1 4728 104 NOTCH SIGNALING PROMOTES DISEASE INITIATION AND PROGRESSION IN MURINE CHRONIC LYMPHOCYTIC LEUKEMIA. NOTCH1 GAIN-OF-FUNCTION MUTATIONS ARE RECURRENT IN B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL), WHERE THEY ARE ASSOCIATED WITH ACCELERATED DISEASE PROGRESSION AND REFRACTORINESS TO CHEMOTHERAPY. THE SPECIFIC ROLE OF NOTCH1 IN THE DEVELOPMENT AND PROGRESSION OF THIS MALIGNANCY IS UNCLEAR. HERE, WE ASSESS THE IMPACT OF LOSS OF NOTCH SIGNALING AND PATHWAY HYPERACTIVATION IN AN IN VIVO MOUSE MODEL OF CLL (IGH.TEMU) THAT FAITHFULLY REPLICATES MANY FEATURES OF THE HUMAN PATHOLOGY. ABLATION OF CANONICAL NOTCH SIGNALING USING CONDITIONAL GENE INACTIVATION OF RBP-J IN IMMATURE HEMATOPOIETIC OR B-CELL PROGENITORS DELAYED CLL INDUCTION AND REDUCED INCIDENCE OF MICE DEVELOPING DISEASE. IN CONTRAST, FORCED EXPRESSION OF A DOMINANT ACTIVE FORM OF NOTCH RESULTED IN MORE ANIMALS DEVELOPING CLL WITH EARLY DISEASE ONSET. COMPARATIVE ANALYSIS OF GENE EXPRESSION AND EPIGENETIC FEATURES OF NOTCH GAIN-OF-FUNCTION AND CONTROL CLL CELLS REVEALED DIRECT AND INDIRECT REGULATION OF CELL CYCLE-ASSOCIATED GENES, WHICH LED TO INCREASED PROLIFERATION OF NOTCH GAIN-OF-FUNCTION CLL CELLS IN VIVO. THESE RESULTS DEMONSTRATE THAT NOTCH SIGNALING FACILITATES DISEASE INITIATION AND PROMOTES CLL CELL PROLIFERATION AND DISEASE PROGRESSION. 2021 2 2025 41 EPIGENETIC CHANGES DURING DISEASE PROGRESSION IN A MURINE MODEL OF HUMAN CHRONIC LYMPHOCYTIC LEUKEMIA. EPIGENETIC ALTERATIONS, INCLUDING GAIN OR LOSS OF DNA METHYLATION, ARE A HALLMARK OF NEARLY EVERY MALIGNANCY. CHANGES IN DNA METHYLATION CAN IMPACT EXPRESSION OF CANCER-RELATED GENES INCLUDING APOPTOSIS REGULATORS AND TUMOR SUPPRESSORS. BECAUSE SUCH EPIGENETIC CHANGES ARE REVERSIBLE, THEY ARE BEING AGGRESSIVELY INVESTIGATED AS POTENTIAL THERAPEUTIC TARGETS. HERE WE USE THE EMU-TCL1 TRANSGENIC MOUSE MODEL OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) TO DETERMINE THE TIMING AND PATTERNS OF ABERRANT DNA METHYLATION, AND TO INVESTIGATE THE MECHANISMS THAT LEAD TO ABERRANT DNA METHYLATION. WE SHOW THAT CLL CELLS FROM EMU-TCL1 MICE AT VARIOUS STAGES RECAPITULATE EPIGENETIC ALTERATIONS SEEN IN HUMAN CLL. ABERRANT METHYLATION OF PROMOTER SEQUENCES IS OBSERVED AS EARLY AS 3 MONTHS OF AGE IN THESE ANIMALS, WELL BEFORE DISEASE ONSET. ABNORMALLY METHYLATED PROMOTER REGIONS INCLUDE BINDING SITES FOR THE TRANSCRIPTION FACTOR FOXD3. WE SHOW THAT LOSS OF FOXD3 EXPRESSION DUE TO AN NF-KAPPAB P50/P50:HDAC1 REPRESSOR COMPLEX OCCURS IN TCL1-POSITIVE B CELLS BEFORE METHYLATION. THEREFORE, SPECIFIC TRANSCRIPTIONAL REPRESSION IS AN EARLY EVENT LEADING TO EPIGENETIC SILENCING OF TARGET GENES IN MURINE AND HUMAN CLL. THESE RESULTS PROVIDE STRONG RATIONALE FOR THE DEVELOPMENT OF STRATEGIES TO TARGET NF-KAPPAB COMPONENTS IN CLL AND POTENTIALLY OTHER B-CELL MALIGNANCIES. 2009 3 5691 37 SILENCING OF HDAC6 AS A THERAPEUTIC TARGET IN CHRONIC LYMPHOCYTIC LEUKEMIA. ALTHOUGH THE TREATMENT PARADIGM FOR CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS RAPIDLY CHANGING, THE DISEASE REMAINS INCURABLE, EXCEPT WITH ALLOGENEIC BONE MARROW TRANSPLANTATION, AND RESISTANCE, RELAPSED DISEASE, AND PARTIAL RESPONSES PERSIST AS SIGNIFICANT CHALLENGES. RECENT STUDIES HAVE UNCOVERED ROLES FOR EPIGENETIC MODIFICATION IN THE REGULATION OF MECHANISMS CONTRIBUTING TO MALIGNANT PROGRESSION OF CLL B CELLS. HOWEVER, THE EXTENT TO WHICH