1 3756 191 INTEGRATED GENOMIC SEQUENCING IN MYELOID BLAST CRISIS CHRONIC MYELOID LEUKEMIA (MBC-CML), IDENTIFIED POTENTIALLY IMPORTANT FINDINGS IN THE CONTEXT OF LEUKEMOGENESIS MODEL. CHRONIC MYELOID LEUKEMIA (CML) IS A MODEL OF LEUKEMOGENESIS IN WHICH THE EXACT MOLECULAR MECHANISMS UNDERLYING BLAST CRISIS STILL REMAINED UNEXPLORED. THE CURRENT STUDY IDENTIFIED MULTIPLE COMMON AND RARE IMPORTANT FINDINGS IN MYELOID BLAST CRISIS CML (MBC-CML) USING INTEGRATED GENOMIC SEQUENCING, COVERING ALL CLASSES OF GENES IMPLICATED IN THE LEUKEMOGENESIS MODEL. INTEGRATED GENOMIC SEQUENCING VIA WHOLE EXOME SEQUENCING (WES), CHROMOSOME-SEQ AND RNA-SEQUENCING WERE CONDUCTED ON THE PERIPHERAL BLOOD SAMPLES OF THREE CML PATIENTS IN THE MYELOID BLAST CRISIS. AN IN-HOUSE FILTERING PIPELINE WAS APPLIED TO ASSESS IMPORTANT VARIANTS IN CANCER-RELATED GENES. STANDARD VARIANT INTERPRETATION GUIDELINES WERE USED FOR THE INTERPRETATION OF POTENTIALLY IMPORTANT FINDINGS (PIFS) AND POTENTIALLY ACTIONABLE FINDINGS (PAFS). SINGLE NUCLEOTIDE VARIATION (SNV) AND SMALL INDEL ANALYSIS BY WES DETECTED SIXTEEN PIFS AFFECTING ALL FIVE KNOWN CLASSES OF LEUKEMOGENIC GENES IN MYELOID MALIGNANCIES INCLUDING SIGNALING PATHWAY COMPONENTS (ABL1, PIK3CB, PTPN11), TRANSCRIPTION FACTORS (GATA2, PHF6, IKZF1, WT1), EPIGENETIC REGULATORS (ASXL1), TUMOR SUPPRESSOR AND DNA REPAIR GENES (BRCA2, ATM, CHEK2) AND COMPONENTS OF SPLICEOSOME (PRPF8). THESE VARIANTS AFFECT GENES INVOLVED IN LEUKEMIA STEM CELL PROLIFERATION, SELF-RENEWAL, AND DIFFERENTIATION. BOTH PATIENTS NO.1 AND NO.2 HAD ACTIONABLE KNOWN MISSENSE VARIANTS ON ABL1 (P.Y272H, P.F359V) AND FRAMESHIFT VARIANTS ON ASXL1 (P.A627GFS*8, P.G646WFS*12). THE GATA2-L359S IN PATIENT NO.1, PTPN11-G503V AND IKZF1-R208Q VARIANTS IN THE PATIENT NO.3 WERE ALSO PAFS. RNA-SEQUENCING WAS USED TO CONFIRM ALL OF THE IDENTIFIED VARIANTS. IN THE PATIENT NO. 3, CHROMOSOME SEQUENCING REVEALED MULTIPLE PATHOGENIC DELETIONS IN THE SHORT AND LONG ARMS OF CHROMOSOME 7, AFFECTING AT LEAST THREE CRITICAL LEUKEMOGENIC GENES (IKZF1, EZH2, AND CUX1). THE LARGE DELETION DISCOVERED ON THE SHORT ARM OF CHROMOSOME 17 IN PATIENT NO. 2 RESULTED IN THE DELETION OF TP53 GENE AS WELL. INTEGRATED GENOMIC SEQUENCING COMBINED WITH RNA-SEQUENCING CAN SUCCESSFULLY DISCOVER AND CONFIRM A WIDE RANGE OF VARIANTS, FROM SNVS TO CNVS. THIS STRATEGY MAY BE AN EFFECTIVE METHOD FOR IDENTIFYING ACTIONABLE FINDINGS AND UNDERSTANDING THE PATHOPHYSIOLOGICAL MECHANISMS UNDERLYING MBC-CML, AS WELL AS PROVIDING FURTHER INSIGHTS INTO THE GENETIC BASIS OF MBC-CML AND ITS MANAGEMENT IN THE FUTURE.	2022	
                                                                                                                                                                             
2 2888  47 GAIN-OF-FUNCTION MUTATION OF GATA-2 IN ACUTE MYELOID TRANSFORMATION OF CHRONIC MYELOID LEUKEMIA. ACQUISITION OF ADDITIONAL GENETIC AND/OR EPIGENETIC ABNORMALITIES OTHER THAN THE BCR/ABL FUSION GENE IS BELIEVED TO CAUSE DISEASE PROGRESSION IN CHRONIC MYELOID LEUKEMIA (CML) FROM CHRONIC PHASE TO BLAST CRISIS (BC). TO GAIN INSIGHTS INTO THE UNDERLYING MECHANISMS OF PROGRESSION TO BC, WE SCREENED DNA SAMPLES FROM CML PATIENTS DURING BLAST TRANSFORMATION FOR MUTATIONS IN A NUMBER OF TRANSCRIPTION FACTOR GENES THAT ARE CRITICAL FOR MYELOID-LYMPHOID DEVELOPMENT. IN 85 CASES OF CML BLAST TRANSFORMATION, WE IDENTIFIED TWO NEW MUTATIONS IN THE CODING REGION OF GATA-2, A NEGATIVE REGULATOR OF HEMATOPOIETIC STEM/PROGENITOR CELL DIFFERENTIATION. A L359V SUBSTITUTION WITHIN ZINC FINGER DOMAIN (ZF) 2 OF GATA-2 WAS FOUND IN EIGHT CASES WITH MYELOMONOBLASTIC FEATURES, WHEREAS AN IN-FRAME DELETION OF 6 AA (DELTA341-346) SPANNING THE C-TERMINAL BORDER OF ZF1 WAS DETECTED IN ONE PATIENT AT MYELOID BC WITH EOSINOPHILIA. FURTHER STUDIES INDICATED THAT L359V NOT ONLY INCREASED TRANSACTIVATION ACTIVITY OF GATA-2 BUT ALSO ENHANCED ITS INHIBITORY EFFECTS ON THE ACTIVITY OF PU.1, A MAJOR REGULATOR OF MYELOPOIESIS. CONSISTENT WITH THE MYELOMONOBLASTIC FEATURES OF CML TRANSFORMATION WITH THE GATA-2 L359V MUTANT, TRANSDUCTION OF THE GATA-2 L359V MUTANT INTO HL-60 CELLS OR BCR/ABL-HARBORING MURINE CELLS DISTURBED MYELOMONOCYTIC DIFFERENTIATION/PROLIFERATION IN VITRO AND IN VIVO, RESPECTIVELY. THESE DATA STRONGLY SUGGEST THAT GATA-2 MUTATIONS MAY PLAY A ROLE IN ACUTE MYELOID TRANSFORMATION IN A SUBSET OF CML PATIENTS.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
