1  3469 162 HYPOXIA-INDUCIBLE HISTONE LYSINE DEMETHYLASES: IMPACT ON THE AGING PROCESS AND AGE-RELATED DISEASES. HYPOXIA IS AN ENVIRONMENTAL STRESS AT HIGH ALTITUDE AND UNDERGROUND CONDITIONS BUT IT IS ALSO PRESENT IN MANY CHRONIC AGE-RELATED DISEASES, WHERE BLOOD FLOW INTO TISSUES IS IMPAIRED. THE OXYGEN-SENSING SYSTEM STIMULATES GENE EXPRESSION PROTECTING TISSUES AGAINST HYPOXIC INSULTS. HYPOXIA STABILIZES THE EXPRESSION OF HYPOXIA-INDUCIBLE TRANSCRIPTION FACTOR-1ALPHA (HIF-1ALPHA), WHICH CONTROLS THE EXPRESSION OF HUNDREDS OF SURVIVAL GENES RELATED TO E.G. ENHANCED ENERGY METABOLISM AND AUTOPHAGY. MOREOVER, MANY STRESS-RELATED SIGNALING MECHANISMS, SUCH AS OXIDATIVE STRESS AND ENERGY METABOLIC DISTURBANCES, AS WELL AS THE SIGNALING CASCADES VIA CERAMIDE, MTOR, NF-KAPPAB, AND TGF-BETA PATHWAYS, CAN ALSO INDUCE THE EXPRESSION OF HIF-1ALPHA PROTEIN TO FACILITATE CELL SURVIVAL IN NORMOXIA. HYPOXIA IS LINKED TO PROMINENT EPIGENETIC CHANGES IN CHROMATIN LANDSCAPE. SCREENING STUDIES HAVE INDICATED THAT THE STABILIZATION OF HIF-1ALPHA INCREASES THE EXPRESSION OF DISTINCT HISTONE LYSINE DEMETHYLASES (KDM). HIF-1ALPHA STIMULATES THE EXPRESSION OF KDM3A, KDM4B, KDM4C, AND KDM6B, WHICH ENHANCE GENE TRANSCRIPTION BY DEMETHYLATING H3K9 AND H3K27 SITES (REPRESSIVE EPIGENETIC MARKS). IN ADDITION, HIF-1ALPHA INDUCES THE EXPRESSION OF KDM2B AND KDM5B, WHICH REPRESS TRANSCRIPTION BY DEMETHYLATING H3K4ME2,3 SITES (ACTIVATING MARKS). HYPOXIA-INDUCIBLE KDMS SUPPORT LOCALLY THE GENE TRANSCRIPTION INDUCED BY HIF-1ALPHA, ALTHOUGH THEY CAN ALSO CONTROL GENOME-WIDE CHROMATIN LANDSCAPE, ESPECIALLY KDMS WHICH DEMETHYLATE H3K9 AND H3K27 SITES. THESE EPIGENETIC MARKS HAVE IMPORTANT ROLE IN THE CONTROL OF HETEROCHROMATIN SEGMENTS AND 3D FOLDING OF CHROMOSOMES, AS WELL AS THE GENETIC LOCI REGULATING CELL TYPE COMMITMENT, PROLIFERATION, AND CELLULAR SENESCENCE, E.G. THE INK4 BOX. A CHRONIC STIMULATION OF HIF-1ALPHA CAN PROVOKE TISSUE FIBROSIS AND CELLULAR SENESCENCE, WHICH BOTH ARE INCREASINGLY PRESENT WITH AGING AND AGE-RELATED DISEASES. WE WILL REVIEW THE REGULATION OF HIF-1ALPHA-DEPENDENT INDUCTION OF KDMS AND CLARIFY THEIR ROLE IN PATHOLOGICAL PROCESSES EMPHASIZING THAT LONG-TERM STRESS-RELATED INSULTS CAN IMPAIR THE MAINTENANCE OF CHROMATIN LANDSCAPE AND PROVOKE CELLULAR SENESCENCE AND TISSUE FIBROSIS ASSOCIATED WITH AGING AND AGE-RELATED DISEASES.	2016	
                                                                                                                                                                                                            
2  6302  33 THE PUTATIVE ROLE OF VIRUSES, BACTERIA, AND CHRONIC FUNGAL BIOTOXIN EXPOSURE IN THE GENESIS OF INTRACTABLE FATIGUE ACCOMPANIED BY COGNITIVE AND PHYSICAL DISABILITY. PATIENTS WHO PRESENT WITH SEVERE INTRACTABLE APPARENTLY IDIOPATHIC FATIGUE ACCOMPANIED BY PROFOUND PHYSICAL AND OR COGNITIVE DISABILITY PRESENT A SIGNIFICANT THERAPEUTIC CHALLENGE. THE EFFECT OF PSYCHOLOGICAL COUNSELING IS LIMITED, WITH SIGNIFICANT BUT VERY SLIGHT IMPROVEMENTS IN PSYCHOMETRIC MEASURES OF FATIGUE AND DISABILITY BUT NO IMPROVEMENT ON SCIENTIFIC MEASURES OF PHYSICAL IMPAIRMENT COMPARED TO CONTROLS. SIMILARLY, EXERCISE REGIMES EITHER PRODUCE SIGNIFICANT, BUT PRACTICALLY UNIMPORTANT, BENEFIT OR PROVOKE SYMPTOM EXACERBATION. MANY SUCH PATIENTS ARE AFFORDED THE EXCLUSIONARY, NON-SPECIFIC DIAGNOSIS OF CHRONIC FATIGUE SYNDROME IF RUDIMENTARY TESTING FAILS TO DISCOVER THE CAUSE OF THEIR SYMPTOMS. MORE SOPHISTICATED INVESTIGATIONS OFTEN REVEAL THE PRESENCE OF A RANGE OF PATHOGENS CAPABLE OF ESTABLISHING LIFE-LONG INFECTIONS WITH SOPHISTICATED IMMUNE EVASION STRATEGIES, INCLUDING PARVOVIRUSES, HHV6, VARIANTS OF EPSTEIN-BARR, CYTOMEGALOVIRUS, MYCOPLASMA, AND BORRELIA BURGDORFERI. OTHER PATIENTS HAVE A HISTORY OF CHRONIC FUNGAL OR OTHER BIOTOXIN EXPOSURE. HEREIN, WE EXPLAIN THE EPIGENETIC FACTORS THAT MAY RENDER SUCH INDIVIDUALS SUSCEPTIBLE TO THE CHRONIC PATHOLOGY INDUCED BY SUCH AGENTS, HOW SUCH AGENTS INDUCE PATHOLOGY, AND, INDEED, HOW SUCH PATHOLOGY CAN PERSIST AND EVEN AMPLIFY EVEN WHEN INFECTIONS HAVE CLEARED OR WHEN BIOTOXIN EXPOSURE HAS CEASED. THE PRESENCE OF ACTIVE, REACTIVATED, OR EVEN LATENT HERPES VIRUS COULD BE A POTENTIAL SOURCE OF INTRACTABLE FATIGUE ACCOMPANIED BY PROFOUND PHYSICAL AND OR COGNITIVE DISABILITY IN SOME PATIENTS, AND THE SAME MAY BE TRUE OF PERSISTENT PARVOVIRUS B12 AND MYCOPLASMA INFECTION. A HISTORY OF CHRONIC MOLD EXPOSURE IS A FEASIBLE EXPLANATION FOR SUCH SYMPTOMS, AS IS THE PRESENCE OF B. BURGDORFERI. THE COMPLEX TROPISM, LIFE CYCLES, GENETIC VARIABILITY, AND LOW TITER OF MANY OF THESE PATHOGENS MAKES THEIR DETECTION IN BLOOD A CHALLENGE. EXAMINATION OF LYMPHOID TISSUE OR CSF IN SUCH CIRCUMSTANCES MAY BE WARRANTED.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                   
