1 3644 101 INCREASED LEVELS OF ENDOGENOUS RETROVIRUSES TRIGGER FIBROINFLAMMATION AND PLAY A ROLE IN KIDNEY DISEASE DEVELOPMENT. INFLAMMATION IS A COMMON FEATURE OF ALL FORMS OF CHRONIC KIDNEY DISEASE; HOWEVER, THE UNDERLYING MECHANISM REMAINS POORLY UNDERSTOOD. EVOLUTIONARILY INHERITED ENDOGENOUS RETROVIRUSES (ERVS) HAVE THE POTENTIAL TO TRIGGER AN IMMUNE REACTION. COMPREHENSIVE RNA-SEQUENCING OF CONTROL AND DISEASED KIDNEYS FROM HUMAN AND MOUSE DISEASE MODELS INDICATED HIGHER EXPRESSION OF TRANSPOSABLE ELEMENTS (TES) AND ERVS IN DISEASED KIDNEYS. LOSS OF CYTOSINE METHYLATION CAUSING EPIGENETIC DEREPRESSION LIKELY CONTRIBUTES TO AN INCREASE IN ERV LEVELS. GENETIC DELETION/PHARMACOLOGICAL INHIBITION OF DNA METHYLTRANSFERASE 1 (DNMT1) INDUCES ERV EXPRESSION. IN CULTURED KIDNEY TUBULE CELLS, ERVS ELICIT THE ACTIVATION OF CYTOSOLIC NUCLEOTIDE SENSORS SUCH AS RIG-I, MDA5, AND STING. ERVS EXPRESSIONS IN KIDNEY TUBULES TRIGGER RIG-I/STING, AND CYTOKINE EXPRESSION, AND CORRELATE WITH THE PRESENCE OF IMMUNE CELLS. GENETIC DELETION OF RIG-I OR STING OR TREATMENT WITH REVERSE TRANSCRIPTASE INHIBITOR AMELIORATES KIDNEY FIBROINFLAMMATION. OUR DATA INDICATE AN IMPORTANT ROLE OF EPIGENETIC DEREPRESSION-INDUCED ERV ACTIVATION TRIGGERING RENAL FIBROINFLAMMATION. 2023 2 3845 19 IS AGING A "RETRO"SPECTIVE EVENT? REACTIVATION OF ENDOGENOUS RETROVIRUSES (ERVS), THE RELICS OF ANCIENT INFECTIONS, HAS BEEN IMPLICATED IN A NUMBER OF DISEASE CONTEXTS. IN THIS ISSUE OF CELL, LIU ET AL. SHOW HOW REACTIVATION OF ERVS IN OLD AGE CAN INDUCE SENESCENCE. THIS AWAKENING OF ERVS IS ASSOCIATED WITH THEIR EPIGENETIC DEREPRESSION AND CONTRIBUTES TO AGE-ASSOCIATED CHRONIC INFLAMMATION. 2023 3 3798 26 INTERPLAY BETWEEN ACTIVATION OF ENDOGENOUS RETROVIRUSES AND INFLAMMATION AS COMMON PATHOGENIC MECHANISM IN NEUROLOGICAL AND PSYCHIATRIC DISORDERS. HUMAN ENDOGENOUS RETROVIRUSES (ERVS) ARE ANCESTORIAL RETROVIRAL ELEMENTS THAT WERE INTEGRATED INTO OUR GENOME THROUGH GERMLINE INFECTIONS AND INSERTIONS DURING EVOLUTION. THEY HAVE REPEATEDLY BEEN IMPLICATED IN THE AETIOLOGY AND PATHOPHYSIOLOGY OF NUMEROUS HUMAN DISORDERS, PARTICULARLY IN THOSE THAT AFFECT THE CENTRAL NERVOUS SYSTEM. IN ADDITION TO THE KNOWN ASSOCIATION OF ERVS WITH MULTIPLE SCLEROSIS AND AMYOTROPHIC LATERAL SCLEROSIS, A GROWING NUMBER OF STUDIES LINKS THE INDUCTION AND EXPRESSION OF THESE RETROVIRAL ELEMENTS WITH THE ONSET AND SEVERITY OF NEURODEVELOPMENTAL AND PSYCHIATRIC DISORDERS. ALTHOUGH THESE DISORDERS DIFFER IN TERMS OF OVERALL DISEASE PATHOLOGY AND CAUSALITIES, A CERTAIN DEGREE OF (SUBCLINICAL) CHRONIC INFLAMMATION CAN BE IDENTIFIED IN ALL OF THEM. BASED ON THESE COMMONALITIES, WE DISCUSS THE BIDIRECTIONAL RELATIONSHIP BETWEEN ERV EXPRESSION AND INFLAMMATION AND HIGHLIGHT THAT NUMEROUS ENTRY POINTS TO THIS RECIPROCAL SEQUENCE OF EVENTS EXIST, INCLUDING INITIAL INFECTIONS WITH ERV-ACTIVATING PATHOGENS, EXPOSURE TO NON-INFECTIOUS INFLAMMATORY STIMULI, AND CONDITIONS IN WHICH EPIGENETIC SILENCING OF ERV ELEMENTS IS DISRUPTED. 2023 4 6657 25 UPREGULATED KAT7 IN SYNOVIAL FIBROBLASTS PROMOTES TH17 CELL DIFFERENTIATION AND INFILTRATION IN RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC AUTOIMMUNE DISEASE INVOLVING MULTIPLE CELLULAR PARTICIPANTS, OF WHICH SYNOVIAL FIBROBLASTS (SFS) ARE TIGHTLY CONNECTED WITH THE DEVELOPMENT AND PROGRESSION OF RA. HERE, WE PROVIDE EVIDENCE CONFIRMING THAT KAT7, AN H4-SPECIFIC HISTONE ACETYLASE, IS UPREGULATED IN SFS OF RA PATIENTS, WHICH IS AT LEAST ATTRIBUTED TO THE STIMULATION BY RA-ASSOCIATED PROINFLAMMATORY CYTOKINES, SUCH AS TNF-ALPHA, IL-1BETA OR IFN-GAMMA. IN ADDITION, KAT7 OVEREXPRESSION IN CULTURED HUMAN FIBROBLAST-LIKE SYNOVIOCYTES (HFLSS) INDUCES IL-6 AND TGF-BETA EXPRESSION THROUGH AN EPIGENETIC MECHANISM, AND IN VITRO T HELPER 17 (TH17) CELL POLARIZATION CULTURED IN THESE SUPERNATANTS SHOWS PROMOTED CELL DIFFERENTIATION. MOREOVER, KAT7 OVEREXPRESSION IN HFLSS INDUCES CCL20 EXPRESSION VIA P44/42 MAPK PATHWAY, WHEREBY PROMOTING TH17 CELL MIGRATION. THESE TWO ACTIVITIES OF KAT7 IN RA SFS INDICATE ITS POTENTIAL ROLES IN ACCELERATING RA PATHOLOGY. OVERALL, THESE RESULTS DEMONSTRATE SOME CONNECTIONS BETWEEN KAT7 UPREGULATED IN RA SFS AND RA PROGRESSION AND PRESENT THE INHIBITION OF KAT7 ACTIVITY AS A NOVEL THERAPEUTIC TARGET FOR INTERFERING RA DISEASE. 2017 5 6236 29 THE MACROPHAGE IRF8/IRF1 REGULOME IS REQUIRED FOR PROTECTION AGAINST INFECTIONS AND IS ASSOCIATED WITH CHRONIC INFLAMMATION. IRF8 AND IRF1 ARE TRANSCRIPTIONAL REGULATORS THAT PLAY CRITICAL ROLES IN THE DEVELOPMENT AND FUNCTION OF MYELOID CELLS, INCLUDING ACTIVATION OF MACROPHAGES BY PROINFLAMMATORY SIGNALS SUCH AS INTERFERON-GAMMA (IFN-GAMMA). LOSS OF IRF8 OR IRF1 FUNCTION CAUSES SEVERE SUSCEPTIBILITY TO INFECTIONS IN MICE AND IN HUMANS. WE USED CHROMATIN IMMUNOPRECIPITATION SEQUENCING AND RNA SEQUENCING IN WILD TYPE AND INIRF8ANDIRF1MUTANT PRIMARY MACROPHAGES TO SYSTEMATICALLY CATALOG ALL OF THE GENES BOUND BY (CISTROMES) AND TRANSCRIPTIONALLY ACTIVATED BY (REGULOMES) IRF8, IRF1, PU.1, AND STAT1, INCLUDING MODULATION OF EPIGENETIC HISTONE MARKS. OF THE SEVEN BINDING COMBINATIONS IDENTIFIED, TWO (CLUSTER 1 [IRF8/IRF1/STAT1/PU.1] AND CLUSTER 5 [IRF1/STAT1/PU.1]) WERE FOUND TO HAVE A MAJOR ROLE IN CONTROLLING MACROPHAGE TRANSCRIPTIONAL PROGRAMS BOTH AT THE BASAL LEVEL AND AFTER IFN-GAMMA ACTIVATION. THEY DIRECT THE EXPRESSION OF A SET OF GENES, THE IRF8/IRF1 REGULOME, THAT PLAY CRITICAL ROLES IN HOST INFLAMMATORY AND ANTIMICROBIAL DEFENSES IN MOUSE MODELS OF NEUROINFLAMMATION AND OF PULMONARY TUBERCULOSIS, RESPECTIVELY. IN ADDITION, THIS IRF8/IRF1 REGULOME IS ENRICHED FOR GENES MUTATED IN HUMAN PRIMARY IMMUNODEFICIENCIES AND WITH LOCI ASSOCIATED WITH SEVERAL INFLAMMATORY DISEASES IN HUMANS. 2016 6 1679 24 DRUG RESISTANCE IN GIARDIA DUODENALIS. GIARDIA DUODENALIS IS A MICROAEROPHILIC PARASITE OF THE HUMAN GASTROINTESTINAL TRACT AND A MAJOR CONTRIBUTOR TO DIARRHEAL AND POST-INFECTIOUS CHRONIC GASTROINTESTINAL DISEASE WORLD-WIDE. TREATMENT OF G. DUODENALIS INFECTION CURRENTLY RELIES ON A SMALL NUMBER OF DRUG CLASSES. NITROHETEROCYCLICS, IN PARTICULAR METRONIDAZOLE, HAVE REPRESENTED THE FRONT LINE TREATMENT FOR THE LAST 40 YEARS. NITROHETEROCYCLIC-RESISTANT G. DUODENALIS HAVE BEEN ISOLATED FROM PATIENTS AND CREATED IN VITRO, PROMPTING CONSIDERABLE RESEARCH INTO THE BIOMOLECULAR MECHANISMS OF RESISTANCE. THESE COMPOUNDS ARE REDOX-ACTIVE AND ARE BELIEVED TO DAMAGE PROTEINS AND DNA AFTER BEING ACTIVATED BY OXIDOREDUCTASE ENZYMES IN METABOLICALLY ACTIVE CELLS. IN THIS REVIEW, WE EXPLORE THE MOLECULAR PHENOTYPES OF NITROHETEROCYCLIC-RESISTANT G. DUODENALIS DESCRIBED TO DATE IN THE CONTEXT OF THE PROTIST'S UNUSUAL GLYCOLYTIC AND ANTIOXIDANT SYSTEMS. WE PROPOSE THAT RESISTANCE MECHANISMS ARE LIKELY TO EXTEND WELL BEYOND CURRENTLY DESCRIBED RESISTANCE-ASSOCIATED ENZYMES (I.E., PYRUVATE FERREDOXIN OXIDOREDUCTASES AND NITROREDUCTASES), TO INCLUDE NAD(P)H- AND FLAVIN-GENERATING PATHWAYS, AND POSSIBLY REDOX-SENSITIVE EPIGENETIC REGULATION. MECHANISMS THAT ALLOW G. DUODENALIS TO TOLERATE OXIDATIVE STRESS MAY LEAD TO RESISTANCE AGAINST BOTH OXYGEN AND NITROHETEROCYCLICS, WITH IMPLICATIONS FOR CLINICAL CONTROL. THE PRESENT REVIEW HIGHLIGHTS THE POTENTIAL FOR SYSTEMS BIOLOGY TOOLS AND ADVANCED BIOINFORMATICS TO FURTHER INVESTIGATE THE MULTIFACETED MECHANISMS OF NITROHETEROCYCLIC RESISTANCE IN THIS IMPORTANT PATHOGEN. 