1 1002 148 CHRONIC TREATMENT OF NON-SMALL-CELL LUNG CANCER CELLS WITH GEFITINIB LEADS TO AN EPIGENETIC LOSS OF EPITHELIAL PROPERTIES ASSOCIATED WITH REDUCTIONS IN MICRORNA-155 AND -200C. BACKGROUND: THE EGFR TYROSINE KINASE INHIBITOR GEFITINIB IS USED IN THERAPY FOR NON-SMALL-CELL LUNG CANCER (NSCLC). HOWEVER, ITS APPLICATION IS LIMITED BY RESISTANCE-ACCELERATED DISEASE PROGRESSION, WHICH IS ACCOMPANIED BY THE EPITHELIAL-TO-MESENCHYMAL TRANSITION (EMT). IN THE PRESENT STUDY, WE PERFORMED MULTIPLE EXPRESSION ANALYSES OF MICRORNAS (MIRNAS) AND QUANTIFIED THE EXPRESSION OF SEVERAL RELATED EMT PLAYERS IN GEFITINIB-RESISTANT NSCLC CELLS. METHODS AND RESULTS: TO ESTABLISH GEFITINIB-RESISTANT NSCLC CELLS, GEFITINIB-SENSITIVE HCC827 CELLS, WHICH EXHIBIT AN IN-FRAME DELETION [E746-A750] IN EGFR EXON 19, WERE EXPOSED TO GEFITINIB FOR AT LEAST 1.5 MONTHS. NEXT, TO PROFILE "GEFITINIB-RESISTANT HCC827 (HCC827GR)" CELLS, WHICH HAVE A SECONDARY T790M MUTATION IN EGFR EXON 20, A MIRNA ARRAY ANALYSIS WAS PERFORMED IN HCC827 AND HCC827GR CELLS. THE GREATEST DIFFERENCES WERE SEEN IN THE LEVELS OF MIR-155 AND MIR-200C, WHICH ESSENTIALLY DISAPPEARED IN HCC827GR CELLS. IN ADDITION TO THESE REDUCTIONS, THE LEVELS OF SMAD2 AND ZEB1, WHICH ARE BOTH KEY PLAYERS IN EMT AND TARGETS FOR MIR-155 AND MIR-200C, RESPECTIVELY, WERE DRAMATICALLY INCREASED IN HCC827GR CELLS. IN HCC827GR CELLS, THE EXPRESSION OF EPITHELIAL-CADHERIN (E-CADHERIN) WAS GREATLY REDUCED WITH REPRESSIVE HISTONE MODIFICATIONS, WHEREAS VIMENTIN, WHICH IS EXPRESSED IN MESENCHYMAL CELLS, WAS DRAMATICALLY INCREASED WITH ACTIVE HISTONE MODIFICATIONS. IN ANOTHER GEFITINIB-RESISTANT NSCLC CELL LINE (H1975 CELLS), SIMILAR TO THE FINDINGS IN HCC827GR CELLS, BOTH MIR-155 AND MIR-200C WERE ABSENT, AND THE EMT WAS INDUCED ALONG WITH EPIGENETIC MODIFICATIONS. INTERESTINGLY, THE INHIBITION OF BOTH MIR-155 AND MIR-200C IN HCC827 CELLS WITHOUT GEFITINIB INDUCED SIGNIFICANT INCREASES IN SMAD2 AND ZEB1 ALONG WITH A DRAMATIC DECREASE IN E-CADHERIN AND A SLIGHT INCREASE IN VIMENTIN. FURTHERMORE, ALTHOUGH THE INHIBITION OF THESE MIRNAS IN HCC827 CELLS DECREASED GEFITINIB SENSITIVITY, THIS DUAL-INHIBITION IN HCC827 CELLS WITHOUT GEFITINIB DID NOT PRODUCE A SECONDARY T790M MUTATION IN EGFR EXON 20. CONCLUSION AND IMPLICATIONS: THESE RESULTS SUGGEST THAT CHRONIC TREATMENT OF NSCLC CELLS WITH GEFITINIB CHANGES THE EXPRESSION OF MIRNAS, INCLUDING DRAMATIC REDUCTIONS IN MIR-155 AND MIR-200C ALONG WITH AN EGFR MUTATION. FURTHERMORE, THIS DEPLETION OF MIR-155 AND MIR-200C MAY BE ASSOCIATED WITH THE EMT ALONG WITH HISTONE MODIFICATIONS, AND MAY CONTRIBUTE TO THE DECREASE IN THE SENSITIVITY TO GEFITINIB INDEPENDENT OF A SECONDARY EGFR MUTATION. 2017 2 1966 34 EPIGENETIC ALTERATION OF PRKCDBP IN COLORECTAL CANCERS AND ITS IMPLICATION IN TUMOR CELL RESISTANCE TO TNFALPHA-INDUCED APOPTOSIS. PURPOSE: PRKCDBP IS A PUTATIVE TUMOR SUPPRESSOR IN WHICH ALTERATION HAS BEEN OBSERVED IN SEVERAL HUMAN CANCERS. WE INVESTIGATED EXPRESSION AND FUNCTION OF PRKCDBP IN COLORECTAL CELLS AND TISSUES TO EXPLORE ITS CANDIDACY AS A SUPPRESSOR IN COLORECTAL TUMORIGENESIS. EXPERIMENTAL DESIGN: EXPRESSION AND METHYLATION STATUS OF PRKCDBP AND ITS EFFECT ON TUMOR GROWTH WERE EVALUATED. TRANSCRIPTIONAL REGULATION BY NF-KAPPAB SIGNALING WAS DEFINED BY LUCIFERASE REPORTER AND CHROMATIN IMMUNOPRECIPITATION ASSAYS. RESULTS: PRKCDBP EXPRESSION WAS HARDLY DETECTABLE IN 29 OF 80 (36%) PRIMARY TUMORS AND 11 OF 19 (58%) CELL LINES, AND ITS ALTERATION CORRELATED WITH TUMOR STAGE AND GRADE. PROMOTER HYPERMETHYLATION WAS COMMONLY FOUND IN CANCERS. PRKCDBP EXPRESSION INDUCED THE G(1) CELL-CYCLE ARREST AND INCREASED CELLULAR SENSITIVITY TO VARIOUS APOPTOTIC STRESSES. PRKCDBP WAS INDUCED BY TNFALPHA, AND ITS LEVEL CORRELATED WITH TUMOR CELL SENSITIVITY TO TNFALPHA-INDUCED APOPTOSIS. PRKCDBP INDUCTION BY TNFALPHA WAS DISRUPTED BY BLOCKING NF-KAPPAB SIGNALING WHILE IT WAS ENHANCED BY RELA TRANSFECTION. THE PRKCDBP PROMOTER ACTIVITY WAS INCREASED IN RESPONSE TO TNFALPHA, AND THIS RESPONSE WAS ABOLISHED BY DISRUPTION OF A KAPPAB SITE IN THE PROMOTER. PRKCDBP DELAYED THE FORMATION AND GROWTH OF XENOGRAFT TUMORS AND IMPROVED TUMOR RESPONSE TO TNFALPHA-INDUCED APOPTOSIS. CONCLUSIONS: PRKCDBP IS A PROAPOPTOTIC TUMOR SUPPRESSOR WHICH IS COMMONLY ALTERED IN COLORECTAL CANCER BY PROMOTER HYPERMETHYLATION, AND ITS GENE TRANSCRIPTION IS DIRECTLY ACTIVATED BY NF-KAPPAB IN RESPONSE TO TNFALPHA. THIS SUGGESTS THAT PRKCDBP INACTIVATION MAY CONTRIBUTE TO TUMOR PROGRESSION BY REDUCING CELLULAR SENSITIVITY TO TNFALPHA AND OTHER STRESSES, PARTICULARLY UNDER CHRONIC INFLAMMATORY MICROENVIRONMENT. 