3  5702  27 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
4  2095  33 EPIGENETIC EFFECTS OF BENZENE IN HEMATOLOGIC NEOPLASMS: THE ALTERED GENE EXPRESSION. BENZENE CARCINOGENIC ABILITY HAS BEEN REPORTED, AND CHRONIC EXPOSURE TO BENZENE CAN BE ONE OF THE RISK ELEMENTS FOR SOLID CANCERS AND HEMATOLOGICAL NEOPLASMS. BENZENE IS ACKNOWLEDGED AS A MYELOTOXIN, AND IT IS ABLE TO AUGMENT THE RISK FOR THE ONSET OF ACUTE MYELOID LEUKEMIA, MYELODYSPLASTIC SYNDROMES, APLASTIC ANEMIA, AND LYMPHOMAS. POSSIBLE MECHANISMS OF BENZENE INITIATION OF HEMATOLOGICAL TUMORS HAVE BEEN IDENTIFIED, AS A GENOTOXIC EFFECT, AN ACTION ON OXIDATIVE STRESS AND INFLAMMATION AND THE PROVOCATION OF IMMUNOSUPPRESSION. HOWEVER, IT IS BECOMING EVIDENT THAT GENETIC ALTERATIONS AND THE OTHER CAUSES ARE INSUFFICIENT TO FULLY JUSTIFY SEVERAL PHENOMENA THAT INFLUENCE THE ONSET OF HEMATOLOGIC MALIGNANCIES. ACQUIRED EPIGENETIC ALTERATIONS MAY PARTICIPATE WITH BENZENE LEUKEMOGENESIS, AS BENZENE MAY AFFECT NUCLEAR RECEPTORS, AND PROVOKE POST-TRANSLATIONAL ALTERATIONS AT THE PROTEIN LEVEL, THEREBY TOUCHING THE FUNCTION OF REGULATORY PROTEINS, COMPRISING ONCOPROTEINS AND TUMOR SUPPRESSOR PROTEINS. DNA HYPOMETHYLATION CORRELATES WITH STIMULATION OF ONCOGENES, WHILE THE HYPERMETHYLATION OF CPG ISLANDS IN PROMOTER REGIONS OF SPECIFIC TUMOR SUPPRESSOR GENES INHIBITS THEIR TRANSCRIPTION AND STIMULATES THE ONSET OF TUMORS. THE DISCOVERY OF THE SYSTEMS OF EPIGENETIC INDUCTION OF BENZENE-CAUSED HEMATOLOGICAL TUMORS HAS ALLOWED THE POSSIBILITY TO OPERATE WITH PHARMACOLOGICAL INTERVENTIONS ABLE OF STOPPING OR OVERTURNING THE NEGATIVE EFFECTS OF BENZENE.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
5  6444  47 THERAPEUTIC ASPECTS OF C-MYC SIGNALING IN INFLAMMATORY AND CANCEROUS COLONIC DISEASES. COLONIC INFLAMMATION IS REQUIRED TO HEAL INFECTIONS, WOUNDS, AND MAINTAIN TISSUE HOMEOSTASIS. AS THE SEVENTH HALLMARK OF CANCER, HOWEVER, IT MAY AFFECT ALL PHASES OF TUMOR DEVELOPMENT, INCLUDING TUMOR INITIATION, PROMOTION, INVASION AND METASTATIC DISSEMINATION, AND ALSO EVASION IMMUNE SURVEILLANCE. INFLAMMATION ACTS AS A CELLULAR STRESSOR AND MAY TRIGGER DNA DAMAGE OR GENETIC INSTABILITY, AND, FURTHER, CHRONIC INFLAMMATION CAN PROVOKE GENETIC MUTATIONS AND EPIGENETIC MECHANISMS THAT PROMOTE MALIGNANT CELL TRANSFORMATION. BOTH SPORADICAL AND COLITIS-ASSOCIATED COLORECTAL CARCINOGENESIS ARE MULTI-STEP, COMPLEX PROCESSES ARISING FROM THE UNCONTROLLED PROLIFERATION AND SPREADING OF MALIGNANTLY TRANSFORMED CELL CLONES WITH THE OBVIOUS ABILITY TO EVADE THE HOST'S PROTECTIVE IMMUNITY. IN CELLS UPON DNA DAMAGE SEVERAL PROTO-ONCOGENES, INCLUDING C-MYC ARE ACTIVATED IN PARELELL WITH THE INACTIVATION OF TUMOR SUPPRESSOR GENES. THE TARGET GENES OF THE C-MYC PROTEIN PARTICIPATE IN DIFFERENT CELLULAR FUNCTIONS, INCLUDING CELL CYCLE, SURVIVAL, PROTEIN SYNTHESIS, CELL ADHESION, AND MICRO-RNA EXPRESSION. THE TRANSCRIPTIONAL PROGRAM REGULATED BY C-MYC IS CONTEXT DEPENDENT, THEREFORE THE FINAL CELLULAR RESPONSE TO ELEVATED C-MYC LEVELS MAY RANGE FROM INCREASED PROLIFERATION TO AUGMENTED APOPTOSIS. CONSIDERING PHYSIOLOGICAL INTESTINAL HOMEOSTASIS, C-MYC DISPLAYS A FUNDAMENTAL ROLE IN THE REGULATION OF CELL PROLIFERATION AND CRYPT CELL NUMBER. HOWEVER, C-MYC GENE IS FREQUENTLY DEREGULATED IN INFLAMMATION, AND OVEREXPRESSED IN BOTH SPORADIC AND COLITIS-ASSOCIATED COLON ADENOCARCINOMAS. RECENT RESULTS DEMONSTRATED THAT ENDOGENOUS C-MYC IS ESSENTIAL FOR EFFICIENT INDUCTION OF P53-DEPENDENT APOPTOSIS FOLLOWING DNA DAMAGE, BUT C-MYC FUNCTION IS ALSO INVOLVED IN AND REGULATED BY AUTOPHAGY-RELATED MECHANISMS, WHILE ITS EXPRESSION IS AFFECTED BY DNA-METHYLATION, OR HISTONE ACETYLATION. MOLECULES DIRECTLY TARGETING C-MYC, OR AGENTS ACTING ON OTHER GENES INVOLVED IN THE C-MYC PATHWAY COULD BE SELECTED FOR COMBINED REGIMENTS. HOWEVER, DUE TO ITS CONTEXT-DEPENDENT CELLULAR FUNCTION, IT IS CLINICALLY ESSENTIAL TO CONSIDER WHICH CYTOTOXIC DRUGS ARE USED IN COMBINATION WITH C-MYC TARGETED AGENTS IN VARIOUS TISSUES. INCREASING OUR KNOWLEDGE ABOUT MYC-DEPENDENT PATHWAYS MIGHT PROVIDE DIRECTION TO NOVEL ANTI-INFLAMMATORY AND COLORECTAL CANCER THERAPIES.	2016	
                                                                                                                
