1 3316 112 HISTIOCYTIC SARCOMA AS A SECONDARY MALIGNANCY: PATHOBIOLOGY, DIAGNOSIS, AND TREATMENT. HISTIOCYTIC SARCOMA (HS) IS AN EXTREMELY RARE NON-LANGERHANS CELL DISORDER WITH AN AGGRESSIVE COURSE AND LIMITED TREATMENT OPTIONS. RECENT ADVANCES IN MOLECULAR/GENETIC SEQUENCING HAVE SUGGESTED A COMMON CLONAL ORIGIN BETWEEN VARIOUS HEMATOLYMPHOID DISORDERS AND CASES OF SECONDARY HS. DERIVING CONCLUSIONS FROM PREVIOUSLY REPORTED CASES OF HS ARISING SECONDARILY TO CERTAIN HEMATOLYMPHOID DISORDERS, HERE WE HAVE TRIED TO PROVIDE INSIGHT INTO THE MECHANISMS INFLUENCING THIS EVOLUTION. WE ALSO DISCUSS A CLINICAL CASE OF A 72-YEAR-OLD MAN WITH A DIAGNOSIS OF CHRONIC MYELOID LEUKEMIA (CML), PRESENTING SUBSEQUENTLY WITH A HETEROGENEOUS LIVER MASS POSITIVE WITH A DIAGNOSIS OF HS. THE LIVER MASS SHOWED A RETAINED BCR-ABL1 TRANSLOCATION SUGGESTING CLONALITY BETWEEN THE CML AND HS. AS SEEN IN OUR CASE AND OTHER REPORTED CASES OF HS DERIVED SECONDARILY, THE CONCURRENT EXPRESSION OF IMMUNOGLOBULIN HEAVY (IGH)-/LIGHT-CHAIN REARRANGEMENTS OR CYTOGENETIC MARKERS COMMON TO THE PRIMARY MALIGNANCY SUGGESTS AN EVOLUTIONARY MECHANISM INVOLVING LINEAGE SWITCHING THAT COULD POTENTIALLY BE INFLUENCED BY GENETIC OR EPIGENETIC CUES WHICH MAY OCCUR AT THE LEVEL OF A PROGENITOR OR THE MALIGNANT CELL ITSELF. 2016 2 3565 37 IMPACT OF GENETIC POLYMORPHISMS AND BIOMARKERS ON THE EFFECTIVENESS AND TOXICITY OF TREATMENT OF CHRONIC MYELOID LEUKEMIA AND ACUTE MYELOID LEUKEMIA. MOST MALIGNANT HEMATOLOGICAL DISEASES ARE GENERALLY A CONSEQUENCE OF ACQUIRED MUTATIONS OR REARRANGEMENTS IN CELL REPLICATION PROCESSES. ACUTE MYELOID LEUKEMIA (AML) IS A CLINICALLY AND MOLECULARLY HETEROGENEOUS DISEASE THAT RESULTS FROM ACQUIRED GENETIC AND EPIGENETIC ALTERATIONS IN HEMATOPOIETIC PROGENITOR CELLS. DESPITE THE ADVANCES MADE IN UNDERSTANDING THE PATHOGENESIS OF THIS DISEASE, THE OVERALL SURVIVAL OF PATIENTS REMAINS VERY LOW DUE TO THE HIGH RELAPSE RATE. PHARMACOGENETICS AND MASSIVE SEQUENCING STUDIES HAVE ALLOWED THE IDENTIFICATION OF NEW RECURRENT MUTATIONS WITH SIGNIFICANT PROGNOSTIC IMPACT IN AML; FURTHERMORE, IT SEEMS LIKELY THAT WHOLE GENOME SEQUENCING WILL SOON BECOME A STANDARD DIAGNOSTIC TEST, WHICH WILL ALLOW THE MOLECULAR DIAGNOSIS OF PATIENTS. THEREFORE, IT IS NECESSARY TO DEVELOP MOLECULAR TARGETS THAT OPEN NEW THERAPEUTIC PERSPECTIVES AND ALLOW INDIVIDUALIZED TREATMENT OF PATIENTS WITH THIS AGGRESSIVE DISEASE. CHRONIC MYELOID LEUKEMIA (CML) IS THE FIRST NEOPLASTIC DISEASE FOR WHICH A CHARACTERISTIC GENETIC ALTERATION WAS DESCRIBED. IT HAS, BY DEFINITION, A GENETIC MARKER, THE BCR::ABL1 REARRANGEMENT, AS A CONSEQUENCE OF THE T9;22(Q34;Q11) TRANSLOCATION. ITS STUDY IS ESSENTIAL FOR THE DIAGNOSIS OF THIS ENTITY AND ALSO FOR MONITORING THE RESPONSE TO TREATMENT. DRUGS KNOWN AS TYROSINE KINASE INHIBITORS (TKIS) THAT TARGET THE BCR::ABL1 PROTEIN (ORAL TARGETED THERAPY) ARE THE CONVENTIONAL TREATMENT OF CML, REPRESENTING A CHANGE OF PARADIGM IN THE MANAGEMENT OF ONCOHEMATOLOGICAL PATIENTS. 