1 5980 108 TET2 MUTATIONS WERE PREDICTIVE OF INFERIOR PROGNOSIS IN THE PRESENCE OF ASXL1 MUTATIONS IN PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA. BACKGROUND: SOMATIC MUTATIONS INVOLVING EPIGENETIC REGULATORS, HISTONE MODIFICATION AND CHROMATIN REGULATION, SPLICING COMPONENTS, TRANSCRIPTION FACTORS AND SIGNALING REGULATOR GENES ARE COMMON IN CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) PATIENTS. IT HAS BEEN CONSENSUS THAT ASXL1 MUTATIONS HAVE ADVERSELY IMPACT ON OVERALL SURVIVAL (OS), WHILE THE EFFECT OF TET2 MUTATIONS REMAINS CONTROVERSIAL AND UNDEFINED. METHODS: ASXL1 AND TET2 MUTATIONS WERE ANALYZED IN 141 PATIENTS WITH CMML USING SANGER SEQUENCING, WITH THE AIM TO IDENTIFY THE INTERPLAY OF ASXL1 AND TET2 MUTATIONS IN THE PROGNOSIS OF CMML. RESULTS: SIXTY-FIVE (46.1%) OF THE CMML PATIENTS HARBORED ASXL1 MUTATIONS (FRAMESHIFT AND NONSENSE), AND 46 (32.6%) HAD TET2 MUTATIONS (FRAME SHIFT, NONSENSE AND MISSENSE). IN A SEPARATE MULTIVARIABLE ANALYSIS THAT INCLUDED THE MAYO PROGNOSTIC MODEL AS A SINGLE VARIABLE ALONG WITH ASXL1WT/TET2WT, THE RESPECTIVE HAZARD RATIOS OF ASXL1MUT/TET2MUT, ASXL1MUT/TET2WT AND ASXL1WT/TET2MUT WERE 4.7 (95% CI, 2.2-10.3; P<0.001), 2.2 (95% CI, 1.1-4.2; P=0.025) AND 1.3 (95% CI, 0.6-2.5; P=0.521). CONCLUSIONS: OUR STUDY SHOWED THAT ASXL1 MUTATIONS PREDICT INFERIOR OS, AND ADDITIONAL TET2 MUTATIONS WERE ASSOCIATED WITH POOR SURVIVAL IN THE PRESENCE OF ASXL1 MUTATIONS OF CMML PATIENTS. 2016 2 5244 39 PROGNOSTIC INTERACTION BETWEEN ASXL1 AND TET2 MUTATIONS IN CHRONIC MYELOMONOCYTIC LEUKEMIA. MUTATIONS INVOLVING EPIGENETIC REGULATORS (TET2~60% AND ASXL1~40%) AND SPLICING COMPONENTS (SRSF2~50%) ARE FREQUENT IN CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML). ON A 27-GENE TARGETED CAPTURE PANEL PERFORMED ON 175 CMML PATIENTS (66% MALES, MEDIAN AGE 70 YEARS), COMMON MUTATIONS INCLUDED: TET2 46%, ASXL1 47%, SRSF2 45% AND SETBP1 19%. A TOTAL OF 172 (98%) PATIENTS HAD AT LEAST ONE MUTATION, 21 (12%) HAD 2, 24 (14%) HAD 3 AND 30 (17%) HAD >3 MUTATIONS. IN A UNIVARIATE ANALYSIS, THE PRESENCE OF ASXL1 MUTATIONS (P=0.02) AND THE ABSENCE OF TET2 MUTATIONS (P=0.03), ADVERSELY IMPACTED SURVIVAL; WHILE THE NUMBER OF CONCURRENT MUTATIONS HAD NO IMPACT (P=0.3). IN A MULTIVARIABLE ANALYSIS THAT INCLUDED HEMOGLOBIN, PLATELET COUNT, ABSOLUTE MONOCYTE COUNT AND CIRCULATING IMMATURE MYELOID CELLS (MAYO MODEL), THE PRESENCE OF ASXL1 MUTATIONS (P=0.01) AND ABSENCE OF TET2 MUTATIONS (P=0.003) RETAINED PROGNOSTIC SIGNIFICANCE. PATIENTS WERE STRATIFIED INTO FOUR CATEGORIES: ASXL1WT/TET2WT (N=56), ASXL1MUT/TET2WT (N=31), ASXL1MUT/TET2MUT (N=50) AND ASXL1WT/TET2MUT (N=38). SURVIVAL DATA DEMONSTRATED A SIGNIFICANT DIFFERENCE IN FAVOR OF ASXL1WT/TET2MUT (38 MONTHS; P=0.016), COMPARED WITH THOSE WITH ASXL1WT/TET2WT (19 MONTHS), ASXL1MUT/TET2WT (21 MONTHS) AND ASXL1MUT/TET2MUT (16 MONTHS) (P=0.3). WE CONFIRM THE NEGATIVE PROGNOSTIC IMPACT IMPARTED BY ASXL1 MUTATIONS AND SUGGEST A FAVORABLE IMPACT FROM TET2 MUTATIONS IN THE ABSENCE OF ASXL1 MUTATIONS. 2016 3 867 24 CHRONIC ACTIVE EPSTEIN-BARR VIRUS INFECTION OF T/NK-CELL TYPE MIMICKING CLASSIC HODGKIN LYMPHOMA: CLINICOPATHOLOGIC AND GENETIC FEATURES OF 8 CASES SUPPORTING A VARIANT WITH "HODGKIN/REED-STERNBERG-LIKE" CELLS OF NK PHENOTYPE. CHRONIC ACTIVE EPSTEIN-BARR VIRUS (EBV) INFECTION OF T-CELL AND NK-CELL TYPE, SYSTEMIC FORM (CAEBV-T/NK-S) IS CHARACTERIZED BY EBV T-CELL AND/OR NK-CELL PROLIFERATION WITH NO CHANGES SUGGESTING MALIGNANCY. THEREFORE, WHEN HODGKIN/REED-STERNBERG (HRS)-LIKE CELLS ARE SCATTERED IN CAEBV-T/NK-S, IT IS MORE LIKELY TO BE MISDIAGNOSED AS CLASSIC HODGKIN LYMPHOMA. WE ENCOUNTERED A CASE WHEREIN THE PATIENT SHOWED HRS-LIKE CELLS WITH TYPICAL NK PHENOTYPE. THEREFORE, WE FURTHER INVESTIGATED 8 SIMILAR CASES TO PROVIDE CLINICOPATHOLOGIC AND GENETIC FEATURES AND DISCUSS THEIR DISTINCTION FROM OTHER RELATED DISEASES. CLINICALLY, ALL CASES MET THE DIAGNOSTIC CRITERIA OF CAEBV. MOREOVER, 4/8 PATIENTS HAD HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS. THE MEDIAN SURVIVAL WAS 16 MONTHS (RANGE, 5 TO 35 MO). PATHOLOGICALLY, ALL LYMPH NODE SAMPLES HAD A REMARKABLY SIMILAR MORPHOLOGY WITH SCATTERED HRS-LIKE CELLS SURROUNDED BY A MIXTURE OF SMALL-SIZED LYMPHOCYTES, PLASMA CELLS, AND MACROPHAGES THAT MASQUERADED CLASSIC HODGKIN LYMPHOMA. BESIDES, ERYTHROPHAGOCYTOSIS WAS DETECTED IN 4/11 SAMPLES. THE HRS-LIKE CELLS WERE POSITIVE FOR CD2, CD3P, CD30, CD56, GRB, AND EBER-ISH, BUT NEGATIVE FOR CD20, CD5, PAX-5, AND LMP-1. THE SURROUNDING LYMPHOCYTES WERE MAINLY CD8 CYTOTOXIC T CELLS, WITHOUT OBVIOUS ABERRANT EXPRESSION. IN ADDITION, ALL PATIENTS WERE POLYCLONAL IN THE T-CELL RECEPTOR GAMMA REARRANGEMENT TEST. THE HARBORED MUTATIONS WERE MAINLY IN EPIGENETIC MODIFIERS, JAK-STAT SIGNALING PATHWAY, AND APOPTOSIS/CELL CYCLE PATHWAY, INCLUDING SOCS1, DDX3X, AND KMT2D, SIMILAR TO OTHER EBV-ASSOCIATED T/NK-CELL LYMPHOPROLIFERATIVE DISORDERS. THEREFORE, THE EVIDENCE INDICATES THAT "HRS-LIKE CELLS OF NK PHENOTYPE" IS A VARIANT OF CAEBV-T/NK-S. THIS STUDY MAY RAISE AWARENESS OF SUCH CONFOUNDING CAEBV-T/N-S CASES IN CLINICAL PRACTICE TO AVOID MISDIAGNOSIS AND TREATMENT DELAY. 