1 3768 106 INTEGRATIVE EPIGENOMICS IN CHRONIC LYMPHOCYTIC LEUKAEMIA: BIOLOGICAL INSIGHTS AND CLINICAL APPLICATIONS. CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS NOT ONLY CHARACTERISED BY DRIVER GENETIC ALTERATIONS BUT BY EXTENSIVE EPIGENETIC CHANGES. OVER THE LAST DECADE, EPIGENOMIC STUDIES HAVE DESCRIBED THE DNA METHYLOME, CHROMATIN ACCESSIBILITY, HISTONE MODIFICATIONS AND THE THREE-DIMENSIONAL (3D) GENOME ARCHITECTURE OF CLL. BEYOND ITS REGULATORY ROLE, THE DNA METHYLOME CONTAINS IMPRINTS OF THE CELLULAR ORIGIN AND PROLIFERATIVE HISTORY OF CLL CELLS. THESE TWO ASPECTS ARE STRONG INDEPENDENT PROGNOSTIC FACTORS. INTEGRATIVE ANALYSES OF CHROMATIN MARKS HAVE UNCOVERED NOVEL REGULATORY ELEMENTS AND ALTERED TRANSCRIPTION FACTOR NETWORKS AS NON-GENETIC MEANS MEDIATING GENE DEREGULATION IN CLL. ADDITIONALLY, CLL CELLS DISPLAY A DISEASE-SPECIFIC PATTERN OF 3D GENOME INTERACTIONS. FROM THE TECHNOLOGICAL PERSPECTIVE, WE ARE CURRENTLY WITNESSING A TRANSITION FROM BULK OMICS TO SINGLE-CELL ANALYSES. THIS REVIEW AIMS AT SUMMARISING THE MAJOR FINDINGS FROM THE EPIGENOMICS FIELD AS WELL AS PROVIDING A PROSPECT OF THE PRESENT AND FUTURE OF SINGLE-CELL ANALYSES IN CLL. 2023 2 3949 28 LNCRNAS IN T LYMPHOCYTES: RNA REGULATION AT THE HEART OF THE IMMUNE RESPONSE. GENOME-WIDE ANALYSES IN THE LAST DECADE HAVE UNCOVERED THE PRESENCE OF A LARGE NUMBER OF LONG NON-PROTEIN-CODING TRANSCRIPTS THAT SHOW HIGHLY TISSUE- AND STATE-SPECIFIC EXPRESSION PATTERNS. HIGH-THROUGHPUT SEQUENCING ANALYSES IN DIVERSE SUBSETS OF IMMUNE CELLS HAVE REVEALED A COMPLEX AND DYNAMIC EXPRESSION PATTERN FOR THESE LONG NONCODING RNAS (LNCRNAS) THAT CORRELATE WITH THE FUNCTIONAL STATES OF IMMUNE CELLS. ALTHOUGH THE VAST MAJORITY OF LNCRNAS EXPRESSED IN IMMUNE CELLS REMAIN UNSTUDIED, FUNCTIONAL STUDIES PERFORMED ON A SMALL SUBSET HAVE INDICATED THAT THEIR STATE-SPECIFIC EXPRESSIONS PATTERN FREQUENTLY HAS A REGULATORY IMPACT ON THE FUNCTION OF IMMUNE CELLS. IN VIVO AND IN VITRO STUDIES HAVE POINTED TO THE INVOLVEMENT OF LNCRNAS IN A WIDE VARIETY OF CELLULAR PROCESSES, INCLUDING BOTH THE INNATE AND ADAPTIVE IMMUNE RESPONSE THROUGH MECHANISMS RANGING FROM EPIGENETIC AND TRANSCRIPTIONAL REGULATION TO SEQUESTRATION OF FUNCTIONAL MOLECULES IN SUBCELLULAR COMPARTMENTS. THIS REVIEW WILL FOCUS MAINLY ON THE ROLE OF LNCRNAS IN CD4(+) AND CD8(+) T CELLS, WHICH PLAY PIVOTAL ROLES IN ADAPTIVE IMMUNITY. RECENT STUDIES HAVE POINTED TO KEY PHYSIOLOGICAL FUNCTIONS FOR LNCRNAS DURING SEVERAL DEVELOPMENTAL AND FUNCTIONAL STAGES OF THE LIFE CYCLE OF LYMPHOCYTES. ALTHOUGH LNCRNAS PLAY IMPORTANT PHYSIOLOGICAL ROLES IN LYMPHOCYTIC RESPONSE TO ANTIGENIC STIMULATION, DIFFERENTIATION INTO EFFECTOR CELLS, AND SECRETION OF CYTOKINES, THEIR DYSREGULATED EXPRESSION CAN PROMOTE OR SUSTAIN PATHOLOGICAL STATES SUCH AS AUTOIMMUNITY, CHRONIC INFLAMMATION, CANCER, AND VIREMIA. THIS, TOGETHER WITH THEIR HIGHLY CELL TYPE-SPECIFIC EXPRESSION PATTERNS, MAKES LNCRNAS IDEAL THERAPEUTIC TARGETS AND UNDERSCORES THE NEED FOR ADDITIONAL STUDIES INTO THE ROLE OF THESE UNDERSTUDIED TRANSCRIPTS IN ADAPTIVE IMMUNE RESPONSE. 