EPIGENETIC MODIFIERS CAN BE TARGETED FOR THERAPEUTIC BENEFIT IN CLL PATIENTS REMAINS POORLY EXPLORED. WE REPORT FOR THE FIRST TIME THAT EXPRESSION OF EPIGENETIC MODIFIER HISTONE DEACETYLASE 6 (HDAC6) IS UPREGULATED IN CLL PATIENT SAMPLES, CELL LINES, AND EUTCL1 TRANSGENIC MOUSE MODELS COMPARED WITH HDAC6 IN NORMAL CONTROLS. GENETIC SILENCING OF HDAC6 CONFERRED SURVIVAL BENEFIT IN EUTCL1 MICE. ADMINISTRATION OF ISOFORM-SPECIFIC HDAC6 INHIBITOR ACY738 IN THE EUTCL1 AGING AND ADOPTIVE TRANSFER MODELS DETERRED PROLIFERATION OF CLL B CELLS, DELAYED DISEASE ONSET VIA DISRUPTION OF B-CELL RECEPTOR SIGNALING, AND SENSITIZED CLL B CELLS TO APOPTOSIS. FURTHERMORE, COADMINISTRATION OF ACY738 AND IBRUTINIB DISPLAYED SYNERGISTIC CELL KILL AGAINST CLL CELL LINES AND IMPROVED OVERALL SURVIVAL COMPARED WITH EITHER SINGLE AGENT IN VIVO. THESE RESULTS DEMONSTRATE FOR THE FIRST TIME THE THERAPEUTIC EFFICACY OF SELECTIVE HDAC6 INHIBITION IN PRECLINICAL CLL MODELS AND SUGGEST A RATIONALE FOR THE CLINICAL DEVELOPMENT OF HDAC6 INHIBITORS FOR CLL TREATMENT, EITHER ALONE OR IN COMBINATION WITH BRUTON TYROSINE KINASE INHIBITION. 2018 4 1976 30 EPIGENETIC ALTERATIONS IN A MURINE MODEL FOR CHRONIC LYMPHOCYTIC LEUKEMIA. EARLY STAGES IN THE DEVELOPMENT OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAVE NOT BEEN EXPLORED MAINLY DUE TO THE INABILITY TO STUDY NORMAL B-CELLS EN ROUTE TO TRANSFORMATION. IN ORDER TO DETERMINE SUCH EARLY EVENTS OF LEUKEMOGENESIS, WE HAVE USED A WELL ESTABLISHED MOUSE MODEL FOR CLL. OVER-EXPRESSION OF HUMAN TCL1, A KNOWN CLL ONCOGENE IN MURINE B-CELLS LEADS TO THE DEVELOPMENT OF MATURE CD19+/CD5+/IGM+ CLONAL LEUKEMIA WITH A DISEASE PHENOTYPE SIMILAR TO THAT SEEN IN HUMAN CLL. HEREIN, WE REVIEW OUR RECENT STUDY USING THIS TCL1-DRIVEN MOUSE MODEL FOR CLL AND CORRESPONDING HUMAN CLL SAMPLES IN A CROSS-SPECIES EPIGENOMICS APPROACH TO ADDRESS THE TIMING AND RELEVANCE OF EPIGENETIC EVENTS OCCURRING DURING LEUKEMOGENESIS. WE DEMONSTRATED THAT THE MOUSE MODEL RECAPITULATES THE EPIGENETIC EVENTS THAT HAVE BEEN REPORTED FOR HUMAN CLL, AFFIRMING THE POWER AND VALIDITY OF THIS MOUSE MODEL TO STUDY EARLY EPIGENETIC EVENTS IN CANCER PROGRESSION. EPIGENETIC ALTERATIONS ARE DETECTED AS EARLY AS THREE MONTHS AFTER BIRTH, FAR BEFORE DISEASE MANIFESTS AT ABOUT 11 MONTHS OF AGE. THESE MICE UNDERGO NFKAPPAB REPRESSOR COMPLEX MEDIATED INACTIVATION OF THE TRANSCRIPTION FACTOR FOXD3, WHOSE TARGETS BECOME ABERRANTLY METHYLATED AND SILENCED IN MOUSE AND HUMAN CLL. OVERALL, OUR DATA SUGGEST THE ACCUMULATED EPIGENETIC ALTERATIONS DURING CLL PATHOGENESIS AS A CONSEQUENCE OF GENE SILENCING THROUGH TCL1 AND NFKAPPAB REPRESSOR COMPLEX, SUGGESTING THE RELEVANCE FOR NFKAPPAB AS A THERAPEUTIC TARGET IN CLL. 2009 5 5475 24 RESTORING MLL REACTIVATES LATENT TUMOR SUPPRESSION-MEDIATED VULNERABILITY TO PROTEASOME INHIBITORS. MLL UNDERGOES MULTIPLE DISTINCT CHROMOSOMAL TRANSLOCATIONS TO YIELD AGGRESSIVE LEUKEMIA WITH DISMAL OUTCOMES. BESIDES THEIR WELL-ESTABLISHED ROLE IN LEUKEMOGENESIS, MLL FUSIONS ALSO POSSESS LATENT TUMOR-SUPPRESSIVE ACTIVITY, WHICH CAN BE EXPLOITED AS EFFECTIVE CANCER TREATMENT STRATEGIES USING PHARMACOLOGICAL MEANS SUCH AS PROTEASOME INHIBITORS (PIS). HERE, USING MLL-REARRANGED XENOGRAFTS AND MLL LEUKEMIC CELLS AS MODELS, WE SHOW THAT WILD-TYPE MLL IS INDISPENSABLE FOR THE LATENT TUMOR-SUPPRESSIVE ACTIVITY OF MLL FUSIONS. MLL DYSFUNCTION, SHOWN AS LOSS