2019 4 5246 44 PROGNOSTIC SCORE INCLUDING GENE MUTATIONS IN CHRONIC MYELOMONOCYTIC LEUKEMIA. PURPOSE: SEVERAL PROGNOSTIC SCORING SYSTEMS HAVE BEEN PROPOSED FOR CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML), A DISEASE IN WHICH SOME GENE MUTATIONS-INCLUDING ASXL1-HAVE BEEN ASSOCIATED WITH POOR PROGNOSIS IN UNIVARIABLE ANALYSES. WE DEVELOPED AND VALIDATED A PROGNOSTIC SCORE FOR OVERALL SURVIVAL (OS) BASED ON MUTATIONAL STATUS AND STANDARD CLINICAL VARIABLES. PATIENTS AND METHODS: WE GENOTYPED ASXL1 AND UP TO 18 OTHER GENES INCLUDING EPIGENETIC (TET2, EZH2, IDH1, IDH2, DNMT3A), SPLICING (SF3B1, SRSF2, ZRSF2, U2AF1), TRANSCRIPTION (RUNX1, NPM1, TP53), AND SIGNALING (NRAS, KRAS, CBL, JAK2, FLT3) REGULATORS IN 312 PATIENTS WITH CMML. GENOTYPES AND CLINICAL VARIABLES WERE INCLUDED IN A MULTIVARIABLE COX MODEL OF OS VALIDATED BY BOOTSTRAPPING. A SCORING SYSTEM WAS DEVELOPED USING REGRESSION COEFFICIENTS FROM THIS MODEL. RESULTS: ASXL1 MUTATIONS (P < .0001) AND, TO A LESSER EXTENT, SRSF2 (P = .03), CBL (P = .003), AND IDH2 (P = .03) MUTATIONS PREDICTED INFERIOR OS IN UNIVARIABLE ANALYSIS. THE RETAINED INDEPENDENT PROGNOSTIC FACTORS INCLUDED ASXL1 MUTATIONS, AGE OLDER THAN 65 YEARS, WBC COUNT GREATER THAN 15 X10(9)/L, PLATELET COUNT LESS THAN 100 X10(9)/L, AND ANEMIA (HEMOGLOBIN < 10 G/DL IN FEMALE PATIENTS, < 11G/DL IN MALE PATIENTS). THE RESULTING FIVE-PARAMETER PROGNOSTIC SCORE DELINEATED THREE GROUPS OF PATIENTS WITH MEDIAN OS NOT REACHED, 38.5 MONTHS, AND 14.4 MONTHS, RESPECTIVELY (P < .0001), AND WAS VALIDATED IN AN INDEPENDENT COHORT OF 165 PATIENTS (P < .0001). CONCLUSION: A NEW PROGNOSTIC SCORE INCLUDING ASXL1 STATUS, AGE, HEMOGLOBIN, WBC, AND PLATELET COUNTS DEFINES THREE GROUPS OF CMML PATIENTS WITH DISTINCT OUTCOMES. BASED ON CONCORDANCE ANALYSIS, THIS SCORE APPEARS MORE DISCRIMINATIVE THAN THOSE BASED SOLELY ON CLINICAL PARAMETERS. 2013 5 817 31 CHARACTERISTIC PATTERNS OF ALTERED DNA METHYLATION PREDICT EMERGENCE OF HUMAN HEPATOCELLULAR CARCINOMA. WE AIMED TO IDENTIFY THE SPECIFIC SUBSET OF TUMOR SUPPRESSOR GENES (TSGS) THAT ARE METHYLATION-SILENCED DURING THE EARLIEST STEPS OF HEPATOCARCINOGENESIS, AND TO FURTHER EVALUATE WHETHER THESE GENES CAN SERVE AS PREDICTIVE BIOMARKERS OF HEPATOCELLULAR CARCINOMA (HCC) EMERGENCE. A TOTAL OF 482 LIVER TISSUES INCLUDING 177 PAIRS OF HCCS AND MATCHED NONTUMOR LIVERS AND 128 LIVER BIOPSIES FROM CHRONIC HEPATITIS C (CHC) PATIENTS WERE ANALYZED FOR QUANTITATIVE METHYLATION ANALYSIS IN 24 TSG PROMOTERS AND THREE MINT LOCI. THE TUMORS WERE CLASSIFIED AS EARLY, LESS-PROGRESSED, AND HIGHLY PROGRESSED HCCS USING HISTOLOGY AND RADIOLOGICAL APPROACHES. A SUBSET OF TSGS THAT HARBORED DISTINCTLY HIGH LEVELS OF METHYLATION IN EARLY HCCS WERE SELECTED. BASED ON THE METHYLATION PROFILES OF THESE GENES, KAPLAN-MEIER ANALYSES WERE PERFORMED TO DETERMINE TIME-TO-HCC OCCURRENCE IN CHC PATIENTS. SUBSEQUENTLY, MULTIVARIATE ANALYSIS WAS PERFORMED USING AGE, GENDER, FIBROSIS STAGE, AND NUMBER OF METHYLATED TSGS AS COVARIATES. AMONG TSGS ANALYZED, A SUBSET OF EIGHT TSGS (HIC1, GSTP1, SOCS1, RASSF1, CDKN2A, APC, RUNX3, AND PRDM2) DEMONSTRATED A DISTINCT CLUSTER BY HIERARCHICAL CLUSTERING AND RECEIVER OPERATING CHARACTERISTIC ANALYSES. THIS SUBSET OF TSGS SHOWED SIGNIFICANTLY HIGHER METHYLATION LEVELS IN THE EARLY HCCS (P < 0.0001). IN THE CHC PATIENTS, METHYLATION FREQUENCIES IN THESE TSGS WERE ASSOCIATED WITH SHORTER TIME-TO-HCC OCCURRENCE (P < 0.0001), AND NUMBER OF METHYLATED GENES WAS AN INDEPENDENT RISK FACTOR FOR HCC (HAZARD RATIO = 5.21, 95% CONFIDENCE INTERVAL = 2.25-11.76, P = 0.0002). CONCLUSION: EPIGENETIC INACTIVATION OF A SUBSET OF TSGS PLAYS A CRITICAL ROLE IN THE EARLIEST STEPS OF HEPATOCARCINOGENESIS. FURTHERMORE, EPIGENETIC INACTIVATION OF THESE GENES IN CHC PROVIDES A PROGNOSTIC VALUE FOR DETERMINING THE RISK FOR DEVELOPING HCC LATER IN LIFE. 2012 6 1100 24 COMBINATION OF MYELOPROLIFERATIVE NEOPLASM DRIVER GENE ACTIVATION WITH MUTATIONS OF SPLICE FACTOR OR EPIGENETIC