1   417 111 ANATOMIC SITE-SPECIFIC PATTERNS OF GENE COPY NUMBER GAINS IN SKIN, MUCOSAL, AND UVEAL MELANOMAS DETECTED BY FLUORESCENCE IN SITU HYBRIDIZATION. TO ASSESS THE DIFFERENCES BETWEEN MELANOMAS OF DIFFERENT LOCATION AND DIFFERENT ETIOLOGY, 372 MALIGNANT MELANOMAS WERE BROUGHT IN A TISSUE MICROARRAY FORMAT. THE COLLECTION INCLUDED 23 ACRAL AND 118 NON-ACRAL SKIN MELANOMAS, 9 MUCOSAL MELANOMAS, 100 UVEAL MELANOMAS, AND 122 MELANOMA METASTASES. FLUORESCENCE IN SITU HYBRIDIZATION (FISH) WAS USED TO ASSESS COPY NUMBER CHANGES OF THE CYCLIN D1 (CCND1), MDM2, C-MYC (MYC), AND HER2 GENES. FISH ANALYSIS REVEALED DISTINCT DIFFERENCES BETWEEN MELANOMAS FROM DIFFERENT LOCATIONS. CCND1 AMPLIFICATIONS WERE DETECTED IN SKIN MELANOMAS FROM SITES WITH CHRONIC SUN EXPOSURE (6 OF 32 CASES), ACRAL MELANOMAS (4 OF 17 CASES), AND MUCOSAL MELANOMAS (ONE OF TEN CASES) BUT NOT IN UVEAL MELANOMAS. HIGH-LEVEL MDM2 AMPLIFICATIONS WERE EXCLUSIVELY PRESENT IN ACRAL MELANOMAS (2 OF 19 CASES). MYC COPY NUMBER GAINS WERE DETECTED IN 32 OF 71 UVEAL MELANOMAS, FIVE OF EIGHT MUCOSAL MELANOMAS, AND 6 OF 67 MELANOMAS FROM SITES WITH INTERMITTENT SUN EXPOSURE BUT NOT IN ACRAL MELANOMAS NOR MELANOMAS FROM SITES WITH CHRONIC SUN EXPOSURE. ALTERATIONS OF THE MYC GENE WERE ASSOCIATED WITH ADVANCED TUMOR STAGE. THERE WERE NO HIGH-LEVEL HER2 AMPLIFICATIONS. SITE-SPECIFIC GENETIC AND EPIGENETIC FEATURES MAY IMPACT THE RESPONSE OF MELANOMAS TO VARIOUS ANTI-CANCER DRUGS AND SHOULD BE CONSIDERED IN FUTURE STUDIES ON THE MOLECULAR PATHOGENESIS OF MALIGNANT MELANOMAS.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
2  2830  26 FOCAL 9P INSTABILITY IN HEMATOLOGIC NEOPLASIAS REVEALED BY COMPARATIVE GENOMIC HYBRIDIZATION AND SINGLE-NUCLEOTIDE POLYMORPHISM MICROARRAY ANALYSES. COPY NUMBER LOSSES IN CHROMOSOME ARM 9P ARE WELL-KNOWN ABERRATIONS IN MALIGNANCIES, INCLUDING LEUKEMIAS. THE CDKN2A GENE IS SUGGESTED TO PLAY A KEY ROLE IN THESE ABERRATIONS. IN THIS STUDY OVERVIEWING 9P LOSSES IN HEMATOLOGIC NEOPLASIAS, WE INTRODUCE THE TERM FOCAL 9P INSTABILITY TO INDICATE MULTIPLE AREAS OF COPY NUMBER LOSS OR HOMOZYGOUS LOSS WITHIN A LARGER HETEROZYGOUS ONE IN 9P. WE HAVE USED MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION TO STUDY PATIENTS WITH ACUTE LYMPHOBLASTIC LEUKEMIA (ALL, N = 140), ACUTE MYELOID LEUKEMIA (N = 50), CHRONIC LYMPHOCYTIC LEUKEMIA (N = 20), AND MYELODYSPLASTIC SYNDROMES (N = 37). OUR RESULTS SHOW THAT 9P INSTABILITY IS RESTRICTED TO ALL. IN TOTAL, 58/140 (41%) PATIENTS WITH ALL HAD A LOSS IN 9P. THE 9P INSTABILITY WAS DETECTED IN 19% OF THE PATIENTS WITH ALL AND ALWAYS INCLUDED HOMOZYGOUS LOSS OF CDKN2A ALONG WITH LOSS OF CDKN2B. OTHER POSSIBLY IMPORTANT GENES INCLUDED MTAP, IFN, MLLT3, JAK2, PTPLAD2, AND PAX5. 13/27 (48%) PATIENTS WITH THE INSTABILITY HAD THE BCR/ABL1 FUSION GENE OR OTHER ONCOGENE-ACTIVATING TRANSLOCATION OR STRUCTURAL ABERRATIONS. TWO PATIENTS HAD HOMOZYGOUS LOSS OF HSA-MIR -31, A MICRORNA KNOWN TO REGULATE IKZF1. IKZF1 DELETION AT 7P12.1 WAS SEEN IN 10 (37%) PATIENTS WITH THE 9P INSTABILITY. THESE FINDINGS SUGGEST THAT, IN ALL LEUKEMOGENESIS, LOSS OF CDKN2A AND OTHER TARGET GENES IN THE INSTABILITY REGION IS FREQUENTLY ASSOCIATED WITH BCR/ABL1 AND IKZF1 DYSFUNCTION. THE MULTIPLE MECHANISMS LEADING TO 9P INSTABILITY INCLUDING PHYSICAL OR EPIGENETIC LOSS OF THE TARGET GENES, LOSS OF THE MICRORNA CLUSTER, AND THE ROLE OF FRA9G FRAGILE SITE ARE DISCUSSED.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