2021 3 1468 35 DISTINCT EPIGENETIC PROGRAMS REGULATE CARDIAC MYOCYTE DEVELOPMENT AND DISEASE IN THE HUMAN HEART IN VIVO. EPIGENETIC MECHANISMS AND TRANSCRIPTION FACTOR NETWORKS ESSENTIAL FOR DIFFERENTIATION OF CARDIAC MYOCYTES HAVE BEEN UNCOVERED. HOWEVER, RESHAPING OF THE EPIGENOME OF THESE TERMINALLY DIFFERENTIATED CELLS DURING FETAL DEVELOPMENT, POSTNATAL MATURATION, AND IN DISEASE REMAINS UNKNOWN. HERE, WE INVESTIGATE THE DYNAMICS OF THE CARDIAC MYOCYTE EPIGENOME DURING DEVELOPMENT AND IN CHRONIC HEART FAILURE. WE FIND THAT PRENATAL DEVELOPMENT AND POSTNATAL MATURATION ARE CHARACTERIZED BY A COOPERATION OF ACTIVE CPG METHYLATION AND HISTONE MARKS AT CIS-REGULATORY AND GENIC REGIONS TO SHAPE THE CARDIAC MYOCYTE TRANSCRIPTOME. IN CONTRAST, PATHOLOGICAL GENE EXPRESSION IN TERMINAL HEART FAILURE IS ACCOMPANIED BY CHANGES IN ACTIVE HISTONE MARKS WITHOUT MAJOR ALTERATIONS IN CPG METHYLATION AND REPRESSIVE CHROMATIN MARKS. NOTABLY, CIS-REGULATORY REGIONS IN CARDIAC MYOCYTES ARE SIGNIFICANTLY ENRICHED FOR CARDIOVASCULAR DISEASE-ASSOCIATED VARIANTS. THIS STUDY UNCOVERS DISTINCT LAYERS OF EPIGENETIC REGULATION NOT ONLY DURING PRENATAL DEVELOPMENT AND POSTNATAL MATURATION BUT ALSO IN DISEASED HUMAN CARDIAC MYOCYTES. 2018 4 4473 25 MOLECULAR PATHOGENESIS OF CLL AND ITS EVOLUTION. IN SPITE OF BEING THE MOST PREVALENT ADULT LEUKEMIA IN WESTERN COUNTRIES, THE MOLECULAR MECHANISMS DRIVING THE ESTABLISHMENT AND PROGRESSION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) REMAIN LARGELY UNKNOWN. IN RECENT YEARS, THE USE OF NEXT-GENERATION SEQUENCING TECHNIQUES HAS UNCOVERED NEW AND, IN SOME CASES, UNEXPECTED DRIVER GENES WITH PROGNOSTIC AND THERAPEUTIC VALUE. THE MUTATIONAL LANDSCAPE OF CLL IS CHARACTERIZED BY HIGH-GENETIC AND EPIGENETIC HETEROGENEITY, LOW MUTATION RECURRENCE AND A LONG TAIL OF CASES WITH UNDEFINED DRIVER GENES. ON THE OTHER HAND, THE USE OF DEEP SEQUENCING HAS ALSO REVEALED HIGH INTRA-TUMOR HETEROGENEITY AND PROVIDED A DETAILED PICTURE OF CLONAL EVOLUTION PROCESSES. THIS PHENOMENON, IN WHICH ABERRANT DNA METHYLATION CAN ALSO PARTICIPATE, APPEARS TO BE TIGHTLY ASSOCIATED TO POOR OUTCOMES AND CHEMO-REFRACTORINESS, THUS PROVIDING A NEW SUBJECT FOR THERAPEUTIC INTERVENTION. HENCE, AND HAVING IN MIND THE LIMITATIONS DERIVED FROM THE CLL COMPLEXITY THUS DESCRIBED, THE APPLICATION OF MASSIVELY PARALLEL SEQUENCING STUDIES HAS UNVEILED A WEALTH OF INFORMATION THAT IS EXPECTED TO SUBSTANTIALLY IMPROVE PATIENT STAGING SCHEMES AND CLL CLINICAL MANAGEMENT. 2015 5 3918 41 LINKING ABERRANT CHROMATIN FEATURES IN CHRONIC LYMPHOCYTIC LEUKEMIA TO TRANSCRIPTION FACTOR NETWORKS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A DIVERSE SET OF GENETIC MUTATIONS IS EMBEDDED IN A DEREGULATED EPIGENETIC LANDSCAPE THAT DRIVES CANCEROGENESIS. TO ELUCIDATE THE ROLE OF ABERRANT CHROMATIN FEATURES, WE MAPPED DNA METHYLATION, SEVEN HISTONE MODIFICATIONS, NUCLEOSOME POSITIONS, CHROMATIN ACCESSIBILITY, BINDING OF EBF1 AND CTCF, AS WELL AS THE TRANSCRIPTOME OF B CELLS FROM CLL PATIENTS AND HEALTHY DONORS. A GLOBALLY INCREASED HISTONE DEACETYLASE ACTIVITY WAS DETECTED AND HALF OF THE GENOME COMPRISED TRANSCRIPTIONALLY DOWNREGULATED PARTIALLY DNA METHYLATED DOMAINS DEMARCATED BY CTCF CLL SAMPLES DISPLAYED A H3K4ME3 REDISTRIBUTION AND NUCLEOSOME GAIN AT PROMOTERS AS WELL AS CHANGES OF ENHANCER ACTIVITY AND ENHANCER LINKAGE TO TARGET GENES. A DNA BINDING MOTIF ANALYSIS IDENTIFIED TRANSCRIPTION FACTORS THAT GAINED OR LOST BINDING IN CLL AT SITES WITH ABERRANT CHROMATIN FEATURES. THESE FINDINGS WERE INTEGRATED INTO A GENE REGULATORY ENHANCER CONTAINING NETWORK ENRICHED FOR B-CELL RECEPTOR SIGNALING PATHWAY COMPONENTS. OUR STUDY PREDICTS NOVEL MOLECULAR LINKS TO TARGETS OF CLL THERAPIES AND PROVIDES A VALUABLE RESOURCE FOR FURTHER STUDIES ON THE EPIGENETIC CONTRIBUTION TO THE DISEASE. 