2022 3 358 35 ALTERNATIVE SPLICING IN CHRONIC MYELOID LEUKEMIA (CML): A NOVEL THERAPEUTIC TARGET? ALTHOUGH THE IMATINIB BASED THERAPY OF CHRONIC MYELOID LEUKEMIA (CML) REPRESENTS A TRIUMPH OF MEDICINE, NOT ALL PATIENTS WITH CML BENEFIT FROM THIS DRUG DUE TO THE DEVELOPMENT OF RESISTANCE AND INTOLERANCE. THE INTERRUPTION OF IMATINIB TREATMENT IS OFTEN FOLLOWED BY CLINICAL RELAPSE, SUGGESTING A FAILURE IN THE KILLING OF RESIDUAL LEUKAEMIC STEM CELLS. THERE IS NEED TO IDENTIFY ALTERNATIVE SELECTIVE MOLECULAR TARGETS FOR THIS DISEASE AND DEVELOP MORE EFFECTIVE THERAPEUTIC APPROACHES. ALTERNATIVE PRE-MRNA SPLICING (AS) IS AN EPIGENETIC PROCESS THAT GREATLY DIVERSIFIES THE REPERTOIRE OF THE TRANSCRIPTOME. AS ORCHESTRATES INTERACTIONS BETWEEN VARIOUS TYPES OF PROTEINS AND BETWEEN PROTEINS AND NUCLEIC ACIDS. CHANGES CAUSED BY INDIVIDUAL SPLICING EVENTS IN THE CELLS ARE SMALL, HOWEVER, "SPLICING PROGRAMS" TYPICALLY REACT TO THESE INDIVIDUAL CHANGES WITH CONSIDERABLE EFFECTS IN CELL PROLIFERATION, CELL SURVIVAL, AND APOPTOSIS. CURRENT EVIDENCE SUGGESTS A PIVOTAL ROLE OF AS IN LEUKEMIAS, PARTICULARLY IN MYELODISPLASTIC SYNDROME (MDS) AND CHRONIC LYMPHOCYTE LEUKEMIA (CLL). FROM THESE STUDIES AND STUDIES IN OTHER MALIGNANCES, IT IS CLEAR THAT SPLICING ABNORMALITIES PLAY A SIGNIFICANT ROLE IN MALIGNANT TRANSFORMATION. EVALUATION OF AS EVENTS IN CML CAN BE USED TO IDENTIFY NOVEL DISEASE MARKERS AND DRUGSENSITIVE TARGETS TO OVERCOME THE LIMITS OF THE SMALL MOLECULE INHIBITORS CURRENTLY USED FOR TREATING PATIENTS WITH CML. THE USE OF ABERRANT SPLICE VARIANTS AS DISEASE MARKERS HAS BEEN REPORTED, HOWEVER, LITTLE IS KNOWN ABOUT THE USE OF SPLICING ABNORMALITIES AS DRUG TARGETS IN CML. HEREIN WE DISCUSS POTENTIAL THERAPEUTIC APPROACHES THAT CAN BE USED TO TARGET SPLICING ABNORMALITIES IN CML. 2013 4 3091 25 GENOMIC AND EPIGENOMIC HETEROGENEITY IN CHRONIC LYMPHOCYTIC LEUKEMIA. DEFINING FEATURES OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ARE NOT ONLY ITS IMMUNOPHENOTYPE OF CD19(+)CD5(+)CD23(+)SIGDIM EXPRESSING CLONAL MATURE B CELLS BUT ALSO ITS HIGHLY VARIABLE CLINICAL COURSE. IN RECENT YEARS, ADVANCES IN MASSIVELY PARALLEL SEQUENCING TECHNOLOGIES HAVE LED TO RAPID PROGRESS IN OUR UNDERSTANDING OF THE CLL GENOME AND EPIGENOME. OVERALL, THESE STUDIES HAVE CLEARLY DEMARCATED NOT ONLY THE VAST DEGREE OF GENETIC AND EPIGENETIC HETEROGENEITY AMONG INDIVIDUALS WITH CLL BUT ALSO EVEN WITHIN INDIVIDUAL PATIENT LEUKEMIAS. WE HEREIN REVIEW THE RAPIDLY GROWING SERIES OF STUDIES ASSESSING THE GENETIC AND EPIGENETIC FEATURES OF CLL WITHIN CLINICALLY DEFINED PERIODS OF ITS GROWTH. THESE STUDIES STRONGLY SUGGEST AN EVOLVING SPECTRUM OF LESIONS OVER TIME AND THAT THESE FEATURES MAY HAVE CLINICAL IMPACT. 2015 5 732 26 CANCER DRUG RESISTANCE: THE CENTRAL ROLE OF THE KARYOTYPE. CURRENT GENETIC AND EPIGENETIC THEORIES OF CANCER-SPECIFIC DRUG RESISTANCE DO NOT ADEQUATELY EXPLAIN: (I) THE KARYOTYPIC CHANGES THAT COINCIDE WITH RESISTANCE, (II) THE HIGH RATES AT WHICH CANCER CELLS ACQUIRE AND ENHANCE RESISTANCE COMPARED TO THE RATES OF CONVENTIONAL MUTATION, (III) THE WIDE RANGES OF RESISTANCE SUCH AS MULTIDRUG RESISTANCE, (IV) THE FREQUENT OCCURRENCE OF INTRINSIC DRUG RESISTANCE. WE HAVE RECENTLY PROPOSED, THAT SPECIFIC KARYOTYPIC ALTERATIONS ARE SUFFICIENT FOR DRUG RESISTANCE VIA NEW TRANSCRIPTOMES OF COOPERATIVE GENES, INDEPENDENT OF GENE MUTATION. THIS MECHANISM GENERATES NEW PHENOTYPES JUST LIKE TRISOMY 21 GENERATES DOWN SYNDROME. THESE KARYOTYPIC CHANGES ARE GENERATED BY CANCER-SPECIFIC ANEUPLOIDY AUTOCATALYTICALLY, BECAUSE ANEUPLOIDY DESTABILIZES THE KARYOTYPE BY MISBALANCING TEAMS OF PROTEINS THAT SYNTHESIZE, REPAIR AND SEGREGATE CHROMOSOMES. EVIDENCE