3  493  36 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
4 2763  34 EXPRESSION OF THE LEUKEMIC PROGNOSTIC MARKER CD7 IS LINKED TO EPIGENETIC MODIFICATIONS IN CHRONIC MYELOID LEUKEMIA. BACKGROUND: EXPRESSION LEVELS OF THE CELL SURFACE GLYCOPROTEIN, CD7, AND THE SERINE PROTEASE, ELASTASE 2 (ELA2), IN THE LEUKEMIC CELLS OF PATIENTS WITH CHRONIC MYELOID LEUKEMIA (CML) HAVE BEEN ASSOCIATED WITH CLINICAL OUTCOME. HOWEVER, LITTLE IS KNOWN ABOUT THE MECHANISMS THAT UNDERLIE THE VARIABLE EXPRESSION OF THESE GENES IN THE LEUKEMIC CELLS. RESULTS: TO ADDRESS THIS QUESTION, WE COMPARED THE LEVEL OF THEIR EXPRESSION WITH THE DNA METHYLATION AND HISTONE ACETYLATION STATUS OF 5' SEQUENCES OF BOTH GENES IN LEUKEMIC CELL LINES AND PRIMITIVE (LIN-CD34+) LEUKEMIC CELLS FROM CHRONIC PHASE CML PATIENTS. DNA METHYLATION OF THE ELA2 GENE PROMOTER DID NOT CORRELATE WITH ITS EXPRESSION PATTERN IN LIN-CD34+ CELLS FROM CHRONIC PHASE CML PATIENT SAMPLES EVEN THOUGH THERE WAS CLEAR DIFFERENTIAL DNA METHYLATION OF THIS LOCUS IN ELA2-EXPRESSING AND NON-EXPRESSING CELL LINES. IN CONTRAST, WE FOUND A STRONG RELATION BETWEEN CD7 EXPRESSION AND TRANSCRIPTION-PERMISSIVE CHROMATIN MODIFICATIONS, BOTH AT THE LEVEL OF DNA METHYLATION AND HISTONE ACETYLATION WITH EVIDENCE OF HYPOMETHYLATION OF THE CD7 PROMOTER REGION IN THE LIN-CD34+ CELLS FROM CML PATIENTS WITH HIGH CD7 EXPRESSION. CONCLUSION: THESE FINDINGS INDICATE A LINK BETWEEN EPIGENETIC MODIFICATIONS AND CD7 EXPRESSION IN PRIMITIVE CML CELLS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
5 2088  41 EPIGENETIC DYSREGULATION OF SECRETED FRIZZLED-RELATED PROTEINS IN MYELOPROLIFERATIVE NEOPLASMS COMPLEMENTS THE JAK2V617F-MUTATION. BACKGROUND: SECRETED FRIZZLED-RELATED PROTEINS (SFRPS) ARE ANTAGONISTS OF THE WNT SIGNALING PATHWAY, WHICH PLAYS A CENTRAL ROLE IN STEM CELL MAINTENANCE AND DIFFERENTIATION OF STEM CELLS AND HEMATOPOIETIC PROGENITORS. EPIGENETIC DOWNREGULATION OF SFRPS BY PROMOTER HYPERMETHYLATION HAS BEEN DESCRIBED TO BE INVOLVED IN THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES. THERE IS AN ASSOCIATION BETWEEN ABERRANT WNT SIGNALING AND THE ESTABLISHED CANCER STEM CELL CONCEPT. IN CONTRAST TO BCR-ABL1-POSITIVE CHRONIC MYELOID LEUKEMIA CML, BCR-ABL1-NEGATIVE MYELOPROLIFERATIVE NEOPLASMS (PH-MPN) ARE CHARACTERIZED BY THE FREQUENT OCCURRENCE OF AN AUTOACTIVATING MUTATION IN THE JAK2 TYROSINE KINASE (JAK2V617F) OR OTHER MUTATIONS IN THE JAK-STAT PATHWAY. HOWEVER, PATHOGENETIC MECHANISMS OF JAK2 MUTATED OR UNMUTATED PH-MPN REMAIN NOT COMPLETELY UNDERSTOOD. WE DETERMINED THE PROMOTER METHYLATION STATUS OF SFRP-1, -2, -4, AND -5 IN 57 MPN PATIENT SAMPLES BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) (MSP). JAK2V617F WAS ASSESSED BY ALLELE-SPECIFIC PCR. RESULTS: ABERRANT METHYLATION AMONG PRIMARY MPN SAMPLES WAS 4% FOR SFRP-1, 25% FOR SFRP-2, 2% FOR SFRP-4, AND 0% FOR SFRP-5. HYPERMETHYLATION OF SFRP-2, WHICH WAS THE MOST FREQUENTLY HYPERMETHYLATED GENE IN OUR STUDY, COULD NOT BE CORRELATED TO ANY SPECIFIC MPN SUBTYPE. HOWEVER, WE DETECTED A SIGNIFICANT CORRELATION BETWEEN SFRP-2 METHYLATION AND PRESENCE OF A JAK2V617F MUTATION (P = 0.008). NONE OF THE 10 CML SAMPLES SHOWED ANY SFRP-METHYLATION. CONCLUSIONS: OUR DATA INDICATE THAT EPIGENETIC DYSREGULATION OF THE WNT SIGNALING PATHWAY IS A COMMON EVENT IN MPN WITH ABERRANT METHYLATION OF AT LEAST ONE SFRP BEING DETECTED IN 25% OF THE PRIMARY PATIENT SAMPLES AND IN 30% IF ONLY ACCOUNTING FOR PH-MPN. A SIGNIFICANT CORRELATION BETWEEN SFRP-2 METHYLATION AND PRESENCE OF JAK2V617F IN OUR DATA SUPPORTS THE HYPOTHESIS THAT EPIGENETIC DYSREGULATION MAY BE A COMPLEMENTARY MECHANISM TO GENETIC ABERRATIONS. ABERRANT METHYLATION OF CRUCIAL STEM CELL MAINTENANCE GENES SEEMS TO CONTRIBUTE TO DISEASE PATHOGENESIS IN PH-MPN.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
