1 1380 160 DEVELOPMENTAL SUBTYPES ASSESSED BY DNA METHYLATION-IPLEX FORECAST THE NATURAL HISTORY OF CHRONIC LYMPHOCYTIC LEUKEMIA. ALTERATIONS IN GLOBAL DNA METHYLATION PATTERNS ARE A MAJOR HALLMARK OF CANCER AND REPRESENT ATTRACTIVE BIOMARKERS FOR PERSONALIZED RISK STRATIFICATION. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK STRATIFICATION STUDIES TYPICALLY FOCUS ON TIME TO FIRST TREATMENT (TTFT), TIME TO PROGRESSION (TTP) AFTER TREATMENT, AND OVERALL SURVIVAL (OS). WHEREAS TTFT RISK STRATIFICATION REMAINS SIMILAR OVER TIME, TTP AND OS HAVE CHANGED DRAMATICALLY WITH THE INTRODUCTION OF TARGETED THERAPIES, SUCH AS THE BRUTON TYROSINE KINASE INHIBITOR IBRUTINIB. WE HAVE SHOWN THAT GENOME-WIDE DNA METHYLATION PATTERNS IN CLL ARE STRONGLY ASSOCIATED WITH PHENOTYPIC DIFFERENTIATION AND PATIENT OUTCOMES. HERE, WE DEVELOPED A NOVEL ASSAY, TERMED METHYLATION-IPLEX (ME-IPLEX), FOR HIGH-THROUGHPUT QUANTIFICATION OF TARGETED PANELS OF SINGLE CYTOSINE GUANINE DINUCLEOTIDES FROM MULTIPLE INDEPENDENT LOCI. ME-IPLEX WAS USED TO CLASSIFY CLL SAMPLES INTO 1 OF 3 KNOWN EPIGENETIC SUBTYPES (EPITYPES). WE EXAMINED THE IMPACT OF EPITYPE IN 1286 CLL PATIENTS FROM 4 INDEPENDENT COHORTS REPRESENTING A COMPREHENSIVE VIEW OF CLL DISEASE COURSE AND THERAPIES. WE FOUND THAT EPITYPE SIGNIFICANTLY PREDICTED TTFT AND OS AMONG NEWLY DIAGNOSED CLL PATIENTS. ADDITIONALLY, EPITYPE PREDICTED TTP AND OS WITH 2 COMMON CLL THERAPIES: CHEMOIMMUNOTHERAPY AND IBRUTINIB. EPITYPE RETAINED SIGNIFICANCE AFTER STRATIFYING BY BIOLOGICALLY RELATED BIOMARKERS, IMMUNOGLOBULIN HEAVY CHAIN MUTATIONAL STATUS, AND ZAP70 EXPRESSION, AS WELL AS OTHER COMMON PROGNOSTIC MARKERS. FURTHERMORE, AMONG SEVERAL BIOLOGICAL TRAITS ENRICHED BETWEEN EPITYPES, WE FOUND HIGHLY BIASED IMMUNOGENETIC FEATURES, INCLUDING IGLV3-21 USAGE IN THE POORLY CHARACTERIZED INTERMEDIATE-PROGRAMMED CLL EPITYPE. IN SUMMARY, ME-IPLEX IS AN ELEGANT METHOD TO ASSESS EPIGENETIC SIGNATURES, INCLUDING ROBUST CLASSIFICATION OF CLL EPITYPES THAT INDEPENDENTLY STRATIFY PATIENT RISK AT DIAGNOSIS AND TIME OF TREATMENT. 2019 2 3125 34 GHSR DNA HYPERMETHYLATION IS A COMMON EPIGENETIC ALTERATION OF HIGH DIAGNOSTIC VALUE IN A BROAD SPECTRUM OF CANCERS. IDENTIFICATION OF A SINGLE MOLECULAR TRAIT THAT IS DETERMINANT OF COMMON MALIGNANCIES MAY SERVE AS A POWERFUL DIAGNOSTIC SUPPLEMENT TO CANCER TYPE-SPECIFIC MARKERS. HERE, WE REPORT A DNA METHYLATION MARK THAT IS CHARACTERISTIC OF SEVEN STUDIED MALIGNANCIES, NAMELY CANCERS OF LUNG, BREAST, PROSTATE, PANCREAS, COLORECTUM, GLIOBLASTOMA AND B CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) (N = 137). THIS MARK WAS DEFINED BY SUBSTANTIAL HYPERMETHYLATION AT THE PROMOTER AND FIRST EXON OF GROWTH HORMONE SECRETAGOUGE RECEPTOR (GHSR) THROUGH BISULFITE PYROSEQUENCING. THE DEGREE OF ABERRANT METHYLATION WAS CAPABLE OF ACCURATE DISCRIMINATION BETWEEN CANCER AND CONTROL SAMPLES. THE HIGHEST SENSITIVITY AND SPECIFICITY OF CANCER DETECTION WAS ACHIEVED FOR CANCERS OF PANCREAS, LUNG, BREAST AND CLL YIELDING THE AREA UNDER THE CURVE (AUC) VALUES OF 1.0000, 0.9952, 0.9800 AND 0.9400, RESPECTIVELY. NARROWING TO A SINGLE CPG SITE WITHIN THE GENE'S PROMOTER OR FOUR CONSECUTIVE CPG UNITS OF THE HIGHEST METHYLATION LEVELS WITHIN THE FIRST EXON IMPROVED THE DETECTION POWER. GHSR HYPERMETHYLATION WAS DETECTED ALREADY AT THE EARLY STAGE TUMORS. THE ACCURATE PERFORMANCE OF THIS MARKER WAS FURTHER REPLICATED IN AN INDEPENDENT SET OF PANCREATIC CANCER AND CONTROL SAMPLES (N = 78). THESE FINDINGS SUPPORT THE CANDIDATURE OF GHSR METHYLATION AS A HIGHLY ACCURATE PAN-CANCER MARKER. 