1 3024 149 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 2 4432 34 MOLECULAR CHARACTERIZATION OF RICHTER SYNDROME IDENTIFIES DE NOVO DIFFUSE LARGE B-CELL LYMPHOMAS WITH POOR PROGNOSIS. RICHTER SYNDROME (RS) IS THE TRANSFORMATION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) INTO AGGRESSIVE LYMPHOMA, MOST COMMONLY DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL). WE CHARACTERIZE 58 PRIMARY HUMAN RS SAMPLES BY GENOME-WIDE DNA METHYLATION AND WHOLE-TRANSCRIPTOME PROFILING. OUR COMPREHENSIVE APPROACH DETERMINES RS DNA METHYLATION PROFILE AND UNRAVELS A CLL EPIGENETIC IMPRINT, ALLOWING CLL-RS CLONAL RELATIONSHIP ASSESSMENT WITHOUT THE NEED OF THE INITIAL CLL TUMOR DNA. DNA METHYLATION- AND TRANSCRIPTOMIC-BASED CLASSIFIERS WERE DEVELOPED, AND TESTING ON LANDMARK DLBCL DATASETS IDENTIFIES A POOR-PROGNOSIS, ACTIVATED B-CELL-LIKE DLBCL SUBSET IN 111/1772 SAMPLES. THE CLASSIFICATION ROBUSTLY IDENTIFIES PHENOTYPES VERY SIMILAR TO RS WITH A SPECIFIC GENOMIC PROFILE, ACCOUNTING FOR 4.3-8.3% OF DE NOVO DLBCLS. IN THIS WORK, RS MULTI-OMICS CHARACTERIZATION DETERMINES ONCOGENIC MECHANISMS, ESTABLISHES A SURROGATE MARKER FOR CLL-RS CLONAL RELATIONSHIP, AND PROVIDES A CLINICALLY RELEVANT CLASSIFIER FOR A SUBSET OF PRIMARY "RS-TYPE DLBCL" WITH UNFAVORABLE PROGNOSIS. 2023 3 1693 40 DUSP4 DEFICIENCY CAUSED BY PROMOTER HYPERMETHYLATION DRIVES JNK SIGNALING AND TUMOR CELL SURVIVAL IN DIFFUSE LARGE B CELL LYMPHOMA. THE EPIGENETIC DYSREGULATION OF TUMOR SUPPRESSOR GENES IS AN IMPORTANT DRIVER OF HUMAN CARCINOGENESIS. WE HAVE COMBINED GENOME-WIDE DNA METHYLATION ANALYSES AND GENE EXPRESSION PROFILING AFTER PHARMACOLOGICAL DNA DEMETHYLATION WITH FUNCTIONAL SCREENING TO IDENTIFY NOVEL TUMOR SUPPRESSORS IN DIFFUSE LARGE B CELL LYMPHOMA (DLBCL). WE FIND THAT A CPG ISLAND IN THE PROMOTER OF THE DUAL-SPECIFICITY PHOSPHATASE DUSP4 IS ABERRANTLY METHYLATED IN NODAL AND EXTRANODAL DLBCL, IRRESPECTIVE OF ABC OR GCB SUBTYPE, RESULTING IN LOSS OF DUSP4 EXPRESSION IN 75% OF >200 EXAMINED CASES. THE DUSP4 GENOMIC LOCUS IS FURTHER DELETED IN UP TO 13% OF AGGRESSIVE B CELL LYMPHOMAS, AND THE LACK OF DUSP4 IS A NEGATIVE PROGNOSTIC FACTOR IN THREE INDEPENDENT COHORTS OF DLBCL PATIENTS. ECTOPIC EXPRESSION OF WILD-TYPE DUSP4, BUT NOT OF A PHOSPHATASE-DEFICIENT MUTANT, DEPHOSPHORYLATES C-JUN N-TERMINAL KINASE (JNK) AND INDUCES APOPTOSIS IN DLBCL CELLS. PHARMACOLOGICAL OR DOMINANT-NEGATIVE JNK INHIBITION RESTRICTS DLBCL SURVIVAL IN VITRO AND IN VIVO AND SYNERGIZES STRONGLY WITH THE BRUTON'S TYROSINE KINASE INHIBITOR IBRUTINIB. OUR RESULTS INDICATE THAT DLBCL CELLS DEPEND ON JNK SIGNALING FOR SURVIVAL. THIS FINDING PROVIDES A MECHANISTIC BASIS FOR THE CLINICAL DEVELOPMENT OF JNK INHIBITORS IN DLBCL, IDEALLY IN SYNTHETIC LETHAL COMBINATIONS WITH INHIBITORS OF CHRONIC ACTIVE B CELL RECEPTOR SIGNALING. 2015 4 628 34 BIOLOGICAL AND CLINICAL INSIGHT FROM ANALYSIS OF THE TUMOR B-CELL RECEPTOR STRUCTURE AND FUNCTION IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE B-CELL RECEPTOR (BCR) IS ESSENTIAL TO THE BEHAVIOR OF THE MAJORITY OF NORMAL AND NEOPLASTIC MATURE B CELLS. THE IDENTIFICATION IN 1999 OF THE TWO MAJOR CLL SUBSETS EXPRESSING UNMUTATED IMMUNOGLOBULIN (IG) VARIABLE REGION GENES (U-IGHV, U-CLL) OF PRE-GERMINAL CENTER ORIGIN AND POOR PROGNOSIS, AND MUTATED IGHV (M-CLL) OF POST-GERMINAL CENTER ORIGIN AND GOOD PROGNOSIS, IGNITED INTENSIVE INVESTIGATIONS ON STRUCTURE AND FUNCTION OF THE TUMOR BCR. THESE