1 5606 133 RPPA-BASED PROTEOMICS RECOGNIZES DISTINCT EPIGENETIC SIGNATURES IN CHRONIC LYMPHOCYTIC LEUKEMIA WITH CLINICAL CONSEQUENCES. THE CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ARMAMENTARIUM HAS EVOLVED SIGNIFICANTLY, WITH NOVEL THERAPIES THAT INHIBIT BRUTON TYROSINE KINASE, PI3K DELTA AND/OR THE BCL2 PROTEIN IMPROVING OUTCOMES. STILL, THE CLINICAL COURSE OF CLL PATIENTS IS HIGHLY VARIABLE AND MOST PREVIOUSLY RECOGNIZED PROGNOSTIC FEATURES LACK THE CAPACITY TO PREDICT RESPONSE TO MODERN TREATMENTS INDICATING THE NEED FOR NEW PROGNOSTIC MARKERS. IN THIS STUDY, WE IDENTIFIED FOUR EPIGENETICALLY DISTINCT PROTEOMIC SIGNATURES OF A LARGE COHORT OF CLL AND RELATED DISEASES DERIVED SAMPLES (N = 871) USING REVERSE PHASE PROTEIN ARRAY TECHNOLOGY. THESE SIGNATURES ARE ASSOCIATED WITH CLINICAL FEATURES INCLUDING AGE, CYTOGENETIC ABNORMALITIES [TRISOMY 12, DEL(13Q) AND DEL(17P)], IMMUNOGLOBULIN HEAVY-CHAIN LOCUS (IGHV) MUTATIONAL LOAD, ZAP-70 STATUS, BINET AND RAI STAGING AS WELL AS WITH THE OUTCOME MEASURES OF TIME TO TREATMENT AND OVERALL SURVIVAL. PROTEIN SIGNATURE MEMBERSHIP WAS IDENTIFIED AS PREDICTIVE MARKER FOR OVERALL SURVIVAL REGARDLESS OF OTHER CLINICAL FEATURES. AMONG THE ANALYZED EPIGENETIC PROTEINS, EZH2, HDAC6, AND LOSS OF H3K27ME3 LEVELS WERE THE MOST INDEPENDENTLY ASSOCIATED WITH POOR SURVIVAL. THESE FINDINGS DEMONSTRATE THAT PROTEOMIC BASED EPIGENETIC BIOMARKERS CAN BE USED TO BETTER CLASSIFY CLL PATIENTS AND PROVIDE THERAPEUTIC GUIDANCE. 2022 2 1561 36 DNA METHYLATION OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH DIFFERENTIAL RESPONSE TO CHEMOTHERAPY. ACQUIRED RESISTANCE TO CHEMOTHERAPY IS AN IMPORTANT CLINICAL PROBLEM AND CAN ALSO OCCUR WITHOUT DETECTABLE CYTOGENETIC ABERRATIONS OR GENE MUTATIONS. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS MOLECULARLY WELL CHARACTERIZED AND HAS BEEN ELEMENTAL FOR ESTABLISHING CENTRAL PARADIGMS IN ONCOLOGY. THIS PROMPTED US TO CHECK WHETHER SPECIFIC EPIGENETIC CHANGES AT THE LEVEL OF DNA METHYLATION MIGHT UNDERLIE DEVELOPMENT OF TREATMENT RESISTANCE. WE USED ILLUMINA INFINIUM HUMANMETHYLATION450 BEADCHIPS TO OBTAIN DNA METHYLATION PROFILES OF 71 CLL PATIENTS WITH DIFFERENTIAL RESPONSES. THIRTY-SIX PATIENTS WERE CATEGORIZED AS RELAPSED/REFRACTORY AFTER TREATMENT WITH FLUDARABINE OR BENDAMUSTINE AND 21 OF THEM HAD GENETIC ABERRATIONS OF TP53. THE OTHER 35 PATIENTS WERE UNTREATED AT THE TIME OF SAMPLING AND 15 OF THEM HAD GENETIC ABERRATION OF TP53. ALTHOUGH WE COULD NOT CORRELATE CHEMORESISTANCE WITH EPIGENETIC CHANGES, THE PATIENTS WERE COMPREHENSIVELY CHARACTERIZED REGARDING RELEVANT PROGNOSTIC AND MOLECULAR MARKERS (E.G. IGHV MUTATION STATUS, CHROMOSOME ABERRATIONS, TP53 MUTATION STATUS, CLINICAL PARAMETERS), WHICH MAKES OUR DATASET A UNIQUE AND VALUABLE RESOURCE THAT CAN BE USED BY RESEARCHERS TO TEST ALTERNATIVE HYPOTHESES. 2020 3 3309 34 HIGHER GENE EXPRESSION VARIABILITY IN THE MORE AGGRESSIVE SUBTYPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PRESENTS TWO SUBTYPES WHICH HAVE DRASTICALLY DIFFERENT CLINICAL OUTCOMES, IGVH MUTATED (M-CLL) AND IGVH UNMUTATED (U-CLL). SO FAR, THESE TWO SUBTYPES ARE NOT ASSOCIATED TO CLEAR DIFFERENCES IN GENE EXPRESSION PROFILES. INTERESTINGLY, RECENT RESULTS HAVE HIGHLIGHTED IMPORTANT ROLES FOR HETEROGENEITY, BOTH AT THE GENETIC AND AT THE EPIGENETIC LEVEL IN CLL PROGRESSION. METHODS: WE ANALYZED GENE EXPRESSION DATA OF