1 214 160 ACUTE AND CHRONIC MOLECULAR SIGNATURES AND ASSOCIATED SYMPTOMS OF BLAST EXPOSURE IN MILITARY BREACHERS. INJURIES FROM EXPOSURE TO EXPLOSIONS ROSE DRAMATICALLY DURING THE IRAQ AND AFGHANISTAN WARS, WHICH MOTIVATED INVESTIGATIONS OF BLAST-RELATED NEUROTRAUMA AND OPERATIONAL BREACHING. IN THIS STUDY, MILITARY "BREACHERS" WERE EXPOSED TO CONTROLLED, LOW-LEVEL BLAST DURING A 10-DAY EXPLOSIVE BREACHING COURSE. USING AN OMICS APPROACH, WE ASSESSED EPIGENETIC, TRANSCRIPTIONAL, AND INFLAMMATORY PROFILE CHANGES IN BLOOD FROM OPERATIONAL BREACHING TRAINEES, WITH VARYING LEVELS OF LIFETIME BLAST EXPOSURE, ALONG WITH DAILY SELF-REPORTED SYMPTOMS (WITH TINNITUS, HEADACHES, AND SLEEP DISTURBANCES AS THE MOST FREQUENTLY REPORTED). ALTHOUGH ACUTE EXPOSURE TO BLAST DID NOT CONFER EPIGENETIC CHANGES, SPECIFICALLY IN DNA METHYLATION, DIFFERENTIALLY METHYLATED REGIONS (DMRS) WITH COORDINATED GENE EXPRESSION CHANGES ASSOCIATED WITH LIFETIME CUMULATIVE BLAST EXPOSURES WERE IDENTIFIED. THE ACCUMULATIVE EFFECT OF BLAST SHOWED INCREASED METHYLATION OF PAX8 ANTISENSE TRANSCRIPT WITH COORDINATED REPRESSION OF GENE EXPRESSION, WHICH HAS BEEN ASSOCIATED WITH SLEEP DISTURBANCE. DNA METHYLATION ANALYSES CONDUCTED IN CONJUNCTION WITH REPORTED SYMPTOMS OF TINNITUS IN THE LOW VERSUS HIGH BLAST INCIDENTS GROUPS IDENTIFIED DMRS IN KCNE1 AND CYP2E1 GENES. KCNE1 AND CYP2E1 SHOWED THE EXPECTED INVERSE CORRELATION BETWEEN DNA METHYLATION AND GENE EXPRESSION, WHICH HAVE BEEN PREVIOUSLY IMPLICATED IN NOISE-RELATED HEARING LOSS. ALTHOUGH NO SIGNIFICANT TRANSCRIPTIONAL CHANGES WERE OBSERVED IN SAMPLES OBTAINED AT THE ONSET OF THE TRAINING COURSE RELATIVE TO CHRONIC CUMULATIVE BLAST, WE IDENTIFIED A LARGE NUMBER OF TRANSCRIPTIONAL PERTURBATIONS ACUTELY PRE- VERSUS POST-BLAST EXPOSURE. ACUTELY, 67 ROBUSTLY DIFFERENTIALLY EXPRESSED GENES (FOLD CHANGE >/=1.5), INCLUDING UFC1 AND YOD1 UBIQUITIN-RELATED PROTEINS, WERE IDENTIFIED. INFLAMMATORY ANALYSES OF CYTOKINES AND CHEMOKINES REVEALED DYSREGULATION OF MCP-1, GCSF, HGF, MCSF, AND RANTES ACUTELY AFTER BLAST EXPOSURE. THESE DATA SHOW THE IMPORTANCE OF AN OMICS APPROACH, REVEALING THAT TRANSCRIPTIONAL AND INFLAMMATORY BIOMARKERS CAPTURE ACUTE LOW-LEVEL BLAST OVERPRESSURE EXPOSURE, WHEREAS DNA METHYLATION MARKS ENCAPSULATE CHRONIC LONG-TERM SYMPTOMS. 2020 2 5453 26 REPROGRAMMING OF COPD LUNG FIBROBLASTS THROUGH FORMATION OF INDUCED PLURIPOTENT STEM CELLS. REPROGRAMMING SOMATIC CELLS TO INDUCED PLURIPOTENT STEM CELLS (IPSCS) ELIMINATES MANY EPIGENETIC MODIFICATIONS THAT CHARACTERIZE DIFFERENTIATED CELLS. IN THIS STUDY, WE TESTED WHETHER FUNCTIONAL DIFFERENCES BETWEEN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND NON-COPD FIBROBLASTS COULD BE REDUCED UTILIZING THIS APPROACH. PRIMARY FIBROBLASTS FROM NON-COPD AND COPD PATIENTS WERE REPROGRAMMED TO IPSCS. REPROGRAMMED IPSCS WERE POSITIVE FOR OCT3/4, NANOG, AND SOX2, FORMED EMBRYOID BODIES IN VITRO, AND INDUCED TERATOMAS IN NONOBESE DIABETIC/SEVERE COMBINED IMMUNODEFICIENT MICE. REPROGRAMMED IPSCS WERE THEN DIFFERENTIATED INTO FIBROBLASTS (NON-COPD-I AND COPD-I) AND WERE ASSESSED EITHER FUNCTIONALLY BY CHEMOTAXIS AND GEL CONTRACTION OR FOR GENE EXPRESSION BY MICROARRAYS AND COMPARED WITH THEIR CORRESPONDING PRIMARY FIBROBLASTS. PRIMARY COPD FIBROBLASTS CONTRACTED THREE-DIMENSIONAL COLLAGEN GELS AND MIGRATED TOWARD FIBRONECTIN LESS ROBUSTLY THAN NON-COPD FIBROBLASTS. IN CONTRAST, REDIFFERENTIATED FIBROBLASTS FROM IPSCS DERIVED FROM THE NON-COPD AND COPD FIBROBLASTS WERE SIMILAR IN RESPONSE IN BOTH FUNCTIONAL ASSAYS. MICROARRAY ANALYSIS IDENTIFIED 1,881 GENES THAT WERE DIFFERENTIALLY EXPRESSED BETWEEN PRIMARY COPD AND NON-COPD FIBROBLASTS, WITH 605 GENES DIFFERING BY MORE THAN TWOFOLD. AFTER