OF THE CHROMATIN ACCUMULATION AND SUBSEQUENT DEGRADATION OF MLL, COMPROMISES THE LATENT TUMOR SUPPRESSION OF MLL-AF4 AND IS INSTRUMENTAL FOR THE ACQUIRED PI RESISTANCE. MECHANISTICALLY, MLL DYSFUNCTION IS CAUSED BY CHRONIC PI TREATMENT-INDUCED EPIGENETIC REPROGRAMMING THROUGH THE H2BUB-ASH2L-MLL AXIS AND CAN BE SPECIFICALLY RESTORED BY HISTONE DEACETYLASE (HDAC) INHIBITORS, WHICH INDUCE HISTONE ACETYLATION AND RECRUITS MLL ON CHROMATIN TO PROMOTE CELL CYCLE GENE EXPRESSION. OUR FINDINGS NOT ONLY DEMONSTRATE THE MECHANISM UNDERLYING THE INEVITABLE ACQUISITION OF PI RESISTANCE IN MLL LEUKEMIC CELLS, BUT ALSO ILLUSTRATE THAT PREVENTING THE EMERGENCE OF PI-RESISTANT CELLS CONSTITUTES A NOVEL RATIONALE FOR COMBINATION THERAPY WITH PIS AND HDAC INHIBITORS IN MLL LEUKEMIAS. 2020 6 3415 33 HSP90 INHIBITION INCREASES SOCS3 TRANSCRIPT AND REGULATES MIGRATION AND CELL DEATH IN CHRONIC LYMPHOCYTIC LEUKEMIA. EPIGENETIC OR TRANSCRIPTIONAL SILENCING OF IMPORTANT TUMOR SUPPRESSORS HAS BEEN DESCRIBED TO CONTRIBUTE TO CELL SURVIVAL AND TUMORIGENESIS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). USING GENE EXPRESSION MICROARRAY ANALYSIS, WE FOUND THAT THOUSANDS OF GENES ARE REPRESSED MORE THAN 2-FOLD IN CLL COMPARED TO NORMAL B CELLS; HOWEVER THERAPEUTIC APPROACHES TO REVERSE THIS HAVE BEEN LIMITED IN CLL. FOLLOWING TREATMENT WITH THE HSP90 INHIBITOR 17-DMAG, A SIGNIFICANT NUMBER OF THESE REPRESSED GENES WERE SIGNIFICANTLY RE-EXPRESSED. ONE OF THE GENES SIGNIFICANTLY REPRESSED IN CLL AND UP-REGULATED BY 17-DMAG WAS SUPPRESSOR OF CYTOKINE SIGNALING 3, (SOCS3). SOCS3 HAS BEEN SHOWN TO BE SILENCED IN SOLID TUMORS AS WELL AS MYELOID LEUKEMIA; HOWEVER LITTLE IS KNOWN ABOUT THE REGULATION IN CLL. WE FOUND THAT 17-DMAG INDUCES EXPRESSION OF SOCS3 BY VIA THE ACTIVATION OF P38 SIGNALING, AND SUBSEQUENTLY INHIBITS AKT AND STAT3 PHOSPHORYLATION RESULTING IN DOWNSTREAM EFFECTS ON CELL MIGRATION AND SURVIVAL. WE THEREFORE SUGGEST THAT SOCS3 IS AN IMPORTANT SIGNALING PROTEIN IN CLL, AND HSP90 INHIBITORS REPRESENT A NOVEL APPROACH TO TARGET TRANSCRIPTIONAL REPRESSION IN B CELL LYMPHOPROLIFERATIVE DISORDERS WHICH EXHIBIT A SUBSTANTIAL DEGREE OF GENE REPRESSION. 2016 7 206 44 ACTIVATION OF NOTCH AND MYC SIGNALING VIA B-CELL-RESTRICTED DEPLETION OF DNMT3A GENERATES A CONSISTENT MURINE MODEL OF CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY DISORDERED DNA METHYLATION, SUGGESTING THESE EPIGENETIC CHANGES MIGHT PLAY A CRITICAL ROLE IN DISEASE ONSET AND PROGRESSION. THE METHYLTRANSFERASE DNMT3A IS A KEY REGULATOR OF DNA METHYLATION. ALTHOUGH DNMT3A SOMATIC MUTATIONS IN CLL ARE RARE, WE FOUND THAT LOW DNMT3A EXPRESSION IS ASSOCIATED WITH MORE AGGRESSIVE DISEASE. A CONDITIONAL KNOCKOUT MOUSE MODEL SHOWED THAT HOMOZYGOUS DEPLETION OF DNMT3A FROM B CELLS RESULTS IN THE DEVELOPMENT OF CLL WITH 100% PENETRANCE AT A MEDIAN AGE OF ONSET OF 5.3 MONTHS, AND HETEROZYGOUS DNMT3A DEPLETION YIELDS A DISEASE PENETRANCE OF 89% WITH A MEDIAN ONSET AT 18.5 MONTHS, CONFIRMING ITS ROLE AS A HAPLOINSUFFICIENT TUMOR SUPPRESSOR. B1A CELLS WERE CONFIRMED AS THE CELL OF ORIGIN OF DISEASE IN THIS MODEL, AND DNMT3A DEPLETION RESULTED IN FOCAL HYPOMETHYLATION AND ACTIVATION OF NOTCH AND MYC SIGNALING. AMPLIFICATION OF CHROMOSOME 15 CONTAINING THE MYC GENE WAS DETECTED IN ALL CLL MICE TESTED, AND INFILTRATION OF HIGH-MYC-EXPRESSING CLL CELLS IN THE SPLEEN WAS OBSERVED. NOTABLY, HYPERACTIVATION