TWO LARGE COHORTS OF CLL PATIENTS AND QUANTIFIED EXPRESSION VARIABILITY ACROSS INDIVIDUALS TO INVESTIGATE DIFFERENCES BETWEEN THE TWO SUBTYPES USING DIFFERENT MEASURES AND STATISTICAL TESTS. FUNCTIONAL SIGNIFICANCE WAS EXPLORED BY PATHWAY ENRICHMENT AND NETWORK ANALYSES. FURTHERMORE, WE IMPLEMENTED A RANDOM FOREST APPROACH BASED ON EXPRESSION VARIABILITY TO CLASSIFY PATIENTS INTO DISEASE SUBTYPES. RESULTS: WE FOUND THAT U-CLL, THE MORE AGGRESSIVE TYPE OF THE DISEASE, SHOWS SIGNIFICANTLY INCREASED VARIABILITY OF GENE EXPRESSION ACROSS PATIENTS AND THAT, OVERALL, GENES THAT SHOW HIGHER VARIABILITY IN THE AGGRESSIVE SUBTYPE ARE RELATED TO CELL CYCLE, DEVELOPMENT AND INTER-CELLULAR COMMUNICATION. THESE FUNCTIONS INDICATE A POTENTIAL RELATION BETWEEN GENE EXPRESSION VARIABILITY AND THE FASTER PROGRESSION OF THIS CLL SUBTYPE. FINALLY, A CLASSIFIER BASED ON GENE EXPRESSION VARIABILITY WAS ABLE TO CORRECTLY PREDICT THE DISEASE SUBTYPE OF CLL PATIENTS. CONCLUSIONS: THERE ARE STRONG RELATIONS BETWEEN GENE EXPRESSION VARIABILITY AND DISEASE SUBTYPE LINKING SIGNIFICANTLY INCREASED EXPRESSION VARIABILITY TO PHENOTYPES SUCH AS AGGRESSIVENESS AND RESISTANCE TO THERAPY IN CLL. 2015 4 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 5 4426 47 MOLECULAR BASIS OF CHRONIC LYMPHOCYTIC LEUKEMIA DIAGNOSIS AND PROGNOSIS. BACKGROUNDS: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON TYPE OF LEUKEMIA IN ADULTS AND IS CHARACTERIZED BY A CLONAL ACCUMULATION OF MATURE APOPTOSIS-RESISTANT NEOPLASTIC CELLS. IT IS ALSO A HETEROGENEOUS DISEASE WITH A VARIABLE CLINICAL OUTCOME. HERE, WE PRESENT A REVIEW OF CURRENTLY KNOWN (EPI)GENETIC ALTERATIONS THAT ARE RELATED TO THE ETIOLOGY, PROGRESSION AND CHEMO-REFRACTORINESS OF CLL. RELEVANT LITERATURE WAS IDENTIFIED THROUGH A PUBMED SEARCH (1994-2014) OF ENGLISH-LANGUAGE PAPERS USING THE TERMS CLL, SIGNALING PATHWAY, CYTOGENETIC ABNORMALITY, SOMATIC MUTATION, EPIGENETIC ALTERATION AND MICRO-RNA. RESULTS: CLL IS CHARACTERIZED BY THE PRESENCE OF GROSS CHROMOSOMAL ABNORMALITIES, EPIGENETIC ALTERATIONS, MICRO-RNA EXPRESSION ALTERATIONS, IMMUNOGLOBULIN HEAVY CHAIN GENE MUTATIONS AND OTHER GENETIC LESIONS. THE EXPRESSION OF UNMUTATED IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION (IGHV) GENES, ZAP-70 AND CD38 PROTEINS, THE OCCURRENCE OF CHROMOSOMAL ABNORMALITIES SUCH AS 17P AND 11Q DELETIONS AND MUTATIONS OF THE NOTCH1, SF3B1 AND BIRC3 GENES HAVE BEEN ASSOCIATED WITH A POOR PROGNOSIS. IN ADDITION, MUTATIONS IN TUMOR SUPPRESSOR GENES, SUCH AS TP53 AND ATM, HAVE BEEN ASSOCIATED WITH REFRACTORINESS TO CONVENTIONAL CHEMOTHERAPEUTIC AGENTS. MICRO-RNA EXPRESSION ALTERATIONS AND ABERRANT METHYLATION PATTERNS IN GENES THAT ARE SPECIFICALLY DEREGULATED IN CLL, INCLUDING THE BCL-2, TCL1 AND ZAP-70 GENES, HAVE ALSO BEEN ENCOUNTERED AND LINKED TO DISTINCT CLINICAL PARAMETERS. CONCLUSIONS: SPECIFIC CHROMOSOMAL ABNORMALITIES AND GENE MUTATIONS MAY SERVE AS DIAGNOSTIC AND PROGNOSTIC INDICATORS FOR DISEASE PROGRESSION AND SURVIVAL. THE IDENTIFICATION OF THESE ANOMALIES BY STATE-OF-THE-ART MOLECULAR (CYTO)GENETIC TECHNIQUES SUCH AS FLUORESCENCE IN SITU HYBRIDIZATION (FISH), COMPARATIVE GENOMIC HYBRIDIZATION (CGH), SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MICROARRAY-BASED GENOMIC PROFILING AND NEXT-GENERATION SEQUENCING (NGS) CAN BE OF PARAMOUNT HELP FOR THE CLINICAL MANAGEMENT OF THESE PATIENTS, INCLUDING OPTIMAL TREATMENT DESIGN. THE EFFICACY OF NOVEL THERAPEUTICS SHOULD TO BE TESTED ACCORDING TO THE PRESENCE OF THESE MOLECULAR LESIONS IN CLL PATIENTS. 