FOR THIS CHROMOSOMAL MECHANISM IS AS FOLLOWS: (I) RESISTANCE IS PROPORTIONAL TO THE NUMBER OF CLONAL CHROMOSOMAL ALTERATIONS COMPARED TO DRUG-SENSITIVE PRECURSORS. (II) THE HIGH RATES AT WHICH CANCER CELLS ACQUIRE DRUG RESISTANCE ARE COMPARABLE WITH THE RATES, AS HIGH AS 10(-2) PER CELL GENERATION, AT WHICH THEIR KARYOTYPES CHANGE-DIMMING HOPES FOR GENE-SPECIFIC THERAPIES. (III) MULTIDRUG RESISTANCE PROBABLY REFLECTS UN-SELECTED TRANSCRIPTOMES OF KARYOTYPES SELECTED FOR RESISTANCE AGAINST SPECIFIC DRUGS. (IV) INTRINSIC DRUG RESISTANCE PROBABLY REFLECTS UNSELECTED TRANSCRIPTOMES OF KARYOTYPES SELECTED FOR ONCOGENICITY. WE ALSO ADDUCE EVIDENCE THAT RESISTANCE OF CHRONIC MYELOID LEUKEMIA AGAINST THE DRUG IMATINIB IS CHROMOSOMAL, ALTHOUGH IT IS WIDELY BELIEVED TO BE DUE TO MUTATION OF A KINASE. 2007 6 2652 31 EPIGENOMICS OF LEUKEMIA: FROM MECHANISMS TO THERAPEUTIC APPLICATIONS. LEUKEMOGENESIS IS A MULTISTEP PROCESS IN WHICH SUCCESSIVE TRANSFORMATIONAL EVENTS ENHANCE THE ABILITY OF A CLONAL POPULATION ARISING FROM HEMATOPOIETIC PROGENITOR CELLS TO PROLIFERATE, DIFFERENTIATE AND SURVIVE. CLINICALLY AND PATHOLOGICALLY, LEUKEMIA IS SUBDIVIDED INTO FOUR MAIN CATEGORIES: CHRONIC LYMPHOCYTIC LEUKEMIA, CHRONIC MYELOID LEUKEMIA, ACUTE LYMPHOCYTIC LEUKEMIA AND ACUTE MYELOID LEUKEMIA. LEUKEMIA HAS BEEN PREVIOUSLY CONSIDERED ONLY AS A GENETIC DISEASE. HOWEVER, IN RECENT YEARS, SIGNIFICANT ADVANCES HAVE BEEN MADE IN THE ELUCIDATION OF THE LEUKEMOGENESIS-ASSOCIATED PROCESSES. THUS, WE HAVE COME TO UNDERSTAND THAT EPIGENETIC ALTERATIONS INCLUDING DNA METHYLATION, HISTONE MODIFICATIONS AND MIRNA ARE INVOLVED IN THE PERMANENT CHANGES OF GENE EXPRESSION CONTROLLING THE LEUKEMIA PHENOTYPE. IN THIS ARTICLE, WE WILL FOCUS ON THE EPIGENETIC DEFECTS ASSOCIATED WITH LEUKEMIA AND THEIR IMPLICATIONS AS BIOMARKERS FOR DIAGNOSTIC, PROGNOSTIC AND THERAPEUTIC APPLICATIONS. 2011 7 2689 23 EVOLUTION OF DNA METHYLATION IS LINKED TO GENETIC ABERRATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA. ALTHOUGH CLONAL SELECTION BY GENETIC DRIVER ABERRATIONS IN CANCER IS WELL DOCUMENTED, THE ABILITY OF EPIGENETIC ALTERATIONS TO PROMOTE TUMOR EVOLUTION IS UNDEFINED. WE USED 450K ARRAYS AND NEXT-GENERATION SEQUENCING TO EVALUATE INTRATUMOR HETEROGENEITY AND EVOLUTION OF DNA METHYLATION AND GENETIC ABERRATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). CLL CASES EXHIBIT VAST INTERPATIENT DIFFERENCES IN INTRATUMOR METHYLATION HETEROGENEITY, WITH GENETICALLY CLONAL CASES MAINTAINING LOW METHYLATION HETEROGENEITY AND UP TO 10% OF TOTAL CPGS IN A MONOALLELICALLY METHYLATED STATE. INCREASING METHYLATION HETEROGENEITY CORRELATES WITH ADVANCED GENETIC SUBCLONAL COMPLEXITY. SELECTION OF NOVEL DNA METHYLATION PATTERNS IS OBSERVED ONLY IN CASES THAT UNDERGO GENETIC EVOLUTION, AND INDEPENDENT GENETIC EVOLUTION IS UNCOMMON AND IS RESTRICTED TO LOW-RISK ALTERATIONS. THESE RESULTS REVEAL THAT ALTHOUGH EVOLUTION OF DNA METHYLATION OCCURS IN HIGH-RISK, CLINICALLY PROGRESSIVE CASES, POSITIVE SELECTION OF NOVEL METHYLATION PATTERNS ENTAILS COEVOLUTION OF GENETIC ALTERATION(S) IN CLL. 2014 8 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 9 3089 24 GENOMIC AND EPIGENOMIC ALTERATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA IS A COMMON DISEASE IN WESTERN COUNTRIES AND HAS HETEROGENEOUS CLINICAL BEHAVIOR. THE