INVESTIGATIONS HAVE PROVIDED FUNDAMENTAL INSIGHT INTO CLL BIOLOGY AND EVENTUALLY THE MECHANISTIC RATIONALE FOR THE DEVELOPMENT OF SUCCESSFUL THERAPIES TARGETING BCR SIGNALING. U-CLL AND M-CLL ARE CHARACTERIZED BY VARIABLE LOW SURFACE IGM (SIGM) EXPRESSION AND SIGNALING CAPACITY. VARIABILITY OF SIGM CAN IN PART BE EXPLAINED BY CHRONIC ENGAGEMENT WITH (AUTO)ANTIGEN AT TISSUE SITES. HOWEVER, OTHER ENVIRONMENTAL ELEMENTS, GENETIC CHANGES, AND EPIGENETIC SIGNATURES ALSO CONTRIBUTE TO THE SIGM VARIABILITY. THE VARIABLE LEVELS HAVE CONSEQUENCES ON THE BEHAVIOR OF CLL, WHICH IS IN A STATE OF ANERGY WITH AN INDOLENT CLINICAL COURSE WHEN SIGM EXPRESSION IS LOW, OR PUSHED TOWARDS PROLIFERATION AND A MORE AGGRESSIVE CLINICAL COURSE WHEN SIGM EXPRESSION IS HIGH. EFFICACY OF THERAPIES THAT TARGET BTK MAY ALSO BE AFFECTED BY THE VARIABLE SIGM LEVELS AND SIGNALING AND, IN PART, EXPLAIN THE DEVELOPMENT OF RESISTANCE. 2022 5 1467 49 DISTINCT CLINICAL AND GENETIC FEATURES OF HEPATITIS B VIRUS-ASSOCIATED FOLLICULAR LYMPHOMA IN CHINESE PATIENTS. HEPATITIS B VIRUS (HBV) INFECTION HAS BEEN ASSOCIATED WITH AN INCREASED RISK FOR B-CELL LYMPHOMAS. WE PREVIOUSLY SHOWED THAT 20% OF DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) PATIENTS FROM CHINA, AN ENDEMIC AREA OF HBV INFECTION, HAVE CHRONIC HBV INFECTION (SURFACE ANTIGEN-POSITIVE, HBSAG+) AND ARE CHARACTERIZED BY DISTINCT CLINICAL AND GENETIC FEATURES. HERE, WE SHOWED THAT 24% OF FOLLICULAR LYMPHOMA (FL) CHINESE PATIENTS ARE HBSAG+. COMPARED WITH THE HBSAG- FL PATIENTS, HBSAG+ PATIENTS ARE YOUNGER, HAVE A HIGHER HISTOLOGICAL GRADE AT DIAGNOSIS, AND HAVE A HIGHER INCIDENCE OF DISEASE PROGRESSION WITHIN 24 MONTHS. MOREOVER, BY SEQUENCING THE GENOMES OF 109 FL TUMORS, WE OBSERVED ENHANCED MUTAGENESIS AND DISTINCT GENETIC PROFILE IN HBSAG+ FLS, WITH A UNIQUE SET OF PREFERENTIALLY MUTATED GENES (TNFAIP3, FAS, HIST1H1C, KLF2, TP53, PIM1, TMSB4X, DUSP2, TAGAP, LYN, AND SETD2) BUT LACK OF THE HALLMARK OF HBSAG- FLS (IE, IGH/BCL2 TRANSLOCATIONS AND CREBBP MUTATIONS). TRANSCRIPTOMIC ANALYSES FURTHER SHOWED THAT HBSAG+ FLS DISPLAYED GENE-EXPRESSION SIGNATURES RESEMBLING THE ACTIVATED B-CELL-LIKE SUBTYPE OF DIFFUSE LARGE B-CELL LYMPHOMA, INVOLVING IRF4-TARGETED GENES AND NF-KAPPAB/MYD88 SIGNALING PATHWAYS. FINALLY, WE IDENTIFIED AN INCREASED INFILTRATION OF CD8+ MEMORY T CELLS, CD4+ TH1 CELLS, AND M1 MACROPHAGES AND HIGHER T-CELL EXHAUSTION GENE SIGNATURE IN HBSAG+ FL SAMPLES. TAKEN TOGETHER, WE PRESENT NEW GENETIC/EPIGENETIC EVIDENCE THAT LINKS CHRONIC HBV INFECTION TO B-CELL LYMPHOMAGENESIS, AND HBV-ASSOCIATED FL IS LIKELY TO HAVE A DISTINCT CELL-OF-ORIGIN AND REPRESENT AS A SEPARATE SUBTYPE OF FL. TARGETABLE GENETIC/EPIGENETIC ALTERATIONS IDENTIFIED IN TUMORS AND THEIR ASSOCIATED TUMOR MICROENVIRONMENT MAY PROVIDE POTENTIAL NOVEL THERAPEUTIC APPROACHES FOR THIS SUBGROUP OF PATIENTS. 2022 6 6468 29 TISSUE-SPECIFIC ENRICHMENT OF LYMPHOMA RISK LOCI IN REGULATORY ELEMENTS. THOUGH NUMEROUS POLYMORPHISMS HAVE BEEN ASSOCIATED WITH RISK OF DEVELOPING LYMPHOMA, HOW THESE VARIANTS FUNCTION TO PROMOTE TUMORIGENESIS IS POORLY UNDERSTOOD. HERE, WE REPORT THAT LYMPHOMA RISK SNPS, ESPECIALLY IN THE NON-HODGKIN'S LYMPHOMA SUBTYPE CHRONIC LYMPHOCYTIC LEUKEMIA, ARE SIGNIFICANTLY ENRICHED FOR CO-LOCALIZATION WITH EPIGENETIC MARKS OF ACTIVE GENE REGULATION. THESE ENRICHMENTS WERE SEEN IN A LYMPHOID-SPECIFIC MANNER FOR NUMEROUS ENCODE DATASETS, INCLUDING DNASE-HYPERSENSITIVITY AS WELL AS