY BOWEL DISEASE (IBD).	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
15 1461 33 DISRUPTION OF RCAN1.4 EXPRESSION MEDIATED BY YY1/HDAC2 MODULATES CHRONIC RENAL ALLOGRAFT INTERSTITIAL FIBROSIS. CHRONIC ALLOGRAFT DYSFUNCTION (CAD) IS A MAJOR FACTOR THAT HINDERS KIDNEY TRANSPLANT SURVIVAL IN THE LONG RUN. EPITHELIAL-MESENCHYMAL TRANSITION (EMT) HAS BEEN CONFIRMED TO SIGNIFICANTLY CONTRIBUTE TO INTERSTITIAL FIBROSIS/TUBULAR ATROPHY (IF/TA), WHICH IS THE MAIN HISTOPATHOLOGICAL FEATURE OF CAD. ABERRANT EXPRESSION OF THE REGULATOR OF CALCINEURIN 1 (RCAN1), RECOGNIZED AS AN ENDOGENOUS INHIBITOR OF THE CALCINEURIN PHOSPHATASE, HAS BEEN SHOWN TO BE EXTENSIVELY INVOLVED IN VARIOUS KIDNEY DISEASES. HOWEVER, IT REMAINS UNCLEAR HOW RCAN1.4 REGULATES IF/TA FORMATION IN CAD PATIENTS. HEREIN, AN IN VIVO MOUSE RENAL TRANSPLANTATION MODEL AND AN IN VITRO MODEL OF HUMAN RENAL TUBULAR EPITHELIAL CELLS (HK-2) TREATED WITH TUMOR NECROSIS FACTOR-ALPHA (TNF-ALPHA) WERE EMPLOYED. OUR RESULTS PROVED THAT RCAN1.4 EXPRESSION WAS DECREASED IN VIVO AND IN VITRO, IN ADDITION TO THE UP-REGULATION OF YIN YANG 1 (YY1), A TRANSCRIPTION FACTOR THAT HAS BEEN REPORTED TO CONVEY MULTIPLE FUNCTIONS IN CHRONIC KIDNEY DISEASE (CKD). KNOCKING IN OF RCAN1.4 EFFICIENTLY ATTENUATED CHRONIC RENAL ALLOGRAFT INTERSTITIAL FIBROSIS IN VIVO AND INHIBITED TNF-ALPHA-INDUCED EMT IN VITRO THROUGH REGULATING ANTI-OXIDATIVE STRESS AND THE CALCINEURIN/NUCLEAR FACTOR OF ACTIVATED T CELLS CYTOPLASMIC 1 (NFATC1) SIGNALING PATHWAY. IN ADDITION, SUPPRESSION OF YY1 MEDIATED BY SHRNA OR SIRNA ALLEVIATED TNF-ALPHA-INDUCED EMT THROUGH ABOLISHING REACTIVE SPECIES PARTLY IN AN RCAN1.4-DEPENDENT MANNER. NOTABLY, WE CONFIRMED THAT YY1 NEGATIVELY REGULATED RCAN1.4 TRANSCRIPTION BY DIRECTLY INTERACTING WITH THE RCAN1.4 PROMOTER. IN ADDITION, HISTONE DEACETYLASE 2 (HDAC2) INTERACTED WITH YY1 TO FORM A MULTI-MOLECULAR COMPLEX, WHICH WAS INVOLVED IN TNF-ALPHA-INDUCED RCAN1.4 TRANSCRIPTIONAL REPRESSION. THEREFORE, RCAN1.4 IS SUGGESTED TO BE MODULATED BY THE YY1/HDAC2 TRANSCRIPTION REPRESSOR COMPLEX IN AN EPIGENETIC MANNER, WHICH IS A MEDIATED NEPHROPROTECTIVE EFFECT PARTLY THROUGH MODULATING O2?- GENERATION AND THE CALCINEURIN/NFATC1 SIGNALING PATHWAY. THUS, THE YY1-RCAN1.4 AXIS CONSTITUTES AN INNOVATIVE TARGET FOR IF/TA TREATMENT IN CAD PATIENTS.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                 