2019 6 3375 22 HISTONE POSTTRANSLATIONAL MODIFICATIONS PREDICT SPECIFIC ALTERNATIVE EXON SUBTYPES IN MAMMALIAN BRAIN. A COMPELLING BODY OF LITERATURE, BASED ON NEXT GENERATION CHROMATIN IMMUNOPRECIPITATION AND RNA SEQUENCING OF REWARD BRAIN REGIONS INDICATES THAT THE REGULATION OF THE EPIGENETIC LANDSCAPE LIKELY UNDERLIES CHRONIC DRUG ABUSE AND ADDICTION. IT IS NOW CRITICAL TO DEVELOP HIGHLY INNOVATIVE COMPUTATIONAL STRATEGIES TO REVEAL THE RELEVANT REGULATORY TRANSCRIPTIONAL MECHANISMS THAT MAY UNDERLIE NEUROPSYCHIATRIC DISEASE. WE HAVE ANALYZED CHROMATIN REGULATION OF ALTERNATIVE SPLICING, WHICH IS IMPLICATED IN COCAINE EXPOSURE IN MICE. RECENT LITERATURE HAS DESCRIBED CHROMATIN-REGULATED ALTERNATIVE SPLICING, SUGGESTING A NOVEL FUNCTION FOR DRUG-INDUCED NEUROEPIGENETIC REMODELING. HOWEVER, THE EXTENT OF THE GENOME-WIDE ASSOCIATION BETWEEN PARTICULAR HISTONE MODIFICATIONS AND ALTERNATIVE SPLICING REMAINS UNEXPLORED. TO ADDRESS THIS, WE HAVE DEVELOPED NOVEL COMPUTATIONAL APPROACHES TO MODEL THE ASSOCIATION BETWEEN ALTERNATIVE SPLICING AND HISTONE POSTTRANSLATIONAL MODIFICATIONS IN THE NUCLEUS ACCUMBENS (NAC), A BRAIN REWARD REGION. USING CLASSICAL STATISTICAL METHODS AND MACHINE LEARNING TO COMBINE CHIP-SEQ AND RNA-SEQ DATA, WE FOUND THAT SPECIFIC HISTONE MODIFICATIONS ARE STRONGLY ASSOCIATED WITH VARIOUS ASPECTS OF DIFFERENTIAL SPLICING. H3K36ME3 AND H3K4ME1 HAVE THE STRONGEST ASSOCIATION WITH SPLICING INDICATING THEY PLAY A SIGNIFICANT ROLE IN ALTERNATIVE SPLICING IN BRAIN REWARD TISSUE. 2017 7 5702 25 SINGLE-CELL GENOMICS FOR INVESTIGATING PATHOGENESIS OF INFLAMMATORY DISEASES. RECENT TECHNICAL ADVANCES HAVE ENABLED UNBIASED TRANSCRIPTOMIC AND EPIGENETIC ANALYSIS OF EACH CELL, KNOWN AS "SINGLE-CELL ANALYSIS". SINGLE-CELL ANALYSIS HAS A VARIETY OF TECHNICAL APPROACHES TO INVESTIGATE THE STATE OF EACH CELL, INCLUDING MRNA LEVELS (TRANSCRIPTOME), THE IMMUNE REPERTOIRE (IMMUNE REPERTOIRE ANALYSIS), CELL SURFACE PROTEINS (SURFACE PROTEOME ANALYSIS), CHROMATIN ACCESSIBILITY (EPIGENOME), AND ACCORDANCE WITH GENOME VARIANTS (EQTLS; EXPRESSION QUANTITATIVE TRAIT LOCI). AS AN EFFECTIVE TOOL FOR INVESTIGATING ROBUST IMMUNE RESPONSES IN CORONAVIRUS DISEASE 2019 (COVID-19), MANY RESEARCHERS PERFORMED SINGLE-CELL ANALYSIS TO CAPTURE THE DIVERSE, UNBIASED IMMUNE CELL ACTIVATION AND DIFFERENTIATION. DESPITE CHALLENGES ELUCIDATING THE COMPLICATED IMMUNE MICROENVIRONMENTS OF CHRONIC INFLAMMATORY DISEASES USING EXISTING EXPERIMENTAL METHODS, IT IS NOW POSSIBLE TO CAPTURE THE SIMULTANEOUS IMMUNE FEATURES OF DIFFERENT CELL TYPES ACROSS INFLAMED TISSUES USING VARIOUS SINGLE-CELL TOOLS. IN THIS REVIEW, WE INTRODUCE PATIENT-BASED AND EXPERIMENTAL MOUSE MODEL RESEARCH UTILIZING SINGLE-CELL ANALYSES IN THE FIELD OF CHRONIC INFLAMMATORY DISEASES, AS WELL AS MULTI-ORGAN ATLAS TARGETING IMMUNE CELLS. 2023 8 6616 44 UNCOVERING THE DNA METHYLOME IN CHRONIC LYMPHOCYTIC LEUKEMIA. OVER THE PAST TWO DECADES, ABERRANT DNA METHYLATION HAS EMERGED AS A KEY PLAYER IN THE PATHOGENESIS OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), AND KNOWLEDGE REGARDING ITS BIOLOGICAL AND CLINICAL CONSEQUENCES IN THIS DISEASE HAS EVOLVED RAPIDLY. SINCE THE INITIAL STUDIES RELATING DNA HYPOMETHYLATION TO GENOMIC INSTABILITY IN CLL, A PLETHORA OF REPORTS HAVE FOLLOWED SHOWING THE IMPACT OF DNA HYPERMETHYLATION IN SILENCING VITAL SINGLE GENE PROMOTERS AND THE REVERSIBLE NATURE OF DNA METHYLATION THROUGH INHIBITOR DRUGS. WITH THE RECOGNITION THAT DNA HYPERMETHYLATION EVENTS COULD POTENTIALLY ACT AS NOVEL PROGNOSTIC AND TREATMENT TARGETS IN CLL, THE SEARCH FOR ABERRANTLY METHYLATED GENES, GENE FAMILIES AND PATHWAYS HAS ENSUED. SUBSEQUENTLY, THE ADVENT OF MICROARRAY AND NEXT-GENERATION SEQUENCING TECHNOLOGIES HAS SUPPORTED THE HUNT FOR SUCH TARGETS, ALLOWING EXPLORATION OF THE METHYLATION LANDSCAPE IN CLL AT AN UNPRECEDENTED SCALE. IN LIGHT OF THESE ANALYSES, WE NOW UNDERSTAND