1  3908 138 LICHEN SCLEROSUS: AN AUTOIMMUNOPATHOGENIC AND GENOMIC ENIGMA WITH EMERGING GENETIC AND IMMUNE TARGETS. LICHEN SCLEROSUS (LS) IS AN INFLAMMATORY DERMATOSIS WITH A PREDILECTION FOR ANOGENITAL SKIN. DEVELOPING LESIONS LEAD TO VULVAR PAIN AND SEXUAL DYSFUNCTION, WITH A SIGNIFICANT LOSS OF STRUCTURAL ANATOMICAL ARCHITECTURE, SCLEROSIS, AND INCREASED RISK OF MALIGNANCY. ONSET MAY OCCUR AT ANY AGE IN BOTH SEXES, BUT TYPICALLY AFFECTS MORE FEMALES THAN MALES, PRESENTING IN A BIMODAL FASHION AMONG PRE-PUBERTAL CHILDREN AND MIDDLE-AGED ADULTS. A DEFINITIVE CURE REMAINS ELUSIVE AS THE EXACT PATHOGENESIS OF LS REMAINS UNKNOWN. A GENERAL REVIEW OF LS, HISTOLOGIC CHALLENGES, ALONG WITH AMOUNTING SUPPORT FOR LS AS AN AUTOIMMUNE DISEASE WITH PREFERENCE FOR A T(H)1 IMMUNE RESPONSE AGAINST A GENETIC BACKGROUND IS SUMMARIZED. IN ADDITION TO THE CLASSICALLY REFERENCED ECM1 (EXTRACELLULAR MATRIX PROTEIN 1), A FOLLOWING DISCUSSION OF OTHER IMMUNE AND GENETIC TARGETS MORE RECENTLY IMPLICATED AS CAUSATIVE OR ACCELERANT AGENTS OF DISEASE, PARTICULARLY MIR-155, DOWNSTREAM TARGETS OF ECM1, GALECTIN-7, P53, AND EPIGENETIC MODIFICATIONS TO CDKN2A, ARE ADDRESSED FROM THE VIEWPOINT OF THEIR INVOLVEMENT IN THREE DIFFERENT, BUT INTERCONNECTED ASPECTS OF LS PATHOLOGY. COLLECTIVELY, THESE EMERGING TARGETS SERVE NOT ONLY AS INHERENTLY POTENTIAL THERAPEUTIC TARGETS FOR TREATMENT, BUT MAY ALSO PROVIDE FURTHER INSIGHT INTO THIS DEBILITATING AND CRYPTIC DISEASE.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
2  5848  22 SUBCLONES IN B-LYMPHOMA CELL LINES: ISOGENIC MODELS FOR THE STUDY OF GENE REGULATION. GENETIC HETEROGENEITY THOUGH COMMON IN TUMORS HAS BEEN RARELY DOCUMENTED IN CELL LINES. TO EXAMINE HOW OFTEN B-LYMPHOMA CELL LINES ARE COMPRISED OF SUBCLONES, WE PERFORMED IMMUNOGLOBULIN (IG) HEAVY CHAIN HYPERMUTATION ANALYSIS. REVEALING THAT SUBCLONES ARE NOT RARE IN B-CELL LYMPHOMA CELL LINES, 6/49 IG HYPERMUTATED CELL LINES (12%) CONSISTED OF SUBCLONES WITH INDIVIDUAL IG MUTATIONS. SUBCLONES WERE ALSO IDENTIFIED IN 2/284 LEUKEMIA/LYMPHOMA CELL LINES EXHIBITING BIMODAL CD MARKER EXPRESSION. WE SUCCESSFULLY ISOLATED 10 SUBCLONES FROM FOUR CELL LINES (HG3, SU-DHL-5, TMD-8, U-2932). WHOLE EXOME SEQUENCING WAS PERFORMED TO MOLECULARLY CHARACTERIZE THESE SUBCLONES. WE DESCRIBE IN DETAIL THE CLONAL STRUCTURE OF CELL LINE HG3, DERIVED FROM CHRONIC LYMPHOCYTIC LEUKEMIA. HG3 CONSISTS OF THREE SUBCLONES EACH BEARING CLONE-SPECIFIC ABERRATIONS, GENE EXPRESSION AND DNA METHYLATION PATTERNS. WHILE DONOR PATIENT LEUKEMIC CELLS WERE CD5+, TWO OF THREE HG3 SUBCLONES HAD INDEPENDENTLY LOST THIS MARKER. CD5 ON HG3 CELLS WAS REGULATED BY EPIGENETIC/TRANSCRIPTIONAL MECHANISMS RATHER THAN BY ALTERNATIVE SPLICING AS REPORTED HITHERTO. IN CONCLUSION, WE SHOW THAT THE PRESENCE OF SUBCLONES IN CELL LINES CARRYING INDIVIDUAL MUTATIONS AND CHARACTERIZED BY SETS OF DIFFERENTIALLY EXPRESSED GENES IS NOT UNCOMMON. WE SHOW ALSO THAT THESE SUBCLONES CAN BE USEFUL ISOGENIC MODELS FOR REGULATORY AND FUNCTIONAL STUDIES.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
3  1432  30 DIFFERENTIAL GENE HYPERMETHYLATION IN GENITAL LICHEN SCLEROSUS AND CANCER: A COMPARATIVE STUDY. AIMS: LICHEN SCLEROSUS (LS) IS A CHRONIC INFLAMMATORY DISEASE OF THE GENITAL SKIN OF UNKNOWN AETIOLOGY. THE ROLE OF LS IN PENILE SQUAMOUS CELL CARCINOGENESIS IS NOT WELL CHARACTERIZED. HPV HAS BEEN IMPLICATED IN BOTH, AS HAVE EPIGENETIC CHANGES. THE PRESENCE OF HPV AND HYPERMETHYLATION OF THE MGMT, P16, RASSF1, RASSF2, TSLC1 AND TSP1 GENES WERE STUDIED IN PENILE LS; MGMT, RASSF2 AND TSLC1 HYPERMETHYLATION IN PENILE CANCER AND TSLC1 HYPERMETHYLATION IN VULVAR LS AND CANCER EXTENDS PREVIOUS RESULTS REPORTED BY OUR GROUP. METHODS AND RESULTS: THIRTY-SEVEN HPV GENOTYPES AND HYPERMETHYLATION WERE EVALUATED BY PCR/REVERSE-LINE-BLOT AND METHYLATION-SPECIFIC PCR RESPECTIVELY, IN 27 PREPUTIAL LS, 24 PENILE SCC, 30 VULVAR SCC, 21 VULVAR LS AND 22 NORMAL SKIN CASES. HPV66 WAS PRESENT IN 3.7% OF PENILE LS CASES, AND P16 AND RASSF2 HYPERMETHYLATION WERE MORE FREQUENT IN PENILE CANCER THAN IN PENILE LS. P16, RASSF1, RASSF2 AND TSP1 HYPERMETHYLATION WERE SIMILAR IN PENILE AND VULVAR LS. CONCLUSIONS: GENE HYPERMETHYLATION IS A COMMON EVENT IN PENILE LS, AND OCCURS APPROXIMATELY AS FREQUENTLY AS IN VULVAR LS. CERTAIN GENES CAN BE HYPERMETHYLATED AS AN EARLY OR LATE EVENT IN LS OR CANCER, RESPECTIVELY. THIS SUGGESTS A POSSIBLE SEQUENTIAL ROLE FOR THESE ALTERATIONS IN THE TRANSITION FROM BENIGN TO MALIGNANT LESIONS.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