2011 3 3468 47 HYPOXIA-INDUCED DNA HYPERMETHYLATION IN HUMAN PULMONARY FIBROBLASTS IS ASSOCIATED WITH THY-1 PROMOTER METHYLATION AND THE DEVELOPMENT OF A PRO-FIBROTIC PHENOTYPE. BACKGROUND: PULMONARY FIBROSIS IS A DEBILITATING AND LETHAL DISEASE WITH NO EFFECTIVE TREATMENT OPTIONS. UNDERSTANDING THE PATHOLOGICAL PROCESSES AT PLAY WILL DIRECT THE APPLICATION OF NOVEL THERAPEUTIC AVENUES. HYPOXIA HAS BEEN IMPLICATED IN THE PATHOGENESIS OF PULMONARY FIBROSIS YET THE PRECISE MECHANISM BY WHICH IT CONTRIBUTES TO DISEASE PROGRESSION REMAINS TO BE FULLY ELUCIDATED. IT HAS BEEN SHOWN THAT CHRONIC HYPOXIA CAN ALTER DNA METHYLATION PATTERNS IN TUMOUR-DERIVED CELL LINES. THIS EPIGENETIC ALTERATION CAN INDUCE CHANGES IN CELLULAR PHENOTYPE WITH PROMOTER METHYLATION BEING ASSOCIATED WITH GENE SILENCING. OF PARTICULAR RELEVANCE TO IDIOPATHIC PULMONARY FIBROSIS (IPF) IS THE OBSERVATION THAT THY-1 PROMOTER METHYLATION IS ASSOCIATED WITH A MYOFIBROBLAST PHENOTYPE WHERE LOSS OF THY-1 OCCURS ALONGSIDE INCREASED ALPHA SMOOTH MUSCLE ACTIN (ALPHA-SMA) EXPRESSION. THE INITIAL AIM OF THIS STUDY WAS TO DETERMINE WHETHER HYPOXIA REGULATES DNA METHYLATION IN NORMAL HUMAN LUNG FIBROBLASTS (CCD19LU). AS IT HAS BEEN REPORTED THAT HYPOXIA SUPPRESSES THY-1 EXPRESSION DURING LUNG DEVELOPMENT WE ALSO STUDIED THE EFFECT OF HYPOXIA ON THY-1 PROMOTER METHYLATION AND GENE EXPRESSION. METHODS: CCD19LU WERE GROWN FOR UP TO 8 DAYS IN HYPOXIA AND ASSESSED FOR GLOBAL CHANGES IN DNA METHYLATION USING FLOW CYTOMETRY. REAL-TIME PCR WAS USED TO QUANTIFY EXPRESSION OF THY-1, ALPHA-SMA, COLLAGEN I AND III. GENOMIC DNA WAS BISULPHITE TREATED AND METHYLATION SPECIFIC PCR (MSPCR) WAS USED TO EXAMINE THE METHYLATION STATUS OF THE THY-1 PROMOTER. RESULTS: SIGNIFICANT GLOBAL HYPERMETHYLATION WAS DETECTED IN HYPOXIC FIBROBLASTS RELATIVE TO NORMOXIC CONTROLS AND WAS ACCOMPANIED BY INCREASED EXPRESSION OF MYOFIBROBLAST MARKERS. THY-1 MRNA EXPRESSION WAS SUPPRESSED IN HYPOXIC CELLS, WHICH WAS RESTORED WITH THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE. MSPCR REVEALED THAT THY-1 BECAME METHYLATED FOLLOWING FIBROBLAST EXPOSURE TO 1% O2. CONCLUSION: THESE DATA SUGGEST THAT GLOBAL AND GENE-SPECIFIC CHANGES IN DNA METHYLATION MAY PLAY AN IMPORTANT ROLE IN FIBROBLAST FUNCTION IN HYPOXIA. 2012 4 3049 28 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 5 2453 30 EPIGENETIC SUPPRESSION OF THE IMMUNOREGULATOR MZB1 IS ASSOCIATED WITH THE MALIGNANT PHENOTYPE OF GASTRIC CANCER. PREDICTION OF TUMOR RECURRENCE AFTER CURATIVE RESECTION IS CRITICAL FOR DETERMINING THE PROGNOSIS OF PATIENTS WITH GASTRIC CANCER (GC). THE INITIATION AND PROGRESSION OF GC ARE ASSOCIATED WITH INAPPROPRIATE IMMUNE RESPONSES CAUSED BY CHRONIC INFLAMMATION OF THE GASTRIC MUCOSA. TO IDENTIFY IMMUNOREGULATORY MOLECULES INVOLVED IN GC PROGRESSION, GC CELL LINES AND 200 PAIRS OF TUMOR AND NORMAL TISSUES FROM PATIENTS WITH GC WERE ANALYZED FOR GENE EXPRESSION, AMPLIFICATION AND METHYLATION AS WELL AS FUNCTION OF A DIFFERENTIALLY EXPRESSED GENE. THE TRANSCRIPTOME ANALYSIS REVEALED THAT MARGINAL ZONE B AND B1 CELL SPECIFIC PROTEIN (MZB1) WAS EXPRESSED AT SIGNIFICANTLY DECREASED LEVELS IN PRIMARY GC TISSUES WHEN COMPARED WITH THE CORRESPONDING NORMAL GASTRIC MUCOSA. PCR ARRAY ANALYSIS EXPLORING GENES EXPRESSED COOPERATIVELY WITH MZB1 REVEALED THAT DIFFERENTIAL EXPRESSION OF MZB1 MRNA IN GC CELL LINES CORRELATED POSITIVELY WITH THE LEVELS OF THE MRNAS ENCODING ESTROGEN RECEPTOR 1 AND DESUMOYLATING ISOPEPTIDASE 1. HYPERMETHYLATION OF THE MZB1 PROMOTER WAS FREQUENT IN CELL LINES WITH DECREASED LEVELS OF MZB1 MRNA. SIRNA-MEDIATED KNOCKDOWN OF MZB1 SIGNIFICANTLY INCREASED PROLIFERATION, INVASION AND MIGRATION OF GC CELL LINES. LOW MZB1 EXPRESSION WAS AN INDEPENDENT PROGNOSTIC FACTOR FOR RECURRENCE AFTER CURATIVE GASTRECTOMY AND WAS ASSOCIATED SIGNIFICANTLY WITH INCREASED HEMATOGENOUS RECURRENCE. MZB1 ACTS AS A SUPPRESSOR OF GC. LOW MZB1 EXPRESSION IN THE PRIMARY GC TISSUE IS PREDICTIVE OF RECURRENCE AFTER CURATIVE RESECTION. 