RELEVANCE OF THE GENETIC BASIS OF THE DISEASE HAS COME TO THE FOREFRONT RECENTLY, WITH GENOME-WIDE STUDIES THAT HAVE PROVIDED A COMPREHENSIVE VIEW OF STRUCTURAL VARIANTS, SOMATIC MUTATIONS, AND DIFFERENT LAYERS OF EPIGENETIC CHANGES. THE MUTATIONAL LANDSCAPE IS CHARACTERIZED BY RELATIVELY COMMON COPY NUMBER ALTERATIONS, A FEW MUTATED GENES OCCURRING IN 10-15% OF CASES, AND A LARGE NUMBER OF GENES MUTATED IN A SMALL NUMBER OF CASES. THE EPIGENOMIC PROFILE HAS REVEALED A MARKED REPROGRAMMING OF REGULATORY REGIONS IN TUMOR CELLS COMPARED WITH NORMAL B CELLS. ALL OF THESE ALTERATIONS ARE DIFFERENTIALLY DISTRIBUTED IN CLINICAL AND BIOLOGICAL SUBSETS OF THE DISEASE, INDICATING THAT THEY MAY UNDERLIE THE HETEROGENEOUS EVOLUTION OF THE DISEASE. THESE GLOBAL STUDIES ARE REVEALING THE MOLECULAR COMPLEXITY OF CHRONIC LYMPHOCYTIC LEUKEMIA AND PROVIDE NEW PERSPECTIVES THAT HAVE HELPED TO UNDERSTAND ITS PATHOGENIC MECHANISMS AND IMPROVE THE CLINICAL MANAGEMENT OF PATIENTS. 2020 10 2966 27 GENETIC AND EPIGENETIC PROFILING OF CLL DISEASE PROGRESSION REVEALS LIMITED SOMATIC EVOLUTION AND SUGGESTS A RELATIONSHIP TO MEMORY-CELL DEVELOPMENT. WE EXAMINED GENETIC AND EPIGENETIC CHANGES THAT OCCUR DURING DISEASE PROGRESSION FROM INDOLENT TO AGGRESSIVE FORMS OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) USING SERIAL SAMPLES FROM 27 PATIENTS. ANALYSIS OF DNA MUTATIONS GROUPED THE LEUKEMIA CASES INTO THREE CATEGORIES: EVOLVING (26%), EXPANDING (26%) AND STATIC (47%). THUS, APPROXIMATELY THREE-QUARTERS OF THE CLL CASES HAD LITTLE TO NO GENETIC SUBCLONAL EVOLUTION. HOWEVER, WE IDENTIFIED SIGNIFICANT RECURRENT DNA METHYLATION CHANGES DURING PROGRESSION AT 4752 CPGS ENRICHED FOR REGIONS NEAR POLYCOMB 2 REPRESSIVE COMPLEX (PRC2) TARGETS. PROGRESSION-ASSOCIATED CPGS NEAR THE PRC2 TARGETS UNDERGO METHYLATION CHANGES IN THE SAME DIRECTION DURING DISEASE PROGRESSION AS DURING NORMAL DEVELOPMENT FROM NAIVE TO MEMORY B CELLS. OUR STUDY SHOWS THAT CLL PROGRESSION DOES NOT TYPICALLY OCCUR VIA SUBCLONAL EVOLUTION, BUT THAT CERTAIN CPG SITES UNDERGO RECURRENT METHYLATION CHANGES. OUR RESULTS SUGGEST CLL PROGRESSION MAY INVOLVE DEVELOPMENTAL PROCESSES SHARED IN COMMON WITH THE GENERATION OF NORMAL MEMORY B CELLS. 2015 11 1164 23 CONTRIBUTION OF CHRONIC MYELOID LEUKAEMIA (CML) AS A DISEASE MODEL TO DEFINE AND STUDY CLONAL HETEROGENEITY. ALTHOUGH TUMOUR CELL INTRA-CLONAL HETEROGENEITY HAS BEEN KNOWN FOR MANY YEARS, ITS APPLICATION IN THE ONCOLOGY CLINICAL PRACTICE (PATIENT MANAGEMENT, PROGNOSIS, ETC.) REMAINS LIMITED. FOR THIS, CHRONIC MYELOID LEUKAEMIA (CML) IS A REMARKABLE MODEL. BASIC RESEARCH STUDIES REVEALED THE HETEROGENEITY OF THE INITIAL CLONE, AND LED TO THE HYPOTHESIS OF THE EXISTENCE OF LEUKEMIC STEM CELLS. NEVERTHELESS, THE INDISPUTABLE EVIDENCE OF THE INTRA-CLONAL HETEROGENEITY ROLE IN THE THERAPEUTIC RESPONSE CAME FROM THE OUTCOMES OF THE TREATMENT WITH TYROSINE KINASE INHIBITORS (THE FIRST TARGETED THERAPY IN MEDICINE) COMBINED WITH THE EARLY AND RIGOROUS CLINICAL AND MOLECULAR MONITORING OF THESE PATIENTS. CML MANAGEMENT ALREADY TAKES THIS HETEROGENEITY INTO ACCOUNT FOR PERSONALIZED PATIENT FOLLOW-UP. THE ADVENTURE CONTINUES WITH THE OBJECTIVES OF BETTER TAILORING THE TREATMENT AND OF CURING THE DISEASE IN MOST OF THE PATIENTS. 2019 12 4320 24 MICRORNAS IN CHRONIC LYMPHOCYTIC LEUKEMIA: AN OLD DISEASE WITH NEW GENETIC INSIGHTS. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON LEUKEMIA AMONG ADULT POPULATION IN WESTERN COUNTRY. IN THE LAST DECADE, SEVERAL FINDINGS HAVE SUBSTANTIALLY REVOLUTIONIZED THE OLD CONCEPT THAT CLL IS A DISEASE ORIGINATING FROM MATURE, NOT-DIVIDING CELL WITH INDOLENT CLINICAL COURSE. NOTABLY, NEXT GENERATION SEQUENCING (NGS) HAS CONTRIBUTED TO DEEPEN THE KNOWLEDGE OF THE CELLULAR NETWORKS THAT IMPLY THE ONSET AND THE PROGRESSION OF CLL. AMONG GENETIC ABERRATIONS THAT ARE RECURRENTLY OBSERVED IN B-CELLS FROM PATIENTS WITH CLL, MICRORNA DEREGULATION REPRESENTED THE FIRST EPIGENETIC MECHANISM THAT HAS BEEN IDENTIFIED. THROUGH EPIGENETIC MECHANISM THEY CAN MODULATE GENE EXPRESSION AND INTERFERE WITH CELLULAR PATHWAYS THAT ARE INVOLVED IN CELL CYCLE, APOPTOSIS AND B-CELL RECEPTOR (BCR) ACTIVATION. ALTHOUGH FEW STUDIES HAVE SHOWN THE PROGNOSTIC AND PREDICTIVE VALUE OF MICRORNA EXPRESSION LEVELS, THEIR VALIDATION WITHIN PROSPECTIVE CLINICAL TRIALS IS WARRANTED. 2016 13 6618 34 UNDERSTANDING AND MONITORING CHRONIC MYELOID LEUKEMIA BLAST CRISIS: HOW TO BETTER MANAGE PATIENTS. CHRONIC MYELOID LEUKEMIA (CML) IS TRIGGERED PRIMARILY BY THE T(9;22) (Q34.13; Q11.23) TRANSLOCATION. THIS RECIPROCAL CHROMOSOMAL TRANSLOCATION LEADS TO THE FORMATION OF THE BCR-ABL FUSION GENE. PATIENTS IN THE CHRONIC PHASE (CP) EXPERIENCE A GOOD CURATIVE EFFECT WITH TYROSINE KINASE INHIBITORS. HOWEVER, CASES ARE TREATMENT REFRACTORY, WITH A DISMAL PROGNOSIS, WHEN THE DISEASE HAS PROGRESSED TO THE ACCELERATED PHASE (AP) OR BLAST PHASE (BP). UNTIL NOW, FEW REPORTS HAVE PROVIDED A COMPREHENSIVE DESCRIPTION OF THE MECHANISMS INVOLVED AT DIFFERENT MOLECULAR LEVELS. INDEED, THE UNDERLYING PATHOGENESIS OF CML EVOLUTION COMPRISES GENETIC ABERRATIONS, CHROMOSOMAL TRANSLOCATIONS (EXCEPT FOR THE PHILADELPHIA CHROMOSOME), TELOMERE BIOLOGY, AND EPIGENETIC ANOMALIES. HEREIN, WE PROVIDE KNOWLEDGE OF THE BIOLOGY RESPONSIBLE FOR BLAST TRANSFORMATION OF CML AT SEVERAL LEVELS, SUCH AS GENETICS, TELOMERE BIOLOGY, AND EPIGENETIC ANOMALIES. BECAUSE OF THE LIMITED TREATMENT OPTIONS AVAILABLE AND POOR OUTCOMES, ONLY THE THERAPEUTIC RESPONSE IS MONITORED REGULARLY, WHICH INVOLVES BCR-ABL TRANSCRIPT LEVEL ASSESSMENT AND IMMUNOLOGIC SURVEILLANCE, WITH THE OPTIMAL TREATMENT STRATEGY FOR PATIENTS IN CP ADAPTED TO EVALUATE DISEASE RECURRENCE OR PROGRESSION. OVERALL, SELECTING OPTIMAL TREATMENT ENDPOINTS TO PREDICT SURVIVAL AND SUCCESSFUL TFR IMPROVES THE QUALITY OF LIFE OF PATIENTS. THUS, IDENTIFYING RISK FACTORS AND DEVELOPING RISK-ADAPTED THERAPEUTIC OPTIONS MAY CONTRIBUTE TO A BETTER OUTCOME FOR ADVANCED-PHASE PATIENTS. 2021 14 2991 30 GENETIC INSTABILITY IN INHERITED AND SPORADIC LEUKEMIAS. GENETIC INSTABILITY DUE TO INCREASED DNA DAMAGE AND ALTERED DNA REPAIR IS OF CENTRAL SIGNIFICANCE IN THE INITIATION AND PROGRESSION OF INHERITED AND SPORADIC HUMAN LEUKEMIAS. ALTHOUGH VERY RARE, SOME INHERITED DNA REPAIR INSUFFICIENCY SYNDROMES (E.G., FANCONI ANEMIA, BLOOM'S SYNDROME) HAVE ADDED SUBSTANTIALLY TO OUR UNDERSTANDING OF CRUCIAL MECHANISMS OF LEUKEMOGENESIS IN RECENT YEARS. CONVERSELY, SPORADIC LEUKEMIAS ACCOUNT FOR THE MAIN PROPORTION OF LEUKEMIAS AND HERE DNA DAMAGING REACTIVE OXYGEN SPECIES (ROS) PLAY A CENTRAL ROLE. ALTHOUGH THE EXACT MECHANISMS OF INCREASED ROS PRODUCTION REMAIN LARGELY UNKNOWN AND NO SINGLE