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The oral mucosa is the first site of SARS-CoV-2 entry and replication, and it plays a central role in the early defense against infection. Thus, the SARS-CoV-2 viral load, miRNAs, cytokines, and neutralizing activity (NA) were assessed in saliva and plasma from mild (MD) and severe (SD) COVID-19 patients. Here we showed that of the 84 miRNAs analyzed, 8 were differently expressed in the plasma and saliva of SD patients. In particular: (1) miRNAs let-7a-5p, let-7b-5p, and let-7c-5p were significantly downregulated; and (2) miR-23a and b and miR-29c, as well as three immunomodulatory miRNAs (miR-34a-5p, miR-181d-5p, and miR-146) were significantly upregulated. The production of pro-inflammatory cytokines (IL-1β, IL-2, IL-6, IL-8, IL-9, and TNFα) and chemokines (CCL2 and RANTES) increased in both the saliva and plasma of SD and MD patients. Notably, disease severity correlated with NA and immune activation. Monitoring these parameters could help predict disease outcomes and identify new markers of disease progression.

Primary non-functional pancreatic neuroendocrine tumors (NF-PanNETs) are a heterogeneous group of neuroendocrine neoplasms that display highly variable clinical behavior. Therefore, NF-PanNETs often present clinical teams with a dilemma: the uncertain metastatic potential of the tumor has to be weighed against the morbidity associated with surgical resection. Thus, rather than utilizing current radiologic thresholds, there is an urgent need for improved prognostic biomarkers. Recent studies aimed at understanding the epigenetic underpinnings of NF-PanNETs have led to the identification of tumor subgroups based on histone modification and DNA methylation patterns. These molecular profiles tend to resemble the cellular origins of PanNETs. Subsequent retrospective analyses have demonstrated that these molecular signatures are of prognostic value and, importantly, may be useful in the preoperative setting. These studies have highlighted that sporadic NF-PanNETs displaying biomarkers associated with disease progression and poor prognosis, such as alternative lengthening of telomeres, inactivating alpha thalassemia/mental retardation X-linked (ATRX) or death domain-associated protein (DAXX) gene mutations, or copy number variations, more often display alpha cell characteristics. Conversely, NF-PanNETs with beta cell characteristics often lack these unfavorable biomarkers. Alternative lengthening of telomeres, transcription factor protein expression, and possibly DNA methylation can be assessed in endoscopic ultrasound-guided tumor biopsies. Prospective studies focusing on cell-of-origin and epigenetic profile-driven decision making prior to surgery are likely to be routinely implemented into clinical practice in the near future. © 2021 The Authors. The Journal of Pathology published by John WileySons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Made available in DSpace on 2022-04-28T19:43:12Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-01 Background: Mesenchymal cells’ biology has been an important investigative tool to maximize bone regeneration through tissue engineering. Here we used mesenchymal cells from periodontal ligament (PDLCs) with high (h-) and low (l-) osteogenic potential, isolated from different donors, to investigate the impact of the individual epigenetic and transcriptional profiles on the osteogenic potential. Methods: Genome-wide and gene-specific DNA (hydroxy) methylation, mRNA expression and immunofluorescence analysis were carried out in h- and l-PDLCs at DMEM (non-induced to osteogenesis) and OM (induced—3rd and 10th days of osteogenic differentiation) groups in vitro. Results: Genome-wide results showed distinct epigenetic profile among PDLCs with most of the differences on 10th day of OM; DMEMs showed higher concentrations (xOM) of differentially methylated probes in gene body, intronic and open sea (3rd day), increasing this concentration in TSS200 and island regions, at 10 days. At basal levels, h- and l-PDLCs showed different transcriptional profiles; l-PDLCs demonstrated higher levels of NANOG/OCT4/SOX2, BAPX1, DNMT3A, TET1/3, and lower levels of RUNX2 transcripts, confirmed by NANOG/OCT4 and RUNX2 immunofluorescence. After osteogenic induction, the distinct transcriptional profile of multipotentiality genes was maintained among PDLCs. In l-PDLCs, the anti-correlation between DNA methylation and gene expression in RUNX2 and NANOG indicates methylation could play a role in modulating both transcripts. Conclusions: Epigenetic and transcriptional distinct profiles detected at basal levels among PDLCs were maintained after osteogenic induction. We cannot discard the existence of a complex that represses osteogenesis, suggesting the individual donors’ characteristics have significant impact on the osteogenic phenotype acquisition. School of Dentistry Health Science Institute Paulista University Department of Prosthodontics and Periodontics Piracicaba Dental School University of Campinas Department of Chemical and Biological Sciences Institute of Biosciences São Paulo State University Department of Dentistry University of Taubaté Program in Environmental and Experimental Pathology Paulista University Department of Chemical and Biological Sciences Institute of Biosciences São Paulo State University

To investigate whether epigenetic profiles of mural granulosa cells (MGC) and leukocytes from women with diminished ovarian reserve (DOR) differ from those of women with normal or high ovarian reserve.Prospectively collected material from a multicenter cohort of women undergoing fertility treatment.Private and university-based facilities for clinical services and research.One hundred and nineteen women of various ages and ovarian reserve status (antimüllerian hormone level) who provided blood samples and MGC.None.Measures of epigenetic aging rates from whole-genome methylation array data: DNA methylation variability, age acceleration, DNA methylation telomere length estimator (DNAmTL), and accumulation of epimutations.Comparison of DOR or high ovarian reserve samples to controls (normal ovarian reserve) showed differential methylation variability between DOR and normal samples at 4,199 CpGs in MGC, and 447 between high and normal (false-discovery rate0.05). Variable sites in MGC from DOR were enriched in regions marked with the repressive histone modification H3K27me3, and also included genes involved in folliculogenesis, such as insulin growth factor 2 (IGF2) and antimüllerian hormone (AMH). Regardless of ovarian reserve, very few signals were detected in leukocytes, and no overlaps with those in MGC were found. Furthermore, we found a higher number of epimutations in MGC from women with DOR (Kruskal-Wallis test, difference in mean = 3,485).The somatic cells of human ovarian follicles have a distinctive epigenetic profile in women with DOR. A high frequency of epimutations suggests premature aging. Ovarian reserve status was not reflected in the leukocyte epigenetic profile.