REDIFFERENTIATION, 112 GENES WERE DIFFERENTIALLY EXPRESSED BETWEEN COPD-I AND NON-COPD-I WITH ONLY THREE GENES BY MORE THAN TWOFOLD. SIMILAR FINDINGS WERE OBSERVED WITH MICRORNA (MIRNA) EXPRESSION: 56 MIRNAS WERE DIFFERENTIALLY EXPRESSED BETWEEN NON-COPD AND COPD PRIMARY CELLS; AFTER REDIFFERENTIATION, ONLY 3 MIRNAS WERE DIFFERENTIALLY EXPRESSED BETWEEN NON-COPD-I AND COPD-I FIBROBLASTS. INTERESTINGLY, OF THE 605 GENES THAT WERE DIFFERENTIALLY EXPRESSED BETWEEN COPD AND NON-COPD FIBROBLASTS, 293 GENES WERE CHANGED TOWARD CONTROL AFTER REDIFFERENTIATION. IN CONCLUSION, FUNCTIONAL AND EPIGENETIC ALTERATIONS OF COPD FIBROBLASTS CAN BE REPROGRAMMED THROUGH FORMATION OF IPSCS. 2014 3 138 37 ABERRANT DNA METHYLATION AT HOXA4 AND HOXA5 GENES ARE ASSOCIATED WITH RESISTANCE TO IMATINIB MESYLATE AMONG CHRONIC MYELOID LEUKEMIA PATIENTS. BACKGROUND: IMATINIB MESYLATE IS A MOLECULARLY TARGETED TYROSINE KINASE INHIBITOR DRUG. IT IS EFFECTIVELY USED IN THE TREATMENT OF CHRONIC MYELOID LEUKEMIA (CML) PATIENTS. HOWEVER, DEVELOPMENT OF RESISTANCE TO IMATINIB MESYLATE AS A RESULT OF BCR-ABL DEPENDENT AND BCR-ABL INDEPENDENT MECHANISMS HAS EMERGED AS A DAUNTING PROBLEM IN THE MANAGEMENT OF CML PATIENTS. BETWEEN THESE MECHANISMS, BCR-ABL INDEPENDENT MECHANISMS ARE STILL NOT ROBUSTLY UNDERSTOOD. AIM: TO INVESTIGATE THE CORRELATION OF HOXA4 AND HOXA5 PROMOTER DNA HYPERMETHYLATION WITH IMATINIB RESISTANCE AMONG CML PATIENTS. METHODS AND RESULTS: SAMPLES FROM 175 PHILADELPHIA POSITIVE CML PATIENTS (83 GOOD RESPONSE AND 92 BCR-ABL NON-MUTATED IMATINIB RESISTANT PATIENTS) WERE SUBJECTED TO METHYLATION SPECIFIC HIGH RESOLUTION MELT ANALYSIS FOR METHYLATION LEVELS QUANTIFICATION OF THE HOXA4 AND HOXA5 PROMOTER REGIONS. RECEIVER OPERATING CHARACTERISTIC CURVE ANALYSIS WAS DONE TO ELUCIDATE THE OPTIMAL METHYLATION CUT-OFF POINT FOLLOWED BY MULTIPLE LOGISTIC REGRESSION ANALYSIS. LOG-RANK ANALYSIS WAS DONE TO MEASURE THE OVERALL SURVIVAL DIFFERENCE BETWEEN CML GROUPS. THE OPTIMAL METHYLATION CUT-OFF POINT WAS FOUND TO BE AT 62.5% FOR BOTH HOXA4 AND HOXA5. CHRONIC MYELOID LEUKEMIA PATIENTS WITH >/=63% HOXA4 AND HOXA5 METHYLATION LEVEL WERE SHOWN TO HAVE 3.78 AND 3.95 TIMES THE ODDS, RESPECTIVELY, TO ACQUIRE RESISTANCE TO IMATINIB. HOWEVER, OVERALL SURVIVAL OF CML PATIENTS THAT HAVE /= 63% METHYLATION LEVELS OF HOXA4 AND HOXA5 GENES WERE FOUND TO BE NOT SIGNIFICANT (P-VALUE = 0.126 FOR HOXA4; P-VALUE = 0.217 FOR HOXA5). CONCLUSION: HYPERMETHYLATION OF THE HOXA4 AND HOXA5 PROMOTER IS CORRELATED WITH IMATINIB RESISTANCE AND WITH FURTHER INVESTIGATION, IT COULD BE A POTENTIAL EPIGENETIC BIOMARKER IN SUPPLEMENT TO THE BCR-ABL GENE MUTATION IN PREDICTING IMATINIB TREATMENT RESPONSE AMONG CML PATIENTS BUT COULD NOT BE CONSIDERED AS A PROGNOSTIC MARKER. 2018 4 1904 27 ENHANCED RETINAL GANGLION CELL SURVIVAL IN GLAUCOMA BY HYPOXIC POSTCONDITIONING AFTER DISEASE ONSET. THE NEUROPROTECTIVE EFFICACY OF ADAPTIVE EPIGENETICS, WHEREIN BENEFICIAL GENE EXPRESSION CHANGES ARE INDUCED BY NONHARMFUL "CONDITIONING" STIMULI, IS NOW WELL ESTABLISHED IN SEVERAL ACUTE, PRECLINICAL CENTRAL NERVOUS SYSTEM INJURY MODELS. RECENTLY, IN A MOUSE MODEL OF GLAUCOMA, WE DEMONSTRATED RETINAL GANGLION CELL (RGC) PROTECTION BY REPETITIVELY "PRECONDITIONING" WITH HYPOXIA PRIOR TO DISEASE ONSET, INDICATING AN EPIGENETIC APPROACH MAY ALSO YIELD BENEFITS IN CHRONIC NEURODEGENERATIVE DISEASE. HEREIN, WE DETERMINED WHETHER PRESENTING THE REPETITIVE HYPOXIC STIMULUS AFTER DISEASE INITIATION [REPETITIVE HYPOXIC "POSTCONDITIONING" (RH-POST)] COULD AFFORD SIMILAR FUNCTIONAL AND MORPHOLOGIC PROTECTION AGAINST GLAUCOMATOUS RGC INJURY. CHRONIC ELEVATIONS IN INTRAOCULAR PRESSURE (IOP) WERE INDUCED UNILATERALLY IN ADULT MALE C57BL/6 MICE BY EPISCLERAL