2015 7 4561 31 MYD88 HYPERMETHYLATION MEDIATED BY DNMT1 IS ASSOCIATED WITH LTA-INDUCED INFLAMMATORY RESPONSE IN HUMAN ODONTOBLAST-LIKE CELLS. DENTAL CARIES IS A CHRONIC, INFECTIOUS, AND DESTRUCTIVE DISEASE THAT ALLOWS BACTERIA TO BREAK INTO THE DENTAL PULP TISSUE. AS CARIES-RELATED BACTERIA INVADE THE HUMAN DENTINAL TUBULES, ODONTOBLASTS ARE THE FIRST LINE OF DENTAL PULP THAT TRIGGER THE INITIAL INFLAMMATORY AND IMMUNE RESPONSES. DNA METHYLATION IS A KEY EPIGENETIC MODIFICATION THAT PLAYS A FUNDAMENTAL ROLE IN GENE TRANSCRIPTION, AND ITS ROLE IN INFLAMMATION-RELATED DISEASES HAS RECENTLY ATTRACTED ATTENTION. HOWEVER, WHETHER DNA METHYLATION REGULATES THE INFLAMMATORY RESPONSE OF HUMAN ODONTOBLASTS IS STILL UNKNOWN. IN THE PRESENT STUDY, WE INVESTIGATED THE EXPRESSION OF DNA METHYLTRANSFERASE (DNMT)-1 IN LIPOTEICHOIC ACID (LTA)-STIMULATED HUMAN ODONTOBLAST-LIKE CELLS (HOBS) AND FOUND THAT DNMT1 EXPRESSION SHOWED A DECLINE THAT IS CONTRARY TO THE TRANSCRIPTION OF INFLAMMATORY CYTOKINES. KNOCKDOWN OF THE DNMT1 GENE INCREASED THE EXPRESSION OF SEVERAL CYTOKINES, INCLUDING IL-6 AND IL-8, IN THE LTA-INDUCED INFLAMMATORY RESPONSE. DNMT1 KNOCKDOWN INCREASED THE PHOSPHORYLATION OF IKKALPHA/BETA, IKAPPABALPHA, AND P65 IN THE NF-KAPPAB PATHWAY AND THE PHOSPHORYLATION OF P38 AND ERK IN THE MAPK PATHWAY; HOWEVER, ONLY THE NF-KAPPAB PATHWAY INHIBITOR PDTC SUPPRESSED BOTH IL-6 AND IL-8 EXPRESSION, WHEREAS INHIBITORS OF THE MAPK PATHWAY (U0126, SB2035580, AND SP600125) DID NOT. FURTHERMORE, DNMT1 KNOCKDOWN UPREGULATED THE EXPRESSION OF MYD88 AND TRAF6 BUT ONLY ATTENUATED THE MYD88 GENE PROMOTER METHYLATION IN LTA-TREATED HOBS. TAKEN TOGETHER, THESE RESULTS DEMONSTRATED THAT DNMT1 DEPLETION CAUSED HYPOMETHYLATION AND UPREGULATION OF MYD88, WHICH RESULTED IN ACTIVATION OF THE NF-KAPPAB PATHWAY AND THE SUBSEQUENT RELEASE OF LTA-INDUCED INFLAMMATORY CYTOKINES IN HOBS. THIS STUDY EMPHASIZES THE CRITICAL ROLE OF DNA METHYLATION IN THE IMMUNE DEFENSE OF ODONTOBLASTS WHEN DENTAL PULP REACTED TO CARIES. 2019 8 850 34 CHILDREN WITH CHRONIC IMMUNE THROMBOCYTOPENIA EXHIBIT HIGH EXPRESSION OF HUMAN ENDOGENOUS RETROVIRUSES TRIM28 AND SETDB1. CHRONIC IMMUNE THROMBOCYTOPENIA (CITP) IS AN AUTOIMMUNE DISEASE WHOSE UNDERLYING BIOLOGIC MECHANISMS REMAIN ELUSIVE. HUMAN ENDOGENOUS RETROVIRUSES (HERVS) DERIVE FROM ANCESTRAL INFECTIONS AND CONSTITUTE ABOUT 8% OF OUR GENOME. A WEALTH OF CLINICAL AND EXPERIMENTAL STUDIES HIGHLIGHTS THEIR PIVOTAL PATHOGENETIC ROLE IN AUTOIMMUNE DISEASES. EPIGENETIC MECHANISMS, SUCH AS THOSE MODULATED BY TRIM28 AND SETDB1, ARE INVOLVED IN HERV ACTIVATION AND REGULATION OF IMMUNE RESPONSE. WE ASSESSED, THROUGH A POLYMERASE CHAIN REACTION REAL-TIME TAQMAN AMPLIFICATION ASSAY, THE TRANSCRIPTION LEVELS OF POL GENES OF HERV-H, HERV-K, AND HERV-W; ENV GENES OF SYNCYTIN (SYN)1, SYN2, AND HERV-W; AS WELL AS TRIM28 AND SETDB1 IN WHOLE BLOOD FROM 34 CHILDREN WITH CITP AND AGE-MATCHED HEALTHY CONTROLS (HC). THE TRANSCRIPTIONAL LEVELS OF ALL HERV SEQUENCES, WITH THE EXCEPTION OF HERV-W-ENV, WERE SIGNIFICANTLY ENHANCED IN CHILDREN WITH CITP AS COMPARED TO HC. PATIENTS ON ELTROMBOPAG TREATMENT EXHIBITED LOWER EXPRESSION OF SYN1, SYN2, AND HERV-W-ENV AS COMPARED TO UNTREATED PATIENTS. THE MRNA CONCENTRATIONS OF TRIM28 AND SETDB1 WERE SIGNIFICANTLY HIGHER AND WERE POSITIVELY CORRELATED WITH THOSE OF HERVS IN CITP PATIENTS. THE OVER-EXPRESSIONS OF HERVS AND TRIM28/SETDB1 AND THEIR POSITIVE CORRELATIONS IN PATIENTS WITH CITP ARE SUGGESTIVE CLUES OF THEIR CONTRIBUTION TO THE PATHOGENESIS OF THE DISEASE AND SUPPORT INNOVATIVE INTERVENTIONS TO INHIBIT HERV AND TRIM28/SETDB1 EXPRESSIONS IN PATIENTS UNRESPONSIVE TO STANDARD THERAPIES. 