Background The brain of chronically ventilated preterm human infants is vulnerable to collateral damage during invasive mechanical ventilation (IMV). Damage is manifest, in part, by learning and memory impairments, which are hippocampal functions. A molecular regulator of hippocampal development is insulin-like growth factor 1 (IGF1). A gentler ventilation strategy is noninvasive respiratory support (NRS). We tested the hypotheses that NRS leads to greater levels of IGF1 messenger RNA (mRNA) variants and distinct epigenetic profile along the IGF1 gene locus in the hippocampus compared to IMV. Methods Preterm lambs were managed by NRS or IMV for 3 or 21 days. Isolated hippocampi were analyzed for IGF1 mRNA levels and splice variants for promoter 1 (P1), P2, and IGF1A and 1B, DNA methylation in P1 region, and histone covalent modifications along the gene locus. Results NRS had significantly greater levels of IGF1 P1 (predominant transcript), and 1A and 1B mRNA variants compared to IMV at 3 or 21 days. NRS also led to more DNA methylation and greater occupancy of activating mark H3K4 trimethylation (H3K4me3), repressive mark H3K27me3, and elongation mark H3K36me3 compared to IMV. Conclusions NRS leads to distinct IGF1 mRNA variant levels and epigenetic profile in the hippocampus compared to IMV. Impact Our study shows that 3 or 21 days of NRS of preterm lambs leads to distinct IGF1 mRNA variant levels and epigenetic profile in the hippocampus compared to IMV. Preterm infant studies suggest that NRS leads to better neurodevelopmental outcomes later in life versus IMV. Also, duration of IMV is directly related to hippocampal damage; however, molecular players remain unknown. NRS, as a gentler mode of respiratory management of preterm neonates, may reduce damage to the immature hippocampus through an epigenetic mechanism.

Introduction: DNA methylation constitutes one important epigenetic mechanism that regulates gene expression in human cells. With regard to obesity, bariatric surgery-induced weight loss has been associated with promoter methylation changes in several genes. Hyperleptinemia is a characteristic feature of obesity. The underlying regulating mechanisms have not yet been completely elucidated. Methods: We investigated the methylation of the promoters of the leptin gene (LEP) and the leptin receptor gene (LEPR) as well as leptin expression in pre- and postbariatric surgery patients using a comparative cross-sectional design. Results: Our results revealed significantly higher LEP promoter methylation patterns in prebariatric surgery patients compared to postoperatively. DNA methylation of the LEPR promoter was significantly higher in the postoperative group. Moreover, we found significantly higher leptin serum levels in patients before the bariatric surgery than afterwards. Discussion: These findings strengthen the suggestion that there is an association between LEP expression and LEP methylation in obesity. We suggest that the epigenetic profile of LEP might be influenced by leptin serum levels in the form of a regulating feedback mechanism.

Alzheimer disease (AD) is the primary form of dementia that occurs spontaneously in older adults. Interestingly, the epigenetic profile of the cells forming the central nervous system changes during aging and may contribute to the progression of some neurodegenerative diseases such as AD. In this review, we present general insights into relevant epigenetic mechanisms and their relationship with aging and AD. The data suggest that some epigenetic changes during aging could be utilized as biomarkers and target molecules for the prevention and control of AD.

Amaç: Çalışmanın amacı mesane tümörlü hastalarda ve sağlıklı kontrollerde protokaderin gen ailesine ait olan protokaderin 8 (PCDH8), protokaderin 10 (PCDH10) ve protokaderin 17 (PCDH17) genlerinin periferal kan DNA metilasyon profillerini analiz ederek bu profillerin tümör-spesifik olası etkilerini değerlendirmektir. Araştırılan üç genin metilasyon profiliyle spesifik demografik ve/veya klinikopatolojik veriler arasındaki olası ilişkinin araştırılması da çalışmanın ikinci hedefidir.Gereç ve Yöntemler: Mesane karsinomalı (n=80; düşük dereceli: 40, yüksek dereceli: 40) ve sağlıklı kontrollerin (n=40) periferal kan örneklerinden ekstrakte edilen genomik DNA promotor bölgelerinin hipermetilasyon analizi için bisülfit modifikasyon ve metilasyon-spesifik PCR işlemine maruz bırakılmıştır.Bulgular: PCDH8 metilasyon profilinin yaşla birlikte artış gösterdiği gözlenmiştir. Neredeyse kontrollerin tamamında da bu genler bakımından kısmi metilasyon profilleri belirlendiği için hasta örneklerindeki PCDH10 ve PCDH17 metilasyon paternleri bir farklılık oluşturmamakla beraber PCDH8 daha farklı bir kan epigenetik profili sergilemiştir.Sonuç: PCDH8 geninin kandaki metilasyon modelinin yaşlanma süreciyle ilişkisi çalışmamızda gösterilmiştir. Mesane kanserindeki etkisi açısından daha kesin bir sonuca varabilmek için PCDH8’in kandaki metilasyon durumunun daha yüksek sayılı kohortta ve MethyLight gibi daha duyarlı metotlarla araştırılmasını tavsiye etmekteyiz.

The gut microbiota has an extremely important role within the body and it is necessary for the regulation of the metabolism of the host and also for the development of metabolic diseases such as obesity. Here, we show several different factors leading to obesity such as epigenetic changes and how they result in differences to occur in the gut microbiota, along with gut dysbiosis which is caused by disturbances in the microbiota homeostasis. Several studies have been explained in this paper, providing evidence in how these findings can actually decrease the susceptibility of obesity, whether it be by changing an individual's diet pattern or observing the epigenetic changes which are taking place. KEY POINTS: • The microbiota depends on an individual's diet, lifestyle, environment, genetics and epigenetic profile. • Changes of the gut microbiota can increase obesity susceptibility. • Non-coding RNA has an important role in the metabolic homeostasis in check so if a disturbance occurs it can lead to resistance to obesity.