6 4556  28 MUTATIONAL SPECTRUM OF MYELOID MALIGNANCIES WITH INV(3)/T(3;3) REVEALS A PREDOMINANT INVOLVEMENT OF RAS/RTK SIGNALING PATHWAYS. MYELOID MALIGNANCIES BEARING CHROMOSOMAL INV(3)/T(3;3) ABNORMALITIES ARE AMONG THE MOST THERAPY-RESISTANT LEUKEMIAS. DEREGULATED EXPRESSION OF EVI1 IS THE MOLECULAR HALLMARK OF THIS DISEASE; HOWEVER, THE GENOME-WIDE SPECTRUM OF COOPERATING MUTATIONS IN THIS DISEASE SUBSET HAS NOT BEEN SYSTEMATICALLY ELUCIDATED. HERE, WE SHOW THAT 98% OF INV(3)/T(3;3) MYELOID MALIGNANCIES HARBOR MUTATIONS IN GENES ACTIVATING RAS/RECEPTOR TYROSINE KINASE (RTK) SIGNALING PATHWAYS. IN ADDITION, HEMIZYGOUS MUTATIONS IN GATA2, AS WELL AS HETEROZYGOUS ALTERATIONS IN RUNX1, SF3B1, AND GENES ENCODING EPIGENETIC MODIFIERS, FREQUENTLY CO-OCCUR WITH THE INV(3)/T(3;3) ABERRATION. NOTABLY, NEITHER MUTATIONAL PATTERNS NOR GENE EXPRESSION PROFILES DIFFER ACROSS INV(3)/T(3;3) ACUTE MYELOID LEUKEMIA, CHRONIC MYELOID LEUKEMIA, AND MYELODYSPLASTIC SYNDROME CASES, SUGGESTING RECOGNITION OF INV(3)/T(3;3) MYELOID MALIGNANCIES AS A SINGLE DISEASE ENTITY IRRESPECTIVE OF BLAST COUNT. THE HIGH INCIDENCE OF ACTIVATING RAS/RTK SIGNALING MUTATIONS MAY PROVIDE A TARGET FOR A RATIONAL TREATMENT STRATEGY IN THIS HIGH-RISK PATIENT GROUP.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
7 3898  32 LARGE-SCALE TOPOLOGICAL DISRUPTION OF CHROMOSOME TERRITORIES 9 AND 22 IS ASSOCIATED WITH NONRESPONSE TO TREATMENT IN CML. CHRONIC MYELOID LEUKEMIA (CML) IS A MYELOPROLIFERATIVE NEOPLASM DEFINED BY THE PRESENCE OF T(9;22) TRANSLOCATION WHOSE ORIGIN HAS BEEN ASSOCIATED WITH THE TRIDIMENSIONAL GENOME ORGANIZATION. THIS REARRANGEMENT LEADS TO THE FUSION OF BCR AND ABL1 GENES GIVING RISE TO A CHIMERIC PROTEIN WITH CONSTITUTIVE KINASE ACTIVITY. IMATINIB, A TYROSINE KINASE INHIBITOR (TKI), IS USED AS A FIRST-LINE TREATMENT FOR CML, THOUGH ~40% OF CML PATIENTS DO NOT RESPOND. HERE, USING STRUCTURED ILLUMINATION MICROSCOPY (SIM) AND 3D RECONSTRUCTION, WE STUDIED THE 3D ORGANIZATION PATTERNS OF THE ABL1 AND BCR GENES, AND THEIR CHROMOSOME TERRITORIES (CTS) CT9 AND CT22, IN CD34+ CELLS FROM CML PATIENTS THAT RESPONDED OR NOT TO TKI. WE FOUND THAT TKI RESISTANCE IN CML IS ASSOCIATED WITH HIGH LEVELS OF STRUCTURAL DISRUPTION OF CT9 AND CT22 IN CD34+ CELLS, INCREASED CT VOLUMES (ESPECIALLY FOR CT22), INTERMINGLING BETWEEN CT9 AND CT22, AND AN OPEN-CHROMATIN EPIGENETIC MARK IN CT22. ALTOGETHER OUR RESULTS SUGGEST THAT LARGE-SCALE DISRUPTION OF CT9 AND CT22 CORRELATES WITH THE CLINICAL RESPONSE OF CML PATIENTS, WHICH COULD BE TRANSLATED INTO A POTENTIAL PROGNOSTIC MARKER OF RESPONSE TO TREATMENT IN THIS DISEASE AND PROVIDE NOVEL INSIGHTS INTO THE MECHANISMS UNDERLYING RESISTANCE TO TKI IN CML.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
8 2761  35 EXPRESSION OF TESTIS-SPECIFIC GENES, TEX101 AND ODF4, IN CHRONIC MYELOID LEUKEMIA AND EVALUATION OF TEX101 IMMUNOGENICITY. BACKGROUND AND OBJECTIVES: CANCER-TESTIS (CT) ANTIGENS ARE A GROUP OF ANTIGENS WITH A RESTRICTED EXPRESSION IN NORMAL TISSUES, EXCEPT TESTIS, AND THEY HAVE ABERRANT EXPRESSION IN DIFFERENT TUMORS. THIS PATTERN OF EXPRESSION HAS MADE THEM PROMISING TARGETS FOR IMMUNOTHERAPY AND CANCER DETECTION. OUR AIM WAS TO FIND NEW MEMBERS OF THIS GROUP THAT MIGHT BE USEFUL AS MARKERS IN THE DETECTION OF CANCER AND IMMUNOTHERAPY. DESIGN AND SETTING: A DESCRIPTIVE STUDY CONDUCTED IN REFERRAL CENTERS OF TEHRAN UNIVERSITY OF MEDICAL SCIENCE FROM JANUARY 2008 TO JANUARY 2009. PATIENTS AND METHODS: WE ANALYZED THE EXPRESSION OF TWO TESTIS-SPECIFIC GENES NAMED ODF4 (OUTER DENSE FIBER OF SPERM TAILS 4) AND TEX101 (TESTIS EXPRESSED 101) IN 20 CHRONIC MYELOID LEUKEMIA (CML) AND 20 NORMAL SAMPLES BY REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION AND SEQUENCING. IMMUNOGENICITY