2015 3 2753 40 EXPRESSION OF BCL2L12 IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS: ASSOCIATION WITH CLINICAL AND MOLECULAR PROGNOSTIC MARKERS. DYSREGULATION OF APOPTOSIS IS A DISTINCTIVE FEATURE OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), ALTHOUGH A UNIQUE MECHANISM UNDERLYING APOPTOSIS RESISTANCE OF CLL B LYMPHOCYTES HAS NOT BEEN IDENTIFIED YET. ABERRANT EXPRESSION AS WELL AS GENETIC AND EPIGENETIC ALTERATIONS OF NUMEROUS GENES INVOLVED IN DIFFERENT PATHWAYS OF APOPTOSIS REGULATION HAS BEEN DESCRIBED IN CLL. HERE, WE REPORT THE EXPRESSION ANALYSIS OF BCL2L12 (BCL2-LIKE 12), A NOVEL APOPTOTIC GENE BELONGING TO BCL2 FAMILY, IN 58 SERBIAN CLL PATIENTS. QUANTITATIVE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION (QRT-PCR) ANALYSIS REVEALED A SIGNIFICANT OVEREXPRESSION OF BCL2L12 MRNA IN CLL SAMPLES COMPARED TO NON-LEUKEMIC SAMPLES, IMPLYING ITS ROLE IN THE PATHOGENESIS OF THE DISEASE. RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS SHOWED THAT BCL2L12 EXPRESSION EFFICIENTLY DISCRIMINATES CLL CASES FROM HEALTHY CONTROLS. HOWEVER, RELATIVELY HOMOGENOUS BCL2L12 MRNA EXPRESSION AMONG PATIENTS DID NOT REFLECT THEIR CLINICAL CHARACTERISTICS (WITH THE EXCEPTION OF LACTATE DEHYDROGENASE STATUS AND TIME FROM DIAGNOSIS TO TREATMENT) AND FAILED TO SHOW ASSOCIATION WITH THE MOST INFORMATIVE PROGNOSTIC MARKERS, NAMELY THE MUTATIONAL STATUS OF REARRANGED IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION GENES, CD38 AND LIPOPROTEIN LIPASE GENE (LPL) EXPRESSION. 2013 4 27 49 A B-CELL EPIGENETIC SIGNATURE DEFINES THREE BIOLOGIC SUBGROUPS OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH CLINICAL IMPACT. PROSPECTIVE IDENTIFICATION OF PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DESTINED TO PROGRESS WOULD GREATLY FACILITATE THEIR CLINICAL MANAGEMENT. RECENTLY, WHOLE-GENOME DNA METHYLATION ANALYSES IDENTIFIED THREE CLINICOBIOLOGIC CLL SUBGROUPS WITH AN EPIGENETIC SIGNATURE RELATED TO DIFFERENT NORMAL B-CELL COUNTERPARTS. HERE, WE DEVELOPED A CLINICALLY APPLICABLE METHOD TO IDENTIFY THESE SUBGROUPS AND TO STUDY THEIR CLINICAL RELEVANCE. USING A SUPPORT VECTOR MACHINE APPROACH, WE BUILT A PREDICTION MODEL USING FIVE EPIGENETIC BIOMARKERS THAT WAS ABLE TO CLASSIFY CLL PATIENTS ACCURATELY INTO THE THREE SUBGROUPS, NAMELY NAIVE B-CELL-LIKE, INTERMEDIATE AND MEMORY B-CELL-LIKE CLL. DNA METHYLATION WAS QUANTIFIED BY HIGHLY REPRODUCIBLE BISULFITE PYROSEQUENCING ASSAYS IN TWO INDEPENDENT CLL SERIES. IN THE INITIAL SERIES (N=211), THE THREE SUBGROUPS SHOWED DIFFERENTIAL LEVELS OF IGHV (IMMUNOGLOBULIN HEAVY-CHAIN LOCUS) MUTATION (P<0.001) AND VH USAGE (P<0.03), AS WELL AS DIFFERENT CLINICAL FEATURES AND OUTCOME IN TERMS OF TIME TO FIRST TREATMENT (TTT) AND OVERALL SURVIVAL (P<0.001). A MULTIVARIATE COX MODEL SHOWED THAT EPIGENETIC CLASSIFICATION WAS THE STRONGEST PREDICTOR OF TTT (P<0.001) ALONG WITH BINET STAGE (P<0.001). THESE FINDINGS WERE CORROBORATED IN A VALIDATION SERIES (N=97). IN THIS STUDY, WE DEVELOPED A SIMPLE AND ROBUST METHOD USING EPIGENETIC BIOMARKERS TO CATEGORIZE CLLS INTO THREE SUBGROUPS WITH DIFFERENT CLINICOBIOLOGIC FEATURES AND OUTCOME. 2015 5 4694 37 NEXT-GENERATION SEQUENCING IDENTIFIES MAJOR DNA METHYLATION CHANGES DURING PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA. LITTLE IS KNOWN ABOUT THE IMPACT OF DNA METHYLATION ON THE EVOLUTION/PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA (CML). WE INVESTIGATED THE METHYLOME OF CML PATIENTS IN CHRONIC PHASE (CP-CML), ACCELERATED PHASE (AP-CML) AND BLAST CRISIS (BC-CML) AS WELL AS IN CONTROLS BY REDUCED REPRESENTATION BISULFITE SEQUENCING. ALTHOUGH ONLY ~600 DIFFERENTIALLY METHYLATED CPG SITES WERE IDENTIFIED IN SAMPLES OBTAINED FROM CP-CML PATIENTS COMPARED WITH CONTROLS, ~6500 DIFFERENTIALLY METHYLATED CPG SITES WERE FOUND IN SAMPLES FROM BC-CML PATIENTS. IN THE MAJORITY OF AFFECTED CPG SITES, METHYLATION WAS INCREASED. IN CP-CML PATIENTS WHO PROGRESSED TO AP-CML/BC-CML, WE IDENTIFIED UP TO 897 