2016 6 2767 49 EXPRESSION, PROGNOSTIC VALUE, AND FUNCTIONAL MECHANISM OF THE KDM5 FAMILY IN PANCREATIC CANCER. BACKGROUND: THE HISTONE LYSINE DEMETHYLASE KDM5 FAMILY IS AN IMPORTANT EPIGENETIC STATE-MODIFYING ENZYME FAMILY. INCREASING EVIDENCE SUPPORTS THAT EPIGENETIC ABNORMALITIES IN THE KDM5 FAMILY ARE RELATED TO MULTIPLE CANCERS IN HUMANS. HOWEVER, THE ROLE OF THE KDM5 FAMILY IN PANCREATIC CANCER IS NOT CLEAR, AND RELATED RESEARCH IS VERY SCARCE. METHODS: R SOFTWARE, KAPLAN-MEIER PLOTTER, CBIOPORTAL, TIMER, LINKEDOMICS, STRING, METASCAPE, TISIDB, AND THE GSCA LITE ONLINE TOOL WERE UTILIZED FOR BIOINFORMATICS ANALYSIS. RESULTS: KDM5A/B/C WAS SIGNIFICANTLY OVEREXPRESSED IN MANY KINDS OF TUMOR TISSUES, INCLUDING PANCREATIC ADENOCARCINOMA (PAAD), WHILE THE EXPRESSION OF KDM5D WAS SIGNIFICANTLY DOWNREGULATED. THE HIGH EXPRESSION OF KDM5A/B/C WAS RELATED TO POOR CLINICAL FEATURES, SUCH AS WORSE TREATMENT EFFICACY, HIGHER TUMOR GRADE, AND MORE ADVANCED CLINICAL STAGE. PATIENTS WITH A FAMILY HISTORY OF BREAST CANCER AND MELANOMA, HISTORY OF DRINKING OR HISTORY CHRONIC PANCREATITIS WERE MORE LIKELY TO HAVE KDM5A/B/C GENE ABNORMALITIES, WHICH WERE RELATED TO A VARIETY OF ADVERSE CLINICAL FEATURES. THE RESULTS OF GENE ONTOLOGY (GO) AND KYOTO ENCYCLOPEDIA OF GENES AND GENOMES (KEGG) PATHWAY ANALYSES OF THE KDM5 FAMILY AND ITS 800 CO-EXPRESSED GENES SHOWED THAT MANY GENE TERMS RELATED TO CELL PROLIFERATION, MIGRATION AND MANY CARCINOGENIC PATHWAYS. NOTABLY, WE FOUND THAT THE EXPRESSION LEVEL OF KDM5A/B/C WAS POSITIVELY CORRELATED WITH THE EXPRESSION OF MULTIPLE KEY DRIVER GENES SUCH AS KRAS, BRCA1, AND BRCA2 ETC. IN ADDITION, PPI NETWORK ANALYSIS SHOWED KDM5 FAMILY PROTEINS HAVE STRONG INTERACTIONS WITH HISTONE DEACETYLASE FAMILY 1 (HDAC1), WHICH COULD MODIFY THE LYSINES OF HISTONE H3, AND CO-ACT ON MANY PATHWAYS, INCLUDING THE "LONGEVITY-REGULATING PATHWAY" AND "NOTCH SIGNALING PATHWAY". MOREOVER, THE UPREGULATION OF KDM5A/B/C EXPRESSION WAS ASSOCIATED WITH AN INCREASE IN THE INFILTRATION OF B CELLS, CD8(+) T CELLS AND OTHER INFILTRATING IMMUNE LYMPHOCYTES AND THE EXPRESSION LEVELS OF IMMUNE MOLECULES SUCH AS NT5E AND CD274. INTERESTINGLY, THE OVEREXPRESSION OF KDM5A/C WAS ALSO CORELATED WITH REDUCED SENSITIVITY OF PANCREATIC CANCER CELLS TO MANY KINDS OF PANCREATIC CANCER-TARGETING OR CHEMOTHERAPEUTIC DRUGS, INCLUDING AXITINIB AND GEMCITABINE. CONCLUSION: KDM5 FAMILY MEMBERS MAY BE PROGNOSTIC MARKERS AND NEW THERAPEUTIC TARGETS FOR PATIENTS WITH PANCREATIC CANCER. 2022 7 155 34 ABERRANT METHYLATION OF POLO-LIKE KINASE CPG ISLANDS IN PLK4 HETEROZYGOUS MICE. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC), ONE OF THE MOST COMMON CANCERS WORLD-WIDE OCCURS TWICE AS OFTEN IN MEN COMPARED TO WOMEN. PREDISPOSING CONDITIONS SUCH AS ALCOHOLISM, CHRONIC VIRAL HEPATITIS, AFLATOXIN B1 INGESTION, AND CIRRHOSIS ALL CONTRIBUTE TO THE DEVELOPMENT OF HCC. METHODS: WE USED A COMBINATION OF METHYLATION SPECIFIC PCR AND BISULFITE SEQUENCING, QREAL-TIME PCR (QPCR), AND WESTERN BLOT ANALYSIS TO EXAMINE EPIGENETIC CHANGES FOR THE POLO-LIKE KINASES (PLKS) DURING THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) IN PLK4 HETEROZYGOUS MICE AND MURINE EMBRYONIC FIBROBLASTS (MEFS). RESULTS: HERE WE REPORT THAT THE PROMOTER METHYLATION OF PLK4 CPG ISLANDS INCREASES WITH AGE, WAS MORE PREVALENT IN MALES AND THAT PLK4 EPIGENETIC MODIFICATION AND SUBSEQUENT DOWNREGULATION OF EXPRESSION WAS ASSOCIATED WITH THE DEVELOPMENT OF HCC IN PLK4 MUTANT MICE. INTERESTINGLY, THE OPPOSITE OCCURS WITH ANOTHER PLK FAMILY MEMBER, PLK1 WHICH WAS TYPICALLY HYPERMETHYLATED IN NORMAL LIVER TISSUE BUT BECAME HYPOMETHYLATED AND UPREGULATED IN LIVER TUMOURS. FURTHERMORE, UPON ALCOHOL EXPOSURE MURINE