THAT DIFFERENT CLL PROGNOSTIC SUBGROUPS ARE CHARACTERIZED BY DIFFERENTIAL METHYLATION PROFILES; WE RECOGNIZE DNA METHYLATION OF A NUMBER OF SIGNALING PATHWAYS GENES TO BE ALTERED IN CLL, AND ACKNOWLEDGE THE ROLE OF DNA METHYLATION OUTSIDE OF TRADITIONAL CPG ISLAND PROMOTERS AS FUNDAMENTAL PLAYERS IN THE REGULATION OF GENE EXPRESSION. TODAY, THE SIGNIFICANCE AND TIMING OF ALTERED DNA METHYLATION WITHIN THE COMPLEX EPIGENETIC NETWORK OF CONCOMITANT EPIGENETIC MESSENGERS SUCH AS HISTONES AND MIRNAS IS AN INTENSIVE AREA OF RESEARCH. IN CLL, IT APPEARS THAT DNA METHYLATION IS A RATHER STABLE EPIGENETIC MARK OCCURRING RATHER EARLY IN THE DISEASE PATHOGENESIS. HOWEVER, OTHER CONSEQUENCES, SUCH AS HOW AND WHY ABERRANT METHYLATION MARKS OCCUR, ARE LESS EXPLORED. IN THIS REVIEW, WE WILL NOT ONLY PROVIDE A COMPREHENSIVE SUMMARY OF THE CURRENT LITERATURE WITHIN THE EPIGENETICS FIELD OF CLL, BUT ALSO HIGHLIGHT SOME OF THE NOVEL FINDINGS RELATING TO WHEN, WHERE, WHY AND HOW ALTERED DNA METHYLATION MATERIALIZES IN CLL. 2013 9 1533 26 DNA METHYLATION DYNAMICS DURING B CELL MATURATION UNDERLIE A CONTINUUM OF DISEASE PHENOTYPES IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHARTING DIFFERENCES BETWEEN TUMORS AND NORMAL TISSUE IS A MAINSTAY OF CANCER RESEARCH. HOWEVER, CLONAL TUMOR EXPANSION FROM COMPLEX NORMAL TISSUE ARCHITECTURES POTENTIALLY OBSCURES CANCER-SPECIFIC EVENTS, INCLUDING DIVERGENT EPIGENETIC PATTERNS. USING WHOLE-GENOME BISULFITE SEQUENCING OF NORMAL B CELL SUBSETS, WE OBSERVED BROAD EPIGENETIC PROGRAMMING OF SELECTIVE TRANSCRIPTION FACTOR BINDING SITES COINCIDENT WITH THE DEGREE OF B CELL MATURATION. BY COMPARING NORMAL B CELLS TO MALIGNANT B CELLS FROM 268 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), WE SHOWED THAT TUMORS DERIVE LARGELY FROM A CONTINUUM OF MATURATION STATES REFLECTED IN NORMAL DEVELOPMENTAL STAGES. EPIGENETIC MATURATION IN CLL WAS ASSOCIATED WITH AN INDOLENT GENE EXPRESSION PATTERN AND INCREASINGLY FAVORABLE CLINICAL OUTCOMES. WE FURTHER UNCOVERED THAT MOST PREVIOUSLY REPORTED TUMOR-SPECIFIC METHYLATION EVENTS ARE NORMALLY PRESENT IN NON-MALIGNANT B CELLS. INSTEAD, WE IDENTIFIED A POTENTIAL PATHOGENIC ROLE FOR TRANSCRIPTION FACTOR DYSREGULATION IN CLL, WHERE EXCESS PROGRAMMING BY EGR AND NFAT WITH REDUCED EBF AND AP-1 PROGRAMMING IMBALANCES THE NORMAL B CELL EPIGENETIC PROGRAM. 2016 10 945 32 CHRONIC LYMPHOCYTIC LEUKEMIA: MOLECULAR HETEROGENEITY REVEALED BY HIGH-THROUGHPUT GENOMICS. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS BEEN CONSISTENTLY AT THE FOREFRONT OF GENETIC RESEARCH OWING TO ITS PREVALENCE AND THE ACCESSIBILITY OF SAMPLE MATERIAL. RECENTLY, GENOME-WIDE TECHNOLOGIES HAVE BEEN INTENSIVELY APPLIED TO CLL GENETICS, WITH REMARKABLE PROGRESS. SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS HAVE IDENTIFIED RECURRING CHROMOSOMAL ABERRATIONS, THEREBY FOCUSING FUNCTIONAL STUDIES ON DISCRETE GENOMIC LESIONS AND LEADING TO THE FIRST IMPLICATION OF SOMATIC MICRORNA DISRUPTION IN CANCER. NEXT-GENERATION SEQUENCING (NGS) HAS FURTHER TRANSFORMED OUR UNDERSTANDING OF CLL BY IDENTIFYING NOVEL RECURRENTLY MUTATED PUTATIVE DRIVERS, INCLUDING THE UNEXPECTED DISCOVERY OF SOMATIC MUTATIONS AFFECTING SPLICEOSOME FUNCTION. NGS HAS FURTHER ENABLED IN-DEPTH EXAMINATION OF THE TRANSCRIPTIONAL AND EPIGENETIC CHANGES IN CLL THAT ACCOMPANY GENETIC LESIONS, AND HAS SHED LIGHT ON HOW DIFFERENT DRIVER EVENTS APPEAR AT DIFFERENT STAGES OF DISEASE PROGRESSION AND CLONALLY EVOLVE WITH RELAPSED DISEASE. IN ADDITION TO PROVIDING IMPORTANT INSIGHTS INTO DISEASE BIOLOGY, THESE DISCOVERIES HAVE SIGNIFICANT TRANSLATIONAL POTENTIAL. THEY ENHANCE PROGNOSIS BY HIGHLIGHTING SPECIFIC LESIONS ASSOCIATED WITH POOR CLINICAL OUTCOMES (FOR EXAMPLE, DRIVER EVENTS SUCH AS MUTATIONS IN THE SPLICING FACTOR SUBUNIT GENE SF3B1) OR WITH INCREASED CLONAL HETEROGENEITY (FOR EXAMPLE, THE PRESENCE OF SUBCLONAL DRIVER MUTATIONS). HERE, WE REVIEW NEW GENOMIC DISCOVERIES IN CLL AND DISCUSS THEIR POSSIBLE IMPLICATIONS IN THE ERA OF PRECISION MEDICINE. 