MODIFIER GENES INCREASES RISK OF RAPID BLASTIC PROGRESSION. OBJECTIVES: MYELOPROLIFERATIVE NEOPLASMS (MPN) COMPRISING POLYCYTHEMIA VERA (PV), ESSENTIAL THROMBOCYTHEMIA (ET) AND PRIMARY MYELOFIBROSIS (PMF) FOLLOW A BI-PHASIC COURSE OF DISEASE WITH FIBROTIC AND/OR BLASTIC PROGRESSION. AT PRESENTATION IN THE CHRONIC PHASE, CURRENTLY THERE ARE ONLY INSUFFICIENT TOOLS TO PREDICT THE RISK OF PROGRESSION IN INDIVIDUAL CASES. METHODS: IN THIS STUDY, CHRONIC PHASE MPN (16 PMF, 11 PV, AND 11 MPN UNCLASSIFIED) WITH BLASTIC TRANSFORMATION DURING COURSE OF DISEASE (N = 38, MEDIAN FOLLOW-UP 5.3 YEARS) WERE ANALYZED BY HIGH-THROUGHPUT SEQUENCING. MPN CASES WITH A COMPARABLE FOLLOW-UP PERIOD AND WITHOUT EVIDENCE OF BLAST INCREASE SERVED AS CONTROL (N = 63, MEDIAN FOLLOW-UP 5.8 YEARS). RESULTS: FREQUENT ARCH/CHIP-ASSOCIATED MUTATIONS (TET2, ASXL1, DNMT3A) FOUND AT PRESENTATION WERE NOT SIGNIFICANTLY ASSOCIATED WITH BLASTIC TRANSFORMATION. BY CONTRAST, MUTATIONS OF SRSF2, U2AF1, AND IDH1/2 AT FIRST PRESENTATION WERE FREQUENTLY OBSERVED IN THE PROGRESSION COHORT (13/38, 34.2%) AND WERE COMPLETELY MISSING IN THE CONTROL GROUP WITHOUT BLAST TRANSFORMATION DURING FOLLOW-UP (P = .0007 FOR SRSF2; P = .0063 FOR U2AF1 AND IDH1/2). CONCLUSION: UNLIKE FREQUENT ARCH/CHIP ALTERATIONS (TET2, ASXL1, DNMT3A), MUTATIONS IN SRSF2, IDH1/2, AND U2AF1 WHEN MANIFEST ALREADY AT FIRST PRESENTATION PROVIDE AN INDEPENDENT RISK FACTOR FOR RAPID BLAST TRANSFORMATION OF MPN. 2021 7 472 31 ARRAY COMPARATIVE GENOMIC HYBRIDIZATION AND SEQUENCING OF 23 GENES IN 80 PATIENTS WITH MYELOFIBROSIS AT CHRONIC OR ACUTE PHASE. MYELOFIBROSIS IS A MYELOPROLIFERATIVE NEOPLASM THAT OCCURS DE NOVO (PRIMARY MYELOFIBROSIS) OR RESULTS FROM THE PROGRESSION OF POLYCYTHEMIA VERA OR ESSENTIAL THROMBOCYTEMIA (HEREAFTER DESIGNATED AS SECONDARY MYELOFIBROSIS OR POST-POLYCYTHEMIA VERA/ ESSENTIAL THROMBOCYTHEMIA MYELOFIBROSIS). TO PROGRESS IN THE UNDERSTANDING OF MYELOFIBROSIS AND TO FIND MOLECULAR PROGNOSTIC MARKERS WE STUDIED 104 SAMPLES OF PRIMARY AND SECONDARY MYELOFIBROSIS AT CHRONIC (N=68) AND ACUTE PHASES (N=12) FROM 80 PATIENTS, BY USING ARRAY-COMPARATIVE GENOMIC HYBRIDIZATION AND SEQUENCING OF 23 GENES (ASXL1, BMI1, CBL, DNMT3A, EZH2, IDH1/2, JAK2, K/NRAS, LNK, MPL, NF1, PPP1R16B, PTPN11, RCOR1, SF3B1, SOCS2, SRSF2, SUZ12, TET2, TP53, TRPS1). WE FOUND COPY NUMBER ABERRATIONS IN 54% OF SAMPLES, OFTEN INVOLVING GENES WITH A KNOWN OR POTENTIAL ROLE IN LEUKEMOGENESIS. WE SHOW THAT CASES CARRYING A DEL(20Q), DEL(17) OR DEL(12P) EVOLVE IN ACUTE MYELOID LEUKEMIA (P=0.03). WE FOUND THAT 88% OF THE CASES WERE MUTATED, MAINLY IN SIGNALING PATHWAY (JAK2 69%, NF1 6%) AND EPIGENETIC GENES (ASXL1 26%, TET2 14%, EZH2 8%). OVERALL SURVIVAL WAS POOR IN PATIENTS WITH MORE THAN ONE MUTATION (P=0.001) AND IN PATIENTS WITH JAK2/ASXL1 MUTATIONS (P=0.02). OUR STUDY HIGHLIGHTS THE HETEROGENEITY OF MYELOFIBROSIS, AND POINTS TO SEVERAL INTERESTING COPY NUMBER ABERRATIONS AND GENES WITH DIAGNOSTIC AND PROGNOSTIC IMPACT. 2014 8 5984 30 TET2, DNMT3A, IDH1, AND JAK2 MUTATION IN MYELOPROLIFERATIVE NEOPLASMS IN SOUTHERN IRAN. BACKGROUND: FIVE EPIGENETIC REGULATOR MUTATIONS ARE CONSIDERED IN MYELOPROLIFERATIVE NEOPLASMS (MPN) THAT HAVE PROGNOSTIC AND THERAPEUTIC VALUES. OBJECTIVE: WE AIMED TO EVALUATE THESE MUTATIONS IN MPNS AMONG THE IRANIAN POPULATION. METHODS: WE SELECTED 5 MUTATIONS IN 4 EPIGENETIC REGULATORY GENES [TET2, DNMT3A, IDH1 (RS147001633&RS121913499), AND JAK2)] AND EVALUATED 130 PATIENTS WITH MPNS INCLUDING 78 PHILADELPHIA CHROMOSOME NEGATIVE (49 ETS, 20 PVS, AND 9 PMFS) AND 52 PHILADELPHIA CHROMOSOME-POSITIVE PATIENTS AS WELL AS 51 HEALTHY CONTROLS. RESULTS: EIGHT PATIENTS (6.5%) CARRIED THE DNMT3A MUTATION, 35 (27%) WERE POSITIVE FOR TET2 MUTATION AND 64 (49.3%) HAD THE JAK2V617F MUTATION. IN THE HEALTHY CONTROLS, 16 (31.4%) CASES HAD THE TET2 MUTATION (15 HETEROZYGOTE + 1 HOMOZYGOTE) AND ONE HAD HETEROZYGOTE JAK2 MUTATION. THERE WAS NO STATISTICALLY SIGNIFICANT DIFFERENCE BETWEEN PATIENT GROUPS FOR ANY OF THESE MUTATIONS, EXCEPT FOR JAK2. THE JAK2 MUTATION RATE WAS 18 (90%), 25 (51%), 7 (77.8%), 14 (26.9%) IN POLYCYTHEMIA VERA, ESSENTIAL THROMBOCYTHEMIA, PRIMARY MYELOFIBROSIS, AND CHRONIC MYELOCYTIC LEUKEMIA, RESPECTIVELY. PATIENTS AGED 60 AND OLDER WERE MORE LIKELY TO CARRY THE TET2 MUTATION (23% VS. 39% IN YOUNGER AND OLDER THAN 60 YEARS OLD INDIVIDUALS, P=0.025). IDH1 WAS NOT DETECTED AT ALL AND PV HAD THE HIGHEST TET2 MUTATION 7(35%). TWO PMF PATIENTS HAD A HISTORY OF BONE MARROW TRANSPLANTATION THAT WERE NEGATIVE FOR IDH1AND DNMT3A AND ONE WAS POSITIVE FOR TET2 