PATHWAY HAS BEEN DETECTED THUS FAR, SOME ONCOGENIC PROTEINS (E.G., THE ACTIVATED TYROSINE KINASES BCR-ABL1 AND FLT3-ITD) SEEM TO PLAY A KEY ROLE IN DRIVING GENETIC INSTABILITY BY INCREASED ROS GENERATION WHICH INFLUENCES THE DISEASE COURSE (E.G., BLAST CRISIS IN CHRONIC MYELOID LEUKEMIA OR RELAPSE IN FLT3-ITD POSITIVE ACUTE MYELOID LEUKEMIA). OF COURSE OTHER MECHANISMS, WHICH PROMOTE GENETIC INSTABILITY IN LEUKEMIA ALSO EXIST. A NEWLY EMERGING MECHANISM IS THE GENOME-WIDE ALTERATION OF EPIGENETIC MARKS (E.G., HYPOMETHYLATION OF HISTONE H3K79), WHICH PROMOTES CHROMOSOMAL INSTABILITY. TAKEN TOGETHER GENETIC INSTABILITY PLAYS A CRITICAL ROLE BOTH IN INHERITED AND SPORADIC LEUKEMIAS AND EMERGES AS A COMMON THEME IN BOTH INHERITED AND SPORADIC LEUKEMIAS. BEYOND ITS THEORETICAL IMPACT, THE ANALYSIS OF GENETIC INSTABILITY MAY LEAD THE WAY TO THE DEVELOPMENT OF INNOVATIVE THERAPY STRATEGIES. 2010 15 4487 36 MOLECULARLY TARGETED DRUG COMBINATIONS DEMONSTRATE SELECTIVE EFFECTIVENESS FOR MYELOID- AND LYMPHOID-DERIVED HEMATOLOGIC MALIGNANCIES. TRANSLATING THE GENETIC AND EPIGENETIC HETEROGENEITY UNDERLYING HUMAN CANCERS INTO THERAPEUTIC STRATEGIES IS AN ONGOING CHALLENGE. LARGE-SCALE SEQUENCING EFFORTS HAVE UNCOVERED A SPECTRUM OF MUTATIONS IN MANY HEMATOLOGIC MALIGNANCIES, INCLUDING ACUTE MYELOID LEUKEMIA (AML), SUGGESTING THAT COMBINATIONS OF AGENTS WILL BE REQUIRED TO TREAT THESE DISEASES EFFECTIVELY. COMBINATORIAL APPROACHES WILL ALSO BE CRITICAL FOR COMBATING THE EMERGENCE OF GENETICALLY HETEROGENEOUS SUBCLONES, RESCUE SIGNALS IN THE MICROENVIRONMENT, AND TUMOR-INTRINSIC FEEDBACK PATHWAYS THAT ALL CONTRIBUTE TO DISEASE RELAPSE. TO IDENTIFY NOVEL AND EFFECTIVE DRUG COMBINATIONS, WE PERFORMED EX VIVO SENSITIVITY PROFILING OF 122 PRIMARY PATIENT SAMPLES FROM A VARIETY OF HEMATOLOGIC MALIGNANCIES AGAINST A PANEL OF 48 DRUG COMBINATIONS. THE COMBINATIONS WERE DESIGNED AS DRUG PAIRS THAT TARGET NONOVERLAPPING BIOLOGICAL PATHWAYS AND COMPRISE DRUGS FROM DIFFERENT CLASSES, PREFERABLY WITH FOOD AND DRUG ADMINISTRATION APPROVAL. A COMBINATION RATIO (CR) WAS DERIVED FOR EACH DRUG PAIR, AND CRS WERE EVALUATED WITH RESPECT TO DIAGNOSTIC CATEGORIES AS WELL AS AGAINST GENETIC, CYTOGENETIC, AND CELLULAR PHENOTYPES OF SPECIMENS FROM THE TWO LARGEST DISEASE CATEGORIES: AML AND CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). NEARLY ALL TESTED COMBINATIONS INVOLVING A BCL2 INHIBITOR SHOWED ADDITIONAL BENEFIT IN PATIENTS WITH MYELOID MALIGNANCIES, WHEREAS SELECT COMBINATIONS INVOLVING PI3K, CSF1R, OR BROMODOMAIN INHIBITORS SHOWED PREFERENTIAL BENEFIT IN LYMPHOID MALIGNANCIES. EXPANDED ANALYSES OF PATIENTS WITH AML AND CLL REVEALED SPECIFIC PATTERNS OF EX VIVO DRUG COMBINATION EFFICACY THAT WERE ASSOCIATED WITH SELECT GENETIC, CYTOGENETIC, AND PHENOTYPIC DISEASE SUBSETS, WARRANTING FURTHER EVALUATION. THESE FINDINGS HIGHLIGHT THE HEURISTIC VALUE OF AN INTEGRATED FUNCTIONAL GENOMIC APPROACH TO THE IDENTIFICATION OF NOVEL TREATMENT STRATEGIES FOR HEMATOLOGIC MALIGNANCIES. 