MULTIPLE SEGMENTATION-DEFINED ENHANCER REGIONS. FURTHERMORE, WE IDENTIFY PUTATIVELY FUNCTIONAL SNPS THAT ARE BOTH IN REGULATORY ELEMENTS IN LYMPHOCYTES AND ARE ASSOCIATED WITH GENE EXPRESSION CHANGES IN BLOOD. WE DEVELOPED AN ALGORITHM, UES, THAT USES A MONTE CARLO SIMULATION APPROACH TO CALCULATE THE ENRICHMENT OF PREVIOUSLY IDENTIFIED RISK SNPS IN VARIOUS FUNCTIONAL ELEMENTS. THIS MULTISCALE APPROACH INTEGRATING MULTIPLE DATASETS HELPS DISENTANGLE THE UNDERLYING BIOLOGY OF LYMPHOMA, AND MORE BROADLY, IS GENERALLY APPLICABLE TO GWAS RESULTS FROM OTHER DISEASES AS WELL. 2015 7 2469 15 EPIGENETIC TRAJECTORIES OF THE PREMALIGNANT-TO-MALIGNANT TRANSITION OF CHRONIC LYMPHOCYTIC LEUKEMIA. KRETZMER AND COLLEAGUES SHOW THAT THE TRANSITION TO ALTERED METHYLOME OCCURS VERY EARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA, AND ONCE ACQUIRED, IT IS A CLONAL AND EXTREMELY STABLE CHANGE. HOWEVER, THE PRECISE TIME POINT WHEN THE LEUKEMIC CLONE STARTS DEVIATING SIGNIFICANTLY FROM THE NORMAL B-CELL DIFFERENTIATION TRAJECTORY IS STILL ELUSIVE. SEE RELATED ARTICLE BY KRETZMER ET AL., P. 54. 2021 8 493 35 ASSESSMENT OF P53 AND ATM FUNCTIONALITY IN CHRONIC LYMPHOCYTIC LEUKEMIA BY MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION. THE ATM-P53 DNA-DAMAGE RESPONSE (DDR) PATHWAY HAS A CRUCIAL ROLE IN CHEMORESISTANCE IN CLL, AS INDICATED BY THE ADVERSE PROGNOSTIC IMPACT OF GENETIC ABERRATIONS OF TP53 AND ATM. IDENTIFYING AND DISTINGUISHING TP53 AND ATM FUNCTIONAL DEFECTS HAS BECOME RELEVANT AS EPIGENETIC AND POSTTRANSCRIPTIONAL DYSREGULATION OF THE ATM/P53 AXIS IS INCREASINGLY BEING RECOGNIZED AS THE UNDERLYING CAUSE OF CHEMORESISTANCE. ALSO, SPECIFIC TREATMENTS SENSITIZING TP53- OR ATM-DEFICIENT CLL CELLS ARE EMERGING. WE THEREFORE DEVELOPED A NEW ATM-P53 FUNCTIONAL ASSAY WITH THE AIM TO (I) IDENTIFY AND (II) DISTINGUISH ABNORMALITIES OF TP53 VERSUS ATM AND (III) ENABLE THE IDENTIFICATION OF ADDITIONAL DEFECTS IN THE ATM-P53 PATHWAY. REVERSED TRANSCRIPTASE MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (RT-MLPA) WAS USED TO MEASURE ATM AND/OR P53-DEPENDENT GENES AT THE RNA LEVEL FOLLOWING DNA DAMAGE USING IRRADIATION. HERE, WE SHOWED THAT THIS ASSAY IS ABLE TO IDENTIFY AND DISTINGUISH THREE SUBGROUPS OF CLL TUMORS (I.E., TP53-DEFECTIVE, ATM-DEFECTIVE AND WT) AND IS ALSO ABLE TO DETECT ADDITIONAL SAMPLES WITH A DEFECTIVE DDR, WITHOUT MOLECULAR ABERRATIONS IN TP53 AND/OR ATM. THESE FINDINGS MAKE THE ATM-P53 RT-MLPA FUNCTIONAL ASSAY A PROMISING PROGNOSTIC TOOL FOR PREDICTING TREATMENT RESPONSES IN CLL. 2015 9 2935 39 GENETIC ALTERATION ASSOCIATED WITH CHRONIC LYMPHOCYTIC LEUKEMIA. THE GENETICS OF B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) DIFFER CONSIDERABLY FROM MOST OTHER FORMS OF HEMATOLOGIC MALIGNANCY WHICH ARE USUALLY CHARACTERIZED BY CHROMOSOME TRANSLOCATIONS. B-CLL TYPICALLY CONTAINS CHROMOSOMAL DELETIONS AND CHROMOSOMES 13Q14 AND 11Q22-->Q23 ARE THE MOST COMMON. THESE TWO REGIONS APPEAR TO SHARE A COMMON ANCESTRAL ORIGIN (AUER ET AL., 2007B). OVERALL, CHROMOSOMAL ABNORMALITIES CAN BE FOUND IN THE MAJORITY OF PATIENTS WITH B-CLL WHEN USING SENSITIVE TECHNIQUES (DOHNERET AL., 2000) AND POSSIBLY REFLECTS AN UNDERLYING PREDISPOSITION, WITH A SMALL BUT SIGNIFICANT NUMBER OF FAMILIAL CASES. ALTHOUGH SINGLE AND CONSISTENT ABNORMALITIES ARE MOST COMMON, MULTIPLE REARRANGEMENTS CAN OCCUR, OFTEN WITH DISEASE PROGRESSION (FEGANETAL., 1995; DOHNER ET AL., 2000). REGIONS OF RECURRENT