MUTATION. CONCLUSION: IN THE NORMAL IRANIAN POPULATION, THE HETEROZYGOTE FORM OF TET2 MUTATION IS SIGNIFICANT, ESPECIALLY IN THE ELDERLY. NO ASSOCIATION WAS FOUND BETWEEN JAK2 AND TET2 MUTATIONS. BOTH OF THEM ARE MORE PREVALENT IN THE AGE GROUP OF 60 YEARS AND OLDER. DNMT3A MUTATION HAS A LOW PREVALENCE AND OCCURS IN BOTH POSITIVE AND NEGATIVE MPNS. 2021 9 1431 21 DIFFERENTIAL FREQUENCIES OF P16(INK4A) PROMOTER HYPERMETHYLATION, P53 MUTATION, AND K-RAS MUTATION IN EXFOLIATIVE MATERIAL MARK THE DEVELOPMENT OF LUNG CANCER IN SYMPTOMATIC CHRONIC SMOKERS. PURPOSE: THE AIM OF THIS STUDY WAS TO INVESTIGATE THE FREQUENCY OF THREE (EPI)GENETIC ALTERATIONS (P53 AND K-RAS MUTATIONS AND P16(INK4A) PROMOTER HYPERMETHYLATION) IN SYMPTOMATIC CHRONIC SMOKERS COMPARED WITH PATIENTS WITH LUNG CANCER AND TO EVALUATE THE USE OF EXFOLIATIVE MATERIAL FOR SUCH ANALYSES. PATIENTS AND METHODS: FIFTY-ONE PATIENTS WITH HISTOLOGICALLY CONFIRMED LUNG CANCER AND 25 CHRONIC SMOKERS (> 20 PACK-YEARS) WERE INVESTIGATED FOR MUTATIONS IN THE K-RAS (CODON 12) AND P53 (CODONS 248, 249, AND 273) GENES AND FOR ALLELIC HYPERMETHYLATION OF THE P16(INK4A) GENE. DNA WAS ISOLATED FROM SPUTUM AND BILATERAL BRONCHIAL LAVAGE, AND BRUSHINGS WERE TAKEN AT BRONCHOSCOPY. RESULTS: FORTY-ONE GENETIC LESIONS WERE DETECTED WITHIN EXFOLIATIVE MATERIAL FROM THE GROUP OF 51 PATIENTS WITH LUNG CANCER AND 10 LESIONS IN THE CHRONIC SMOKER GROUP. K-RAS MUTATIONS OCCURRED EXCLUSIVELY IN THE LUNG CANCER GROUP, WHEREAS P53 MUTATIONS AND P16(INK4A) PROMOTER HYPERMETHYLATION WERE ALSO FOUND IN CHRONIC SMOKERS. THREE OF EIGHT CHRONIC SMOKERS WHO HARBORED AN (EPI)GENETIC ALTERATION WERE SUBSEQUENTLY DIAGNOSED WITH LUNG CANCER. ANALYSIS OF SPUTUM YIELDED INFORMATION EQUIVALENT TO THAT OF SAMPLES OBTAINED DURING BRONCHOSCOPY. CONCLUSION: P16(INK4A) PROMOTER HYPERMETHYLATION AND P53 MUTATIONS CAN OCCUR IN CHRONIC SMOKERS BEFORE ANY CLINICAL EVIDENCE OF NEOPLASIA AND MAY BE INDICATIVE OF AN INCREASED RISK OF DEVELOPING LUNG CANCER OR OF EARLY DISEASE. K-RAS MUTATIONS OCCUR EXCLUSIVELY IN THE PRESENCE OF CLINICALLY DETECTABLE NEOPLASTIC TRANSFORMATION. MOLECULAR ANALYSIS OF SPUTUM FOR SUCH MARKERS MAY PROVIDE AN EFFECTIVE MEANS OF SCREENING CHRONIC SMOKERS TO ENABLE EARLIER DETECTION AND THERAPEUTIC INTERVENTION OF LUNG CANCER. 2000 10 4553 46 MUTATIONAL LANDSCAPE OF CHRONIC MYELOMONOCYTIC LEUKEMIA IN CHINESE PATIENTS. BACKGROUND: CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) IS A RARE AND HETEROGENEOUS HEMATOLOGICAL MALIGNANCY. IT HAS BEEN SHOWN THAT THE MOLECULAR ABNORMALITIES SUCH AS ASXL1, TET2, SETBP1, AND SRSF2 MUTATIONS ARE COMMON IN CAUCASIAN POPULATION. METHODS: WE RETROSPECTIVELY ANALYZED 178 CHINESE CMML PATIENTS. THE TARGETED NEXT GENERATION SEQUENCING (NGS) WAS USED TO EVALUATE 114 GENE VARIATIONS, AND THE PROGNOSTIC FACTORS FOR OS WERE DETERMINED BY COX REGRESSION ANALYSIS. RESULTS: THE CMML PATIENTS SHOWED A UNIQUE MUTATIONAL SPECTRUM, INCLUDING TET2 (36.5%), NRAS (31.5%), ASXL1 (28.7%), SRSF2 (24.7%), AND RUNX1 (21.9%). OF THE 102 PATIENTS WITH CLONAL ANALYSIS, THE ANCESTRAL EVENTS PREFERENTIALLY OCCURRED IN TET2 (18.5%), SPLICING FACTORS (16.5%), RAS (14.0%), AND ASXL1 (7.8%), AND THE SUBCLONAL GENES WERE MAINLY ASXL1, TET2, AND RAS. IN ADDITION, THE SECONDARY ACUTE MYELOID LEUKEMIA (SAML) TRANSFORMED FROM CMML OFTEN HAD MUTATIONS IN DNMT3A, ETV6, FLT3, AND NPM1, WHILE THE PRIMARY AML (PAML) DEMONSTRATED MORE MUTATIONS IN CEBPA, DNMT3A, FLT3, IDH1/2, NPM1, AND WT1. IT WAS OF NOTE THAT A SERIES OF CLONES WERE EMERGED DURING THE PROGRESSION FROM CMML TO AML, INCLUDING DNMT3A, FLT3, AND NPM1. BY UNIVARIATE ANALYSIS, ASXL1 MUTATION, INTERMEDIATE- AND HIGH-RISK CYTOGENETIC ABNORMALITY, CMML-SPECIFIC PROGNOSTIC SCORING SYSTEM (CPSS) STRATIFICATIONS (INTERMEDIATE-2 AND HIGH GROUP), AND TREATMENT OPTIONS (BEST SUPPORTIVE CARE) PREDICTED FOR WORSE OS. MULTIVARIATE ANALYSIS REVEALED A SIMILAR OUTCOME. CONCLUSIONS: THE COMMON MUTATIONS IN CHINESE CMML PATIENTS INCLUDED EPIGENETIC MODIFIERS (TET2 AND ASXL1), SIGNALING TRANSDUCTION PATHWAY COMPONENTS (NRAS), AND SPLICING FACTOR (SRSF2). THE CMML PATIENTS WITH DNMT3A, ETV6, FLT3, AND NPM1 MUTATIONS TENDED TO PROGRESS TO SAML. ASXL1 MUTATION AND THERAPEUTIC MODALITIES WERE INDEPENDENT PROGNOSTIC FACTORS FOR CMML. 2022 11 1043 26 CLINICAL CHARACTERISTICS AND WHOLE EXOME/TRANSCRIPTOME SEQUENCING OF COEXISTING CHRONIC MYELOID LEUKEMIA AND MYELOFIBROSIS. MYELOPROLIFERATIVE NEOPLASMS (MPNS) ARE CLONAL HEMATOPOIETIC STEM CELL (HSC) DISORDERS THAT CAN BE CLASSIFIED ON THE BASIS OF GENETIC, CLINICAL, PHENOTYPIC