VEIN LIGATION. MICE WERE RANDOMIZED TO AN RH-POST [1 H OF SYSTEMIC HYPOXIA (11% OXYGEN) EVERY OTHER DAY, STARTING 4 DAYS AFTER IOP ELEVATION] OR AN UNTREATED CONTROL GROUP. AFTER 3 WEEKS OF EXPERIMENTAL GLAUCOMA, THE 21-27% REDUCTION AND 5-25% PROLONGATION IN FLASH VISUAL-EVOKED POTENTIAL AMPLITUDES AND LATENCIES, RESPECTIVELY, AND THE 30% IMPAIRMENT IN VISUAL ACUITY WERE ROBUSTLY IMPROVED IN RH-POST-TREATED MICE, AS WAS THE 17% LOSS IN RGC SOMA NUMBER AND 20% REDUCTION IN AXON INTEGRITY. THESE PROTECTIVE EFFECTS WERE OBSERVED WITHOUT RH-POST AFFECTING IOP. THE PRESENT FINDINGS DEMONSTRATE THAT FUNCTIONAL AND MORPHOLOGIC PROTECTION OF RGCS CAN BE REALIZED BY STIMULATING EPIGENETIC RESPONSES DURING THE EARLY STAGES OF DISEASE, AND THUS CONSTITUTE A NEW CONCEPTUAL APPROACH TO GLAUCOMA THERAPEUTICS. 2015 5 3021 29 GENETICS AND EPIGENETICS OF PRIMARY SJOGREN SYNDROME: IMPLICATIONS FOR FUTURE THERAPIES. IN PRIMARY SJOGREN SYNDROME (PSS), CHRONIC INFLAMMATION OF EXOCRINE GLANDS RESULTS IN TISSUE DESTRUCTION AND SICCA SYMPTOMS, PRIMARILY OF THE MOUTH AND EYES. FATIGUE, ARTHRALGIA AND MYALGIA ARE ALSO COMMON SYMPTOMS, WHEREAS EXTRAGLANDULAR MANIFESTATIONS THAT INVOLVE THE RESPIRATORY, NERVOUS AND VASCULAR SYSTEMS OCCUR IN A SUBSET OF PATIENTS. THE DISEASE PREDOMINANTLY AFFECTS WOMEN, WITH AN ESTIMATED FEMALE TO MALE RATIO OF 14 TO 1. THE AETIOLOGY OF PSS, HOWEVER, REMAINS INCOMPLETELY UNDERSTOOD, AND EFFECTIVE TREATMENT IS LACKING. LARGE-SCALE GENETIC AND EPIGENETIC INVESTIGATIONS HAVE REVEALED ASSOCIATIONS BETWEEN PSS AND GENES IN BOTH INNATE AND ADAPTIVE IMMUNE PATHWAYS. THE GENETIC VARIANTS MEDIATE CONTEXT-DEPENDENT EFFECTS, AND BOTH SEX AND ENVIRONMENTAL FACTORS CAN INFLUENCE THE OUTCOME. AS SUCH, GENETIC AND EPIGENETIC STUDIES CAN PROVIDE INSIGHT INTO THE DYSREGULATED MOLECULAR MECHANISMS, WHICH IN TURN MIGHT REVEAL NEW THERAPEUTIC POSSIBILITIES. THIS REVIEW DISCUSSES THE GENETIC AND EPIGENETIC FEATURES THAT HAVE BEEN ROBUSTLY CONNECTED WITH PSS, PUTTING THEM INTO THE CONTEXT OF CELLULAR FUNCTION, CARRIER SEX AND ENVIRONMENTAL CHALLENGES. IN ALL, THE OBSERVATIONS POINT TO SEVERAL NOVEL OPPORTUNITIES FOR EARLY DETECTION, TREATMENT DEVELOPMENT AND THE PATHWAY TOWARDS PERSONALIZED MEDICINE. 2023 6 5872 25 SUSTAINED TNF-ALPHA STIMULATION LEADS TO TRANSCRIPTIONAL MEMORY THAT GREATLY ENHANCES SIGNAL SENSITIVITY AND ROBUSTNESS. TRANSCRIPTIONAL MEMORY ALLOWS CERTAIN GENES TO RESPOND TO PREVIOUSLY EXPERIENCED SIGNALS MORE ROBUSTLY. HOWEVER, WHETHER AND HOW THE KEY PROINFLAMMATORY CYTOKINE TNF-ALPHA MEDIATES TRANSCRIPTIONAL MEMORY ARE POORLY UNDERSTOOD. USING HEK293F CELLS AS A MODEL SYSTEM, WE REPORT THAT SUSTAINED TNF-ALPHA STIMULATION INDUCES TRANSCRIPTIONAL MEMORY DEPENDENT ON TET ENZYMES. THE HYPOMETHYLATED STATUS OF TRANSCRIPTIONAL REGULATORY REGIONS CAN BE INHERITED, FACILITATING NF-KAPPAB BINDING AND MORE ROBUST SUBSEQUENT ACTIVATION. A HIGH INITIAL METHYLATION LEVEL AND CPG DENSITY AROUND KAPPAB SITES ARE CORRELATED WITH THE FUNCTIONAL POTENTIAL OF TRANSCRIPTIONAL MEMORY MODULES. INTERESTINGLY, THE CALCB GENE, ENCODING THE PROVEN MIGRAINE THERAPEUTIC TARGET CGRP, EXHIBITS THE BEST TRANSCRIPTIONAL MEMORY. A NEIGHBORING PRIMATE-SPECIFIC ENDOGENOUS RETROVIRUS STIMULATES MORE RAPID, MORE STRONG, AND AT LEAST 100-FOLD MORE SENSITIVE CALCB INDUCTION IN SUBSEQUENT TNF-ALPHA STIMULATION. OUR STUDY REVEALS THAT TNF-ALPHA-MEDIATED TRANSCRIPTIONAL MEMORY IS GOVERNED BY ACTIVE DNA DEMETHYLATION AND GREATLY SENSITIZES MEMORY GENES TO MUCH LOWER DOSES OF INFLAMMATORY CUES. 2020 7 4432 23 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 8 5320 30 PU.1 IS REQUIRED TO RESTRAIN MYELOPOIESIS DURING CHRONIC INFLAMMATORY STRESS. CHRONIC INFLAMMATION IS A COMMON FEATURE OF AGING