Translocations of the KMT2A (MLL) gene define a biologically distinct and clinically aggressive subtype of acute myeloid leukaemia (AML), marked by a characteristic gene expression profile and few cooperating mutations. Although dysregulation of the epigenetic landscape in this leukaemia is particularly interesting given the low mutation frequency, its comprehensive analysis using whole genome bisulphite sequencing (WGBS) has not been previously performed. Here we investigated epigenetic dysregulation in nine MLL-rearranged (MLL-r) AML samples by comparing them to six normal myeloid controls, using a computational method that encapsulates mean DNA methylation measurements along with analyses of methylation stochasticity. We discovered a dramatically altered epigenetic profile in MLL-r AML, associated with genome-wide hypomethylation and a markedly increased DNA methylation entropy reflecting an increasingly disordered epigenome. Methylation discordance mapped to key genes and regulatory elements that included bivalent promoters and active enhancers. Genes associated with significant changes in methylation stochasticity recapitulated known MLL-r AML expression signatures, suggesting a role for the altered epigenetic landscape in the transcriptional programme initiated by MLL translocations. Accordingly, we established statistically significant associations between discordances in methylation stochasticity and gene expression in MLL-r AML, thus providing a link between the altered epigenetic landscape and the phenotype.

Cancer stem cells (CSC) can be identified by modifications in their genomic DNA. Here, we report a concept of precisely shrinking an organic semiconductor surface-enhanced Raman scattering (SERS) probe to quantum size, for investigating the epigenetic profile of CSC. The probe is used for tag-free genomic DNA detection, an approach towards the advancement of single-molecule DNA detection. The sensor detected structural, molecular and gene expression aberrations of genomic DNA in femtomolar concentration simultaneously in a single test. In addition to pointing out the divergences in genomic DNA of cancerous and non-cancerous cells, the quantum scale organic semiconductor was able to trace the expression of two genes which are frequently used as CSC markers. The quantum scale organic semiconductor holds the potential to be a new tool for label-free, ultra-sensitive multiplexed genomic analysis., The low detection sensitivity of organic semiconductors has limited their use in biomedical surface-enhanced Raman scattering applications. Here, the authors use quantum scale organic semiconductors and show detection of genomic DNA methylation as well as gene expression.

Exposure to bisphenol A (BPA) has been related to male reproductive disorders. Since this endocrine disruptor also displays genotoxic and epigenotoxic effects, it likely alters the spermatogenesis, a process in which both hormones and chromatin remodeling play crucial roles. The hypothesis of this work is that BPA impairs early embryo development by modifying the spermatic genetic and epigenetic information. Zebrafish males were exposed to 100 and 2000 μg/L BPA during early spermatogenesis and during the whole process. Genotoxic and epigenotoxic effects on spermatozoa (comet assay and immunocytochemistry) as well as progeny development (mortality, DNA repairing activity, apoptosis and epigenetic profile) were evaluated. Exposure to 100 µg/L BPA during mitosis slightly increased sperm chromatin fragmentation, enhancing DNA repairing activity in embryos. The rest of treatments promoted high levels of sperm DNA damage, triggering apoptosis in early embryo and severely impairing survival. Regarding epigenetics, histone acetylation (H3K9Ac and H3K27Ac) was similarly enhanced in spermatozoa and embryos from males exposed to all the treatments. Therefore, BPA male exposure jeopardizes embryonic survival and development due to the transmission of a paternal damaged genome and of a hyper-acetylated histone profile, both alterations depending on the dose of the toxicant and the temporal window of exposure.

How the local inflammatory environment regulates epigenetic changes in the context of autoimmune diseases remains unclear. Here we assessed the transcriptional and active enhancer profile of monocytes derived from the inflamed joints of Juvenile Idiopathic Arthritis (JIA) patients, a model well-suited for studying autoimmune diseases. RNA-sequencing analysis demonstrated that synovial-derived monocytes display an activated phenotype, characterized by increased expression of surface activation markers and multiple chemokines and cytokines. This increased expression is regulated on the epigenetic level, as ChIP-sequencing indicated increased H3K27 acetylation of genes upregulated in synovial monocytes. IFN signaling-associated genes are increased and epigenetically altered in synovial monocytes, suggesting a role for IFN in establishing the inflammatory phenotype. Treatment of human synovial monocytes with the Janus-associated kinase (JAK) inhibitor Ruxolitinib, which inhibits IFN signaling, transformed the activated enhancer landscape and reduced disease-associated gene expression, thereby inhibiting the inflammatory phenotype. Taken together, these data provide novel insight into epigenetic regulation of autoimmune disease-patient derived monocytes and suggest that altering the epigenetic profile can be a therapeutic approach for the treatment of autoimmune diseases.

Environmental stimuli, including sex hormones and oxidative stress (OS), affect bone balance, modifying the epigenetic profiles of key osteogenic genes. Nonetheless, the interplay between sex steroids, epigenome and OS has yet be fully elucidated. This paper aims to study in vitro the role of sex steroids in OS-induced alteration in bone cells’ homeostasis, and to assess the possible contribution of epigenetic modifications. Toward this purpose, osteoblast (MC3T3-E1) and osteocyte (MLOY-4) cell lines were exposed to two different sources of free oxygen radicals, i.e., tert-butyl hydroperoxide and dexamethasone, and the protective effect of pre-treatment with androgens and estrogens was evaluated. In particular, we analyzed parameters that reflect bone cell homeostasis such as cell viability, cell migration, transcriptomic profile, transcriptional activity, and epigenetic signature. Our findings indicate that estrogens and androgens counteract OS effects. Using partially overlapping strategies, they reduce OS outcomes regarding cell viability, cell migration, the transcriptomic profile of gene families involved in bone remodeling, and epigenetic profile, i.e., H3K4me3 level. Additionally, we demonstrated that the protective effect of steroids against OS on bone homeostasis is partially mediated by the Akt pathway. Overall, these results suggest that the hormonal milieu may influence the mechanisms of age-related bone disease.