4  6600  21 TWIST2 DEMONSTRATES DIFFERENTIAL METHYLATION IN IMMUNOGLOBULIN VARIABLE HEAVY CHAIN MUTATED AND UNMUTATED CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A CLINICALLY HETEROGENEOUS DISEASE FOR WHICH NATURAL HISTORY CAN BE PREDICTED BASED ON THE PRESENCE OR ABSENCE OF IMMUNOGLOBULIN (IG) VARIABLE HEAVY CHAIN (V(H)) GENE MUTATIONS. HEREIN WE REPORT SELECTIVE EPIGENETIC SILENCING OF THE TRANSCRIPTION FACTOR TWIST2 (DERMO1) IN IG V(H) MUTATED CLL AND DESCRIBE A SEMIQUANTITATIVE ASSAY TO STUDY PROMOTER METHYLATION OF THIS GENE IN PRIMARY TUMOR CELLS. MATERIALS AND METHODS: TWIST2 PROMOTER METHYLATION WAS IDENTIFIED BY RESTRICTION LANDMARK GENOME SCANNING. SOUTHERN BLOT (SB), BISULFITE SEQUENCING, AND COMBINED BISULFITE RESTRICTION ANALYSIS (COBRA), AND QUANTITATIVE SB-COBRA WAS PERFORMED TO STUDY METHYLATION OF THE TWIST2 PROMOTER. REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION ASSAYS WERE USED TO STUDY TWIST2 EXPRESSION IN CLL CELLS. RESULTS: FOLLOWING IDENTIFICATION AND CONFIRMATION OF TWIST2 METHYLATION IN CLL PATIENTS, WE DEMONSTRATED THAT EXPRESSION OF THIS TRANSCRIPTION FACTOR IS RELATED TO THE DEGREE OF PROMOTER METHYLATION. EXPRESSION OF TWIST2 IN A CLL CELL LINE IN WHICH THE PROMOTER IS METHYLATED WAS INCREASED FOLLOWING DECITABINE TREATMENT. WE NEXT STUDIED 53 PATIENTS BY COBRA AND DEMONSTRATED THAT 72% OF PATIENT SAMPLES WITH MUTATED IG V(H) SHOW TWIST2 METHYLATION, WHILE ONLY 16% OF PATIENT SAMPLES WITH UNMUTATED IG V(H) WERE METHYLATED (P < .001). IN A SUBSET OF PATIENTS, METHYLATION OF TWIST2 CORRELATED WITH MRNA EXPRESSION. CONCLUSION: TWIST2 IS DIFFERENTIALLY METHYLATED IN CLL CELLS RELATIVE TO IG V(H) MUTATIONAL STATUS AND CAN BE QUANTITATIVELY MONITORED BY SB-COBRA. BASED ON THE KNOWN ROLE OF TWIST2 IN SILENCING P53 FUNCTION IN OTHER MALIGNANCIES, FUTURE STUDIES SHOULD FOCUS ON THE ROLE OF TWIST2 IN CLL AND RELATED LYMPHOPROLIFERATIVE DISEASES.	2005	
                                                                                                                                 
5  1937  25 EOMES IS ESSENTIAL FOR ANTITUMOR ACTIVITY OF CD8(+) T CELLS IN CHRONIC LYMPHOCYTIC LEUKEMIA. GENOME-WIDE ASSOCIATION STUDIES IDENTIFIED A SINGLE-NUCLEOTIDE POLYMORPHISM (SNP) AFFECTING THE TRANSCRIPTION FACTOR EOMESODERMIN (EOMES) ASSOCIATED WITH A SIGNIFICANTLY INCREASED RISK TO DEVELOP CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). EPIGENETIC ANALYSES, RNA SEQUENCING, AND FLOW CYTOMETRY REVEALED THAT EOMES IS NOT EXPRESSED IN CLL CELLS, BUT IN CD8(+) T CELLS FOR WHICH EOMES IS A KNOWN MASTER REGULATOR. WE THUS HYPOTHESIZED THAT THE INCREASED CLL RISK ASSOCIATED WITH THE EOMES SNP MIGHT BE EXPLAINED BY ITS NEGATIVE IMPACT ON CD8(+) T-CELL-MEDIATED IMMUNE CONTROL OF CLL. FLOW CYTOMETRY ANALYSES REVEALED A HIGHER EOMES EXPRESSION IN CD8(+) T CELLS OF CLL PATIENTS COMPARED TO HEALTHY INDIVIDUALS, AND AN ACCUMULATION OF PD-1(+) EOMES(+) CD8(+) T CELLS IN LYMPH NODES RATHER THAN BLOOD OR BONE MARROW IN CLL. THIS WAS IN LINE WITH AN OBSERVED EXPANSION OF EOMES(+) CD8(+) T CELLS IN THE SPLEEN OF LEUKEMIC EMICRO-TCL1 MICE. AS EOMES EXPRESSION WAS HIGHEST IN CD8(+) T CELLS THAT EXPRESS INHIBITORY RECEPTORS, AN INVOLVEMENT OF EOMES IN T-CELL EXHAUSTION AND DYSFUNCTION SEEMS LIKELY. INTERESTINGLY, EOMES-DEFICIENCY IN CD8(+) T CELLS RESULTED IN THEIR IMPAIRED EXPANSION ASSOCIATED WITH DECREASED CLL CONTROL IN MICE. OVERALL, THESE OBSERVATIONS SUGGEST THAT EOMES IS ESSENTIAL FOR CD8(+) T-CELL EXPANSION AND/OR MAINTENANCE, AND THEREFORE INVOLVED IN ADAPTIVE IMMUNE CONTROL OF CLL.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