2017 16 943 27 CHRONIC LYMPHOCYTIC LEUKEMIA. PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA CAN BE DIVIDED INTO THREE CATEGORIES: THOSE WHO ARE MINIMALLY AFFECTED BY THE PROBLEM, OFTEN NEVER REQUIRING THERAPY; THOSE THAT INITIALLY FOLLOW AN INDOLENT COURSE BUT SUBSEQUENTLY PROGRESS AND REQUIRE THERAPY; AND THOSE THAT FROM THE POINT OF DIAGNOSIS EXHIBIT AN AGGRESSIVE DISEASE NECESSITATING TREATMENT. LIKEWISE, SUCH PATIENTS PASS THROUGH THREE PHASES: DEVELOPMENT OF THE DISEASE, DIAGNOSIS, AND NEED FOR THERAPY. FINALLY, THE LEUKEMIC CLONES OF ALL PATIENTS APPEAR TO REQUIRE CONTINUOUS INPUT FROM THE EXTERIOR, MOST OFTEN THROUGH MEMBRANE RECEPTORS, TO ALLOW THEM TO SURVIVE AND GROW. THIS REVIEW IS PRESENTED ACCORDING TO THE TEMPORAL COURSE THAT THE DISEASE FOLLOWS, FOCUSING ON THOSE EXTERNAL INFLUENCES FROM THE TISSUE MICROENVIRONMENT (TME) THAT SUPPORT THE TIME LINES AS WELL AS THOSE INTERNAL INFLUENCES THAT ARE INHERITED OR DEVELOP AS GENETIC AND EPIGENETIC CHANGES OCCURRING OVER THE TIME LINE. REGARDING THE FORMER, SPECIAL EMPHASIS IS PLACED ON THE INPUT PROVIDED VIA THE B-CELL RECEPTOR FOR ANTIGEN AND THE C-X-C-MOTIF CHEMOKINE RECEPTOR-4 AND THE THERAPEUTIC AGENTS THAT BLOCK THESE INPUTS. REGARDING THE LATTER, PROMINENCE IS LAID UPON INHERITED SUSCEPTIBILITY GENES AND THE GENETIC AND EPIGENETIC ABNORMALITIES THAT LEAD TO THE DEVELOPMENTAL AND PROGRESSION OF THE DISEASE. 2021 17 1628 27 DNMT3A AND TET2 DOMINATE CLONAL HEMATOPOIESIS AND DEMONSTRATE BENIGN PHENOTYPES AND DIFFERENT GENETIC PREDISPOSITIONS. AGE-ASSOCIATED CLONAL HEMATOPOIESIS CAUSED BY ACQUIRED MUTATIONS IN MYELOID CANCER-ASSOCIATED GENES IS HIGHLY PREVALENT IN THE NORMAL POPULATION. ITS ETIOLOGY, BIOLOGICAL IMPACT ON HEMATOPOIESIS, AND ONCOGENIC RISK IS POORLY DEFINED AT THIS TIME. TO GAIN INSIGHT INTO THIS PHENOMENON, WE ANALYZED A COHORT OF 2530 RELATED AND UNRELATED HEMATOLOGICALLY NORMAL INDIVIDUALS (AGES 55 TO 101 YEARS). WE USED A SENSITIVE GENE-TARGETED DEEP SEQUENCING APPROACH TO GAIN PRECISION ON THE EXACT PREVALENCE OF DRIVER MUTATIONS AND THE PROPORTIONS OF AFFECTED GENES. MUTATIONAL STATUS WAS CORRELATED WITH BIOLOGICAL PARAMETERS. WE REPORT A HIGHER OVERALL PREVALENCE OF DRIVER MUTATIONS (13.7%), WHICH OCCURRED MOSTLY (93%) IN DNMT3A OR TET2 AND WERE HIGHLY AGE-CORRELATED. MUTATION IN THESE 2 GENES HAD SOME DISTINCTIVE EFFECTS ON END POINTS. TET2 MUTATIONS WERE MORE AGE-DEPENDENT, ASSOCIATED WITH A MODEST NEUTROPENIC EFFECT (9%, P = .012), DEMONSTRATED FAMILIAL AGGREGATION, AND ASSOCIATED WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE. MUTATIONS IN DNMT3A HAD NO IMPACT ON BLOOD COUNTS OR INDICES. MUTATIONAL BURDEN OF BOTH GENES CORRELATED WITH X-INACTIVATION SKEWING BUT NO SIGNIFICANT ASSOCIATION WITH AGE-ADJUSTED TELOMERE LENGTH REDUCTION WAS DOCUMENTED. THE DISCORDANCE BETWEEN THE HIGH PREVALENCE OF MUTATIONS IN THESE 2 GENES AND THEIR LIMITED BIOLOGICAL IMPACT RAISE THE QUESTION OF THE POTENTIAL ROLE OF DYSREGULATED EPIGENETIC MODIFIERS IN NORMAL AGING HEMATOPOIESIS, WHICH MAY INCLUDE SUPPORT TO FAILING HEMATOPOIESIS. 2017 18 5905 24 TACKLING THE HETEROGENEITY OF CVID. PURPOSE OF REVIEW: COMMON VARIABLE IMMUNODEFICIENCY IS CLINICALLY THE MOST RELEVANT PRIMARY IMMUNODEFICIENCY OF THE ADULT. ITS HETEROGENEITY HAS HINDERED PROGRESS IN THE PATHOGENETIC UNDERSTANDING OF THE MAJORITY OF COMMON VARIABLE IMMUNODEFICIENCY PATIENTS. THIS ABSTRACT SUMMARIZES RECENT ASPECTS OF THE FIELD AND EMPHASIZES THE NEED FOR A COMMONLY ACCEPTED APPROACH TO CLASSIFY COMMON VARIABLE IMMUNODEFICIENCY. RECENT FINDINGS: IN THE LAST 2 YEARS, THE FIRST GENETIC DEFECTS UNDERLYING COMMON VARIABLE IMMUNODEFICIENCY, INCLUDING ICOS, TACI, BAFF-R AND