BackgroundObesity is a major risk factor for dysglycemic disorders, including type 2 diabetes (T2D). However, there is wide phenotypic variation in metabolic profiles. Tissue-specific epigenetic modifications could be partially accountable for the observed phenotypic variability.ScopeThe aim of this systematic review was to summarize the available data on epigenetic signatures in human adipose tissue (AT) that characterize overweight or obesity-related insulin resistance (IR) and dysglycemia states and to identify potential underlying mechanisms through the use of unbiased bioinformatics approaches.MethodsOriginal data published in the last decade concerning the comparison of epigenetic marks in human AT of individuals with metabolically unhealthy overweight/obesity (MUHO) versus normal weight individuals or individuals with metabolically healthy overweight/obesity (MHO) was assessed. Furthermore, association of these epigenetic marks with IR/dysglycemic traits, including T2D, was compiled.ResultsWe catalogued more than two thousand differentially methylated regions (DMRs; above the cut-off of 5%) in the AT of individuals with MUHO compared to individuals with MHO. These DNA methylation changes were less likely to occur around the promoter regions and were enriched at loci implicated in intracellular signaling (signal transduction mediated by small GTPases, ERK1/2 signaling and intracellular trafficking). We also identified a network of seven transcription factors that may play an important role in targeting DNA methylation changes to specific genes in the AT of subjects with MUHO, contributing to the pathogeny of obesity-related IR/T2D. Furthermore, we found differentially methylated CpG sites at 8 genes that were present in AT and whole blood, suggesting that DMRs in whole blood could be potentially used as accessible biomarkers of MUHO.ConclusionsThe overall evidence linking epigenetic alterations in key tissues such AT to metabolic complications in human obesity is still very limited, highlighting the need for further studies, particularly those focusing on epigenetic marks other than DNA methylation. Our initial analysis suggests that DNA methylation patterns can potentially discriminate between MUHO from MHO and provide new clues into why some people with obesity are less susceptible to dysglycemia. Identifying AT-specific epigenetic targets could also lead to novel approaches to modify the progression of individuals with obesity towards metabolic disease.Systematic Review RegistrationPROSPERO, identifier CRD42021227237.

Drug addiction results in part from maladaptive learning, including the formation of strong associations between the drug and the circumstances of consumption. However, drug-induced changes in gene expression underlying the saliency of these associations remain understudied. Consolidation of explicit memories occurs within the hippocampus, and we have shown that spatial learning induces expression of the transcription factor ΔFosB in hippocampus and that this induction is critical for learning. Drugs of abuse also upregulate ΔFosB in hippocampus, but the mechanism of its induction by cocaine and its role in hippocampus-dependent cocaine responses is unknown. We investigated differences in mouse dorsal and ventral hippocampal ΔFosB expression in response to chronic cocaine, because these regions appear to regulate distinct cocaine-related behaviors. We found that cocaine-mediated induction of ΔFosB was subregion-specific, and that ΔFosB transcriptional activity in both the dorsal and ventral hippocampus is necessary for cocaine conditioned place preference. Further, we characterize changes in histone modifications at theFosBpromoter in hippocampus in response to chronic cocaine and found that locus-specific epigenetic modification is essential forFosBinduction and multiple hippocampus-dependent behaviors, including cocaine place preference. Collectively, these findings suggest that exposure to cocaine induces histone modification at the hippocampalFosBgene promoter to cause ΔFosB induction critical for cocaine-related learning.SIGNIFICANCE STATEMENTAlthough cocaine addiction is driven in part by the formation of indelible associations between the drug and the environment, paraphernalia, and circumstances of use, and although this type of associative learning is dependent upon changes in gene expression in a brain region called the hippocampus, the mechanisms by which cocaine alters hippocampal gene expression to drive formation of these associations is poorly understood. Here, we demonstrate that chronic cocaine engages locus-specific changes in the epigenetic profile of theFosBgene in the hippocampus, and that these alterations are required for cocaine-dependent gene expression and cocaine–environment associations. This work provides novel insight into addiction etiology and potential inroads for therapeutic intervention in cocaine addiction.

Caspase-10 belongs to the class of initiator caspases and is a close homolog of caspase-8. However, the lack of caspase-10 in mice and limited substrate repertoire restricts the understanding of its physiological functions. Here, we report that ATP-citrate lyase (ACLY) is a caspase-10 substrate. Caspase-10 cleaves ACLY at the conserved Asp1026 site under conditions of altered metabolic homeostasis. Cleavage of ACLY abrogates its enzymatic activity and suppresses the generation of acetyl-CoA, which is critical for lipogenesis and histone acetylation. Thus, caspase-10-mediated ACLY cleavage results in reduced intracellular lipid levels and represses GCN5-mediated histone H3 and H4 acetylation. Furthermore, decline in GCN5 activity alters the epigenetic profile, resulting in downregulation of proliferative and metastatic genes. Thus caspase-10 suppresses ACLY-promoted malignant phenotype. These findings expand the substrate repertoire of caspase-10 and highlight its pivotal role in inhibiting tumorigenesis through metabolic and epigenetic mechanisms., Caspases are most closely associated with cell death, but many have other cellular functions. Here, Das et al. find that upon metabolic stress, caspase-10 cleaves ACLY to regulate metabolic homeostasis and epigenetic reprogramming by altering Acetyl-CoA levels.