FEATURES. GENETIC LESIONS SUCH AS JAK2 MUTATIONS AND BCR-ABL TRANSLOCATION ARE OFTEN MUTUALLY EXCLUSIVE IN MPN PATIENTS AND LEAD TO ESSENTIAL THROMBOCYTHEMIA, POLYCYTHEMIA VERA, OR MYELOFIBROSIS OR CHRONIC MYELOID LEUKEMIA, RESPECTIVELY. NEVERTHELESS, COEXISTENCE OF THESE GENETIC ABERRATIONS IN THE SAME PATIENT HAS BEEN REPORTED. WHETHER THESE ABERRATIONS OCCUR IN THE SAME STEM CELL OR A DIFFERENT CELL IS UNCLEAR, BUT AN UNSTABLE GENOME IN THE HSCS SEEMS TO BE THE COMMON ANTECEDENT. IN AN EFFORT TO CHARACTERIZE THE UNDERLYING GENETIC EVENTS THAT MIGHT CONTRIBUTE TO THE APPEARANCE OF MORE THAN ONE MPN IN A PATIENT, WE STUDIED NEOPLASTIC CELLS FROM PATIENTS WITH DUAL MPNS BY NEXT-GENERATION SEQUENCING. WE OBSERVED THAT MOST PATIENTS WITH TWO MPNS HARBORED MUTATIONS IN GENES KNOWN TO CONTRIBUTE TO CLONAL HEMATOPOIESIS THROUGH ALTERED EPIGENETIC REGULATION SUCH AS TET2, ASXL1/2, SRSF2, AND IDH2 AT VARYING FREQUENCIES (1%-47%). IN ADDITION, WE FOUND THAT SOME PATIENTS ALSO HARBORED ONCOGENIC MUTATIONS IN N/KRAS, TP53, BRAF, EZH2, AND GNAS AT LOW FREQUENCIES, WHICH PROBABLY REPRESENT CLONAL EVOLUTION. THESE FINDINGS SUPPORT THE HYPOTHESIS THAT HEMATOPOIETIC CELLS FROM MPN PATIENTS HARBOR MULTIPLE GENETIC ABERRATIONS, SOME OF WHICH CAN CONTRIBUTE TO CLONAL DOMINANCE. ACQUIRING MUTATIONS IN JAK2/CALR/MPL OR THE BCR-ABL TRANSLOCATION PROBABLY DRIVE THE ONCOGENIC PHENOTYPE TOWARDS A SPECIFIC MPN. FURTHER, WE PROPOSE THAT THE ACQUISITION OF BCR-ABL IN THESE PATIENTS IS FREQUENTLY A SECONDARY EVENT RESULTING FROM AN UNSTABLE GENOME. 2017 12 2678 31 EVALUATION OF A PROGNOSTIC EPIGENETIC CLASSIFICATION SYSTEM IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS. BACKGROUND: METHYLATION AT 5 CPG SITES WAS PREVIOUSLY SHOWN TO CLASSIFY CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) INTO 3 PROGNOSTIC SUBGROUPS. HERE, WE AIMED TO VALIDATE THE MARKER SET IN AN ADDITIONAL COHORT AND TO EVALUATE ITS CLINICAL UTILITY FOR CLL PATIENT STRATIFICATION. METHODS: WE EVALUATED THIS EPIGENETIC MARKER SET IN 79 GERMAN PATIENTS USING BISULFITE TREATMENT FOLLOWED BY PYROSEQUENCING AND CLASSIFICATION USING A SUPPORT VECTOR MACHINE-LEARNING TOOL. RESULTS: THE N-CLL, I-CLL, AND M-CLL CLASSIFICATION WAS DETECTED IN 28 (35%), 10 (13%), AND 41 (51%) PATIENTS, RESPECTIVELY. EPIGENETIC GROUPING WAS ASSOCIATED WITH IGHV MUTATIONAL STATUS (P = 2 X 10(-12)), ISOLATED DEL13Q (P = 9 X 10(-6)), DEL17P (P = .015), COMPLEX KARYOTYPE (P = .005), VH-USAGE, AND CLINICAL OUTCOME AS TIME TO FIRST TREATMENT (P = 1.4 X 10(-12)) AND OVERALL SURVIVAL (P = .003). MULTIVARIATE COX REGRESSION ANALYSIS IDENTIFIED N-CLL AS A FACTOR FOR EARLIER TREATMENT HAZARD RATIO (HR), 6.3 (95% CONFIDENCE INTERVAL [CI] 2.4-16.4; P = .0002) COMPARED TO IGHV MUTATIONAL STATUS (HR 4.6, 95% CI 1.9-11.3, P = .0008). IN ADDITION, WHEN COMPARING THE PROGNOSTIC VALUE OF THE EPIGENETIC CLASSIFICATION SYSTEM WITH THE IGHV CLASSIFICATION, EPIGENETIC GROUPING PERFORMED BETTER COMPARED TO IGHV MUTATIONAL STATUS USING KAPLAN-MEIER ESTIMATION AND ALLOWED THE IDENTIFICATION OF A THIRD, INTERMEDIATE (I-CLL) GROUP. THUS, OUR STUDY CONFIRMED THE PROGNOSTIC VALUE OF THE EPIGENETIC MARKER SET FOR PATIENT STRATIFICATION IN ROUTINE CLINICAL DIAGNOSTICS. 2022 13 5665 41 SF3B1, RUNX1 AND TP53 MUTATIONS SIGNIFICANTLY IMPACT THE OUTCOME OF PATIENTS WITH LOWER-RISK MYELODYSPLASTIC SYNDROME. INTRODUCTION: PROGNOSIS OF PATIENTS WITH MYELODYSPLASTIC SYNDROME (MDS), PARTICULARLY THE GROUP WITH LOWER-RISK DISEASE (LR-MDS) IS VERY HETEROGENEOUS. SEVERAL STUDIES HAVE DESCRIBED THE PROGNOSTIC VALUE OF RECURRENT SOMATIC MUTATIONS IN MDS INCLUDING ALL RISK CATEGORIES. RECENTLY, THE INCORPORATION OF GENOMIC DATA TO CLINICAL PARAMETERS DEFINED THE NEW MOLECULAR INTERNATIONAL PROGNOSTIC SCORING SYSTEM (IPSS-M). MATERIALS AND METHODS: IN THIS STUDY, WE EVALUATED THE IMPACT OF MOLECULAR PROFILE IN A SERIES OF 181 PATIENTS WITH LR-MDS AND NON-PROLIFERATIVE CHRONIC MYELOMONOCYTIC LEUKEMIA. RESULTS: EPIGENETIC REGULATORS (TET2, ASXL1) AND SPLICING (SF3B1) WERE THE MOST RECURRENT MUTATED PATHWAYS. IN UNIVARIATE ANALYSIS, RUNX1 OR TP53 MUTATIONS CORRELATED WITH LOWER MEDIAN OVERALL SURVIVAL (OS). IN CONTRAST, SF3B1 MUTATION WAS ASSOCIATED WITH PROLONGED MEDIAN OS [95 MONTHS (95% IC, 32-157) VS. 33 MONTHS (95% CI, 19-46) IN UNMUTATED PATIENTS (P < 0.01)]. IN A MULTIVARIATE COX REGRESSION MODEL, RUNX1 MUTATIONS INDEPENDENTLY ASSOCIATED WITH SHORTER OS, WHILE SF3B1 MUTATION RETAINED ITS FAVORABLE IMPACT ON OUTCOME (HR: 0.24, 95% CI, 0.1-0.5; P = 0.001). IN ADDITION, TP53 OR RUNX1 MUTATIONS WERE IDENTIFIED AS PREDICTIVE COVARIATES FOR THE PROBABILITY OF LEUKEMIC PROGRESSION (P < 0.001). CONCLUSION: INCORPORATION OF MOLECULAR TESTING IN LR-MDS IDENTIFIED A SUBSET OF PATIENTS WITH EXPECTED POORER OUTCOME, EITHER DUE TO LOWER SURVIVAL OR PROBABILITY OF LEUKEMIC PROGRESSION. 