1 4248 130 METHYLATION STATUS, MRNA AND PROTEIN EXPRESSION OF THE SMAD4 GENE IN PATIENTS WITH NON-MELANOCYTIC SKIN CANCERS. BACKGROUND: SMAD4 IS A POTENT TUMOR SUPPRESSOR. SMAD4 LOSS INCREASES GENOMIC INSTABILITY AND PLAYS A CRITICAL ROLE IN THE DNA DAMAGE RESPONSE THAT LEADS TO SKIN CANCER DEVELOPMENT. WE AIMED TO INVESTIGATE SMAD4 METHYLATION EFFECTS ON MRNA AND PROTEIN EXPRESSION OF SMAD4 IN CANCER AND HEALTHY TISSUES FROM PATIENTS WITH BASAL CELL CARCINOMA (BCC), CUTANEOUS SQUAMOUS CELL CARCINOMA (CSCC), AND BASOSQUAMOUS SKIN CANCER (BSC). METHODS AND RESULTS: THE STUDY INCLUDED 17 BCC, 24 CSCC AND NINE BSC PATIENTS. DNA AND RNA WERE ISOLATED FROM CANCEROUS AND HEALTHY TISSUES FOLLOWING PUNCH BIOPSY. METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) AND REAL-TIME QUANTITATIVE PCR METHODS WERE USED TO EXAMINE SMAD4 PROMOTER METHYLATION AND SMAD4 MRNA LEVELS, RESPECTIVELY. THE PERCENTAGE AND INTENSITY OF STAINING OF THE SMAD4 PROTEIN WERE DETERMINED BY IMMUNOHISTOCHEMISTRY. THE PERCENTAGE OF SMAD4 METHYLATION WAS INCREASED IN THE PATIENTS WITH BCC (P = 0.007), CSCC (P = 0.004), AND BSC (P = 0.018) COMPARED TO THE HEALTHY TISSUE. SMAD4 MRNA EXPRESSION WAS DECREASED IN THE PATIENTS WITH BCC (P<0.001), CSCC (P<0.001), AND BSC (P = 0.008). THE STAINING CHARACTERISTIC OF SMAD4 PROTEIN WAS NEGATIVE IN THE CANCER TISSUES OF THE PATIENTS WITH CSCC (P = 0.00). LOWER SMAD4 MRNA LEVELS WERE OBSERVED IN THE POORLY DIFFERENTIATED CSCC PATIENTS (P = 0.001). THE STAINING CHARACTERISTICS OF THE SMAD4 PROTEIN WERE RELATED TO AGE AND CHRONIC SUN EXPOSURE. CONCLUSIONS: HYPERMETHYLATION OF SMAD4 AND REDUCED SMAD4 MRNA EXPRESSION WERE FOUND TO PLAY A ROLE IN THE PATHOGENESIS OF BCC, CSCC, AND BSC. A DECREASE IN SMAD4 PROTEIN EXPRESSION LEVEL WAS OBSERVED ONLY IN CSCC PATIENTS. THIS SUGGESTS THAT EPIGENETIC ALTERATIONS TO THE SMAD4 GENE ARE ASSOCIATED WITH CSCC. TRIAL REGISTRATION: THE NAME OF THE TRIAL REGISTER: SMAD4 METHYLATION AND EXPRESSION LEVELS IN NON-MELANOCYTIC SKIN CANCERS; SMAD4 PROTEIN POSITIVITY. THE REGISTRATION NUMBER: NCT04759261 ( HTTPS://CLINICALTRIALS.GOV/CT2/RESULTS?TERM=NCT04759261 ). 2023 2 1284 26 DECIPHERING THE MOLECULAR LANDSCAPE OF CUTANEOUS SQUAMOUS CELL CARCINOMA FOR BETTER DIAGNOSIS AND TREATMENT. CUTANEOUS SQUAMOUS CELL CARCINOMA (CSCC) IS A COMMON TYPE OF NEOPLASIA, REPRESENTING A TERRIBLE BURDEN ON PATIENTS' LIFE AND CLINICAL MANAGEMENT. ALTHOUGH IT SELDOM METASTASIZES, AND MOST CASES CAN BE EFFECTIVELY TREATED WITH SURGICAL INTERVENTION, ONCE METASTATIC CSCC DISPLAYS CONSIDERABLE AGGRESSIVENESS LEADING TO THE DEATH OF AFFECTED INDIVIDUALS. NO CONSENSUS HAS BEEN REACHED AS TO WHICH FEATURES BETTER CHARACTERIZE THE AGGRESSIVE BEHAVIOR OF CSCC, AN ACHIEVEMENT HINDERED BY THE HIGH MUTATIONAL BURDEN CAUSED BY CHRONIC ULTRAVIOLET LIGHT EXPOSURE. EVEN THOUGH SOME SUBTYPES HAVE BEEN RECOGNIZED AS HIGH RISK VARIANTS, DEPENDING ON CERTAIN TUMOR FEATURES, CSCC THAT ARE NORMALLY THOUGHT OF AS LOW RISK COULD POSE AN INCREASED DANGER TO THE PATIENTS. IN LIGHT OF THIS, SPECIFIC GENETIC AND EPIGENETIC MARKERS FOR CUTANEOUS SCC, WHICH COULD SERVE AS RELIABLE DIAGNOSTIC MARKERS AND POSSIBLE TARGETS FOR NOVEL TREATMENT DEVELOPMENT, HAVE BEEN SEARCHED FOR. THIS REVIEW AIMS TO GIVE AN OVERVIEW OF THE MUTATIONAL LANDSCAPE OF CSCC, POINTING OUT ESTABLISHED BIOMARKERS, AS WELL AS NOVEL CANDIDATES, AND FUTURE POSSIBLE MOLECULAR THERAPIES FOR CSCC. 2020 3 6655 25 UPDATE ON THE MOLECULAR PATHOLOGY OF CUTANEOUS SQUAMOUS CELL CARCINOMA. CUTANEOUS SQUAMOUS CELL CARCINOMA (CSCC) IS THE SECOND MOST COMMON SKIN CANCER, ORIGINATING FROM KERATINOCYTES OF THE SPINOUS LAYER. NUMEROUS RISK FACTORS HAVE BEEN DISCOVERED FOR THE INITIATION AND GROWTH OF THIS TYPE OF CANCER, SUCH AS EXPOSURE TO UV AND IONIZING RADIATION, CHEMICAL CARCINOGENS, THE PRESENCE OF IMMUNOSUPPRESSION STATES, CHRONIC INFLAMMATION, INFECTIONS WITH HIGH-RISK VIRAL STRAINS, AND, LAST BUT NOT LEAST, THE PRESENCE OF DISEASES ASSOCIATED WITH GENETIC ALTERATIONS. THE IMPORTANT SOCIO-ECONOMIC IMPACT, AS WELL AS THE DIFFICULTY ASSOCIATED WITH THERAPY FOR ADVANCED FORMS, HAS MADE THE MOLECULAR MECHANISMS UNDERLYING THIS NEOPLASIA MORE AND MORE INTENSIVELY STUDIED, WITH THE INTENTION OF ACHIEVING A BETTER UNDERSTANDING AND ADVANCING THE TREATMENT OF THIS PATHOLOGY. THIS REVIEW AIMS TO PROVIDE A BRIEF FORAY INTO THE MOLECULAR, GENETIC, AND EPIGENETIC ASPECTS OF THIS CANCER, AS WELL AS THE TREATMENT METHODS, RANGING FROM THE FIRST USED TO THE LATEST TARGETED THERAPIES. 