AIM: To investigate the degree by which epigenetic signatures in children from mothers with gestational diabetes mellitus (GDM) are influenced by environmental factors.METHODS: We profiled the DNA methylation signature of blood from lean, obese and GDM mothers and their respective newborns.RESULTS: DNA methylation profiles of mothers showed high similarity across groups, while newborns from GDM mothers showed a marked distinct epigenetic profile compared with newborns of both lean and obese mothers. Analysis of variance in DNA methylation levels between newborns showed higher variance in the GDM group.CONCLUSION: Our results suggest that environmental factors, rather than direct transmission of epigenetic marks from the mother, are involved in establishing the epigenetic signature associated with GDM.CLINICAL TRIAL REGISTRATION NUMBER: Dnr 402-08.

Disruption of epigenetic mechanisms has been intimately linked to the etiology of human cancer. Understanding how these epigenetic mechanisms (including DNA methylation (5mC), hydroxymethylation (5hmC), and histone post-translational modifications) work in concert to drive cancer initiation and progression still remains unknown. Hepatocellular carcinoma (HCC) is increasing in frequency in western countries but lacks efficacious treatments. The epigenome of HCC remains understudied. To better understand the epigenetic underpinnings of HCC, we performed a genome-wide assessment of 5mC, 5hmC, four histone modifications linked to promoter/enhancer function (H3K4me1, H3K27ac, H3K4me3, and H3K27me3), and transcription across normal, cirrhotic, and HCC liver tissue. Implementation of bioinformatic strategies integrated these epigenetic marks with each other and with transcription to provide a comprehensive epigenetic profile of how and when the liver epigenome is perturbed during progression to HCC. Our data demonstrate significant deregulation of epigenetic regulators combined with disruptions in the epigenome hallmarked by profound loss of 5hmC, locus-specific gains in 5mC and 5hmC, and markedly altered histone modification profiles, particularly remodeling of enhancers. Data integration demonstrates that these marks collaborate to influence transcription (e.g. hyper-5hmC in HCC-gained active enhancers is linked to elevated expression) of genes regulating HCC proliferation. Two such putative epigenetic driver loci identified through our integrative approach, COMT and FMO3, increase apoptosis and decrease cell viability in liver-derived cancer cell lines when ectopically re-expressed. CONCLUSION: Altogether, integration of multiple epigenetic parameters is a powerful tool for identifying epigenetically regulated drivers of HCC and elucidating how epigenome deregulation contributes to liver disease and HCC.

Endometriosis, which has been considered an epigenetic disease, is a prevalent gynecological disorder worldwide. With an emphasis on changes in the HOXA10 gene expression of the endometrium of women with endometriosis, the aim of this study was to investigate HOXA10 gene expression and its correlation with the epigenetic characteristics of the specific promoter region of the gene in the eutopic and ectopic endometrium of women with endometriosis. Thirty-six patients and 21 healthy fertile women were recruited as participants of this study. In this study group, chromatin immunoprecipitation and real-time polymerase chain reaction technique were performed to quantify the epigenetic profile of HOXA10, parallel to its expression. During the secretory phase in eutopic tissues, reduction in HOXA10 gene expression was identified along with lower acetylation and higher methylation of H3K9 as well as higher incorporation of MeCP2 on the HOXA10 gene promoter. In contrast with control group, studies of ectopic endometriotic lesions in the secretory phase demonstrate a correlation between induction of HOXA10 gene and higher levels of H3K9ac, H3K27me3, and H3K4me3 in the promoter region of the HOXA10 gene. Further distinctions from the control group were revealed in the proliferative phase of the ectopic endometrium, where upregulation of HOXA10 coincided with lower incorporation of MeCP2 and higher levels of H3K4me3 in the promoter region. Since it is well known that aberrant expression of HOXA10 is involved in pathogenesis of the endometrium, our data emphasized the epigenetic role of this gene aberration related to clinical pathophysiology of endometriosis.

BACKGROUNDSpermatozoa acquire their motility and fertilizing abilities during their maturation through the epididymis. This process is controlled by epididymal epithelial cells that possess features adapted to sense and respond to their surrounding environment and to communicate with spermatozoa. During the past decade, new intercellular communication processes have been discovered, including the secretion and transport of molecules from the epithelium to spermatozoa via extracellular vesicles (EVs), as well as sensing of the intraluminal milieu by cellular extensions.OBJECTIVE AND RATIONALEThis review addresses recent findings regarding epididymal epithelial cell features and interactions between spermatozoa and the epididymal epithelium as well as epigenetic modifications undergone by spermatozoa during transit through the epididymal microenvironment.SEARCH METHODSA systematic search was conducted in Pubmed with the keyword ‘epididymis’. Results were filtered on original research articles published from 2009 to 2021 and written in the English language. One hundred fifteen original articles presenting recent advancements on the epididymis contribution to sperm maturation were selected. Some additional papers cited in the primary reference were also included. A special focus was given to higher mammalian species, particularly rodents, bovines and humans, that are the most studied in this field.OUTCOMESThis review provides novel insights into the contribution of epididymal epithelium and EVs to post-testicular sperm maturation. First, new immune cell populations have been described in the epididymis, where they are proposed to play a role in protecting the environment surrounding sperm against infections or autoimmune responses. Second, novel epididymal cell extensions, including dendrites, axopodia and primary cilia, have been identified as sensors of the environment surrounding sperm. Third, new functions have been outlined for epididymal EVs, which modify the sperm epigenetic profile and participate in transgenerational epigenetic inheritance of paternal traits.WIDER IMPLICATIONSAlthough the majority of these findings result from studies in rodents, this fundamental research will ultimately improve our knowledge of human reproductive physiopathologies. Recent discoveries linking sperm epigenetic modifications with paternal environmental exposure and progeny outcome further stress the importance of advancing fundamental research on the epididymis. From this, new therapeutic options for infertile couples and better counseling strategies may arise to increase positive health outcomes in children conceived either naturally or with ART.