2015 6 4446 36 MOLECULAR MAP OF CHRONIC LYMPHOCYTIC LEUKEMIA AND ITS IMPACT ON OUTCOME. RECENT ADVANCES IN CANCER CHARACTERIZATION HAVE CONSISTENTLY REVEALED MARKED HETEROGENEITY, IMPEDING THE COMPLETION OF INTEGRATED MOLECULAR AND CLINICAL MAPS FOR EACH MALIGNANCY. HERE, WE FOCUS ON CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A B CELL NEOPLASM WITH VARIABLE NATURAL HISTORY THAT IS CONVENTIONALLY CATEGORIZED INTO TWO SUBTYPES DISTINGUISHED BY EXTENT OF SOMATIC MUTATIONS IN THE HEAVY-CHAIN VARIABLE REGION OF IMMUNOGLOBULIN GENES (IGHV). TO BUILD THE 'CLL MAP,' WE INTEGRATED GENOMIC, TRANSCRIPTOMIC AND EPIGENOMIC DATA FROM 1,148 PATIENTS. WE IDENTIFIED 202 CANDIDATE GENETIC DRIVERS OF CLL (109 NEW) AND REFINED THE CHARACTERIZATION OF IGHV SUBTYPES, WHICH REVEALED DISTINCT GENOMIC LANDSCAPES AND LEUKEMOGENIC TRAJECTORIES. DISCOVERY OF NEW GENE EXPRESSION SUBTYPES FURTHER SUBCATEGORIZED THIS NEOPLASM AND PROVED TO BE INDEPENDENT PROGNOSTIC FACTORS. CLINICAL OUTCOMES WERE ASSOCIATED WITH A COMBINATION OF GENETIC, EPIGENETIC AND GENE EXPRESSION FEATURES, FURTHER ADVANCING OUR PROGNOSTIC PARADIGM. OVERALL, THIS WORK REVEALS FRESH INSIGHTS INTO CLL ONCOGENESIS AND PROGNOSTICATION. 2022 7 4487 38 MOLECULARLY TARGETED DRUG COMBINATIONS DEMONSTRATE SELECTIVE EFFECTIVENESS FOR MYELOID- AND LYMPHOID-DERIVED HEMATOLOGIC MALIGNANCIES. TRANSLATING THE GENETIC AND EPIGENETIC HETEROGENEITY UNDERLYING HUMAN CANCERS INTO THERAPEUTIC STRATEGIES IS AN ONGOING CHALLENGE. LARGE-SCALE SEQUENCING EFFORTS HAVE UNCOVERED A SPECTRUM OF MUTATIONS IN MANY HEMATOLOGIC MALIGNANCIES, INCLUDING ACUTE MYELOID LEUKEMIA (AML), SUGGESTING THAT COMBINATIONS OF AGENTS WILL BE REQUIRED TO TREAT THESE DISEASES EFFECTIVELY. COMBINATORIAL APPROACHES WILL ALSO BE CRITICAL FOR COMBATING THE EMERGENCE OF GENETICALLY HETEROGENEOUS SUBCLONES, RESCUE SIGNALS IN THE MICROENVIRONMENT, AND TUMOR-INTRINSIC FEEDBACK PATHWAYS THAT ALL CONTRIBUTE TO DISEASE RELAPSE. TO IDENTIFY NOVEL AND EFFECTIVE DRUG COMBINATIONS, WE PERFORMED EX VIVO SENSITIVITY PROFILING OF 122 PRIMARY PATIENT SAMPLES FROM A VARIETY OF HEMATOLOGIC MALIGNANCIES AGAINST A PANEL OF 48 DRUG COMBINATIONS. THE COMBINATIONS WERE DESIGNED AS DRUG PAIRS THAT TARGET NONOVERLAPPING BIOLOGICAL PATHWAYS AND COMPRISE DRUGS FROM DIFFERENT CLASSES, PREFERABLY WITH FOOD AND DRUG ADMINISTRATION APPROVAL. A COMBINATION RATIO (CR) WAS DERIVED FOR EACH DRUG PAIR, AND CRS WERE EVALUATED WITH RESPECT TO DIAGNOSTIC CATEGORIES AS WELL AS AGAINST GENETIC, CYTOGENETIC, AND CELLULAR PHENOTYPES OF SPECIMENS FROM THE TWO LARGEST DISEASE CATEGORIES: AML AND CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). NEARLY ALL TESTED COMBINATIONS INVOLVING A BCL2 INHIBITOR SHOWED ADDITIONAL BENEFIT IN PATIENTS WITH MYELOID MALIGNANCIES, WHEREAS SELECT COMBINATIONS INVOLVING PI3K, CSF1R, OR BROMODOMAIN INHIBITORS SHOWED PREFERENTIAL BENEFIT IN LYMPHOID MALIGNANCIES. EXPANDED ANALYSES OF PATIENTS WITH AML AND CLL REVEALED SPECIFIC PATTERNS OF EX VIVO DRUG COMBINATION EFFICACY THAT WERE ASSOCIATED WITH SELECT GENETIC, CYTOGENETIC, AND PHENOTYPIC DISEASE SUBSETS, WARRANTING FURTHER EVALUATION. THESE FINDINGS HIGHLIGHT THE HEURISTIC VALUE OF AN INTEGRATED FUNCTIONAL GENOMIC APPROACH TO THE IDENTIFICATION OF NOVEL TREATMENT STRATEGIES FOR HEMATOLOGIC MALIGNANCIES. 