2023 9 3941 25 LNCRNA DRAIR IS DOWNREGULATED IN DIABETIC MONOCYTES AND MODULATES THE INFLAMMATORY PHENOTYPE VIA EPIGENETIC MECHANISMS. LONG NONCODING RNAS (LNCRNAS) ARE INCREASINGLY IMPLICATED IN THE PATHOLOGY OF DIABETIC COMPLICATIONS. HERE, WE EXAMINED THE ROLE OF LNCRNAS IN MONOCYTE DYSFUNCTION AND INFLAMMATION ASSOCIATED WITH HUMAN TYPE 2 DIABETES MELLITUS (T2D). RNA SEQUENCING ANALYSIS OF CD14+ MONOCYTES FROM PATIENTS WITH T2D VERSUS HEALTHY CONTROLS REVEALED DOWNREGULATION OF ANTIINFLAMMATORY AND ANTIPROLIFERATIVE GENES, ALONG WITH SEVERAL LNCRNAS, INCLUDING A POTENTIALLY NOVEL DIVERGENT LNCRNA DIABETES REGULATED ANTIINFLAMMATORY RNA (DRAIR) AND ITS NEARBY GENE CPEB2. HIGH GLUCOSE AND PALMITIC ACID DOWNREGULATED DRAIR IN CULTURED CD14+ MONOCYTES, WHEREAS ANTIINFLAMMATORY CYTOKINES AND MONOCYTE-TO-MACROPHAGE DIFFERENTIATION UPREGULATED DRAIR VIA KLF4 TRANSCRIPTION FACTOR. DRAIR OVEREXPRESSION INCREASED ANTIINFLAMMATORY AND MACROPHAGE DIFFERENTIATION GENES BUT INHIBITED PROINFLAMMATORY GENES. CONVERSELY, DRAIR KNOCKDOWN ATTENUATED ANTIINFLAMMATORY GENES, PROMOTED INFLAMMATORY RESPONSES, AND INHIBITED PHAGOCYTOSIS. DRAIR REGULATED TARGET GENE EXPRESSION THROUGH INTERACTION WITH CHROMATIN, AS WELL AS INHIBITION OF THE REPRESSIVE EPIGENETIC MARK H3K9ME2 AND ITS CORRESPONDING METHYLTRANSFERASE G9A. MOUSE ORTHOLOGOUS DRAIR AND CPEB2 WERE ALSO DOWNREGULATED IN PERITONEAL MACROPHAGES FROM T2D DB/DB MICE, AND DRAIR KNOCKDOWN IN NONDIABETIC MICE ENHANCED PROINFLAMMATORY GENES IN MACROPHAGES. THUS, DRAIR MODULATES THE INFLAMMATORY PHENOTYPE OF MONOCYTES/MACROPHAGES VIA EPIGENETIC MECHANISMS, AND ITS DOWNREGULATION IN T2D MAY PROMOTE CHRONIC INFLAMMATION. AUGMENTATION OF ENDOGENOUS LNCRNAS LIKE DRAIR COULD SERVE AS NOVEL ANTIINFLAMMATORY THERAPIES FOR DIABETIC COMPLICATIONS. 2021 10 6327 24 THE ROLE OF CD4(+) RESIDENT MEMORY T CELLS IN LOCAL IMMUNITY IN THE MUCOSAL TISSUE - PROTECTION VERSUS PATHOLOGY. MEMORY T CELLS ARE CRUCIAL FOR BOTH LOCAL AND SYSTEMIC PROTECTION AGAINST PATHOGENS OVER A LONG PERIOD OF TIME. THREE MAJOR SUBSETS OF MEMORY T CELLS; EFFECTOR MEMORY T (T(EM)) CELLS, CENTRAL MEMORY T (T(CM)) CELLS, AND TISSUE-RESIDENT MEMORY T (T(RM)) CELLS HAVE BEEN IDENTIFIED. THE MOST RECENTLY IDENTIFIED SUBSET, T(RM) CELLS, IS CHARACTERIZED BY THE EXPRESSION OF THE C-TYPE LECTIN CD69 AND/OR THE INTEGRIN CD103. T(RM) CELLS PERSIST LOCALLY AT SITES OF MUCOSAL TISSUE, SUCH AS THE LUNG, WHERE THEY PROVIDE FRONTLINE DEFENSE AGAINST VARIOUS PATHOGENS. IMPORTANTLY, HOWEVER, T(RM) CELLS ARE ALSO INVOLVED IN SHAPING THE PATHOLOGY OF INFLAMMATORY DISEASES. A NUMBER OF PIONEERING STUDIES REVEALED IMPORTANT ROLES OF CD8(+) T(RM) CELLS, PARTICULARLY THOSE IN THE LOCAL CONTROL OF VIRAL INFECTION. HOWEVER, THE PROTECTIVE FUNCTION AND PATHOGENIC ROLE OF CD4(+) T(RM) CELLS THAT RESIDE WITHIN THE MUCOSAL TISSUE REMAIN LARGELY UNKNOWN. IN THIS REVIEW, WE DISCUSS THE AMBIVALENT FEATURE OF CD4(+) T(RM) CELLS IN THE PROTECTIVE AND PATHOLOGICAL IMMUNE RESPONSES. WE ALSO REVIEW THE TRANSCRIPTIONAL AND EPIGENETIC CHARACTERISTICS OF CD4(+) T(RM) CELLS IN THE LUNG THAT HAVE BEEN ELUCIDATED BY RECENT TECHNICAL APPROACHES. A BETTER UNDERSTANDING OF THE FUNCTION OF CD4(+) T(RM) CELLS IS CRUCIAL FOR THE DEVELOPMENT OF BOTH EFFECTIVE VACCINATION AGAINST PATHOGENS AND NEW THERAPEUTIC STRATEGIES FOR INTRACTABLE INFLAMMATORY DISEASES, SUCH AS INFLAMMATORY BOWEL DISEASES AND CHRONIC ALLERGIC DISEASES. 