The mammalian genome has a complex 3D organization, serving vital functional purposes, yet it remains largely unknown how the multitude of specific DNA contacts, e.g., between transcribed and regulatory regions, is orchestrated by chromatin organizers, such as Transcription Factors. Here, we implement a method combining machine learning and polymer physics to infer from only Hi-C data the genomic 1D arrangement of the minimal set of binding sites sufficient to recapitulate, through only physics, 3D contact patterns genome-wide in human and mouse cells. The inferred binding sites are validated by their predictions on how chromatin refolds in a set of duplications at the Sox9 locus against available independent cHi-C data, showing that their different phenotypes originate from distinct enhancer hijackings in their 3D structure. Albeit derived from only Hi-C, our binding sites fall in epigenetic classes that well match chromatin states from epigenetic segmentation studies, such as active, poised and repressed states. However, the inferred binding domains have an overlapping, combinatorial organization along chromosomes, missing in epigenetic segmentations, which is required to explain Hi-C contact specificity with high accuracy. In a reverse approach, the epigenetic profile of binding domains provides a code to derive from only epigenetic marks the DNA binding sites and, hence, the 3D architecture, as validated by successful predictions of Hi-C matrices in an independent set of chromosomes. Overall, our results shed light on how complex 3D architectural information is encrypted in 1D epigenetics via the related, combinatorial arrangement of specific binding sites along the genome.

Overcoming anticancer drug resistance is a major challenge in cancer therapy, requiring innovative strategies that consider the extensive tumor heterogeneity and adaptability. We provide recent evidence highlighting the key role of amino acid (AA) metabolic reprogramming in cancer cells and the supportive microenvironment in driving resistance to anticancer therapies. AAs sustain the acquisition of anticancer resistance by providing essential building blocks for biosynthetic pathways and for maintaining a balanced redox status, and modulating the epigenetic profile of both malignant and non-malignant cells. In addition, AAs support the reduced intrinsic susceptibility of cancer stem cells to antineoplastic therapies. These findings shed new light on the possibility of targeting nonresponding tumors by modulating AA availability through pharmacological or dietary interventions.

Germ cells reset their epigenome to form a proper epigenetic state for development of the next generation, a process termed epigenome reprogramming. During this process, primordial germ cells (PGCs), the first germ cells and origin of the germ cell lineages, acquire a unique epigenetic profile that includes events such as genome-wide DNA demethylation, large-scale chromatin remodeling, erasure of genomic imprinting, and female X-reactivation. These features crosstalk with each other to regulate the gene expression dynamics of PGCs, and underlie the formation of the totipotent epigenome in the next generation. During the last decade, low-input genomics and in vitro reconstitution of mammalian germ cells have advanced our understanding of epigenome reprogramming. Key findings include details of the dynamics of DNA methylome and histone modifications during PGC development, the formation of sexual dimorphisms in more differentiated germ cells, and the acquisition of a unique epigenome during gametogenesis. Detailed epigenome analyses may also be important for evaluation of germline development in vivo and in vitro.

The preimplantation stages cover a very dynamic phase of development with respect to epigenetic programming. The epigenetic reprogramming during preimplantation development erases gametic epigenetic patterns and allows the embryo to establish an epigenetic profile that is relevant for early development and that is essential for the developing conceptus. Our knowledge of epigenetic programming during these early stages of development is improving, but is far from complete. The use of better methodology to assess epigenetic marks is already providing a much more comprehensive picture of epigenetic reprogramming during preimplantation development. This work is being complemented by targeted functional assessment of epigenetic regulators to understand their roles in preimplantation epigenetic reprogramming. The findings of these studies may for example have ramifications in human assisted reproduction where preimplantation embryos are handled in vitro. Here we explore some of the main epigenetic features, mechanisms and mediators of these dynamic stages of development.

Atherosclerosis, which is also an indirect cause of restenosis, is one of the major cardiovascular complications seen worldwide and is the underlying cause of roughly 50% of deaths in the Western hemisphere. It is a progressive disease characterized by the accumulation of lipids, necrotic cells, calcium, and fibrous elements in arteries culminating in the formation of an arterial plaque. The growth and presence of this plaque is primarily a subclinical existence, but if it grows large enough and/or dislodges, the plaque can cause cardiac events with various ischemic implications based on where it is localized in the blood vessel. Several characteristic cellular and histological events occur during plaque development which are predictable and mark the progression of the disease. When mature, the developed plaque has the potential to block vasculature as a thrombus or embolus, and the blockage of blood flow has potent ischemic effects on distal tissues. The disease holds macroscopic implications, such as ischemia, myocardial infarction, and sudden death in patients if the intervention was not initiated. Angioplasty, followed by a prolonged oral statin regimen has been the current standard of care for the past few decades, although the incidence of atherosclerosis is continuously rising. In atherosclerotic plaques, epigenetic changes encourage its progression and remove protective factors. A careful examination of atherosclerosis’ epigenetic profile shows that the pathology incites alterations in the genome pushing the disease to more serious stages. Thus, gleaning a better understanding of these epigenetic changes might birth novel therapies. This chapter seeks to highlight atherosclerosis’ epigenetic profile in relation to the agents DNMT1 and HDAC2.

In the past, many attempts were made to solve the molecular mechanisms of cancer biology using a single OMICS approach through transcriptomics or proteomics for screening gene-level cancer-specific mutations, changed epigenetic profile, or varied mRNA and protein expressions. Apart from the contribution of these approaches in the identification of cancer-related mutations, alterations, these have lacked in establishing a direct link between molecular signatures and phenotypic examination of cancer hallmarks. Nevertheless, multi-OMICS approaches will reveal the underlying complex molecular mechanism of cancer hallmark stages like metastasis and angiogenesis. These approaches can very well be used to analyze cellular response to various cancer treatment therapies as well as find out molecular candidates having the potential to diagnose or cure. This chapter deals with applications of diverse OMICS approaches in the varied and dynamic field of cancer biology and also confers how these multi-OMICS approaches can be decisive in the personalized medicine field. The unified experimental data along with computational or mathematical data models have been accumulated in the Cancer Genome Atlas (TCGA) consortium, which further with the multi-OMICS approach will provide an opportunity to deal with the cancer cells complexity. This chapter will encourage the readers to integrate these OMICS approaches together to analyze the oncogenesis at different cellular, molecular, and system basis.