6  1659  23 DOWN-REGULATION OF CANDIDATE TUMOR SUPPRESSOR GENES WITHIN CHROMOSOME BAND 13Q14.3 IS INDEPENDENT OF THE DNA METHYLATION PATTERN IN B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA. LOSS OF GENOMIC MATERIAL FROM CHROMOSOMAL BAND 13Q14.3 IS THE MOST COMMON GENETIC IMBALANCE IN B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) AND MANTLE CELL LYMPHOMA, POINTING TO THE INVOLVEMENT OF THIS REGION IN A TUMOR SUPPRESSOR MECHANISM. FROM THE MINIMALLY DELETED REGION, 3 CANDIDATE GENES HAVE BEEN ISOLATED, RFP2, BCMS, AND BCMSUN. DNA SEQUENCE ANALYSES HAVE FAILED TO DETECT SMALL MUTATIONS IN ANY OF THESE GENES, SUGGESTING A DIFFERENT PATHOMECHANISM, MOST LIKELY HAPLOINSUFFICIENCY. WE, THEREFORE, TESTED B-CLL PATIENTS FOR EPIGENETIC ABERRATIONS BY MEASURING EXPRESSION OF GENES FROM 13Q14.3 AND METHYLATION OF THEIR PROMOTOR REGION. RB1, CLLD7, KPNA3, CLLD6, AND RFP2 WERE DOWN-REGULATED IN B-CLL PATIENTS AS COMPARED WITH B CELLS OF HEALTHY DONORS, WITH RFP2 SHOWING THE MOST PRONOUNCED LOSS OF EXPRESSION. TO TEST WHETHER THIS LOSS OF GENE EXPRESSION IS ASSOCIATED WITH METHYLATION OF CPG ISLANDS IN THE RESPECTIVE PROMOTOR REGIONS, WE PERFORMED METHYLATION-SENSITIVE QUANTITATIVE POLYMERASE CHAIN REACTION ANALYSES AND BISULFITE SEQUENCING ON DNA FROM B-CLL PATIENTS. NO DIFFERENCE IN THE METHYLATION PATTERNS COULD BE DETECTED IN ANY CPG ISLAND OF THE MINIMALLY DELETED REGION. DOWN-REGULATION OF GENES WITHIN CHROMOSOMAL BAND 13Q14.3 IN B-CLL IS IN LINE WITH THE CONCEPT OF HAPLOINSUFFICIENCY, BUT THIS TUMOR-SPECIFIC PHENOMENON IS NOT ASSOCIATED WITH DNA METHYLATION.	2002	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
7  3500  23 IDENTIFICATION OF NOVEL, CLONALLY STABLE, SOMATIC MUTATIONS TARGETING TRANSCRIPTION FACTORS PAX5 AND NKX2-3, THE EPIGENETIC REGULATOR LRIF1, AND BRAF IN A CASE OF ATYPICAL B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA HARBORING A T(14;18)(Q32;Q21). DIAGNOSIS OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) IS USUALLY STRAIGHTFORWARD, INVOLVING CLINICAL, IMMUNOPHENOTYPIC (MATUTES SCORE), AND (IMMUNO)GENETIC ANALYSES (TO REFINE PATIENT PROGNOSIS FOR TREATMENT). CLL CASES WITH ATYPICAL PRESENTATION (E.G., MATUTES </= 3) ARE ALSO ENCOUNTERED, AND FOR THESE DISEASES, BIOLOGY AND PROGNOSTIC IMPACT ARE LESS CLEAR. HERE WE REPORT THE GENOMIC CHARACTERIZATION OF A CASE OF ATYPICAL B-CLL IN A 70-YR-OLD MALE PATIENT; B-CLL CELLS SHOWED A MATUTES SCORE OF 3, CHROMOSOMAL TRANSLOCATION T(14;18)(Q32;Q21) (BCL2/IGH), MUTATED IGHV, DELETION 17P, AND MUTATIONS IN BCL2, NOTCH1 (SUBCLONAL), AND TP53 (SUBCLONAL). QUITE STRIKINGLY, A NOVEL PAX5 MUTATION THAT WAS PREDICTED TO BE LOSS OF FUNCTION WAS ALSO SEEN. EXOME SEQUENCING IDENTIFIED, IN ADDITION, A POTENTIALLY ACTIONABLE BRAF MUTATION, TOGETHER WITH NOVEL SOMATIC MUTATIONS AFFECTING THE HOMEOBOX TRANSCRIPTION FACTOR NKX2-3, KNOWN TO CONTROL B-LYMPHOCYTE DEVELOPMENT AND HOMING, AND THE EPIGENETIC REGULATOR LRIF1, WHICH IS IMPLICATED IN CHROMATIN COMPACTION AND GENE SILENCING. NEITHER NKX2-3 NOR LRIF1 MUTATIONS, PREDICTED TO BE LOSS OF FUNCTION, HAVE PREVIOUSLY BEEN REPORTED IN B-CLL. SEQUENCING CONFIRMED THE PRESENCE OF THESE MUTATIONS TOGETHER WITH BCL2, NOTCH1, AND BRAF MUTATIONS, WITH THE T(14;18)(Q32;Q21) TRANSLOCATION, IN THE INITIAL DIAGNOSTIC SAMPLE OBTAINED 12 YR PRIOR. THIS IS SUGGESTIVE OF A ROLE FOR THESE NOVEL MUTATIONS IN B-CLL INITIATION AND STABLE CLONAL EVOLUTION, INCLUDING UPON TREATMENT WITHDRAWAL. THIS CASE EXTENDS THE SPECTRUM OF ATYPICAL B-CLL WITH T(14;18)(Q32;Q21) AND HIGHLIGHTS THE VALUE OF MORE GLOBAL PRECISION GENOMICS FOR PATIENT FOLLOW-UP AND TREATMENT IN THESE PATIENTS.	2021	
                                                                                                 