OF TEX101 WAS EVALUATED BY MEANS OF ENZYME-LINKED IMMUNOSORBENT ASSAY. RESULTS: THESE TWO GENES WERE EXPRESSED IN 30% OF CML PATIENTS BUT NOT IN ANY OF THE HEALTHY DONORS. HUMORAL RESPONSE AGAINST TEX101 WAS NOT DETECTED IN ANY SAMPLES. CONCLUSIONS: TEX101 AND ODF4 ARE CT GENES USEFUL FOR DETECTION OF CML. UNLIKE MANY CT GENES, OVEREXPRESSION OF TEX101 WAS NOT SHOWN TO INDUCE IMMUNOLOGIC RESPONSES IN THESE SAMPLES. ACCORDING TO THE PREVIOUS STUDIES, OVEREXPRESSION OF TEX101 LEADS TO SUPPRESSION OF CANCER INVASION AND METASTASIS; THUS, THE INDUCTION OF THE EXPRESSION OF TEX101 IN CANCER BY EPIGENETIC MECHANISMS MAY BE A TREATMENT STRATEGY.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
9 5608  40 RUNX1-EVI1 DISRUPTS LINEAGE DETERMINATION AND THE CELL CYCLE BY INTERFERING WITH RUNX1 AND EVI1 DRIVEN GENE REGULATORY NETWORKS. HEMATOLOGICAL MALIGNANCIES ARE CHARACTERISED BY A BLOCK IN DIFFERENTIATION, WHICH IN MANY CASES IS CAUSED BY RECURRENT MUTATIONS AFFECTING THE ACTIVITY OF HEMATOPOIETIC TRANSCRIPTION FACTORS. RUNX1-EVI1 IS A FUSION PROTEIN FORMED BY THE T(3;21) TRANSLOCATION LINKING TWO TRANSCRIPTION FACTORS REQUIRED FOR NORMAL HEMATOPOIESIS. RUNX1-EVI1 EXPRESSION IS FOUND IN MYELODYSPLASTIC SYNDROME, SECONDARY ACUTE MYELOID LEUKEMIA, AND BLAST CRISIS OF CHRONIC MYELOID LEUKEMIA; WITH CLINICAL OUTCOMES BEING WORSE THAN IN PATIENTS WITH RUNX1-ETO, RUNX1 OR EVI1 MUTATIONS ALONE. RUNX1-EVI1 IS USUALLY FOUND AS A SECONDARY MUTATION, THEREFORE THE MOLECULAR MECHANISMS UNDERLYING HOW RUNX1-EVI1 ALONE CONTRIBUTES TO POOR PROGNOSIS ARE UNKNOWN. TO ADDRESS THIS QUESTION, WE INDUCED EXPRESSION OF RUNX1-EVI1 IN HEMATOPOIETIC CELLS DERIVED FROM AN EMBRYONIC STEM CELL DIFFERENTIATION MODEL. INDUCTION RESULTED IN DISRUPTION OF THE RUNX1-DEPENDENT ENDOTHELIAL-HEMATOPOIETIC TRANSITION, BLOCKED THE CELL CYCLE AND UNDERMINED CELL FATE DECISIONS IN MULTIPOTENT HEMATOPOIETIC PROGENITOR CELLS. INTEGRATIVE ANALYSES OF GENE EXPRESSION WITH CHROMATIN AND TRANSCRIPTION FACTOR BINDING DATA DEMONSTRATED THAT RUNX1-EVI1 BINDING CAUSED THE RE-DISTRIBUTION OF ENDOGENOUS RUNX1 WITHIN THE GENOME AND INTERFERED WITH BOTH RUNX1 AND EVI1 REGULATED GENE EXPRESSION PROGRAMS. IN SUMMARY, RUNX1-EVI1 EXPRESSION ALONE LEADS TO EXTENSIVE EPIGENETIC REPROGRAMMING WHICH IS INCOMPATIBLE WITH HEALTHY BLOOD PRODUCTION.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
10 1629  25 DNMT3A ARG882 MUTATION DRIVES CHRONIC MYELOMONOCYTIC LEUKEMIA THROUGH DISTURBING GENE EXPRESSION/DNA METHYLATION IN HEMATOPOIETIC CELLS. THE GENE ENCODING DNA METHYLTRANSFERASE 3A (DNMT3A) IS MUTATED IN APPROXIMATELY 20% OF ACUTE MYELOID LEUKEMIA CASES, WITH ARG882 (R882) AS THE HOTSPOT. HERE, WE ADDRESSED THE TRANSFORMATION ABILITY OF THE DNMT3A-ARG882HIS (R882H) MUTANT BY USING A RETROVIRAL TRANSDUCTION AND BONE MARROW TRANSPLANTATION (BMT) APPROACH AND FOUND THAT THE MUTANT GENE CAN INDUCE ABERRANT PROLIFERATION OF HEMATOPOIETIC STEM/PROGENITOR CELLS. AT 12 MO POST-BMT, ALL MICE DEVELOPED CHRONIC MYELOMONOCYTIC LEUKEMIA WITH THROMBOCYTOSIS. RNA MICROARRAY ANALYSIS REVEALED ABNORMAL EXPRESSIONS OF SOME HEMATOPOIESIS-RELATED GENES, AND THE DNA METHYLATION ASSAY IDENTIFIED CORRESPONDING CHANGES IN METHYLATION PATTERNS IN GENE BODY REGIONS. MOREOVER, DNMT3A-R882H INCREASED THE CDK1 PROTEIN LEVEL AND ENHANCED CELL-CYCLE ACTIVITY, THEREBY CONTRIBUTING TO LEUKEMOGENESIS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