3  2261  18 EPIGENETIC PROFILE IN CHRONIC LYMPHOCYTIC LEUKEMIA USING METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION. AIM: TO ANALYZE THE METHYLATION STATUS OF 35 TUMOR SUPPRESSOR GENES USING METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (MS-MLPA) IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). MATERIALS & METHODS: THE DNA OF 37 SAMPLES FROM PATIENTS WITH CLL, SIX HEALTHY DONORS, AND JURKAT AND RAMOS CELL LINES WAS ANALYZED BY MS-MLPA. RESULTS: OUR RESULTS CONFIRM THAT HYPERMETHYLATION IS A COMMON AND NOT RANDOMLY DISTRIBUTED EVENT IN CLL, AND SOME GENES, SUCH AS WT1, CDH13, IGSF4/TSLC1, GATA5, DAPK1 AND RARB, ARE HYPERMETHYLATED IN MORE THAN 25% OF THE ANALYZED SAMPLES. IMPORTANTLY, MS-MLPA ALSO DETECTED HYPERMETHYLATION OF SOME GENES NOT REPORTED PREVIOUSLY IN CLL, AND THEIR METHYLATION STATUS WAS CONFIRMED BY BISULFITE SEQUENCING. CONCLUSION: THESE RESULTS INDICATE THAT MS-MLPA IS A USEFUL TECHNIQUE FOR THE DETECTION OF METHYLATION IN CLL SAMPLES. SELECTING CLL-SPECIFIC METHYLATION TARGETS IN ORDER TO GENERATE A CLL-SPECIFIC MS-MLPA PROBE SET COULD ENHANCE ITS USEFULNESS AS A TOOL IN STUDIES OF RISK STRATIFICATION AND GUIDING THE BEST THERAPEUTIC DECISION.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
4  4371  20 MIRNAS POTENTIALLY INVOLVED IN POST LUNG TRANSPLANT-OBLITERATIVE BRONCHIOLITIS: THE ROLE OF MIR-21-5P. EPIGENETIC CHANGES, INCLUDING MIRNAS DEREGULATION, HAVE BEEN SUGGESTED TO PLAY A SIGNIFICANT ROLE IN DEVELOPMENT OF OBLITERATIVE BRONCHIOLITIS (OB) IN TRANSPLANTED LUNGS. MANY STUDIES HAVE TRIED TO IDENTIFY IDEAL CANDIDATE MIRNAS AND THE DOWNSTREAM PATHWAYS IMPLICATED IN THE BRONCHIOLAR FIBRO-OBLITERATIVE PROCESS. SEVERAL CANDIDATE MIRNAS, PREVIOUSLY INDICATED AS POSSIBLY BEING ASSOCIATED WITH OB, WERE ANALYZED BY COMBINING THE QUANTITATIVE REAL TIME-POLYMERASE CHAIN REACTION (QRT-PCR) AND IN SITU HYBRIDIZATION (ISH) OF LUNG TISSUES OF OB AFFECTED PATIENTS. DISEASE AND OB-LESION-SPECIFIC EXPRESSION OF MIR-21-5P WAS CONFIRMED AND BY COMPUTATIONAL ANALYSIS WE WERE ABLE TO IDENTIFY THE NETWORK OF GENES MOST PROBABLY ASSOCIATED MIR-21-5P IN THE CONTEXT OF OB FIBROGENESIS. AMONG ALL POTENTIALLY ASSOCIATED GENES, STAT3 HAD A VERY HIGH PROBABILITY SCORE. IMMUNOHISTOCHEMISTRY SHOWED THAT STAT3/MIR-21-5P WERE CO-OVER EXPRESSED IN OB LESIONS, THUS, SUGGESTING MIR-21-5P COULD REGULATE STAT3 EXPRESSION. HOWEVER, MIR-21-5P INHIBITION IN CULTURES OF BRONCHIOLITIS OBLITERANS SYNDROME (BOS) DERIVED MYOFIBROBLASTS DID NOT SIGNIFICANTLY AFFECT STAT3 MRNA AND PROTEIN EXPRESSION LEVELS. THIS STUDY DEMONSTRATES THE SPECIFICITY OF MIR-21-5P OVER-EXPRESSION IN OB LESIONS AND CONTRIBUTES TO EXISTING KNOWLEDGE ON THE MIR-21-5P DOWNSTREAM PATHWAY. ACTIVATION OF STAT3 IS ASSOCIATED WITH MIR-21-5P UPREGULATION, HOWEVER, STAT-3 NETWORK ACTIVATION IS MOST LIKELY COMPLEX AND MIR-21-5P IS NOT THE SOLE REGULATOR OF STAT3.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
5  2678  18 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
6  4485  28 MOLECULAR SIMILARITY BETWEEN MYELODYSPLASTIC FORM OF CHRONIC MYELOMONOCYTIC LEUKEMIA AND REFRACTORY ANEMIA WITH RING SIDEROBLASTS. CHRONIC MYELOMONOCYTIC LEUKEMIA IS SIMILAR TO BUT A SEPARATE ENTITY FROM BOTH MYELOPROLIFERATIVE NEOPLASMS AND MYELODYSPLASTIC SYNDROMES, AND SHOWS EITHER MYELOPROLIFERATIVE OR MYELODYSPLASTIC FEATURES. WE ASK WHETHER THIS DISTINCTION MAY HAVE A MOLECULAR BASIS. WE ESTABLISHED THE GENE EXPRESSION PROFILES OF 39 SAMPLES OF CHRONIC MYELOMONOCYTIC LEUKEMIA (INCLUDING 12 CD34-POSITIVE) AND 32 CD34-POSITIVE SAMPLES OF MYELODYSPLASTIC SYNDROMES BY USING AFFYMETRIX MICROARRAYS, AND STUDIED THE STATUS OF 18 GENES BY SANGER SEQUENCING AND ARRAY-COMPARATIVE GENOMIC HYBRIDIZATION IN 53 SAMPLES. ANALYSIS OF 12 MRNAS FROM CHRONIC MYELOMONOCYTIC LEUKEMIA ESTABLISHED A GENE EXPRESSION SIGNATURE OF 122 PROBE SETS DIFFERENTIALLY EXPRESSED BETWEEN PROLIFERATIVE AND DYSPLASTIC CASES OF CHRONIC MYELOMONOCYTIC LEUKEMIA. AS COMPARED TO PROLIFERATIVE CASES, DYSPLASTIC CASES OVER-EXPRESSED GENES INVOLVED IN RED BLOOD CELL BIOLOGY. WHEN APPLIED TO 32 MYELODYSPLASTIC SYNDROMES, THIS GENE EXPRESSION SIGNATURE WAS ABLE TO DISCRIMINATE REFRACTORY ANEMIAS WITH RING SIDEROBLASTS FROM REFRACTORY ANEMIAS WITH EXCESS OF BLASTS. BY COMPARING MRNAS FROM THESE TWO FORMS OF MYELODYSPLASTIC SYNDROMES WE DERIVED A SECOND GENE EXPRESSION SIGNATURE. THIS SIGNATURE SEPARATED THE MYELODYSPLASTIC AND MYELOPROLIFERATIVE FORMS OF CHRONIC MYELOMONOCYTIC LEUKEMIAS. THESE RESULTS WERE VALIDATED USING TWO INDEPENDENT GENE EXPRESSION DATA SETS. WE FOUND THAT MYELODYSPLASTIC CHRONIC MYELOMONOCYTIC LEUKEMIAS ARE CHARACTERIZED BY MUTATIONS IN TRANSCRIPTION/EPIGENETIC REGULATORS (ASXL1, RUNX1, TET2) AND SPLICING GENES (SRSF2) AND THE ABSENCE OF MUTATIONS IN SIGNALING GENES. MYELODYSPLASTIC CHRONIC MYELOMONOCYTIC LEUKEMIAS AND REFRACTORY ANEMIAS WITH RING SIDEROBLASTS SHARE A COMMON EXPRESSION PROGRAM SUGGESTING THEY ARE PART OF A CONTINUUM, WHICH IS NOT TOTALLY EXPLAINED BY THEIR SIMILAR BUT NOT, HOWEVER, IDENTICAL MUTATION SPECTRUM.