AND NUMEROUS DISEASES SUCH AS DIABETES, OBESITY, AND AUTOIMMUNE SYNDROMES AND HAS BEEN LINKED TO THE DEVELOPMENT OF HEMATOLOGICAL MALIGNANCY. BLOOD-FORMING HEMATOPOIETIC STEM CELLS (HSC) CAN CONTRIBUTE TO THESE DISEASES VIA THE PRODUCTION OF TISSUE-DAMAGING MYELOID CELLS AND/OR THE ACQUISITION OF MUTATIONS IN EPIGENETIC AND TRANSCRIPTIONAL REGULATORS THAT INITIATE EVOLUTION TOWARD LEUKEMOGENESIS. WE PREVIOUSLY SHOWED THAT THE MYELOID "MASTER REGULATOR" TRANSCRIPTION FACTOR PU.1 IS ROBUSTLY INDUCED IN HSC BY PRO-INFLAMMATORY CYTOKINES SUCH AS INTERLEUKIN (IL)-1BETA AND LIMITS THEIR PROLIFERATIVE ACTIVITY. HERE, WE USED A PU.1-DEFICIENT MOUSE MODEL TO INVESTIGATE THE BROADER ROLE OF PU.1 IN REGULATING HEMATOPOIETIC ACTIVITY IN RESPONSE TO CHRONIC INFLAMMATORY CHALLENGES. WE FOUND THAT PU.1 IS CRITICAL IN RESTRAINING INFLAMMATORY MYELOPOIESIS VIA SUPPRESSION OF CELL CYCLE AND SELF-RENEWAL GENE PROGRAMS IN MYELOID-BIASED MULTIPOTENT PROGENITOR (MPP) CELLS. OUR DATA SHOW THAT WHILE PU.1 FUNCTIONS AS A KEY DRIVER OF MYELOID DIFFERENTIATION, IT PLAYS AN EQUALLY CRITICAL ROLE IN TAILORING HEMATOPOIETIC RESPONSES TO INFLAMMATORY STIMULI WHILE LIMITING EXPANSION AND SELF-RENEWAL GENE EXPRESSION IN MPPS. THESE DATA IDENTIFY PU.1 AS A KEY REGULATOR OF "EMERGENCY" MYELOPOIESIS RELEVANT TO INFLAMMATORY DISEASE AND LEUKEMOGENESIS. 2023 9 2928 21 GENERATION OF IPSCS FROM CULTURED HUMAN MALIGNANT CELLS. INDUCED PLURIPOTENT STEM CELLS (IPSCS) CAN BE GENERATED FROM VARIOUS DIFFERENTIATED CELL TYPES BY THE EXPRESSION OF A SET OF DEFINED TRANSCRIPTION FACTORS. SO FAR, IPSCS HAVE BEEN GENERATED FROM PRIMARY CELLS, BUT IT IS UNCLEAR WHETHER HUMAN CANCER CELL LINES CAN BE REPROGRAMMED. HERE WE DESCRIBE THE GENERATION AND CHARACTERIZATION OF IPSCS DERIVED FROM HUMAN CHRONIC MYELOID LEUKEMIA CELLS. WE SHOW THAT, DESPITE THE PRESENCE OF ONCOGENIC MUTATIONS, THESE CELLS ACQUIRED PLURIPOTENCY BY THE EXPRESSION OF 4 TRANSCRIPTION FACTORS AND UNDERWENT DIFFERENTIATION INTO CELL TYPES DERIVED OF ALL 3 GERM LAYERS DURING TERATOMA FORMATION. INTERESTINGLY, ALTHOUGH THE PARENTAL CELL LINE WAS STRICTLY DEPENDENT ON CONTINUOUS SIGNALING OF THE BCR-ABL ONCOGENE, ALSO TERMED ONCOGENE ADDICTION, REPROGRAMMED CELLS LOST THIS DEPENDENCY AND BECAME RESISTANT TO THE BCR-ABL INHIBITOR IMATINIB. THIS FINDING INDICATES THAT THE THERAPEUTIC AGENT IMATINIB TARGETS CELLS IN A SPECIFIC EPIGENETIC DIFFERENTIATED CELL STATE, AND THIS MAY CONTRIBUTE TO ITS INABILITY TO FULLY ERADICATE DISEASE IN CHRONIC MYELOID LEUKEMIA PATIENTS. 2010 10 2002 27 EPIGENETIC AND POST-TRANSCRIPTIONAL REPRESSION SUPPORT METABOLIC SUPPRESSION IN CHRONICALLY HYPOXIC GOLDFISH. GOLDFISH ENTER A HYPOMETABOLIC STATE TO SURVIVE CHRONIC HYPOXIA. WE RECENTLY DESCRIBED TISSUE-SPECIFIC CONTRIBUTIONS OF MEMBRANE LIPID COMPOSITION REMODELING AND MITOCHONDRIAL FUNCTION TO METABOLIC SUPPRESSION ACROSS DIFFERENT GOLDFISH TISSUES. HOWEVER, THE MOLECULAR AND ESPECIALLY EPIGENETIC FOUNDATIONS OF HYPOXIA TOLERANCE IN GOLDFISH UNDER METABOLIC SUPPRESSION ARE NOT WELL UNDERSTOOD. HERE WE SHOW THAT COMPONENTS OF THE MOLECULAR OXYGEN-SENSING MACHINERY ARE ROBUSTLY ACTIVATED ACROSS TISSUES IRRESPECTIVE OF HYPOXIA DURATION. INDUCTION OF GENE EXPRESSION OF ENZYMES INVOLVED IN DNA METHYLATION TURNOVER AND MICRORNA BIOGENESIS SUGGEST A ROLE FOR EPIGENETIC TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL SUPPRESSION OF GENE EXPRESSION IN THE HYPOXIA-ACCLIMATED BRAIN. CONVERSELY, MECHANISTIC TARGET OF RAPAMYCIN-DEPENDENT TRANSLATIONAL MACHINERY ACTIVITY IS NOT REDUCED IN LIVER AND WHITE MUSCLE, SUGGESTING THIS PATHWAY DOES NOT CONTRIBUTE TO LOWERING CELLULAR ENERGY EXPENDITURE. FINALLY, MOLECULAR EVIDENCE SUPPORTS PREVIOUSLY REPORTED CHRONIC HYPOXIA-DEPENDENT