2023 4 564 42 BASAL CELL CARCINOMAS OF THE SCALP AFTER RADIOTHERAPY FOR TINEA CAPITIS IN CHILDHOOD: A GENETIC AND EPIGENETIC STUDY WITH COMPARISON WITH BASAL CELL CARCINOMAS EVOLVING IN CHRONICALLY SUN-EXPOSED AREAS. BACKGROUND: BASAL CELL CARCINOMA (BCC) HAS BEEN MOSTLY ASSOCIATED WITH SUN EXPOSURE, BUT IONIZING RADIATION IS ALSO A KNOWN RISK FACTOR. IT IS NOT CLEAR IF THE PATHOGENESIS OF BCC, NAMELY AT A GENOMIC AND EPIGENETIC LEVEL, DIFFERS ACCORDING TO THE UNDERLYING TRIGGERING FACTORS. OBJECTIVE: THE PRESENT STUDY AIMS TO COMPARE GENETIC AND EPIGENETIC CHANGES IN BCCS RELATED TO IONIZING RADIATION AND CHRONIC SUN EXPOSURE. METHODS: TUMOR SAMPLES FROM BCCS OF THE SCALP IN PATIENTS SUBMITTED TO RADIOTHERAPY TO TREAT TINEA CAPITIS IN CHILDHOOD AND BCCS FROM SUN-EXPOSED AREAS WERE ANALYSED THROUGH ARRAY COMPARATIVE GENOMIC HYBRIDIZATION (ARRAY-CGH) AND METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (MS-MLPA) TO DETECT COPY NUMBER ALTERATIONS AND METHYLATION STATUS OF SPECIFIC GENES. RESULTS: GENOMIC CHARACTERIZATION OF TUMOR SAMPLES REVEALED SEVERAL COPY NUMBER GAINS AND LOSSES IN ALL CHROMOSOMES, WITH THE MOST FREQUENT GAINS OBSERVED AT 2P, 6P, 12P, 14Q, 15Q, 18Q, XP AND YP, AND THE MOST FREQUENT LOSSES OBSERVED AT 3Q, 14Q, 16P, 17Q, 22Q, XP, YP AND YQ. WE DEVELOPED A STATISTICAL MODEL, ENCOMPASSING GAINS IN 3P AND 16P AND LOSSES IN 14Q AND 20P, WITH POTENTIAL TO DISCRIMINATE BCC SAMPLES WITH SPORADIC AETIOLOGY FROM BCC SAMPLES THAT EVOLVE AFTER RADIOTHERAPY IN CHILDHOOD FOR THE TREATMENT OF TINEA CAPITIS, WHICH PRESENTED STATISTICAL SIGNIFICANCE (P = 0.003). FEW METHYLATED GENES WERE DETECTED THROUGH MS-MLPA, MOST FREQUENTLY RARB AND CD44. CONCLUSIONS: OUR STUDY REPRESENTS A STEP FORWARD IN THE UNDERSTANDING OF THE GENETIC MECHANISMS UNDERLYING THE PATHOGENESIS OF BCC AND SUGGESTS POTENTIAL DIFFERENCES ACCORDING TO THE UNDERLYING RIS K FACTORS. 2021 5 1065 42 CLINICAL SIGNIFICANCE OF SERUM DRAM1 MRNA, ARSA MRNA, HSA-MIR-2053 AND LNCRNA-RP1-86D1.3 AXIS EXPRESSION IN MALIGNANT PLEURAL MESOTHELIOMA. AIM AND BACKGROUND: MALIGNANT PLEURAL MESOTHELIOMA (MPM) IS A LETHAL CANCER MAINLY CAUSED BY CHRONIC EXPOSURE OF ASBESTOS. IN THIS PILOT STUDY, WE AIMED TO ASSESS THE EXPRESSION OF SERUM RNA-BASED BIOMARKER PANEL EXPLORING THEIR CLINICAL UTILITY AS DIAGNOSTIC AND PROGNOSTIC BIOMARKERS FOR MPM. METHODS: WE HAVE SELECTED AN MPM-SPECIFIC RNA-BASED BIOMARKER PANEL THROUGH BIOINFORMATICS ANALYSIS BASED ON THE INTEGRATION OF DNA DAMAGE REGULATED AUTOPHAGY MODULATOR 1 (DRAM1) AND ARYLSULFATASE A ( ARSA) GENE EXPRESSION WITH THEIR EPIGENETIC REGULATORS MICRORNA ( MIR-2053) AND LONG NONCODING RNA ( LNCRNA-RP1-86D1.3). THEN, QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (QPCR) VALIDATION IN SERA OF 60 MPM PATIENTS, 20 CHRONIC ASBESTOS EXPOSURE PATIENTS, AND 20 HEALTHY VOLUNTEERS WAS DONE. LASTLY, THE PROGNOSTIC POWER OF THE SELECTED PANEL WAS ASSESSED. RESULTS: THE EXPRESSION OF SERUM DRAM1 MESSENGER RNA (MRNA), ARSA MRNA, HSA-MIR-2053 AND LNCRNA-RP1-86D1.3 WERE POSITIVE IN 78.3%, 90%, 85%, AND 83.3% OF MPM PATIENTS, RESPECTIVELY. THE RNA-BASED BIOMARKER PANEL WAS ABLE TO DISCRIMINATE BETWEEN MPM PATIENTS AND CONTROLS WITH HIGH ACCURACY AND THEIR COMBINED SENSITIVITY REACHED 100% FOR THE DIAGNOSIS OF MPM. KAPLAN-MEIER ANALYSIS SHOWED THAT HSA-MIR-2053 IS AN INDEPENDENT PROGNOSTIC FACTOR OF MPM. CONCLUSION: OUR PRELIMINARY DATA REVEALED THAT THE CHOSEN RNAS PLAY AN IMPORTANT ROLE IN DRIVING MPM DEVELOPMENT AND PROGRESSION. 