2017 8 5687 31 SIGNIFICANCE OF INACTIVATED GENES IN LEUKEMIA: PATHOGENESIS AND PROGNOSIS. EPIGENETIC AND GENETIC ALTERATIONS ARE TWO MECHANISMS PARTICIPATING IN LEUKEMIA, WHICH CAN INACTIVATE GENES INVOLVED IN LEUKEMIA PATHOGENESIS OR PROGRESSION. THE PURPOSE OF THIS REVIEW WAS TO INTRODUCE VARIOUS INACTIVATED GENES AND EVALUATE THEIR POSSIBLE ROLE IN LEUKEMIA PATHOGENESIS AND PROGNOSIS. BY SEARCHING THE MESH WORDS "GENE, SILENCING AND LEUKEMIA" IN PUBMED WEBSITE, RELEVANT ENGLISH ARTICLES DEALT WITH HUMAN SUBJECTS AS OF 2000 WERE INCLUDED IN THIS STUDY. GENE INACTIVATION IN LEUKEMIA IS LARGELY MEDIATED BY PROMOTER'S HYPERMETHYLATION OF GENE INVOLVING IN CELLULAR FUNCTIONS SUCH AS CELL CYCLE, APOPTOSIS, AND GENE TRANSCRIPTION. INACTIVATED GENES, SUCH AS ASPP1, TP53, IKZF1 AND P15, MAY CORRELATE WITH POOR PROGNOSIS IN ACUTE LYMPHOID LEUKEMIA (ALL), CHRONIC LYMPHOID LEUKEMIA (CLL), CHRONIC MYELOGENOUS LEUKEMIA (CML) AND ACUTE MYELOID LEUKEMIA (AML), RESPECTIVELY. GENE INACTIVATION MAY PLAY A CONSIDERABLE ROLE IN LEUKEMIA PATHOGENESIS AND PROGNOSIS, WHICH CAN BE CONSIDERED AS COMPLEMENTARY DIAGNOSTIC TESTS TO DIFFERENTIATE DIFFERENT LEUKEMIA TYPES, DETERMINE LEUKEMIA PROGNOSIS, AND ALSO DETECT RESPONSE TO THERAPY. IN GENERAL, THIS REVIEW SHOWED SOME GENES INACTIVATED ONLY IN LEUKEMIA (WITH DIFFERENCES BETWEEN B-ALL, T-ALL, CLL, AML AND CML). THESE DIFFERENCES COULD BE OF INTEREST AS AN ADDITIONAL TOOL TO BETTER CATEGORIZE LEUKEMIA TYPES. FURTHERMORE; BASED ON INACTIVATED GENES, A DIVERSE CLASSIFICATION OF LEUKEMIAS COULD REPRESENT A POWERFUL METHOD TO ADDRESS A TARGETED THERAPY OF THE PATIENTS, IN ORDER TO MINIMIZE SIDE EFFECTS OF CONVENTIONAL THERAPIES AND TO ENHANCE NEW DRUG STRATEGIES. 2017 9 27 46 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 10 4678 42 NEW MOLECULAR MARKERS IN RESISTANT B-CLL. B-CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) IS CHARACTERIZED BY A HIGHLY VARIABLE CLINICAL COURSE WHICH HAS LONG REMAINED A STUMBLING BLOCK FOR CLINICIANS. THIS VARIABILITY APPEARS TO ARISE FROM COMPLEX MOLECULAR ALTERATIONS IDENTIFIED IN MALIGNANT CELLS FROM PATIENT SUBSETS. RECENT STUDIES HAVE FOCUSED IN PARTICULAR ON IDENTIFYING NEW MOLECULAR MARKERS TO HELP PREDICT THE MOST EFFECTIVE AND ADAPTED TREATMENTS. IN ADDITION TO THE MUTATION STATUS OF IMMUNOGLOBULIN VARIABLE HEAVY-CHAIN REGION (IGVH) GENES, WHICH IS A WELL-ESTABLISHED PREDICTIVE FACTOR IN B-CLL, THESE NEW MARKERS INCLUDE DEFECTS OF CELL FACTORS INVOLVED IN THE MAINTENANCE OF GENOME STABILITY, SUCH AS TELOMERE FUNCTION, DNA REPAIR, ATM AND P53. OTHER PREDICTIVE FACTORS, SUCH AS TYROSINE KINASE ZAP-70 AND SOLUBLE FACTORS FOUND IN PATIENT SERA, MAY BE ASSOCIATED WITH B-CELL RECEPTOR SIGNAL TRANSDUCTION. INTERESTINGLY, AN ALTERATION OF THESE FACTORS FITS CLOSELY, THOUGH NOT STRIKINGLY, WITH THE ABSENCE OF SOMATIC MUTATIONS IN IGVH GENES, SUGGESTING THAT THE LATTER MAY BE DUE EITHER TO EPIGENETIC EVENTS LEADING TO AN UNSTABLE GENOME OR TO AN INHERITED DEFECT IN THE IMMUNE RESPONSE OF MALIGNANT B-CELLS. RECENT LESSONS FROM ZAP-70 EXPRESSION/PHOSPHORYLATION SUGGEST THAT SOME OF THESE MARKERS MAY REFLECT THE DEFECTIVE PATHWAYS IN B-CLL CELLS RATHER THAN BEING MARKERS OF CELL MALIGNANCY PER SE. FURTHERMORE, SPECIFIC SUBSETS OF MARKERS ARE FOUND IN PATIENT CELLS RESISTANT TO TREATMENT. CURRENT STUDIES ON GENE EXPRESSION PROFILING