2013 11 862 27 CHROMATIN REMODELING IN MONOCYTE AND MACROPHAGE ACTIVATION. INCREASING EVIDENCE COLLECTED DURING THE LAST YEARS SUPPORTS THE IDEA THAT MONOCYTE AND MACROPHAGE ACTIVATION IS NOT ONLY ASSOCIATED WITH TRANSCRIPTIONAL CHANGES BUT ALSO CHANGES IN THE CHROMATIN LANDSCAPE. MOREOVER, THE INTRODUCTION OF A MULTIDIMENSIONAL MODEL OF MACROPHAGE ACTIVATION ALLOWS A MORE PRECISE DESCRIPTION OF MONOCYTES AND MACROPHAGES UNDER HOMEOSTATIC AND PATHOPHYSIOLOGICAL CONDITIONS. MONOCYTES AND MACROPHAGES ARE MASTERS OF INTEGRATING MICROENVIRONMENTAL SIGNALS, THEREBY RESHAPING THEIR CHROMATIN LANDSCAPE AND AS A CONSEQUENCE THEIR TRANSCRIPTIONAL AND FUNCTIONAL PROGRAMS. ALBEIT THESE CELLS SHARE A LARGE NUMBER OF EPIGENETIC LANDMARKS, THEIR CHROMATIN IS SIGNIFICANTLY SHAPED BY ENVIRONMENTAL SIGNALS. THE CHROMATIN LANDSCAPE OF ANY GIVEN TISSUE MACROPHAGE IS A RATHER SPECIFIC FINGERPRINT OF THESE CELLS, WHICH IS DIRECTLY LINKED TO TISSUE-SPECIFIC FUNCTIONS OF THESE CELLS. MOREOVER, CHROMATIN REMODELING IN RESPONSE TO STRESS SIGNALS ALSO SEEMS TO BE AN IMPORTANT MECHANISM OF THESE CELLS TO INCREASE THEIR READINESS FOR FUTURE STRESSORS. UNDERSTANDING THIS SOPHISTICATED EPIGENETIC REGULATORY NETWORK IN MONOCYTES AND MACROPHAGES WILL OPEN UP NEW AVENUES TOWARD TISSUE- AND DISEASE-SPECIFIC THERAPEUTIC STRATEGIES IN MANY OF THE CHRONIC INFLAMMATORY DISEASES OUR SOCIETIES ARE CURRENTLY FACING. 2017 12 6307 34 THE REFERENCE EPIGENOME AND REGULATORY CHROMATIN LANDSCAPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A FREQUENT HEMATOLOGICAL NEOPLASM IN WHICH UNDERLYING EPIGENETIC ALTERATIONS ARE ONLY PARTIALLY UNDERSTOOD. HERE, WE ANALYZE THE REFERENCE EPIGENOME OF SEVEN PRIMARY CLLS AND THE REGULATORY CHROMATIN LANDSCAPE OF 107 PRIMARY CASES IN THE CONTEXT OF NORMAL B CELL DIFFERENTIATION. WE IDENTIFY THAT THE CLL CHROMATIN LANDSCAPE IS LARGELY INFLUENCED BY DISTINCT DYNAMICS DURING NORMAL B CELL MATURATION. BEYOND THIS, WE DEFINE EXTENSIVE CATALOGUES OF REGULATORY ELEMENTS DE NOVO REPROGRAMMED IN CLL AS A WHOLE AND IN ITS MAJOR CLINICO-BIOLOGICAL SUBTYPES CLASSIFIED BY IGHV SOMATIC HYPERMUTATION LEVELS. WE UNCOVER THAT IGHV-UNMUTATED CLLS HARBOR MORE ACTIVE AND OPEN CHROMATIN THAN IGHV-MUTATED CASES. FURTHERMORE, WE SHOW THAT DE NOVO ACTIVE REGIONS IN CLL ARE ENRICHED FOR NFAT, FOX AND TCF/LEF TRANSCRIPTION FACTOR FAMILY BINDING SITES. ALTHOUGH MOST GENETIC ALTERATIONS ARE NOT ASSOCIATED WITH CONSISTENT EPIGENETIC PROFILES, CLLS WITH MYD88 MUTATIONS AND TRISOMY 12 SHOW DISTINCT CHROMATIN CONFIGURATIONS. FURTHERMORE, WE OBSERVE THAT NON-CODING MUTATIONS IN IGHV-MUTATED CLLS ARE ENRICHED IN H3K27AC-ASSOCIATED REGULATORY ELEMENTS OUTSIDE ACCESSIBLE CHROMATIN. OVERALL, THIS STUDY PROVIDES AN INTEGRATIVE PORTRAIT OF THE CLL EPIGENOME, IDENTIFIES EXTENSIVE NETWORKS OF ALTERED REGULATORY ELEMENTS AND SHEDS LIGHT ON THE RELATIONSHIP BETWEEN THE GENETIC AND EPIGENETIC ARCHITECTURE OF THE DISEASE. 