2019 6 5289 45 PROSTANOID RECEPTOR GENES CONFER POOR PROGNOSIS IN HEAD AND NECK SQUAMOUS CELL CARCINOMA VIA EPIGENETIC INACTIVATION. BACKGROUND: CHRONIC INFLAMMATION IS A RISK FACTOR FOR HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) AND OTHER DISEASES. PROSTANOID RECEPTORS ARE CLEARLY INVOLVED IN THE DEVELOPMENT OF MANY TYPES OF CANCER. HOWEVER, THEIR ROLE IS NOT SIMPLE AND IS POORLY UNDERSTOOD IN HNSCC. METHODS: METHYLATION PROFILES OF PROSTANOID RECEPTOR FAMILY GENES WERE GENERATED FOR TUMOUR SAMPLES OBTAINED FROM 274 PATIENTS WITH HNSCC, INCLUDING 69 HYPOPHARYNX, 51 LARYNX, 79 ORAL CAVITY, AND 75 OROPHARYNX TUMOUR SAMPLES, BY QUANTITATIVE METHYLATION-SPECIFIC PCR. PROMOTER METHYLATION WAS THEN EVALUATED WITH RESPECT TO VARIOUS CLINICAL CHARACTERISTICS AND PATIENT SURVIVAL. RESULTS: THE MEAN NUMBER OF METHYLATED GENES PER SAMPLE WAS 2.05 +/- 2.59 (RANGE 0 TO 9). PROMOTERS OF PTGDR1, PTGDR2, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, AND TBXA2R WERE METHYLATED IN 43.8%, 18.2%, 25.5%, 17.5%, 41.2%, 8.0%, 19.3%, 20.4%, AND 11.3% OF THE SAMPLES, RESPECTIVELY. METHYLATION INDICES FOR PROSTANOID RECEPTOR FAMILY GENES TENDED TO BE HIGHER AS THE NUMBER OF TET METHYLATION EVENTS INCREASED. PATIENTS WITH 5-9 METHYLATED GENES HAD A SIGNIFICANTLY LOWER SURVIVAL RATE THAN THAT OF PATIENTS WITH 0-4 METHYLATED GENES (LOG-RANK TEST, P= 0.007). IN MULTIVARIATE ANALYSES, PTGDR1 METHYLATION WAS MOST HIGHLY CORRELATED WITH RECURRENCE IN PATIENTS WITH HYPOPHARYNGEAL CANCER (P = 0.014). A SIMILAR CORRELATION WAS OBSERVED FOR PTGER4 IN PATIENTS WITH LARYNGEAL CANCER (P = 0.046). METHYLATION OF THE PTGIR AND TBXA2R PROMOTERS WAS POSITIVELY CORRELATED WITH RECURRENCE IN OROPHARYNGEAL CANCER (P = 0.028 AND P = 0.006, RESPECTIVELY). MOREOVER, PATIENTS WITH 5-9 METHYLATED GENES WERE EXTREMELY LOWER OF 5HMC LEVELS (P = 0.035) AND WAS CORRELATED WITH INCREASING EXPRESSION OF DNMT3A AND DNMT3B (P < 0.05 AND P < 0.05, RESPECTIVELY). CONCLUSION: WE CHARACTERISED THE RELATIONSHIP BETWEEN THE METHYLATION STATUS OF PROSTANOID RECEPTOR GENES AND RECURRENCE IN HNSCC. THESE RESULTS PROVIDE NEW PERSPECTIVES FOR THE DEVELOPMENT OF MOLECULAR TARGETED TREATMENT APPROACHES. 2020 7 6686 29 VALIDATION OF EPIGENETIC MARKERS TO IDENTIFY COLITIS ASSOCIATED CANCER: RESULTS OF MODULE 1 OF THE ENDCAP-C STUDY. BACKGROUND: CHRONIC INFLAMMATION CAUSED BY ULCERATIVE COLITIS (UC) CAUSES A PRO-NEOPLASTIC DRIVE IN THE INFLAMED COLON, LEADING TO A MARKEDLY GREATER RISK OF INVASIVE MALIGNANCY COMPARED TO THE GENERAL POPULATION. DESPITE SURVEILLANCE PROTOCOLS, 50% OF CASES PROCEED TO CANCER BEFORE NEOPLASIA IS DETECTED. THE ENHANCED NEOPLASIA DETECTION AND CANCER PREVENTION IN CHRONIC COLITIS (ENDCAP-C) TRIAL IS AN OBSERVATIONAL MULTI-CENTRE TEST ACCURACY STUDY TO ASCERTAIN THE ROLE OF MOLECULAR MARKERS IN IMPROVING THE DETECTION OF DYSPLASIA. WE AIMED TO VALIDATE PREVIOUSLY IDENTIFIED BIOMARKERS OF NEOPLASIA IN A RETROSPECTIVE COHORT AND CREATE PREDICTIVE MODELS FOR LATER VALIDATION IN A PROSPECTIVE COHORT. METHODS: A RETROSPECTIVE ANALYSIS USING BISULPHITE PYROSEQUENCING OF AN 11 MARKER PANEL (SFRP1, SFRP2, SRP4, SRP5, WIF1, TUBB6, SOX7, APC1A, APC2, MINT1, RUNX3) IN SAMPLES FROM 35 PATIENTS WITH CANCER, 78 WITH DYSPLASIA AND 343 WITHOUT NEOPLASIA UNDERGOING SURVEILLANCE FOR UC ASSOCIATED NEOPLASIA ACROSS 6 MEDICAL CENTRES. PREDICTIVE MODELS FOR UC ASSOCIATED CANCER/DYSPLASIA WERE CREATED IN THE SETTING OF NEOPLASTIC AND NON-NEOPLASTIC MUCOSA. FINDINGS: FOR NEOPLASTIC MUCOSA A FIVE MARKER PANEL (SFRP2, SFRP4, WIF1, APC1A, APC2) WAS ACCURATE IN DETECTING PRE-CANCEROUS AND INVASIVE NEOPLASIA (AUC = 0.83; 95% CI: 0.79, 0.88), AND DYSPLASIA (AUC = 0.88; (0.84, 0.91). FOR NON-NEOPLASTIC MUCOSA A FOUR MARKER PANEL (APC1A, SFRP4, SFRP5, SOX7) HAD MODEST ACCURACY (AUC = 0.68; 95% CI: 0.62,0.73) IN PREDICTING ASSOCIATED BOWEL NEOPLASIA THROUGH THE METHYLATION SIGNATURE OF DISTANT NON-NEOPLASTIC COLONIC MUCOSA. INTERPRETATION: THIS MULTIPLEX METHYLATION MARKER PANEL IS ACCURATE IN THE DETECTION OF ULCERATIVE COLITIS ASSOCIATED DYSPLASIA AND NEOPLASIA AND IS CURRENTLY BEING VALIDATED IN A PROSPECTIVE CLINICAL TRIAL. FUNDING: THE ENDCAP-C STUDY WAS FUNDED BY THE NATIONAL INSTITUTE FOR HEALTH RESEARCH EFFICACY AND MECHANISM EVALUATION (EME) PROGRAMME (11/100/29). 