DELETION SUGGEST THE PRESENCE OF TUMOR SUPPRESSOR GENES IF FOLLOWING KNUDSON'S THEORETICAL 2-HIT MODEL. HOWEVER, DESPITE EXTENSIVE SEQUENCING ANALYSIS OVER THE LAST DECADE AND LACK OF PATHOGENIC MUTATIONS IDENTIFIED, THERE HAS BEEN A MOVE AWAY FROM THIS SUGGESTED HYPOTHESIS AND ALTERNATIVE MECHANISMS OF GENE INACTIVATION INVOLVING EPIGENETIC SILENCING OR HAPLOINSUFFICIENCY MAY BE CONSIDERED AS MORE LIKELY IN THIS DISEASE. THIS REVIEW FOCUSES ON THE COMMON GENETIC ABNORMALITIES IN B-CLL AND RELATES THEM TO SOME OF THE MORE RECENT HYPOTHESES ON INACTIVATION OF GENES WITHIN THESE REGIONS OF DELETION. 2007 10 2637 39 EPIGENOME-WIDE STUDY IDENTIFIES EPIGENETIC OUTLIERS IN NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. NONGENETIC PREDISPOSITION TO COLORECTAL CANCER CONTINUES TO BE DIFFICULT TO MEASURE PRECISELY, HAMPERING EFFORTS IN TARGETED PREVENTION AND SCREENING. EPIGENETIC CHANGES IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER CAN SERVE AS A TOOL IN PREDICTING COLORECTAL CANCER OUTCOMES. WE IDENTIFIED EPIGENETIC CHANGES AFFECTING THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. DNA METHYLATION PROFILING ON NORMAL COLON MUCOSA FROM 77 PATIENTS WITH COLORECTAL CANCER AND 68 CONTROLS IDENTIFIED A DISTINCT SUBGROUP OF NORMALLY-APPEARING MUCOSA WITH MARKEDLY DISRUPTED DNA METHYLATION AT A LARGE NUMBER OF CPGS, TERMED AS "OUTLIER METHYLATION PHENOTYPE" (OMP) AND ARE PRESENT IN 15 OF 77 PATIENTS WITH CANCER VERSUS 0 OF 68 CONTROLS (P < 0.001). SIMILAR FINDINGS WERE ALSO SEEN IN PUBLICLY AVAILABLE DATASETS. COMPARISON OF NORMAL COLON MUCOSA TRANSCRIPTION PROFILES OF PATIENTS WITH OMP CANCER WITH THOSE OF PATIENTS WITH NON-OMP CANCER INDICATES GENES WHOSE PROMOTERS ARE HYPERMETHYLATED IN THE OMP PATIENTS ARE ALSO TRANSCRIPTIONALLY DOWNREGULATED, AND THAT MANY OF THE GENES MOST AFFECTED ARE INVOLVED IN INTERACTIONS BETWEEN EPITHELIAL CELLS, THE MUCUS LAYER, AND THE MICROBIOME. ANALYSIS OF 16S RRNA PROFILES SUGGESTS THAT NORMAL COLON MUCOSA OF OMPS ARE ENRICHED IN BACTERIAL GENERA ASSOCIATED WITH COLORECTAL CANCER RISK, ADVANCED TUMOR STAGE, CHRONIC INTESTINAL INFLAMMATION, MALIGNANT TRANSFORMATION, NOSOCOMIAL INFECTIONS, AND KRAS MUTATIONS. IN CONCLUSION, OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. PROSPECTIVE STUDIES ARE NEEDED TO DETERMINE WHETHER OMP COULD SERVE AS A BIOMARKER FOR AN ELEVATED EPIGENETIC RISK FOR COLORECTAL CANCER DEVELOPMENT. PREVENTION RELEVANCE: OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. IDENTIFICATION OF OMPS IN HEALTHY CONTROLS AND PATIENTS WITH COLORECTAL CANCER WILL LEAD TO PREVENTION AND BETTER PROGNOSIS, RESPECTIVELY. 2022 11 2753 31 EXPRESSION OF BCL2L12 IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS: ASSOCIATION WITH CLINICAL AND MOLECULAR PROGNOSTIC MARKERS. DYSREGULATION OF APOPTOSIS IS A DISTINCTIVE FEATURE OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), ALTHOUGH A UNIQUE MECHANISM UNDERLYING APOPTOSIS RESISTANCE OF CLL B LYMPHOCYTES HAS NOT BEEN IDENTIFIED YET. ABERRANT EXPRESSION AS WELL AS GENETIC AND EPIGENETIC ALTERATIONS OF NUMEROUS GENES INVOLVED IN DIFFERENT PATHWAYS OF APOPTOSIS REGULATION HAS BEEN DESCRIBED IN CLL. HERE, WE REPORT THE EXPRESSION ANALYSIS OF BCL2L12 (BCL2-LIKE 12), A NOVEL APOPTOTIC GENE BELONGING TO BCL2 FAMILY, IN 58 SERBIAN CLL PATIENTS. QUANTITATIVE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION (QRT-PCR) ANALYSIS REVEALED A SIGNIFICANT OVEREXPRESSION OF