6  1110  35 COMMON GENETIC POLYMORPHISMS INFLUENCE BLOOD BIOMARKER MEASUREMENTS IN COPD. IMPLEMENTING PRECISION MEDICINE FOR COMPLEX DISEASES SUCH AS CHRONIC OBSTRUCTIVE LUNG DISEASE (COPD) WILL REQUIRE EXTENSIVE USE OF BIOMARKERS AND AN IN-DEPTH UNDERSTANDING OF HOW GENETIC, EPIGENETIC, AND ENVIRONMENTAL VARIATIONS CONTRIBUTE TO PHENOTYPIC DIVERSITY AND DISEASE PROGRESSION. A META-ANALYSIS FROM TWO LARGE COHORTS OF CURRENT AND FORMER SMOKERS WITH AND WITHOUT COPD [SPIROMICS (N = 750); COPDGENE (N = 590)] WAS USED TO IDENTIFY SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) ASSOCIATED WITH MEASUREMENT OF 88 BLOOD PROTEINS (PROTEIN QUANTITATIVE TRAIT LOCI; PQTLS). PQTLS CONSISTENTLY REPLICATED BETWEEN THE TWO COHORTS. FEATURES OF PQTLS WERE COMPARED TO PREVIOUSLY REPORTED EXPRESSION QTLS (EQTLS). INFERENCE OF CAUSAL RELATIONS OF PQTL GENOTYPES, BIOMARKER MEASUREMENTS, AND FOUR CLINICAL COPD PHENOTYPES (AIRFLOW OBSTRUCTION, EMPHYSEMA, EXACERBATION HISTORY, AND CHRONIC BRONCHITIS) WERE EXPLORED USING CONDITIONAL INDEPENDENCE TESTS. WE IDENTIFIED 527 HIGHLY SIGNIFICANT (P < 8 X 10-10) PQTLS IN 38 (43%) OF BLOOD PROTEINS TESTED. MOST PQTL SNPS WERE NOVEL WITH LOW OVERLAP TO EQTL SNPS. THE PQTL SNPS EXPLAINED >10% OF MEASURED VARIATION IN 13 PROTEIN BIOMARKERS, WITH A SINGLE SNP (RS7041; P = 10-392) EXPLAINING 71%-75% OF THE MEASURED VARIATION IN VITAMIN D BINDING PROTEIN (GENE = GC). SOME OF THESE PQTLS [E.G., PQTLS FOR VDBP, SRAGE (GENE = AGER), SURFACTANT PROTEIN D (GENE = SFTPD), AND TNFRSF10C] HAVE BEEN PREVIOUSLY ASSOCIATED WITH COPD PHENOTYPES. MOST PQTLS WERE LOCAL (CIS), BUT DISTANT (TRANS) PQTL SNPS IN THE ABO BLOOD GROUP LOCUS WERE THE TOP PQTL SNPS FOR FIVE PROTEINS. THE INCLUSION OF PQTL SNPS IMPROVED THE CLINICAL PREDICTIVE VALUE FOR THE ESTABLISHED ASSOCIATION OF SRAGE AND EMPHYSEMA, AND THE EXPLANATION OF VARIANCE (R2) FOR EMPHYSEMA IMPROVED FROM 0.3 TO 0.4 WHEN THE PQTL SNP WAS INCLUDED IN THE MODEL ALONG WITH CLINICAL COVARIATES. CAUSAL MODELING PROVIDED INSIGHT INTO SPECIFIC PQTL-DISEASE RELATIONSHIPS FOR AIRFLOW OBSTRUCTION AND EMPHYSEMA. IN CONCLUSION, GIVEN THE FREQUENCY OF HIGHLY SIGNIFICANT LOCAL PQTLS, THE LARGE AMOUNT OF VARIANCE POTENTIALLY EXPLAINED BY PQTL, AND THE DIFFERENCES OBSERVED BETWEEN PQTLS AND EQTLS SNPS, WE RECOMMEND THAT PROTEIN BIOMARKER-DISEASE ASSOCIATION STUDIES TAKE INTO ACCOUNT THE POTENTIAL EFFECT OF COMMON LOCAL SNPS AND THAT PQTLS BE INTEGRATED ALONG WITH EQTLS TO UNCOVER DISEASE MECHANISMS. LARGE-SCALE BLOOD BIOMARKER STUDIES WOULD ALSO BENEFIT FROM CLOSE ATTENTION TO THE ABO BLOOD GROUP.	2016	

7  1173  34 CONTRIBUTION OF TLR SIGNALING TO THE PATHOGENESIS OF COLITIS-ASSOCIATED CANCER IN INFLAMMATORY BOWEL DISEASE. IN THE INTESTINE A BALANCE BETWEEN PROINFLAMMATORY AND REPAIR SIGNALS OF THE IMMUNE SYSTEM IS ESSENTIAL FOR THE MAINTENANCE OF INTESTINAL HOMEOSTASIS. THE INNATE IMMUNITY ENSURES A PRIMARY HOST RESPONSE TO MICROBIAL INVASION, WHICH INDUCES AN INFLAMMATORY PROCESS TO LOCALIZE THE INFECTION AND PREVENT SYSTEMIC DISSEMINATION OF PATHOGENS. THE KEY ELEMENTS OF THIS PROCESS ARE THE GERMLINE ENCODED PATTERN RECOGNITION RECEPTORS INCLUDING TOLL-LIKE RECEPTORS (TLRS). IF PATHOGENS CANNOT BE ELIMINATED, THEY MAY ELICIT CHRONIC INFLAMMATION, WHICH MAY BE PARTLY MEDIATED VIA TLRS. ADDITIONALLY, CHRONIC INFLAMMATION HAS LONG BEEN SUGGESTED TO TRIGGER TISSUE TUMOROUS TRANSFORMATION. INFLAMMATION, THE SEVENTH HALLMARK OF CANCER, MAY AFFECT ALL PHASES OF TUMOR DEVELOPMENT, AND EVADE THE IMMUNE SYSTEM. INFLAMMATION ACTS AS A CELLULAR STRESSOR AND MAY TRIGGER DNA DAMAGE OR GENETIC INSTABILITY. FURTHERMORE, CHRONIC INFLAMMATION CAN PROVOKE GENETIC MUTATIONS AND EPIGENETIC MECHANISMS THAT PROMOTE MALIGNANT CELL TRANSFORMATION. COLORECTAL CANCERS IN INFLAMMATORY BOWEL DISEASE PATIENTS ARE CONSIDERED TYPICAL EXAMPLES OF INFLAMMATION-RELATED CANCERS. ALTHOUGH DATA REGARDING THE ROLE OF TLRS IN THE PATHOMECHANISM OF CANCER-ASSOCIATED COLITIS ARE RATHER CONFLICTING, FUNCTIONALLY THESE MOLECULES CAN BE CLASSIFIED AS "LARGELY ANTITUMORIGENIC" AND "LARGELY PRO-TUMORIGENIC" WITH THE CAVEAT THAT THE UNDERLYING SIGNALING PATHWAYS ARE MAINLY CONTEXT (I.E., ORGAN-, TISSUE-, CELL-) AND LIGAND-DEPENDENT.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