OF NOTCH AND MYC SIGNALING WAS EXCLUSIVELY OBSERVED IN THE DNMT3A CLL MICE, BUT NOT IN THREE OTHER CLL MOUSE MODELS TESTED (SF3B1-ATM, IKZF3, AND MDR), AND DNMT3A-DEPLETED CLL WERE SENSITIVE TO PHARMACOLOGIC INHIBITION OF NOTCH SIGNALING IN VITRO AND IN VIVO. CONSISTENT WITH THESE FINDINGS, HUMAN CLL SAMPLES WITH LOWER DNMT3A EXPRESSION WERE MORE SENSITIVE TO NOTCH INHIBITION THAN THOSE WITH HIGHER DNMT3A EXPRESSION. ALTOGETHER, THESE RESULTS SUGGEST THAT DNMT3A DEPLETION INDUCES CLL THAT IS HIGHLY DEPENDENT ON ACTIVATION OF NOTCH AND MYC SIGNALING. SIGNIFICANCE: LOSS OF DNMT3A EXPRESSION IS A DRIVING EVENT IN CLL AND IS ASSOCIATED WITH AGGRESSIVE DISEASE, ACTIVATION OF NOTCH AND MYC SIGNALING, AND ENHANCED SENSITIVITY TO NOTCH INHIBITION. 2021 8 2389 30 EPIGENETIC REPOLARIZATION OF T LYMPHOCYTES FROM CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS USING 5-AZA-2'-DEOXYCYTIDINE. T CELL IMMUNE DYSFUNCTION HAS AN IMPORTANT ROLE IN THE PROFOUND IMMUNE SUPPRESSION THAT CHARACTERIZES CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). IMPROPER POLARIZATION OF T CELLS HAS BEEN PROPOSED AS ONE OF THE MECHANISM INVOLVED. MOUNTING DATA IMPLICATES CHROMATIN REGULATION, NAMELY PROMOTER METHYLATION, IN THE PLASTICITY OF NAIVE HUMAN T CELLS. RECENT IN VITRO EVIDENCE INDICATES THAT THIS PLASTICITY MAY BE PHENOTYPICALLY ALTERED BY USING METHYLATION INHIBITORS WHICH ARE APPROVED FOR CLINICAL USE IN CERTAIN TYPES OF CANCER. THESE RESULTS BEG THE QUESTION: CAN THE INEFFECTIVE POLARIZATION OF T LYMPHOCYTES IN THE CONTEXT OF CLL BE EFFECTIVELY MODULATED USING METHYLATION INHIBITORS IN A SUSTAINABLE THERAPEUTIC FASHION? TO ANSWER THIS QUESTION OUR LABORATORY HAS STUDIED THE EFFECTS OF 5-AZA-2'-DEOXYCYTIDINE (5A2) IN HELPER AND CYTOTOXIC T LYMPHOCYTES FROM HEALTHY DONORS AND CLL PATIENTS IN WELL CHARACTERIZED MOLECULAR AND EPIGENETIC SIGNALING PATHWAYS INVOLVED IN EFFECTIVE POLARIZATION. MOREOVER, WE SOUGHT TO INVESTIGATE THE CONSEQUENCES OF METHYLATION INHIBITOR TREATMENT ON LYMPHOCYTE SURVIVAL, ACTIVATION INTENSITY, AND NAIVE CELL POLARIZATION. OUR DATA INDICATES THAT 5A2 TREATMENT CAN DEPOLARIZE TH2 CELLS TO EFFECTIVELY SECRETE INTERFERON GAMMA, SIGNAL VIA T-BET, AND ACHIEVE DEMETHYLATION OF CRITICAL TH1 SPECIFIC PROMOTERS. MOREOVER, WE DEMONSTRATE THAT 5A2 CAN FORCE TH1 POLARIZATION OF NAIVE T CELLS DESPITE A STRONG IL-4 STIMULI AND A LACK OF IL-12. IN CONCLUSION OUR DATA SEEKS TO DEFINE A MODALITY IN WHICH IMPROPER OR INEFFECTIVE T CELL POLARIZATION CAN BE ALTERED BY 5AZA AND COULD BE INCORPORATED IN FUTURE THERAPEUTIC INTERVENTIONS. 2011 9 5030 27 PERSPECTIVES ON PRECISION MEDICINE IN CHRONIC LYMPHOCYTIC LEUKEMIA: TARGETING RECURRENT MUTATIONS-NOTCH1, SF3B1, MYD88, BIRC3. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS HIGHLY HETEROGENEOUS, WITH EXTREMELY VARIABLE CLINICAL COURSE. THE CLINICAL HETEROGENEITY OF CLL REFLECTS DIFFERENCES IN THE BIOLOGY OF THE DISEASE, INCLUDING CHROMOSOMAL ALTERATIONS, SPECIFIC IMMUNOPHENOTYPIC PATTERNS AND SERUM MARKERS. THE APPLICATION OF NEXT-GENERATION SEQUENCING TECHNIQUES HAS DEMONSTRATED THE HIGH GENETIC AND EPIGENETIC HETEROGENEITY IN CLL. THE NOVEL MUTATIONS COULD BE PHARMACOLOGICALLY TARGETED FOR INDIVIDUALIZED APPROACH IN SOME OF THE CLL PATIENTS. POTENTIAL NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 (NOTCH1) SIGNALLING TARGETING MECHANISMS IN CLL INCLUDE SECRETASE