16  197 28 ACINAR ATP8B1/LPC PATHWAY PROMOTES MACROPHAGE EFFEROCYTOSIS AND CLEARANCE OF INFLAMMATION DURING CHRONIC PANCREATITIS DEVELOPMENT. NONINFLAMMATORY CLEARANCE OF DYING CELLS BY PROFESSIONAL PHAGOCYTES, TERMED EFFEROCYTOSIS, IS FUNDAMENTAL IN BOTH HOMEOSTASIS AND INFLAMMATORY FIBROSIS DISEASE BUT HAS NOT BEEN CONFIRMED TO OCCUR IN CHRONIC PANCREATITIS (CP). HERE, WE INVESTIGATED WHETHER EFFEROCYTOSIS CONSTITUTES A NOVEL REGULATORY TARGET IN CP AND ITS MECHANISMS. PRSS1 TRANSGENIC (PRSS1(TG)) MICE WERE TREATED WITH CAERULEIN TO MIMIC CP DEVELOPMENT. PHOSPHOLIPID METABOLITE PROFILING AND EPIGENETIC ASSAYS WERE PERFORMED WITH PRSS1(TG) CP MODELS. THE POTENTIAL FUNCTIONS OF ATP8B1 IN CP MODEL WERE CLARIFIED USING ATP8B1-OVEREXPRESSING ADENO-ASSOCIATED VIRUS, IMMUNOFLUORESCENCE, ENZYME-LINKED IMMUNOSORBENT ASSAY(ELISA), AND LIPID METABOLOMIC APPROACHES. ATAC-SEQ COMBINED WITH RNA-SEQ WAS THEN USED TO IDENTIFY TRANSCRIPTION FACTORS BINDING TO THE ATP8B1 PROMOTER, AND CHIP-QPCR AND LUCIFERASE ASSAYS WERE USED TO CONFIRM THAT THE IDENTIFIED TRANSCRIPTION FACTOR BOUND TO THE ATP8B1 PROMOTER, AND TO IDENTIFY THE SPECIFIC BINDING SITE. FLOW CYTOMETRY WAS PERFORMED TO ANALYZE THE PROPORTION OF PANCREATIC MACROPHAGES. DECREASED EFFEROCYTOSIS WITH AGGRAVATED INFLAMMATION WAS IDENTIFIED IN CP. THE LYSOPHOSPHATIDYLCHOLINE (LPC) PATHWAY WAS THE MOST OBVIOUSLY DYSREGULATED PHOSPHOLIPID PATHWAY, AND LPC AND ATP8B1 EXPRESSION GRADUALLY DECREASED DURING CP DEVELOPMENT. H3K27ME3 CHIP-SEQ SHOWED THAT INCREASED ATP8B1 PROMOTER METHYLATION LED TO TRANSCRIPTIONAL INHIBITION. ATP8B1 COMPLEMENTATION SUBSTANTIALLY INCREASED THE LPC CONCENTRATION AND IMPROVED CP OUTCOMES. BHLHA15 WAS IDENTIFIED AS A TRANSCRIPTION FACTOR THAT BINDS TO THE ATP8B1 PROMOTER AND REGULATES PHOSPHOLIPID METABOLISM. OUR STUDY INDICATES THAT THE ACINAR ATP8B1/LPC PATHWAY ACTS AS AN IMPORTANT "FIND-ME" SIGNAL FOR MACROPHAGES AND PLAYS A PROTECTIVE ROLE IN CP, WITH ATP8B1 TRANSCRIPTION PROMOTED BY THE ACINAR CELL-SPECIFIC TRANSCRIPTION FACTOR BHLHA15. BHLHA15, ATP8B1, AND LPC COULD BE CLINICALLY TRANSLATED INTO VALUABLE THERAPEUTIC TARGETS TO OVERCOME THE LIMITATIONS OF CURRENT CP THERAPIES.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