AND PROTEOMIC ANALYSES SHOULD SOON LEAD TO A BETTER UNDERSTANDING OF HOW THESE PATHWAYS ARE AFFECTED, ESPECIALLY IN MULTI-DRUG RESISTANT B-CLL. 2006 11 2966 23 GENETIC AND EPIGENETIC PROFILING OF CLL DISEASE PROGRESSION REVEALS LIMITED SOMATIC EVOLUTION AND SUGGESTS A RELATIONSHIP TO MEMORY-CELL DEVELOPMENT. WE EXAMINED GENETIC AND EPIGENETIC CHANGES THAT OCCUR DURING DISEASE PROGRESSION FROM INDOLENT TO AGGRESSIVE FORMS OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) USING SERIAL SAMPLES FROM 27 PATIENTS. ANALYSIS OF DNA MUTATIONS GROUPED THE LEUKEMIA CASES INTO THREE CATEGORIES: EVOLVING (26%), EXPANDING (26%) AND STATIC (47%). THUS, APPROXIMATELY THREE-QUARTERS OF THE CLL CASES HAD LITTLE TO NO GENETIC SUBCLONAL EVOLUTION. HOWEVER, WE IDENTIFIED SIGNIFICANT RECURRENT DNA METHYLATION CHANGES DURING PROGRESSION AT 4752 CPGS ENRICHED FOR REGIONS NEAR POLYCOMB 2 REPRESSIVE COMPLEX (PRC2) TARGETS. PROGRESSION-ASSOCIATED CPGS NEAR THE PRC2 TARGETS UNDERGO METHYLATION CHANGES IN THE SAME DIRECTION DURING DISEASE PROGRESSION AS DURING NORMAL DEVELOPMENT FROM NAIVE TO MEMORY B CELLS. OUR STUDY SHOWS THAT CLL PROGRESSION DOES NOT TYPICALLY OCCUR VIA SUBCLONAL EVOLUTION, BUT THAT CERTAIN CPG SITES UNDERGO RECURRENT METHYLATION CHANGES. OUR RESULTS SUGGEST CLL PROGRESSION MAY INVOLVE DEVELOPMENTAL PROCESSES SHARED IN COMMON WITH THE GENERATION OF NORMAL MEMORY B CELLS. 2015 12 1682 35 DRUG-MICROENVIRONMENT PERTURBATIONS REVEAL RESISTANCE MECHANISMS AND PROGNOSTIC SUBGROUPS IN CLL. THE TUMOUR MICROENVIRONMENT AND GENETIC ALTERATIONS COLLECTIVELY INFLUENCE DRUG EFFICACY IN CANCER, BUT CURRENT EVIDENCE IS LIMITED AND SYSTEMATIC ANALYSES ARE LACKING. USING CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) AS A MODEL DISEASE, WE INVESTIGATED THE INFLUENCE OF 17 MICROENVIRONMENTAL STIMULI ON 12 DRUGS IN 192 GENETICALLY CHARACTERISED PATIENT SAMPLES. BASED ON MICROENVIRONMENTAL RESPONSE, WE IDENTIFIED FOUR SUBGROUPS WITH DISTINCT CLINICAL OUTCOMES BEYOND KNOWN PROGNOSTIC MARKERS. RESPONSE TO MULTIPLE MICROENVIRONMENTAL STIMULI WAS AMPLIFIED IN TRISOMY 12 SAMPLES. TRISOMY 12 WAS ASSOCIATED WITH A DISTINCT EPIGENETIC SIGNATURE. BROMODOMAIN INHIBITION REVERSED THIS EPIGENETIC PROFILE AND COULD BE USED TO TARGET MICROENVIRONMENTAL SIGNALLING IN TRISOMY 12 CLL. WE QUANTIFIED THE IMPACT OF MICROENVIRONMENTAL STIMULI ON DRUG RESPONSE AND THEIR DEPENDENCE ON GENETIC ALTERATIONS, IDENTIFYING INTERLEUKIN 4 (IL4) AND TOLL-LIKE RECEPTOR (TLR) STIMULATION AS THE STRONGEST ACTUATORS OF DRUG RESISTANCE. IL4 AND TLR SIGNALLING ACTIVITY WAS INCREASED IN CLL-INFILTRATED LYMPH NODES COMPARED WITH HEALTHY SAMPLES. HIGH IL4 ACTIVITY CORRELATED WITH FASTER DISEASE PROGRESSION. THE PUBLICLY AVAILABLE DATASET CAN FACILITATE THE INVESTIGATION OF CELL-EXTRINSIC MECHANISMS OF DRUG RESISTANCE AND DISEASE PROGRESSION. 2022 13 1577 33 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES. 2018 14 2494 23 EPIGENETICS AND CHRONIC LYMPHOCYTIC LEUKEMIA. THE DNA METHYLATION LEVEL IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS GENERALLY LOWER THAN HEALTHY INDIVIDUALS. ALTHOUGH DNA METHYLATION IS GLOBALLY DECREASED, REGIONAL HYPERMETHYLATION OF GENE PROMOTERS LEADS TO GENE SILENCING. MANY OF THESE GENES HAVE TUMOR SUPPRESSOR PHENOTYPES. UNLIKE MUTATIONS OR DELETIONS, HYPERMETHYLATION IS POTENTIALLY REVERSIBLE AFTER INHIBITION WITH DNA METHYLATION MODULATORS. MYELODYSPLASTIC