2019 8 2996 21 GENETIC PROFILE AND MICROSATELLITE INSTABILITY IN A CASE OF SECONDARY ESOPHAGEAL SQUAMOUS CELL CARCINOMA 12 YEARS AFTER ALLOGENEIC HEMATOPOIETIC STEM CELL TRANSPLANTATION FOR APLASTIC ANEMIA. WE REPORT ON A 16-YEAR-OLD JAPANESE BOY IN WHOM AN ESOPHAGEAL SQUAMOUS CELL CARCINOMA (ESCC) DEVELOPED 12 YEARS AFTER ALLOGENEIC HEMATOPOIETIC STEM CELL TRANSPLANTATION WAS PERFORMED FOR APLASTIC ANEMIA. A HIGH FREQUENCY OF MICROSATELLITE INSTABILITY WAS DETECTED IN SAMPLES OF ESCC. MOREOVER, THE DETECTION OF PATHOGENIC VARIANTS, INCLUDING SINGLE NUCLEOTIDE SUBSTITUTION OF TP53 (C.346C>T) AND BRCA2 (C.6952C>T) AND SPLICING OF KDM6A (C.1194+2T>G), SUGGEST THAT THE DEVELOPMENT OF ESCC IN THE PATIENT WAS TRIGGERED BY IMPAIRMENT OF CHECKPOINT AND REPAIR FOR DNA DAMAGE AND EPIGENETIC MODIFICATION THROUGH ACCUMULATION OF GENE MUTATIONS INDUCED BY CHRONIC GRAFT-VERSUS-HOST DISEASE AND PROLONGED ADMINISTRATION OF TACROLIMUS. 2020 9 3629 37 INACTIVATION OF P15(INK4B) IN CHRONIC ARSENIC POISONING CASES. ARSENIC EXPOSURE FROM BURNING HIGH ARSENIC-CONTAINING COAL HAS BEEN ASSOCIATED WITH HUMAN SKIN LESION AND CANCER. HOWEVER, THE MECHANISMS OF ARSENIC-RELATED CARCINOGENESIS ARE NOT FULLY UNDERSTOOD. INACTIVATION OF CRITICAL TUMOR SUPPRESSION GENES BY EPIGENETIC REGULATION OR GENETIC MODIFICATION MIGHT CONTRIBUTE TO ARSENIC-INDUCED CARCINOGENICITY. THIS STUDY AIMS TO CLARIFY THE CORRELATION BETWEEN ARSENIC POLLUTION AND FUNCTIONAL DEFECT OF P15(INK4B) GENE IN ARSENIC EXPOSURE RESIDENTS FROM A REGION OF GUIZHOU PROVINCE, CHINA. TO THIS END, 103 ARSENIC EXPOSURE RESIDENTS AND 105 CONTROL SUBJECTS WERE RECRUITED IN THIS STUDY. THE RESULTS SHOWED THAT THE EXPOSURE GROUP EXHIBITED HIGHER LEVELS OF URINARY AND HAIR ARSENIC COMPARED WITH THE CONTROL GROUP (55.28 VS 28.87 MUG/L, 5.16 VS 1.36 MUG/G). SUBJECTS WITH HIGHER ARSENIC CONCENTRATIONS ARE MORE LIKELY TO HAVE P15(INK4B) METHYLATION AND GENE DELETION (CHI(2) = 4.28, P = 0.04 AND CHI(2) = 4.31, P = 0.04). WE ALSO FOUND THAT THE DEGREE OF P15(INK4B) HYPERMETHYLATION AND GENE DELETION OCCURRED AT HIGHER INCIDENCE IN THE POISONING CASES WITH SKIN CANCER (3.7% AND 14.81% IN NON-SKIN CANCER GROUP, 41.18% AND 47.06 IN SKIN CANCER GROUP), AND WERE SIGNIFICANTLY ASSOCIATED WITH THE STAGE OF SKIN LESIONS (CHI(2) = 12.82, P < 0.01 AND CHI(2) = 7.835, P = 0.005). THESE OBSERVATIONS INDICATE THAT INACTIVATION OF P15(INK4B) THROUGH GENETIC ALTERATION OR EPIGENETIC MODIFICATION IS A COMMON EVENT THAT IS ASSOCIATED WITH ARSENIC EXPOSURE AND THE DEVELOPMENT OF ARSENICOSIS. 2014 10 417 29 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 11 5382 28 RECURRENT CHROMOSOMAL AND EPIGENETIC ALTERATIONS IN ORAL SQUAMOUS CELL CARCINOMA AND ITS PUTATIVE PREMALIGNANT CONDITION ORAL LICHEN PLANUS. HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) AFFECTS ABOUT 700.000 INDIVIDUALS PER YEAR WORLDWIDE WITH ORAL SQUAMOUS CELL CARCINOMA (OSCC) AS A MAJOR SUBCATEGORY. DESPITE A COMPREHENSIVE TREATMENT CONCEPT INCLUDING SURGERY, RADIATION, AND CHEMOTHERAPY THE 5-YEAR SURVIVAL RATE IS STILL ONLY ABOUT 50 PERCENT. CHRONIC INFLAMMATION IS ONE OF THE HALLMARKS OF CARCINOGENESIS. UNTIL NOW, LITTLE IS KNOWN ABOUT THE PREMALIGNANT STATUS OF ORAL LICHEN PLANUS (OLP) AND MOLECULAR ALTERATIONS IN OLP ARE STILL POORLY CHARACTERIZED. OUR STUDY AIMS TO DELINEATE DIFFERENTIAL DNA METHYLATION PATTERNS IN OLP, OSCC, AND NORMAL ORAL MUCOSA. BY APPLYING A BEAD CHIP APPROACH, WE IDENTIFIED ALTERED CHROMOSOMAL PATTERNS CHARACTERISTIC FOR OSCC WHILE FINDING NO RECURRENT ALTERATIONS IN OLP. IN CONTRAST, WE IDENTIFIED NUMEROUS ALTERATIONS IN THE DNA