11 3484  44 IDENTIFICATION OF CHROMATIN REMODELING GENES ARID4A AND ARID4B AS LEUKEMIA SUPPRESSOR GENES. BACKGROUND: LEUKEMIA EVOLVES THROUGH A MULTISTEP PROCESS FROM PREMALIGNANCY TO MALIGNANCY. EPIGENETIC ALTERATIONS, INCLUDING HISTONE MODIFICATIONS, HAVE BEEN PROPOSED TO PLAY AN IMPORTANT ROLE IN TUMORIGENESIS. THE INVOLVEMENT OF TWO CHROMATIN REMODELING GENES, RETINOBLASTOMA-BINDING PROTEIN 1 (RBBP1/ARID4A) AND RBBP1-LIKE 1 (RBBP1L1/ARID4B), IN LEUKEMOGENESIS WAS NOT CHARACTERIZED. METHODS: THE LEUKEMIC PHENOTYPE OF MICE DEFICIENT FOR ARID4A WITH OR WITHOUT HAPLOINSUFFICIENCY FOR ARID4B WAS INVESTIGATED BY SERIALLY MONITORING COMPLETE BLOOD COUNTS TOGETHER WITH MICROSCOPIC HISTOLOGIC ANALYSIS AND FLOW CYTOMETRIC ANALYSIS OF BONE MARROW AND SPLEEN FROM THE ARID4A(-/-) MICE OR ARID4A(-/-)ARID4B(+/-) MICE. REGULATION IN BONE MARROW CELLS OF DOWNSTREAM GENES IMPORTANT FOR NORMAL HEMATOPOIESIS WAS ANALYZED BY REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION. GENOTYPIC EFFECTS ON HISTONE MODIFICATIONS WERE EXAMINED BY WESTERN BLOTTING AND IMMUNOFLUORESCENCE ANALYSIS. ALL STATISTICAL TESTS WERE TWO-SIDED. RESULTS: YOUNG (2-5 MONTHS OLD) ARID4A-DEFICIENT MICE HAD INEFFECTIVE BLOOD CELL PRODUCTION IN ALL HEMATOPOIETIC LINEAGES. BEYOND 5 MONTHS OF AGE, THE ARID4A(-/-) MICE MANIFESTED MONOCYTOSIS, ACCOMPANIED BY SEVERE ANEMIA AND THROMBOCYTOPENIA. THESE SICK ARID4A(-/-) MICE SHOWED BONE MARROW FAILURE WITH MYELOFIBROSIS ASSOCIATED WITH SPLENOMEGALY AND HEPATOMEGALY. FIVE OF 42 ARID4A(-/-) MICE AND 10 OF 12 ARID4A(-/-)ARID4B(+/-) MICE PROGRESSED TO ACUTE MYELOID LEUKEMIA (AML) AND HAD RAPID FURTHER INCREASES OF LEUKOCYTE COUNTS. EXPRESSION OF HOX GENES (HOXB3, HOXB5, HOXB6, AND HOXB8) WAS DECREASED IN ARID4A-DEFICIENT BONE MARROW CELLS WITH OR WITHOUT ARID4B HAPLOINSUFFICIENCY, AND FOXP3 EXPRESSION WAS REDUCED IN ARID4A(-/-)ARID4B(+/-) BONE MARROW. INCREASES OF HISTONE TRIMETHYLATION OF H3K4, H3K9, AND H4K20 (FOLD INCREASES IN TRIMETHYLATION = 32, 95% CONFIDENCE INTERVAL [CI] = 27 TO 32; 45, 95% CI = 41 TO 49; AND 2.2, 95% CI = 1.7 TO 2.7, RESPECTIVELY) WERE OBSERVED IN THE BONE MARROW OF ARID4A-DEFICIENT MICE. CONCLUSIONS: ARID4A-DEFICIENT MICE INITIALLY DISPLAY INEFFECTIVE HEMATOPOIESIS, FOLLOWED BY TRANSITION TO CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML)-LIKE MYELODYSPLASTIC/MYELOPROLIFERATIVE DISORDER, AND THEN TRANSFORMATION TO AML. THE DISEASE PROCESSES IN THE ARID4A-DEFICIENT MICE ARE VERY SIMILAR TO THE COURSE OF EVENTS IN HUMANS WITH CMML AND AML. THIS MOUSE MODEL HAS THE POTENTIAL TO FURNISH ADDITIONAL INSIGHTS INTO THE ROLE OF EPIGENETIC ALTERATIONS IN LEUKEMOGENESIS, AND IT MAY BE USEFUL IN DEVELOPING NOVEL PHARMACOLOGICAL APPROACHES TO TREATMENT OF PRELEUKEMIC AND LEUKEMIC STATES.	2008	
                         
12  409  33 ANALYSIS OF GENES ENCODING EPIGENETIC REGULATORS IN MYELOPROLIFERATIVE NEOPLASMS: COEXISTENCE OF A NOVEL SETBP1 MUTATION IN A PATIENT WITH A P.V617F JAK2 POSITIVE MYELOFIBROSIS. IN RECENT YEARS IT HAS BEEN SHOWN THAT THE CAUSES OF CHRONIC MYELOPROLIFERATIVE NEOPLASMS (MPNS) ARE MORE COMPLEX THAN A SIMPLE SIGNALING ABERRATION AND MANY OTHER MUTATED GENES AFFECTING DIFFERENT CELL PROCESSES HAVE BEEN DESCRIBED. FOR INSTANCE, MUTATIONS IN GENES ENCODING EPIGENETIC REGULATORS ARE MORE FREQUENT THAN EXPECTED. ONE OF THE LATEST GENES DESCRIBED AS MUTATED IS SET BINDING PROTEIN 1 (SETBP1). IN SILICO TOOLS HAVE REVEALED THAT THERE ARE SEVERAL HUMAN SETBP1 PARALOGOUS TO NUCLEAR RECEPTOR BINDING SET DOMAIN PROTEIN 1 (NSD1), NSD2 AND NSD3, FOR EXAMPLE, WHICH ARE ALSO INVOLVED IN THE DEVELOPMENT OF OTHER HEMATOLOGICAL MALIGNANCIES. THEREFORE, THE PRESENT STUDY ANALYZED THE MUTATIONAL STATUS OF NSD1, NSD2, NSD3 AND SETBP1 IN BCR-ABL1 NEGATIVE MPNS WITH OR WITHOUT JANUS KINASE 2 (JAK2) P.V617F MUTATION. THE PRESENT STUDY REVEALED THAT THE NSD GENES ARE NOT FREQUENTLY MUTATED IN MPNS. HOWEVER, A NOVEL SETBP1 MUTATION WAS IDENTIFIED IN A PATIENT WITH P.V617F JAK2 POSITIVE PRIMARY MYELOFIBROSIS. THESE RESULTS PROVIDE FURTHER INSIGHT INTO THE GENETIC COMPLEXITY OF MPNS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