BCL2L12 MRNA IN CLL SAMPLES COMPARED TO NON-LEUKEMIC SAMPLES, IMPLYING ITS ROLE IN THE PATHOGENESIS OF THE DISEASE. RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS SHOWED THAT BCL2L12 EXPRESSION EFFICIENTLY DISCRIMINATES CLL CASES FROM HEALTHY CONTROLS. HOWEVER, RELATIVELY HOMOGENOUS BCL2L12 MRNA EXPRESSION AMONG PATIENTS DID NOT REFLECT THEIR CLINICAL CHARACTERISTICS (WITH THE EXCEPTION OF LACTATE DEHYDROGENASE STATUS AND TIME FROM DIAGNOSIS TO TREATMENT) AND FAILED TO SHOW ASSOCIATION WITH THE MOST INFORMATIVE PROGNOSTIC MARKERS, NAMELY THE MUTATIONAL STATUS OF REARRANGED IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION GENES, CD38 AND LIPOPROTEIN LIPASE GENE (LPL) EXPRESSION. 2013 12 1424 30 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 13 3125 27 GHSR DNA HYPERMETHYLATION IS A COMMON EPIGENETIC ALTERATION OF HIGH DIAGNOSTIC VALUE IN A BROAD SPECTRUM OF CANCERS. IDENTIFICATION OF A SINGLE MOLECULAR TRAIT THAT IS DETERMINANT OF COMMON MALIGNANCIES MAY SERVE AS A POWERFUL DIAGNOSTIC SUPPLEMENT TO CANCER TYPE-SPECIFIC MARKERS. HERE, WE REPORT A DNA METHYLATION MARK THAT IS CHARACTERISTIC OF SEVEN STUDIED MALIGNANCIES, NAMELY CANCERS OF LUNG, BREAST, PROSTATE, PANCREAS, COLORECTUM, GLIOBLASTOMA AND B CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) (N = 137). THIS MARK WAS DEFINED BY SUBSTANTIAL HYPERMETHYLATION AT THE PROMOTER AND FIRST EXON OF GROWTH HORMONE SECRETAGOUGE RECEPTOR (GHSR) THROUGH BISULFITE PYROSEQUENCING. THE DEGREE OF ABERRANT METHYLATION WAS CAPABLE OF ACCURATE DISCRIMINATION BETWEEN CANCER AND CONTROL SAMPLES. THE HIGHEST SENSITIVITY AND SPECIFICITY OF CANCER DETECTION WAS ACHIEVED FOR CANCERS OF PANCREAS, LUNG, BREAST AND CLL YIELDING THE AREA UNDER THE CURVE (AUC) VALUES OF 1.0000, 0.9952, 0.9800 AND 0.9400, RESPECTIVELY. NARROWING TO A SINGLE CPG SITE WITHIN THE GENE'S PROMOTER OR FOUR CONSECUTIVE CPG UNITS OF THE HIGHEST METHYLATION LEVELS WITHIN THE FIRST EXON IMPROVED THE DETECTION POWER. GHSR HYPERMETHYLATION WAS DETECTED ALREADY AT THE EARLY STAGE TUMORS. THE ACCURATE PERFORMANCE OF THIS MARKER WAS FURTHER REPLICATED IN AN INDEPENDENT SET OF PANCREATIC CANCER AND CONTROL SAMPLES (N = 78). THESE FINDINGS SUPPORT THE CANDIDATURE OF GHSR METHYLATION AS A HIGHLY ACCURATE PAN-CANCER MARKER. 2015 14 1995 36 EPIGENETIC AND GENETIC ALTERATIONS AND THEIR INFLUENCE ON GENE REGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: TO UNDERSTAND THE CHANGES OF GENE REGULATION IN CARCINOGENESIS, WE EXPLORED SIGNALS OF DNA METHYLATION - A STABLE EPIGENETIC MARK OF GENE REGULATORY ELEMENTS - AND DESIGNED A COMPUTATIONAL MODEL TO PROFILE LOSS AND GAIN OF REGULATORY ELEMENTS (RES) DURING CARCINOGENESIS. WE ALSO UTILIZED SEQUENCING DATA TO ANALYZE THE ALLELE FREQUENCY OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AND DETECTED THE CANCER-ASSOCIATED SNPS, I.E., THE SNPS DISPLAYING THE SIGNIFICANT ALLELE FREQUENCY DIFFERENCE BETWEEN CANCER AND NORMAL SAMPLES. RESULTS: AFTER APPLYING THIS MODEL TO CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DATA, WE IDENTIFIED RES DIFFERENTIALLY ACTIVATED (DRES) BETWEEN NORMAL AND CLL CELLS, CONSISTING OF 6,802 DRES GAINED AND 4,606 DRES LOST IN CLL. THE IDENTIFIED REGULATORY PERTURBATIONS COINCIDE WITH CHANGES IN THE EXPRESSION OF TARGET GENES. IN PARTICULAR, THE GENES ENCODING DNA METHYLTRANSFERASES HARBOR MULTIPLE LOST-IN-CANCER DRES AND ZERO GAINED-IN-CANCER DRES, INDICATING THAT THE DAMAGED REGULATION