GENES THAT WERE METHYLATED AT THE TIME OF PROGRESSION BUT NOT AT THE TIME OF DIAGNOSIS. USING RNA-SEQUENCING, WE OBSERVED DOWNREGULATED EXPRESSION OF MANY OF THESE GENES IN BC-CML COMPARED WITH CP-CML SAMPLES. SEVERAL OF THEM ARE WELL-KNOWN TUMOR-SUPPRESSOR GENES OR REGULATORS OF CELL PROLIFERATION, AND GENE RE-EXPRESSION WAS OBSERVED BY THE USE OF EPIGENETIC ACTIVE DRUGS. TOGETHER, OUR RESULTS DEMONSTRATE THAT CPG SITE METHYLATION CLEARLY INCREASES DURING CML PROGRESSION AND THAT IT MAY PROVIDE A USEFUL BASIS FOR REVEALING NEW TARGETS OF THERAPY IN ADVANCED CML. 2016 6 4221 39 METHYLATION AND SILENCING OF PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE O IN CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE: PREVIOUS STUDIES IN OUR LABORATORY HAVE SHOWN THE PROGRESSIVE METHYLATION AND SUPPRESSION OF THE GENE ENCODING PROTEIN TYROSINE PHOSPHATASE, PTPRO, IN THE LIVERS OF RATS FED A METHYL-DEFICIENT DIET THAT INDUCES HEPATOCARCINOGENESIS. SUBSEQUENTLY, WE OBSERVED THE METHYLATION OF PTPRO IN PRIMARY HUMAN LUNG TUMORS AND ALSO SHOWED ITS POTENTIAL TUMOR SUPPRESSOR CHARACTERISTICS. THE PRESENT STUDY WAS UNDERTAKEN TO INVESTIGATE WHETHER THE TRUNCATED FORM OF PTPRO (PTPROT), SPECIFICALLY EXPRESSED IN NAIVE B LYMPHOCYTES, WAS ALSO METHYLATED AND SUPPRESSED IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A DISEASE GENERALLY AFFECTING B LYMPHOCYTES. EXPERIMENTAL DESIGN AND RESULTS: INITIAL SCREENING SHOWED THAT 60% OF THE 52 CLL SAMPLES ANALYZED USING METHYLATION-SPECIFIC PCR ASSAY WERE METHYLATED COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS, WHICH WERE NOT METHYLATED. THE EXPRESSION OF PTPROT, AS MEASURED BY SEMIQUANTITATIVE REVERSE TRANSCRIPTION-PCR, INVERSELY CORRELATED WITH METHYLATION IN THE FEW SAMPLES TESTED. ANALYSIS OF ADDITIONAL SAMPLES (N = 50) BY COMBINED BISULFITE RESTRICTION ANALYSIS SHOWED THAT THE PTPRO CPG ISLAND WAS METHYLATED IN 82% OF PATIENTS WITH CLL COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS. FURTHERMORE, OVERALL EXPRESSION OF PTPRO WAS REDUCED IN CLL RELATIVE TO NORMAL LYMPHOCYTES. THE PTPRO GENE WAS ALSO SUPPRESSED BY METHYLATION IN THE CLL CELL LINE WAC3CD5, WHERE IT COULD BE REACTIVATED UPON TREATMENT WITH THE DNA HYPOMETHYLATING AGENT 5-AZAC. ECTOPIC EXPRESSION OF PTPROT IN A NONEXPRESSING CELL LINE INCREASED GROWTH INHIBITION WITH FLUDARABINE TREATMENT, A THERAPY COMMONLY USED FOR CLL. CONCLUSION: THIS STUDY REVEALS THE POTENTIAL ROLE OF PTPRO METHYLATION AND SILENCING IN CLL TUMORIGENESIS AND ALSO PROVIDES A NOVEL MOLECULAR TARGET IN THE EPIGENETIC THERAPY. 2007 7 15 37 450K-ARRAY ANALYSIS OF CHRONIC LYMPHOCYTIC LEUKEMIA CELLS REVEALS GLOBAL DNA METHYLATION TO BE RELATIVELY STABLE OVER TIME AND SIMILAR IN RESTING AND PROLIFERATIVE COMPARTMENTS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE MICROENVIRONMENT INFLUENCES GENE EXPRESSION PATTERNS; HOWEVER, KNOWLEDGE IS LIMITED REGARDING THE EXTENT TO WHICH METHYLATION CHANGES WITH TIME AND EXPOSURE TO SPECIFIC MICROENVIRONMENTS. USING HIGH-RESOLUTION 450K ARRAYS, WE PROVIDE THE MOST COMPREHENSIVE DNA METHYLATION STUDY OF CLL TO DATE, ANALYZING PAIRED DIAGNOSTIC/FOLLOW-UP SAMPLES FROM IGHV-MUTATED/UNTREATED AND IGHV-UNMUTATED/TREATED PATIENTS (N=36) AND PATIENT-MATCHED PERIPHERAL BLOOD AND LYMPH NODE SAMPLES (N=20). ON AN UNPRECEDENTED SCALE, WE REVEALED 2239 DIFFERENTIALLY METHYLATED CPG SITES BETWEEN IGHV-MUTATED AND UNMUTATED PATIENTS, WITH THE MAJORITY OF SITES POSITIONED OUTSIDE ANNOTATED CPG ISLANDS. INTRIGUINGLY, CLL PROGNOSTIC GENES (FOR EXAMPLE, CLLU1, LPL, ZAP70 AND NOTCH1), EPIGENETIC REGULATOR (FOR EXAMPLE, HDAC9, HDAC4 AND DNMT3B), B-CELL SIGNALING (FOR EXAMPLE, IBTK) AND NUMEROUS TGF-BETA AND NF-KAPPAB/TNF PATHWAY GENES WERE ALTERNATIVELY METHYLATED BETWEEN SUBGROUPS. CONTRARY, DNA METHYLATION OVER TIME WAS DEEMED RATHER STABLE WITH FEW RECURRENT CHANGES NOTED WITHIN SUBGROUPS. ALTHOUGH A LARGER NUMBER OF NON-RECURRENT CHANGES WERE IDENTIFIED AMONG IGHV-UNMUTATED RELATIVE TO MUTATED CASES OVER TIME, THESE EQUATED TO A LOW GLOBAL CHANGE. SIMILARLY, FEW CHANGES WERE IDENTIFIED BETWEEN COMPARTMENT CASES. ALTOGETHER, WE REVEAL CLL SUBGROUPS TO DISPLAY UNIQUE METHYLATION PROFILES AND UNVEIL METHYLATION AS RELATIVELY STABLE OVER TIME AND SIMILAR WITHIN DIFFERENT CLL COMPARTMENTS, IMPLYING ABERRANT METHYLATION AS AN EARLY LEUKEMOGENIC EVENT. 