13 5101  29 POLYCOMB FACTOR PHF19 CONTROLS CELL GROWTH AND DIFFERENTIATION TOWARD ERYTHROID PATHWAY IN CHRONIC MYELOID LEUKEMIA CELLS. POLYCOMB GROUP (PCG) OF PROTEINS ARE A GROUP OF HIGHLY CONSERVED EPIGENETIC REGULATORS INVOLVED IN MANY BIOLOGICAL FUNCTIONS, SUCH AS EMBRYONIC DEVELOPMENT, CELL PROLIFERATION, AND ADULT STEM CELL DETERMINATION. PHD FINGER PROTEIN 19 (PHF19) IS AN ASSOCIATED FACTOR OF POLYCOMB REPRESSOR COMPLEX 2 (PRC2), OFTEN UPREGULATED IN HUMAN CANCERS. IN PARTICULAR, MYELOID LEUKEMIA CELL LINES SHOW INCREASED LEVELS OF PHF19, YET LITTLE IS KNOWN ABOUT ITS FUNCTION. HERE, WE HAVE CHARACTERIZED THE ROLE OF PHF19 IN MYELOID LEUKEMIA CELLS. WE DEMONSTRATED THAT PHF19 DEPLETION DECREASES CELL PROLIFERATION AND PROMOTES CHRONIC MYELOID LEUKEMIA (CML) DIFFERENTIATION. MECHANISTICALLY, WE HAVE SHOWN HOW PHF19 REGULATES THE PROLIFERATION OF CML THROUGH A DIRECT REGULATION OF THE CELL CYCLE INHIBITOR P21. FURTHERMORE, WE OBSERVED THAT MTF2, A PHF19 HOMOLOG, PARTIALLY COMPENSATES FOR PHF19 DEPLETION IN A SUBSET OF TARGET GENES, INSTRUCTING SPECIFIC ERYTHROID DIFFERENTIATION. TAKEN TOGETHER, OUR RESULTS SHOW THAT PHF19 IS A KEY TRANSCRIPTIONAL REGULATOR FOR CELL FATE DETERMINATION AND COULD BE A POTENTIAL THERAPEUTIC TARGET FOR MYELOID LEUKEMIA TREATMENT.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
14 4837  29 ONCOGENIC GENE EXPRESSION AND EPIGENETIC REMODELING OF CIS-REGULATORY ELEMENTS IN ASXL1-MUTANT CHRONIC MYELOMONOCYTIC LEUKEMIA. MYELOID NEOPLASMS ARE CLONAL HEMATOPOIETIC STEM CELL DISORDERS DRIVEN BY THE SEQUENTIAL ACQUISITION OF RECURRENT GENETIC LESIONS. TRUNCATING MUTATIONS IN THE CHROMATIN REMODELER ASXL1 (ASXL1(MT)) ARE ASSOCIATED WITH A HIGH-RISK DISEASE PHENOTYPE WITH INCREASED PROLIFERATION, EPIGENETIC THERAPEUTIC RESISTANCE, AND POOR SURVIVAL OUTCOMES. WE PERFORMED A MULTI-OMICS INTERROGATION TO DEFINE GENE EXPRESSION AND CHROMATIN REMODELING ASSOCIATED WITH ASXL1(MT) IN CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML). ASXL1(MT) ARE ASSOCIATED WITH A LOSS OF REPRESSIVE HISTONE METHYLATION AND INCREASE IN PERMISSIVE HISTONE METHYLATION AND ACETYLATION IN PROMOTER REGIONS. ASXL1(MT) ARE FURTHER ASSOCIATED WITH DE NOVO ACCESSIBILITY OF DISTAL ENHANCERS BINDING ETS TRANSCRIPTION FACTORS, TARGETING IMPORTANT LEUKEMOGENIC DRIVER GENES. CHROMATIN REMODELING OF PROMOTERS AND ENHANCERS IS STRONGLY ASSOCIATED WITH GENE EXPRESSION AND HETEROGENOUS AMONG OVEREXPRESSED GENES. THESE RESULTS PROVIDE A COMPREHENSIVE MAP OF THE TRANSCRIPTOME AND CHROMATIN LANDSCAPE OF ASXL1(MT) CMML, FORMING AN IMPORTANT FRAMEWORK FOR THE DEVELOPMENT OF NOVEL THERAPEUTIC STRATEGIES TARGETING ONCOGENIC CIS INTERACTIONS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
15 3168  36 GTPASE REGULATOR ASSOCIATED WITH THE FOCAL ADHESION KINASE (GRAF) TRANSCRIPT WAS DOWN-REGULATED IN PATIENTS WITH MYELOID MALIGNANCIES. BACKGROUND: GTPASE REGULATOR ASSOCIATED WITH THE FOCAL ADHESION KINASE (GRAF), A PUTATIVE TUMOR SUPPRESSOR GENE, IS FOUND INACTIVATED IN HEMATOPOIETIC MALIGNANCIES BY EITHER GENETIC OR EPIGENETIC ABNORMALITIES. HOWEVER, THE EXPRESSION LEVEL OF GRAF GENE HAS NOT YET BEEN STUDIED IN LEUKEMIA. THE AIM OF THIS STUDY WAS TO INVESTIGATE THE EXPRESSION LEVEL OF GRAF GENE IN THOSE PATIENTS WITH MYELOID MALIGNANCIES INCLUDING ACUTE MYELOID LEUKEMIA (AML), MYELODYSPLASTIC SYNDROME (MDS) AND CHRONIC MYELOID LEUKEMIA (CML). METHODS: THE EXPRESSION LEVELS OF GRAF TRANSCRIPT WERE DETERMINED IN 94 PATIENTS USING REAL-TIME QUANTITATIVE PCR (RQ-PCR). CLINICAL AND LABORATORY DATA OF THESE PATIENTS WERE COLLECTED AND ANALYZED. RESULTS: THE SIGNIFICANTLY DECREASED LEVEL OF GRAF TRANSCRIPT WAS OBSERVED IN THREE MYELOID MALIGNANCIES COMPARED TO CONTROLS. WITHIN AML, THERE WAS NO DIFFERENCE IN THE LEVEL OF GRAF TRANSCRIPT AMONG DIFFERENT FAB SUBTYPES (P > 0.05). DIFFERENCE WAS NOT OBSERVED IN THE AMOUNT OF GRAF MRNA BETWEEN CML AT CHRONIC PHASE AND CONTROLS. AS CML PROGRESSED, GRAF TRANSCRIPT SIGNIFICANTLY DECREASED. IN MDS, THREE CASES WITH 5Q DELETION HAD LOWER GRAF TRANSCRIPT THAN FOUR WITHOUT 5Q DELETION (MEDIAN 0.76 VS 2.99) (P > 0.05). CONCLUSION: OUR RESULTS DEMONSTRATE THAT THE GRAF TRANSCRIPT IS DECREASED IN MYELOID MALIGNANCIES.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