In the most recent decades, oxaliplatin has been used as a chemotherapeutic agent for colorectal cancer and other malignancies as well. Oxaliplatin interferes with tumor growth predominantly exerting its action in DNA synthesis inhibition by the formation of DNA-platinum adducts that, in turn, leads to cancer cell death. On the other hand, unfortunately, this interaction leads to a plethora of systemic side effects, including those affecting the peripheral and central nervous system. Oxaliplatin therapy has been associated with acute and chronic neuropathic pain that induces physicians to reduce the dose of medication or discontinue treatment. Recently, the capability of oxaliplatin to alter the genetic and epigenetic profiles of the nervous cells has been documented, and the understanding of gene expression and transcriptional changes may help to find new putative treatments for neuropathy. The present article is aimed to review the effects of oxaliplatin on genetic and epigenetic mechanisms to better understand how to ameliorate neuropathic pain in order to enhance the anti-cancer potential and improve patients’ quality of life.

Nutrition plays a critical role during the reproductive phases of an individual's life. It is well known that under or over nutrition can affect the reproductive functions. However, the underlying regulatory mechanisms are poorly understood. In recent years, epigenetics is suggested to be a new link between nutrition and health. Maternal nutrition plays a significant role in establishing the fetal epigenetic profile that may influence the health of the offspring in later life. Understanding the relation between nutrition, reproductive health and epigenetic mechanisms represents an interesting field. In the current chapter, we discuss the role of nutrition in influencing epigenome. This chapter also reviews studies examining epigenetic changes in pregnancy complications, endometriosis and polycystic ovary syndrome (PCOS). However, there are limited studies describing the effect of nutrition on epigenome in reproductive health. Hence, there is a need to understand the role of nutrition in determining the reproductive outcome of an individual via underlying epigenetic modifications.

Prenatal adversity or stress can have long-term consequences on developmental trajectories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional implications. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early development. As these insults can have sex-specific effects on biological outcomes, we analyzed epigenome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cognition, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may reflect the sex-specific effects of prenatal insults on long-term functional and health outcomes and have important implications for understanding possible mechanisms underlying fetal alcohol spectrum disorder and other neurodevelopmental disorders.

Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function, not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mechanisms that is in turn orchestrated by genetic and environmental factors. The epigenetic profile captures the unique regulatory landscape and the exposure to environmental stimuli of an individual. It thus constitutes a valuable reservoir of information for personalized medicine, which is aimed at customizing health-care interventions based on the unique characteristics of each individual. Nowadays, the complex milieu of epigenomic marks can be studied at the genome-wide level thanks to massive, high-throughput technologies. This new experimental approach is opening up new and interesting knowledge perspectives. However, the analysis of these complex omic data requires to face important analytic issues. Artificial Intelligence, and in particular Machine Learning, are emerging as powerful resources to decipher epigenomic data. In this review, we will first describe the most used ML approaches in epigenomics. We then will recapitulate some of the recent applications of ML to epigenomic analysis. Finally, we will provide some examples of how the ML approach to epigenetic data can be useful for personalized medicine.

Topologically associated domains (TADs) are one of the important higher order chromatin structures with various sizes in the eukaryotic genomes. TAD boundaries, as the flanking regions between adjacent domains, can restrict the interactions of regulatory elements, including enhancers and promoters, and are generally dynamic and variable in different cells. However, the influence of sequence and epigenetic profile-based features in the identification of TAD boundaries is largely unknown. In this work, we proposed a method called pTADS (prediction of TAD boundary and strength), to predict TAD boundaries and boundary strength across multiple cell lines with DNA sequence and epigenetic profile information. The performance was assessed in seven cell lines and three TAD calling methods. The results demonstrate that the TAD boundary can be well predicted by the selected shared features across multiple cell lines. Especially, the model can be transferable to predict the TAD boundary from one cell line to other cell lines. The boundary strength can be characterized by boundary score with good performance. The predicted TAD boundary and TAD boundary strength are further confirmed by three Hi-C contact matrix-based methods across multiple cell lines. The codes and datasets are available at https://github.com/chrom3DEpi/pTADS.

Nutritional intake impacts the human epigenome by directing epigenetic pathways in normal cell development via as yet unknown molecular mechanisms. Consequently, imbalance in the nutritional intake is able to dysregulate the epigenetic profile and drive cells towards malignant transformation. Herein, we present a novel epigenetic effect of the essential nutrient, NAD. We demonstrate that impairment of DNMT1 enzymatic activity by NAD-promoted ADP-ribosylation, leads to demethylation and transcriptional activation ofCEBPAgene, suggesting the existence of an unknown NAD-controlled region within the locus. In addition to the molecular events, NAD treated cells exhibit significant morphological and phenotypical changes that correspond to myeloid differentiation.Collectively, these results delineate a novel role for NAD in cell differentiation and indicate novel nutri-epigenetic strategy to regulate and control gene expression in human cells.

A balance between co-inhibitory and co-stimulatory signals in the tumor microenvironment (TME) is critical to suppress tumor development and progression, primarily via maintaining effective immunosurveillance. Aberrant expression of immune checkpoints (ICs), including programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), lymphocyte-activation gene 3 (LAG-3) and T cell immunoreceptor with Ig and ITIM domains (TIGIT), can create an immune-subversive environment, which helps tumor cells to evade immune destruction. Recent studies showed that epigenetic modifications play critical roles in regulating the expression of ICs and their ligands in the TME. Reports showed that the promoter regions of genes encoding ICs/IC ligands can undergo inherent epigenetic alterations, such as DNA methylation and histone modifications (acetylation and methylation). These epigenetic aberrations can significantly contribute to the transcriptomic upregulation of ICs and their ligands. Epigenetic therapeutics, including DNA methyltransferase and histone deacetylase inhibitors, can be used to revert these epigenetic anomalies acquired during the progression of disease. These discoveries have established a promising therapeutic modality utilizing the combination of epigenetic and immunotherapeutic agents to restore the physiological epigenetic profile and to re-establish potent host immunosurveillance mechanisms. In this review, we highlight the roles of epigenetic modifications on the upregulation of ICs, focusing on tumor development, and progression. We discuss therapeutic approaches of epigenetic modifiers, including clinical trials in various cancer settings and their impact on current and future anti-cancer therapies.