SYNDROME HAS BEEN A MODEL DISEASE IN WHICH TREATMENT OF PATIENTS RESULTS IN DEMETHYLATION OF SPECIFIC GENES. THE STORY IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS SLOWLY UNRAVELING AS EPIGENETIC MODIFICATIONS LIKELY ALSO PLAY AN IMPORTANT ROLE. ONGOING CLINICAL TRIALS CORRELATING CLINICAL RESPONSE TO GENE EXPRESSION AFTER TREATMENT WITH DNA METHYLATION INHIBITORS WILL ULTIMATELY ALLOW US TO BETTER RISK STRATIFY AND PREDICT THE SUBGROUP OF PATIENTS WHO WILL BENEFIT FROM TREATMENT WITH THIS CLASS OF DRUGS. 2006 15 2074 38 EPIGENETIC DEREGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA: CLINICAL AND BIOLOGICAL IMPACT. DEREGULATED TRANSCRIPTIONAL CONTROL CAUSED BY ABERRANT DNA METHYLATION AND/OR HISTONE MODIFICATIONS IS A HALLMARK OF CANCER CELLS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE MOST COMMON ADULT LEUKEMIA, THE EPIGENETIC 'LANDSCAPE' HAS ADDED A NEW LAYER OF COMPLEXITY TO OUR UNDERSTANDING OF THIS CLINICALLY AND BIOLOGICALLY HETEROGENEOUS DISEASE. EARLY STUDIES IDENTIFIED ABERRANT DNA METHYLATION, OFTEN BASED ON SINGLE GENE PROMOTER ANALYSIS WITH BOTH BIOLOGICAL AND CLINICAL IMPACT. SUBSEQUENT GENOME-WIDE PROFILING STUDIES REVEALED DIFFERENTIAL DNA METHYLATION BETWEEN CLLS AND CONTROLS AND IN PROGNOSTICS SUBGROUPS OF THE DISEASE. FROM THESE STUDIES, IT BECAME APPARENT THAT DNA METHYLATION IN REGIONS OUTSIDE OF PROMOTERS, SUCH AS ENHANCERS, IS IMPORTANT FOR THE REGULATION OF CODING GENES AS WELL AS FOR THE REGULATION OF NON-CODING RNAS. ALTHOUGH DNA METHYLATION PROFILES ARE REPORTEDLY STABLE OVER TIME AND IN RELATION TO THERAPY, A HIGHER EPIGENETIC HETEROGENEITY OR 'BURDEN' IS SEEN IN MORE AGGRESSIVE CLL SUBGROUPS, ALBEIT AS NON-RECURRENT 'PASSENGER' EVENTS. MORE RECENTLY, DNA METHYLATION PROFILES IN CLL ANALYZED IN RELATION TO DIFFERENTIATING NORMAL B-CELL POPULATIONS REVEALED THAT THE MAJORITY OF THE CLL EPIGENOME REFLECTS THE EPIGENOMES PRESENT IN THE CELL OF ORIGIN AND THAT ONLY A SMALL FRACTION OF THE EPIGENETIC ALTERATIONS REPRESENTS TRULY CLL-SPECIFIC CHANGES. FURTHERMORE, CLL PATIENTS CAN BE GROUPED INTO AT LEAST THREE CLINICALLY RELEVANT EPIGENETIC SUBGROUPS, POTENTIALLY ORIGINATING FROM DIFFERENT CELLS AT VARIOUS STAGES OF DIFFERENTIATION AND ASSOCIATED WITH DISTINCT OUTCOMES. IN THIS REVIEW, WE SUMMARIZE THE CURRENT UNDERSTANDING OF THE DNA METHYLOME IN CLL, THE ROLE OF HISTONE MODIFYING ENZYMES, HIGHLIGHT INSIGHTS DERIVED FROM ANIMAL MODELS AND ATTEMPTS MADE TO TARGET EPIGENETIC REGULATORS IN CLL ALONG WITH THE FUTURE DIRECTIONS OF THIS RAPIDLY ADVANCING FIELD. 2018 16 1068 32 CLL INTRACLONAL FRACTIONS EXHIBIT ESTABLISHED AND RECENTLY ACQUIRED PATTERNS OF DNA METHYLATION. INTRACLONAL SUBPOPULATIONS OF CIRCULATING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS WITH DIFFERENT PROLIFERATIVE HISTORIES AND RECIPROCAL SURFACE EXPRESSION OF CXCR4 AND CD5 HAVE BEEN OBSERVED IN THE PERIPHERAL BLOOD OF CLL PATIENTS AND NAMED PROLIFERATIVE (PF), INTERMEDIATE (IF), AND RESTING (RF) CELLULAR FRACTIONS. HERE, WE FOUND THAT THESE INTRACLONAL CIRCULATING FRACTIONS SHARE PERSISTENT DNA METHYLATION SIGNATURES LARGELY ASSOCIATED WITH THE MUTATION STATUS OF THE IMMUNOGLOBULIN HEAVY CHAIN LOCUS (IGHV) AND THEIR ORIGINS FROM DISTINCT STAGES OF DIFFERENTIATION OF ANTIGEN-EXPERIENCED B CELLS. INCREASED LEUKEMIC BIRTH RATE, HOWEVER, SHOWED A VERY LIMITED IMPACT ON DNA METHYLATION OF CIRCULATING CLL