16  145  43 ABERRANT DNA METHYLATION STATUS AND MRNA EXPRESSION LEVEL OF SMG1 GENE IN CHRONIC MYELOID LEUKEMIA: A CASE-CONTROL STUDY. OOBJECTIVE: CHRONIC MYELOID LEUKEMIA (CML) IS A MYELOPROLIFERATIVE MALIGNANCY WITH DIFFERENT STAGES. ABERRANT EPIGENETIC MODIFICATIONS, SUCH AS DNA METHYLATION, HAVE BEEN INTRODUCED AS A SIGNATURE FOR DIVERSE CANCERS WHICH ALSO PLAYS A CRUCIAL ROLE IN CML PATHOGENESIS AND DEVELOPMENT. SUPPRESSOR WITH MORPHOGENETIC EFFECT ON GENITALIA (SMG1) GENE RECENTLY HAS BEEN BROUGHT TO THE SPOTLIGHT AS A POTENT TUMOR SUPPRESSOR GENE THAT CAN BE SUPPRESSED BY TUMORS FOR FURTHER PROGRESS. THE PRESENT STUDY AIMS TO INVESTIGATE SMG1 STATUS IN CML PATIENTS. MATERIALS AND METHODS: IN THIS CASE-CONTROL STUDY, PERIPHERAL BLOOD FROM 30 PATIENTS WITH DIFFERENT PHASES OF CML [NEW CASE (N)=10, COMPLETE MOLECULAR REMISSION (CMR)=10, BLASTIC PHASE (BP)=10] AND 10 HEALTHY SUBJECTS WERE COLLECTED. METHYLATION STATUS AND EXPRESSION LEVEL OF SMG1 GENE PROMOTER WAS ASSESSED BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) AND QUANTITATIVE REVERSE-TRANSCRIPTION PCR, RESPECTIVELY. RESULTS: MSP RESULTS OF SMG1 GENE PROMOTOR IN THE NEW CASE GROUP WERE METHYLATED (60% METHYLATED, 30% HEMIMETHYLATED AND 10% UNMETHYLATED). ALL CMR AND CONTROL GROUP PATIENTS WERE UNMETHYLATED IN THE SMG1 GENE PROMOTER. IN THE BP GROUP, METHYLATED SMG1 PROMOTER WAS SEEN (50% OF PATIENTS HAD A METHYLATED STATUS AND 50% HAD HEMIMETHYLATED STATUS). IN COMPARISON WITH THE HEALTHY SUBJECTS, EXPRESSION LEVEL OF SMG1 IN THE NEW CASE GROUP WAS DECREASED (P<0.01); IN THE CMR GROUP AND BP-CML GROUPS, IT WAS INCREASED (P<0.05). NO SIGNIFICANT CORRELATION BETWEEN PATIENTS' HEMATOLOGICAL FEATURES AND SMG1 METHYLATION WAS SEEN. CONCLUSION: OUR RESULTS DEMONSTRATED THAT ABERRANT METHYLATION OF SMG1 OCCURRED IN CML PATIENTS AND IT HAD A SIGNIFICANT ASSOCIATION WITH SMG1 EXPRESSION. SMG1 GENE PROMOTER SHOWED DIVERSE METHYLATED STATUS AND SUBSEQUENT EXPRESSION LEVELS IN DIFFERENT PHASES OF CML. THESE FINDINGS SUGGESTED POSSIBLE PARTICIPATION OF SMG1 SUPPRESSION IN THE CML PATHOGENESIS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
17 4388  43 MLL2/KMT2D AND MLL3/KMT2C EXPRESSION CORRELATES WITH DISEASE PROGRESSION AND RESPONSE TO IMATINIB MESYLATE IN CHRONIC MYELOID LEUKEMIA. BACKGROUND: CHRONIC MYELOID LEUKEMIA (CML) IS A CLONAL MYELOPROLIFERATIVE NEOPLASM WHOSE PATHOGENESIS IS LINKED TO THE PHILADELPHIA CHROMOSOME PRESENCE THAT GENERATES THE BCR-ABL1 FUSION ONCOGENE. TYROSINE KINASE INHIBITORS (TKI) SUCH AS IMATINIB MESYLATE (IM) DRAMATICALLY IMPROVED THE TREATMENT EFFICIENCY AND SURVIVAL OF CML PATIENTS BY TARGETING BCR-ABL TYROSINE KINASE. THE DISEASE SHOWS THREE DISTINCT CLINICAL-LABORATORY STAGES: CHRONIC PHASE, ACCELERATED PHASE AND BLAST CRISIS. ALTHOUGH PATIENTS IN THE CHRONIC PHASE RESPOND WELL TO TREATMENT, PATIENTS IN THE ACCELERATED PHASE OR BLAST CRISIS USUALLY SHOW THERAPY RESISTANCE AND CML RELAPSE. IT IS CRUCIAL, THEREFORE, TO IDENTIFY BIOMARKERS TO PREDICT CML GENETIC EVOLUTION AND RESISTANCE TO TKI THERAPY, CONSIDERING NOT ONLY THE EFFECTS OF GENETIC ABERRATIONS BUT ALSO THE ROLE OF EPIGENETIC ALTERATIONS DURING THE DISEASE. ALTHOUGH DYSREGULATIONS IN EPIGENETIC MODULATORS SUCH AS HISTONE METHYLTRASNFERASES HAVE ALREADY BEEN DESCRIBED FOR SOME HEMATOLOGIC MALIGNANCIES, TO DATE VERY LIMITED DATA IS AVAILABLE FOR CML, ESPECIALLY WHEN CONSIDERING THE LYSINE METHYLTRANSFERASE MLL2/KMT2D AND MLL3/KMT2C. METHODS: HERE WE INVESTIGATED THE EXPRESSION PROFILE OF BOTH GENES IN CML PATIENTS IN DIFFERENT STAGES OF THE DISEASE, IN PATIENTS SHOWING DIFFERENT RESPONSES TO THERAPY WITH IM AND IN NON-NEOPLASTIC CONTROL SAMPLES. IMATINIB SENSITIVE AND RESISTANT CML CELL LINES WERE ALSO USED TO INVESTIGATE WHETHER TREATMENT WITH OTHER TYROSINE KINASE INHIBITORS INTERFERED IN THEIR EXPRESSION. RESULTS: IN PATIENTS, BOTH METHYLTRANSFERASES WERE EITHER UPREGULATED OR WITH BASAL EXPRESSION LEVEL DURING THE CHRONIC PHASE COMPARED TO CONTROLS. INTERESTINGLY, MLL3/KMT2C AND SPECIALLY MLL2/KMT2D LEVELS DECREASED DURING DISEASE PROGRESSION CORRELATING WITH DISTINCT CLINICAL STAGES. FURTHERMORE, MLL2/KMT2D WAS DECREASED IN PATIENTS RESISTANT TO IM TREATMENT. A RESCUE IN THE EXPRESSION OF BOTH MLL GENES WAS