2013 8 628 34 BIOLOGICAL AND CLINICAL INSIGHT FROM ANALYSIS OF THE TUMOR B-CELL RECEPTOR STRUCTURE AND FUNCTION IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE B-CELL RECEPTOR (BCR) IS ESSENTIAL TO THE BEHAVIOR OF THE MAJORITY OF NORMAL AND NEOPLASTIC MATURE B CELLS. THE IDENTIFICATION IN 1999 OF THE TWO MAJOR CLL SUBSETS EXPRESSING UNMUTATED IMMUNOGLOBULIN (IG) VARIABLE REGION GENES (U-IGHV, U-CLL) OF PRE-GERMINAL CENTER ORIGIN AND POOR PROGNOSIS, AND MUTATED IGHV (M-CLL) OF POST-GERMINAL CENTER ORIGIN AND GOOD PROGNOSIS, IGNITED INTENSIVE INVESTIGATIONS ON STRUCTURE AND FUNCTION OF THE TUMOR BCR. THESE INVESTIGATIONS HAVE PROVIDED FUNDAMENTAL INSIGHT INTO CLL BIOLOGY AND EVENTUALLY THE MECHANISTIC RATIONALE FOR THE DEVELOPMENT OF SUCCESSFUL THERAPIES TARGETING BCR SIGNALING. U-CLL AND M-CLL ARE CHARACTERIZED BY VARIABLE LOW SURFACE IGM (SIGM) EXPRESSION AND SIGNALING CAPACITY. VARIABILITY OF SIGM CAN IN PART BE EXPLAINED BY CHRONIC ENGAGEMENT WITH (AUTO)ANTIGEN AT TISSUE SITES. HOWEVER, OTHER ENVIRONMENTAL ELEMENTS, GENETIC CHANGES, AND EPIGENETIC SIGNATURES ALSO CONTRIBUTE TO THE SIGM VARIABILITY. THE VARIABLE LEVELS HAVE CONSEQUENCES ON THE BEHAVIOR OF CLL, WHICH IS IN A STATE OF ANERGY WITH AN INDOLENT CLINICAL COURSE WHEN SIGM EXPRESSION IS LOW, OR PUSHED TOWARDS PROLIFERATION AND A MORE AGGRESSIVE CLINICAL COURSE WHEN SIGM EXPRESSION IS HIGH. EFFICACY OF THERAPIES THAT TARGET BTK MAY ALSO BE AFFECTED BY THE VARIABLE SIGM LEVELS AND SIGNALING AND, IN PART, EXPLAIN THE DEVELOPMENT OF RESISTANCE. 2022 9 493 33 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 10 4907 32 P53 ABERRATIONS DO NOT PREDICT INDIVIDUAL RESPONSE TO FLUDARABINE IN PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKAEMIA IN ADVANCED STAGES RAI III/IV. ABNORMALITIES OF P53 HAVE BEEN ASSOCIATED WITH SHORT SURVIVAL AND NON-RESPONSE TO THERAPY IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL). WE HAVE EVALUATED THE RATE OF RESPONSE TO FLUDARABINE AS FIRST-LINE THERAPY IN 54 PATIENTS WITH ADVANCED STAGE CLL, ANALYSING THE CYTOGENETIC PROFILE, ABERRATIONS IN P53, INCLUDING THE METHYLATION STATUS OF ITS PROMOTER, AND THE IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE-REGION (IGVH) MUTATION STATUS. ACCORDING TO THE ADVANCED STAGE OF THE DISEASE IN THIS SERIES, 75% OF PATIENTS PRESENTED GENETIC ABERRATIONS ASSOCIATED WITH POOR PROGNOSIS: DEL(17P) AND/OR DEL(11Q), AND NO-MUTATED IGVH GENES. TEN PATIENTS (18.5%) HAD METHYLATION IN THE PROMOTER REGION OF P53. EIGHTY-THREE PER CENT OF PATIENTS TREATED ACHIEVED A RESPONSE, WITH A HIGH RATE OF COMPLETE REMISSION (47.6%). ALTHOUGH WE FOUND A SIGNIFICANT CORRELATION BETWEEN FAILURES AND THE PRESENCE OF P53 ABERRATIONS (P = 0.0065), EITHER WITH METHYLATION (P = 0.018) OR DELETION (P = 0.015), 64% OF THE PATIENTS WITH ABERRATIONS IN THIS GENE RESPONDED TO TREATMENT (11/17), SUGGESTING THAT FLUDARABINE INDUCES HIGH REMISSION RATES, EVEN IN THESE PATIENTS. THIS IS THE FIRST TIME THAT THE SIGNIFICANCE OF P53 PROMOTER METHYLATION STATUS IS DESCRIBED IN THIS PATHOLOGY, AND OUR DATA SUPPORT THAT THIS EPIGENETIC PHENOMENON COULD BE INVOLVED IN THE PATHOGENESIS AND CLINICAL EVOLUTION OF CLL. 2005 11 1995 38 EPIGENETIC AND GENETIC