2021 11 5231 16 PROBIOTICS AND AMELIORATION OF RHEUMATOID ARTHRITIS: SIGNIFICANT ROLES OF LACTOBACILLUS CASEI AND LACTOBACILLUS ACIDOPHILUS. RHEUMATOID ARTHRITIS IS A CHRONIC AUTOIMMUNE DISORDER THAT CAN LEAD TO DISABILITY CONDITIONS WITH SWOLLEN JOINTS, PAIN, STIFFNESS, CARTILAGE DEGRADATION, AND OSTEOPOROSIS. GENETIC, EPIGENETIC, SEX-SPECIFIC FACTORS, SMOKING, AIR POLLUTION, FOOD, ORAL HYGIENE, PERIODONTITIS, PREVOTELLA, AND IMBALANCE IN THE GASTROINTESTINAL MICROBIOTA ARE POSSIBLE SOURCES OF THE INITIATION OR PROGRESSION OF RHEUMATOID ARTHRITIS, ALTHOUGH THE DETAILED MECHANISMS STILL NEED TO BE ELUCIDATED. PROBIOTICS CONTAINING LACTOBACILLUS SPP. ARE COMMONLY USED AS ALLEVIATING AGENTS OR FOOD SUPPLEMENTS TO MANAGE DIARRHEA, DYSENTERY, DEVELOP IMMUNITY, AND MAINTAIN GENERAL HEALTH. THE MECHANISM OF ACTION OF LACTOBACILLUS SPP. AGAINST RHEUMATOID ARTHRITIS IS STILL NOT CLEARLY KNOWN TO DATE. IN THIS NARRATIVE REVIEW, WE RECAPITULATE THE FINDINGS OF RECENT STUDIES TO UNDERSTAND THE OVERALL PATHOGENESIS OF RHEUMATOID ARTHRITIS AND THE ROLES OF PROBIOTICS, PARTICULARLY L. CASEI OR L. ACIDOPHILUS, IN THE MANAGEMENT OF RHEUMATOID ARTHRITIS IN CLINICAL AND PRECLINICAL STUDIES. 2021 12 6397 28 THE ROLE OF TRANSPOSABLE ELEMENTS IN AGING AND CANCER. TRANSPOSABLE ELEMENTS (TES) CONSTITUTE A LARGE PORTION OF THE HUMAN GENOME. VARIOUS MECHANISMS AT THE TRANSCRIPTION AND POST-TRANSCRIPTION LEVELS DEVELOPED TO SUPPRESS TE ACTIVITY IN HEALTHY CONDITIONS. HOWEVER, A GROWING BODY OF EVIDENCE SUGGESTS THAT TE DYSREGULATION IS INVOLVED IN VARIOUS HUMAN DISEASES, INCLUDING AGE-RELATED DISEASES AND CANCER. IN THIS REVIEW, WE EXPLAINED HOW SENSING TES BY THE IMMUNE SYSTEM COULD INDUCE INNATE IMMUNE RESPONSES, CHRONIC INFLAMMATION, AND FOLLOWING AGE-RELATED DISEASES. WE ALSO NOTED THAT INFLAMMAGEING AND EXOGENOUS CARCINOGENS COULD TRIGGER THE UPREGULATION OF TES IN PRECANCEROUS CELLS. INCREASED INFLAMMATION COULD ENHANCE EPIGENETIC PLASTICITY AND UPREGULATION OF EARLY DEVELOPMENTAL TES, WHICH REWIRES THE TRANSCRIPTIONAL NETWORKS AND GIFT THE SURVIVAL ADVANTAGE TO THE PRECANCEROUS CELLS. IN ADDITION, UPREGULATED TES COULD INDUCE GENOME INSTABILITY, ACTIVATION OF ONCOGENES, OR INHIBITION OF TUMOR SUPPRESSORS AND CONSEQUENT CANCER INITIATION AND PROGRESSION. SO, WE SUGGEST THAT TES COULD BE CONSIDERED THERAPEUTIC TARGETS IN AGING AND CANCER. 2023 13 460 30 ARACHIDONIC ACID 15-LIPOXYGENASE: EFFECTS OF ITS EXPRESSION, METABOLITES, AND GENETIC AND EPIGENETIC VARIATIONS ON AIRWAY INFLAMMATION. ARACHIDONIC ACID 15-LIPOXYGENASE (ALOX15) IS AN ENZYME THAT CAN OXIDIZE POLYUNSATURATED FATTY ACIDS. ALOX15 IS STRONGLY EXPRESSED IN AIRWAY EPITHELIAL CELLS, WHERE IT CATALYZES THE CONVERSION OF ARACHIDONIC ACID TO 15-HYDROXYEICOSATETRAENOIC ACID (15-HETE) INVOLVED IN VARIOUS AIRWAY INFLAMMATORY DISEASES. INTERLEUKIN (IL)-4 AND IL-13 INDUCE ALOX15 EXPRESSION BY ACTIVATING JAK2 AND TYK2 KINASES AS WELL AS SIGNAL TRANSDUCERS AND ACTIVATORS OF TRANSCRIPTION (STATS) 1/3/5/6. ALOX15 UP-REGULATION AND SUBSEQUENT ASSOCIATION WITH PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN 1 (PEBP1) ACTIVATE THE MITOGEN-ACTIVATED EXTRACELLULAR SIGNAL-REGULATED KINASE (MEK)-EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) PATHWAY, THUS INDUCING EOSINOPHIL-MEDIATED AIRWAY INFLAMMATION. IN ADDITION, ALOX15 PLAYS A SIGNIFICANT ROLE IN PROMOTING THE MIGRATION OF IMMUNE CELLS, SUCH AS IMMATURE DENDRITIC CELLS, ACTIVATED T CELLS, AND MAST CELLS, AND AIRWAY REMODELING, INCLUDING GOBLET CELL DIFFERENTIATION. GENOME-WIDE ASSOCIATION STUDIES HAVE REVEALED MULTIPLE ALOX15 VARIANTS AND THEIR SIGNIFICANT CORRELATION WITH THE RISK OF DEVELOPING AIRWAY DISEASES. THE EPIGENETIC MODIFICATIONS OF THE ALOX15 GENE, SUCH AS DNA METHYLATION AND HISTONE MODIFICATIONS, HAVE BEEN SHOWN TO CLOSELY RELATE WITH AIRWAY INFLAMMATION. THIS REVIEW SUMMARIZES THE ROLE OF ALOX15 IN DIFFERENT PHENOTYPES OF ASTHMA, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, CHRONIC RHINOSINUSITIS, ASPIRIN-EXACERBATED RESPIRATORY DISEASE, AND NASAL POLYPS, SUGGESTING NEW TREATMENT STRATEGIES FOR THESE AIRWAY INFLAMMATORY DISEASES WITH COMPLEX ETIOLOGY AND POOR TREATMENT RESPONSE. 