METHYLATION PATTERN IN OLP, AS COMPARED TO NORMAL CONTROLS, THAT WERE ALSO PRESENT IN OSCC. OUR DATA SUPPORT THE HYPOTHESIS THAT OLP IS A PRECURSOR LESION OF OSCC SHARING MULTIPLE EPIGENETIC ALTERATIONS WITH OSCC. 2019 12 1044 31 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 13 4232 35 METHYLATION OF RUNX3 IN VARIOUS TYPES OF HUMAN CANCERS AND PREMALIGNANT STAGES OF GASTRIC CARCINOMA. ACCUMULATING EVIDENCE HAS IDENTIFIED A MECHANISM POTENTIALLY RESPONSIBLE FOR THE INACTIVATION OF TUMOR SUPPRESSOR GENES, NAMELY TRANSCRIPTIONAL SILENCING BY ABERRANT METHYLATION OF CPG ISLANDS. A PREVIOUS STUDY HAS SHOWN THE LOSS OF RUNX3 EXPRESSION, DUE TO ABERRANT METHYLATION OF ITS CPG ISLAND, IN GASTRIC CANCER CELL LINES, SUGGESTING THAT RUNX3 IS A TARGET FOR EPIGENETIC GENE SILENCING IN GASTRIC CARCINOGENESIS. HOWEVER, THERE ARE LIMITED DATA ON THE METHYLATION STATUS OF RUNX3 IN THE NEOPLASTIC AND NON-NEOPLASTIC TISSUES IN VARIOUS TYPES OF HUMAN CANCERS, INCLUDING GASTRIC CANCER. HERE, WE REPORT THAT 60% OF GASTRIC CANCER CELL LINES AND 64% OF PRIMARY GASTRIC CARCINOMAS (N=75) WERE METHYLATED AT THE RUNX3 CPG ISLAND. RUNX3 METHYLATION WAS ALSO DETECTED IN HEPATOCELLULAR CARCINOMAS (73%, N=48), LARYNX CANCERS (62%, N=37), LUNG CANCERS (46%, N=24), BREAST CANCERS (25%, N=25), PROSTATE CANCERS (23%, N=44), ENDOMETRIAL CANCERS (12.5%, N=24), COLON CANCERS (4.9%, N=61) AND UTERINE CERVICAL CANCERS (2.5%, N=40), SHOWING THAT RUNX3 METHYLATION IS NOT RESTRICTED TO GASTRIC CANCER. INTERESTINGLY, THE RUNX3 METHYLATION WAS ESPECIALLY FREQUENT IN TUMORS FROM TISSUES OF A FOREGUT DERIVATIVE, THAT IS, THE STOMACH, LIVER, LARYNX AND LUNG. NEXT, THE METHYLATION STATUS OF RUNX3 IN VARIOUS NON-NEOPLASTIC TISSUES WAS EXAMINED, INCLUDING THE PREMALIGNANT LESIONS OF GASTRIC CARCINOMAS. THE RUNX3 METHYLATION WAS FOUND IN 8.1% OF CHRONIC GASTRITIS (N=99), 28.1% OF INTESTINAL METAPLASIA (N=32), 27.3% OF GASTRIC ADENOMAS (N=77) AND 64% OF GASTRIC CARCINOMAS (N=75), BUT NOT IN CHRONIC HEPATITIS B, NORMAL PROSTATE AND COLON MUCOSA, EVEN THOUGH IN CASES OF CHRONIC HEPATITIS, THE METHYLATION FREQUENCY OF ITS NEOPLASTIC TISSUES WAS VERY HIGH. IN CONCLUSION, RUNX3 METHYLATION IS FREQUENTLY FOUND IN HUMAN CANCERS, INCLUDING GASTRIC CANCER, AND IS MOSTLY CANCER SPECIFIC, WITH THE EXCEPTION OF THE STOMACH, AND THUS, MIGHT BE USEFUL AS A POTENTIAL DIAGNOSTIC BIOMARKER OF CANCER. 2004 14 116 43 A STUDY OF DNA METHYLATION OF BLADDER CANCER BIOMARKERS IN THE URINE OF PATIENTS WITH NEUROGENIC LOWER URINARY TRACT DYSFUNCTION. BACKGROUND: BLADDER CANCER (BCA) IN PATIENTS SUFFERING FROM NEUROGENIC LOWER URINARY TRACT DYSFUNCTION (NLUTD) IS A SIGNIFICANT CONCERN DUE TO ITS ADVANCED STAGE AT DIAGNOSIS AND HIGH MORTALITY RATE. CURRENTLY, THERE IS A SCARCITY OF SPECIFIC GUIDELINES FOR BCA SCREENING IN THESE PATIENTS. THE DEVELOPMENT OF URINE BIOMARKERS FOR BCA SEEMS TO BE AN ATTRACTIVE NON-INVASIVE METHOD OF SCREENING OR RISK STRATIFICATION IN THIS PATIENT POPULATION. DNA METHYLATION IS AN EPIGENETIC MODIFICATION, RESULTING IN THE TRANSCRIPTIONAL SILENCING OF TUMOR SUPPRESSION GENES, THAT IS FREQUENTLY DETECTED IN THE URINE OF BCA PATIENTS. OBJECTIVES: WE AIMED TO INVESTIGATE DNA HYPERMETHYLATION IN FIVE GENE PROMOTERS, PREVIOUSLY ASSOCIATED WITH BCA, IN THE URINE OF NLUTD PATIENTS, AND IN COMPARISON WITH HEALTHY CONTROLS. DESIGN, SETTING AND PARTICIPANTS: THIS WAS A PROSPECTIVE CASE-CONTROL STUDY THAT RECRUITED NEUROUROLOGY OUTPATIENTS FROM A PUBLIC TEACHING HOSPITAL WHO HAD SUFFERED FROM NLUTD FOR AT LEAST 5 YEARS. THEY ALL UNDERWENT CYSTOSCOPY COMBINED WITH BIOPSY FOR BCA SCREENING FOLLOWING WRITTEN INFORMED CONSENT. DNA WAS EXTRACTED AND DNA METHYLATION WAS ASSESSED FOR THE RASSF1, RARBETA, DAPK, TERT AND APC GENE PROMOTERS VIA QUANTITATIVE METHYLATION-SPECIFIC PCR IN URINE SPECIMENS FROM THE PATIENTS AND CONTROLS. RESULTS: FORTY-ONE PATIENTS OF MIXED NLUTD ETIOLOGY AND 35 CONTROLS WERE ENROLLED. DNA WAS DETECTED IN 36 PATIENTS' URINE SPECIMENS AND IN