8   437  27 ANTIGEN RECEPTOR STEREOTYPY IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE DISCOVERY OF ALMOST IDENTICAL OR 'STEREOTYPED' B-CELL RECEPTOR IMMUNOGLOBULINS (BCR IG) AMONG UNRELATED PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CEMENTED THE IDEA OF ANTIGEN SELECTION IN DISEASE ONTOGENY AND EVOLUTION. THE SYSTEMATIC ANALYSIS OF THE STEREOTYPY PHENOMENON IN CLL REVEALED THAT AROUND ONE-THIRD OF CLL PATIENTS MAY BE GROUPED INTO SUBSETS BASED ON SHARED SEQUENCE MOTIFS WITHIN THE VARIABLE HEAVY COMPLEMENTARITY DETERMINING REGION 3. STEREOTYPED SUBSETS DISPLAY A STRIKINGLY SIMILAR BIOLOGY OF THE LEUKEMIC CLONES, REFERRING TO MANY DIFFERENT LEVELS, FROM THE IMMUNOGENETIC AND GENETIC AND EXTENDING TO THE EPIGENETIC AND FUNCTIONAL LEVELS. EVEN MORE IMPORTANTLY, THE HOMOGENEITY OF STEREOTYPED SUBSETS HAS CLINICAL CONSEQUENCES AS PATIENTS ASSIGNED TO THE SAME STEREOTYPED SUBSET GENERALLY EXHIBIT AN OVERALL SIMILAR DISEASE COURSE AND OUTCOME. IN OTHER WORDS, STEREOTYPY-BASED PATIENT CLASSIFICATION OF CLL HAS ALREADY PROVIDED A MORE COMPARTMENTALIZED VIEW OF THIS OTHERWISE HETEROGENEOUS DISEASE AND CAN ASSIST IN REFINING PROGNOSTICATION MODELS. WHILE THIS IS RELEVANT ONLY FOR THE ONE-THIRD OF CASES EXPRESSING STEREOTYPED BCR IG; IN PRINCIPLE, HOWEVER, THE FINDINGS FROM FURTHER ANALYSIS OF THE STEREOTYPED SUBSETS MAY ALSO CONTRIBUTE TOWARDS IMPROVED UNDERSTANDING OF THE REMAINING NON-STEREOTYPED FRACTION OF CLL PATIENTS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
9  5663  23 SEZARY SYNDROME COEXISTING WITH B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA: CASE REPORT AND REVIEW OF THE LITERATURE. INTRODUCTION: THE SIMULTANEOUS PRESENTATION OF CHRONIC B-CELL LYMPHOCYTIC LEUKEMIA (B-CLL) AND CUTANEOUS T-CELL LYMPHOMA (CTCL) IS EXTREMELY RARE. CASE REPORT: WE DESCRIBE A PATIENT WITH B-CLL AND SEZARY SYNDROME (SS), AN ERYTHRODERMIC AND LEUKEMIC VARIANT OF CTCL. DESPITE TREATMENT, THE SS PROGRESSED TO INVOLVE INTERNAL ORGANS AND EVENTUAL DEATH OF THE PATIENT FROM SEPSIS. THIS IS THE FIRST REPORTED CASE OF SS COEXISTING WITH CHRONIC LYMPHOCYTIC LEUKEMIA IN WHICH AN ANTI-V BETA 13.6 ANTIBODY WAS USED TO SERIALLY TRACK CHANGES IN CIRCULATING NEOPLASTIC T CELLS VIS-A-VIS NEOPLASTIC B CELLS AND TO DETECT NEOPLASTIC T CELLS IN ASCITIC FLUID NEAR THE END OF THE PATIENT'S LIFE. DISCUSSION: WE SPECULATE THAT THE COEXISTENCE OF B-CLL AND CTCL IS THE RESULT OF AN INITIATING GENETIC OR EPIGENETIC DEFECT AT THE LEVEL OF THE COMMON LYMPHOID STEM CELL THAT PREDISPOSES BOTH B-CELL AND T-CELL LINEAGES TO ADDITIONAL ONCOGENIC CHANGES AT A MORE ADVANCED STAGE OF DIFFERENTIATION.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
10  5243  20 PROGNOSTIC IMPACT OF EPIGENETIC CLASSIFICATION IN CHRONIC LYMPHOCYTIC LEUKEMIA: THE CASE OF SUBSET #2. BASED ON THE METHYLATION STATUS OF 5 SINGLE CPG SITES, A NOVEL EPIGENETIC CLASSIFICATION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WAS RECENTLY PROPOSED, CLASSIFYING CLL PATIENTS INTO 3 CLINICO-BIOLOGICAL SUBGROUPS WITH DIFFERENT OUTCOME, TERMED MEMORY LIKE CLL (M-CLL), NAIVE LIKE CLL (N-CLL), AND A THIRD INTERMEDIATE CLL SUBGROUP (I-CLL). WHILE M-CLL AND N-CLL PATIENTS AT LARGE CORRESPONDED TO PATIENTS CARRYING MUTATED AND UNMUTATED IGHV GENES, RESPECTIVELY, LIMITED INFORMATION EXISTS REGARDING THE LESS DEFINED I-CLL GROUP. USING PYROSEQUENCING, WE INVESTIGATED THE PROGNOSTIC IMPACT OF THE PROPOSED 5 CPG SIGNATURE IN A WELL-CHARACTERIZED CLL COHORT (135 CASES), INCLUDING IGHV-MUTATED AND UNMUTATED PATIENTS AS WELL AS CLINICALLY AGGRESSIVE STEREOTYPED SUBSET #2 PATIENTS. OVERALL, WE CONFIRMED THE SIGNATURE'S ASSOCIATION WITH ESTABLISHED PROGNOSTIC MARKERS. MOREOVER, IN THE PRESENCE OF THE IGHV MUTATIONAL STATUS, THE EPIGENETIC SIGNATURE REMAINED INDEPENDENTLY ASSOCIATED WITH BOTH TIME-TO-FIRST-TREATMENT AND OVERALL SURVIVAL IN MULTIVARIATE ANALYSES. AS A PRIME FINDING, WE OBSERVED THAT SUBSET #2 PATIENTS WERE PREDOMINANTLY CLASSIFIED AS I-CLL, PROBABLY REFLECTING THEIR BORDERLINE IGHV MUTATIONAL STATUS (97-99% GERMLINE IDENTITY), THOUGH HAVING A SIMILARLY POOR PROGNOSIS AS N-CLL PATIENTS. IN SUMMARY, WE VALIDATED THE EPIGENETIC CLASSIFIER AS AN INDEPENDENT FACTOR IN CLL PROGNOSTICATION AND PROVIDE FURTHER EVIDENCE THAT SUBSET #2 IS A MEMBER OF THE I-CLL GROUP, HENCE SUPPORTING THE EXISTENCE OF A THIRD, INTERMEDIATE EPIGENETIC SUBGROUP.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                   