CHANGES IN MEMBRANE CHOLESTEROL, LIPID METABOLISM AND MITOCHONDRIAL FUNCTION VIA CHANGES IN TRANSCRIPTS INVOLVED IN CHOLESTEROL BIOSYNTHESIS, BETA-OXIDATION, AND MITOCHONDRIAL FUSION IN MULTIPLE TISSUES. OVERALL, THIS STUDY SHOWS THAT CHRONIC HYPOXIA ROBUSTLY INDUCES EXPRESSION OF OXYGEN-SENSING MACHINERY ACROSS TISSUES, INDUCES REPRESSIVE TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL EPIGENETIC MARKS ESPECIALLY IN THE CHRONIC HYPOXIA-ACCLIMATED BRAIN AND SUPPORTS A ROLE FOR MEMBRANE REMODELING AND MITOCHONDRIAL FUNCTION AND DYNAMICS IN PROMOTING METABOLIC SUPPRESSION. 2022 11 2619 35 EPIGENOME-WIDE ANALYSIS REVEALS FUNCTIONAL MODULATORS OF DRUG SENSITIVITY AND POST-TREATMENT SURVIVAL IN CHRONIC LYMPHOCYTIC LEUKAEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) PATIENTS DISPLAY A HIGHLY VARIABLE CLINICAL COURSE, WITH PROGRESSIVE ACQUISITION OF DRUG RESISTANCE. WE SOUGHT TO IDENTIFY ABERRANT EPIGENETIC TRAITS THAT ARE ENRICHED FOLLOWING EXPOSURE TO TREATMENT THAT COULD IMPACT PATIENT RESPONSE TO THERAPY. METHODS: EPIGENOME-WIDE ANALYSIS OF DNA METHYLATION WAS PERFORMED FOR 20 PATIENTS AT TWO TIMEPOINTS DURING TREATMENT. THE PROGNOSTIC SIGNIFICANCE OF DIFFERENTIALLY METHYLATED REGIONS (DMRS) WAS ASSESSED IN INDEPENDENT COHORTS OF 139 AND 163 PATIENTS. THEIR FUNCTIONAL ROLE IN DRUG SENSITIVITY WAS ASSESSED IN VITRO. RESULTS: WE IDENTIFIED 490 DMRS FOLLOWING EXPOSURE TO THERAPY, OF WHICH 31 WERE CLL-SPECIFIC AND INDEPENDENT OF CHANGES OCCURRING IN NORMAL B-CELL DEVELOPMENT. SEVENTEEN DMR-ASSOCIATED GENES WERE IDENTIFIED AS DIFFERENTIALLY EXPRESSED FOLLOWING TREATMENT IN AN INDEPENDENT COHORT. METHYLATION OF THE HOXA4, MAFB AND SLCO3A1 DMRS WAS ASSOCIATED WITH POST-TREATMENT PATIENT SURVIVAL, WITH HOXA4 DISPLAYING THE STRONGEST ASSOCIATION. RE-EXPRESSION OF HOXA4 IN CELL LINES AND PRIMARY CLL CELLS SIGNIFICANTLY INCREASED APOPTOSIS IN RESPONSE TO TREATMENT WITH FLUDARABINE, IBRUTINIB AND IDELALISIB. CONCLUSION: OUR STUDY DEMONSTRATES ENRICHMENT FOR MULTIPLE CLL-SPECIFIC EPIGENETIC TRAITS IN RESPONSE TO CHEMOTHERAPY THAT PREDICT PATIENT OUTCOMES, AND PARTICULARLY IMPLICATE EPIGENETIC SILENCING OF HOXA4 IN REDUCING THE SENSITIVITY OF CLL CELLS TO THERAPY. 2021 12 3409 31 HOXA4 GENE PROMOTER HYPERMETHYLATION AS AN EPIGENETIC MECHANISM MEDIATING RESISTANCE TO IMATINIB MESYLATE IN CHRONIC MYELOID LEUKEMIA PATIENTS. DEVELOPMENT OF RESISTANCE TO IMATINIB MESYLATE (IM) IN CHRONIC MYELOID LEUKEMIA (CML) PATIENTS HAS EMERGED AS A SIGNIFICANT CLINICAL PROBLEM. THE OBSERVATION THAT INCREASED EPIGENETIC SILENCING OF POTENTIAL TUMOR SUPPRESSOR GENES CORRELATES WITH DISEASE PROGRESSION IN SOME CML PATIENTS TREATED WITH IM SUGGESTS A RELATIONSHIP BETWEEN EPIGENETIC SILENCING AND RESISTANCE DEVELOPMENT. WE HYPOTHESIZE THAT PROMOTER HYPERMETHYLATION OF HOXA4 COULD BE AN EPIGENETIC MECHANISM MEDIATING IM RESISTANCE IN CML PATIENTS. THUS A STUDY WAS UNDERTAKEN TO INVESTIGATE THE PROMOTER HYPERMETHYLATION STATUS OF HOXA4 IN CML PATIENTS ON IM TREATMENT AND TO DETERMINE ITS ROLE IN MEDIATING RESISTANCE TO IM. GENOMIC DNA WAS EXTRACTED FROM PERIPHERAL BLOOD SAMPLES OF 95 CML PATIENTS (38 GOOD RESPONDERS AND 57 RESISTANT) AND 12 NORMAL CONTROLS. ALL SAMPLES WERE BISULFITE TREATED AND ANALYSED BY METHYLATION-SPECIFIC HIGH-RESOLUTION MELT ANALYSIS. COMPARED TO THE GOOD RESPONDERS, THE HOXA4 HYPERMETHYLATION LEVEL WAS SIGNIFICANTLY HIGHER (P = 0.002) IN IM-RESISTANT CML PATIENTS. ON COMPARING THE RISK, HOXA4 HYPERMETHYLATION WAS ASSOCIATED WITH A HIGHER RISK FOR IM RESISTANCE (OR 4.658; 95% CI, 1.673-12.971; P = 0.003). THUS, IT IS REASONABLE TO SUGGEST THAT PROMOTER HYPERMETHYLATION OF HOXA4 GENE COULD BE AN EPIGENETIC MECHANISM MEDIATING IM RESISTANCE IN CML PATIENTS. 