CD19, HAVE BEEN IDENTIFIED. THE ANALYSIS OF DENDRITIC CELLS DEMONSTRATED ALTERATIONS IN A MAJORITY OF PATIENTS IN ADDITION TO THE DISTURBED T AND B-CELL FUNCTION. SEVERAL CHANGES OF THE ADAPTIVE IMMUNE SYSTEM MIGHT BE SECONDARY TO AN UNDERLYING CHRONIC INFLAMMATORY SETTING POSSIBLY DUE TO A HHV8 INFECTION IN A SUBGROUP OF PATIENTS WITH GRANULOMATOUS DISEASE, AUTOIMMUNE PHENOMENA AND T-CELL DYSFUNCTION. THE OCCURRENCE OF GRANULOMATOUS INFLAMMATION IS ASSOCIATED WITH A WORSE PROGNOSIS COMPARED WITH COMMON VARIABLE IMMUNODEFICIENCY PATIENTS WITHOUT GRANULOMA. SUMMARY: THE PATHOGENESIS OF COMMON VARIABLE IMMUNODEFICIENCY INCLUDES DISTURBANCES OF THE ADAPTIVE AS WELL AS INNATE IMMUNE SYSTEM. IDENTIFIED MONOGENIC DEFECTS ACCOUNT FOR ABOUT 10% OF CASES, LEAVING THE MAJORITY OF DEFECTS UNDEFINED AND CERTAINLY IN PART EPIGENETIC. TO COMBINE THE KNOWN ASPECTS OF THE PATHOGENESIS OF COMMON VARIABLE IMMUNODEFICIENCY TO A CONCLUSIVE PICTURE, THE CLINICAL AND IMMUNOLOGIC PHENOTYPING OF PATIENTS NEEDS TO BE STANDARDIZED. 2005 19 3015 27 GENETICS AND EPIGENETICS OF CLL. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS A HETEROGENEOUS BIOLOGICAL BEHAVIOR, WHICH IS HIGHLY INFLUENCED BY ITS IMMUNOGENETIC, EPIGENETIC, AND GENOMIC PROPERTIES. THE REMARKABLY VARIABLE CLINICAL COURSE OF THE DISEASE HAS BEEN ASSOCIATED WITH GENETIC FEATURES SUCH AS CHROMOSOMAL ABNORMALITIES, THE PRESENCE OF EITHER HIGH OR LOW NUMBERS OF SOMATIC HYPERMUTATIONS (SHM) IN THE VARIABLE REGION OF THE IMMUNOGLOBULIN HEAVY CHAIN LOCUS (IGHV), AND SOMATIC MUTATIONS OF SEVERAL SPECIFIC DRIVER GENES. NEXT-GENERATION SEQUENCING (NGS) TECHNOLOGIES HAVE PROVIDED A COMPREHENSIVE CHARACTERIZATION OF THE GENOMIC AND EPIGENOMIC LANDSCAPE IN CLL, ELUCIDATING IMPORTANT UNDERLYING MECHANISMS OF THE DISEASE'S BIOLOGY. THE SCOPE OF THIS REVIEW IS TO SUMMARIZE THE MOST RECENT DISCOVERIES ABOUT NOVEL GENETIC AND EPIGENETIC ALTERATIONS, DISCUSSING THEIR IMPACT ON CLINICAL OUTCOMES AND RESPONSE TO CURRENTLY AVAILABLE THERAPY. 2023 20 4028 32 LUNG TUMORS, COPD AND IMMUNE RESPONSE: IS EPIGENETICS THE BOTTOM LINE? NSCLC IS A HETEROGENEOUS DISORDER CONSISTING OF DISTINCT MOLECULAR SUBTYPES WHICH CAN BE TREATED BY USING SPECIFIC DRUGS TARGETED TO DISTINCT GENETIC LESIONS. IT IS WELL KNOWN THAT NSCLS INCIDENCE IS HIGHER IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) PATIENTS BECAUSE THEY SHARE A COMMON RISK FACTOR (CIGARETTE SMOKING) AND IT IS BELIEVED THAT THE TYPICAL INFLAMMATORY MICROENVIRONMENT OBSERVED IN COPD MAY INFLUENCE THE MOLECULAR MECHANISMS RESPONSIBLE OF CARCINOGENESIS. IN THE LAST YEARS, THE ROLE OF EPIGENETIC PROCESSES IN CELL BIOLOGY AND TISSUE PATHOLOGY HAS BEEN EXTENSIVELY STUDIED BOTH IN COPD AND NSCLC. THE RECENT PAPER BY WAUTERS ET AL. SHOWED A SPECIFIC PATTERN OF DRIVER MUTATIONS AND MOLECULAR FEATURES IN NSCLC RAISING IN THE CONTEXT OF COPD. ALL THESE FINDINGS HAVE SHOWN FOR THE FIRST TIME THAT LUNG TUMORS FOUND IN COPD PATIENTS DIFFER FROM THOSE OBSERVED IN PATIENT WITHOUT COPD DUE TO THE PRESENCE OF A SPECIFIC TUMOR MICROENVIRONMENT WHICH IS CHARACTERIZED BY REDUCED CD4+ TREG CELLS. ON THIS BASIS, THE PRESENT WORK AIMS AT DISCUSSING AND ANALYZING THE CONTEXT-SPECIFIC MECHANISMS OF CLONAL SELECTION AND EVOLUTION MAINLY FOCUSING ON THE EPIGENETIC ALTERATIONS AND AT POINTING OUT THE POTENTIAL THERAPEUTIC IMPLICATIONS. 2016