OBSERVED IN KCL22S, A CML CELL LINE SENSITIVE TO IM, AFTER TREATMENT WITH DASATINIB OR NILOTINIB WHICH WAS ASSOCIATED WITH A HIGHER RATE OF APOPTOSIS, AN ENHANCED EXPRESSION OF P21 (CDKN1A) AND A CONCOMITANT DECREASE IN THE EXPRESSION OF CDK2, CDK4 AND CYCLIN B1 (CCNB1) IN COMPARISON TO UNTREATED KCL22S CONTROL OR IM RESISTANT KCL22R CELL LINE, WHICH SUGGESTS INVOLVEMENT OF P53 REGULATED PATHWAY. CONCLUSION: OUR RESULTS ESTABLISHED A NEW ASSOCIATION BETWEEN MLL2/KMT2D AND MLL3/KMT2C GENES WITH CML AND SUGGEST THAT MLL2/KMT2D IS ASSOCIATED WITH DISEASE EVOLUTION AND MAY BE A POTENTIAL MARKER TO PREDICT THE DEVELOPMENT OF THERAPY RESISTANCE.	2018	

18  102  30 A REGULATORY ROLE FOR CHD2 IN MYELOPOIESIS. THE TRANSCRIPTIONAL PROGRAM THAT DICTATES HAEMATOPOIETIC CELL FATE AND DIFFERENTIATION REQUIRES AN EPIGENETIC REGULATORY AND MEMORY FUNCTION, PROVIDED BY A NETWORK OF EPIGENETIC FACTORS THAT REGULATE DNA METHYLATION, POST-TRANSLATIONAL HISTONE MODIFICATIONS AND CHROMATIN STRUCTURE. DISTURBED EPIGENETIC REGULATION CAUSES PERTURBATIONS IN THE BLOOD CELL DIFFERENTIATION PROGRAM THAT RESULTS IN VARIOUS TYPES OF HAEMATOPOIETIC DISORDERS. THUS, ACCURATE EPIGENETIC REGULATION IS ESSENTIAL FOR FUNCTIONAL HAEMATOPOIESIS. IN THIS STUDY, WE USED A CRISPR-CAS9 SCREENING APPROACH TO IDENTIFY NEW EPIGENETIC REGULATORS IN MYELOID DIFFERENTIATION. WE DESIGNED A CHROMATIN-UMI CRISPR GUIDE LIBRARY TARGETING 1092 EPIGENETIC REGULATORS. PHORBOL 12-MYRISTATE 13-ACETATE (PMA) TREATMENT OF THE CHRONIC MYELOID LEUKAEMIA CELL LINE K-562 WAS USED AS A MEGAKARYOCYTIC MYELOID DIFFERENTIATION MODEL. BOTH PREVIOUSLY DESCRIBED DEVELOPMENTAL EPIGENETIC REGULATORS AND NOVEL FACTORS WERE IDENTIFIED IN OUR SCREEN. IN THIS STUDY, WE VALIDATED AND CHARACTERIZED A ROLE FOR THE CHROMATIN REMODELLER CHD2 IN MYELOID PROLIFERATION AND MEGAKARYOCYTIC DIFFERENTIATION.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
19 3500  39 IDENTIFICATION OF NOVEL, CLONALLY STABLE, SOMATIC MUTATIONS TARGETING TRANSCRIPTION FACTORS PAX5 AND NKX2-3, THE EPIGENETIC REGULATOR LRIF1, AND BRAF IN A CASE OF ATYPICAL B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA HARBORING A T(14;18)(Q32;Q21). DIAGNOSIS OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) IS USUALLY STRAIGHTFORWARD, INVOLVING CLINICAL, IMMUNOPHENOTYPIC (MATUTES SCORE), AND (IMMUNO)GENETIC ANALYSES (TO REFINE PATIENT PROGNOSIS FOR TREATMENT). CLL CASES WITH ATYPICAL PRESENTATION (E.G., MATUTES </= 3) ARE ALSO ENCOUNTERED, AND FOR THESE DISEASES, BIOLOGY AND PROGNOSTIC IMPACT ARE LESS CLEAR. HERE WE REPORT THE GENOMIC CHARACTERIZATION OF A CASE OF ATYPICAL B-CLL IN A 70-YR-OLD MALE PATIENT; B-CLL CELLS SHOWED A MATUTES SCORE OF 3, CHROMOSOMAL TRANSLOCATION T(14;18)(Q32;Q21) (BCL2/IGH), MUTATED IGHV, DELETION 17P, AND MUTATIONS IN BCL2, NOTCH1 (SUBCLONAL), AND TP53 (SUBCLONAL). QUITE STRIKINGLY, A NOVEL PAX5 MUTATION THAT WAS PREDICTED TO BE LOSS OF FUNCTION WAS ALSO SEEN. EXOME SEQUENCING IDENTIFIED, IN ADDITION, A POTENTIALLY ACTIONABLE BRAF MUTATION, TOGETHER WITH NOVEL SOMATIC MUTATIONS AFFECTING THE HOMEOBOX TRANSCRIPTION FACTOR NKX2-3, KNOWN TO CONTROL B-LYMPHOCYTE DEVELOPMENT AND HOMING, AND THE EPIGENETIC REGULATOR LRIF1, WHICH IS IMPLICATED IN CHROMATIN COMPACTION AND GENE SILENCING. NEITHER NKX2-3 NOR LRIF1 MUTATIONS, PREDICTED TO BE LOSS OF FUNCTION, HAVE PREVIOUSLY BEEN REPORTED IN B-CLL. SEQUENCING CONFIRMED THE PRESENCE OF THESE MUTATIONS TOGETHER WITH BCL2, NOTCH1, AND BRAF MUTATIONS, WITH THE T(14;18)(Q32;Q21) TRANSLOCATION, IN THE INITIAL DIAGNOSTIC SAMPLE OBTAINED 12 YR PRIOR. THIS IS SUGGESTIVE OF A ROLE FOR THESE NOVEL MUTATIONS IN B-CLL INITIATION AND STABLE CLONAL EVOLUTION, INCLUDING UPON TREATMENT WITHDRAWAL. THIS CASE EXTENDS THE SPECTRUM OF ATYPICAL B-CLL WITH T(14;18)(Q32;Q21) AND HIGHLIGHTS THE VALUE OF MORE GLOBAL PRECISION GENOMICS FOR PATIENT FOLLOW-UP AND TREATMENT IN THESE PATIENTS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
20 4694  42 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