OF THESE GENES MIGHT BE ONE OF THE KEY CAUSES OF TUMOR FORMATION. DRES DISPLAY A SIGNIFICANTLY ELEVATED DENSITY OF THE GENOME-WIDE ASSOCIATION STUDY (GWAS) SNPS ASSOCIATED WITH CLL AND CLL-RELATED TRAITS. WE OBSERVED THAT MOST OF DRE GWAS SNPS ASSOCIATED WITH CLL AND CLL-RELATED TRAITS (83%) DISPLAY A SIGNIFICANT HAPLOTYPE ASSOCIATION AMONG THE IDENTIFIED CANCER-ASSOCIATED ALLELES AND THE RISK ALLELES THAT HAVE BEEN REPORTED IN GWAS. ALSO DRES ARE ENRICHED FOR THE BINDING SITES OF THE WELL-ESTABLISHED B-CELL AND CLL TRANSCRIPTION FACTORS (TFS) NF-KB, AP2, P53, E2F1, PAX5, AND SP1. WE ALSO IDENTIFIED CLL-ASSOCIATED SNPS AND DEMONSTRATED THAT THE MUTATIONS AT THESE SNPS CHANGE THE BINDING SITES OF KEY TFS MUCH MORE FREQUENTLY THAN EXPECTED. CONCLUSIONS: THROUGH EXPLORING SEQUENCING DATA MEASURING DNA METHYLATION, WE IDENTIFIED THE EPIGENETIC ALTERATIONS (MORE SPECIFICALLY, DNA METHYLATION) AND GENETIC MUTATIONS ALONG NON-CODING GENOMIC REGIONS CLL, AND DEMONSTRATED THAT THESE CHANGES PLAY A CRITICAL ROLE IN CARCINOGENESIS THROUGH DAMAGING THE REGULATION OF KEY GENES AND ALTERNATING THE BINDING OF KEY TFS IN B AND CLL CELLS. 2017 15 4517 30 MULTI-OMICS FACTOR ANALYSIS-A FRAMEWORK FOR UNSUPERVISED INTEGRATION OF MULTI-OMICS DATA SETS. MULTI-OMICS STUDIES PROMISE THE IMPROVED CHARACTERIZATION OF BIOLOGICAL PROCESSES ACROSS MOLECULAR LAYERS. HOWEVER, METHODS FOR THE UNSUPERVISED INTEGRATION OF THE RESULTING HETEROGENEOUS DATA SETS ARE LACKING. WE PRESENT MULTI-OMICS FACTOR ANALYSIS (MOFA), A COMPUTATIONAL METHOD FOR DISCOVERING THE PRINCIPAL SOURCES OF VARIATION IN MULTI-OMICS DATA SETS. MOFA INFERS A SET OF (HIDDEN) FACTORS THAT CAPTURE BIOLOGICAL AND TECHNICAL SOURCES OF VARIABILITY. IT DISENTANGLES AXES OF HETEROGENEITY THAT ARE SHARED ACROSS MULTIPLE MODALITIES AND THOSE SPECIFIC TO INDIVIDUAL DATA MODALITIES. THE LEARNT FACTORS ENABLE A VARIETY OF DOWNSTREAM ANALYSES, INCLUDING IDENTIFICATION OF SAMPLE SUBGROUPS, DATA IMPUTATION AND THE DETECTION OF OUTLIER SAMPLES. WE APPLIED MOFA TO A COHORT OF 200 PATIENT SAMPLES OF CHRONIC LYMPHOCYTIC LEUKAEMIA, PROFILED FOR SOMATIC MUTATIONS, RNA EXPRESSION, DNA METHYLATION AND EX VIVO DRUG RESPONSES. MOFA IDENTIFIED MAJOR DIMENSIONS OF DISEASE HETEROGENEITY, INCLUDING IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE REGION STATUS, TRISOMY OF CHROMOSOME 12 AND PREVIOUSLY UNDERAPPRECIATED DRIVERS, SUCH AS RESPONSE TO OXIDATIVE STRESS. IN A SECOND APPLICATION, WE USED MOFA TO ANALYSE SINGLE-CELL MULTI-OMICS DATA, IDENTIFYING COORDINATED TRANSCRIPTIONAL AND EPIGENETIC CHANGES ALONG CELL DIFFERENTIATION. 2018 16 4549 29 MUTATION ANALYSIS OF THERAPY-RELATED MYELOID NEOPLASMS. WE ANALYZED THE GENETIC MUTATION STATUS OF 13 PATIENTS WITH THERAPY-RELATED MYELOID NEOPLASMS (T-MN). CONSISTENT WITH PREVIOUS REPORTS, T-MN CELLS PREFERENTIALLY ACQUIRED MUTATIONS IN TP53 AND EPIGENETIC MODIFYING GENES, INSTEAD OF MUTATIONS IN TYROSINE KINASE AND SPLICEOSOME GENES. FURTHERMORE, WE COMPARED THE MUTATION STATUS OF THREE T-MN CELLS WITH EACH OF THE INITIAL LYMPHOID MALIGNANT CELLS, AND IDENTIFIED COMMON MUTATIONS AMONG T-MN AND THE INITIAL MALIGNANT CELLS IN TWO PATIENTS. IN A PATIENT WHO DEVELOPED CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AFTER FOLLICULAR LYMPHOMA (FL), TET2 MUTATION WAS IDENTIFIED IN BOTH CMML AND FL CELLS. NOTABLY, THE TET2 MUTATION WAS ALSO IDENTIFIED IN PERIPHERAL BLOOD CELLS IN THE DISEASE-FREE PERIOD WITH THE SAME ALLELIC