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7  2135  31 EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IN SERUM OF PATIENTS WITH CUTANEOUS MELANOMA. SMALL AMOUNTS OF CELL-FREE DNA CIRCULATE IN BOTH HEALTHY AND DISEASED HUMAN BLOOD, WHILE INCREASED CONCENTRATIONS OF DNA ARE PRESENT IN THE SERUM OF CANCER PATIENTS. TUMOR-SPECIFIC MUTATIONS OR EPIGENETIC MODIFICATIONS HAVE PREDOMINANTLY BEEN DETECTED IN TISSUE SPECIMENS. THE PURPOSE OF THIS STUDY WAS TO INVESTIGATE METHYLATION OF FIVE DIFFERENT GENES INVOLVED IN TUMOR SUPPRESSION AND DNA REPAIR (SUPPRESSORS OF CYTOKINE SIGNALING 1 AND 2 (SOCS1, SOCS2)), RAS-ASSOCIATION DOMAIN FAMILY PROTEIN 1A (RASSF1A), D-TYPE P16(INK4A) CYCLIN-DEPENDENT KINASE INHIBITOR (CDKN), AND O6-METHYLGUANINE DNA-METHYLTRANSFERASE (MGMT)) IN THE SERUM OF 100 PATIENTS USING METHYLATION-SPECIFIC PCR. IN ALL, 41 MELANOMA PATIENTS (STAGE I = 18; STAGE II = 10; STAGE III/IV = 13), 13 HEALTHY CONTROLS WITHOUT NEVI, AND 10 INDIVIDUALS WITH MORE THAN 15 NEVI OF >5 MM IN SIZE WERE INVESTIGATED. FOR COMPARISON, SERA FROM PATIENTS WITH OTHER SKIN TUMORS (NINE BASAL CELL CANCERS, FIVE KAPOSI'S SARCOMA), DIFFERENT METASTASIZED CANCERS (FIVE BREAST CANCERS, FIVE COLON CANCERS), AND SEVERAL CHRONIC INFLAMMATORY DISEASES (N = 12) WERE ALSO ANALYZED. IN ADDITION, WE EXAMINED IF METHYLATION WAS INVOLVED IN SILENCING TRANSCRIPTION OF THESE GENES IN 12 MELANOMA SPECIMENS. SOCS1, SOCS2, RASSF1A, CDKN2A, AND MGMT WERE METHYLATED IN 75, 43, 64, 75, AND 64% OF MELANOMA SAMPLES, RESPECTIVELY. OF THE 41 MELANOMA PATIENTS, 83% HAD ONE HYPERMETHYLATED GENE, WHILE 66, 51, AND 41% HAD TWO, THREE, OR FOUR HYPERMETHYLATED GENES, RESPECTIVELY. ALSO, 20% OF THESE PATIENTS SHOWED HYPERMETHYLATION FOR ALL GENES, WHILE ONLY 17% SHOWED NO METHYLATION. IMPORTANTLY, THE METHYLATION PROFILE OF THE SELECTED GENES FROM MELANOMA PATIENTS WAS DISTINCT FROM THE OTHER ANALYZED TUMORS. TRANSCRIPTION OF SOCS1, SOCS2, CDKN2A, AND RASSF1A GENES WAS SIGNIFICANTLY REDUCED IN FRESH MELANOMA SAMPLES, WHILE MGMT SHOWED A 12-FOLD UPREGULATION AT THE MESSENGER RIBONUCLEIC ACID LEVEL (P < 0.001). OUR FINDINGS SUGGEST THAT EPIGENETIC SILENCING OF THE STUDIED TUMOR SUPPRESSOR GENES IS A COMMON AND PROBABLY IMPORTANT MECHANISM FOR MELANOMA FORMATION. THIS CONVENIENT METHOD USING A SIMPLE BLOOD SAMPLE MAY CONTRIBUTE TO CLASSIFICATION OF MELANOMA AND AWAITS CLINICAL VALIDATION.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
8  2960  20 GENETIC AND EPIGENETIC MARKERS IN THE EVALUATION OF PANCREATIC MASSES. BACKGROUND: METHYLATION MARKERS HAVE SHOWN PROMISE IN THE EARLY DIAGNOSIS OF PANCREATIC CARCINOMA. THE AIM OF THIS STUDY WAS TO ASSESS THE DIAGNOSTIC UTILITY OF HYPERMETHYLATION STATUS OF CANDIDATE GENES IN COMBINATION WITH KRAS MUTATION DETECTION IN THE EVALUATION OF PANCREATIC MASSES. EXPERIMENTAL DESIGN: SIXTY-ONE FINE NEEDLE ASPIRATES OF PANCREATIC MASSES (43 PANCREATIC ADENOCARCINOMAS AND 18 CHRONIC PANCREATITIS) WERE STUDIED. METHYLATION STATUS OF HRH2, EN1, SPARC, CDH13 AND APC WERE ANALYSED USING MELTING CURVE ANALYSIS AFTER DNA BISULFITE TREATMENT. KRAS MUTATIONS WERE ALSO ANALYSED. RESULTS: THE METHYLATION PANEL HAD A SENSITIVITY OF 73% (27 OF 37, CI 95% 56 TO 86%) AND A SPECIFICITY OF 100% WHENEVER TWO OR MORE PROMOTERS WERE FOUND HYPERMETHYLATED. KRAS MUTATIONS SHOWED A SENSITIVITY OF 77% (33 OF 43, CI 95% 62 TO 88%) AND A SPECIFICITY OF 100%. BOTH MOLECULAR ANALYSES ADDED USEFUL INFORMATION TO CYTOLOGY BY INCREASING THE NUMBER OF INFORMATIVE CASES. WHEN GENETIC AND EPIGENETIC ANALYSES WERE COMBINED SENSITIVITY WAS 84% (36 OF 43 CI 95% 69 TO 93%) MAINTAINING A 100% SPECIFICITY. CONCLUSIONS: ANALYSIS OF HYPERMETHYLATION STATUS OF A PANEL OF GENES AND KRAS MUTATION DETECTION OFFER A SIMILAR DIAGNOSTIC YIELD IN THE EVALUATION OF PANCREATIC MASSES. THE COMBINED MOLECULAR ANALYSIS INCREASES THE NUMBER OF INFORMATIVE CASES WITHOUT DIMINISHING SPECIFICITY.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