EMBRYONIC FIBROBLASTS EXHIBITED INCREASED PLK4 HYPERMETHYLATION AND DOWNREGULATION ALONG WITH INCREASED CENTROSOME NUMBERS AND MULTINUCLEATION. CONCLUSIONS: THESE RESULTS SUGGEST THAT ABERRANT PLK METHYLATION IS CORRELATED WITH THE DEVELOPMENT OF HCC IN MICE. 2011 8 3128 41 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 9 6294 29 THE PROINFLAMMATORY CYTOKINE TNFALPHA INDUCES DNA DEMETHYLATION-DEPENDENT AND -INDEPENDENT ACTIVATION OF INTERLEUKIN-32 EXPRESSION. IL-32 IS A CYTOKINE INVOLVED IN PROINFLAMMATORY IMMUNE RESPONSES TO BACTERIAL AND VIRAL INFECTIONS. HOWEVER, THE ROLE OF EPIGENETIC EVENTS IN THE REGULATION OF IL-32 GENE EXPRESSION IS UNDERSTUDIED. HERE WE SHOW THAT IL-32 IS REPRESSED BY DNA METHYLATION IN HEK293 CELLS. USING CHIP SEQUENCING, LOCUS-SPECIFIC METHYLATION ANALYSIS, CRISPR/CAS9-MEDIATED GENOME EDITING, AND RT-QPCR (QUANTITATIVE RT-PCR) AND IMMUNOBLOT ASSAYS, WE FOUND THAT SHORT-TERM TREATMENT (A FEW HOURS) WITH THE PROINFLAMMATORY CYTOKINE TUMOR NECROSIS FACTOR ALPHA (TNFALPHA) ACTIVATES IL-32 IN A DNA DEMETHYLATION-INDEPENDENT MANNER. IN CONTRAST, PROLONGED TNFALPHA TREATMENT (SEVERAL DAYS) INDUCED DNA DEMETHYLATION AT THE PROMOTER AND A CPG ISLAND IN THE IL-32 GENE IN A TET (TEN-ELEVEN TRANSLOCATION) FAMILY ENZYME- AND NF-KAPPAB-DEPENDENT MANNER. NOTABLY, THE HYPOMETHYLATION STATUS OF TRANSCRIPTIONAL REGULATORY ELEMENTS IN IL-32 WAS MAINTAINED FOR A LONG TIME (SEVERAL WEEKS), CAUSING ELEVATED IL-32 EXPRESSION EVEN IN THE ABSENCE OF TNFALPHA. CONSIDERING THAT IL-32 CAN, IN TURN, INDUCE TNFALPHA EXPRESSION, WE SPECULATE THAT SUCH FEEDFORWARD EVENTS MAY CONTRIBUTE TO THE TRANSITION FROM AN ACUTE INFLAMMATORY RESPONSE TO CHRONIC INFLAMMATION. 2019 10 3198 33 HDAC-LINKED "PROLIFERATIVE" MIRNA EXPRESSION PATTERN IN PANCREATIC NEUROENDOCRINE TUMORS. EPIGENETIC FACTORS ARE ESSENTIALLY INVOLVED IN CARCINOGENESIS, TUMOR PROMOTION, AND CHEMORESISTANCE. TWO EPIGENETIC KEY PLAYERS ARE MIRNAS AND HISTONE DEACETYLASES (HDACS). AS PREVIOUSLY SHOWN BY OWN THEORETICAL DATABANK ANALYSIS, THE CROSSTALK BETWEEN MIRNAS AND HDACS IS RELEVANT IN DIFFERENT HUMAN CHRONIC DISEASES AND CANCEROGENIC PATHWAYS. WE AIMED TO INVESTIGATE A POTENTIAL CONNECTION BETWEEN THE EXPRESSION OF A WELL-DEFINED SUBSET OF "PROLIFERATION-ASSOCIATED" MIRNAS AND THE EXPRESSION OF HDACS AS WELL AS CLINICAL PARAMETERS IN PANCREATIC NEUROENDOCRINE TUMORS (PNETS). MATERIALS AND METHODS: EXPRESSION LEVELS OF MIRNA132-3P, MIRNA145-5P, MIRNA183-5P, MIRNA34A-5P, AND MIRNA449A IN 57 PNETS RESECTED BETWEEN 1997 AND 2015 WERE MEASURED AND LINKED TO THE IMMUNOHISTOCHEMICAL EXPRESSION PATTERN OF MEMBERS OF THE FOUR HDAC CLASSES ON HUMAN TISSUE MICROARRAYS. ALL PNET CASES WERE CLINICALLY AND PATHOLOGICALLY CHARACTERIZED ACCORDING TO PUBLISHED GUIDELINES. CORRELATION ANALYSIS REVEALED A SIGNIFICANT ASSOCIATION BETWEEN EXPRESSION OF SPECIFIC MIRNAS AND TWO MEMBERS OF THE HDAC FAMILY (HDAC3 AND HDAC4). ADDITIONALLY, A LINKAGE BETWEEN MIRNA EXPRESSION AND CLINICO-PATHOLOGICAL PARAMETERS LIKE GRADING, TNM-STAGING, AND HORMONE ACTIVITY WAS FOUND. MOREOVER, OVERALL AND DISEASE-FREE SURVIVAL IS STATISTICALLY CORRELATED WITH THE EXPRESSION OF THE INVESTIGATED MIRNAS. OVERALL, WE DEMONSTRATED THAT SPECIFIC MIRNAS COULD BE LINKED TO HDAC EXPRESSION IN PNETS. ESPECIALLY MIRNA449A (ASSOCIATED WITH HDAC3/4) SEEMS TO PLAY AN IMPORTANT ROLE IN PNET PROLIFERATION AND COULD BE A POTENTIAL PROGNOSTIC FACTOR FOR POOR SURVIVAL. THESE FIRST DATA COULD HELP, TO IMPROVE OUR KNOWLEDGE OF THE COMPLEX INTERACTIONS OF THE EPIGENETIC DRIVERS IN PNETS FOR FURTHER THERAPEUTIC APPROACHES. 