FREQUENCY AS CMML AND FL CELLS, BUT NOT IN A GERM-LINE CONTROL, INDICATING THAT THE TET2 MUTATION OCCURRED SOMATICALLY IN THE INITIATING CLONE FOR BOTH MALIGNANT CELLS. ON THE OTHER HAND, A GERM-LINE MYB MUTATION WAS IDENTIFIED IN A PATIENT WHO DEVELOPED MYELODYSPLASTIC SYNDROMES (MDS) AFTER FL. THESE RESULTS SUGGEST THAT GERM-LINE DEPOSITION AND CLONAL HEMATOPOIESIS ARE CLOSELY ASSOCIATED WITH T-MN SUSCEPTIBILITY; HOWEVER, FURTHER ANALYSIS IS NECESSARY TO CLARIFY THE MECHANISM REQUIRED TO PROVIDE THE INITIATING CLONE WITH LINEAGE COMMITMENT AND CLONAL EXPANSION. 2018 17 6222 23 THE LANDSCAPE OF SOMATIC MUTATIONS IN LYMPHOBLASTOID CELL LINES. SOMATIC MUTATIONS HAVE IMPORTANT BIOLOGICAL RAMIFICATIONS WHILE EXERTING SUBSTANTIAL RATE, TYPE, AND GENOMIC LOCATION HETEROGENEITY. YET, THEIR SPORADIC OCCURRENCE MAKES THEM DIFFICULT TO STUDY AT SCALE AND ACROSS INDIVIDUALS. LYMPHOBLASTOID CELL LINES (LCLS), A MODEL SYSTEM FOR HUMAN POPULATION AND FUNCTIONAL GENOMICS, HARBOR LARGE NUMBERS OF SOMATIC MUTATIONS AND HAVE BEEN EXTENSIVELY GENOTYPED. BY COMPARING 1,662 LCLS, WE REPORT THAT THE MUTATIONAL LANDSCAPE OF THE GENOME VARIES ACROSS INDIVIDUALS IN TERMS OF THE NUMBER OF MUTATIONS, THEIR GENOMIC LOCATIONS, AND THEIR SPECTRA; THIS VARIATION MAY ITSELF BE MODULATED BY SOMATIC TRANS-ACTING MUTATIONS. MUTATIONS ATTRIBUTED TO THE TRANSLESION DNA POLYMERASE ETA FOLLOW TWO DIFFERENT MODES OF FORMATION, WITH ONE MODE ACCOUNTING FOR THE HYPERMUTABILITY OF THE INACTIVE X CHROMOSOME. NONETHELESS, THE DISTRIBUTION OF MUTATIONS ALONG THE INACTIVE X CHROMOSOME APPEARS TO FOLLOW AN EPIGENETIC MEMORY OF THE ACTIVE FORM. 2023 18 1380 39 DEVELOPMENTAL SUBTYPES ASSESSED BY DNA METHYLATION-IPLEX FORECAST THE NATURAL HISTORY OF CHRONIC LYMPHOCYTIC LEUKEMIA. ALTERATIONS IN GLOBAL DNA METHYLATION PATTERNS ARE A MAJOR HALLMARK OF CANCER AND REPRESENT ATTRACTIVE BIOMARKERS FOR PERSONALIZED RISK STRATIFICATION. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK STRATIFICATION STUDIES TYPICALLY FOCUS ON TIME TO FIRST TREATMENT (TTFT), TIME TO PROGRESSION (TTP) AFTER TREATMENT, AND OVERALL SURVIVAL (OS). WHEREAS TTFT RISK STRATIFICATION REMAINS SIMILAR OVER TIME, TTP AND OS HAVE CHANGED DRAMATICALLY WITH THE INTRODUCTION OF TARGETED THERAPIES, SUCH AS THE BRUTON TYROSINE KINASE INHIBITOR IBRUTINIB. WE HAVE SHOWN THAT GENOME-WIDE DNA METHYLATION PATTERNS IN CLL ARE STRONGLY ASSOCIATED WITH PHENOTYPIC DIFFERENTIATION AND PATIENT OUTCOMES. HERE, WE DEVELOPED A NOVEL ASSAY, TERMED METHYLATION-IPLEX (ME-IPLEX), FOR HIGH-THROUGHPUT QUANTIFICATION OF TARGETED PANELS OF SINGLE CYTOSINE GUANINE DINUCLEOTIDES FROM MULTIPLE INDEPENDENT LOCI. ME-IPLEX WAS USED TO CLASSIFY CLL SAMPLES INTO 1 OF 3 KNOWN EPIGENETIC SUBTYPES (EPITYPES). WE EXAMINED THE IMPACT OF EPITYPE IN 1286 CLL PATIENTS FROM 4 INDEPENDENT COHORTS REPRESENTING A COMPREHENSIVE VIEW OF CLL DISEASE COURSE AND THERAPIES. WE FOUND THAT EPITYPE SIGNIFICANTLY PREDICTED TTFT AND OS AMONG NEWLY DIAGNOSED CLL PATIENTS. ADDITIONALLY, EPITYPE PREDICTED TTP AND OS WITH 2 COMMON CLL THERAPIES: CHEMOIMMUNOTHERAPY AND IBRUTINIB. EPITYPE RETAINED SIGNIFICANCE AFTER STRATIFYING BY BIOLOGICALLY RELATED BIOMARKERS, IMMUNOGLOBULIN HEAVY CHAIN MUTATIONAL STATUS, AND ZAP70 EXPRESSION, AS WELL AS OTHER COMMON PROGNOSTIC MARKERS. FURTHERMORE, AMONG SEVERAL BIOLOGICAL TRAITS ENRICHED BETWEEN EPITYPES, WE FOUND HIGHLY BIASED IMMUNOGENETIC FEATURES, INCLUDING IGLV3-21 USAGE IN THE POORLY CHARACTERIZED INTERMEDIATE-PROGRAMMED CLL EPITYPE. IN SUMMARY, ME-IPLEX IS AN ELEGANT METHOD TO ASSESS EPIGENETIC SIGNATURES, INCLUDING ROBUST CLASSIFICATION OF CLL EPITYPES THAT INDEPENDENTLY STRATIFY PATIENT RISK AT DIAGNOSIS AND TIME OF TREATMENT. 