2021 14 5601 18 RORALPHA IS CRUCIAL FOR ATTENUATED INFLAMMATORY RESPONSE TO MAINTAIN INTESTINAL HOMEOSTASIS. RETINOIC ACID-RELATED ORPHAN RECEPTOR ALPHA (RORALPHA) FUNCTIONS AS A TRANSCRIPTION FACTOR FOR VARIOUS BIOLOGICAL PROCESSES, INCLUDING CIRCADIAN RHYTHM, CANCER, AND METABOLISM. HERE, WE GENERATE INTESTINAL EPITHELIAL CELL (IEC)-SPECIFIC RORALPHA-DEFICIENT (RORALPHA(DELTAIEC)) MICE AND FIND THAT RORALPHA IS CRUCIAL FOR MAINTAINING INTESTINAL HOMEOSTASIS BY ATTENUATING NUCLEAR FACTOR KAPPAB (NF-KAPPAB) TRANSCRIPTIONAL ACTIVITY. RORALPHA(DELTAIEC) MICE EXHIBIT EXCESSIVE INTESTINAL INFLAMMATION AND HIGHLY ACTIVATED INFLAMMATORY RESPONSES IN THE DEXTRAN SULFATE SODIUM (DSS) MOUSE COLITIS MODEL. TRANSCRIPTOME ANALYSIS REVEALS THAT DELETION OF RORALPHA LEADS TO UP-REGULATION OF NF-KAPPAB TARGET GENES IN IECS. CHROMATIN IMMUNOPRECIPITATION ANALYSIS REVEALS CORECRUITMENT OF RORALPHA AND HISTONE DEACETYLASE 3 (HDAC3) ON NF-KAPPAB TARGET PROMOTERS AND SUBSEQUENT DISMISSAL OF CREB BINDING PROTEIN (CBP) AND BROMODOMAIN-CONTAINING PROTEIN 4 (BRD4) FOR TRANSCRIPTIONAL REPRESSION. TOGETHER, WE DEMONSTRATE THAT RORALPHA/HDAC3-MEDIATED ATTENUATION OF NF-KAPPAB SIGNALING CONTROLS THE BALANCE OF INFLAMMATORY RESPONSES, AND THERAPEUTIC STRATEGIES TARGETING THIS EPIGENETIC REGULATION COULD BE BENEFICIAL TO THE TREATMENT OF CHRONIC INFLAMMATORY DISEASES, INCLUDING INFLAMMATORY BOWEL DISEASE (IBD). 2019 15 3716 21 INHIBITING INFLAMMATION WITH MYELOID CELL-SPECIFIC NANOBIOLOGICS PROMOTES ORGAN TRANSPLANT ACCEPTANCE. INDUCING GRAFT ACCEPTANCE WITHOUT CHRONIC IMMUNOSUPPRESSION REMAINS AN ELUSIVE GOAL IN ORGAN TRANSPLANTATION. USING AN EXPERIMENTAL TRANSPLANTATION MOUSE MODEL, WE DEMONSTRATE THAT LOCAL MACROPHAGE ACTIVATION THROUGH DECTIN-1 AND TOLL-LIKE RECEPTOR 4 (TLR4) DRIVES TRAINED IMMUNITY-ASSOCIATED CYTOKINE PRODUCTION DURING ALLOGRAFT REJECTION. WE CONDUCTED NANOIMMUNOTHERAPEUTIC STUDIES AND FOUND THAT A SHORT-TERM MTOR-SPECIFIC HIGH-DENSITY LIPOPROTEIN (HDL) NANOBIOLOGIC TREATMENT (MTORI-HDL) AVERTED MACROPHAGE AEROBIC GLYCOLYSIS AND THE EPIGENETIC MODIFICATIONS UNDERLYING INFLAMMATORY CYTOKINE PRODUCTION. THE RESULTING REGULATORY MACROPHAGES PREVENTED ALLOREACTIVE CD8(+) T CELL-MEDIATED IMMUNITY AND PROMOTED TOLEROGENIC CD4(+) REGULATORY T (TREG) CELL EXPANSION. TO ENHANCE THERAPEUTIC EFFICACY, WE COMPLEMENTED THE MTORI-HDL TREATMENT WITH A CD40-TRAF6-SPECIFIC NANOBIOLOGIC (TRAF6I-HDL) THAT INHIBITS CO-STIMULATION. THIS SYNERGISTIC NANOIMMUNOTHERAPY RESULTED IN INDEFINITE ALLOGRAFT SURVIVAL. TOGETHER, WE SHOW THAT HDL-BASED NANOIMMUNOTHERAPY CAN BE EMPLOYED TO CONTROL MACROPHAGE FUNCTION IN VIVO. OUR STRATEGY, FOCUSED ON PREVENTING INFLAMMATORY INNATE IMMUNE RESPONSES, PROVIDES A FRAMEWORK FOR DEVELOPING TARGETED THERAPIES THAT PROMOTE IMMUNOLOGICAL TOLERANCE. 2018 16 5153 24 PPP2R2B HYPERMETHYLATION CAUSES ACQUIRED APOPTOSIS DEFICIENCY IN SYSTEMIC AUTOIMMUNE DISEASES. CHRONIC INFLAMMATION CAUSES TARGET ORGAN DAMAGE IN PATIENTS WITH SYSTEMIC AUTOIMMUNE DISEASES. THE FACTORS THAT ALLOW THIS PROTRACTED RESPONSE ARE POORLY UNDERSTOOD. WE ANALYZED THE TRANSCRIPTIONAL REGULATION OF PPP2R2B (B55SS), A MOLECULE NECESSARY FOR THE TERMINATION OF THE IMMUNE RESPONSE, IN PATIENTS WITH AUTOIMMUNE DISEASES. ALTERED EXPRESSION OF B55SS CONDITIONED RESISTANCE TO CYTOKINE WITHDRAWAL-INDUCED DEATH (CWID) IN PATIENTS WITH AUTOIMMUNE DISEASES. THE IMPAIRED UPREGULATION OF B55SS