9  3495  17 IDENTIFICATION OF MIRNAS POTENTIALLY INVOLVED IN BRONCHIOLITIS OBLITERANS SYNDROME: A COMPUTATIONAL STUDY. THE PATHOGENESIS OF BRONCHIOLITIS OBLITERANS SYNDROME (BOS), THE MAIN CLINICAL PHENOTYPE OF CHRONIC LUNG ALLOGRAFT DYSFUNCTION, IS POORLY UNDERSTOOD. RECENT STUDIES SUGGEST THAT EPIGENETIC REGULATION OF MICRORNAS MIGHT PLAY A ROLE IN ITS DEVELOPMENT. IN THIS PAPER WE PRESENT THE APPLICATION OF A COMPLEX COMPUTATIONAL PIPELINE TO PERFORM ENRICHMENT ANALYSIS OF MIRNAS IN PATHWAYS APPLIED TO THE STUDY OF BOS. THE ANALYSIS CONSIDERED THE FULL SET OF MIRNAS ANNOTATED IN MIRBASE (VERSION 21), AND APPLIED A SEQUENCE OF FILTERING APPROACHES AND STATISTICAL ANALYSES TO REDUCE THIS SET AND TO SCORE THE CANDIDATE MIRNAS ACCORDING TO THEIR POTENTIAL INVOLVEMENT IN BOS DEVELOPMENT. DYSREGULATION OF TWO OF THE SELECTED CANDIDATE MIRNAS-MIR-34A AND MIR-21 -WAS CLEARLY SHOWN IN IN-SITU HYBRIDIZATION (ISH) ON FIVE EXPLANTED HUMAN BOS LUNGS AND ON A RAT MODEL OF ACUTE AND CHRONIC LUNG REJECTION, THUS DEFINITELY IDENTIFYING MIR-34A AND MIR-21 AS PATHOGENIC FACTORS IN BOS AND CONFIRMING THE EFFECTIVENESS OF THE COMPUTATIONAL PIPELINE.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
10  2151  27 EPIGENETIC MECHANISM IN SEARCH FOR THE PATHOMECHANISM OF DIABETIC NEUROPATHY DEVELOPMENT IN DIABETES MELLITUS TYPE 1 (T1DM). OBJECTIVE: THE AIM OF THIS STUDY WAS TO CHECK THE HYPOTHESIS CONCERNING THE CRUCIAL ROLE OF DNA METHYLATION (ONE OF THE EPIGENETIC MECHANISMS) WITHIN SELECTED GENES RELATED TO THE DESTRUCTION AND REGENERATION OF NEURAL CELLS AND ITS INPUT IN THE PATHOGENESIS OF DIABETIC NEUROPATHY, USING A MODEL OF THE DNA IN PERIPHERAL BLOOD CELLS. METHODS: A CROSS-SECTIONAL, CASE-CONTROL STUDY WAS CONDUCTED, CONSISTING OF 24 ADULT TYPE 1 DIABETES MELITUS (T1DM) PATIENTS WITH AUTONOMIC NEUROPATHY (CAN), 25 T1DM PATIENTS WITHOUT NEUROPATHY AND 25 MATCHED, HEALTHY ADULTS ACTING AS A CONTROL (CTRL). THE EWING'S TESTS, USING THE PROSCICARD APPARATUS (MEWICON CATEEM-TEC GMBH), WAS EMPLOYED TO ASSESS THE SEVERITY OF THE PATIENTS' SYMPTOMS OF AUTONOMIC NEUROPATHY. FOR DNA METHYLATION ANALYSIS, DNA MATERIAL OF EACH SAMPLE DNA AFTER BISULFITE CONVERSION WAS USED FOR THE HYBRIDIZATION OF BEADCHIPS (INFINIUM METHYLATION EPIC KIT, ILLUMINA), AND IMAGED ON THE ILLUMINA HISCAN. THE CHANGES IN THE EXPRESSION OF SELECTED GENES WERE EXAMINED USING REAL-TIME PCR. PROBES WERE LABELED USING FLUORESCEIN AMIDITE, FAM (THERMO FISHER SCIENTIFIC). AMPLIFICATION WAS PERFORMED USING THE CONTINUOUS FLUORESCENCE DETECTION 7900 HT FAST REAL-TIME PCR SYSTEM (THERMO FISHER SCIENTIFIC). THE EXPRESSION RATIO OF THE TARGET MRNA WAS NORMALIZED TO THE LEVEL OF 18S RNA AND COMPARED WITH THE CONTROL. STATISTICAL ANALYSIS WAS PERFORMED USING STATISTICA VERSION 13.1. THE STATISTICALLY SIGNIFICANT RESULTS WERE RECOGNIZED, WITH A VALUE OF P < 0.05. RESULTS: CLINICAL ANALYSIS OF THE INVESTIGATED GROUPS REVEALED A SIGNIFICANTLY HIGHER PERCENTAGE OF PERSONAL INSULIN PUMP USERS IN THE GROUP WITHOUT NEUROPATHY. THE GLUCOSE METABOLIC CONTROL, BASED ON THE HBA1C LEVEL ANALYSIS, WAS ALSO SIGNIFICANTLY BETTER IN T1DM PATIENTS WITHOUT CAN. THE BUMPHUNTER METHOD FOR DNA METHYLATION ANALYSIS SHOWED STATISTICALLY SIGNIFICANT REGIONS RELATED TO THE GENES INVOLVED IN NERVE REGENERATION NINJURIN 2 (NINJ2) AND FUNCTIONALITY (BR SERINE/THREONINE KINASE 2 BRSK2, CLAUDIN 4 CLDN4). WHEN COMPARED WITH T1DM PATIENTS WITHOUT NEUROPATHY, T1DM PATIENTS WITH NEUROPATHY SHOWED SIGNIFICANTLY INCREASED METHYLATION IN THE FIRST NINJ2 AXON, AND A LOWER LEVEL OF DNA METHYLATION IN THE REGION OF THE FIRST INTRON OF BRSK2, AS WELL AS THE CLDN4 5'UTR REGIONS. THE QRT-PCR RESULTS CONFIRMED THE DECREASED EXPRESSION OF NINJ2 AND CLDN4 GENES IN PATIENTS WITH T1DM WITH CAN. CONCLUSIONS: THE DIFFERENT DNA METHYLATION PROFILES, CORRELATING WITH THE EXPRESSION OF GENES RELATED TO NERVOUS TISSUE DEVELOPMENT AND REGENERATION IN PATIENTS WITH T1DM WITH AUTONOMIC NEUROPATHY PROVIDE EVIDENCE FOR THE ROLE OF EPIGENETIC MECHANISMS PROMOTING THE DEVELOPMENT OF CAN, A CHRONIC COMPLICATION OF T1DM.	2020	