2013 13 942 32 CHRONIC LYMPHOCYTIC LEUKEMIA PRESENCE IMPAIRS ANTIGEN-SPECIFIC CD8(+) T-CELL RESPONSES THROUGH EPIGENETIC REPROGRAMMING TOWARDS SHORT-LIVED EFFECTORS. T-CELL DYSREGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ASSOCIATES WITH LOW RESPONSE RATES TO AUTOLOGOUS T CELL-BASED THERAPIES. HOW CLL AFFECTS ANTIGEN-SPECIFIC T-CELL RESPONSES REMAINS LARGELY UNKNOWN. WE INVESTIGATED (EPI)GENETIC AND FUNCTIONAL CONSEQUENCES OF ANTIGEN-SPECIFIC T-CELL RESPONSES IN PRESENCE OF CLL IN VITRO AND IN AN ADOPTIVE-TRANSFER MURINE MODEL. ALREADY AT STEADY-STATE, ANTIGEN-EXPERIENCED PATIENT-DERIVED T CELLS WERE SKEWED TOWARDS SHORT-LIVED EFFECTOR CELLS (SLEC) AT THE EXPENSE OF MEMORY-PRECURSOR EFFECTOR CELLS (MPEC). STIMULATION OF THESE T CELLS IN VITRO SHOWED RAPID INDUCTION OF EFFECTOR GENES AND SUPPRESSION OF KEY MEMORY TRANSCRIPTION FACTORS ONLY IN PRESENCE OF CLL CELLS, INDICATING EPIGENETIC REGULATION. THIS WAS INVESTIGATED IN VIVO BY FOLLOWING ANTIGEN-SPECIFIC RESPONSES OF NAIVE OT-I CD8(+) CELLS TO MCMV-OVA IN PRESENCE/ABSENCE OF TCL1 B-CELL LEUKEMIA. PRESENCE OF LEUKEMIA RESULTED IN INCREASED SLEC FORMATION, WITH DISTURBED INFLAMMATORY CYTOKINE PRODUCTION. CHROMATIN AND TRANSCRIPTOME PROFILING REVEALED STRONG EPIGENETIC MODIFICATIONS, LEADING TO ACTIVATION OF AN EFFECTOR AND SILENCING OF A MEMORY PROFILE THROUGH PRESENCE OF CLL CELLS. SECONDARY CHALLENGE IN VIVO CONFIRMED DYSFUNCTIONAL MEMORY RESPONSES BY ANTIGEN-EXPERIENCED OT-I CELLS GENERATED IN PRESENCE OF CLL. ALTOGETHER, WE SHOW THAT PRESENCE OF CLL INDUCES A SHORT-LIVED EFFECTOR PHENOTYPE AND IMPAIRED MEMORY RESPONSES BY EPIGENETIC REPROGRAMMING DURING PRIMARY RESPONSES. 2023 14 3522 29 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 15 2639 31 EPIGENOMIC ANALYSIS DETECTS WIDESPREAD GENE-BODY DNA HYPOMETHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. WE HAVE EXTENSIVELY CHARACTERIZED THE DNA METHYLOMES OF 139 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WITH MUTATED OR UNMUTATED IGHV AND OF SEVERAL MATURE B-CELL SUBPOPULATIONS THROUGH THE USE OF WHOLE-GENOME BISULFITE SEQUENCING AND HIGH-DENSITY MICROARRAYS. THE TWO MOLECULAR SUBTYPES OF CLL HAVE DIFFERING DNA METHYLOMES THAT SEEM TO REPRESENT EPIGENETIC IMPRINTS FROM DISTINCT NORMAL B-CELL SUBPOPULATIONS. DNA HYPOMETHYLATION IN THE GENE BODY, TARGETING MOSTLY ENHANCER SITES, WAS THE MOST FREQUENT DIFFERENCE BETWEEN NAIVE AND MEMORY B CELLS AND BETWEEN THE TWO MOLECULAR SUBTYPES OF CLL AND NORMAL B CELLS. ALTHOUGH DNA METHYLATION AND GENE EXPRESSION WERE POORLY CORRELATED, WE IDENTIFIED GENE-BODY CPG DINUCLEOTIDES WHOSE METHYLATION WAS POSITIVELY OR NEGATIVELY ASSOCIATED WITH EXPRESSION. WE HAVE ALSO RECOGNIZED A DNA METHYLATION SIGNATURE THAT DISTINGUISHES NEW CLINICO-BIOLOGICAL SUBTYPES OF CLL. WE PROPOSE AN EPIGENOMIC SCENARIO IN WHICH DIFFERENTIAL METHYLATION IN THE GENE BODY MAY HAVE FUNCTIONAL AND CLINICAL IMPLICATIONS IN LEUKEMOGENESIS. 2012 16 3896 32 LARGE-SCALE ANALYSIS OF DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. AIMS: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A HETEROGENEOUS MALIGNANCY THAT CLINICALLY RANGES FROM INDOLENT TO RAPIDLY PROGRESSIVE. CLL, LIKE OTHER CANCERS, CAN BE AFFECTED BY EPIGENETIC ALTERATIONS. MATERIALS & METHODS: A MICROARRAY DISCOVERY-BASED STUDY WAS INITIATED TO DETERMINE DNA METHYLATION IN CLL CASES WITH A RANGE OF CD38 EXPRESSION (1-92%). RESULTS: MANY LOCI WERE EITHER METHYLATED OR UNMETHYLATED ACROSS ALL CD38 LEVELS, BUT DIFFERENTIAL METHYLATION WAS ALSO OBSERVED FOR SOME GENES. GENOMIC SEQUENCING OF DLEU7 CONFIRMED EXTENSIVE CYTOSINE METHYLATION PREFERENTIALLY IN PATIENT SAMPLES WITH LOW CD38 EXPRESSION, WHEREAS NRP2, SFRP2 AND ADAM12 WERE MORE COMMONLY