FRACTIONS INDEPENDENT OF IGHV MUTATION STATUS. ADDITIONALLY, DNA METHYLATION HETEROGENEITY INCREASED AS LEUKEMIC CELLS ADVANCED FROM PF TO RF IN THE PERIPHERAL BLOOD. THIS FREQUENTLY CO-OCCURRED WITH HETEROCHROMATIN HYPOMETHYLATION AND HYPERMETHYLATION OF POLYCOMB-REPRESSED REGIONS IN THE PF, SUGGESTING ACCUMULATION OF LONGEVITY-ASSOCIATED EPIGENETIC FEATURES IN RECENTLY BORN CELLS. ON THE OTHER HAND, TRANSCRIPTIONAL DIFFERENCES BETWEEN PAIRED INTRACLONAL FRACTIONS CONFIRMED THEIR PROLIFERATIVE EXPERIENCE AND FURTHER SUPPORTED A LINEAR ADVANCEMENT FROM PF TO RF IN THE PERIPHERAL BLOOD. SEVERAL OF THESE DIFFERENTIALLY EXPRESSED GENES SHOWED UNIQUE ASSOCIATIONS WITH CLINICAL OUTCOME NOT EVIDENT IN THE BULK CLONE, SUPPORTING THE PATHOLOGICAL AND THERAPEUTIC RELEVANCE OF STUDYING INTRACLONAL CLL FRACTIONS. WE CONCLUDE THAT INDEPENDENT METHYLATION AND TRANSCRIPTIONAL LANDSCAPES REFLECT BOTH PREEXISTING CELL-OF-ORIGIN FINGERPRINTS AND MORE RECENTLY ACQUIRED HALLMARKS ASSOCIATED WITH THE LIFE CYCLE OF CIRCULATING CLL CELLS. 2020 17 3896 31 LARGE-SCALE ANALYSIS OF DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. AIMS: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A HETEROGENEOUS MALIGNANCY THAT CLINICALLY RANGES FROM INDOLENT TO RAPIDLY PROGRESSIVE. CLL, LIKE OTHER CANCERS, CAN BE AFFECTED BY EPIGENETIC ALTERATIONS. MATERIALS & METHODS: A MICROARRAY DISCOVERY-BASED STUDY WAS INITIATED TO DETERMINE DNA METHYLATION IN CLL CASES WITH A RANGE OF CD38 EXPRESSION (1-92%). RESULTS: MANY LOCI WERE EITHER METHYLATED OR UNMETHYLATED ACROSS ALL CD38 LEVELS, BUT DIFFERENTIAL METHYLATION WAS ALSO OBSERVED FOR SOME GENES. GENOMIC SEQUENCING OF DLEU7 CONFIRMED EXTENSIVE CYTOSINE METHYLATION PREFERENTIALLY IN PATIENT SAMPLES WITH LOW CD38 EXPRESSION, WHEREAS NRP2, SFRP2 AND ADAM12 WERE MORE COMMONLY METHYLATED IN THOSE WITH HIGH CD38 EXPRESSION. CONCLUSION: THIS STUDY DEMONSTRATES THAT CLL IS AFFECTED BY CPG ISLAND METHYLATION IN SOME GENES THAT SEGREGATE WITH CD38 EXPRESSION LEVELS, WHILE MOST OTHERS SHOW SIMILAR METHYLATION PATTERNS ACROSS ALL LEVELS. THE CPG ISLAND METHYLATION IN CERTAIN FUNCTIONAL GENE GROUPS AND PATHWAY-ASSOCIATED GENES THAT ARE KNOWN TO BE DEREGULATED IN CLL PROVIDES ADDITIONAL INSIGHTS INTO THE CLL METHYLOME AND EPIGENETIC CONTRIBUTION TO CELLULAR DYSFUNCTION. IT WILL NOW BE USEFUL TO INVESTIGATE THE EFFECTIVENESS OF EPIGENETIC THERAPEUTIC REVERSAL OF THESE ALTERATIONS TO DEVELOP EFFECTIVE TREATMENTS FOR THE DISEASE. 2009 18 941 30 CHRONIC LYMPHOCYTIC LEUKEMIA B-CELL NORMAL CELLULAR COUNTERPART: CLUES FROM A FUNCTIONAL PERSPECTIVE. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY THE CLONAL EXPANSION OF SMALL MATURE-LOOKING CD19+ CD23+ CD5+ B-CELLS THAT ACCUMULATE IN THE BLOOD, BONE MARROW, AND LYMPHOID ORGANS. TO DATE, NO CONSENSUS HAS BEEN REACHED CONCERNING THE NORMAL CELLULAR COUNTERPART OF CLL B-CELLS AND SEVERAL B-CELL TYPES HAVE BEEN PROPOSED. CLL B-CELLS HAVE REMARKABLE PHENOTYPIC AND GENE EXPRESSION PROFILE HOMOGENEITY. IN RECENT YEARS, THE MOLECULAR AND CELLULAR BIOLOGY OF CLL HAS BEEN ENRICHED BY SEMINAL INSIGHTS THAT ARE LEADING TO A BETTER UNDERSTANDING OF THE NATURAL HISTORY OF THE DISEASE. IMMUNOPHENOTYPIC AND MOLECULAR APPROACHES (INCLUDING IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE GENE MUTATIONAL STATUS, TRANSCRIPTIONAL AND EPIGENETIC PROFILING) COMPARING THE NORMAL B-CELL SUBSET AND CLL B-CELLS