WAS CAUSED BY INFLAMMATION-DRIVEN HYPERMETHYLATION OF SPECIFIC CYTOSINES LOCATED WITHIN A REGULATORY ELEMENT OF PPP2R2B PREVENTING CTCF BINDING. THIS PHENOTYPE COULD BE INDUCED IN HEALTHY T CELLS BY EXPOSURE TO TNF-ALPHA. OUR RESULTS REVEAL A GENE WHOSE EXPRESSION IS AFFECTED BY AN ACQUIRED DEFECT, THROUGH AN EPIGENETIC MECHANISM, IN THE SETTING OF SYSTEMIC AUTOIMMUNITY. BECAUSE FAILURE TO REMOVE ACTIVATED T CELLS THROUGH CWID COULD CONTRIBUTE TO AUTOIMMUNE PATHOLOGY, THIS MECHANISM ILLUSTRATES A VICIOUS CYCLE THROUGH WHICH AUTOIMMUNE INFLAMMATION CONTRIBUTES TO ITS OWN PERPETUATION. 2019 17 374 31 AN ENDOSIRNA-BASED REPRESSION MECHANISM COUNTERACTS TRANSPOSON ACTIVATION DURING GLOBAL DNA DEMETHYLATION IN EMBRYONIC STEM CELLS. ERASURE OF DNA METHYLATION AND REPRESSIVE CHROMATIN MARKS IN THE MAMMALIAN GERMLINE LEADS TO RISK OF TRANSCRIPTIONAL ACTIVATION OF TRANSPOSABLE ELEMENTS (TES). HERE, WE USED MOUSE EMBRYONIC STEM CELLS (ESCS) TO IDENTIFY AN ENDOSIRNA-BASED MECHANISM INVOLVED IN SUPPRESSION OF TE TRANSCRIPTION. IN ESCS WITH DNA DEMETHYLATION INDUCED BY ACUTE DELETION OF DNMT1, WE SAW AN INCREASE IN SENSE TRANSCRIPTION AT TES, RESULTING IN AN ABUNDANCE OF SENSE/ANTISENSE TRANSCRIPTS LEADING TO HIGH LEVELS OF ARGONAUTE2 (AGO2)-BOUND SMALL RNAS. INHIBITION OF DICER OR AGO2 EXPRESSION REVEALED THAT SMALL RNAS ARE INVOLVED IN AN IMMEDIATE RESPONSE TO DEMETHYLATION-INDUCED TRANSPOSON ACTIVATION, WHILE THE DEPOSITION OF REPRESSIVE HISTONE MARKS FOLLOWS AS A CHRONIC RESPONSE. IN VIVO, WE ALSO FOUND TE-SPECIFIC ENDOSIRNAS PRESENT DURING PRIMORDIAL GERM CELL DEVELOPMENT. OUR RESULTS SUGGEST THAT ANTISENSE TE TRANSCRIPTION IS A "TRAP" THAT ELICITS AN ENDOSIRNA RESPONSE TO RESTRAIN ACUTE TRANSPOSON ACTIVITY DURING EPIGENETIC REPROGRAMMING IN THE MAMMALIAN GERMLINE. 2017 18 568 21 BATF REGULATES PROGENITOR TO CYTOLYTIC EFFECTOR CD8(+) T CELL TRANSITION DURING CHRONIC VIRAL INFECTION. DURING CHRONIC VIRAL INFECTION, CD8(+) T CELLS DEVELOP INTO THREE MAJOR PHENOTYPICALLY AND FUNCTIONALLY DISTINCT SUBSETS: LY108(+)TCF-1(+) PROGENITORS, LY108(-)CX(3)CR1(-) TERMINALLY EXHAUSTED CELLS AND THE RECENTLY IDENTIFIED CX(3)CR1(+) CYTOTOXIC EFFECTOR CELLS. NEVERTHELESS, HOW CX(3)CR1(+) EFFECTOR CELL DIFFERENTIATION IS TRANSCRIPTIONALLY AND EPIGENETICALLY REGULATED REMAINS ELUSIVE. HERE, WE IDENTIFY DISTINCT GENE REGULATORY NETWORKS AND EPIGENETIC LANDSCAPES UNDERPINNING THE FORMATION OF THESE SUBSETS. NOTABLY, OUR DATA DEMONSTRATE THAT CX(3)CR1(+) EFFECTOR CELLS BEAR A STRIKING SIMILARITY TO SHORT-LIVED EFFECTOR CELLS DURING ACUTE INFECTION. GENETIC DELETION OF TBX21 SIGNIFICANTLY DIMINISHED FORMATION OF THE CX(3)CR1(+) SUBSET. IMPORTANTLY, WE FURTHER IDENTIFY A PREVIOUSLY UNAPPRECIATED ROLE FOR THE TRANSCRIPTION FACTOR BATF IN MAINTAINING A PERMISSIVE CHROMATIN STRUCTURE THAT ALLOWS THE TRANSITION FROM TCF-1(+) PROGENITORS TO CX(3)CR1(+) EFFECTOR CELLS. BATF DIRECTLY BOUND TO REGULATORY REGIONS NEAR TBX21 AND KLF2, MODULATING THEIR ENHANCER ACCESSIBILITY TO FACILITATE THE TRANSITION. THESE MECHANISTIC INSIGHTS CAN POTENTIALLY BE HARNESSED TO OVERCOME T CELL EXHAUSTION DURING CHRONIC INFECTION AND CANCER. 