17 1334 24 DEREGULATION OF AIOLOS EXPRESSION IN CHRONIC LYMPHOCYTIC LEUKEMIA IS ASSOCIATED WITH EPIGENETIC MODIFICATIONS. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF MATURE NEOPLASTIC B CELLS THAT ARE RESISTANT TO APOPTOSIS. AIOLOS, A MEMBER OF THE IKAROS FAMILY OF ZINC-FINGER TRANSCRIPTION FACTORS, PLAYS AN IMPORTANT ROLE IN THE CONTROL OF MATURE B LYMPHOCYTE DIFFERENTIATION AND MATURATION. IN THIS STUDY, WE SHOWED THAT AIOLOS EXPRESSION IS UP-REGULATED IN B-CLL CELLS. THIS OVEREXPRESSION DOES NOT IMPLICATE ISOFORM IMBALANCE OR DISTURB AIOLOS SUBCELLULAR LOCALIZATION. THE CHROMATIN STATUS AT THE AIOLOS PROMOTER IN CLL IS DEFINED BY THE DEMETHYLATION OF DNA AND AN ENRICHMENT OF EUCHROMATIN ASSOCIATED HISTONE MARKERS, SUCH AS THE DIMETHYLATION OF THE LYSINE 4 ON HISTONE H3. THESE EPIGENETIC MODIFICATIONS SHOULD ALLOW ITS UPSTREAM EFFECTORS, SUCH AS NUCLEAR FACTOR-KAPPAB, CONSTITUTIVELY ACTIVATED IN CLL, TO GAIN ACCESS TO PROMOTER, RESULTING UP-REGULATION OF AIOLOS. TO DETERMINE THE CONSEQUENCES OF AIOLOS DEREGULATION IN CLL, WE ANALYZED THE EFFECTS OF AIOLOS OVEREXPRESSION OR DOWN-REGULATION ON APOPTOSIS. AIOLOS IS INVOLVED IN CELL SURVIVAL BY REGULATING THE EXPRESSION OF SOME BCL-2 FAMILY MEMBERS. OUR RESULTS STRONGLY SUGGEST THAT AIOLOS DEREGULATION BY EPIGENETIC MODIFICATIONS MAY BE A HALLMARK OF CLL.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
18 1806 26 EFFECT OF TRANSCRIPTION INHIBITION AND GENERATION OF SUPPRESSIVE VIRAL NON-CODING RNAS. BACKGROUND: HIV-1 PATIENTS RECEIVING COMBINATION ANTIRETROVIRAL THERAPY (CART) SURVIVE INFECTION BUT REQUIRE LIFE-LONG ADHERENCE AT HIGH EXPENSE. IN CHRONIC CART-TREATED PATIENTS WITH UNDETECTABLE VIRAL TITERS, CELL-ASSOCIATED VIRAL RNA IS STILL DETECTABLE, POINTING TO LOW-LEVEL VIRAL TRANSCRIPTIONAL LEAKINESS. TO DATE, THERE ARE NO FDA-APPROVED DRUGS AGAINST HIV-1 TRANSCRIPTION. WE HAVE PREVIOUSLY SHOWN THAT F07#13, A THIRD GENERATION TAT PEPTIDE MIMETIC WITH COMPETITIVE ACTIVITY AGAINST CDK9/T1-TAT BINDING SITES, INHIBITS HIV-1 TRANSCRIPTION IN VITRO AND IN VIVO. RESULTS: HERE, WE DEMONSTRATE THAT INCREASING CONCENTRATIONS OF F07#13 (0.01, 0.1, 1 MICROM) CAUSE A DECREASE IN TAT LEVELS IN A DOSE-DEPENDENT MANNER BY INHIBITING THE CDK9/T1-TAT COMPLEX FORMATION AND SUBSEQUENT UBIQUITIN-MEDIATED TAT SEQUESTRATION AND DEGRADATION. OUR DATA INDICATE THAT COMPLEXES I AND IV CONTAIN DISTINCT PATTERNS OF UBIQUITINATED TAT AND THAT TRANSCRIPTIONAL INHIBITION INDUCED BY F07#13 