2019 19 27 30 A B-CELL EPIGENETIC SIGNATURE DEFINES THREE BIOLOGIC SUBGROUPS OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH CLINICAL IMPACT. PROSPECTIVE IDENTIFICATION OF PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DESTINED TO PROGRESS WOULD GREATLY FACILITATE THEIR CLINICAL MANAGEMENT. RECENTLY, WHOLE-GENOME DNA METHYLATION ANALYSES IDENTIFIED THREE CLINICOBIOLOGIC CLL SUBGROUPS WITH AN EPIGENETIC SIGNATURE RELATED TO DIFFERENT NORMAL B-CELL COUNTERPARTS. HERE, WE DEVELOPED A CLINICALLY APPLICABLE METHOD TO IDENTIFY THESE SUBGROUPS AND TO STUDY THEIR CLINICAL RELEVANCE. USING A SUPPORT VECTOR MACHINE APPROACH, WE BUILT A PREDICTION MODEL USING FIVE EPIGENETIC BIOMARKERS THAT WAS ABLE TO CLASSIFY CLL PATIENTS ACCURATELY INTO THE THREE SUBGROUPS, NAMELY NAIVE B-CELL-LIKE, INTERMEDIATE AND MEMORY B-CELL-LIKE CLL. DNA METHYLATION WAS QUANTIFIED BY HIGHLY REPRODUCIBLE BISULFITE PYROSEQUENCING ASSAYS IN TWO INDEPENDENT CLL SERIES. IN THE INITIAL SERIES (N=211), THE THREE SUBGROUPS SHOWED DIFFERENTIAL LEVELS OF IGHV (IMMUNOGLOBULIN HEAVY-CHAIN LOCUS) MUTATION (P<0.001) AND VH USAGE (P<0.03), AS WELL AS DIFFERENT CLINICAL FEATURES AND OUTCOME IN TERMS OF TIME TO FIRST TREATMENT (TTT) AND OVERALL SURVIVAL (P<0.001). A MULTIVARIATE COX MODEL SHOWED THAT EPIGENETIC CLASSIFICATION WAS THE STRONGEST PREDICTOR OF TTT (P<0.001) ALONG WITH BINET STAGE (P<0.001). THESE FINDINGS WERE CORROBORATED IN A VALIDATION SERIES (N=97). IN THIS STUDY, WE DEVELOPED A SIMPLE AND ROBUST METHOD USING EPIGENETIC BIOMARKERS TO CATEGORIZE CLLS INTO THREE SUBGROUPS WITH DIFFERENT CLINICOBIOLOGIC FEATURES AND OUTCOME. 2015 20 230 29 ADAPTIVE AND INNATE CYTOTOXIC EFFECTORS IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) SUBJECTS WITH STABLE DISEASE. CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS CHARACTERISED BY THE EXPANSION OF A NEOPLASTIC MATURE B CELL CLONE. CLL CLINICAL OUTCOME IS VERY HETEROGENEOUS, WITH SOME SUBJECTS NEVER REQUIRING THERAPY AND SOME SHOWING AN AGGRESSIVE DISEASE. GENETIC AND EPIGENETIC ALTERATIONS AND PRO-INFLAMMATORY MICROENVIRONMENT INFLUENCE CLL PROGRESSION AND PROGNOSIS. THE INVOLVEMENT OF IMMUNE-MEDIATED MECHANISMS IN CLL CONTROL NEEDS TO BE INVESTIGATED. WE ANALYSE THE ACTIVATION PROFILE OF INNATE AND ADAPTIVE CYTOTOXIC IMMUNE EFFECTORS IN A COHORT OF 26 CLL PATIENTS WITH STABLE DISEASE, AS KEY ELEMENTS FOR IMMUNE-MEDIATED CONTROL OF CANCER PROGRESSION. WE OBSERVED AN INCREASE IN CD54 EXPRESSION AND INTERFERON (IFN)-GAMMA PRODUCTION BY CYTOTOXIC T CELLS (CTL). CTL ABILITY TO RECOGNISE TUMOUR-TARGETS DEPENDS ON HUMAN LEUKOCYTE ANTIGENS (HLA)-CLASS I EXPRESSION. WE OBSERVED A DECREASED EXPRESSION OF HLA-A AND HLA-BC ON B CELLS OF CLL SUBJECTS, ASSOCIATED WITH A SIGNIFICANT REDUCTION IN INTRACELLULAR CALNEXIN THAT IS RELEVANT FOR HLA SURFACE EXPRESSION. NATURAL KILLER (NK) CELLS AND CTL FROM CLL SUBJECTS SHOW AN INCREASED EXPRESSION OF THE ACTIVATING RECEPTOR KIR2DS2 AND A REDUCTION OF 3DL1 AND NKG2A INHIBITING MOLECULES. THEREFORE, AN ACTIVATION PROFILE CHARACTERISES CTL AND NK CELLS OF CLL SUBJECTS WITH STABLE DISEASE. THIS PROFILE IS CONCEIVABLE WITH THE FUNCTIONAL INVOLVEMENT OF CYTOTOXIC EFFECTORS IN CLL CONTROL. 2023