INHIBITORS AND SPECIFIC ANTIBODIES TO BLOCK NOTCH LIGAND/RECEPTOR INTERACTIONS. IN VITRO STUDIES CHARACTERIZING THE EFFECT OF THE SPLICING INHIBITORS RESULTED IN INCREASED APOPTOSIS OF CLL CELLS REGARDLESS OF SPLICING FACTOR 3B SUBUNIT 1 (SF3B1) STATUS. SEVERAL THERAPEUTIC STRATEGIES HAVE BEEN ALSO PROPOSED TO DIRECTLY OR INDIRECTLY INHIBIT THE TOLL-LIKE RECEPTOR/MYELOID DIFFERENTIATION PRIMARY RESPONSE GENE 88 (TLR/MYD88) PATHWAY. ANOTHER POTENTIAL APPROACH IS TARGETING NUCLEAR FACTOR KAPPA-LIGHT-CHAIN-ENHANCER OF ACTIVATED B CELLS (NF-KAPPAB) AND INHIBITION OF THIS PROSURVIVAL PATHWAY. NEWLY DISCOVERED MUTATIONS AND THEIR SIGNALLING PATHWAYS PLAY KEY ROLES IN THE COURSE OF THE DISEASE. THIS OPENS NEW OPPORTUNITIES IN THE MANAGEMENT AND TREATMENT OF CLL. 2021 10 1568 21 DNA METHYLATION OF TUMOR-SUPPRESSOR MIRNA GENES IN CHRONIC LYMPHOCYTIC LEUKEMIA. DNA METHYLATION IS ONE OF THE MOST IMPORTANT EPIGENETIC MODIFICATIONS OF THE GENOME INVOLVED IN THE REGULATION OF NUMEROUS CELLULAR PROCESSES THROUGH GENE SILENCING WITHOUT ALTERING DNA SEQUENCES. MIRNAS, A CLASS OF SINGLE-STRANDED NONCODING RNAS OF 19-25 NUCLEOTIDES IN LENGTH, FUNCTION AS POST-TRANSCRIPTIONAL REGULATORS OF GENE EXPRESSION LEADING TO MRNA CLEAVAGE OR TRANSLATIONAL REPRESSION OF THEIR CORRESPONDING TARGET PROTEIN-CODING GENES. RECENTLY, DYSREGULATION OF TUMOR SUPPRESSOR MIRNAS MEDIATED BY PROMOTER DNA HYPERMETHYLATION IS IMPLICATED IN HUMAN CANCERS, INCLUDING B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). MOREOVER, IT APPEARS THAT METHYLATED MIRNA GENES COULD BE POTENTIAL BIOMARKERS FOR CLL DIAGNOSIS OR THERAPY. THIS REVIEW WILL HIGHLIGHT THE ROLE OF ABERRANT METHYLATION OF MIRNA GENES IN THE PATHOGENESIS OF CLL. 2015 11 6762 16 ZAP70 IN CHRONIC LYMPHOCYTIC LEUKAEMIA. THE PROTEIN TYROSINE KINASE ZETA-CHAIN ASSOCIATED PROTEIN KINASE (ZAP70), NORMALLY EXPRESSED IN T CELLS AND A SUBSET OF B CELLS, IS SOLELY EXPRESSED IN POOR PROGNOSIS CHRONIC LYMPHOCYTIC LEUKAEMIA AND IMPLICATED IN ENHANCED B CELL RECEPTOR SIGNALLING. AS A RESULT, THE EXPRESSION OF THIS PROTEIN PROVIDES AN IDEAL PROGNOSTIC MARKER FOR THE DISEASE. A PREVIOUS STUDY HAS SHOWN DIFFERENTIAL CPG METHYLATION OF A 5' REGION OF ZAP70 IN LEUKAEMIC LYMPHOID CELLS, ALTHOUGH NO FURTHER EPIGENETIC STUDIES HAVE BEEN REPORTED. FURTHER INVESTIGATION INTO THE EXPRESSION OF ZAP70 MAY THEREFORE PROVIDE TARGETS FOR THERAPIES. 2008 12 5871 35 SUSTAINED NF-KAPPAB ACTIVITY IN CHRONIC LYMPHOCYTIC LEUKEMIA IS INDEPENDENT OF GENETIC AND EPIGENETIC ALTERATIONS IN THE TNFAIP3 (A20) LOCUS. INAPPROPRIATE NUCLEAR FACTOR (NF) KAPPAB ACTIVITY IS ONE MAJOR HALLMARK OF B-CELL MALIGNANCIES AND CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). NFKAPPAB-DEPENDENT GENES ARE INVOLVED IN ANTIAPOPTOSIS, CELL PROLIFERATION AND METASTASIS AND ARE RESPONSIBLE FOR SURVIVAL AND PROLIFERATION OF TUMORS. HOWEVER, THE MECHANISMS OF NFKAPPAB ACTIVITY IN CLL STILL NEED TO BE ELUCIDATED. PREVIOUSLY, WE IDENTIFIED TRANSLOCATIONS IN A REGION ON CHROMOSOME 6Q THAT ENCODES TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3, WHICH IS A KEY PLAYER IN NEGATIVE FEEDBACK LOOP REGULATION OF NFKAPPAB. INACTIVATION OF THIS UBIQUITIN-EDITING ENZYME IS INVOLVED IN IMMUNOPATHOLOGIES AND IN TUMORIGENESIS. FREQUENT MUTATIONS IN THE A20 LOCUS--LEADING TO SUSTAINED NFKAPPAB ACTIVITY--COULD BE SHOWN TO PLAY A DOMINANT ROLE IN DEVELOPMENT OF DIFFERENT B-CELL