2022 14 1044 33 CLINICAL CHARACTERISTICS OF HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS ASSOCIATED WITH NON-HODGKIN B-CELL LYMPHOMA: A MULTICENTER RETROSPECTIVE STUDY. BACKGROUND: HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS (HLH) ASSOCIATED WITH B-CELL LYMPHOMA IS A HIGHLY AGGRESSIVE DISEASE WITH UNCLEAR CLINICAL FEATURES AND HAS NO STANDARD TREATMENT. PATIENTS AND METHODS: WE ANALYZED THE CLINICAL CHARACTERISTICS OF 31 PATIENTS FROM TWO INDIVIDUAL CENTERS. RESULTS: THE MEDIAN OVERALL SURVIVAL WAS ONLY 1.5 MONTHS. BOTH UNIVARIATE AND MULTIVARIATE ANALYSES, BASED ON LYMPHOMA OR HLH-RELATED CHARACTERISTICS, REVEALED THAT PATIENTS WITH HIGH EPSTEIN-BARR VIRUS (EBV) DNA LOAD AND >/= 2 EXTRANODAL LESIONS, OR HYPOFIBRINOGENEMIA, RESPECTIVELY, SHOWED SIGNIFICANTLY POORER OVERALL SURVIVAL. INTERESTINGLY, SOME PATIENTS WITH HIGH EBV DNA LOAD HAD EBV-POSITIVE NATURAL KILLER (NK) AND/OR T CELLS, WHICH MAY BE RELATED TO THE COEXISTENCE OF IMMUNODEFICIENCY AND/OR CHRONIC ACTIVE EBV INFECTION. MOLECULAR GENETICS EXAMINATION CONFIRMED THAT 47.4% (9/19) OF PATIENTS HAD COMPLEX KARYOTYPES, 37.5% (3/8) OF PATIENTS HAD TP53 DELETIONS, AND 21.34% (3/14) OF PATIENTS HAD TP53 MUTATION OR ALTERATION OF MALIGNANCY-RELATED PATHWAYS, INCLUDING BCR/NF-KAPPAB, JAK-STAT, AND EPIGENETIC REGULATORY PATHWAYS, WHICH MAY PROVIDE CLUES TO CHOOSE TARGETS FOR THERAPY. TREATMENT REGIMENS CONTAINING ETOPOSIDE, ANTI-CD20 MONOCLONAL ANTIBODIES, OR ANTHRACYCLINES IMPROVED PATIENT PROGNOSIS (P = .0183, .025, AND .0436, RESPECTIVELY). PATIENTS WITH INFECTIONS HAD SIGNIFICANTLY SHORTER SURVIVAL THAN THOSE WITHOUT INFECTIONS (P = .00019). CONCLUSION: THE PATIENTS' PERFORMANCE STATUS, NUMBER OF EXTRANODAL LESIONS, HIGH EBV DNA LOAD, AND HYPOFIBRINOGENEMIA ARE POOR PROGNOSTIC FACTORS FOR HLH ASSOCIATED WITH B-CELL LYMPHOMA. MOLECULAR GENETIC HIGH-RISK FACTORS ARE OF PARTICULAR IMPORTANCE BECAUSE THESE FACTORS CAN PROVIDE INFORMATION FOR PROGNOSIS PREDICTION, TREATMENT DECISIONS, AND DISEASE SURVEILLANCE. 2021 15 159 21 ABERRANT PROMOTER HYPERMETHYLATION OF MULTIPLE GENES IN GALLBLADDER CARCINOMA AND CHRONIC CHOLECYSTITIS. PURPOSE: ABERRANT METHYLATION OF 5' GENE PROMOTER REGIONS IS AN EPIGENETIC PHENOMENON THAT IS A MAJOR MECHANISM FOR SILENCING OF TUMOR SUPPRESSOR GENES IN MANY CANCER TYPES. THERE IS LIMITED INFORMATION ABOUT THE MOLECULAR CHANGES INVOLVED IN THE PATHOGENESIS OF GALLBLADDER CARCINOMA (GBC), INCLUDING METHYLATION STATUS. EXPERIMENTAL DESIGN: WE INVESTIGATED THE ABERRANT PROMOTER METHYLATION PROFILE OF 24 KNOWN OR SUSPECTED TUMOR SUPPRESSOR GENES IN 50 GBCS AND COMPARED THOSE RESULTS WITH THE FINDINGS IN 25 CHRONIC CHOLECYSTITIS (CC) SPECIMENS WITHOUT CANCER. THE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION AND COMBINED RESTRICTION ANALYSIS METHODS WERE USED TO DETECT METHYLATION, AND THE RESULTS WERE CONFIRMED BY SEQUENCING OF CLONED POLYMERASE CHAIN REACTION PRODUCTS. RESULTS: IN GBC, GENE METHYLATION FREQUENCIES VARIED FROM 0% TO 80%. TEN GENES DEMONSTRATED RELATIVELY HIGH FREQUENCIES OF ABERRANT METHYLATION: SHP1 (80%), 3-OST-2 (72%), CDH13 (44%), P15INK4B (44%), CDH1 (38%), RUNX3 (32%), APC (30%), RIZ1 (26%), P16INK4A (24%), AND HPP1 (20%). EIGHT GENES (P73, RARBETA2, SOCS-1, DAPK, DCR2, DCR1, HIN1, AND CHFR) SHOWED LOW FREQUENCIES (2-14%) OF METHYLATION, AND NO METHYLATION OF THE REMAINING SIX GENES (TIMP-3, P57, RASSF1A, CRBP1, SYK, AND NORE1) WAS DETECTED. IN CC, METHYLATION WAS DETECTED FOR SEVEN GENES: SHP1 (88%), P15INK4B (28%), 3-OST-2 (12%), CDH1 (12%), CDH13 (8%), DCR2 (4%), AND P16INK4A (4%). SIGNIFICANTLY HIGHER FREQUENCIES OF METHYLATION IN GBC COMPARED WITH CC WERE DETECTED FOR EIGHT GENES (3-OST-2, CDH13, CDH1, RUNX3, APC, RIZ1, P16INK4A, AND HPP1). OF THOSE, FOUR GENES SHOWED FREQUENT METHYLATION (>30%) IN GBCS. THE MEAN METHYLATION INDEX, AN EXPRESSION OF THE AMOUNT OF METHYLATED GENES BY CASE, WAS SIGNIFICANTLY HIGHER IN GBC (0.196 +/- 0.013) COMPARED WITH CC (0.065 +/- 0.008; P < 0.001). CONCLUSIONS: OUR STUDY CONSTITUTES THE MOST COMPREHENSIVE METHYLATION PROFILE REPORT AVAILABLE IN GBC AND DEMONSTRATES THAT THIS NEOPLASM HAS A DISTINCT PATTERN OF ABNORMAL GENE METHYLATION. WHEREAS GALLBLADDERS FROM HEALTHY INDIVIDUAL WERE NOT AVAILABLE, OUR FINDING OF METHYLATION IN CC CASES