11  5979  21 TET2 MUTATIONS ARE ASSOCIATED WITH SPECIFIC 5-METHYLCYTOSINE AND 5-HYDROXYMETHYLCYTOSINE PROFILES IN PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA. CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) HAS RECENTLY BEEN ASSOCIATED WITH A HIGH INCIDENCE OF DIVERSE MUTATIONS IN GENES SUCH AS TET2 OR EZH2 THAT ARE IMPLICATED IN EPIGENETIC MECHANISMS. WE HAVE PERFORMED GENOME-WIDE DNA METHYLATION ARRAYS AND MUTATIONAL ANALYSIS OF TET2, IDH1, IDH2, EZH2 AND JAK2 IN A GROUP OF 24 PATIENTS WITH CMML. 249 GENES WERE DIFFERENTIALLY METHYLATED BETWEEN CMML PATIENTS AND CONTROLS. USING INGENUITY PATHWAY ANALYSIS, WE IDENTIFIED ENRICHMENT IN A GENE NETWORK CENTERED AROUND PLC, JNK AND ERK SUGGESTING THAT THESE PATHWAYS, WHOSE DEREGULATION HAS BEEN RECENTLY DESCRIBED IN CMML, ARE AFFECTED BY EPIGENETIC MECHANISMS. MUTATIONS OF TET2, JAK2 AND EZH2 WERE FOUND IN 15 PATIENTS (65%), 4 PATIENTS (17%) AND 1 PATIENT (4%) RESPECTIVELY WHILE NO MUTATIONS IN THE IDH1 AND IDH2 GENES WERE IDENTIFIED. INTERESTINGLY, PATIENTS WITH WILD TYPE TET2 CLUSTERED SEPARATELY FROM PATIENTS WITH TET2 MUTATIONS, SHOWED A HIGHER DEGREE OF HYPERMETHYLATION AND WERE ASSOCIATED WITH HIGHER RISK KARYOTYPES. OUR RESULTS DEMONSTRATE THE PRESENCE OF ABERRANT DNA METHYLATION IN CMML AND IDENTIFIES TET2 MUTANT CMML AS A BIOLOGICALLY DISTINCT DISEASE SUBTYPE WITH A DIFFERENT EPIGENETIC PROFILE.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
12   472  23 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
13  3506  29 IDENTIFICATION OF SPINAL CORD MICRORNA AND GENE SIGNATURES IN A MODEL OF CHRONIC STRESS-INDUCED VISCERAL HYPERALGESIA IN RAT. INTRODUCTION: ANIMAL STUDIES HAVE SHOWN THAT STRESS COULD INDUCE EPIGENETIC AND TRANSCRIPTOMIC ALTERATIONS ESSENTIAL IN DETERMINING THE BALANCE BETWEEN ADAPTIVE OR MALADAPTIVE RESPONSES TO STRESS. WE TESTED THE HYPOTHESIS THAT CHRONIC STRESS IN RATS DEREGULATES CODING AND NON-CODING GENE EXPRESSION IN THE SPINAL CORD, WHICH MAY UNDERLINE NEUROINFLAMMATION AND NOCICEPTIVE CHANGES PREVIOUSLY OBSERVED IN THIS MODEL. METHODS: MALE WISTAR RATS WERE EXPOSED TO DAILY STRESS OR HANDLED, FOR 10 DAYS. AT DAY 11, LUMBAR SPINAL SEGMENTS WERE COLLECTED AND PROCESSED FOR MRNA/MIRNA ISOLATION FOLLOWED BY EXPRESSION PROFILING USING AGILENT SUREPRINT RAT EXON AND RAT MIRNA MICROARRAY PLATFORMS. DIFFERENTIALLY EXPRESSED GENE LISTS WERE GENERATED USING THE DCHIP PROGRAM. MICROARRAYS WERE ANALYZED USING THE INGENUITY PATHWAYS ANALYSIS (IPA) TOOL FROM INGENUITY SYSTEMS. MULTIPLE METHODS WERE USED FOR THE ANALYSIS OF MIRNA-MRNA FUNCTIONAL MODULES. QUANTITATIVE REAL TIME RT-PCR FOR INTERLEUKIN 6 SIGNAL TRANSDUCER (GP130), THE SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3 (STAT3), GLIAL FIBRILLARY ACIDIC PROTEIN AND MIR-17-5P WERE PERFORMED TO CONFIRM LEVELS OF EXPRESSION. RESULTS: GENE NETWORK ANALYSIS REVEALED THAT STRESS DEREGULATED DIFFERENT INFLAMMATORY (IL-6, JAK/STAT, TNF) AND METABOLIC (PI3K/AKT) SIGNALING PATHWAYS. MICRORNA ARRAY ANALYSIS REVEALED A SIGNATURE OF 39 DEREGULATED MICRORNAS IN STRESSED RATS. MICRORNA-GENE NETWORK ANALYSIS SHOWED THAT MICRORNAS ARE REGULATORS OF TWO GENE NETWORKS RELEVANT TO INFLAMMATORY PROCESSES. SPECIFICALLY, OUR ANALYSIS OF MIRNA-MRNA FUNCTIONAL MODULES IDENTIFIED MIR-17-5P AS AN IMPORTANT REGULATOR IN OUR MODEL. WE VERIFIED MIR-17-5P INCREASED EXPRESSION IN STRESS USING QPCR AND IN SITU HYBRIDIZATION. IN ADDITION, WE OBSERVED CHANGES IN THE EXPRESSION OF GP130 AND STAT3 (INVOLVED IN INTRACELLULAR SIGNALING CASCADES IN RESPONSE TO GP130 ACTIVATION), BOTH PREDICTED TARGETS FOR MIR-17-5P. A MODULATORY ROLE OF SPINAL MIR17-5P IN THE MODULATION OF VISCERAL SENSITIVITY WAS CONFIRMED IN VIVO. CONCLUSION: USING AN INTEGRATIVE HIGH THROUGHPUT APPROACH, OUR FINDINGS SUGGEST A LINK BETWEEN MIR-17-5P INCREASED EXPRESSION AND GP130/STAT3 ACTIVATION PROVIDING NEW INSIGHT INTO THE POSSIBLE MECHANISMS MEDIATING THE EFFECT OF CHRONIC STRESS ON NEUROINFLAMMATION IN THE SPINAL CORD.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                       