METHYLATED IN THOSE WITH HIGH CD38 EXPRESSION. CONCLUSION: THIS STUDY DEMONSTRATES THAT CLL IS AFFECTED BY CPG ISLAND METHYLATION IN SOME GENES THAT SEGREGATE WITH CD38 EXPRESSION LEVELS, WHILE MOST OTHERS SHOW SIMILAR METHYLATION PATTERNS ACROSS ALL LEVELS. THE CPG ISLAND METHYLATION IN CERTAIN FUNCTIONAL GENE GROUPS AND PATHWAY-ASSOCIATED GENES THAT ARE KNOWN TO BE DEREGULATED IN CLL PROVIDES ADDITIONAL INSIGHTS INTO THE CLL METHYLOME AND EPIGENETIC CONTRIBUTION TO CELLULAR DYSFUNCTION. IT WILL NOW BE USEFUL TO INVESTIGATE THE EFFECTIVENESS OF EPIGENETIC THERAPEUTIC REVERSAL OF THESE ALTERATIONS TO DEVELOP EFFECTIVE TREATMENTS FOR THE DISEASE. 2009 17 5865 24 SUPPRESSION OF HDAC2 IN SPINAL CORD ALLEVIATES MECHANICAL HYPERALGESIA AND RESTORES KCC2 EXPRESSION IN A RAT MODEL OF BONE CANCER PAIN. EPIGENETIC MODULATION PARTICIPATES IN THE MECHANISM OF MULTIPLE TYPES OF PATHOLOGICAL PAIN, SO TARGETING THE INVOLVED REGULATORS MAY BE A PROMISING STRATEGY FOR PAIN TREATMENT. OUR PREVIOUS RESEARCH IDENTIFIED THE ANALGESIC EFFECT OF THE HISTONE DEACETYLASE (HDAC) INHIBITOR TRICHOSTATIN A (TSA) ON MECHANICAL HYPERALGESIA IN A RAT MODEL OF BONE CANCER PAIN (BCP) VIA RESTORATION OF MU-OPIOID RECEPTOR (MOR) EXPRESSION. HOWEVER, THE SPECIFIC TYPES OF HDACS CONTRIBUTING TO BCP HAVE NOT BEEN EXPLORED. THE PRESENT STUDY INVESTIGATED THE EXPRESSION PATTERN OF SOME COMMON HDACS AND FOUND THAT HDAC2 WAS UP-REGULATED IN A TIME-DEPENDENT MANNER IN THE LUMBAR SPINAL CORD OF BCP RATS. TSA APPLICATION SUPPRESSED HDAC2 EXPRESSION IN CULTURED PC12 CELLS AND REVERSED THE AUGMENTED HDAC2 IN BCP RATS. AN RNA-INTERFERING STRATEGY CONFIRMED THE ESSENTIAL ROLE OF HDAC2 IN THE MODULATION OF MECHANICAL HYPERALGESIA FOLLOWING TUMOR CELL INOCULATION, AND WE FURTHER EXAMINED ITS POSSIBLE DOWNSTREAM TARGETS. NOTABLY, HDAC2 KNOCK-DOWN DID NOT RESTORE MOR EXPRESSION, BUT IT ROBUSTLY REVERSED THE DOWN-REGULATION OF POTASSIUM-CHLORIDE COTRANSPORTER 2 (KCC2). THE IMPAIRED KCC2 EXPRESSION IS A VITAL MECHANISM OF MANY TYPES OF PATHOLOGICAL PAIN. THEREFORE, OUR RESULTS DEMONSTRATED THAT HDAC2 IN SPINAL CORD CONTRIBUTED TO THE MECHANICAL HYPERALGESIA IN BCP RATS, AND THIS EFFECT MAY BE ASSOCIATED WITH KCC2 MODULATION. 2018 18 1976 31 EPIGENETIC ALTERATIONS IN A MURINE MODEL FOR CHRONIC LYMPHOCYTIC LEUKEMIA. EARLY STAGES IN THE DEVELOPMENT OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAVE NOT BEEN EXPLORED MAINLY DUE TO THE INABILITY TO STUDY NORMAL B-CELLS EN ROUTE TO TRANSFORMATION. IN ORDER TO DETERMINE SUCH EARLY EVENTS OF LEUKEMOGENESIS, WE HAVE USED A WELL ESTABLISHED MOUSE MODEL FOR CLL. OVER-EXPRESSION OF HUMAN TCL1, A KNOWN CLL ONCOGENE IN MURINE B-CELLS LEADS TO THE DEVELOPMENT OF MATURE CD19+/CD5+/IGM+ CLONAL LEUKEMIA WITH A DISEASE PHENOTYPE SIMILAR TO THAT SEEN IN HUMAN CLL. HEREIN, WE REVIEW OUR RECENT STUDY USING THIS TCL1-DRIVEN MOUSE MODEL FOR CLL AND CORRESPONDING HUMAN CLL SAMPLES IN A CROSS-SPECIES EPIGENOMICS APPROACH TO ADDRESS THE TIMING AND RELEVANCE OF EPIGENETIC EVENTS OCCURRING DURING LEUKEMOGENESIS. WE DEMONSTRATED THAT THE MOUSE MODEL RECAPITULATES THE EPIGENETIC EVENTS THAT HAVE BEEN REPORTED FOR HUMAN CLL, AFFIRMING THE POWER AND VALIDITY OF THIS MOUSE MODEL TO STUDY EARLY EPIGENETIC EVENTS IN CANCER PROGRESSION. EPIGENETIC ALTERATIONS ARE DETECTED AS EARLY AS THREE MONTHS AFTER BIRTH, FAR BEFORE DISEASE MANIFESTS AT ABOUT 11 MONTHS OF AGE. THESE MICE UNDERGO NFKAPPAB REPRESSOR COMPLEX MEDIATED INACTIVATION OF THE TRANSCRIPTION FACTOR FOXD3, WHOSE TARGETS BECOME ABERRANTLY METHYLATED AND SILENCED IN MOUSE AND HUMAN CLL. OVERALL, OUR DATA SUGGEST THE ACCUMULATED EPIGENETIC ALTERATIONS DURING CLL PATHOGENESIS AS A CONSEQUENCE OF GENE SILENCING THROUGH TCL1 AND NFKAPPAB REPRESSOR