WITHOUT CANCER SUGGESTS THAT THIS PHENOMENON REPRESENTS AN EARLY EVENT IN THE PATHOGENESIS OF GBC. 2004 16 6770 23 [ABERRANT METHYLATION OF MULTIPLE GENES AND ITS CLINICAL IMPLICATION IN HEPATOCELLULAR CARCINOMA]. OBJECTIVE: TO INVESTIGATE THE METHYLATION FREQUENCIES OF MULTIPLE TUMOR SUPPRESSOR GENES (TSGS) IN HEPATOCELLULAR CARCINOMA (HCC) AND THE CLINICAL IMPLICATION OF ABERRANT DNA METHYLATION IN MOLECULAR CARCINOGENESIS OF HCC. METHODS: SIXTY SAMPLES OF HCC AND THE PAIRED ADJACENT LIVER TISSUE, 16 SAMPLES FROM POST-HEPATITIS CIRRHOTIC LIVERS, 5 FROM LIVERS WITH CHRONIC HEPATITIS AND 5 FROM NORMAL LIVERS WERE COLLECTED. EIGHT TSGS FREQUENTLY SILENCED BY HYPERMETHYLATION OF THEIR PROMOTERS IN VARIOUS TYPES OF DIGESTIVE TUMORS WERE SELECTED, INCLUDING APC, RASSF1A, P16, GSTP1, MGMT, DAPK, SOCS-1 AND RIZ1. THE STATUS OF PROMOTER METHYLATION IN THESE 8 GENES WAS INVESTIGATED USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. THE CLINICOPATHOLOGICAL DATA OF HCC WERE ALSO ANALYZED IN ORDER TO EVALUATE THE CLINICAL IMPLICATION OF ABERRANT METHYLATION IN HCC. RESULTS: METHYLATION OF THE 8 TSGS WAS QUITE FREQUENT IN HCC, WITH A METHYLATION RATE OF 95.0% IN RASSF1A, 90.0% IN APC, 73.3% IN GSTP1, 65.0% IN P16, 61.6% IN RIZ1 AND 60.0% IN MGMT. METHYLATION OF THE 6 GENES WAS MORE FREQUENT IN HCC THAN THAT IN ADJACENT TISSUES (P < 0.05). THE METHYLATION RATE OF MGMT, GSTP1 AND RIZ1 IN THE ADJACENT TISSUES WAS 41.6%, 40.0% AND 25.0%, RESPECTIVELY, SIGNIFICANTLY HIGHER THAN THAT IN CIRRHOTIC LIVER (P < 0.05). P16 METHYLATION WAS MORE FREQUENTLY OBSERVED IN HCC IN ELDERLY PATIENTS. THE FREQUENCY OF MGMT METHYLATION WAS TENDED TO BE HIGHER IN GIANT HCC THAN THAT IN THE OTHER TYPES OF HCC. PATIENTS WITH MGMT METHYLATION IN THE TUMOR WERE FOUND TO HAVE A SHORTER DISEASE FREE SURVIVAL. CONCLUSION: DIFFERENT FREQUENCY OF METHYLATION IN HEPATOCELLULAR CARCINOMAS, ADJACENT LIVER TISSUES AND CIRRHOTIC LIVERS IMPLIES THAT EPIGENETIC ALTERATION IN THE HEPATOCELLULAR CARCINOGENESIS MAY BE A GRADUALLY PROGRESSIVE PROCESS. METHYLATION STATUS OF MGMT, GSTP1 AND RIZ1 MAY BE PROMISING IN RISK ASSESSMENT OF HEPATOCELLULAR CARCINOMA AND IN EARLY DIAGNOSIS. FURTHERMORE, MGMT METHYLATION MIGHT BE ALSO USED AS A POTENTIAL PROGNOSTIC BIOMARKER FOR HEPATOCELLULAR CARCINOMA PATIENTS. 2008 17 4748 28 NOVEL MUTATIONS AND THEIR FUNCTIONAL AND CLINICAL RELEVANCE IN MYELOPROLIFERATIVE NEOPLASMS: JAK2, MPL, TET2, ASXL1, CBL, IDH AND IKZF1. MYELOPROLIFERATIVE NEOPLASMS (MPNS) ORIGINATE FROM GENETICALLY TRANSFORMED HEMATOPOIETIC STEM CELLS THAT RETAIN THE CAPACITY FOR MULTILINEAGE DIFFERENTIATION AND EFFECTIVE MYELOPOIESIS. BEGINNING IN EARLY 2005, A NUMBER OF NOVEL MUTATIONS INVOLVING JANUS KINASE 2 (JAK2), MYELOPROLIFERATIVE LEUKEMIA VIRUS (MPL), TET ONCOGENE FAMILY MEMBER 2 (TET2), ADDITIONAL SEX COMBS-LIKE 1 (ASXL1), CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE (CBL), ISOCITRATE DEHYDROGENASE (IDH) AND IKAROS FAMILY ZINC FINGER 1 (IKZF1) HAVE BEEN DESCRIBED IN BCR-ABL1-NEGATIVE MPNS. HOWEVER, NONE OF THESE MUTATIONS WERE MPN SPECIFIC, DISPLAYED MUTUAL EXCLUSIVITY OR COULD BE TRACED BACK TO A COMMON ANCESTRAL CLONE. JAK2 AND MPL MUTATIONS APPEAR TO EXERT A PHENOTYPE-MODIFYING EFFECT AND ARE DISTINCTLY ASSOCIATED WITH POLYCYTHEMIA VERA, ESSENTIAL THROMBOCYTHEMIA AND PRIMARY MYELOFIBROSIS; THE CORRESPONDING MUTATIONAL FREQUENCIES ARE APPROXIMATELY 99, 55 AND 65% FOR JAK2 AND 0, 3 AND 10% FOR MPL MUTATIONS. THE INCIDENCE OF TET2, ASXL1, CBL, IDH OR IKZF1 MUTATIONS IN THESE DISORDERS RANGES FROM 0 TO 17%; THESE LATTER MUTATIONS ARE MORE COMMON IN CHRONIC (TET2, ASXL1, CBL) OR JUVENILE (CBL) MYELOMONOCYTIC LEUKEMIAS, MASTOCYTOSIS (TET2), MYELODYSPLASTIC SYNDROMES (TET2, ASXL1) AND SECONDARY ACUTE MYELOID LEUKEMIA, INCLUDING BLAST-PHASE MPN (IDH, ASXL1, IKZF1). THE FUNCTIONAL CONSEQUENCES OF MPN-ASSOCIATED MUTATIONS INCLUDE UNREGULATED JAK-STAT (JANUS KINASE/SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION) SIGNALING, EPIGENETIC MODULATION OF TRANSCRIPTION AND ABNORMAL ACCUMULATION OF ONCOPROTEINS. HOWEVER, IT IS NOT CLEAR AS TO WHETHER AND HOW THESE ABNORMALITIES CONTRIBUTE TO DISEASE INITIATION, CLONAL EVOLUTION OR BLASTIC TRANSFORMATION. 