14  1495  23 DNA HYPERMETHYLATION OF CELL CYCLE (P15 AND P16) AND APOPTOTIC (P14, P53, DAPK AND TMS1) GENES IN PERIPHERAL BLOOD OF LEUKEMIA PATIENTS. ABERRANT DNA METHYLATION OF TUMOR SUPPRESSOR GENES HAS BEEN REPORTED IN ALL MAJOR TYPES OF LEUKEMIA WITH POTENTIAL INVOLVEMENT IN THE INACTIVATION OF REGULATORY CELL CYCLE AND APOPTOSIS GENES. HOWEVER, MOST OF THE PREVIOUS REPORTS DID NOT SHOW THE EXTENT OF CONCURRENT METHYLATION OF MULTIPLE GENES IN THE FOUR LEUKEMIA TYPES. HERE, WE ANALYZED SIX KEY GENES (P14, P15, P16, P53, DAPK AND TMS1) FOR DNA METHYLATION USING METHYLATION SPECIFIC PCR TO ANALYZE PERIPHERAL BLOOD OF 78 LEUKEMIA PATIENTS (24 CML, 25 CLL, 12 AML, AND 17 ALL) AND 24 HEALTHY VOLUNTEERS. IN CML, METHYLATION WAS DETECTED FOR P15 (11%), P16 (9%), P53 (23%) AND DAPK (23%), IN CLL, P14 (25%), P15 (19%), P16 (12%), P53 (17%) AND DAPK (36%), IN AML, P14 (8%), P15 (45%), P53 (9%) AND DAPK (17%) AND IN ALL, P15 (14%), P16 (8%), AND P53 (8%). THIS STUDY HIGHLIGHTED AN ESSENTIAL ROLE OF DAPK METHYLATION IN CHRONIC LEUKEMIA IN CONTRAST TO P15 METHYLATION IN THE ACUTE CASES, WHEREAS TMS1 HYPERMETHYLATION WAS ABSENT IN ALL CASES. FURTHERMORE, HYPERMETHYLATION OF MULTIPLE GENES PER PATIENT WAS OBSERVED, WITH OBVIOUS SELECTIVENESS IN THE 9P21 CHROMOSOMAL REGION GENES (P14, P15 AND P16). INTERESTINGLY, METHYLATION OF P15 INCREASED THE RISK OF METHYLATION IN P53, AND VICE VERSA, BY FIVE FOLDS (P=0.03) INDICATING POSSIBLE SYNERGISTIC EPIGENETIC DISRUPTION OF DIFFERENT PHASES OF THE CELL CYCLE OR BETWEEN THE CELL CYCLE AND APOPTOSIS. THE INVESTIGATION OF MULTIPLE RELATIONSHIPS BETWEEN METHYLATED GENES MIGHT SHED LIGHT ON TUMOR SPECIFIC INACTIVATION OF THE CELL CYCLE AND APOPTOTIC PATHWAYS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
15  1107  23 COMBINING CYTOGENETIC AND EPIGENETIC APPROACHES IN CHRONIC LYMPHOCYTIC LEUKEMIA IMPROVES PROGNOSIS PREDICTION FOR PATIENTS WITH ISOLATED 13Q DELETION. BACKGROUND: BOTH DEFECTIVE DNA METHYLATION AND ACTIVE DNA DEMETHYLATION PROCESSES ARE EMERGING AS IMPORTANT RISK FACTORS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). HOWEVER, ASSOCIATIONS BETWEEN 5-CYTOSINE EPIGENETIC MARKERS AND THE MOST FREQUENT CHROMOSOMAL ABNORMALITIES DETECTED IN CLL REMAIN TO BE ESTABLISHED. METHODS: CLL PATIENTS WERE RETROSPECTIVELY CLASSIFIED INTO A CYTOGENETIC LOW-RISK GROUP (ISOLATED 13Q DELETION), AN INTERMEDIATE-RISK GROUP (NORMAL KARYOTYPE OR TRISOMY 12), AND A HIGH-RISK GROUP (11Q DELETION, 17P DELETION, OR COMPLEX KARYOTYPE [>/= 3 BREAKPOINTS]). THE TWO 5-CYTOSINE DERIVATIVES, 5-METHYLCYTOSINE (5-MCYT) AND 5-HYDROXYMETHYLCYTOSINE (5-HMCYT), WERE TESTED BY ELISA (N = 60), WHILE REAL-TIME QUANTITATIVE PCR WAS USED FOR DETERMINING TRANSCRIPTIONAL EXPRESSION LEVELS OF DNMT AND TET (N = 24). RESULTS: BY USING GLOBAL DNA METHYLATION/DEMETHYLATION LEVELS, IN THE LOW-RISK DISEASE GROUP, TWO SUBGROUPS WITH SIGNIFICANTLY DIFFERENT CLINICAL OUTCOMES HAVE BEEN IDENTIFIED (MEDIAN TREATMENT-FREE SURVIVAL [TFS] 45 VERSUS > 120 MONTHS FOR 5-MCYT, P = 0.0008, AND 63 VERSUS > 120 MONTHS FOR 5-HMCYT, P = 0.04). A DEFECTIVE 5-MCYT STATUS WAS FURTHER ASSOCIATED WITH A HIGHER PERCENTAGE OF 13Q DELETED NUCLEI (> 80%), THUS SUGGESTING AN ACQUIRED PROCESS. WHEN CONSIDERING THE CYTOGENETIC INTERMEDIATE/HIGH-RISK DISEASE GROUPS, AN ASSOCIATION OF 5-MCYT STATUS WITH LYMPHOCYTOSIS (P = 0.0008) AND THE LYMPHOCYTE DOUBLING TIME (P = 0.04) BUT NOT WITH TFS WAS OBSERVED, AS WELL AS A REDUCTION OF DNMT3A, TET1, AND TET2 TRANSCRIPTS. CONCLUSIONS: COMBINING CYTOGENETIC STUDIES WITH 5-MCYT ASSESSMENT ADDS ACCURACY TO CLL PATIENTS' PROGNOSES AND PARTICULARLY FOR THOSE WITH 13Q DELETION AS A SOLE CYTOGENETIC ABNORMALITY.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