2018 11 546 33 ATTENUATED EXPRESSION OF SLCO2A1 CAUSED BY DNA METHYLATION IN PEDIATRIC INFLAMMATORY BOWEL DISEASE. BACKGROUND: SLCO2A1 ENCODES A PROSTAGLANDIN (PG) TRANSPORTER, AND AUTOSOMAL RECESSIVE PATHOGENIC VARIANTS OF THIS GENE CAUSE CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1. IT IS UNCLEAR WHETHER A HETEROZYGOUS PATHOGENIC VARIANT OF SLCO2A1 HAS A ROLE IN THE PATHOGENESIS OF OTHER TYPES OF INFLAMMATORY BOWEL DISEASE (IBD). IN THIS STUDY, WE INVESTIGATED THE POSSIBLE INVOLVEMENT OF A LOCAL EPIGENETIC ALTERATION IN SLCO2A1 IN PATIENTS WITH A HETEROZYGOUS PATHOGENIC VARIANT. METHODS: WE CONDUCTED WHOLE-EXOME SEQUENCING OF SAMPLES FROM 2 SISTERS WITH SUSPECTED MONOGENIC IBD. IN ADDITION, WE PERFORMED BISULFITE SEQUENCING USING DNA EXTRACTED FROM THEIR SMALL AND LARGE INTESTINE SAMPLES TO EXPLORE EPIGENETIC ALTERATIONS. RESULTS: A HETEROZYGOUS SPLICING SITE VARIANT, SLCO2A1:C.940 + 1G > A, WAS DETECTED IN BOTH PATIENTS. TO EXPLORE THE POSSIBLE INVOLVEMENT OF EPIGENETIC ALTERATIONS, WE ANALYZED PROTEIN AND MESSENGER RNA EXPRESSION OF SLCO2A1, AND OBSERVED ATTENUATED SLCO2A1 EXPRESSION IN THE INFLAMED LESIONS OF THESE PATIENTS COMPARED WITH THAT IN THE CONTROL INDIVIDUALS. FURTHERMORE, BISULFITE SEQUENCING INDICATED DENSE METHYLATION IN THE PROMOTER REGION OF SLCO2A1 ONLY IN THE INFLAMED LESIONS OF BOTH PATIENTS. THE URINARY PG METABOLITE LEVELS IN THESE PATIENTS WERE COMPARABLE TO THOSE IN PATIENTS WITH CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1 AND HIGHER THAN THOSE IN THE CONTROL INDIVIDUALS. WE FOUND CONSIDERABLY HIGHER LEVELS OF THE METABOLITES IN PATIENT 1, WHO SHOWED MORE SEVERE SYMPTOMS THAN PATIENT 2. CONCLUSIONS: LOCAL DNA METHYLATION ATTENUATED SLCO2A1 EXPRESSION, WHICH MAY EVOKE LOCAL INFLAMMATION OF THE MUCOSA BY THE UNINCORPORATED PG. THESE FINDINGS MAY IMPROVE OUR UNDERSTANDING OF THE EPIGENETIC MECHANISMS UNDERLYING IBD DEVELOPMENT. 2023 12 3764 36 INTEGRATIVE ANALYSIS OF DNA METHYLATION AND GENE EXPRESSION DATA IDENTIFIES EPAS1 AS A KEY REGULATOR OF COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE. GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS ARE KNOWN TO CONTRIBUTE TO COPD RISK AND DISEASE PROGRESSION. THEREFORE WE DEVELOPED A SYSTEMATIC APPROACH TO IDENTIFY KEY REGULATORS OF COPD THAT INTEGRATES GENOME-WIDE DNA METHYLATION, GENE EXPRESSION, AND PHENOTYPE DATA IN LUNG TISSUE FROM COPD AND CONTROL SAMPLES. OUR INTEGRATIVE ANALYSIS IDENTIFIED 126 KEY REGULATORS OF COPD. WE IDENTIFIED EPAS1 AS THE ONLY KEY REGULATOR WHOSE DOWNSTREAM GENES SIGNIFICANTLY OVERLAPPED WITH MULTIPLE GENES SETS ASSOCIATED WITH COPD DISEASE SEVERITY. EPAS1 IS DISTINCT IN COMPARISON WITH OTHER KEY REGULATORS IN TERMS OF METHYLATION PROFILE AND DOWNSTREAM TARGET GENES. GENES PREDICTED TO BE REGULATED BY EPAS1 WERE ENRICHED FOR BIOLOGICAL PROCESSES INCLUDING SIGNALING, CELL COMMUNICATIONS, AND SYSTEM DEVELOPMENT. WE CONFIRMED THAT EPAS1 PROTEIN LEVELS ARE LOWER IN HUMAN COPD LUNG TISSUE COMPARED TO NON-DISEASE CONTROLS AND THAT EPAS1 GENE EXPRESSION IS REDUCED IN MICE CHRONICALLY EXPOSED TO CIGARETTE SMOKE. AS EPAS1 DOWNSTREAM GENES WERE SIGNIFICANTLY ENRICHED FOR HYPOXIA RESPONSIVE GENES IN ENDOTHELIAL CELLS, WE TESTED EPAS1 FUNCTION IN HUMAN ENDOTHELIAL CELLS. EPAS1 KNOCKDOWN BY SIRNA IN ENDOTHELIAL CELLS IMPACTED GENES THAT SIGNIFICANTLY OVERLAPPED WITH EPAS1 DOWNSTREAM GENES IN LUNG TISSUE INCLUDING HYPOXIA RESPONSIVE GENES, AND GENES ASSOCIATED WITH EMPHYSEMA SEVERITY. OUR FIRST INTEGRATIVE ANALYSIS OF GENOME-WIDE DNA METHYLATION AND GENE EXPRESSION PROFILES ILLUSTRATES THAT NOT ONLY DOES DNA METHYLATION PLAY A 'CAUSAL' ROLE IN THE MOLECULAR PATHOPHYSIOLOGY OF COPD, BUT IT CAN BE LEVERAGED TO DIRECTLY IDENTIFY NOVEL KEY MEDIATORS OF THIS PATHOPHYSIOLOGY. 2015 13 493 28 ASSESSMENT OF P53 AND ATM FUNCTIONALITY IN CHRONIC LYMPHOCYTIC LEUKEMIA BY MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION. THE ATM-P53 DNA-DAMAGE RESPONSE (DDR) PATHWAY HAS A CRUCIAL ROLE IN CHEMORESISTANCE IN CLL, AS INDICATED BY THE ADVERSE PROGNOSTIC IMPACT OF GENETIC ABERRATIONS OF TP53 AND ATM. IDENTIFYING AND DISTINGUISHING TP53 AND ATM FUNCTIONAL DEFECTS HAS BECOME RELEVANT AS EPIGENETIC AND POSTTRANSCRIPTIONAL DYSREGULATION OF THE ATM/P53 AXIS IS INCREASINGLY BEING RECOGNIZED AS THE UNDERLYING CAUSE OF CHEMORESISTANCE. ALSO, SPECIFIC TREATMENTS SENSITIZING TP53- OR ATM-DEFICIENT CLL CELLS ARE EMERGING. WE THEREFORE DEVELOPED A NEW ATM-P53 FUNCTIONAL ASSAY WITH THE AIM TO (I) IDENTIFY AND (II) DISTINGUISH ABNORMALITIES OF TP53 VERSUS ATM AND (III) ENABLE THE IDENTIFICATION OF ADDITIONAL DEFECTS IN THE ATM-P53 PATHWAY. REVERSED TRANSCRIPTASE MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (RT-MLPA) WAS USED TO MEASURE ATM AND/OR P53-DEPENDENT GENES AT THE RNA LEVEL FOLLOWING DNA DAMAGE USING IRRADIATION. HERE, WE SHOWED THAT THIS ASSAY IS ABLE TO IDENTIFY AND DISTINGUISH THREE SUBGROUPS OF CLL TUMORS (I.E., TP53-DEFECTIVE, ATM-DEFECTIVE AND WT) AND IS ALSO ABLE TO DETECT ADDITIONAL SAMPLES WITH A DEFECTIVE DDR, WITHOUT MOLECULAR ABERRATIONS IN TP53 AND/OR ATM. THESE FINDINGS MAKE THE ATM-P53 RT-MLPA FUNCTIONAL ASSAY A PROMISING PROGNOSTIC TOOL FOR PREDICTING TREATMENT RESPONSES IN CLL. 2015 14 3296 38 HIGH RESOLUTION INTEGRATIVE ANALYSIS REVEALS WIDESPREAD GENETIC AND EPIGENETIC CHANGES AFTER CHRONIC IN-VITRO ACID AND BILE EXPOSURE IN BARRETT'S EPITHELIUM CELLS. BARRETT'S EPITHELIUM (BE) IS A PREMALIGNANT CONDITION RESULTING FROM CHRONIC GASTROESOPHAGEAL REFLUX THAT MAY PROGRESS TO ESOPHAGEAL ADENOCARCINOMA (EAC). EARLY INTERVENTION HOLDS PROMISE IN PREVENTING BE PROGRESSION. HOWEVER, IDENTIFICATION OF HIGH-RISK BE PATIENTS REMAINS CHALLENGING DUE TO INADEQUATE BIOMARKERS FOR EARLY DIAGNOSIS. WE INVESTIGATED THE EFFECT OF PROLONGED CHRONIC ACID AND BILE EXPOSURE ON TRANSCRIPTOME, METHYLOME, AND MUTATOME OF CELLS IN AN IN-VITRO BE CARCINOGENESIS (BEC) MODEL. TWENTY WEEKS ACID AND BILE EXPOSED CELLS FROM THE BEC MODEL (BEC20W) WERE COMPARED WITH THEIR NAIVE PREDECESSORS HISEQ ILLUMINA BASED RNA SEQUENCING WAS PERFORMED ON RNA FROM BOTH THE CELLS FOR GENE EXPRESSION AND MUTATIONAL ANALYSIS. HELP TAGGING ASSAY WAS PERFORMED FOR DNA METHYLATION ANALYSIS. INGENUITY PATHWAY, GENE ONTOLOGY, AND KEGG PATHWAY ANALYSES WERE THEN PERFORMED ON DATASETS. WIDESPREAD ABERRANT GENETIC AND EPIGENETIC CHANGES WERE OBSERVED IN THE BEC20W CELLS. COMBINATORIAL ANALYSES REVEALED 433 FROM A TOTAL OF 863 DOWNREGULATED GENES HAD ACCOMPANYING HYPERMETHYLATION OF PROMOTERS. SIMULTANEOUSLY, 690 GENES FROM A TOTAL OF 1,492 WERE UPREGULATED WITH ACCOMPANYING PROMOTER HYPOMETHYLATION. IN ADDITION, 763 MUTATIONS WERE IDENTIFIED ON 637 GENES. INGENUITY PATHWAY ANALYSIS, GENE ONTOLOGY, AND KEGG PATHWAY ANALYSES ASSOCIATED THE GENETIC AND EPIGENETIC CHANGES IN BEC20W CELLS WITH CELLULAR AND BIOLOGICAL FUNCTIONS. INTEGRATION OF HIGH RESOLUTION COMPARATIVE ANALYSES OF NAIVE BAR-T AND BEC20W CELLS REVEALED STRIKING GENETIC AND EPIGENETIC CHANGES INDUCED BY CHRONIC ACID AND BILE EXPOSURE THAT MAY DISRUPT NORMAL CELLULAR FUNCTIONS AND PROMOTE CARCINOGENESIS. THIS NOVEL STUDY REVEALS SEVERAL POTENTIAL TARGETS FOR FUTURE BIOMARKERS AND THERAPEUTIC DEVELOPMENT. 2013 15 984 36 CHRONIC PSYCHOLOGICAL STRESS ALTERS GENE EXPRESSION IN RAT COLON EPITHELIAL CELLS PROMOTING CHROMATIN REMODELING, BARRIER DYSFUNCTION AND INFLAMMATION. CHRONIC STRESS IS COMMONLY ASSOCIATED WITH ENHANCED ABDOMINAL PAIN (VISCERAL HYPERSENSITIVITY), BUT THE CELLULAR MECHANISMS UNDERLYING HOW CHRONIC STRESS INDUCES VISCERAL HYPERSENSITIVITY ARE POORLY UNDERSTOOD. IN THIS STUDY, WE EXAMINED CHANGES IN GENE EXPRESSION IN COLON EPITHELIAL CELLS FROM A RAT MODEL USING RNA-SEQUENCING TO EXAMINE STRESS-INDUCED CHANGES TO THE TRANSCRIPTOME. FOLLOWING CHRONIC STRESS, THE MOST SIGNIFICANTLY UP-REGULATED GENES INCLUDED ATG16L1, COQ10B, DCAF13, NAT2, PTBP2, RRAS2, SPINK4 AND DOWN-REGULATED GENES INCLUDING ABAT, CITED2, CNNM2, DAB2IP, PLEKHM1, SCD2, AND TAB2. THE PRIMARY ALTERED BIOLOGICAL PROCESSES REVEALED BY NETWORK ENRICHMENT ANALYSIS WERE INFLAMMATION/IMMUNE RESPONSE, TISSUE MORPHOGENESIS AND DEVELOPMENT, AND NUCLEOSOME/CHROMATIN ASSEMBLY. THE MOST SIGNIFICANTLY DOWN-REGULATED PROCESS WAS THE DIGESTIVE SYSTEM DEVELOPMENT/FUNCTION, WHEREAS THE MOST SIGNIFICANTLY UP-REGULATED PROCESSES WERE INFLAMMATORY RESPONSE, ORGANISMAL INJURY, AND CHROMATIN REMODELING MEDIATED BY H3K9 METHYLATION. FURTHERMORE, A SUBPOPULATION OF STRESSED RATS DEMONSTRATED VERY SIGNIFICANTLY ALTERED GENE EXPRESSION AND TRANSCRIPT ISOFORMS, ENRICHED FOR THE DIFFERENTIAL EXPRESSION OF GENES INVOLVED IN THE INFLAMMATORY RESPONSE, INCLUDING UPREGULATION OF CYTOKINE AND CHEMOKINE RECEPTOR GENE EXPRESSION COUPLED WITH DOWNREGULATION OF EPITHELIAL ADHERENS AND TIGHT JUNCTION MRNAS. IN SUMMARY, THESE FINDINGS SUPPORT THAT CHRONIC STRESS IS ASSOCIATED WITH INCREASED LEVELS OF CYTOKINES AND CHEMOKINES, THEIR DOWNSTREAM SIGNALING PATHWAYS COUPLED TO DYSREGULATION OF INTESTINAL CELL DEVELOPMENT AND FUNCTION. EPIGENETIC REGULATION OF CHROMATIN REMODELING LIKELY PLAYS A PROMINENT ROLE IN THIS PROCESS. RESULTS ALSO SUGGEST THAT SUPER ENHANCERS PLAY A PRIMARY ROLE IN CHRONIC STRESS-ASSOCIATED INTESTINAL BARRIER DYSFUNCTION. 