MALIGNANCIES. TO CHECK IF A20 IS INVOLVED IN UPREGULATION OF NFKAPPAB ACTIVITY IN CLL, WE SEQUENCED EXONS 2-9 OF THE A20 GENE IN 55 CLL DNA SAMPLES. FURTHERMORE, WE DETERMINED THE METHYLATION STATUS OF THE PROMOTER REGION IN 63 CLL DNA SAMPLES AND COMPARED TO 10 CONTROL DNAS OF B CELLS FROM HEALTHY DONORS. CONTRARY TO REPORTS FROM OTHER B-CELL MALIGNANCIES, THE A20 REGION SHOWED NEITHER MUTATIONS NOR ABERRANT DNA METHYLATION. MOREOVER, ITS EXPRESSION COULD BE CONFIRMED BY IMMUNOBLOTTING AND SHOWING COMPARABLE RESULTS TO HEALTHY B CELLS. THESE RESULTS INDICATE THAT MALIGNANT DEVELOPMENT IN CLL DIFFERS FROM MOST OF OTHER B-CELL MALIGNANCIES, WHICH SHOW FREQUENT INACTIVATION OF A20. 2011 13 942 29 CHRONIC LYMPHOCYTIC LEUKEMIA PRESENCE IMPAIRS ANTIGEN-SPECIFIC CD8(+) T-CELL RESPONSES THROUGH EPIGENETIC REPROGRAMMING TOWARDS SHORT-LIVED EFFECTORS. T-CELL DYSREGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ASSOCIATES WITH LOW RESPONSE RATES TO AUTOLOGOUS T CELL-BASED THERAPIES. HOW CLL AFFECTS ANTIGEN-SPECIFIC T-CELL RESPONSES REMAINS LARGELY UNKNOWN. WE INVESTIGATED (EPI)GENETIC AND FUNCTIONAL CONSEQUENCES OF ANTIGEN-SPECIFIC T-CELL RESPONSES IN PRESENCE OF CLL IN VITRO AND IN AN ADOPTIVE-TRANSFER MURINE MODEL. ALREADY AT STEADY-STATE, ANTIGEN-EXPERIENCED PATIENT-DERIVED T CELLS WERE SKEWED TOWARDS SHORT-LIVED EFFECTOR CELLS (SLEC) AT THE EXPENSE OF MEMORY-PRECURSOR EFFECTOR CELLS (MPEC). STIMULATION OF THESE T CELLS IN VITRO SHOWED RAPID INDUCTION OF EFFECTOR GENES AND SUPPRESSION OF KEY MEMORY TRANSCRIPTION FACTORS ONLY IN PRESENCE OF CLL CELLS, INDICATING EPIGENETIC REGULATION. THIS WAS INVESTIGATED IN VIVO BY FOLLOWING ANTIGEN-SPECIFIC RESPONSES OF NAIVE OT-I CD8(+) CELLS TO MCMV-OVA IN PRESENCE/ABSENCE OF TCL1 B-CELL LEUKEMIA. PRESENCE OF LEUKEMIA RESULTED IN INCREASED SLEC FORMATION, WITH DISTURBED INFLAMMATORY CYTOKINE PRODUCTION. CHROMATIN AND TRANSCRIPTOME PROFILING REVEALED STRONG EPIGENETIC MODIFICATIONS, LEADING TO ACTIVATION OF AN EFFECTOR AND SILENCING OF A MEMORY PROFILE THROUGH PRESENCE OF CLL CELLS. SECONDARY CHALLENGE IN VIVO CONFIRMED DYSFUNCTIONAL MEMORY RESPONSES BY ANTIGEN-EXPERIENCED OT-I CELLS GENERATED IN PRESENCE OF CLL. ALTOGETHER, WE SHOW THAT PRESENCE OF CLL INDUCES A SHORT-LIVED EFFECTOR PHENOTYPE AND IMPAIRED MEMORY RESPONSES BY EPIGENETIC REPROGRAMMING DURING PRIMARY RESPONSES. 2023 14 1542 28 DNA METHYLATION IN HAEMATOLOGICAL MALIGNANCIES: THE ROLE OF DECITABINE. NORMAL CELL DEVELOPMENT AND FUNCTION IS DEPENDENT UPON CONTROLLED GENE EXPRESSION. DNA METHYLATION IS AN EPIGENETIC MODIFICATION THAT CAN PLAY AN IMPORTANT ROLE IN THE CONTROL OF GENE EXPRESSION. DNA METHYLATION AT CYTOSINE RESIDUES IN GENE PROMOTER CPG SEQUENCES IS KNOWN TO INHIBIT GENE TRANSCRIPTION. INAPPROPRIATE INHIBITION OF THE TRANSCRIPTION OF TUMOUR SUPPRESSOR GENES, GENES THAT INHIBIT ANGIOGENESIS AND METASTASIS AND GENES INVOLVED IN DNA REPAIR BY UNCONTROLLED METHYLATION, CAN LEAD TO UNREGULATED GROWTH AND PROLIFERATION OF A CELL AND CARCINOGENESIS. PROMOTER HYPERMETHYLATION AFFECTING THE P16 GENE, RESULTING IN GENE SILENCING, HAS BEEN SHOWN TO OCCUR IN MANY HUMAN SOLID TUMOURS AND A 'HYPERMETHYLATION PROFILE' IN SOME LEUKAEMIAS HAS BEEN DEFINED. THE MOLECULAR MECHANISMS BY WHICH ABERRANT DNA METHYLATION TAKES PLACE DURING CARCINOGENESIS ARE STILL NOT CLEAR. HOWEVER, THE LARGE NUMBER OF TARGET GENES (INVOLVED IN TUMORIGENESIS) THAT ARE