2021 19 370 23 AN APICOMPLEXAN BROMODOMAIN PROTEIN, TGBDP1, ASSOCIATES WITH DIVERSE EPIGENETIC FACTORS TO REGULATE ESSENTIAL TRANSCRIPTIONAL PROCESSES IN TOXOPLASMA GONDII. THE PROTOZOAN PATHOGEN TOXOPLASMA GONDII RELIES ON TIGHT REGULATION OF GENE EXPRESSION TO INVADE AND ESTABLISH INFECTION IN ITS HOST. THE DIVERGENT GENE REGULATORY MECHANISMS OF TOXOPLASMA AND RELATED APICOMPLEXAN PATHOGENS RELY HEAVILY ON REGULATORS OF CHROMATIN STRUCTURE AND HISTONE MODIFICATIONS. THE IMPORTANT CONTRIBUTION OF HISTONE ACETYLATION FOR TOXOPLASMA IN BOTH ACUTE AND CHRONIC INFECTION HAS BEEN DEMONSTRATED, WHERE HISTONE ACETYLATION INCREASES AT ACTIVE GENE LOCI. HOWEVER, THE DIRECT CONSEQUENCES OF SPECIFIC HISTONE ACETYLATION MARKS AND THE CHROMATIN PATHWAY THAT INFLUENCES TRANSCRIPTIONAL REGULATION IN RESPONSE TO THE MODIFICATION ARE UNCLEAR. AS A READER OF LYSINE ACETYLATION, THE BROMODOMAIN SERVES AS A MEDIATOR BETWEEN THE ACETYLATED HISTONE AND TRANSCRIPTIONAL REGULATORS. HERE WE SHOW THAT THE BROMODOMAIN PROTEIN, TGBDP1, WHICH IS CONSERVED AMONG APICOMPLEXA AND WITHIN THE ALVEOLATA SUPERPHYLUM, IS ESSENTIAL FOR TOXOPLASMA ASEXUAL PROLIFERATION. USING CLEAVAGE UNDER TARGETS AND TAGMENTATION, WE DEMONSTRATE THAT TGBDP1 IS RECRUITED TO TRANSCRIPTIONAL START SITES OF A LARGE PROPORTION OF PARASITE GENES. TRANSCRIPTIONAL PROFILING DURING TGBDP1 KNOCKDOWN REVEALED THAT LOSS OF TGBDP1 LEADS TO MAJOR DYSREGULATION OF GENE EXPRESSION, IMPLYING MULTIPLE ROLES FOR TGBDP1 IN BOTH GENE ACTIVATION AND REPRESSION. THIS IS SUPPORTED BY INTERACTOME ANALYSIS OF TGBDP1 DEMONSTRATING THAT TGBDP1 FORMS A CORE COMPLEX WITH TWO OTHER BROMODOMAIN PROTEINS AND AN APIAP2 FACTOR. THIS CORE COMPLEX APPEARS TO INTERACT WITH OTHER EPIGENETIC FACTORS SUCH AS NUCLEOSOME REMODELING COMPLEXES. WE CONCLUDE THAT TGBDP1 INTERACTS WITH DIVERSE EPIGENETIC REGULATORS TO EXERT OPPOSING INFLUENCES ON GENE EXPRESSION IN THE TOXOPLASMA TACHYZOITE. IMPORTANCE HISTONE ACETYLATION IS CRITICAL FOR PROPER REGULATION OF GENE EXPRESSION IN THE SINGLE-CELLED EUKARYOTIC PATHOGEN TOXOPLASMA GONDII. BROMODOMAIN PROTEINS ARE "READERS" OF HISTONE ACETYLATION AND MAY LINK THE MODIFIED CHROMATIN TO TRANSCRIPTION FACTORS. HERE, WE SHOW THAT THE BROMODOMAIN PROTEIN TGBDP1 IS ESSENTIAL FOR PARASITE SURVIVAL AND THAT LOSS OF TGBDP1 RESULTS IN GLOBAL DYSREGULATION OF GENE EXPRESSION. TGBDP1 IS RECRUITED TO THE PROMOTER REGION OF A LARGE PROPORTION OF PARASITE GENES, FORMS A CORE COMPLEX WITH TWO OTHER BROMODOMAIN PROTEINS, AND INTERACTS WITH DIFFERENT TRANSCRIPTIONAL REGULATORY COMPLEXES. WE CONCLUDE THAT TGBDP1 IS A KEY FACTOR FOR SENSING SPECIFIC HISTONE MODIFICATIONS TO INFLUENCE MULTIPLE FACETS OF TRANSCRIPTIONAL REGULATION IN TOXOPLASMA GONDII. 2023 20 3384 23 HOFBAUER CELLS: THEIR ROLE IN HEALTHY AND COMPLICATED PREGNANCY. HOFBAUER CELLS ARE PLACENTAL VILLOUS MACROPHAGES OF FETAL ORIGIN THAT ARE PRESENT THROUGHOUT PREGNANCY. ALTHOUGH HOFBAUER CELL POPULATIONS ARE ANTIGENICALLY AND MORPHOLOGICALLY HETEROGENEOUS, THEIR EPIGENETIC, ANTIGENIC, AND FUNCTIONAL PROFILES MOST CLOSELY RESEMBLE ALTERNATIVELY ACTIVATED MACROPHAGES OR WHAT ARE REFERRED TO AS M2A, M2B, M2C, AND M2D POLARITY SUBTYPES. CONSISTENT WITH AN M2-LIKE PROFILE, THESE CELLS PLAY AN IMPORTANT ROLE IN PLACENTAL DEVELOPMENT INCLUDING VASCULOGENESIS AND ANGIOGENESIS. DURING PLACENTAL INFLAMMATION HOFBAUER CELLS MAY PRODUCE PRO-INFLAMMATORY CYTOKINES OR MEDIATORS THAT DAMAGE THE VILLOUS CELL BARRIER, AND INDUCE FIBROTIC RESPONSES WITHIN THE VILLI AS A CONTINUUM OF CHRONIC INFLAMMATION. HOWEVER, TO DATE, THERE IS NO EVIDENCE THAT HOFBAUER CELLS BECOME CLASSICALLY ACTIVATED OR ADOPT AN M1 POLARITY PHENOTYPE THAT IS ABLE TO KILL MICROBES. TO THE CONTRARY, THEIR PREDOMINANT M2 LIKE QUALITIES MAY BE WHY THESE CELLS ARE INEFFECTIVE IN CONTROLLING MOST TORCH INFECTIONS. MOREOVER, HOFBAUER CELLS MAY CONTRIBUTE TO VERTICAL TRANSMISSION OF VARIOUS PATHOGENS TO THE FETUS SINCE THEY CAN HARBOR LIVE VIRUS AND SERVE AS RESERVOIRS WITHIN THE PLACENTA. THE GOAL OF THIS REVIEW IS TO SUMMARIZE WHAT IS CURRENTLY KNOWN ABOUT THE ROLE OF HOFBAUER CELLS IN NORMAL AND COMPLICATED PREGNANCIES THAT INVOLVE IMMUNOLOGIC DISORDERS, INFLAMMATION, AND/OR INFECTION. 2018