ALTERATIONS AND THEIR INFLUENCE ON GENE REGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: TO UNDERSTAND THE CHANGES OF GENE REGULATION IN CARCINOGENESIS, WE EXPLORED SIGNALS OF DNA METHYLATION - A STABLE EPIGENETIC MARK OF GENE REGULATORY ELEMENTS - AND DESIGNED A COMPUTATIONAL MODEL TO PROFILE LOSS AND GAIN OF REGULATORY ELEMENTS (RES) DURING CARCINOGENESIS. WE ALSO UTILIZED SEQUENCING DATA TO ANALYZE THE ALLELE FREQUENCY OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AND DETECTED THE CANCER-ASSOCIATED SNPS, I.E., THE SNPS DISPLAYING THE SIGNIFICANT ALLELE FREQUENCY DIFFERENCE BETWEEN CANCER AND NORMAL SAMPLES. RESULTS: AFTER APPLYING THIS MODEL TO CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DATA, WE IDENTIFIED RES DIFFERENTIALLY ACTIVATED (DRES) BETWEEN NORMAL AND CLL CELLS, CONSISTING OF 6,802 DRES GAINED AND 4,606 DRES LOST IN CLL. THE IDENTIFIED REGULATORY PERTURBATIONS COINCIDE WITH CHANGES IN THE EXPRESSION OF TARGET GENES. IN PARTICULAR, THE GENES ENCODING DNA METHYLTRANSFERASES HARBOR MULTIPLE LOST-IN-CANCER DRES AND ZERO GAINED-IN-CANCER DRES, INDICATING THAT THE DAMAGED REGULATION OF THESE GENES MIGHT BE ONE OF THE KEY CAUSES OF TUMOR FORMATION. DRES DISPLAY A SIGNIFICANTLY ELEVATED DENSITY OF THE GENOME-WIDE ASSOCIATION STUDY (GWAS) SNPS ASSOCIATED WITH CLL AND CLL-RELATED TRAITS. WE OBSERVED THAT MOST OF DRE GWAS SNPS ASSOCIATED WITH CLL AND CLL-RELATED TRAITS (83%) DISPLAY A SIGNIFICANT HAPLOTYPE ASSOCIATION AMONG THE IDENTIFIED CANCER-ASSOCIATED ALLELES AND THE RISK ALLELES THAT HAVE BEEN REPORTED IN GWAS. ALSO DRES ARE ENRICHED FOR THE BINDING SITES OF THE WELL-ESTABLISHED B-CELL AND CLL TRANSCRIPTION FACTORS (TFS) NF-KB, AP2, P53, E2F1, PAX5, AND SP1. WE ALSO IDENTIFIED CLL-ASSOCIATED SNPS AND DEMONSTRATED THAT THE MUTATIONS AT THESE SNPS CHANGE THE BINDING SITES OF KEY TFS MUCH MORE FREQUENTLY THAN EXPECTED. CONCLUSIONS: THROUGH EXPLORING SEQUENCING DATA MEASURING DNA METHYLATION, WE IDENTIFIED THE EPIGENETIC ALTERATIONS (MORE SPECIFICALLY, DNA METHYLATION) AND GENETIC MUTATIONS ALONG NON-CODING GENOMIC REGIONS CLL, AND DEMONSTRATED THAT THESE CHANGES PLAY A CRITICAL ROLE IN CARCINOGENESIS THROUGH DAMAGING THE REGULATION OF KEY GENES AND ALTERNATING THE BINDING OF KEY TFS IN B AND CLL CELLS. 2017 12 2469 18 EPIGENETIC TRAJECTORIES OF THE PREMALIGNANT-TO-MALIGNANT TRANSITION OF CHRONIC LYMPHOCYTIC LEUKEMIA. KRETZMER AND COLLEAGUES SHOW THAT THE TRANSITION TO ALTERED METHYLOME OCCURS VERY EARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA, AND ONCE ACQUIRED, IT IS A CLONAL AND EXTREMELY STABLE CHANGE. HOWEVER, THE PRECISE TIME POINT WHEN THE LEUKEMIC CLONE STARTS DEVIATING SIGNIFICANTLY FROM THE NORMAL B-CELL DIFFERENTIATION TRAJECTORY IS STILL ELUSIVE. SEE RELATED ARTICLE BY KRETZMER ET AL., P. 54. 2021 13 494 29 ASSESSMENT OF PROMOTER METHYLATION IDENTIFIES PTCH AS A PUTATIVE TUMOR-SUPPRESSOR GENE IN HUMAN CLL. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF NEOPLASTIC LYMPHOCYTES, INDICATING DISRUPTION OF APOPTOSIS. PATIENTS AND METHODS: DIFFERENTIAL METHYLATION HYBRIDIZATION ANALYSIS WAS PERFORMED TO IDENTIFY NOVEL TARGET GENES SILENCED BY CPG ISLAND METHYLATION IN PATIENTS WITH CLL. RESULTS: PATCHED (PTCH), A TUMOR-SUPPRESSOR GENE, WAS FOUND TO BE FREQUENTLY METHYLATED IN CLL SAMPLES COMPARED TO SAMPLES DERIVED FROM HEALTHY INDIVIDUALS. DE NOVO METHYLATION OF A CPG ISLAND REGION LOCATED UPSTREAM OF PTCH EXON 1 WAS CONFIRMED BY PYROSEQUENCING IN 17/37 (46%) OF PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH CLL, BUT IN NONE ISOLATED FROM SEVEN HEALTHY INDIVIDUALS. NO ASSOCIATION WAS FOUND BETWEEN PTCH HYPERMETHYLATION AND CURRENTLY USED PROGNOSTIC CLL FACTORS. CONCLUSION: OUR INVESTIGATION SUGGESTS THAT EPIGENETIC SILENCING OF PTCH IS A MECHANISM CONTRIBUTING TO CLL TUMORIGENESIS. 