11  6390  21 THE ROLE OF THE GENETIC ABNORMALITIES, EPIGENETIC AND MICRORNA IN THE PROGNOSIS OF CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS INCREASED PROLIFERATION OF B-CELLS WITH PERIPHERAL BLOOD AND BONE MARROW INVOLVEMENT, WHICH IS USUALLY OBSERVED IN OLDER PEOPLE. GENETIC MUTATIONS, EPIGENETIC CHANGES AND MIRS PLAY A ROLE IN CLL PATHOGENESIS. DEL 11Q, DEL L17Q, DEL 6Q, TRISOMY 12, P53 AND IGVH MUTATIONS ARE THE MOST IMPORTANT GENETIC CHANGES IN CLL. DELETION OF MIR-15A AND MIR-16A CAN INCREASE BCL2 GENE EXPRESSION, MIR-29 AND MIR-181 DELETIONS DECREASE THE EXPRESSION OF TCL1, AND MIR-146A DELETION PREVENTS TUMOR METASTASIS. EPIGENETIC CHANGES SUCH AS HYPO- AND HYPERMETHYLATION, UBIQUITINATION, HYPO- AND HYPERACETYLATION OF GENE PROMOTERS INVOLVED IN CLL PATHOGENESIS CAN ALSO PLAY A ROLE IN CLL. EXPRESSION OF CD38 AND ZAP70, PRESENCE OR ABSENCE OF MUTATION IN IGVH AND P53 MUTATION ARE AMONG THE FACTORS INVOLVED IN CLL PROGNOSIS. USE OF MONOCLONAL ANTIBODIES AGAINST SURFACE MARKERS OF B-CELLS LIKE ANTI-CD20 AS WELL AS TYROSINE KINASE INHIBITORS ARE THE MOST IMPORTANT THERAPEUTIC APPROACHES FOR CLL.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
12  3522  20 IL-10 PRODUCTION BY CLL CELLS IS ENHANCED IN THE ANERGIC IGHV MUTATED SUBSET AND ASSOCIATES WITH REDUCED DNA METHYLATION OF THE IL10 LOCUS. CHRONIC LYMPHOCYTIC LEUKEMIAS (CLLS) WITH UNMUTATED (U-CLL) OR MUTATED (M-CLL) IGHV HAVE VARIABLE FEATURES OF IMMUNOSUPPRESSION, POSSIBLY INFLUENCED BY THOSE CLL CELLS ACTIVATED TO PRODUCE INTERLEUKIN 10 (IL-10). THE TWO SUBSETS DIFFER IN THEIR LEVELS OF ANERGY, DEFINED BY LOW SURFACE IMMUNOGLOBULIN M LEVELS/SIGNALING CAPACITY, AND IN THEIR DNA METHYLATION PROFILE, PARTICULARLY VARIABLE IN M-CLL. WE HAVE NOW FOUND THAT LEVELS OF IL-10 PRODUCED BY ACTIVATED CLL CELLS WERE HIGHLY VARIABLE. LEVELS WERE HIGHER IN M-CLL THAN IN U-CLL AND CORRELATED WITH ANERGY. DNA METHYLATION ANALYSIS OF IL10 LOCUS REVEALED TWO PREVIOUSLY UNCHARACTERIZED 'VARIABLY METHYLATED REGIONS' (CLL-VMRS1/2) IN THE GENE BODY, BUT SIMILARLY LOW METHYLATION IN THE PROMOTER OF BOTH U-CLL AND M-CLL. CLL-VMR1/2 METHYLATION WAS LOWER IN M-CLL THAN IN U-CLL AND INVERSELY CORRELATED WITH IL-10 INDUCTION. A FUNCTIONAL SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3 (STAT3) BINDING SITE IN CLL-VMR2 WAS CONFIRMED BY PROXIMITY LIGATION AND LUCIFERASE ASSAYS, WHEREAS INHIBITION OF SYK-MEDIATED STAT3 ACTIVATION RESULTED IN SUPPRESSION OF IL10. THE DATA SUGGEST EPIGENETIC CONTROL OF IL-10 PRODUCTION. HIGHER TUMOR LOAD MAY COMPENSATE THE REDUCED IL-10 PRODUCTION IN U-CLL, ACCOUNTING FOR CLINICAL IMMUNOSUPPRESSION IN BOTH SUBSETS. THE OBSERVATION THAT SYK INHIBITION ALSO SUPPRESSES IL-10 PROVIDES A POTENTIAL NEW RATIONALE FOR THERAPEUTIC TARGETING AND IMMUNOLOGICAL RESCUE BY SYK INHIBITORS IN CLL.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                               
13  6709  19 VIRAL TRANSDUCTION OF PRIMARY HUMAN LYMPHOMA B CELLS REVEALS MECHANISMS OF NOTCH-MEDIATED IMMUNE ESCAPE. HOTSPOT MUTATIONS IN THE PEST-DOMAIN OF NOTCH1 AND NOTCH2 ARE RECURRENTLY IDENTIFIED IN B CELL MALIGNANCIES. TO ADDRESS HOW NOTCH-MUTATIONS CONTRIBUTE TO A DISMAL PROGNOSIS, WE HAVE GENERATED ISOGENIC PRIMARY HUMAN TUMOR CELLS FROM PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) AND MANTLE CELL LYMPHOMA (MCL), DIFFERING ONLY IN THEIR EXPRESSION OF THE INTRACELLULAR DOMAIN (ICD) OF NOTCH1 OR NOTCH2. OUR DATA DEMONSTRATE THAT BOTH NOTCH-PARALOGS FACILITATE IMMUNE-ESCAPE OF MALIGNANT B CELLS BY UP-REGULATING PD-L1, PARTLY DEPENDENT ON AUTOCRINE INTERFERON-GAMMA SIGNALING. IN ADDITION, NOTCH-ACTIVATION CAUSES SILENCING OF THE ENTIRE HLA-CLASS II LOCUS VIA EPIGENETIC REGULATION OF THE TRANSCRIPTIONAL CO-ACTIVATOR CIITA. NOTABLY, WHILE NOTCH1 AND NOTCH2 GOVERN SIMILAR TRANSCRIPTIONAL PROGRAMS, DISEASE-SPECIFIC DIFFERENCES IN THEIR EXPRESSION LEVELS CAN FAVOR PARALOG-SPECIFIC SELECTION. IMPORTANTLY, NOTCH-ICD ALSO STRONGLY DOWN-REGULATES THE EXPRESSION OF CD19, POSSIBLY LIMITING THE EFFECTIVENESS OF IMMUNE-THERAPIES. THESE NOTCH-MEDIATED IMMUNE ESCAPE MECHANISMS ARE ASSOCIATED WITH THE EXPANSION OF EXHAUSTED CD8(+) T CELLS IN VIVO.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