16  6415  26 THE STUDY OF P16 AND P15 GENE METHYLATION IN HEAD AND NECK SQUAMOUS CELL CARCINOMA AND THEIR QUANTITATIVE EVALUATION IN PLASMA BY REAL-TIME PCR. EPIGENETIC SILENCING OF THE P16 AND P15 GENES BY PROMOTER METHYLATION ARE COMMONLY OBSERVED IN HUMAN EPITHELIAL MALIGNANCIES, INCLUDING HEAD AND NECK SQUAMOUS CELL CARCINOMAS (HNSCC). IN THIS STUDY, A METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) WAS USED TO EVALUATE THE METHYLATION STATUS OF THE P16 AND P15 GENES IN 73 HNSCC SURGICAL SPECIMENS. P16 AND P15 GENE METHYLATION WAS ALSO EXAMINED IN 29 PAIRED METASTATIC LYMPH NODES AND 29 PAIRED HISTOLOGICALLY, NORMAL RESECTION MARGIN MUCOSAE. THE QUANTITY OF CELL-FREE METHYLATED P16 AND P15 DNA IN THE PLASMA SAMPLES OF 20 HNSCC PATIENTS AND 24 HEALTHY CONTROLS WAS ALSO EXAMINED USING A FLUORESCENCE-BASED REAL-TIME PCR ASSAY. THE FREQUENCIES OF P16 AND P15 METHYLATION IN THE PRIMARY TUMOUR WERE 49% AND 60%, RESPECTIVELY. CONCORDANT METHYLATION OF P16 AND P15 IN TUMOUR SAMPLES AND METASTATIC LYMPH NODES WAS FOUND IN 59 AND 38% OF CASES, RESPECTIVELY. A SIGNIFICANTLY HIGHER PREVALENCE OF P15 METHYLATION WAS FOUND IN HISTOLOGICALLY-NORMAL SURGICAL MARGIN EPITHELIA OF HNSCC PATIENTS WITH CHRONIC SMOKING AND DRINKING HABITS COMPARED WITH NON-SMOKERS AND NON-DRINKERS. IN ADDITION, METHYLATED P16 AND P15 DNA LEVELS WERE SIGNIFICANTLY HIGHER IN THE PLASMA OF HNSCC PATIENTS (MEAN 56 COPIES/ML PLASMA AND 65 COPIES/ML PLASMA, RESPECTIVELY) COMPARED WITH NORMAL CONTROLS (MEAN 6 COPIES/ML PLASMA AND 16 COPIES/ML PLASMA, RESPECTIVELY). IN CONCLUSION, PROMOTER METHYLATION OF THE P16 AND P15 GENES IS INVOLVED IN THE PATHOGENESIS OF HNSCC AND MAY BE RELATED TO CHRONIC SMOKING AND DRINKING. THE DIFFERENTIAL LEVELS OF METHYLATED P16 AND P15 DNA IN PLASMA MIGHT BE POTENTIAL USEFUL MARKERS IN SCREENING HIGH-RISK POPULATIONS FOR EARLY HNSCC AND MONITORING THEIR TREATMENT RESPONSE.	2003	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
17  4555  22 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
18  4349  22 MIR-155 AND MIR-122 EXPRESSION OF SPERMATOZOA IN OBESE SUBJECTS. OBESITY IS CHARACTERIZED BY MILD CHRONIC INFLAMMATION THAT IS LINKED WITH IMPAIRED IRON HOMEOSTASIS. STUDIES IN HUMAN AND MURINE SHOW THAT THERE IS A TRANSGENERATIONAL EPIGENETIC INHERITANCE VIA THE GAMETES IN OBESITY; HOWEVER, THERE IS LITTLE INFORMATION ON CHANGES IN THE EXPRESSION OF MICRORNAS RELATED TO INFLAMMATION AND IRON HOMEOSTASIS IN SPERMATOZOA FROM OBESE SUBJECTS. THE PRESENT STUDY INVESTIGATED THE EXPRESSION OF MICRORNAS RELATED TO INFLAMMATION (MIR-21 Y MIR-155) AND IRON NUTRITION (MIR-122 AND MIR-200B) IN PLASMA, PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC) AND SPERMATOZOA FROM NORMOZOOSPERMIC CONTROLS (CN; N = 17; BMI: 24.6 +/- 2.0) AND OBESE (OB; N = 17; BMI: 32.6 +/- 4.4) MEN. TO DETERMINE THE INFLAMMATION LEVELS, WE MEASURED IL-6, TNF-ALPHA, AND MONOCYTE CHEMOATTRACTANT PROTEIN-1 (MCP1) BY MAGNETIC LUMINEX((R)) ASSAY. MRNA EXPRESSION OF IL6, TNF-ALPHA, AND HEPCIDIN (HAMP) IN PBMC WERE EVALUATED BY RT-QPCR. THE ANALYSIS OF MICRORNAS WAS PERFORMED USING THE TAQMAN((R)) ASSAYS. THE IRON CONTENT IN PBMC, SEMINAL PLASMA, AND SPERMATOZOA WAS DETERMINED BY INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (ICP-MS). HIGH SERUM IL6, TNF-ALPHA, AND MCP1 LEVELS WERE OBSERVED IN OB GROUP (P < 0.05). GENE EXPRESSION ANALYSIS SHOWED AN INCREASED ABUNDANCE RELATIVE OF TNF-ALPHA (P = 0.018), HAMP (P = 0.03), AND IL6 (P = 0.02) IN PBMC FROM OBESE SUBJECTS. ALSO, WE OBSERVED HIGH LEVELS OF SERUM FERRITIN (P = 0.03), IRON CONTENT IN SEMINAL PLASMA (P = 0.04), AND SPERMATOZOA (P = 0.002), BUT LOWER SERUM FE (P = 0.007) IN OBESE SUBJECTS. IN THE OB GROUP, A HIGH EXPRESSION OF MIR-155 (P = 0.02) AND MIR-21 (P = 0.03) WAS OBSERVED IN PBMC AND MIR-122 (P = 0.03) IN PLASMA. IN SPERM, BOTH MIR-155 (P = 0.004) AND MIR-122 (P = 0.028) WERE HIGH IN THE OB GROUP. OUR RESULTS SHOWED THAT OBESE SUBJECTS HAVE INCREASED EXPRESSIONS OF MIR-155 AND MIR-122, TWO MICRORNAS THAT WERE PREVIOUSLY RELATED WITH INFLAMMATION AND IRON METABOLISM, RESPECTIVELY, AT BOTH THE SYSTEMIC AND SPERM LEVELS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