2016 14 6468 34 TISSUE-SPECIFIC ENRICHMENT OF LYMPHOMA RISK LOCI IN REGULATORY ELEMENTS. THOUGH NUMEROUS POLYMORPHISMS HAVE BEEN ASSOCIATED WITH RISK OF DEVELOPING LYMPHOMA, HOW THESE VARIANTS FUNCTION TO PROMOTE TUMORIGENESIS IS POORLY UNDERSTOOD. HERE, WE REPORT THAT LYMPHOMA RISK SNPS, ESPECIALLY IN THE NON-HODGKIN'S LYMPHOMA SUBTYPE CHRONIC LYMPHOCYTIC LEUKEMIA, ARE SIGNIFICANTLY ENRICHED FOR CO-LOCALIZATION WITH EPIGENETIC MARKS OF ACTIVE GENE REGULATION. THESE ENRICHMENTS WERE SEEN IN A LYMPHOID-SPECIFIC MANNER FOR NUMEROUS ENCODE DATASETS, INCLUDING DNASE-HYPERSENSITIVITY AS WELL AS MULTIPLE SEGMENTATION-DEFINED ENHANCER REGIONS. FURTHERMORE, WE IDENTIFY PUTATIVELY FUNCTIONAL SNPS THAT ARE BOTH IN REGULATORY ELEMENTS IN LYMPHOCYTES AND ARE ASSOCIATED WITH GENE EXPRESSION CHANGES IN BLOOD. WE DEVELOPED AN ALGORITHM, UES, THAT USES A MONTE CARLO SIMULATION APPROACH TO CALCULATE THE ENRICHMENT OF PREVIOUSLY IDENTIFIED RISK SNPS IN VARIOUS FUNCTIONAL ELEMENTS. THIS MULTISCALE APPROACH INTEGRATING MULTIPLE DATASETS HELPS DISENTANGLE THE UNDERLYING BIOLOGY OF LYMPHOMA, AND MORE BROADLY, IS GENERALLY APPLICABLE TO GWAS RESULTS FROM OTHER DISEASES AS WELL. 2015 15 5275 42 PROMOTER METHYLATION OF THE BONE MORPHOGENETIC PROTEIN-6 GENE IN ASSOCIATION WITH ADULT T-CELL LEUKEMIA. BONE MORPHOGENETIC PROTEINS (BMP), BELONGING TO THE TRANSFORMING GROWTH FACTOR-BETA SUPERFAMILY, ARE MULTIFUNCTIONAL REGULATORS OF CELL PROLIFERATION, DIFFERENTIATION AND APOPTOSIS IN VARIOUS TYPES OF MALIGNANT CELLS. IN THIS STUDY, WE INVESTIGATED BMP-6 PROMOTER METHYLATION IN PATIENTS WITH VARIOUS TYPES OF LEUKEMIAS. THE BMP-6 METHYLATION WAS FOUND PREFERENTIALLY IN ADULT T-CELL LEUKEMIA (ATL) (49 OF 60, 82%) COMPARED WITH OTHER TYPES OF LEUKEMIAS STUDIED INCLUDING ACUTE MYELOID LEUKEMIA (3 OF 67, 5%), ACUTE LYMPHOBLASTIC LEUKEMIA (6 OF 38, 16%) AND CHRONIC LYMPHOCYTIC LEUKEMIA (1 OF 21, 5%). AMONG SUBTYPES OF ATL, THE BMP-6 GENE WAS MORE FREQUENTLY METHYLATED IN AGGRESSIVE ATL FORMS OF ACUTE (96%) AND LYMPHOMA (94%) TYPES THAN LESS MALIGNANT CHRONIC ATL (44%) AND SMOLDERING ATL (20%). WE ALSO ANALYZED THE METHYLATION STATUS OF PERIPHERAL BLOOD MONONUCLEAR CELLS FROM HEALTHY DONORS AND NONMALIGNANT LYMPH NODES WITH REACTIVE LYMPHADENOPATHY, NONE OF WHICH SHOWED DETECTABLE BMP-6 METHYLATION IN THIS STUDY. THE BMP-6 METHYALTION WAS CORRELATED WITH DECREASED MRNA TRANSCRIPT AND PROTEIN EXPRESSION. EXPRESSION OF BMP-6 WAS RESTORED BY THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE, SUGGESTING THAT METHYLATION WAS ASSOCIATED WITH THE TRANSCRIPTIONAL SILENCING. SERIAL ANALYSIS DEMONSTRATED AN INCREASING METHYLATION OF CPG SITES IN THE BMP-6 PROMOTER AND THE RESULTANT SUPPRESSION OF BMP-6 EXPRESSION AS ATL PROGRESSED. THESE FINDINGS SUGGESTED THAT BMP-6 PROMOTER METHYLATION IS LIKELY TO BE A COMMON EPIGENETIC EVENT AT LATER STAGES OF ATL AND THAT THE METHYLATION PROFILES MAY BE USEFUL FOR THE STAGING OF ATL AS WELL AS FOR EVALUATION OF THE INDIVIDUAL RISK OF DEVELOPING THE DISEASE. 2008 16 230 32 ADAPTIVE AND INNATE CYTOTOXIC EFFECTORS IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) SUBJECTS WITH STABLE DISEASE. CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS CHARACTERISED BY THE EXPANSION OF A NEOPLASTIC MATURE B CELL CLONE. CLL CLINICAL OUTCOME IS VERY HETEROGENEOUS, WITH SOME SUBJECTS NEVER REQUIRING THERAPY AND SOME SHOWING AN AGGRESSIVE DISEASE. GENETIC AND EPIGENETIC ALTERATIONS AND PRO-INFLAMMATORY MICROENVIRONMENT INFLUENCE CLL PROGRESSION AND PROGNOSIS. THE INVOLVEMENT OF IMMUNE-MEDIATED MECHANISMS IN CLL CONTROL NEEDS TO BE INVESTIGATED. WE ANALYSE THE ACTIVATION PROFILE OF INNATE AND ADAPTIVE CYTOTOXIC IMMUNE EFFECTORS IN A COHORT OF 26 CLL PATIENTS WITH STABLE DISEASE, AS KEY