2010 18 5911 22 TARGETED NEXT-GENERATION SEQUENCING IN MYELODYSPLASTIC SYNDROME AND CHRONIC MYELOMONOCYTIC LEUKEMIA AIDS DIAGNOSIS IN CHALLENGING CASES AND IDENTIFIES FREQUENT SPLICEOSOME MUTATIONS IN TRANSFORMED ACUTE MYELOID LEUKEMIA. OBJECTIVES: OPTIMAL INTEGRATION OF NEXT-GENERATION SEQUENCING (NGS) INTO CLINICAL PRACTICE IN HEMATOLOGIC MALIGNANCIES REMAINS UNCLEAR. WE EVALUATE THE UTILITY OF NGS IN MYELOID MALIGNANCIES. METHODS: A 42-GENE PANEL WAS USED TO SEQUENCE 109 CASES OF MYELODYSPLASTIC SYNDROME (MDS, N = 38), CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML, N = 14), MYELOPROLIFERATIVE NEOPLASM (MPN, N = 24), AND MDS AND/OR MPN TRANSFORMED TO ACUTE MYELOID LEUKEMIA (AML, N = 33). RESULTS: AT LEAST ONE PATHOGENIC MUTATION WAS IDENTIFIED IN 74% OF CASES OF MDS, 100% OF CMMLS, AND 96% OF MPNS. IN CONTRAST, ONLY 47% OF CASES OF MDS (18/38) AND 7% (1/14) OF CMMLS EXHIBITED ABNORMAL CYTOGENETICS. IN DIAGNOSTICALLY DIFFICULT CASES OF MDS OR CMML WITH NORMAL CYTOGENETICS, NGS IDENTIFIED A PATHOGENIC MUTATION AND WAS CRITICAL IN ESTABLISHING THE CORRECT DIAGNOSIS. SPLICEOSOMAL GENES AND EPIGENETIC MODIFIERS WERE FREQUENTLY MUTATED. SPLICEOSOME MUTATIONS WERE ALSO FREQUENTLY DETECTED IN AML ARISING FROM MDS, CMML, OR MPN (39%) COMPARED WITH THE REPORTED RATE IN DE NOVO AML (7%-14%). CONCLUSIONS: IN DIFFICULT CASES OF MDS OR MPN, NGS FACILITATES DIAGNOSIS BY DETECTION OF GENE MUTATIONS TO CONFIRM CLONALITY, AND AMLS EVOLVING FROM MDS OR MPN CARRY FREQUENT MUTATIONS IN SPLICEOSOMAL GENES. 2016 19 4555 34 MUTATIONAL SPECTRUM ANALYSIS OF CHRONIC MYELOMONOCYTIC LEUKEMIA INCLUDES GENES ASSOCIATED WITH EPIGENETIC REGULATION: UTX, EZH2, AND DNMT3A. CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML), A MYELODYSPLASTIC/MYELOPROLIFERATIVE NEOPLASM, IS CHARACTERIZED BY MONOCYTIC PROLIFERATION, DYSPLASIA, AND PROGRESSION TO ACUTE MYELOID LEUKEMIA. CMML HAS BEEN ASSOCIATED WITH SOMATIC MUTATIONS IN DIVERSE RECENTLY IDENTIFIED GENES. WE ANALYZED 72 WELL-CHARACTERIZED PATIENTS WITH CMML (N = 52) AND CMML-DERIVED ACUTE MYELOID LEUKEMIA (N = 20) FOR RECURRENT CHROMOSOMAL ABNORMALITIES WITH THE USE OF ROUTINE CYTOGENETICS AND SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS ALONG WITH COMPREHENSIVE MUTATIONAL SCREENING. CYTOGENETIC ABERRATIONS WERE PRESENT IN 46% OF CASES, WHEREAS SINGLE NUCLEOTIDE POLYMORPHISM ARRAY INCREASED THE DIAGNOSTIC YIELD TO 60%. AT LEAST 1 MUTATION WAS FOUND IN 86% OF ALL CASES; NOVEL UTX, DNMT3A, AND EZH2 MUTATIONS WERE FOUND IN 8%, 10%, AND 5.5% OF PATIENTS, RESPECTIVELY. TET2 MUTATIONS WERE PRESENT IN 49%, ASXL1 IN 43%, CBL IN 14%, IDH1/2 IN 4%, KRAS IN 7%, NRAS IN 4%, AND JAK2 V617F IN 1% OF PATIENTS. VARIOUS MUTANT GENOTYPE COMBINATIONS WERE OBSERVED, INDICATING MOLECULAR HETEROGENEITY IN CMML. OUR RESULTS SUGGEST THAT MOLECULAR DEFECTS AFFECTING DISTINCT PATHWAYS CAN LEAD TO SIMILAR CLINICAL PHENOTYPES. 2011 20 4229 25 METHYLATION OF INK4 AND CIP/KIP FAMILIES OF CYCLIN-DEPENDENT KINASE INHIBITOR IN CHRONIC LYMPHOCYTIC LEUKAEMIA IN CHINESE PATIENTS. BACKGROUND: INK4 (P15, P16, P18 AND P19) AND CIP/KIP (P21, P27 AND P57) ARE TWO FAMILIES OF CYCLIN-DEPENDENT KINASE INHIBITORS (CKI) TARGETING CDK4/6 AND CDK2, RESPECTIVELY. AIM: TO STUDY THE ROLE OF METHYLATION IN THE INACTIVATION OF CKI IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL). MATERIALS AND METHODS: METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WAS CARRIED OUT ON DNA OBTAINED FROM THE BONE MARROW OF 56 NEWLY DIAGNOSED PATIENTS WITH CLL. RESULTS: SIMILAR DEMOGRAPHIC FEATURES AND CLINICAL OUTCOME WERE OBSERVED IN OUR PATIENTS WHEN COMPARED WITH CAUCASIAN PATIENTS, INCLUDING AN INDOLENT CLINICAL COURSE (10-YEAR OVERALL SURVIVAL 51%) AND ADVANCED RAI STAGE (P = 0.006), AND A HIGH-RISK KARYOTYPE SUCH AS TRISOMY 12 AND COMPLEX ABERRATIONS (P = 0.03). IN THE INK4 FAMILY, METHYLATION IN P15 AND P16 OCCURRED IN 20 (35.7%) AND 8 (14.3%) PATIENTS, RESPECTIVELY. IN ALL, 5 (8.9%) CLL SAMPLES HARBOURED CONCURRENT METHYLATION OF BOTH P15 AND P16. APART FROM AN ASSOCIATION OF P16 METHYLATION WITH HIGHER PRESENTING LEUCOCYTE COUNT (64.5 X 10(9)/L IN METHYLATED P16 AND 16.0 X 10(9)/L IN UNMETHYLATED P16 PATIENTS; P = 0.016), THERE WAS NO ASSOCIATION BETWEEN P15 AND P16 METHYLATION AND AGE, SEX AND RAI STAGE. NO DIFFERENCE WAS OBSERVED IN THE OVERALL SURVIVAL FOR PATIENTS WITH AND WITHOUT P15 AND P16 METHYLATION. BY CONTRAST, P18 AND RB WERE UNMETHYLATED IN ALL SAMPLES. IN THE CIP/KIP FAMILY, APART FROM INFREQUENT METHYLATION OF P57 IN 4 (7.1%) PATIENTS, METHYLATION OF P21 AND P27 WAS UNIFORMLY ABSENT. CONCLUSION: P15 AND, LESS FREQUENTLY, P16 OF THE INK4 FAMILY OF CKI, INSTEAD OF THE CIP OR KIP FAMILY, WERE TARGETED BY METHYLATION IN CLL. P16 METHYLATION WAS ASSOCIATED WITH A HIGHER LYMPHOCYTE COUNT AT PRESENTATION. THIS IS THE FIRST COMPREHENSIVE STUDY OF THE EPIGENETIC DYSREGULATION OF THE INK4 AND CIP/KIP FAMILIES OF CKI IN CHINESE PATIENTS WITH CLL. 2006