14  5462  22 RESEARCH PROGRESS ON EPIGENETICS OF SMALL B-CELL LYMPHOMA. SMALL B-CELL LYMPHOMA IS THE CLASSIFICATION OF B-CELL CHRONIC LYMPHOPROLIFERATIVE DISORDERS THAT INCLUDE CHRONIC LYMPHOCYTIC LEUKAEMIA/SMALL LYMPHOCYTIC LYMPHOMA, FOLLICULAR LYMPHOMA, MANTLE CELL LYMPHOMA, MARGINAL ZONE LYMPHOMA, LYMPHOPLASMACYTIC LYMPHOMA/WALDENSTROM MACROGLOBULINEMIA. THE CLINICAL PRESENTATION IS SOMEWHAT HETEROGENEOUS, AND ITS OCCURRENCE AND DEVELOPMENT MECHANISMS ARE NOT YET PRECISE AND MAY INVOLVE EPIGENETIC CHANGES. EPIGENETIC ALTERATIONS MAINLY INCLUDE DNA METHYLATION, HISTONE MODIFICATION, AND NON-CODING RNA, WHICH ARE ESSENTIAL FOR GENETIC DETECTION, EARLY DIAGNOSIS, AND ASSESSMENT OF TREATMENT RESISTANCE IN SMALL B-CELL LYMPHOMA. AS CHRONIC LYMPHOCYTIC LEUKEMIA/SMALL LYMPHOCYTIC LYMPHOMA HAS ALREADY BEEN REPORTED IN THE LITERATURE, THIS ARTICLE FOCUSES ON SMALL B-CELL LYMPHOMAS SUCH AS FOLLICULAR LYMPHOMA, MANTLE CELL LYMPHOMA, MARGINAL ZONE LYMPHOMA, AND WALDENSTROM MACROGLOBULINEMIA. IT DISCUSSES RECENT DEVELOPMENTS IN EPIGENETIC RESEARCH TO DIAGNOSE AND TREAT THIS GROUP OF LYMPHOMAS. THIS REVIEW PROVIDES NEW IDEAS FOR THE TREATMENT AND PROGNOSIS ASSESSMENT OF SMALL B-CELL LYMPHOMA BY EXPLORING THE CONNECTION BETWEEN SMALL B-CELL LYMPHOMA AND EPIGENETICS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
15  1424  18 DIFFERENTIAL DNA METHYLATION OF GENE PROMOTERS IN SMALL B-CELL LYMPHOMAS. IMPROVED CARE OF PATIENTS WITH SMALL B-CELL LYMPHOMAS (SBCLS) IS LIKELY TO RESULT FROM THE ONGOING DISCOVERY OF MOLECULAR MARKERS THAT BETTER DEFINE THESE MALIGNANT NEOPLASMS. WE IDENTIFIED MULTIPLE GENE LOCI WHOSE DNA METHYLATION PATTERNS DIFFERED BETWEEN 3 TYPES OF SBCL: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA/SMALL LYMPHOCYTIC LYMPHOMA, MANTLE CELL LYMPHOMA, AND GRADES I AND II FOLLICULAR LYMPHOMA. THIS ANALYSIS WAS PERFORMED USING AN OLIGONUCLEOTIDE MICROARRAY THAT ALLOWED DETERMINATION OF THE DNA METHYLATION STATUS OF 156 LOCI IN 38 GENES. COMBINED BISULFITE RESTRICTION ANALYSIS AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WERE USED TO VALIDATE THE DIFFERENTIAL METHYLATION OF 6 OF THESE GENES. BY USING NON-HODGKIN LYMPHOMA CELL LINES AS MODELS, THESE GENES WERE EXAMINED FURTHER FOR METHYLATION AND GENE EXPRESSION RELATIONSHIPS. THIS STUDY ILLUSTRATES NONRANDOM EPIGENETIC ALTERATIONS IN SBCLS THAT SEEM TO PREFERENTIALLY INVOLVE LYMPHOMAS OF GERMINAL CENTER DERIVATION.	2005	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
16  5245  29 PROGNOSTIC RELEVANCE OF INTEGRATED GENETIC PROFILING IN ADULT T-CELL LEUKEMIA/LYMPHOMA. ADULT T-CELL LEUKEMIA/LYMPHOMA (ATL) IS A HETEROGENEOUS GROUP OF PERIPHERAL T-CELL MALIGNANCIES CHARACTERIZED BY HUMAN T-CELL LEUKEMIA VIRUS TYPE-1 INFECTION, WHOSE GENETIC PROFILE HAS RECENTLY BEEN FULLY INVESTIGATED. HOWEVER, IT IS STILL POORLY UNDERSTOOD HOW THESE ALTERATIONS AFFECT CLINICAL FEATURES AND PROGNOSIS. WE INVESTIGATED THE EFFECTS OF GENETIC ALTERATIONS COMMONLY FOUND IN ATL ON DISEASE PHENOTYPES AND CLINICAL OUTCOMES, BASED ON GENOTYPING DATA OBTAINED FROM 414 AND 463 ATL PATIENTS USING TARGETED-CAPTURE SEQUENCING AND SINGLE NUCLEOTIDE POLYMORPHISM ARRAY KARYOTYPING, RESPECTIVELY. AGGRESSIVE (ACUTE/LYMPHOMA) SUBTYPES WERE ASSOCIATED WITH AN INCREASED BURDEN OF GENETIC AND EPIGENETIC ALTERATIONS, HIGHER FREQUENCIES OF TP53 AND IRF4 MUTATIONS, AND MANY COPY NUMBER ALTERATIONS (CNAS), INCLUDING PD-L1 AMPLIFICATIONS AND CDKN2A DELETIONS, COMPARED WITH INDOLENT (CHRONIC/SMOLDERING) SUBTYPES. BY CONTRAST, STAT3 MUTATIONS WERE MORE CHARACTERISTIC OF INDOLENT ATL. HIGHER NUMBERS OF SOMATIC MUTATIONS AND CNAS SIGNIFICANTLY CORRELATED WITH WORSE SURVIVAL. IN A MULTIVARIATE ANALYSIS INCORPORATING BOTH CLINICAL FACTORS AND GENETIC ALTERATIONS, THE JAPAN CLINICAL ONCOLOGY GROUP PROGNOSTIC INDEX HIGH-RISK, OLDER AGE, PRKCB