2018 13 115 22 A STEM CELL AGING FRAMEWORK, FROM MECHANISMS TO INTERVENTIONS. STEM CELLS PLAY CENTRAL ROLES IN TISSUE DEVELOPMENT, HOMEOSTASIS, AND REGENERATION. DECADES OF SCIENTIFIC RESEARCH HAVE UNCOVERED PROCESSES OF STEM CELL DECLINE IN TISSUE AND ORGANISMAL AGING, AND MORE RECENTLY, PIONEERING TECHNOLOGIES PERMIT THE DISSECTION OF ITS UNDERLYING MECHANISMS AND INFORM THERAPEUTIC DEVELOPMENT FOR AGING AND AGING-ASSOCIATED DISORDERS. IN THIS REVIEW, WE ELUCIDATE AGING-RELATED FEATURES ACROSS DIFFERENT SOMATIC STEM CELL TYPES, WITH A SPECIFIC FOCUS ON EPIGENETIC CHANGES, LOSS OF PROTEIN HOMEOSTASIS, AND SYSTEMIC INFLUENCING FACTORS, INCLUDING CHRONIC INFLAMMATION, CIRCADIAN RHYTHM DYSREGULATION, AND METABOLIC DISORDER. OUR SURVEY OF ORGANISMAL STEM CELL AGING SUMMARIZES ITS UNDERLYING BIOLOGICAL IMPLICATIONS, POINTS TO POTENTIAL BIOMARKERS OF STEM CELL AGING, AND DISCUSSES STEM CELL-BASED THERAPEUTIC STRATEGIES WITH THE POTENTIAL FOR PROMOTING HEALTHY AGING AND COMBATING AGING AND AGE-RELATED DISEASES. 2022 14 2944 30 GENETIC AND EPIGENETIC BASIS OF CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE OF REVIEW: NEXT-GENERATION SEQUENCING OF WHOLE GENOMES, EXOMES AND DNA METHYLOMES IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS PROVIDED THE FIRST COMPREHENSIVE VIEW OF SOMATIC MUTATIONS AND METHYLATION CHANGES IN THIS DISEASE. THIS REVIEW SUMMARIZES THE RECENT FINDINGS IN THIS FIELD AND THEIR IMPACT ON OUR CURRENT UNDERSTANDING OF THIS NEOPLASM. RECENT FINDINGS: GENOMIC STUDIES HAVE REVEALED A REMARKABLE MOLECULAR HETEROGENEITY OF THE DISEASE, WITH ONLY FEW GENES MUTATED IN UP TO 10-15% OF THE PATIENTS AND A RELATIVELY LARGE NUMBER OF GENES RECURRENTLY MUTATED AT LOW FREQUENCY. THE MUTATED GENES TEND TO CLUSTER IN DIFFERENT PATHWAYS THAT INCLUDE NOTCH1 SIGNALING, RNA SPLICING, PROCESSING AND TRANSPORT MACHINERY, INNATE INFLAMMATORY RESPONSE, AND DNA DAMAGE AND CELL CYCLE CONTROL, AMONG OTHERS. NOTCH1 AND SF3B1 MUTATIONS ARE EMERGING AS NEW DRIVERS OF AGGRESSIVE FORMS OF THE DISEASE. GENOME-WIDE METHYLATION STUDIES HAVE SHOWN THAT CLL TRANSFORMATION IS ASSOCIATED WITH A MASSIVE HYPOMETHYLATION PHENOMENON FREQUENTLY AFFECTING THE ENHANCER REGIONS. THIS EPIGENETIC REPROGRAMMING MAINTAINS AN IMPRINT OF THE PUTATIVE CELL OF ORIGIN FROM NAIVE AND MEMORY B-CELLS. SUMMARY: GENOMIC AND EPIGENOMIC STUDIES OF CLL ARE RESHAPING OUR UNDERSTANDING OF THE DISEASE AND PROVIDE NEW PERSPECTIVE FOR A MORE INDIVIDUALIZED DIAGNOSIS AND NEW POTENTIAL THERAPEUTIC TARGETS. 2013 15 4132 24 MECHANISMS OF HEPATIC FIBROGENESIS. SUBSTANTIAL IMPROVEMENTS IN THE TREATMENT OF CHRONIC LIVER DISEASE HAVE ACCELERATED INTEREST IN UNCOVERING THE MECHANISMS UNDERLYING HEPATIC FIBROSIS AND ITS RESOLUTION. ACTIVATION OF RESIDENT HEPATIC STELLATE CELLS INTO PROLIFERATIVE, CONTRACTILE, AND FIBROGENIC CELLS IN LIVER INJURY REMAINS A DOMINANT THEME DRIVING THE FIELD. HOWEVER, SEVERAL NEW AREAS OF RAPID PROGRESS IN THE PAST 5-10 YEARS ALSO HAVE TAKEN ROOT, INCLUDING: (1) IDENTIFICATION OF DIFFERENT FIBROGENIC POPULATIONS APART FROM RESIDENT STELLATE CELLS, FOR EXAMPLE, PORTAL FIBROBLASTS, FIBROCYTES, AND BONE-MARROW-DERIVED CELLS, AS WELL AS CELLS DERIVED FROM EPITHELIAL MESENCHYMAL TRANSITION; (2) EMERGENCE OF STELLATE CELLS AS FINELY REGULATED DETERMINANTS OF HEPATIC INFLAMMATION AND IMMUNITY; (3) ELUCIDATION OF MULTIPLE PATHWAYS CONTROLLING GENE EXPRESSION DURING STELLATE CELL ACTIVATION INCLUDING TRANSCRIPTIONAL, POST-TRANSCRIPTIONAL, AND EPIGENETIC MECHANISMS; (4) RECOGNITION OF DISEASE-SPECIFIC PATHWAYS OF FIBROGENESIS; (5) RE-EMERGENCE OF HEPATIC MACROPHAGES AS DETERMINANTS OF MATRIX DEGRADATION IN FIBROSIS RESOLUTION AND THE IMPORTANCE OF MATRIX CROSS-LINKING AND SCAR MATURATION IN DETERMINING REVERSIBILITY; AND (6) HINTS THAT HEPATIC STELLATE CELLS MAY CONTRIBUTE TO HEPATIC STEM CELL BEHAVIOR, CANCER, AND REGENERATION. CLINICAL AND TRANSLATIONAL IMPLICATIONS OF THESE ADVANCES HAVE BECOME CLEAR, AND HAVE BEGUN TO IMPACT SIGNIFICANTLY ON THE MANAGEMENT AND OUTLOOK OF PATIENTS WITH CHRONIC LIVER DISEASE. 