8  2277  28 EPIGENETIC REGULATION BY ASXL1 IN MYELOID MALIGNANCIES. MYELOID MALIGNANCIES ARE CLONAL HEMATOPOIETIC DISORDERS THAT ARE COMPRISED OF A SPECTRUM OF GENETICALLY HETEROGENEOUS DISORDERS, INCLUDING MYELODYSPLASTIC SYNDROMES (MDS), MYELOPROLIFERATIVE NEOPLASMS (MPN), CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML), AND ACUTE MYELOID LEUKEMIA (AML). MYELOID MALIGNANCIES ARE CHARACTERIZED BY EXCESSIVE PROLIFERATION, ABNORMAL SELF-RENEWAL, AND/OR DIFFERENTIATION DEFECTS OF HEMATOPOIETIC STEM CELLS (HSCS) AND MYELOID PROGENITOR CELLS HEMATOPOIETIC STEM/PROGENITOR CELLS (HSPCS). MYELOID MALIGNANCIES CAN BE CAUSED BY GENETIC AND EPIGENETIC ALTERATIONS THAT PROVOKE KEY CELLULAR FUNCTIONS, SUCH AS SELF-RENEWAL, PROLIFERATION, BIASED LINEAGE COMMITMENT, AND DIFFERENTIATION. ADVANCES IN NEXT-GENERATION SEQUENCING LED TO THE IDENTIFICATION OF MULTIPLE MUTATIONS IN MYELOID NEOPLASMS, AND MANY NEW GENE MUTATIONS WERE IDENTIFIED AS KEY FACTORS IN DRIVING THE PATHOGENESIS OF MYELOID MALIGNANCIES. THE POLYCOMB PROTEIN ASXL1 WAS IDENTIFIED TO BE FREQUENTLY MUTATED IN ALL FORMS OF MYELOID MALIGNANCIES, WITH MUTATIONAL FREQUENCIES OF 20%, 43%, 10%, AND 20% IN MDS, CMML, MPN, AND AML, RESPECTIVELY. SIGNIFICANTLY, ASXL1 MUTATIONS ARE ASSOCIATED WITH A POOR PROGNOSIS IN ALL FORMS OF MYELOID MALIGNANCIES. THE FACT THAT ASXL1 MUTATIONS ARE ASSOCIATED WITH POOR PROGNOSIS IN PATIENTS WITH CMML, MDS, AND AML, POINTS TO THE POSSIBILITY THAT ASXL1 MUTATION IS A KEY FACTOR IN THE DEVELOPMENT OF MYELOID MALIGNANCIES. THIS REVIEW SUMMARIZES THE RECENT ADVANCES IN UNDERSTANDING MYELOID MALIGNANCIES WITH A SPECIFIC FOCUS ON ASXL1 MUTATIONS.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
9  1340  28 DESIGNING SAFER DRUGS: (Q)SAR-BASED IDENTIFICATION OF MUTAGENS AND CARCINOGENS. MUTAGENICITY AND CARCINOGENICITY ARE CHRONIC EFFECTS OF PRIMARY CONCERN FOR HUMAN HEALTH. A UNIFYING APPROACH TO THEIR MECHANISTIC UNDERSTANDING IS THE RECOGNITION THAT MANY CHEMICALS PROVOKE BOTH EFFECTS BY ELECTROPHILIC ATTACK TO THE BIOLOGICAL MACROMOLECULES, AS SUCH OR AFTER METABOLISM (GENOTOXIC CARCINOGENICITY). QSARS OF INDIVIDUAL CLASSES OF GENOTOXIC CARCINOGENS HAVE CONTRIBUTED TO THE ELUCIDATION OF THE CHEMICAL DETERMINANTS OF THIS ACTIVITY. LITTLE WORK HAS BEEN DONE ON THE EPIGENETIC CARCINOGENS, ACTING THROUGH NON-GENOTOXIC, VERY SPECIFIC MECHANISMS. HOWEVER, THE EXISTING QSARS FOR INDIVIDUAL CHEMICAL CLASSES ARE TOO FEW TO BE OF REAL USEFULNESS IN THE SCREENING OF MASSES OF CANDIDATE DRUGS. MODELS FOR PREDICTING THE CARCINOGENICITY OF "ANY TYPE" OF CHEMICALS HAVE BEEN PROPOSED: PROSPECTIVE PREDICTION EXERCISES POINTED TO THE SERIOUS LIMITATIONS OF MOST OF THESE APPROACHES. THE BEST ALTERNATIVE IS PROVIDED BY PANELS OF HUMAN EXPERTS. THE ABOVE PREDICTION EXERCISES CONSIDERED SAMPLES OF GENERAL CHEMICALS, THUS WE SPECIFICALLY ADDRESSED IN THIS PAPER THE ISSUE OF PHARMACEUTICAL DRUGS. WE APPLIED OUR EXPERT KNOWLEDGE TO A DATABASE OF DRUGS WHOSE CARCINOGENICITY/NONCARCINOGENICITY STATUS WAS KNOWN. WHEREAS MOST OF THE NONCARCINOGENS WERE CORRECTLY IDENTIFIED, OUR PREDICTION OF CARCINOGENS WAS LESS SUCCESSFUL THAN WITH THE GENERAL CHEMICALS. SEVERAL CARCINOGENIC DRUGS DID NOT SHOW RECOGNIZED STRUCTURAL ALERTS, AND SUPPOSEDLY ACTED BY EPIGENETIC MECHANISMS. WHEREAS THE CONTRIBUTION OF HUMAN EXPERTS IS HIGHLY VALUABLE IN THIS PHASE (E.G. PRIORITY SETTING), MORE WORK IS NECESSARY ON: A) EPIGENETIC CARCINOGENS; B) EFFICIENT COMPUTERIZED MODELS.	2003	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
10  1577  25 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
11   938  41 CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK IS MEDIATED BY MULTIPLE ENHANCER VARIANTS WITHIN CLL RISK LOCI. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON ADULT LEUKEMIA IN WESTERN COUNTRIES. IT HAS A STRONG GENETIC BASIS, SHOWING A ~ 8-FOLD INCREASED RISK OF CLL IN FIRST-DEGREE RELATIVES. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED 41 RISK VARIANTS ACROSS 41 LOCI. HOWEVER, FOR A MAJORITY OF THE LOCI, THE FUNCTIONAL VARIANTS AND THE MECHANISMS UNDERLYING THEIR CAUSAL ROLES REMAIN UNDEFINED. HERE, WE EXAMINED THE GENETIC AND EPIGENETIC FEATURES ASSOCIATED WITH 12 INDEX VARIANTS, ALONG WITH ANY CORRELATED (R2 >/= 0.5) VARIANTS, AT THE CLL RISK LOCI LOCATED OUTSIDE OF GENE PROMOTERS. BASED ON PUBLICLY AVAILABLE CHIP-SEQ AND CHROMATIN ACCESSIBILITY DATA AS WELL AS OUR OWN CHIP-SEQ DATA FROM CLL PATIENTS, WE IDENTIFIED SIX CANDIDATE FUNCTIONAL VARIANTS AT SIX LOCI AND AT LEAST TWO CANDIDATE FUNCTIONAL VARIANTS AT EACH OF THE REMAINING SIX LOCI. THE FUNCTIONAL VARIANTS ARE PREDOMINANTLY LOCATED WITHIN ENHANCERS OR SUPER-ENHANCERS, INCLUDING BI-DIRECTIONALLY TRANSCRIBED ENHANCERS, WHICH ARE OFTEN RESTRICTED TO IMMUNE CELL TYPES. FURTHERMORE, WE FOUND THAT, AT 78% OF THE FUNCTIONAL VARIANTS, THE ALTERNATIVE ALLELES ALTERED THE TRANSCRIPTION FACTOR BINDING MOTIFS OR HISTONE MODIFICATIONS, INDICATING THE INVOLVEMENT OF THESE VARIANTS IN THE CHANGE OF LOCAL CHROMATIN STATE. FINALLY, THE ENHANCERS CARRYING FUNCTIONAL VARIANTS PHYSICALLY INTERACTED WITH GENES ENRICHED IN THE TYPE I INTERFERON SIGNALING PATHWAY, APOPTOSIS, OR TP53 NETWORK THAT ARE KNOWN TO PLAY KEY ROLES IN CLL. THESE RESULTS SUPPORT THE REGULATORY ROLES FOR INHERITED NONCODING VARIANTS IN THE PATHOGENESIS OF CLL.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
12  2106  29 EPIGENETIC EVOLUTION AND LINEAGE HISTORIES OF CHRONIC LYMPHOCYTIC LEUKAEMIA. GENETIC AND EPIGENETIC INTRA-TUMORAL HETEROGENEITY COOPERATE TO SHAPE THE EVOLUTIONARY COURSE OF CANCER(1). CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS A HIGHLY INFORMATIVE MODEL FOR CANCER EVOLUTION AS IT UNDERGOES SUBSTANTIAL GENETIC DIVERSIFICATION AND EVOLUTION AFTER THERAPY(2,3). THE CLL EPIGENOME IS ALSO AN IMPORTANT DISEASE-DEFINING FEATURE(4,5), AND GROWING POPULATIONS OF CELLS IN CLL DIVERSIFY BY STOCHASTIC CHANGES IN DNA METHYLATION KNOWN AS EPIMUTATIONS(6). HOWEVER, PREVIOUS STUDIES USING BULK SEQUENCING METHODS TO ANALYSE THE PATTERNS OF DNA METHYLATION WERE UNABLE TO DETERMINE WHETHER EPIMUTATIONS AFFECT CLL POPULATIONS HOMOGENEOUSLY. HERE, TO MEASURE THE EPIMUTATION RATE AT SINGLE-CELL RESOLUTION, WE APPLIED MULTIPLEXED SINGLE-CELL REDUCED-REPRESENTATION BISULFITE SEQUENCING TO B CELLS FROM HEALTHY DONORS AND PATIENTS WITH CLL. WE OBSERVED THAT THE COMMON CLONAL ORIGIN OF CLL RESULTS IN A CONSISTENTLY INCREASED EPIMUTATION RATE, WITH LOW VARIABILITY IN THE CELL-TO-CELL EPIMUTATION RATE. BY CONTRAST, VARIABLE EPIMUTATION RATES ACROSS HEALTHY B CELLS REFLECT DIVERSE EVOLUTIONARY AGES ACROSS THE TRAJECTORY OF B CELL DIFFERENTIATION, CONSISTENT WITH EPIMUTATIONS SERVING AS A MOLECULAR CLOCK. HERITABLE EPIMUTATION INFORMATION ALLOWED US TO RECONSTRUCT LINEAGES AT HIGH-RESOLUTION WITH SINGLE-CELL DATA, AND TO APPLY THIS DIRECTLY TO PATIENT SAMPLES. THE CLL LINEAGE TREE SHAPE REVEALED EARLIER BRANCHING AND LONGER BRANCH LENGTHS THAN IN NORMAL B CELLS, REFLECTING RAPID DRIFT AFTER THE INITIAL MALIGNANT TRANSFORMATION AND A GREATER PROLIFERATIVE HISTORY. INTEGRATION OF SINGLE-CELL BISULFITE SEQUENCING ANALYSIS WITH SINGLE-CELL TRANSCRIPTOMES AND GENOTYPING CONFIRMED THAT GENETIC SUBCLONES MAPPED TO DISTINCT CLADES, AS INFERRED SOLELY ON THE BASIS OF EPIMUTATION INFORMATION. FINALLY, TO EXAMINE POTENTIAL LINEAGE BIASES DURING THERAPY, WE PROFILED SERIAL SAMPLES DURING IBRUTINIB-ASSOCIATED LYMPHOCYTOSIS, AND IDENTIFIED CLADES OF CELLS THAT WERE PREFERENTIALLY EXPELLED FROM THE LYMPH NODE AFTER TREATMENT, MARKED BY DISTINCT TRANSCRIPTIONAL PROFILES. THE SINGLE-CELL INTEGRATION OF GENETIC, EPIGENETIC AND TRANSCRIPTIONAL INFORMATION THUS CHARTS THE LINEAGE HISTORY OF CLL AND ITS EVOLUTION WITH THERAPY.	2019	
                                                                                                                                                                                                                                                  
13  3445  33 HYPERMETHYLATION OF ITGA4, TFPI2 AND VIMENTIN PROMOTERS IS INCREASED IN INFLAMED COLON TISSUE: PUTATIVE RISK MARKERS FOR COLITIS-ASSOCIATED CANCER. PURPOSE: EPIGENETIC SILENCING OF TUMOR SUPPRESSOR GENES IS INVOLVED IN EARLY TRANSFORMING EVENTS AND HAS A HIGH IMPACT ON COLORECTAL CARCINOGENESIS. LIKEWISE, COLON CANCERS THAT DERIVE FROM CHRONICALLY INFLAMED BOWEL DISEASES FREQUENTLY EXHIBIT EPIGENETIC CHANGES. BUT THERE IS LITTLE DATA ABOUT EPIGENETIC ABERRATIONS CAUSING COLORECTAL CANCER IN CHRONICALLY INFLAMED TISSUE. THE AIM OF THE PRESENT STUDY WAS TO EVALUATE THE ABERRANT GAIN OF METHYLATION IN THE GENE PROMOTERS OF VIM, TFPI2 AND ITGA4 AS PUTATIVE EARLY MARKERS IN THE DEVELOPMENT FROM INFLAMED TISSUE VIA PRECANCEROUS LESIONS TOWARD COLORECTAL CANCER. METHODS: INITIAL SCREENING OF DIFFERENT CANCER CELL LINES BY USING METHYLATION-SPECIFIC PCR REVEALED A PUTATIVE COLON CANCER-SPECIFIC METHYLATION PATTERN. ADDITIONALLY, A