2022 16 4362 45 MIR?152 REGULATES TGF?BETA1?INDUCED EPITHELIAL?MESENCHYMAL TRANSITION BY TARGETING HPIP IN TUBULAR EPITHELIAL CELLS. RENAL FIBROSIS IS A COMMON PATHOLOGICAL FEATURE OF CHRONIC KIDNEY DISEASES, AND THEIR DEVELOPMENT AND PROGRESSION ARE INFLUENCED BY EPIGENETIC MODIFICATIONS INCLUDING ABERRANT MICRORNA (MIRNA OR MIR) EXPRESSION. MIRNAS HAVE BEEN DEMONSTRATED TO MODULATE THE AGGRESSIVENESS OF VARIOUS CANCERS AND HAVE EMERGED AS POSSIBLE THERAPEUTIC AGENTS FOR THE MANAGEMENT OF RENAL FIBROSIS. TRANSFORMING GROWTH FACTOR BETA1 (TGF?BETA1)?INDUCED EPITHELIAL?MESENCHYMAL TRANSITION (EMT) OF TUBULAR EPITHELIAL CELLS SERVES A ROLE IN THE INITIATION AND PROGRESSION OF RENAL FIBROSIS. FURTHERMORE, RECENT RESULTS INDICATED THAT THE PROGRESSION OF EMT IS REVERSIBLE. THE PRESENT STUDY AIMED TO CLARIFY THE ROLE OF MIR?152 IN EMT OF THE TUBULAR EPITHELIAL CELL LINE HK?2, STIMULATED BY TGF?BETA1, USING IN VITRO TRANSFECTION WITH A MIR?152 MIMIC AND TO FURTHER INVESTIGATE THE UNDERLYING MECHANISM OF MIR?152 ACTIVITY. IN THE PRESENT STUDY, MIR?152 EXPRESSION WAS SIGNIFICANTLY REDUCED IN TGF?BETA1?TREATED HK?2 CELLS, ACCOMPANIED BY AN INCREASED EXPRESSION OF HEMATOPOIETIC PRE?B?CELL LEUKEMIA TRANSCRIPTION FACTOR (PBX)?INTERACTING PROTEIN (HPIP). ADDITIONALLY, MIR?152 OVEREXPRESSION INHIBITED TGF?BETA1?INDUCED EMT AND SUPPRESSED HPIP EXPRESSION BY DIRECTLY TARGETING THE 3' UNTRANSLATED REGION OF HPIP IN HK?2 CELLS. FURTHERMORE, UPREGULATION OF HPIP REVERSED MIR?152?MEDIATED INHIBITORY EFFECTS ON THE EMT. COLLECTIVELY, THE RESULTS SUGGEST THAT DOWNREGULATION OF MIR?152 INITIATES THE DEDIFFERENTIATION OF RENAL TUBULES AND PROGRESSION OF RENAL FIBROSIS, WHICH MAY PROVIDE IMPORTANT TARGETS FOR PREVENTION STRATEGIES OF RENAL FIBROSIS. 2018 17 4545 31 MUTANT P53 GAIN OF FUNCTION AND CHEMORESISTANCE: THE ROLE OF MUTANT P53 IN RESPONSE TO CLINICAL CHEMOTHERAPY. PURPOSE: TO REVIEW MECHANISMS UNDERLYING MUTANT P53 (MUTP53) GAIN OF FUNCTION (GOF) AND MUTP53-INDUCED CHEMORESISTANCE, AND TO INVESTIGATE THE ROLE OF MUTP53 IN RESPONSE TO CLINICAL CHEMOTHERAPY. METHODS: WE SEARCHED THE PUBMED DATABASE FOR CLINICAL STUDIES FROM THE PAST DECADE, INCLUDING DATA EVALUATING THE IMPACT OF MUTP53 IN CLINICAL CHEMOTHERAPY RESPONSE. RESULTS: INTERACTIONS BETWEEN MUTP53 AND TRANSCRIPTIONAL FACTORS, PROTEINS OR DNA STRUCTURES, AS WELL AS EPIGENETIC REGULATION, CONTRIBUTE TO MUTP53 GOF. MAJOR MECHANISMS OF MUTP53-INDUCED CHEMORESISTANCE INCLUDE ENHANCED DRUG EFFLUX AND METABOLISM, PROMOTING SURVIVAL, INHIBITING APOPTOSIS, UPREGULATING DNA REPAIR, SUPPRESSING AUTOPHAGY, ELEVATING MICROENVIRONMENTAL RESISTANCE AND INDUCING A STEM-LIKE PHENOTYPE. CLINICALLY, MUTP53 PREDICTED RESISTANCE TO CHEMOTHERAPY IN DIFFUSE LARGE B-CELL LYMPHOMA, AND ESOPHAGEAL AND OROPHARYNGEAL CANCERS, BUT ITS IMPACT ON CHRONIC LYMPHOCYTIC LEUKEMIA WAS UNCLEAR. IN BLADDER CANCER, MUTP53 DID NOT PREDICT RESISTANCE, WHEREAS IN SOME BREAST AND OVARIAN CANCERS, IT WAS ASSOCIATED WITH SENSITIVITY TO CERTAIN CHEMOTHERAPEUTIC AGENTS. CONCLUSION: MUTP53 HAS AN INTRICATE ROLE IN THE RESPONSE TO CLINICAL CHEMOTHERAPY AND SHOULD NOT BE INTERPRETED IN ISOLATION. FURTHERMORE, WHEN PREDICTING TUMOR RESPONSE TO CHEMOTHERAPY BASED ON THE P53 STATUS, THE DRUGS USED SHOULD ALSO BE TAKEN INTO CONSIDERATION. THESE CONCEPTS REQUIRE FURTHER INVESTIGATION. 