MUTATIONS, AND PD-L1 AMPLIFICATIONS WERE INDEPENDENT POOR PROGNOSTIC FACTORS IN AGGRESSIVE ATL. IN INDOLENT ATL, IRF4 MUTATIONS, PD-L1 AMPLIFICATIONS, AND CDKN2A DELETIONS WERE SIGNIFICANTLY ASSOCIATED WITH SHORTER SURVIVAL, ALTHOUGH THE CHRONIC SUBTYPE WITH UNFAVORABLE CLINICAL FACTORS WAS ONLY MARGINALLY SIGNIFICANT. THUS, SOMATIC ALTERATIONS CHARACTERIZING AGGRESSIVE DISEASES PREDICT WORSE PROGNOSIS IN INDOLENT ATL, AMONG WHICH PD-L1 AMPLIFICATIONS ARE A STRONG GENETIC PREDICTOR IN BOTH AGGRESSIVE AND INDOLENT ATL. ATL SUBTYPES ARE FURTHER CLASSIFIED INTO MOLECULARLY DISTINCT SUBSETS WITH DIFFERENT PROGNOSIS. GENETIC PROFILING MIGHT CONTRIBUTE TO IMPROVED PROGNOSTICATION AND MANAGEMENT OF ATL PATIENTS.	2018	

17   939  20 CHRONIC LYMPHOCYTIC LEUKEMIA AND 13Q14: MIRS AND MORE. LOSS OF A CRITICAL REGION IN 13Q14.3 [DEL(13Q)] IS THE MOST COMMON GENOMIC ABERRATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), OCCURRING IN MORE THAN 50% OF PATIENTS (STILGENBAUER ET AL., ONCOGENE 1998;16:1891 - 1897, DOHNER ET AL., N ENGL J MED 2000;343:1910 - 1916). DESPITE EXTENSIVE INVESTIGATIONS, NO POINT MUTATIONS HAVE BEEN FOUND IN THE REMAINING ALLELE THAT WOULD INACTIVATE ONE OF THE CANDIDATE TUMOR SUPPRESSOR GENES AND EXPLAIN THE PATHOMECHANISM POSTULATED FOR THIS REGION. HOWEVER, THE GENES IN THE REGION ARE SIGNIFICANTLY DOWN-REGULATED IN CLL CELLS, MORE THAN WOULD BE EXPECTED BY GENE DOSAGE, AND RECENTLY A COMPLEX EPIGENETIC REGULATORY MECHANISM WAS IDENTIFIED FOR 13Q14.3 IN NON-MALIGNANT CELLS THAT INVOLVES ASYNCHRONOUS REPLICATION TIMING AND MONOALLELIC EXPRESSION OF CANDIDATE TUMOR SUPPRESSOR GENES. HERE, WE PROPOSE A MODEL OF A MULTIGENIC PATHOMECHANISM IN 13Q14.3, WHERE SEVERAL TUMOR SUPPRESSOR GENES, INCLUDING THE MIRNA GENES MIR-16-1 AND MIR-15A, ARE CO-REGULATED BY THE TWO LONG NON-CODING RNA GENES DLEU1 AND DLEU2 THAT SPAN THE CRITICAL REGION. FURTHERMORE, WE PROPOSE THESE CO-REGULATED GENES TO BE INVOLVED IN THE SAME MOLECULAR PATHWAYS, THEREBY ALSO FORMING A FUNCTIONAL GENE CLUSTER. ELUCIDATING THE MOLECULAR AND CELLULAR FUNCTION OF THE 13Q14.3 CANDIDATE GENES WILL SHED LIGHT ON THE UNDERLYING PATHOMECHANISM OF CLL.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
18   940  29 CHRONIC LYMPHOCYTIC LEUKEMIA AND MANTLE CELL LYMPHOMA: CROSSROADS OF GENETIC AND MICROENVIRONMENT INTERACTIONS. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) AND MANTLE CELL LYMPHOMA (MCL) ARE 2 WELL-DEFINED ENTITIES THAT DIVERGE IN THEIR BASIC PATHOGENIC MECHANISMS AND CLINICAL EVOLUTION BUT THEY SHARE EPIDEMIOLOGICAL CHARACTERISTICS, CELLS OF ORIGIN, MOLECULAR ALTERATIONS, AND CLINICAL FEATURES THAT DIFFER FROM OTHER LYMPHOID NEOPLASMS. CLL AND MCL ARE CLASSICALLY CONSIDERED INDOLENT AND AGGRESSIVE NEOPLASMS, RESPECTIVELY. HOWEVER, THE CLINICAL EVOLUTION OF BOTH TUMORS IS VERY HETEROGENEOUS, WITH SUBSETS OF PATIENTS HAVING STABLE DISEASE FOR A LONG TIME WHEREAS OTHERS REQUIRE IMMEDIATE INTERVENTION. BOTH CLL AND MCL INCLUDE 2 MAJOR MOLECULAR SUBTYPES THAT SEEM TO DERIVE FROM ANTIGEN-EXPERIENCED CD5(+) B CELLS THAT RETAIN A NAIVE OR MEMORY-LIKE EPIGENETIC SIGNATURE AND CARRY A VARIABLE LOAD OF IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE REGION SOMATIC MUTATIONS FROM TRULY UNMUTATED TO HIGHLY MUTATED, RESPECTIVELY. THESE 2 SUBTYPES OF TUMORS DIFFER IN THEIR MOLECULAR PATHWAYS, GENOMIC ALTERATIONS, AND CLINICAL BEHAVIOR, BEING MORE AGGRESSIVE IN NAIVE-LIKE THAN MEMORY-LIKE-DERIVED TUMORS IN BOTH CLL AND MCL. THE PATHOGENESIS OF THE 2 ENTITIES INTEGRATES THE RELEVANT INFLUENCE OF B-CELL RECEPTOR SIGNALING, TUMOR CELL MICROENVIRONMENT INTERACTIONS, GENOMIC ALTERATIONS, AND EPIGENOME MODIFICATIONS THAT CONFIGURE THE EVOLUTION OF THE TUMORS AND OFFER NEW POSSIBILITIES FOR THERAPEUTIC INTERVENTION. THIS REVIEW WILL FOCUS ON THE SIMILARITIES AND DIFFERENCES OF THESE 2 TUMORS BASED ON RECENT STUDIES THAT ARE ENHANCING THE UNDERSTANDING OF THEIR PATHOGENESIS AND CREATING SOLID BASES FOR NEW MANAGEMENT STRATEGIES.	2018	
                                                                                                                                                                                                                                                                                                                                             