DEMETHYLATION ASSAY WAS PERFORMED TO INVESTIGATE THE METHYLATION-DEPENDENT GENE SILENCING OF ITGA4. THE CANDIDATE MARKERS WERE ANALYZED IN COLONIC TISSUE SPECIMENS FROM PATIENTS WITH COLORECTAL CANCER (N = 15), ADENOMAS (N = 76), SERRATED LESIONS (N = 13), CHRONIC INFLAMMATION (N = 10) AND NORMAL MUCOSAL SAMPLES (N = 9). RESULTS: A HIGH METHYLATION FREQUENCY OF VIM (55.6 %) WAS OBSERVED IN NORMAL COLON TISSUE, WHEREAS ITGA4 AND TFPI2 WERE COMPLETELY UNMETHYLATED IN CONTROLS. A SIGNIFICANT GAIN OF METHYLATION FREQUENCY WITH PROGRESSION OF DISEASE AS WELL AS AN AGE-DEPENDENT EFFECT WAS DETECTABLE FOR TFPI2. ITGA4 METHYLATION FREQUENCY WAS HIGH IN PRECANCEROUS AND CANCEROUS TISSUES AS WELL AS IN INFLAMMATORY BOWEL DISEASES (IBD). CONCLUSION: THE ALREADY ESTABLISHED METHYLATION MARKER VIM DOES NOT PERMIT A SPECIFIC AND SENSITIVE DISCRIMINATION OF HEALTHY AND NEOPLASTIC TISSUE. THE METHYLATION MARKERS ITGA4 AND TFPI2 SEEM TO BE SUITABLE RISK MARKERS FOR INFLAMMATION-ASSOCIATED COLON CANCER.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
14  2411  25 EPIGENETIC SCORES FOR THE CIRCULATING PROTEOME AS TOOLS FOR DISEASE PREDICTION. PROTEIN BIOMARKERS HAVE BEEN IDENTIFIED ACROSS MANY AGE-RELATED MORBIDITIES. HOWEVER, CHARACTERISING EPIGENETIC INFLUENCES COULD FURTHER INFORM DISEASE PREDICTIONS. HERE, WE LEVERAGE EPIGENOME-WIDE DATA TO STUDY LINKS BETWEEN THE DNA METHYLATION (DNAM) SIGNATURES OF THE CIRCULATING PROTEOME AND INCIDENT DISEASES. USING DATA FROM FOUR COHORTS, WE TRAINED AND TESTED EPIGENETIC SCORES (EPISCORES) FOR 953 PLASMA PROTEINS, IDENTIFYING 109 SCORES THAT EXPLAINED BETWEEN 1% AND 58% OF THE VARIANCE IN PROTEIN LEVELS AFTER ADJUSTING FOR KNOWN PROTEIN QUANTITATIVE TRAIT LOCI (PQTL) GENETIC EFFECTS. BY PROJECTING THESE EPISCORES INTO AN INDEPENDENT SAMPLE (GENERATION SCOTLAND; N = 9537) AND RELATING THEM TO INCIDENT MORBIDITIES OVER A FOLLOW-UP OF 14 YEARS, WE UNCOVERED 137 EPISCORE-DISEASE ASSOCIATIONS. THESE ASSOCIATIONS WERE LARGELY INDEPENDENT OF IMMUNE CELL PROPORTIONS, COMMON LIFESTYLE AND HEALTH FACTORS, AND BIOLOGICAL AGING. NOTABLY, WE FOUND THAT OUR DIABETES-ASSOCIATED EPISCORES HIGHLIGHTED PREVIOUS TOP BIOMARKER ASSOCIATIONS FROM PROTEOME-WIDE ASSESSMENTS OF DIABETES. THESE EPISCORES FOR PROTEIN LEVELS CAN THEREFORE BE A VALUABLE RESOURCE FOR DISEASE PREDICTION AND RISK STRATIFICATION.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
15  5435  25 RELATIVE ROLE OF METHYLATOR AND TUMOR SUPPRESSOR PATHWAYS IN ULCERATIVE COLITIS-ASSOCIATED COLON CANCER. BACKGROUND: CHRONIC ULCERATIVE COLITIS (UC) IS ASSOCIATED WITH AN INCREASED COLORECTAL CANCER RISK WHICH MAY BE SECONDARY TO REPETITIVE MUCOSAL INJURY. BOTH EPIGENETIC METHYLATION AND THE CLASSIC ADENOMA-TO-CARCINOMA SEQUENCE HAVE BEEN IMPLICATED IN THIS MALIGNANT TRANSFORMATION, BUT THE UNDERLYING MOLECULAR MECHANISMS REMAIN POORLY DEFINED. THIS STUDY COMPARES THE MOLECULAR CHARACTERISTICS OF COLITIS-ASSOCIATED AND COMMON COLORECTAL CANCERS. METHODS: NINETEEN PATIENTS WITH COLORECTAL ADENOCARCINOMAS ARISING WITHIN UC WERE MATCHED FOR AGE AND CANCER SITE WITH 54 PATIENTS WITH SPORADIC ADENOCARCINOMAS. TUMOR TISSUE WAS EXAMINED FOR BRAF MUTATIONS, CPG ISLAND METHYLATOR PHENOTYPE (CIMP), AND MLH1 PROMOTER METHYLATION. MUTATIONS OF KRAS AND P53 WERE ASSESSED BY SEQUENCING. RESULTS: PATIENT DEMOGRAPHICS WERE SIMILAR FOR THE TWO GROUPS. CIMP WAS OBSERVED IN 22% OF SPORADIC COLORECTAL CANCERS AND IN 5% OF UC CANCERS (P = 0.162). RATES OF BRAF MUTATION (4% VS 5%, P = 1.0), MLH1 METHYLATION (9% VERSUS 5%, P = 0.682), AND KRAS MUTATIONS (24% VERSUS 32%, P = 0.552) WERE SIMILAR BETWEEN THE GROUPS. HOWEVER, COLITIS-ASSOCIATED COLORECTAL CANCERS WERE MORE LIKELY TO HAVE A P53 MUTATION COMPARED TO SPORADIC ADENOCARCINOMAS (95% VERSUS 53%, P = 0.001). THE DOMINANT MUTATION FOR COLITIS-ASSOCIATED CANCERS WAS A MUTATION IN CODON 4, REPRESENTING HALF OF THE MUTATIONS. FURTHERMORE, COLITIS-ASSOCIATED CANCERS HAD A HIGHER RATE OF MUTATION IN CODON 8 (48% VERSUS 6%, P < 0.001) THAN SPORADIC COUNTERPARTS. CONCLUSIONS: UNLIKE OTHER INFLAMMATORY GASTROINTESTINAL CANCERS, COLITIS-ASSOCIATED COLORECTAL CANCERS DO NOT PREFERENTIALLY ARISE VIA A METHYLATOR PATHWAY WHEN COMPARED TO SPORADIC COLORECTAL CANCERS. CHROMOSOMAL INSTABILITY REMAINS AN IMPORTANT ETIOLOGY, BUT WITH A UNIQUE P53 FREQUENCY AND MUTATION PATTERN.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