2008 16 371 21 AN ATLAS OF THE AGING LUNG MAPPED BY SINGLE CELL TRANSCRIPTOMICS AND DEEP TISSUE PROTEOMICS. AGING PROMOTES LUNG FUNCTION DECLINE AND SUSCEPTIBILITY TO CHRONIC LUNG DISEASES, WHICH ARE THE THIRD LEADING CAUSE OF DEATH WORLDWIDE. HERE, WE USE SINGLE CELL TRANSCRIPTOMICS AND MASS SPECTROMETRY-BASED PROTEOMICS TO QUANTIFY CHANGES IN CELLULAR ACTIVITY STATES ACROSS 30 CELL TYPES AND CHART THE LUNG PROTEOME OF YOUNG AND OLD MICE. WE SHOW THAT AGING LEADS TO INCREASED TRANSCRIPTIONAL NOISE, INDICATING DEREGULATED EPIGENETIC CONTROL. WE OBSERVE CELL TYPE-SPECIFIC EFFECTS OF AGING, UNCOVERING INCREASED CHOLESTEROL BIOSYNTHESIS IN TYPE-2 PNEUMOCYTES AND LIPOFIBROBLASTS AND ALTERED RELATIVE FREQUENCY OF AIRWAY EPITHELIAL CELLS AS HALLMARKS OF LUNG AGING. PROTEOMIC PROFILING REVEALS EXTRACELLULAR MATRIX REMODELING IN OLD MICE, INCLUDING INCREASED COLLAGEN IV AND XVI AND DECREASED FRASER SYNDROME COMPLEX PROTEINS AND COLLAGEN XIV. COMPUTATIONAL INTEGRATION OF THE AGING PROTEOME WITH THE SINGLE CELL TRANSCRIPTOMES PREDICTS THE CELLULAR SOURCE OF REGULATED PROTEINS AND CREATES AN UNBIASED REFERENCE MAP OF THE AGING LUNG. 2019 17 1336 26 DESCRIBING A TRANSCRIPTION FACTOR DEPENDENT REGULATION OF THE MICRORNA TRANSCRIPTOME. WHILE THE TRANSCRIPTION REGULATION OF PROTEIN CODING GENES WAS EXTENSIVELY STUDIED, LITTLE IS KNOWN ON HOW TRANSCRIPTION FACTORS ARE INVOLVED IN TRANSCRIPTION OF NON-CODING RNAS, SPECIFICALLY OF MICRORNAS. HERE, WE PROPOSE A STRATEGY TO STUDY THE POTENTIAL ROLE OF TRANSCRIPTION FACTOR IN REGULATING TRANSCRIPTION OF MICRORNAS USING PUBLICALLY AVAILABLE DATA, COMPUTATIONAL RESOURCES AND HIGH THROUGHPUT DATA. WE USE THE H3K4ME3 EPIGENETIC SIGNATURE TO IDENTIFY MICRORNA PROMOTERS AND CHROMATIN IMMUNOPRECIPITATION (CHIP)-SEQUENCING DATA FROM THE ENCODE PROJECT TO IDENTIFY MICRORNA PROMOTERS THAT ARE ENRICHED WITH TRANSCRIPTION FACTOR BINDING SITES. BY TRANSFECTING CELLS OF INTEREST WITH SHRNA TARGETING A TRANSCRIPTION FACTOR OF INTEREST AND SUBJECTING THE CELLS TO MICRORNA ARRAY, WE STUDY THE EFFECT OF THIS TRANSCRIPTION FACTOR ON THE MICRORNA TRANSCRIPTOME. AS AN ILLUSTRATIVE EXAMPLE WE USE OUR STUDY ON THE EFFECT OF STAT3 ON THE MICRORNA TRANSCRIPTOME OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. 2016 18 1562 35 DNA METHYLATION OF ENHANCER ELEMENTS IN MYELOID NEOPLASMS: THINK OUTSIDE THE PROMOTERS? GENE REGULATION THROUGH DNA METHYLATION IS A WELL DESCRIBED PHENOMENON THAT HAS A PROMINENT ROLE IN PHYSIOLOGICAL AND PATHOLOGICAL CELL-STATES. THIS EPIGENETIC MODIFICATION IS USUALLY GROUPED IN REGIONS DENOMINATED CPG ISLANDS, WHICH FREQUENTLY CO-LOCALIZE WITH GENE PROMOTERS, SILENCING THE TRANSCRIPTION OF THOSE GENES. RECENT GENOME-WIDE DNA METHYLATION STUDIES HAVE CHALLENGED THIS PARADIGM, DEMONSTRATING THAT DNA METHYLATION OF REGULATORY REGIONS OUTSIDE PROMOTERS IS ABLE TO INFLUENCE CELL-TYPE SPECIFIC GENE EXPRESSION PROGRAMS UNDER PHYSIOLOGIC OR PATHOLOGIC CONDITIONS. COUPLING GENOME-WIDE DNA METHYLATION ASSAYS WITH HISTONE MARK ANNOTATION HAS ALLOWED FOR THE IDENTIFICATION OF SPECIFIC EPIGENOMIC CHANGES THAT AFFECT ENHANCER REGULATORY REGIONS, REVEALING AN ADDITIONAL LAYER OF COMPLEXITY TO THE EPIGENETIC REGULATION OF GENE EXPRESSION. IN THIS REVIEW, WE SUMMARIZE THE NOVEL EVIDENCE FOR THE MOLECULAR AND BIOLOGICAL REGULATION OF DNA METHYLATION IN ENHANCER REGIONS AND THE DYNAMISM OF THESE CHANGES CONTRIBUTING TO THE FINE-TUNING OF GENE EXPRESSION. WE ALSO ANALYZE THE CONTRIBUTION OF ENHANCER DNA METHYLATION ON THE EXPRESSION OF RELEVANT GENES IN ACUTE MYELOID LEUKEMIA AND CHRONIC MYELOPROLIFERATIVE NEOPLASMS. THE CHARACTERIZATION OF THE ABERRANT ENHANCER DNA METHYLATION PROVIDES NOT ONLY A NOVEL PATHOGENIC MECHANISM FOR DIFFERENT TUMORS BUT ALSO HIGHLIGHTS NOVEL POTENTIAL THERAPEUTIC TARGETS FOR MYELOID DERIVED NEOPLASMS. 