19  3024  26 GENETICS AND PATHOGENESIS OF DIFFUSE LARGE B-CELL LYMPHOMA. BACKGROUND: DIFFUSE LARGE B-CELL LYMPHOMAS (DLBCLS) ARE PHENOTYPICALLY AND GENETICALLY HETEROGENEOUS. GENE-EXPRESSION PROFILING HAS IDENTIFIED SUBGROUPS OF DLBCL (ACTIVATED B-CELL-LIKE [ABC], GERMINAL-CENTER B-CELL-LIKE [GCB], AND UNCLASSIFIED) ACCORDING TO CELL OF ORIGIN THAT ARE ASSOCIATED WITH A DIFFERENTIAL RESPONSE TO CHEMOTHERAPY AND TARGETED AGENTS. WE SOUGHT TO EXTEND THESE FINDINGS BY IDENTIFYING GENETIC SUBTYPES OF DLBCL BASED ON SHARED GENOMIC ABNORMALITIES AND TO UNCOVER THERAPEUTIC VULNERABILITIES BASED ON TUMOR GENETICS. METHODS: WE STUDIED 574 DLBCL BIOPSY SAMPLES USING EXOME AND TRANSCRIPTOME SEQUENCING, ARRAY-BASED DNA COPY-NUMBER ANALYSIS, AND TARGETED AMPLICON RESEQUENCING OF 372 GENES TO IDENTIFY GENES WITH RECURRENT ABERRATIONS. WE DEVELOPED AND IMPLEMENTED AN ALGORITHM TO DISCOVER GENETIC SUBTYPES BASED ON THE CO-OCCURRENCE OF GENETIC ALTERATIONS. RESULTS: WE IDENTIFIED FOUR PROMINENT GENETIC SUBTYPES IN DLBCL, TERMED MCD (BASED ON THE CO-OCCURRENCE OF MYD88(L265P) AND CD79B MUTATIONS), BN2 (BASED ON BCL6 FUSIONS AND NOTCH2 MUTATIONS), N1 (BASED ON NOTCH1 MUTATIONS), AND EZB (BASED ON EZH2 MUTATIONS AND BCL2 TRANSLOCATIONS). GENETIC ABERRATIONS IN MULTIPLE GENES DISTINGUISHED EACH GENETIC SUBTYPE FROM OTHER DLBCLS. THESE SUBTYPES DIFFERED PHENOTYPICALLY, AS JUDGED BY DIFFERENCES IN GENE-EXPRESSION SIGNATURES AND RESPONSES TO IMMUNOCHEMOTHERAPY, WITH FAVORABLE SURVIVAL IN THE BN2 AND EZB SUBTYPES AND INFERIOR OUTCOMES IN THE MCD AND N1 SUBTYPES. ANALYSIS OF GENETIC PATHWAYS SUGGESTED THAT MCD AND BN2 DLBCLS RELY ON "CHRONIC ACTIVE" B-CELL RECEPTOR SIGNALING THAT IS AMENABLE TO THERAPEUTIC INHIBITION. CONCLUSIONS: WE UNCOVERED GENETIC SUBTYPES OF DLBCL WITH DISTINCT GENOTYPIC, EPIGENETIC, AND CLINICAL CHARACTERISTICS, PROVIDING A POTENTIAL NOSOLOGY FOR PRECISION-MEDICINE STRATEGIES IN DLBCL. (FUNDED BY THE INTRAMURAL RESEARCH PROGRAM OF THE NATIONAL INSTITUTES OF HEALTH AND OTHERS.).	2018	
                                                   
20   326  26 ALLELIC SILENCING AT THE TUMOR-SUPPRESSOR LOCUS 13Q14.3 SUGGESTS AN EPIGENETIC TUMOR-SUPPRESSOR MECHANISM. GENOMIC MATERIAL FROM CHROMOSOME BAND 13Q14.3 DISTAL TO THE RETINOBLASTOMA LOCUS IS RECURRENTLY LOST IN A VARIETY OF HUMAN NEOPLASMS, INDICATING AN AS-YET-UNIDENTIFIED TUMOR-SUPPRESSOR MECHANISM. NO PATHOGENIC MUTATIONS HAVE BEEN FOUND IN THE MINIMALLY DELETED REGION UNTIL NOW. HOWEVER, IN B CELL CHRONIC LYMPHOCYTIC LEUKEMIA TUMORS WITH LOSS OF ONE COPY OF THE CRITICAL REGION, RESPECTIVE CANDIDATE TUMOR-SUPPRESSOR GENES ARE DOWN-REGULATED BY A FACTOR >2, WHICH WOULD BE EXPECTED BY A NORMAL GENE-DOSAGE EFFECT. THIS FINDING POINTS TO AN EPIGENETIC PATHOMECHANISM. WE FIND THAT THE TWO COPIES OF THE CRITICAL REGION REPLICATE ASYNCHRONOUSLY, SUGGESTING DIFFERENTIAL CHROMATIN PACKAGING OF THE TWO COPIES OF 13Q14.3. ALTHOUGH WE ALSO DETECT MONOALLELIC SILENCING OF GENES LOCALIZED IN THE CRITICAL REGION, MONOALLELIC EXPRESSION ORIGINATES FROM EITHER THE MATERNAL OR PATERNAL COPY, EXCLUDING AN IMPRINTING MECHANISM. DNA METHYLATION ANALYSES REVEALED ONE CPG ISLAND OF THE REGION TO BE METHYLATED. DNA DEMETHYLATION OF THIS CPG ISLAND AND GLOBAL HISTONE HYPERACETYLATION INDUCED BIALLELIC EXPRESSION, WHEREAS REPLICATION TIMING WAS NOT AFFECTED. WE PROPOSE THAT DIFFERENTIAL REPLICATION TIMING REPRESENTS AN EARLY EPIGENETIC MARK THAT DISTINGUISHES THE TWO COPIES OF 13Q14.3, RESULTING IN DIFFERENTIAL CHROMATIN PACKAGING AND MONOALLELIC EXPRESSION. ACCORDINGLY, DELETION OF THE SINGLE ACTIVE COPY OF 13Q14.3 RESULTS IN SIGNIFICANT DOWN-REGULATION OF THE CANDIDATE GENES AND LOSS OF FUNCTION, PROVIDING A MODEL FOR THE INTERACTION OF GENETIC LESIONS AND EPIGENETIC SILENCING AT 13Q14.3 IN B CELL CHRONIC LYMPHOCYTIC LEUKEMIA.	2006