COMPLEX, SUGGESTING THE RELEVANCE FOR NFKAPPAB AS A THERAPEUTIC TARGET IN CLL. 2009 19 5513 31 RICHTER SYNDROME: NOVEL INSIGHTS INTO THE BIOLOGY OF TRANSFORMATION. ALTHOUGH THE GENETIC LANDSCAPE OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS BEEN BROADLY PROFILED BY LARGE-SCALE SEQUENCING STUDIES PERFORMED OVER THE PAST DECADE, THE MOLECULAR BASIS OF THE TRANSFORMATION OF CLL INTO AGGRESSIVE LYMPHOMA, OR RICHTER SYNDROME (RS), HAS REMAINED INCOMPLETELY CHARACTERIZED. RECENT ADVANCES IN COMPUTATIONAL METHODS OF CLONAL DECONVOLUTION, AS WELL AS EXTENSIVE SAMPLE COLLECTION EFFORTS IN THIS RAPIDLY PROGRESSIVE MALIGNANCY, HAVE NOW ENABLED COMPREHENSIVE ANALYSIS OF PAIRED CLL AND RS SAMPLES AND HAVE LED TO MULTIPLE NEW STUDIES INVESTIGATING THE GENETIC, TRANSCRIPTOMIC, AND EPIGENETIC ORIGINS OF RS. IN PARALLEL, NEW GENETICALLY ENGINEERED AND XENOGRAFT MOUSE MODELS HAVE PROVIDED THE OPPORTUNITY FOR GLEANING FRESH BIOLOGICAL AND MECHANISTIC INSIGHTS INTO RS DEVELOPMENT AND STEPWISE EVOLUTION FROM ANTECEDENT CLL. ALTOGETHER, THESE STUDIES HAVE DEFINED RS DRIVER LESIONS AND CLL RISK LESIONS AND IDENTIFIED PATHWAYS DYSREGULATED IN TRANSFORMATION. MOREOVER, UNIQUE MOLECULAR SUBTYPES OF RS HAVE BEEN REVEALED, INCLUDING A DISEASE MARKED BY PROFOUND GENOMIC INSTABILITY WITH CHROMOTHRIPSIS/CHROMOPLEXY AND WHOLE GENOME DUPLICATION. NOVEL PROFILING APPROACHES, INCLUDING SINGLE-CELL DNA AND TRANSCRIPTOME SEQUENCING OF RS BIOPSY SPECIMENS AND CELL-FREE DNA PROFILING OF PATIENT PLASMA, DEMONSTRATE PROMISE FOR THE TIMELY IDENTIFICATION OF RS CLONES AND MAY TRANSLATE TO NONINVASIVE IDENTIFICATION AND EARLY DIAGNOSIS OF RS. THIS REVIEW SUMMARIZES THE RECENT SCIENTIFIC ADVANCES IN RS AND SUPPORTS THE INTEGRATED STUDY OF HUMAN GENOMICS WITH MOUSE MODELING TO PROVIDE AN ADVANCED UNDERSTANDING OF THE BIOLOGICAL UNDERPINNINGS OF TRANSFORMATION. THESE RECENT STUDIES HAVE MAJOR IMPLICATIONS FOR MUCH-NEEDED NOVEL THERAPEUTIC STRATEGIES FOR THIS STILL LARGELY INCURABLE MALIGNANCY. 2023 20 3309 33 HIGHER GENE EXPRESSION VARIABILITY IN THE MORE AGGRESSIVE SUBTYPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PRESENTS TWO SUBTYPES WHICH HAVE DRASTICALLY DIFFERENT CLINICAL OUTCOMES, IGVH MUTATED (M-CLL) AND IGVH UNMUTATED (U-CLL). SO FAR, THESE TWO SUBTYPES ARE NOT ASSOCIATED TO CLEAR DIFFERENCES IN GENE EXPRESSION PROFILES. INTERESTINGLY, RECENT RESULTS HAVE HIGHLIGHTED IMPORTANT ROLES FOR HETEROGENEITY, BOTH AT THE GENETIC AND AT THE EPIGENETIC LEVEL IN CLL PROGRESSION. METHODS: WE ANALYZED GENE EXPRESSION DATA OF TWO LARGE COHORTS OF CLL PATIENTS AND QUANTIFIED EXPRESSION VARIABILITY ACROSS INDIVIDUALS TO INVESTIGATE DIFFERENCES BETWEEN THE TWO SUBTYPES USING DIFFERENT MEASURES AND STATISTICAL TESTS. FUNCTIONAL SIGNIFICANCE WAS EXPLORED BY PATHWAY ENRICHMENT AND NETWORK ANALYSES. FURTHERMORE, WE IMPLEMENTED A RANDOM FOREST APPROACH BASED ON EXPRESSION VARIABILITY TO CLASSIFY PATIENTS INTO DISEASE SUBTYPES. RESULTS: WE FOUND THAT U-CLL, THE MORE AGGRESSIVE TYPE OF THE DISEASE, SHOWS SIGNIFICANTLY INCREASED VARIABILITY OF GENE EXPRESSION ACROSS PATIENTS AND THAT, OVERALL, GENES THAT SHOW HIGHER VARIABILITY IN THE AGGRESSIVE SUBTYPE ARE RELATED TO CELL CYCLE, DEVELOPMENT AND INTER-CELLULAR COMMUNICATION. THESE FUNCTIONS INDICATE A POTENTIAL RELATION BETWEEN GENE EXPRESSION VARIABILITY AND THE FASTER PROGRESSION OF THIS CLL SUBTYPE. FINALLY, A CLASSIFIER BASED ON GENE EXPRESSION VARIABILITY WAS ABLE TO CORRECTLY PREDICT THE DISEASE SUBTYPE OF CLL PATIENTS. CONCLUSIONS: THERE ARE STRONG RELATIONS BETWEEN GENE EXPRESSION VARIABILITY AND DISEASE SUBTYPE LINKING SIGNIFICANTLY INCREASED EXPRESSION VARIABILITY TO PHENOTYPES SUCH AS AGGRESSIVENESS AND RESISTANCE TO THERAPY IN CLL. 2015