2019 19 2074 47 EPIGENETIC DEREGULATION IN CHRONIC LYMPHOCYTIC LEUKEMIA: CLINICAL AND BIOLOGICAL IMPACT. DEREGULATED TRANSCRIPTIONAL CONTROL CAUSED BY ABERRANT DNA METHYLATION AND/OR HISTONE MODIFICATIONS IS A HALLMARK OF CANCER CELLS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE MOST COMMON ADULT LEUKEMIA, THE EPIGENETIC 'LANDSCAPE' HAS ADDED A NEW LAYER OF COMPLEXITY TO OUR UNDERSTANDING OF THIS CLINICALLY AND BIOLOGICALLY HETEROGENEOUS DISEASE. EARLY STUDIES IDENTIFIED ABERRANT DNA METHYLATION, OFTEN BASED ON SINGLE GENE PROMOTER ANALYSIS WITH BOTH BIOLOGICAL AND CLINICAL IMPACT. SUBSEQUENT GENOME-WIDE PROFILING STUDIES REVEALED DIFFERENTIAL DNA METHYLATION BETWEEN CLLS AND CONTROLS AND IN PROGNOSTICS SUBGROUPS OF THE DISEASE. FROM THESE STUDIES, IT BECAME APPARENT THAT DNA METHYLATION IN REGIONS OUTSIDE OF PROMOTERS, SUCH AS ENHANCERS, IS IMPORTANT FOR THE REGULATION OF CODING GENES AS WELL AS FOR THE REGULATION OF NON-CODING RNAS. ALTHOUGH DNA METHYLATION PROFILES ARE REPORTEDLY STABLE OVER TIME AND IN RELATION TO THERAPY, A HIGHER EPIGENETIC HETEROGENEITY OR 'BURDEN' IS SEEN IN MORE AGGRESSIVE CLL SUBGROUPS, ALBEIT AS NON-RECURRENT 'PASSENGER' EVENTS. MORE RECENTLY, DNA METHYLATION PROFILES IN CLL ANALYZED IN RELATION TO DIFFERENTIATING NORMAL B-CELL POPULATIONS REVEALED THAT THE MAJORITY OF THE CLL EPIGENOME REFLECTS THE EPIGENOMES PRESENT IN THE CELL OF ORIGIN AND THAT ONLY A SMALL FRACTION OF THE EPIGENETIC ALTERATIONS REPRESENTS TRULY CLL-SPECIFIC CHANGES. FURTHERMORE, CLL PATIENTS CAN BE GROUPED INTO AT LEAST THREE CLINICALLY RELEVANT EPIGENETIC SUBGROUPS, POTENTIALLY ORIGINATING FROM DIFFERENT CELLS AT VARIOUS STAGES OF DIFFERENTIATION AND ASSOCIATED WITH DISTINCT OUTCOMES. IN THIS REVIEW, WE SUMMARIZE THE CURRENT UNDERSTANDING OF THE DNA METHYLOME IN CLL, THE ROLE OF HISTONE MODIFYING ENZYMES, HIGHLIGHT INSIGHTS DERIVED FROM ANIMAL MODELS AND ATTEMPTS MADE TO TARGET EPIGENETIC REGULATORS IN CLL ALONG WITH THE FUTURE DIRECTIONS OF THIS RAPIDLY ADVANCING FIELD. 2018 20 3322 28 HISTONE ACETYLTRANSFERASE P300 INDUCES DE NOVO SUPER-ENHANCERS TO DRIVE CELLULAR SENESCENCE. ACCUMULATION OF SENESCENT CELLS DURING AGING CONTRIBUTES TO CHRONIC INFLAMMATION AND AGE-RELATED DISEASES. WHILE SENESCENCE IS ASSOCIATED WITH PROFOUND ALTERATIONS OF THE EPIGENOME, A SYSTEMATIC VIEW OF EPIGENETIC FACTORS IN REGULATING SENESCENCE IS LACKING. HERE, WE CURATED A LIBRARY OF SHORT HAIRPIN RNAS FOR TARGETED SILENCING OF ALL KNOWN EPIGENETIC PROTEINS AND PERFORMED A HIGH-THROUGHPUT SCREEN TO IDENTIFY KEY CANDIDATES WHOSE DOWNREGULATION CAN DELAY REPLICATIVE SENESCENCE OF PRIMARY HUMAN CELLS. THIS SCREEN IDENTIFIED MULTIPLE NEW PLAYERS INCLUDING THE HISTONE ACETYLTRANSFERASE P300 THAT WAS FOUND TO BE A PRIMARY DRIVER OF THE SENESCENT PHENOTYPE. P300, BUT NOT THE PARALOGOUS CBP, INDUCES A DYNAMIC HYPER-ACETYLATED CHROMATIN STATE AND PROMOTES THE FORMATION OF ACTIVE ENHANCER ELEMENTS IN THE NON-CODING GENOME, LEADING TO A SENESCENCE-SPECIFIC GENE EXPRESSION PROGRAM. OUR WORK ILLUSTRATES A CAUSAL ROLE OF HISTONE ACETYLTRANSFERASES AND ACETYLATION IN SENESCENCE AND SUGGESTS P300 AS A POTENTIAL THERAPEUTIC TARGET FOR SENESCENCE AND AGE-RELATED DISEASES. 2019