ELEMENTS FOR IMMUNE-MEDIATED CONTROL OF CANCER PROGRESSION. WE OBSERVED AN INCREASE IN CD54 EXPRESSION AND INTERFERON (IFN)-GAMMA PRODUCTION BY CYTOTOXIC T CELLS (CTL). CTL ABILITY TO RECOGNISE TUMOUR-TARGETS DEPENDS ON HUMAN LEUKOCYTE ANTIGENS (HLA)-CLASS I EXPRESSION. WE OBSERVED A DECREASED EXPRESSION OF HLA-A AND HLA-BC ON B CELLS OF CLL SUBJECTS, ASSOCIATED WITH A SIGNIFICANT REDUCTION IN INTRACELLULAR CALNEXIN THAT IS RELEVANT FOR HLA SURFACE EXPRESSION. NATURAL KILLER (NK) CELLS AND CTL FROM CLL SUBJECTS SHOW AN INCREASED EXPRESSION OF THE ACTIVATING RECEPTOR KIR2DS2 AND A REDUCTION OF 3DL1 AND NKG2A INHIBITING MOLECULES. THEREFORE, AN ACTIVATION PROFILE CHARACTERISES CTL AND NK CELLS OF CLL SUBJECTS WITH STABLE DISEASE. THIS PROFILE IS CONCEIVABLE WITH THE FUNCTIONAL INVOLVEMENT OF CYTOTOXIC EFFECTORS IN CLL CONTROL. 2023 17 1424 35 DIFFERENTIAL DNA METHYLATION OF GENE PROMOTERS IN SMALL B-CELL LYMPHOMAS. IMPROVED CARE OF PATIENTS WITH SMALL B-CELL LYMPHOMAS (SBCLS) IS LIKELY TO RESULT FROM THE ONGOING DISCOVERY OF MOLECULAR MARKERS THAT BETTER DEFINE THESE MALIGNANT NEOPLASMS. WE IDENTIFIED MULTIPLE GENE LOCI WHOSE DNA METHYLATION PATTERNS DIFFERED BETWEEN 3 TYPES OF SBCL: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA/SMALL LYMPHOCYTIC LYMPHOMA, MANTLE CELL LYMPHOMA, AND GRADES I AND II FOLLICULAR LYMPHOMA. THIS ANALYSIS WAS PERFORMED USING AN OLIGONUCLEOTIDE MICROARRAY THAT ALLOWED DETERMINATION OF THE DNA METHYLATION STATUS OF 156 LOCI IN 38 GENES. COMBINED BISULFITE RESTRICTION ANALYSIS AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WERE USED TO VALIDATE THE DIFFERENTIAL METHYLATION OF 6 OF THESE GENES. BY USING NON-HODGKIN LYMPHOMA CELL LINES AS MODELS, THESE GENES WERE EXAMINED FURTHER FOR METHYLATION AND GENE EXPRESSION RELATIONSHIPS. THIS STUDY ILLUSTRATES NONRANDOM EPIGENETIC ALTERATIONS IN SBCLS THAT SEEM TO PREFERENTIALLY INVOLVE LYMPHOMAS OF GERMINAL CENTER DERIVATION. 2005 18 2637 41 EPIGENOME-WIDE STUDY IDENTIFIES EPIGENETIC OUTLIERS IN NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. NONGENETIC PREDISPOSITION TO COLORECTAL CANCER CONTINUES TO BE DIFFICULT TO MEASURE PRECISELY, HAMPERING EFFORTS IN TARGETED PREVENTION AND SCREENING. EPIGENETIC CHANGES IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER CAN SERVE AS A TOOL IN PREDICTING COLORECTAL CANCER OUTCOMES. WE IDENTIFIED EPIGENETIC CHANGES AFFECTING THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. DNA METHYLATION PROFILING ON NORMAL COLON MUCOSA FROM 77 PATIENTS WITH COLORECTAL CANCER AND 68 CONTROLS IDENTIFIED A DISTINCT SUBGROUP OF NORMALLY-APPEARING MUCOSA WITH MARKEDLY DISRUPTED DNA METHYLATION AT A LARGE NUMBER OF CPGS, TERMED AS "OUTLIER METHYLATION PHENOTYPE" (OMP) AND ARE PRESENT IN 15 OF 77 PATIENTS WITH CANCER VERSUS 0 OF 68 CONTROLS (P < 0.001). SIMILAR FINDINGS WERE ALSO SEEN IN PUBLICLY AVAILABLE DATASETS. COMPARISON OF NORMAL COLON MUCOSA TRANSCRIPTION PROFILES OF PATIENTS WITH OMP CANCER WITH THOSE OF PATIENTS WITH NON-OMP CANCER INDICATES GENES WHOSE PROMOTERS ARE HYPERMETHYLATED IN THE OMP PATIENTS ARE ALSO TRANSCRIPTIONALLY DOWNREGULATED, AND THAT MANY OF THE GENES MOST AFFECTED ARE INVOLVED IN INTERACTIONS BETWEEN EPITHELIAL CELLS, THE MUCUS LAYER, AND THE MICROBIOME. ANALYSIS OF 16S RRNA PROFILES SUGGESTS THAT NORMAL COLON MUCOSA OF OMPS ARE ENRICHED IN BACTERIAL GENERA ASSOCIATED WITH COLORECTAL CANCER RISK, ADVANCED TUMOR STAGE, CHRONIC INTESTINAL INFLAMMATION, MALIGNANT TRANSFORMATION, NOSOCOMIAL INFECTIONS, AND KRAS MUTATIONS. IN CONCLUSION, OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. PROSPECTIVE STUDIES ARE NEEDED TO DETERMINE WHETHER OMP COULD SERVE AS A BIOMARKER FOR AN ELEVATED EPIGENETIC RISK FOR COLORECTAL CANCER DEVELOPMENT. PREVENTION RELEVANCE: OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. IDENTIFICATION OF OMPS IN HEALTHY CONTROLS AND PATIENTS WITH COLORECTAL CANCER WILL LEAD TO PREVENTION AND BETTER PROGNOSIS, RESPECTIVELY. 