THOSE OF 22 CONTROLS. IN THE URINE SPECIMENS, DNA WAS HYPERMETHYLATED IN AT LEAST ONE OF FIVE GENE PROMOTERS IN 17/36 PATIENTS AND IN 3/22 CONTROLS (47.22% VS. 13.64%, RESPECTIVELY, P = 0.009). RASSF1 WAS HYPERMETHYLATED IN 10/17 (58.82%) SPECIMENS WITH DETECTED METHYLATION, APC IN 7/17 (41.18%), DAPK IN 4/17 (23.53%), RAR-BETA2 IN 3/17 (17.56%) AND TERT IN NONE. ACCORDING TO A MULTIVARIATE LOGISTIC REGRESSION ANALYSIS, NLUTD AND MALE GENDER WERE SIGNIFICANTLY ASSOCIATED WITH HYPERMETHYLATION (OR = 7.43, P = 0.007 AND OR = 4.21; P = 0.04, RESPECTIVELY). IN THE TISSUE SPECIMENS, HISTOLOGY REVEALED TALG BCA IN TWO PATIENTS AND UROTHELIAL SQUAMOUS METAPLASIA IN FIVE PATIENTS. CHRONIC BLADDER INFLAMMATION WAS PRESENT IN 35/41 BLADDER BIOPSIES. CONCLUSIONS: DNA HYPERMETHYLATION IN A PANEL OF FIVE BCA-ASSOCIATED GENES IN THE URINE WAS SIGNIFICANTLY MORE FREQUENT IN NLUTD PATIENTS THAN IN THE CONTROLS. OUR RESULTS WARRANT FURTHER EVALUATION IN LONGITUDINAL STUDIES ASSESSING THE CLINICAL IMPLICATIONS AND POSSIBLE ASSOCIATIONS BETWEEN DNA HYPERMETHYLATION, CHRONIC INFLAMMATION AND BCA IN THE NLUTD POPULATION. 2023 15 3879 32 KERATIN 19-EXPRESSING HEPATOCELLULAR CARCINOMA AND SMALL-DUCT TYPE INTRAHEPATIC CHOLANGIOCARCINOMA SHOW A SIMILAR POSTOPERATIVE CLINICAL COURSE BUT HAVE DISTINCT GENETIC FEATURES. AIMS: THE PRESENT STUDY AIMED TO SYSTEMATICALLY COMPARE CLINICOPATHOLOGICAL AND GENETIC FEATURES BETWEEN KERATIN 19 (K19)-EXPRESSING HEPATOCELLULAR CARCINOMA (HCC) AND INTRAHEPATIC CHOLANGIOCARCINOMA (ICCA). METHODS AND RESULTS: CONSECUTIVE CASES OF HCC (N = 430) WERE CLASSIFIED INTO K19(+) AND K19(-) USING IMMUNOHISTOCHEMISTRY. ICCA CASES WERE ALSO SEPARATED INTO SMALL-(S-ICCA; N = 36) AND LARGE-DUCT TYPES (N = 22) BASED ON RECENTLY PROPOSED CRITERIA, WITH THE FORMER BEING USED IN THE PRESENT STUDY. MUTATIONAL HOT-SPOTS IN TERT, CTNNB1, KRAS AND IDH1 WERE SEQUENCED. TWENTY-SIX CASES (6%) OF HCC EXPRESSED K19. K19(+) HCC WAS MORE STRONGLY ASSOCIATED WITH CHRONIC HEPATITIS B THAN K19(-) HCC AND S-ICCA (46% VERSUS 17% AND 6%; BOTH P < 0.001). LYMPH NODE METASTASIS WAS OBSERVED IN K19(+) HCC (8%) AND S-ICCA (22%), BUT WAS EXCEPTIONAL IN K19(-) HCC (1%). K19(+) HCC HAD TERT PROMOTER MUTATIONS LESS FREQUENTLY THAN K19(-) HCC (31% VERSUS 59%; P = 0.022), AND LACKED ALTERATIONS IN KRAS AND IDH1. CTNNB1 MUTATIONS WERE SIMILARLY OBSERVED IN K19(+) AND K19(-) HCC (23% AND 19%, RESPECTIVELY), BUT RARE IN S-ICCA (3%). THE POSTOPERATIVE SURVIVAL CURVE OF K19(+) HCC WAS ALMOST IDENTICAL TO THAT OF S-ICCA IN THE FIRST 5 YEARS (APPROXIMATELY 50% AT 5 YEARS), AND SIGNIFICANTLY WORSE THAN THAT OF K19(-) HCC (P = 0.040). EXTRAHEPATIC RECURRENCE WAS MORE COMMON IN K19(+) HCC (50%) AND S-ICCA (35%) THAN IN K19(-) HCC (15%) (P = 0.001). CONCLUSIONS: ALTHOUGH K19(+) HCC AND S-ICCA SHOWED SIMILAR BIOLOGICAL BEHAVIOURS, THEY DID NOT SHARE ANY DRIVER GENE MUTATIONS, SUGGESTING THE POSSIBLE INVOLVEMENT OF EPIGENETIC ALTERATIONS IN THE ICCA-LIKE FEATURES OF K19(+) HCC. 2019 16 1624 35 DNA-METHYLOME-BASED TUMOR HYPOXIA CLASSIFIER IDENTIFIES HPV-NEGATIVE HEAD AND NECK CANCER PATIENTS AT RISK FOR LOCOREGIONAL RECURRENCE AFTER PRIMARY RADIOCHEMOTHERAPY. PURPOSE: TUMOR HYPOXIA IS A PARADIGMATIC NEGATIVE PROGNOSTICATOR OF TREATMENT RESISTANCE IN HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC). THE LACK OF ROBUST AND RELIABLE HYPOXIA CLASSIFIERS LIMITS THE ADAPTATION OF STRATIFIED THERAPIES. WE HYPOTHESIZED THAT THE TUMOR DNA METHYLATION LANDSCAPE MIGHT INDICATE EPIGENETIC REPROGRAMMING INDUCED BY CHRONIC INTRATUMORAL HYPOXIA. EXPERIMENTAL DESIGN: A DNA-METHYLOME-BASED TUMOR HYPOXIA CLASSIFIER (HYPOXIA-M) WAS TRAINED IN THE TCGA (THE CANCER GENOME ATLAS)-HNSCC COHORT BASED ON MATCHED ASSIGNMENTS USING GENE EXPRESSION-BASED SIGNATURES OF HYPOXIA (HYPOXIA-GES). HYPOXIA-M WAS VALIDATED IN A MULTICENTER DKTK-ROG TRIAL CONSISTING OF HUMAN PAPILLOMAVIRUS (HPV)-NEGATIVE PATIENTS WITH HNSCC TREATED WITH PRIMARY RADIOCHEMOTHERAPY (RCHT). RESULTS: ALTHOUGH HYPOXIA-GES FAILED TO STRATIFY PATIENTS IN THE DKTK-ROG, HYPOXIA-M WAS INDEPENDENTLY PROGNOSTIC FOR LOCAL RECURRENCE (HR, 4.3; P = 0.001) AND OVERALL SURVIVAL (HR, 2.34; P = 0.03) BUT NOT DISTANT METASTASIS AFTER RCHT IN BOTH COHORTS. HYPOXIA-M STATUS WAS INVERSELY ASSOCIATED WITH CD8 T-CELL INFILTRATION IN BOTH COHORTS. HYPOXIA-M WAS FURTHER PROGNOSTIC IN THE TCGA-PANCANCER COHORT (HR, 1.83; P = 0.04), UNDERSCORING THE BREADTH OF THIS CLASSIFIER FOR PREDICTING TUMOR HYPOXIA STATUS. CONCLUSIONS: OUR FINDINGS HIGHLIGHT AN UNEXPLORED AVENUE FOR DNA METHYLATION-BASED CLASSIFIERS AS BIOMARKERS OF TUMORAL HYPOXIA FOR IDENTIFYING HIGH-RISK FEATURES IN PATIENTS WITH HNSCC TUMORS. SEE RELATED COMMENTARY BY HEFT NEAL AND BRENNER, P. 2954. 2023 17 388 43 AN INTEGRATED ANALYSIS OF SOCS1 DOWN-REGULATION IN HBV INFECTION-RELATED HEPATOCELLULAR CARCINOMA. PERSISTENT INFLAMMATION TOGETHER WITH GENETIC/EPIGENETIC ABERRATIONS IS STRONGLY ASSOCIATED WITH CHRONIC HEPATITIS B VIRUS (HBV) INFECTION-RELATED HEPATOCARCINOGENESIS. HERE, WE INVESTIGATED THE ALTERATIONS OF THE SUPPRESSOR OF CYTOKINE SIGNALLING (SOCS) FAMILY GENES IN HBV-RELATED HEPATOCELLULAR CARCINOMA (HCC). A TOTAL OF 116 PATIENTS WITH HCC WERE ENROLLED IN THIS STUDY. THE METHYLATION STATUSES OF SOCS1-7 AND CISH GENES WERE QUANTITATIVELY MEASURED AND CLINICOPATHOLOGICAL SIGNIFICANCE OF SOCS1 METHYLATION WAS STATISTICALLY ANALYSED. THE GENE COPY NUMBER VARIATION WAS ASSAYED BY ACGH. LUCIFERASE REPORTER ASSAY AND WESTERN BLOT WERE USED TO DETECT THE INVOLVEMENT OF SOCS1 IN P53 SIGNALLING. WE FOUND HIGH FREQUENCIES OF SOCS1 GENE HYPERMETHYLATION IN BOTH TUMOUR (56.03%) AND ADJACENT NONTUMOUR TISSUES (54.31%), BUT TUMOUR TISSUES EXHIBITED INCREASED METHYLATION INTENSITY (24.01% VS 13.11%, P < 0.0001), PARTICULARLY IN PATIENTS WITH LARGER TUMOUR SIZE OR CIRRHOSIS BACKGROUND (P < 0.0001). IN ADDITION, THE FREQUENCY AND INTENSITY OF SOCS1 HYPERMETHYLATION IN TUMOUR TISSUES WERE BOTH SIGNIFICANTLY HIGHER THAN THOSE IN NONTUMOUR TISSUES IN MALE GENDER PATIENTS AND IN PATIENTS >/=45 YEARS OLD (P = 0.0214 AND P < 0.0001, P = 0.0232 AND P < 0.0001, RESPECTIVELY). SOCS1 GENE DELETION WAS FOUND IN 8 OF 25 ACGH ASSAYED TUMOUR SPECIMENS, WHICH WAS ASSOCIATED WITH LOWER SOCS1 MRNA EXPRESSION (P = 0.0448). FURTHERMORE, ECTOPIC SOCS1 OVEREXPRESSION COULD ACTIVATE THE P53 SIGNALLING PATHWAY IN HCC CELL LINES. HYPERMETHYLATION OF SOCS2-7 AND CISH GENES WAS SELDOM FOUND IN HCC. OUR RESULTS SUGGESTED THAT THE GENE LOSS AND EPIGENETIC SILENCING OF SOCS1 WERE STRONGLY ASSOCIATED WITH HBV-RELATED HCC. 2014 18 5909 32 TARGETED DEEP SEQUENCING OF PLASMA CIRCULATING CELL-FREE DNA REVEALS VIMENTIN AND FIBULIN 1 AS POTENTIAL EPIGENETIC BIOMARKERS FOR HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMA (HCC) IS THE SECOND MOST COMMON CAUSE OF CANCER DEATH WORLDWIDE, BUT IS STILL LACKING SENSITIVE AND SPECIFIC BIOMARKERS FOR EARLY DIAGNOSIS AND PROGNOSIS. IN THIS STUDY, WE APPLIED TARGETED MASSIVELY PARALLEL SEMICONDUCTOR SEQUENCING TO ASSESS METHYLATION ON A PANEL OF GENES (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM AND YWHAZ) IN PLASMA CIRCULATING CELL-FREE DNA (CFDNA) AND TO EVALUATE THE POTENTIAL OF THESE GENES AS HCC BIOMARKERS IN TWO DIFFERENT SERIES, ONE FROM FRANCE (42 HCC CASES AND 42 CONTROLS) AND ONE FROM THAILAND (42 HCC CASES, 26 CHRONIC LIVER DISEASE CASES AND 42 CONTROLS). WE ALSO ANALYZED A SET OF HCC AND ADJACENT TISSUES AND LIVER CELL LINES TO FURTHER COMPARE WITH 'THE CANCER GENOME ATLAS' (TCGA) DATA. THE METHYLATION IN CFDNA WAS DETECTED FOR FBLN1, PSMA7, PXDN AND VIM, WITH DIFFERENCES IN METHYLATION PATTERNS BETWEEN CASES AND CONTROLS FOR FBLN1 AND VIM. THE AVERAGE METHYLATION LEVEL ACROSS ANALYZED CPG-SITES WAS ASSOCIATED WITH HIGHER ODDS OF HCC FOR VIM (1.48 [1.02, 2.16] FOR FRENCH CASES AND 2.18 [1.28, 3.72] FOR THAI CASES), AND LOWER ODDS OF HCC FOR FBLN1 (0.89 [0.76, 1.03] FOR FRENCH CASES AND 0.75 [0.63, 0.88] FOR THAI CASES). IN CONCLUSION, OUR STUDY PROVIDES EVIDENCE THAT CHANGES IN VIM AND FBLN1 METHYLATION LEVELS IN CFDNA ARE ASSOCIATED WITH HCC AND COULD REPRESENT USEFUL PLASMA-BASED BIOMARKERS. ALSO, THE POTENTIAL TO INVESTIGATE METHYLATION PATTERNS IN CFDNA COULD BRING NEW STRATEGIES FOR HCC DETECTION AND MONITORING HIGH-RISK GROUPS AND RESPONSE TO TREATMENT. 