16  4769  40 NUCLEAR MORPHOMETRY, NUCLEOMICS AND PROSTATE CANCER PROGRESSION. PROSTATE CANCER (PCA) RESULTS FROM A MULTISTEP PROCESS. THIS PROCESS INCLUDES INITIATION, WHICH OCCURS THROUGH VARIOUS AGING EVENTS AND MULTIPLE INSULTS (SUCH AS CHRONIC INFECTION, INFLAMMATION AND GENETIC INSTABILITY THROUGH REACTIVE OXYGEN SPECIES CAUSING DNA DOUBLE-STRAND BREAKS), FOLLOWED BY A MULTISTEP PROCESS OF PROGRESSION. THESE STEPS INCLUDE SEVERAL GENETIC AND EPIGENETIC ALTERATIONS, AS WELL AS ALTERATIONS TO THE CHROMATIN STRUCTURE, WHICH OCCUR IN RESPONSE TO THE CARCINOGENIC STRESS-RELATED EVENTS THAT SUSTAIN PROLIFERATIVE SIGNALING. EVENTS SUCH AS EVADING GROWTH SUPPRESSORS, RESISTING CELL DEATH, ENABLING REPLICATIVE IMMORTALITY, INDUCING ANGIOGENESIS, AND ACTIVATING INVASION AND METASTASIS ARE READILY OBSERVED. IN ADDITION, IN CONJUNCTION WITH THESE CRITICAL DRIVERS OF CARCINOGENESIS, OTHER FACTORS RELATED TO THE ETIOPATHOGENESIS OF PCA, INVOLVING ENERGY METABOLISM AND EVASION OF THE IMMUNE SURVEILLANCE SYSTEM, APPEAR TO BE INVOLVED. IN ADDITION, WHEN CANCER SPREAD AND METASTASIS OCCUR, THE 'TUMOR MICROENVIRONMENT' IN THE BONE OF PCA PATIENTS MAY PROVIDE A WAY TO SUSTAIN DORMANCY OR SENESCENCE AND EVENTUALLY ESTABLISH A 'SEED AND SOIL' SITE WHERE PCA PROLIFERATION AND GROWTH MAY OCCUR OVER TIME. WHEN PCA IS INITIATED AND PROGRESSION ENSUES, SIGNIFICANT ALTERATIONS IN NUCLEAR SIZE, SHAPE AND HETEROCHROMATIN (DNA TRANSCRIPTION) ORGANIZATION ARE FOUND, AND KEY NUCLEAR TRANSCRIPTIONAL AND STRUCTURAL PROTEINS, AS WELL AS MULTIPLE NUCLEAR BODIES CAN LEAD TO PRECANCEROUS AND MALIGNANT CHANGES. THESE SERIES OF CELLULAR AND TISSUE-RELATED MALIGNANCY-ASSOCIATED EVENTS CAN BE QUANTIFIED TO ASSESS DISEASE PROGRESSION AND MANAGEMENT.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
17  4838  32 ONCOGENIC N-RAS AND TET2 HAPLOINSUFFICIENCY COLLABORATE TO DYSREGULATE HEMATOPOIETIC STEM AND PROGENITOR CELLS. CONCURRENT GENETIC LESIONS EXIST IN A MAJORITY OF PATIENTS WITH HEMATOLOGIC MALIGNANCIES. AMONG THESE, SOMATIC MUTATIONS THAT ACTIVATE RAS ONCOGENES AND INACTIVATE THE EPIGENETIC MODIFIER TEN-ELEVEN TRANSLOCATION 2 (TET2) FREQUENTLY CO-OCCUR IN HUMAN CHRONIC MYELOMONOCYTIC LEUKEMIAS (CMMLS) AND ACUTE MYELOID LEUKEMIAS, SUGGESTING A COOPERATIVITY IN MALIGNANT TRANSFORMATION. TO TEST THIS, WE APPLIED A CONDITIONAL MURINE MODEL THAT ENDOGENOUSLY EXPRESSED ONCOGENIC NRAS(G12D) AND MONOALLELIC LOSS OF TET2 AND EXPLORED THE COLLABORATIVE ROLE SPECIFICALLY WITHIN HEMATOPOIETIC STEM AND PROGENITOR CELLS (HSPCS) AT DISEASE INITIATION. WE DEMONSTRATE THAT THE 2 MUTATIONS COLLABORATED TO ACCELERATE A TRANSPLANTABLE CMML-LIKE DISEASE IN VIVO, WITH AN OVERALL SHORTENED SURVIVAL AND INCREASED DISEASE PENETRANCE COMPARED WITH SINGLE MUTANTS. AT PRELEUKEMIC STAGE, N-RAS(G12D) AND TET2 HAPLOINSUFFICIENCY TOGETHER INDUCED BALANCED HEMATOPOIETIC STEM CELL (HSC) PROLIFERATION AND ENHANCED COMPETITIVENESS. NRAS(G12D/+)/TET2(+/-) HSCS DISPLAYED INCREASED SELF-RENEWAL IN PRIMARY AND SECONDARY TRANSPLANTATIONS, WITH SIGNIFICANTLY HIGHER RECONSTITUTION THAN SINGLE MUTANTS. STRIKINGLY, THE 2 MUTATIONS TOGETHER CONFERRED LONG-TERM RECONSTITUTION AND SELF-RENEWAL POTENTIAL TO MULTIPOTENT PROGENITORS, A POOL OF CELLS THAT USUALLY HAVE LIMITED SELF-RENEWAL COMPARED WITH HSCS. MOREOVER, HSPCS FROM NRAS(G12D/+)/TET2(+/-) MICE DISPLAYED INCREASED CYTOKINE SENSITIVITY IN RESPONSE TO THROMBOPOIETIN. THEREFORE, OUR STUDIES ESTABLISH A NOVEL TRACTABLE CMML MODEL AND PROVIDE INSIGHTS INTO HOW DYSREGULATED SIGNALING PATHWAYS AND EPIGENETIC MODIFIERS COLLABORATE TO MODULATE HSPC FUNCTION AND PROMOTE LEUKEMOGENESIS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
18   606  33 BEYOND GENETICS--THE EMERGING ROLE OF EPIGENETIC CHANGES IN HEMATOPOIETIC MALIGNANCIES. THE TERM EPIGENETIC REFERS TO A HERITABLE CHANGE IN GENE EXPRESSION THAT IS MEDIATED BY MECHANISMS OTHER THAN ALTERATIONS IN THE PRIMARY NUCLEOTIDE SEQUENCE. DNA METHYLATION AT CYTOSINE BASES THAT ARE LOCATED 5' TO GUANOSINE WITHIN A CPG DINUCLEOTIDE IS THE MAIN EPIGENETIC MODIFICATION IN HUMANS. PATTERNS OF DNA METHYLATION ARE PROFOUNDLY DERANGED IN HUMAN CANCER AND COMPRISE GENOME-WIDE LOSSES AS WELL AS REGIONAL GAINS IN DNA METHYLATION. HYPERMETHYLATION OF CPG ISLANDS WITHIN GENE PROMOTER REGIONS IS ASSOCIATED WITH TRANSCRIPTIONAL INACTIVATION AND REPRESENTS, IN ADDITION TO GENETIC ABERRATIONS, AN IMPORTANT MECHANISM OF GENE SILENCING IN THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES. THIS EPIGENETIC PHENOMENON