2022 19 6826 35 [GENOME-WIDE ANALYSIS OF DNA METHYLATION IN CD4+ T LYMPHOCYTES OF PATIENTS WITH PRIMARY PROGRESSIVE MULTIPLE SCLEROSIS INDICATES INVOLVEMENT OF THIS EPIGENETIC PROCESS IN THE DISEASE IMMUNOPATHOGENESIS]. THE PATHOGENESIS OF MULTIPLE SCLEROSIS (MS), A CHRONIC DISEASE OF THE CNS, INCLUDES AUTOIMMUNE AND NEURODEGENERATIVE COMPONENTS. IN MOST CASES, PATIENTS DEVELOP RELAPSING-REMITTING MS (RRMS), WHILE 10-15% OF PATIENTS DEVELOP PRIMARY PROGRESSIVE MS (PPMS), WHICH DIFFERS FROM RRMS IN THE MECHANISMS OF THE PATHOLOGICAL PROCESS, SOME DEMOGRAPHIC, AND SOME CLINICAL CHARACTERISTICS. THESE DIFFERENCES MAY BE EXPLAINED BY THE EPIGENETIC REGULATION OF GENE EXPRESSION IN PPMS INCLUDING DNA METHYLATION AS ONE OF THE KEY EPIGENETIC PROCESSES. THE FEATURES OF DNA METHYLATION IN VARIOUS CELL POPULATIONS IN PPMS PATIENTS REMAIN UNDERSTUDIED. THE GOAL OF THIS STUDY IS TO IDENTIFY DIFFERENTIALLY METHYLATED CPG SITES (DMSS) OF THE GENOME OF CD4+ T LYMPHOCYTES, WHICH CHARACTERIZE PPMS. THE STUDY INCLUDED EIGHT TREATMENT-NAIVE PPMS PATIENTS AND EIGHT HEALTHY CONTROLS. GENOME-WIDE ANALYSIS OF DNA METHYLATION OF CD4+ T LYMPHOCYTES WAS PERFORMED USING HIGH-DENSITY DNA MICROARRAYS. WE HAVE IDENTIFIED 108 DMSS, WHICH DISTINGUISH PPMS PATIENTS FROM HEALTHY CONTROLS. IN PPMS PATIENTS 81% OF THE DMSS ARE HYPERMETHYLATED. MORE THAN A HALF OF THE IDENTIFIED DMSS ARE LOCATED IN KNOWN GENES IN CPG ISLANDS AND ADJACENT REGIONS, WHICH INDICATES A HIGH FUNCTIONAL SIGNIFICANCE OF THESE DMSS IN PPMS DEVELOPMENT. ANALYSIS OF THE OVERREPRESENTATION OF DMS-CONTAINING GENES IN THE MAIN BIOLOGICAL PROCESSES DEMONSTRATES THEIR INVOLVEMENT IN THE REGULATION OF CELL ADHESION TO THE EXTRACELLULAR MATRIX AND THE DEVELOPMENT OF THE IMMUNE RESPONSE, I.E., ANTIGEN PROCESSING AND PRESENTATION, AND DEVELOPMENT OF THE IMMUNE SYSTEM. GENOME-WIDE ANALYSIS OF DNA METHYLATION IN CD4+ T LYMPHOCYTES OF PPMS PATIENTS INDICATES THE INVOLVEMENT OF THIS EPIGENETIC PROCESS IN THE IMMUNOPATHOGENESIS OF THE DISEASE. THESE RESULTS MAY HELP BETTER UNDERSTAND THE PATHOGENESIS OF THIS SEVERE FORM OF MS. 2022 20 1473 44 DISTINCT PATTERNS OF GLOBAL PROMOTER METHYLATION IN EARLY STAGE CHRONIC LYMPHOCYTIC LEUKEMIA. GENOMIC AND EPIGENOMIC STUDIES OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ARE RESHAPING OUR UNDERSTANDING OF THE DISEASE AND HAVE PROVIDED NEW PERSPECTIVES FOR A MORE INDIVIDUALIZED DIAGNOSIS AND NEW POTENTIAL THERAPEUTIC TARGETS. IN THIS STUDY, THE GLOBAL PROMOTER METHYLATION PROFILE WAS DETERMINED IN HIGHLY PURIFIED B-CELLS FROM 37 (BINET STAGE A) CLL PATIENTS, USING HIGH-RESOLUTION METHYLATION MICROARRAYS (27,578 CPG). OVERALL, THE METHYLATION PATTERN CORRELATED WITH THE MAJOR BIOLOGICAL (ZAP-70 AND CD38), AND MOLECULAR (IGHV MUTATION) MARKERS, DISTINGUISHING CLL CASES ACCORDING TO IGHV MUTATIONAL STATUS. CELL ADHESION MOLECULES WERE ENRICHED IN THE SIGNATURE OF UNMUTATED (UM) VERSUS MUTATED (M-) CLL. MOREOVER, IN M-CLL CPG HYPER-METHYLATION IN THREE GENES, INCLUDING SPG20, WAS SIGNIFICANTLY ANTI-CORRELATED WITH THE CORRESPONDING GENE EXPRESSION LEVEL. FINALLY, THE CORRELATION BETWEEN THE METHYLATION PATTERN AND CLINICAL PARAMETERS WAS INVESTIGATED. NOTABLY, OUT OF 42 METHYL-PROBES THAT WERE SIGNIFICANTLY ASSOCIATED WITH PROGRESSION FREE SURVIVAL (PFS), HYPER-METHYLATION OF SPG20 WAS ALSO POSITIVELY ASSOCIATED WITH PFS. THESE DATA SUPPORT THE NOTION THAT EPIGENETIC CHANGES HAVE CLINICAL IMPACT IN CLL AND MAY CONTRIBUTE TO THE IDENTIFICATION OF NOVEL CANDIDATE DISEASE-ASSOCIATED GENES POTENTIALLY USEFUL TO PREDICT THE CLINICAL OUTCOME OF EARLY STAGE CLL PATIENTS. 2014