2017 19 2679 37 EVALUATION OF CIRCULATORY RNA-BASED BIOMARKER PANEL IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE CIRCULATING TRANSCRIPTOME (CODING AND NON-CODING) PLAYS A CRITICAL ROLE IN CANCER. NOVEL ACCURATE STRATEGIES FOR EARLY DETECTION OF HEPATOCELLULAR CARCINOMA (HCC) ARE STRONGLY NEEDED. PATIENTS AND METHODS: WE CHOSE AN HCC-SPECIFIC RNA-BASED BIOMARKER PANEL BASED ON THE INTEGRATION OF DIFFERENTIAL LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 2 (LAMP2) GENE EXPRESSION WITH ITS SELECTED EPIGENETIC REGULATORS USING BIOINFORMATIC METHODS. THIS WAS FOLLOWED BY RT-QPCR VALIDATION IN SERUM OF 78 PATIENTS WITH HCC, 36 PATIENTS WITH CHRONIC HEPATITIS C (CHC) INFECTION AND 44 HEALTHY VOLUNTEERS. WE USED RISK-SCORE ANALYSIS TO EVALUATE THE DIAGNOSTIC EFFICACY OF THE SERUM PROFILING SYSTEM. MOREOVER, IN TWENTY OF THE 78 HCC CASES INVOLVED IN THE STUDY WE EXAMINED THE EXPRESSION OF RNA-BASED BIOMARKER PANEL IN BOTH HCC AND ADJACENT NON-TUMOR TISSUES AND ASSESSED THEIR CORRELATION WITH THE SERUM LEVEL OF THIS PANEL. RESULTS: THE FOUR RIBONUCLEIC ACID (RNA)-BASED BIOMARKER PANEL [LONG NON-CODING RNA-C TERMINAL BINDING PROTEIN, ANDROGEN RESPONSIVE (LNCRNA-CTBP), MICRORNA-16-2 (MIR-16-2), MICRORNA-21-5-P (MIR-21-5P) AND LAMP2], HAD HIGH SENSITIVITY AND SPECIFICITY FOR DISCRIMINATING HCC FROM HEALTHY CONTROLS AND ALSO FROM CHC PATIENTS. AMONG THESE FOUR RNAS, SERUM MIR-16-2 AND MIR-21-5P WERE INDEPENDENT PROGNOSTIC FACTORS. CONCLUSION: THE CIRCULATORY RNA-BASED BIOMARKER PANEL CAN SERVE AS A POTENTIAL BIOMARKER FOR HCC DIAGNOSIS AND PROGNOSIS. 2016 20 1273 23 CYTOTOXIC PERIPHERAL T-CELL LYMPHOMAS AND EBV-POSITIVE T/NK-CELL LYMPHOPROLIFERATIVE DISEASES: EMERGING CONCEPTS, RECENT ADVANCES, AND THE PUTATIVE ROLE OF CLONAL HEMATOPOIESIS. A REPORT OF THE 2022 EA4HP/SH LYMPHOMA WORKSHOP. CYTOTOXIC PERIPHERAL T-CELL LYMPHOMAS AND EBV-POSITIVE T/NK-CELL LYMPHOPROLIFERATIVE DISEASES WERE DISCUSSED AT THE 2022 EUROPEAN ASSOCIATION FOR HAEMATOPATHOLOGY/SOCIETY FOR HEMATOPATHOLOGY LYMPHOMA WORKSHOP HELD IN FLORENCE, ITALY. THIS SESSION FOCUSED ON (I) PRIMARY NODAL EBV-POSITIVE T AND NK-CELL LYMPHOMAS (PRIMARY NODAL-EBV-TNKL), (II) EXTRANODAL EBV-POSITIVE T/NK LYMPHOPROLIFERATIVE DISEASES (LPD) IN CHILDREN AND ADULTS, (III) CYTOTOXIC PERIPHERAL T-CELL LYMPHOMAS, NOS (CPTCL-NOS), EBV-NEGATIVE, AND (IV) MISCELLANEOUS CASES. PRIMARY NODAL-EBV-TNKL IS A NEWLY RECOGNIZED ENTITY WHICH IS RARE, AGGRESSIVE, AND ASSOCIATED WITH UNDERLYING IMMUNE DEFICIENCY/IMMUNE DYSREGULATION. ALL CASES PRESENTED WITH LYMPHADENOPATHY BUT SOME DEMONSTRATED INVOLVEMENT OF TONSIL/WALDEYER'S RING AND EXTRANODAL SITES. THE MAJORITY OF TUMORS ARE OF T-CELL LINEAGE, AND THE MOST FREQUENT MUTATIONS INVOLVE THE EPIGENETIC MODIFIER GENES, SUCH AS TET2 AND DNMT3A, AND JAK-STAT GENES. A SPECTRUM OF EBV-POSITIVE T/NK LPD INVOLVING EXTRANODAL SITES WERE DISCUSSED AND HIGHLIGHT THE DIAGNOSTIC CHALLENGE WITH PRIMARY NODAL-EBV-TNKL WHEN THESE EXTRANODAL EBV-POSITIVE T/NK LPD CASES DEMONSTRATE PREDOMINANT NODAL DISEASE EITHER AT PRESENTATION OR DURING DISEASE PROGRESSION FROM CHRONIC ACTIVE EBV DISEASE. THE MAJORITY OF CPTCL-NOS DEMONSTRATED THE TBX21 PHENOTYPE. SOME CASES HAD A BACKGROUND OF IMMUNOSUPPRESSION OR IMMUNE DYSREGULATION. INTERESTINGLY, AN UNEXPECTED ASSOCIATION OF CPTCL-NOS, EBV-POSITIVE AND NEGATIVE, WITH TFH LYMPHOMAS/LPDS WAS OBSERVED IN THE WORKSHOP CASES. SIMILAR TO A PUBLISHED LITERATURE, THE GENETIC LANDSCAPE OF CPTCL-NOS FROM THE WORKSHOP SHOWED FREQUENT MUTATIONS IN EPIGENETIC MODIFIERS, INCLUDING TET2 AND DNMT3A, SUGGESTING A ROLE OF CLONAL HEMATOPOIESIS IN THE DISEASE PATHOGENESIS. 2023