PROVIDE SOME NEW INSIGHTS INTO THE NORMAL CELLULAR COUNTERPART. FUNCTIONAL CHARACTERISTICS (INCLUDING ACTIVATION REQUIREMENTS AND PROPENSITY FOR PLASMA CELL DIFFERENTIATION) OF CLL B-CELLS HAVE NOW BEEN INVESTIGATED FOR 50 YEARS. B-CELL SUBSETS DIFFER SUBSTANTIALLY IN TERMS OF THEIR FUNCTIONAL FEATURES. ANALYSIS OF SHARED FUNCTIONAL CHARACTERISTICS MAY REVEAL SIMILARITIES BETWEEN NORMAL B-CELL SUBSETS AND CLL B-CELLS, ALLOWING SPECULATIVE ASSIGNMENT OF A NORMAL CELLULAR COUNTERPART FOR CLL B-CELLS. IN THIS REVIEW, WE SUMMARIZE CURRENT DATA REGARDING PERIPHERAL B-CELL DIFFERENTIATION AND HUMAN B-CELL SUBSETS AND SUGGEST POSSIBILITIES FOR A NORMAL CELLULAR COUNTERPART BASED ON THE FUNCTIONAL CHARACTERISTICS OF CLL B-CELLS. HOWEVER, A DEFINITIVE NORMAL CELLULAR COUNTERPART CANNOT BE ATTRIBUTED ON THE BASIS OF THE AVAILABLE DATA. WE DISCUSS THE FUNCTIONAL CHARACTERISTICS REQUIRED FOR A CELL TO BE LOGICALLY CONSIDERED TO BE THE NORMAL COUNTERPART OF CLL B-CELLS. 2018 19 2689 21 EVOLUTION OF DNA METHYLATION IS LINKED TO GENETIC ABERRATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA. ALTHOUGH CLONAL SELECTION BY GENETIC DRIVER ABERRATIONS IN CANCER IS WELL DOCUMENTED, THE ABILITY OF EPIGENETIC ALTERATIONS TO PROMOTE TUMOR EVOLUTION IS UNDEFINED. WE USED 450K ARRAYS AND NEXT-GENERATION SEQUENCING TO EVALUATE INTRATUMOR HETEROGENEITY AND EVOLUTION OF DNA METHYLATION AND GENETIC ABERRATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). CLL CASES EXHIBIT VAST INTERPATIENT DIFFERENCES IN INTRATUMOR METHYLATION HETEROGENEITY, WITH GENETICALLY CLONAL CASES MAINTAINING LOW METHYLATION HETEROGENEITY AND UP TO 10% OF TOTAL CPGS IN A MONOALLELICALLY METHYLATED STATE. INCREASING METHYLATION HETEROGENEITY CORRELATES WITH ADVANCED GENETIC SUBCLONAL COMPLEXITY. SELECTION OF NOVEL DNA METHYLATION PATTERNS IS OBSERVED ONLY IN CASES THAT UNDERGO GENETIC EVOLUTION, AND INDEPENDENT GENETIC EVOLUTION IS UNCOMMON AND IS RESTRICTED TO LOW-RISK ALTERATIONS. THESE RESULTS REVEAL THAT ALTHOUGH EVOLUTION OF DNA METHYLATION OCCURS IN HIGH-RISK, CLINICALLY PROGRESSIVE CASES, POSITIVE SELECTION OF NOVEL METHYLATION PATTERNS ENTAILS COEVOLUTION OF GENETIC ALTERATION(S) IN CLL. 2014 20 2639 26 EPIGENOMIC ANALYSIS DETECTS WIDESPREAD GENE-BODY DNA HYPOMETHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. WE HAVE EXTENSIVELY CHARACTERIZED THE DNA METHYLOMES OF 139 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WITH MUTATED OR UNMUTATED IGHV AND OF SEVERAL MATURE B-CELL SUBPOPULATIONS THROUGH THE USE OF WHOLE-GENOME BISULFITE SEQUENCING AND HIGH-DENSITY MICROARRAYS. THE TWO MOLECULAR SUBTYPES OF CLL HAVE DIFFERING DNA METHYLOMES THAT SEEM TO REPRESENT EPIGENETIC IMPRINTS FROM DISTINCT NORMAL B-CELL SUBPOPULATIONS. DNA HYPOMETHYLATION IN THE GENE BODY, TARGETING MOSTLY ENHANCER SITES, WAS THE MOST FREQUENT DIFFERENCE BETWEEN NAIVE AND MEMORY B CELLS AND BETWEEN THE TWO MOLECULAR SUBTYPES OF CLL AND NORMAL B CELLS. ALTHOUGH DNA METHYLATION AND GENE EXPRESSION WERE POORLY CORRELATED, WE IDENTIFIED GENE-BODY CPG DINUCLEOTIDES WHOSE METHYLATION WAS POSITIVELY OR NEGATIVELY ASSOCIATED WITH EXPRESSION. WE HAVE ALSO RECOGNIZED A DNA METHYLATION SIGNATURE THAT DISTINGUISHES NEW CLINICO-BIOLOGICAL SUBTYPES OF CLL. WE PROPOSE AN EPIGENOMIC SCENARIO IN WHICH DIFFERENTIAL METHYLATION IN THE GENE BODY MAY HAVE FUNCTIONAL AND CLINICAL IMPLICATIONS IN LEUKEMOGENESIS. 2012