ACTS AS AN ALTERNATIVE TO MUTATIONS AND DELETIONS TO DISRUPT TUMOR SUPPRESSOR GENE FUNCTION. A LARGE NUMBER OF GENES INVOLVING FUNDAMENTAL CELLULAR PATHWAYS MAY BE AFFECTED IN VIRTUALLY ALL TYPES OF HUMAN CANCER BY ABERRANT CPG ISLAND METHYLATION IN ASSOCIATION WITH TRANSCRIPTIONAL SILENCING. ALTERED METHYLATION PATTERNS CAN BE USED AS BIOMARKERS FOR CANCER DETECTION, ASSESSMENT OF PROGNOSIS, AND PREDICTION OF RESPONSE TO ANTITUMOR TREATMENT. FURTHERMORE, CLINICAL TRIALS USING EPIGENETICALLY TARGETED THERAPIES HAVE YIELDED PROMISING RESULTS FOR ACUTE AND CHRONIC LEUKEMIAS AS WELL AS FOR MYELODYSPLASTIC SYNDROMES. THE EXPLORATION OF OUR GROWING KNOWLEDGE ABOUT EPIGENETIC ABERRATIONS MAY HELP DEVELOP NOVEL STRATEGIES FOR THE DIAGNOSIS AND TREATMENT OF HEMATOPOIETIC MALIGNANCIES IN THE FUTURE.	2004	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
19   930  37 CHRONIC IRRADIATION OF HUMAN CELLS REDUCES HISTONE LEVELS AND DEREGULATES GENE EXPRESSION. OVER THE PAST DECADES, THERE HAVE BEEN HUGE ADVANCES IN UNDERSTANDING CELLULAR RESPONSES TO IONISING RADIATION (IR) AND DNA DAMAGE. THESE STUDIES, HOWEVER, WERE MOSTLY EXECUTED WITH CELL LINES AND MICE USING SINGLE OR MULTIPLE ACUTE DOSES OF RADIATION. HENCE, RELATIVELY LITTLE IS KNOWN ABOUT HOW CONTINUOUS EXPOSURE TO LOW DOSE IONISING RADIATION AFFECTS NORMAL CELLS AND ORGANISMS, EVEN THOUGH OUR CELLS ARE CONSTANTLY EXPOSED TO LOW LEVELS OF RADIATION. WE ADDRESSED THIS ISSUE BY EXAMINING THE CONSEQUENCES OF EXPOSING HUMAN PRIMARY CELLS TO CONTINUOUS IONISING GAMMA-RADIATION DELIVERED AT 6-20 MGY/H. ALTHOUGH THESE DOSE RATES ARE ESTIMATED TO INFLICT FEWER THAN A SINGLE DNA DOUBLE-STRAND BREAK (DSB) PER HOUR PER CELL, THEY STILL CAUSED DOSE-DEPENDENT REDUCTIONS IN CELL PROLIFERATION AND INCREASED CELLULAR SENESCENCE. WE CONCOMITANTLY OBSERVED HISTONE PROTEIN LEVELS TO REDUCE BY UP TO 40%, WHICH IN CONTRAST TO PREVIOUS OBSERVATIONS, WAS NOT MAINLY DUE TO PROTEIN DEGRADATION BUT INSTEAD CORRELATED WITH REDUCED HISTONE GENE EXPRESSION. HISTONE REDUCTIONS WERE ACCOMPANIED BY ENLARGED NUCLEAR SIZE PARALLELED BY AN INCREASE IN GLOBAL TRANSCRIPTION, INCLUDING THAT OF PRO-INFLAMMATORY GENES. THUS, CHRONIC IRRADIATION, EVEN AT LOW DOSE-RATES, CAN INDUCE CELL SENESCENCE AND ALTER GENE EXPRESSION VIA A HITHERTO UNCHARACTERISED EPIGENETIC ROUTE. THESE FEATURES OF CHRONIC RADIATION REPRESENT A NEW ASPECT OF RADIATION BIOLOGY.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
20  4856  41 OPTIMIZING RETROVIRAL GENE EXPRESSION FOR EFFECTIVE THERAPIES. WITH THEIR ABILITY TO INTEGRATE THEIR GENETIC MATERIAL INTO THE TARGET CELL GENOME, RETROVIRAL VECTORS (RV) OF BOTH THE GAMMA-RETROVIRAL (GAMMA-RV) AND LENTIVIRAL VECTOR (LV) CLASSES CURRENTLY REMAIN THE MOST EFFICIENT AND THUS THE SYSTEM OF CHOICE FOR ACHIEVING TRANSGENE RETENTION AND THEREFORE POTENTIALLY LONG-TERM EXPRESSION AND THERAPEUTIC BENEFIT. HOWEVER, GAMMA-RV AND LV INTEGRATION COMES AT A COST IN THAT TRANSCRIPTION UNITS WILL BE PRESENT WITHIN A NATIVE CHROMATIN ENVIRONMENT AND THUS BE SUBJECT TO EPIGENETIC EFFECTS (DNA METHYLATION, HISTONE MODIFICATIONS) THAT CAN NEGATIVELY IMPACT ON THEIR FUNCTION. INDEED, HIGHLY VARIABLE EXPRESSION AND SILENCING OF GAMMA-RV AND LV TRANSGENES ESPECIALLY RESULTING FROM PROMOTER DNA METHYLATION IS WELL DOCUMENTED AND WAS THE CAUSE OF THE FAILURE OF GENE THERAPY IN A CLINICAL TRIAL FOR X-LINKED CHRONIC GRANULOMATOUS DISEASE. THIS REVIEW WILL CRITICALLY EXPLORE THE USE OF DIFFERENT CLASSES OF GENETIC CONTROL ELEMENTS THAT CAN IN PRINCIPLE REDUCE VECTOR INSERTION SITE POSITION EFFECTS AND EPIGENETIC-MEDIATED SILENCING. THESE TRANSCRIPTIONAL REGULATORY ELEMENTS BROADLY DIVIDE THEMSELVES INTO EITHER THOSE WITH A CHROMATIN BOUNDARY OR BORDER FUNCTION (SCAFFOLD/MATRIX ATTACHMENT REGIONS, INSULATORS) OR THOSE WITH A DOMINANT CHROMATIN REMODELING AND TRANSCRIPTIONAL ACTIVATING CAPABILITY (LOCUS CONTROL REGIONS,, UBIQUITOUS CHROMATIN OPENING ELEMENTS). ALL THESE TYPES OF ELEMENTS HAVE THEIR STRENGTHS AND WEAKNESSES WITHIN THE CONSTRAINTS OF A GAMMA-RV AND LV BACKBONE, SHOWING VARYING DEGREES OF EFFICACY IN IMPROVING REPRODUCIBILITY AND STABILITY OF TRANSGENE FUNCTION. COMBINATIONS OF BOUNDARY AND CHROMATIN REMODELING; TRANSCRIPTIONAL ACTIVATING ELEMENTS, WHICH DO NOT IMPEDE VECTOR PRODUCTION; TRANSDUCTION EFFICIENCY; AND STABILITY ARE MOST LIKELY TO MEET THE REQUIREMENTS WITHIN A GENE THERAPY CONTEXT ESPECIALLY WHEN TARGETING A STEM CELL POPULATION.	2013