CAUSES AN OVERALL REDUCTION IN TAT LEVELS. THIS REDUCTION MAY BE TRIGGERED BY F07#13 BUT ULTIMATELY IS MEDIATED BY TAR-GAG VIRAL RNAS THAT BIND SUPPRESSIVE TRANSCRIPTION FACTORS (SIMILAR TO 7SK, NRON, HOTAIR, AND XIST LNCRNAS) TO ENHANCE TRANSCRIPTIONAL GENE SILENCING AND LATENCY. THESE RNAS COMPLEX WITH PRC2, SIN3A, AND CUL4B, RESULTING IN EPIGENETIC MODIFICATIONS. FINALLY, WE OBSERVED AN F07#13-MEDIATED DECREASE OF VIRAL BURDEN BY TARGETING THE R REGION OF THE LONG TERMINAL REPEAT (HIV-1 PROMOTER REGION, LTR), PROMOTING BOTH PAUSED POLYMERASES AND INCREASED EFFICIENCY OF CRISPR/CAS9 EDITING IN INFECTED CELLS. THIS IMPLIES THAT GENE EDITING MAY BE BEST PERFORMED UNDER A REPRESSED TRANSCRIPTIONAL STATE. CONCLUSIONS: COLLECTIVELY, OUR RESULTS INDICATE THAT F07#13, WHICH CAN TERMINATE RNA POLYMERASE II AT DISTINCT SITES, CAN GENERATE SCAFFOLD RNAS, WHICH MAY ASSEMBLE INTO SPECIFIC SETS OF "RNA MACHINES" THAT CONTRIBUTE TO GENE REGULATION. IT REMAINS TO BE SEEN WHETHER THESE EFFECTS CAN ALSO BE SEEN IN VARIOUS CLADES THAT HAVE VARYING PROMOTER STRENGTH, MUTANT LTRS, AND IN PATIENT SAMPLES.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
19 1274 36 DACH1 PROTECTS PODOCYTES FROM EXPERIMENTAL DIABETIC INJURY AND MODULATES PTIP-H3K4ME3 ACTIVITY. DACHSHUND HOMOLOG 1 (DACH1), A KEY CELL-FATE DETERMINANT, REGULATES TRANSCRIPTION BY DNA SEQUENCE-SPECIFIC BINDING. WE IDENTIFIED DIMINISHED DACH1 EXPRESSION IN A LARGE-SCALE SCREEN FOR MUTATIONS THAT CONVERT INJURY-RESISTANT PODOCYTES INTO INJURY-SUSCEPTIBLE PODOCYTES. IN DIABETIC KIDNEY DISEASE (DKD) PATIENTS, PODOCYTE DACH1 EXPRESSION LEVELS ARE DIMINISHED, A CONDITION THAT STRONGLY CORRELATES WITH POOR CLINICAL OUTCOMES. GLOBAL DACH1 KO MICE MANIFEST RENAL HYPOPLASIA AND DIE PERINATALLY. PODOCYTE-SPECIFIC DACH1 KO MICE, HOWEVER, MAINTAIN NORMAL GLOMERULAR ARCHITECTURE AT BASELINE, BUT RAPIDLY EXHIBIT PODOCYTE INJURY AFTER DIABETES ONSET. FURTHERMORE, PODOCYTE-SPECIFIC AUGMENTATION OF DACH1 EXPRESSION IN MICE PROTECTS FROM DKD. COMBINED RNA SEQUENCING AND IN SILICO PROMOTER ANALYSIS REVEAL CONVERSELY OVERLAPPING GLOMERULAR TRANSCRIPTOMIC SIGNATURES BETWEEN PODOCYTE-SPECIFIC DACH1 AND PAX TRANSACTIVATION-DOMAIN INTERACTING PROTEIN (PTIP) KO MICE, WITH UPREGULATED GENES POSSESSING HIGHER-THAN-EXPECTED NUMBERS OF PROMOTER DACH1-BINDING SITES. PTIP, AN ESSENTIAL COMPONENT OF THE