2017 18 3317 38 HISTOLOGICAL TRANSFORMATION TO SIGNET-RING CELL CARCINOMA IN A PATIENT WITH CLINICALLY AGGRESSIVE POORLY DIFFERENTIATED ADENOCARCINOMA OF THE ASCENDING COLON AFTER RESPONSE TO CHEMOTHERAPY PLUS CETUXIMAB: A CASE REPORT. BACKGROUND: ALTERATION OF CHEMOSENSITIVITY OR TUMOR AGGRESSIVENESS IN RESPONSE TO CHEMOTHERAPY HAS BEEN REPORTED, AND LIQUID BIOPSY ASSESSMENT DURING CHEMOTHERAPY FOR COLORECTAL CANCERS HAS CONFIRMED THE ACQUISITION OF MUTATIONS IN VARIOUS ONCOGENES. HOWEVER, THE OCCURRENCE OF HISTOLOGICAL TRANSFORMATION SEEMS TO BE EXTREMELY RARE IN COLORECTAL CANCERS, AND THE FEW EXISTING CASE REPORTS OF THIS TRANSFORMATION ARE FROM LUNG CANCER AND BREAST CANCER. IN THIS REPORT, WE DESCRIBE THE HISTOLOGICAL TRANSFORMATION OF CLINICALLY AGGRESSIVE SCIRRHOUS-TYPE POORLY DIFFERENTIATED ADENOCARCINOMA OF THE ASCENDING COLON TO SIGNET-RING CELL CARCINOMA IN ALMOST ALL RECURRENT TUMORS THAT WERE CONFIRMED BY AUTOPSY AFTER RESPONSE TO CHEMOTHERAPY PLUS CETUXIMAB. CASE PRESENTATION: A 59-YEAR-OLD WOMAN VISITED OUR HOSPITAL WITH WHOLE ABDOMINAL PAIN AND BODY WEIGHT LOSS AND WAS DIAGNOSED WITH SCIRRHOUS-TYPE POORLY DIFFERENTIATED ADENOCARCINOMA OF THE ASCENDING COLON WITH AGGRESSIVE LYMPH NODE METASTASES. THE INTRINSIC CHEMOSENSITIVITY OF THE TUMORS WAS EVIDENT UPON INITIATION OF MFOLFOX6 PLUS CETUXIMAB THERAPY, AND RIGHT HEMICOLECTOMY WAS PERFORMED, AND THE TUMOR OBVIOUSLY REMAINED IN THE PERIPANCREATIC AREA, PARAAORTIC REGION, OR OTHER RETROPERITONEAL AREAS. THE ASCENDING COLON TUMORS MAINLY CONSISTED OF POORLY DIFFERENTIATED ADENOCARCINOMA AND WERE NOT ASSOCIATED WITH SIGNET-RING CELL COMPONENTS EXCEPT FOR MINUTE CLUSTERS IN A FEW LYMPHATIC EMBOLI IN THE MAIN TUMOR. CHEMOTHERAPY WAS CONTINUED, AND METASTASES WERE ELIMINATED AT 8 MONTHS AFTER THE OPERATION; THIS RESPONSE WAS MAINTAINED FOR AN ADDITIONAL 4 MONTHS. DISCONTINUATION OF CHEMOTHERAPY PLUS CETUXIMAB RESULTED IN IMMEDIATE TUMOR RECURRENCE AND RAPID EXPANSION, AND THE PATIENT DIED OF THE RECURRENT TUMOR 1 YEAR AND 2 MONTHS AFTER THE OPERATION. AUTOPSY SPECIMENS REVEALED THAT ALMOST ALL OF THE RECURRENT TUMORS EXHIBITED TRANSFORMATION AND CONSISTED OF SIGNET-RING CELL HISTOLOGY. CONCLUSION: THIS CASE MIGHT SUGGEST THAT VARIOUS ONCOGENE MUTATIONS OR EPIGENETIC CHANGES RESULTING FROM CHEMOTHERAPY, ESPECIALLY REGIMENS THAT INCLUDE CETUXIMAB, CONTRIBUTE TO THE TRANSFORMATION OF NON-SIGNET-RING CELL COLORECTAL CARCINOMA TO SIGNET-RING CELL CARCINOMA HISTOLOGY AND CAN PROMOTE THE AGGRESSIVE CLINICAL PROGRESSION CHARACTERISTIC OF SIGNET-RING CELL CARCINOMA. 2023 19 2395 41 EPIGENETIC REPROGRAMMING IN MIST1(-/-) MICE PREDICTS THE MOLECULAR RESPONSE TO CERULEIN-INDUCED PANCREATITIS. GENE EXPRESSION IS AFFECTED BY MODIFICATIONS TO HISTONE CORE PROTEINS WITHIN CHROMATIN. CHANGES IN THESE MODIFICATIONS, OR EPIGENETIC REPROGRAMMING, CAN DICTATE CELL FATE AND PROMOTE SUSCEPTIBILITY TO DISEASE. THE GOAL OF THIS STUDY WAS TO DETERMINE THE EXTENT OF EPIGENETIC REPROGRAMMING IN RESPONSE TO CHRONIC STRESS THAT OCCURS FOLLOWING ABLATION OF MIST1 (MIST1(-/-) ), WHICH IS REPRESSED IN PANCREATIC DISEASE. CHROMATIN IMMUNOPRECIPITATION FOR TRIMETHYLATION OF LYSINE RESIDUE 4 ON HISTONE 3 (H3K4ME3) IN PURIFIED ACINAR CELLS FROM WILD TYPE AND MIST1(-/-) MICE WAS FOLLOWED BY NEXT GENERATION SEQUENCING (CHIP-SEQ) OR CHIP-QPCR. H3K4ME3-ENRICHED GENES WERE ASSESSED FOR EXPRESSION BY QRT-PCR IN PANCREATIC TISSUE BEFORE AND AFTER INDUCTION OF CERULEIN-INDUCED PANCREATITIS. WHILE MOST OF H3K4ME3-ENRICHMENT IS RESTRICTED TO TRANSCRIPTIONAL START SITES, >25% OF ENRICHMENT SITES ARE FOUND WITHIN, DOWNSTREAM OR BETWEEN ANNOTATED GENES. LESS THAN 10% OF THESE SITES WERE ALTERED IN MIST1(-/-) ACINI, WITH MOST CHANGES IN H3K4ME3 ENRICHMENT NOT REFLECTING ALTERED GENE EXPRESSION. INGENUITY PATHWAY ANALYSIS OF GENES DIFFERENTIALLY-ENRICHED FOR H3K4ME3 REVEALED AN ASSOCIATION WITH PANCREATITIS AND PANCREATIC DUCTAL ADENOCARCINOMA IN MIST1(-/-) TISSUE. MOST OF THESE GENES WERE NOT DIFFERENTIALLY EXPRESSED BUT SEVERAL WERE READILY INDUCED BY ACUTE EXPERIMENTAL PANCREATITIS, WITH SIGNIFICANTLY INCREASED EXPRESSION IN MIST1(-/-) TISSUE RELATIVE TO WILD TYPE MICE. WE SUGGEST THAT THE CHRONIC CELL STRESS OBSERVED IN THE ABSENCE OF MIST1 RESULTS IN EPIGENETIC REPROGRAMMING OF GENES INVOLVED IN PROMOTING PANCREATITIS TO A POISED STATE, THEREBY INCREASING THE SENSITIVITY TO EVENTS THAT PROMOTE DISEASE. 2014 20 1334 33 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