The application of biocontrol biopesticides based on plant growth-promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences' Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140. KEY POINTS: • Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140. • Identification of genetic determinants responsible for PGPR activities. • Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.

Epstein–Barr virus-associated gastric cancer [EBV-associated GC, EBV( +) GC] is a distinct molecular subtype of gastrointestinal (GI) cancers. It accounts for up to 10% of all molecular subtypes of gastric cancer (GC). It has unique genetic and epigenetic features, which determine its definitive phenotype with male and younger age predominance, proximal stomach localization, and diffuse adenocarcinoma histology. EBV( +) GC also has a unique epigenetic profile and mutational status with frequent mutations of PIK3CA, ARID1A and BCOR, and PD-L1 and PD-L2 amplifications, as well. The aim of this review is to highlight clinical significance of EBV( +) GC and prognostic role of EBV infection, and to determine potentially appropriate drug therapy for this disease.

Highly dynamic epigenetic signaling is influenced mainly by (micro)environmental stimuli and genetic factors. The exact mechanisms affecting particular epigenomic patterns differ dependently on the context. In the current review, we focus on the causes and effects of the dynamic signatures of the human epigenome as evaluated with the high-throughput profiling data and single-gene approaches. We will discuss three different aspects of phenotypic outcomes occurring as a consequence of epigenetics interplaying with genotype and environment. The first issue is related to the cases of environmental impacts on epigenetic profile, and its adverse and advantageous effects related to human health and evolutionary adaptation. The next topic will present a model of the interwoven co-evolution of genetic and epigenetic patterns exemplified with transposable elements (TEs) and their epigenetic repressors Krüppel-associated box zinc finger proteins (KRAB–ZNFs). The third aspect concentrates on the mitosis-based microevolution that takes place during carcinogenesis, leading to clonal diversity and expansion of tumor cells. The whole picture of epigenome plasticity and its role in distinct biological processes is still incomplete. However, accumulating data define epigenomic dynamics as an essential co-factor driving adaptation at the cellular and inter-species levels with a benefit or disadvantage to the host.

Genetic and epigenetic factors have an important role during the development of osteoporosis. RANK/RANKL pathway is important for the bone remodeling and NFATC1 and c-FOS are the downtargets of this pathway. Here, we report methylation status of NFATC1 and C-FOS genes in post and premenopausal cases. In this study 30 pre-menopausal and 35 post-menopausal cases were included. MS-HRM was used for identification of NFATC1 and C-FOS metyhylation.NFATC1 were methylated in 11 of the 35 post-menopausal women and C-FOS were methylated in 6 of the postmenopausal women (p >0.005). Here, we found statistically significant association between unmethylation of NFATC1 and post-menopausal status. This result explains the epigenetic regulation of osteoclasts during the menopausal transition and our results can be used for epigenetic explanation of post-menopausal osteoporosis for the first time in the literature. Although the limited number of studies in this field makes our results crucial. Therefore, our results showed great value of epigenetic profile of post-menopausal women.

Dietary intake in early lactating cows is outmatched by milk production. These cows experience a negative energy balance, resulting in a distinct blood metabolism and poor reproductive function due to impaired ovulation and increased embryo loss. We hypothesize that oocytes from lactating cows undergoing transient metabolic stress exhibit a different epigenetic profile crucial for developmental competence. To investigate this, we collected oocytes from metabolically-profiled cows at early- and mid-postpartum stages and characterized their epigenetic landscape compared with control heifers using whole-genome bisulfite sequencing. Early-postpartum cows were metabolically deficient with a significantly lower energy balance and significantly higher concentrations of non-esterified fatty acids and beta-hydroxybutyrate than mid-postpartum animals and control heifers. Accordingly, 32,990 early-postpartum-specific differentially methylated regions (DMRs) were found in genes involved in metabolic pathways, carbon metabolism, and fatty acid metabolism, likely descriptive of the epigenetic regulation of metabolism in early-postpartum oocytes. DMRs found overlapping CpG islands and exons of imprinted genes such as MEST and GNAS in early-postpartum oocytes suggest that early lactation metabolic stress may affect imprint acquisition, which could explain the embryo loss. This whole-genome approach introduces potential candidate genes governing the link between metabolic stress and the reproductive outcome of oocytes.

Ewing sarcoma (ES) is a primary bone marrow tumor that very rarely develops in extra‑osseous tissues, such as lung. The hallmark of ES tumors is a translocation between chromosomes 11 and 22, resulting in a fusion protein, commonly referred to as EWS‑FLI1. The epigenetic profile (histone acetylation and methylation enrichment of the promoter region) that may regulate the expression of the aberrant transcription factor EWS‑FLI1, remains poorly studied and understood. Knowledge of epigenetic patterns associated with covalent histone modification and expression of enzymes associated with this process, can contribute to the understanding of the molecular basis of the disease, as well as to the identification of possible molecular targets involved in expression of the EWS‑FLI1 gene, so that therapeutic strategies may be improved in the future. In the present study, the transcriptional activation and repression of the EWS‑FLI1 fusion gene in ES was accompanied by selective deposition of histone markers on its promoter. The EWS‑FLI1 fusion gene was evaluated in two patients with ES using conventional cytogenetic, fluorescence in situ hybridization and nested PCR assays, which revealed that the aberrant expression of the EWS‑FLI1 gene is accompanied by enrichment of H3K4Me3, H3K9ac and H3K27ac at the promoter region.