19  1433  26 DIFFERENTIAL GENOME-WIDE ARRAY-BASED METHYLATION PROFILES IN PROGNOSTIC SUBSETS OF CHRONIC LYMPHOCYTIC LEUKEMIA. GLOBAL HYPOMETHYLATION AND REGIONAL HYPERMETHYLATION ARE WELL-KNOWN EPIGENETIC FEATURES OF CANCER; HOWEVER, IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), STUDIES ON GENOME-WIDE EPIGENETIC MODIFICATIONS ARE LIMITED. HERE, WE ANALYZED THE GLOBAL METHYLATION PROFILES IN CLL, BY APPLYING HIGH-RESOLUTION METHYLATION MICROARRAYS (27,578 CPG SITES) TO 23 CLL SAMPLES, BELONGING TO THE IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE (IGHV) MUTATED (FAVORABLE) AND IGHV UNMUTATED/IGHV3-21 (POOR-PROGNOSTIC) SUBSETS. OVERALL, RESULTS DEMONSTRATED SIGNIFICANT DIFFERENCES IN METHYLATION PATTERNS BETWEEN THESE SUBGROUPS. SPECIFICALLY, IN IGHV UNMUTATED CLL, WE IDENTIFIED METHYLATION OF 7 KNOWN OR CANDIDATE TUMOR SUPPRESSOR GENES (EG, VHL, ABI3, AND IGSF4) AS WELL AS 8 UNMETHYLATED GENES INVOLVED IN CELL PROLIFERATION AND TUMOR PROGRESSION (EG, ADORA3 AND PRF1 ENHANCING THE NUCLEAR FACTOR-KAPPAB AND MITOGEN-ACTIVATED PROTEIN KINASE PATHWAYS, RESPECTIVELY). IN CONTRAST, THESE LATTER GENES WERE SILENCED BY METHYLATION IN IGHV MUTATED PATIENTS. THE ARRAY DATA WERE VALIDATED FOR SELECTED GENES USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION, QUANTITATIVE REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION, AND BISULFITE SEQUENCING. FINALLY, THE SIGNIFICANCE OF DNA METHYLATION IN REGULATING GENE PROMOTERS WAS SHOWN BY REINDUCING 4 METHYLATED TUMOR SUPPRESSOR GENES (EG, VHL AND ABI3) IN IGHV UNMUTATED SAMPLES USING THE METHYL-INHIBITOR 5-AZA-2'-DEOXYCYTIDINE. TAKEN TOGETHER, OUR DATA FOR THE FIRST TIME REVEAL DIFFERENCES IN GLOBAL METHYLATION PROFILES BETWEEN PROGNOSTIC SUBSETS OF CLL, WHICH MAY UNFOLD EPIGENETIC SILENCING MECHANISMS INVOLVED IN CLL PATHOGENESIS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
20   401  23 ANALYSIS OF ABERRANT METHYLATION ON PROMOTER SEQUENCES OF TUMOR SUPPRESSOR GENES AND TOTAL DNA IN SPUTUM SAMPLES: A PROMISING TOOL FOR EARLY DETECTION OF COPD AND LUNG CANCER IN SMOKERS. BACKGROUND: CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A DISORDER ASSOCIATED TO CIGARETTE SMOKE AND LUNG CANCER (LC). SINCE EPIGENETIC CHANGES IN ONCOGENES AND TUMOR SUPPRESSOR GENES (TSGS) ARE CLEARLY IMPORTANT IN THE DEVELOPMENT OF LC. IN THIS STUDY, WE HYPOTHESIZE THAT TOBACCO SMOKERS ARE SUSCEPTIBLE FOR METHYLATION IN THE PROMOTER REGION OF TSGS IN AIRWAY EPITHELIAL CELLS WHEN COMPARED WITH NON-SMOKER SUBJECTS. THE PURPOSE OF THIS STUDY WAS TO INVESTIGATE THE USEFULNESS OF DETECTION OF GENES PROMOTER METHYLATION IN SPUTUM SPECIMENS, AS A COMPLEMENTARY TOOL TO IDENTIFY LC BIOMARKERS AMONG SMOKERS WITH EARLY COPD. METHODS: WE DETERMINED THE AMOUNT OF DNA IN INDUCED SPUTUM FROM PATIENTS WITH COPD (N = 23), LC (N = 26), AS WELL AS IN HEALTHY SUBJECTS (CTR) (N = 33), USING A COMMERCIAL KIT FOR DNA PURIFICATION, FOLLOWED BY ABSORBANCE MEASUREMENT AT 260 NM. THE FREQUENCY OF CDKN2A, CDH1 AND MGMT PROMOTER METHYLATION IN THE SAME GROUPS WAS DETERMINED BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP). THE FISHER'S EXACT TEST WAS EMPLOYED TO COMPARE FREQUENCY OF RESULTS BETWEEN DIFFERENT GROUPS. RESULTS: DNA CONCENTRATION WAS 7.4 AND 5.8 TIMES HIGHER IN LC AND COPD COMPARED TO THE (CTR) (P < 0.0001), RESPECTIVELY. METHYLATION STATUS OF CDKN2A AND MGMT WAS SIGNIFICANTLY HIGHER IN COPD AND LC PATIENTS COMPARED WITH CTR GROUP (P < 0.0001). FREQUENCY OF CDH1 METHYLATION ONLY SHOWED A STATISTICALLY SIGNIFICANT DIFFERENCE BETWEEN LC PATIENTS AND CTR GROUP (P < 0.05). CONCLUSIONS: WE PROVIDE EVIDENCE THAT ABERRANT METHYLATION OF TSGS IN SAMPLES OF INDUCED SPUTUM IS A USEFUL TOOL FOR EARLY DIAGNOSTIC OF LUNG DISEASES (LC AND COPD) IN SMOKER SUBJECTS. VIRTUAL SLIDES: THE ABSTRACT MUST FINISH WITH THE FOLLOWING TEXT: VIRTUAL SLIDES THE VIRTUAL SLIDE(S) FOR THIS ARTICLE CAN BE FOUND HERE: HTTP://WWW.DIAGNOSTICPATHOLOGY.DIAGNOMX.EU/VS/1127865005664160.	2012