SILENCED BY ABERRANT METHYLATION SUGGESTS THAT INHIBITION OF THIS PROCESS MAY HAVE POTENTIAL AS CANCER THERAPY. DECITABINE (NSC-127716, DACOGEN; SUPERGEN) IS A POTENT AND SPECIFIC HYPOMETHYLATING AGENT AND AN INHIBITOR OF THE DNA METHYLTRANSFERASE ACTIVITY THAT MEDIATES DNA METHYLATION. DECITABINE HAS BEEN SHOWN TO HAVE A BROAD RANGE OF ANTINEOPLASTIC ACTIVITY IN PRECLINICAL STUDIES. THIS AGENT HAS EXHIBITED SIGNIFICANT ACTIVITY IN THE TREATMENT OF PATIENTS WITH MYELODYSPLASTIC SYNDROME, CHRONIC MYELOID LEUKAEMIA AND ACUTE MYELOID LEUKAEMIA, ALTHOUGH CLINICAL PHASE I AND II STUDIES WITH SOLID TUMOURS HAVE NOT BEEN VERY PROMISING. PHASE II AND III STUDIES ARE CURRENTLY ONGOING TO EVALUATE DECITABINE, BOTH ALONE AND IN COMBINATION, IN VARIOUS STAGES OF THESE HAEMATOLOGICAL MALIGNANCIES. 2003 15 3098 34 GENOMIC DISRUPTION OF THE HISTONE METHYLTRANSFERASE SETD2 IN CHRONIC LYMPHOCYTIC LEUKAEMIA. HISTONE METHYLTRANSFERASES (HMTS) ARE IMPORTANT EPIGENETIC REGULATORS OF GENE TRANSCRIPTION AND ARE DISRUPTED AT THE GENOMIC LEVEL IN A SPECTRUM OF HUMAN TUMOURS INCLUDING HAEMATOLOGICAL MALIGNANCIES. USING HIGH-RESOLUTION SINGLE NUCLEOTIDE POLYMORPHISM (SNP) ARRAYS, WE IDENTIFIED RECURRENT DELETIONS OF THE SETD2 LOCUS IN 3% (8/261) OF CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) PATIENTS. FURTHER VALIDATION IN TWO INDEPENDENT COHORTS SHOWED THAT SETD2 DELETIONS WERE ASSOCIATED WITH LOSS OF TP53, GENOMIC COMPLEXITY AND CHROMOTHRIPSIS. WITH NEXT-GENERATION SEQUENCING WE DETECTED MUTATIONS OF SETD2 IN AN ADDITIONAL 3.8% OF PATIENTS (23/602). IN MOST CASES, SETD2 DELETIONS OR MUTATIONS WERE OFTEN OBSERVED AS A CLONAL EVENT AND ALWAYS AS A MONO-ALLELIC LESION, LEADING TO REDUCED MRNA EXPRESSION IN SETD2-DISRUPTED CASES. PATIENTS WITH SETD2 ABNORMALITIES AND WILD-TYPE TP53 AND ATM FROM FIVE CLINICAL TRIALS EMPLOYING CHEMOTHERAPY OR CHEMO-IMMUNOTHERAPY HAD REDUCED PROGRESSION-FREE AND OVERALL SURVIVAL COMPARED WITH CASES WILD TYPE FOR ALL THREE GENES. CONSISTENT WITH ITS POSTULATED ROLE AS A TUMOUR SUPPRESSOR, OUR DATA HIGHLIGHT SETD2 ABERRATION AS A RECURRENT, EARLY LOSS-OF-FUNCTION EVENT IN CLL PATHOBIOLOGY LINKED TO AGGRESSIVE DISEASE. 2016 16 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 17 160 26 ABERRANT PROMOTER HYPOMETHYLATION IN CLL: DOES IT MATTER FOR DISEASE DEVELOPMENT? OVER THE LAST 30 YEARS, STUDIES OF ABERRANT DNA METHYLATION IN HEMATOLOGIC MALIGNANCIES HAVE BEEN DOMINATED BY THE PRIMARY FOCUS OF UNDERSTANDING PROMOTER HYPERMETHYLATION. THESE EFFORTS NOT ONLY RESULTED IN A BETTER UNDERSTANDING OF THE BASIS OF EPIGENETIC SILENCING OF TUMOR SUPPRESSOR GENES BUT ALSO RESULTED IN APPROVAL OF HYPOMETHYLATING AGENTS FOR THE TREATMENT OF SEVERAL MALIGNANCIES, SUCH AS MYELODYSPLASTIC SYNDROME AND ACUTE MYELOID LEUKEMIA. RECENT ADVANCES IN GLOBAL METHYLATION PROFILING COUPLED WITH THE USE OF MOUSE MODELS SUGGEST THAT ABERRANT PROMOTER HYPOMETHYLATION IS ALSO A FREQUENT EVENT IN HEMATOLOGIC MALIGNANCIES, PARTICULARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). PROMOTER HYPOMETHYLATION AFFECTS GENE EXPRESSION AND, THEREFORE, MAY PLAY AN IMPORTANT ROLE IN DISEASE PATHOGENESIS. HERE, WE REVIEW RECENT FINDINGS AND DISCUSS THE POTENTIAL INVOLVEMENT OF ABERRANT PROMOTER HYPOMETHYLATION IN CLL. 2016 18 3740 24 INSIGHT INTO GENETIC PREDISPOSITION TO CHRONIC LYMPHOCYTIC LEUKEMIA FROM INTEGRATIVE EPIGENOMICS. GENOME-WIDE ASSOCIATION