ACTIVATING HISTONE H3 LYSINE 4 TRIMETHYLATION (H3K4ME3) COMPLEX, INTERACTS WITH DACH1 AND IS RECRUITED BY DACH1 TO ITS PROMOTER-BINDING SITES. DACH1-PTIP RECRUITMENT REPRESSES TRANSCRIPTION AND REDUCES PROMOTER H3K4ME3 LEVELS. DACH1 KNOCKDOWN IN PODOCYTES COMBINED WITH HYPERGLYCEMIA TRIGGERS TARGET GENE UPREGULATION AND INCREASES PROMOTER H3K4ME3. THESE FINDINGS REVEAL THAT IN DKD, DIMINISHED DACH1 EXPRESSION ENHANCES PODOCYTE INJURY VULNERABILITY VIA EPIGENETIC DEREPRESSION OF ITS TARGET GENES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
20  136 26 ABERRANT DNA HYPERMETHYLATION PATTERNS LEAD TO TRANSCRIPTIONAL SILENCING OF TUMOR SUPPRESSOR GENES IN UVB-EXPOSED SKIN AND UVB-INDUCED SKIN TUMORS OF MICE. OVEREXPOSURE OF THE HUMAN SKIN TO SOLAR ULTRAVIOLET (UV) RADIATION IS THE MAJOR ETIOLOGIC FACTOR FOR DEVELOPMENT OF SKIN CANCERS. HERE, WE REPORT THE RESULTS OF EPIGENETIC MODIFICATIONS IN UV-EXPOSED SKIN AND SKIN TUMORS IN A SYSTEMATIC MANNER. THE SKIN AND TUMOR SAMPLES WERE COLLECTED AFTER CHRONIC EXPOSURE OF THE SKIN OF SKH-1 HAIRLESS MICE TO UVB RADIATION USING A WELL-ESTABLISHED PHOTOCARCINOGENESIS PROTOCOL. WE FOUND A DISTINCT DNA HYPERMETHYLATION PATTERN IN THE UVB-EXPOSED EPIDERMAL SKIN AND UVB-INDUCED SKIN TUMORS THAT WAS ASSOCIATED WITH THE ELEVATED EXPRESSION AND ACTIVITY OF THE DNA METHYLTRANSFERASES (DNMT) 1, DNMT3A AND DNMT3B. TO EXPLORE THE ROLE OF HYPERMETHYLATION IN SKIN PHOTOCARCINOGENESIS, WE FOCUSED ON THE P16(INK4A) AND RASSF1A TUMOR SUPPRESSOR GENES, WHICH ARE TRANSCRIPTIONALLY SILENCED ON METHYLATION. WE ESTABLISHED THAT THE SILENCING OF THESE GENES IN UVB-EXPOSED EPIDERMIS AND UVB-INDUCED SKIN TUMORS IS ASSOCIATED WITH A NETWORK OF EPIGENETIC MODIFICATIONS, INCLUDING HYPOACETYLATION OF HISTONE H3 AND H4 AND INCREASED HISTONE DEACETYLATION, AS WELL AS RECRUITMENT OF METHYL-BINDING PROTEINS, INCLUDING MECP2 AND MBD1, TO THE METHYLATED CPGS. HIGHER LEVELS OF DNA METHYLATION AND DNMT ACTIVITY IN HUMAN SQUAMOUS CELL CARCINOMA SPECIMENS THAN IN NORMAL HUMAN SKIN SUGGEST THAT THE DATA ARE RELEVANT CLINICALLY. OUR DATA INDICATE FOR THE FIRST TIME THAT UVB-INDUCED DNA HYPERMETHYLATION, ENHANCED DNMT ACTIVITY AND HISTONE MODIFICATIONS OCCUR IN UVB-EXPOSED SKIN AND UVB-INDUCED SKIN TUMORS AND SUGGEST THAT THESE EVENTS ARE INVOLVED IN THE SILENCING OF TUMOR SUPPRESSOR GENES AND IN SKIN TUMOR DEVELOPMENT.	2011