STUDIES HAVE PROVIDED EVIDENCE FOR INHERITED GENETIC PREDISPOSITION TO CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). TO GAIN INSIGHT INTO THE MECHANISMS UNDERLYING CLL RISK WE ANALYZE CHROMATIN ACCESSIBILITY, ACTIVE REGULATORY ELEMENTS MARKED BY H3K27AC, AND DNA METHYLATION AT 42 RISK LOCI IN UP TO 486 PRIMARY CLLS. WE IDENTIFY THAT RISK LOCI ARE SIGNIFICANTLY ENRICHED FOR ACTIVE CHROMATIN IN CLL WITH EVIDENCE OF BEING CLL-SPECIFIC OR DIFFERENTIALLY REGULATED IN NORMAL B-CELL DEVELOPMENT. WE THEN USE IN SITU PROMOTER CAPTURE HI-C, IN CONJUNCTION WITH GENE EXPRESSION DATA TO REVEAL LIKELY TARGET GENES OF THE RISK LOCI. CANDIDATE TARGET GENES ARE ENRICHED FOR PATHWAYS RELATED TO B-CELL DEVELOPMENT SUCH AS MYC AND BCL2 SIGNALLING. AT 14 LOCI THE ANALYSIS HIGHLIGHTS 63 VARIANTS AS THE PROBABLE FUNCTIONAL BASIS OF CLL RISK. BY INTEGRATING GENETIC AND EPIGENETIC INFORMATION OUR ANALYSIS REVEALS NOVEL INSIGHTS INTO THE RELATIONSHIP BETWEEN INHERITED PREDISPOSITION AND THE REGULATORY CHROMATIN LANDSCAPE OF CLL. 2019 19 851 24 CHIP-SEQ ANALYSIS OF HUMAN CHRONIC MYELOID LEUKEMIA CELLS. MANY TRANSCRIPTION FACTORS, CHROMATIN-ASSOCIATED PROTEINS AND REGULATORY DNA ELEMENTS ARE GENETICALLY AND/OR EPIGENETICALLY ALTERED IN CANCER, INCLUDING CHRONIC MYELOID LEUKEMIA (CML). THIS LEADS TO DEREGULATION OF TRANSCRIPTION THAT IS OFTEN CAUSALLY LINKED TO THE TUMORIGENIC STATE. CHROMATIN-IMMUNOPRECIPITATION COUPLED WITH MASSIVELY PARALLEL DNA SEQUENCING (CHIP-SEQ) IS THE KEY TECHNOLOGY TO STUDY TRANSCRIPTION AS IT ALLOWS IN VIVO WHOLE-GENOME MAPPING OF EPIGENETIC MODIFICATIONS AND INTERACTIONS OF PROTEINS WITH DNA OR CHROMATIN. HOWEVER, NUMEROUS DNA/CHROMATIN-BINDING PROTEINS, INCLUDING EZH2, REMAIN DIFFICULT TO "CHIP," THUS YIELDING GENOME-WIDE BINDING MAPS OF ONLY SUBOPTIMAL QUALITY. HERE, WE DESCRIBE A CHIP-SEQ PROTOCOL OPTIMIZED FOR HIGH-QUALITY PROTEIN-GENOME BINDING MAPS THAT HAVE PROVEN ESPECIALLY USEFUL FOR STUDYING DIFFICULT TO 'CHIP' TRANSCRIPTION REGULATORY FACTORS IN CHRONIC MYELOID LEUKEMIA (CML) AND RELATED MALIGNANCIES. 2016 20 1533 30 DNA METHYLATION DYNAMICS DURING B CELL MATURATION UNDERLIE A CONTINUUM OF DISEASE PHENOTYPES IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHARTING DIFFERENCES BETWEEN TUMORS AND NORMAL TISSUE IS A MAINSTAY OF CANCER RESEARCH. HOWEVER, CLONAL TUMOR EXPANSION FROM COMPLEX NORMAL TISSUE ARCHITECTURES POTENTIALLY OBSCURES CANCER-SPECIFIC EVENTS, INCLUDING DIVERGENT EPIGENETIC PATTERNS. USING WHOLE-GENOME BISULFITE SEQUENCING OF NORMAL B CELL SUBSETS, WE OBSERVED BROAD EPIGENETIC PROGRAMMING OF SELECTIVE TRANSCRIPTION FACTOR BINDING SITES COINCIDENT WITH THE DEGREE OF B CELL MATURATION. BY COMPARING NORMAL B CELLS TO MALIGNANT B CELLS FROM 268 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), WE SHOWED THAT TUMORS DERIVE LARGELY FROM A CONTINUUM OF MATURATION STATES REFLECTED IN NORMAL DEVELOPMENTAL STAGES. EPIGENETIC MATURATION IN CLL WAS ASSOCIATED WITH AN INDOLENT GENE EXPRESSION PATTERN AND INCREASINGLY FAVORABLE CLINICAL OUTCOMES. WE FURTHER UNCOVERED THAT MOST PREVIOUSLY REPORTED TUMOR-SPECIFIC METHYLATION EVENTS ARE NORMALLY PRESENT IN NON-MALIGNANT B CELLS. INSTEAD, WE IDENTIFIED A POTENTIAL PATHOGENIC ROLE FOR TRANSCRIPTION FACTOR DYSREGULATION IN CLL, WHERE EXCESS PROGRAMMING BY EGR AND NFAT WITH REDUCED EBF AND AP-1 PROGRAMMING IMBALANCES THE NORMAL B CELL EPIGENETIC PROGRAM. 2016