Overview of Histone Modification

Epigenetics changes during allergen immunotherapy - Review of available literature

Allergic diseases are very broad ranging conditions and affect the health and comfort of patients in different manners. To date, the only effective treatment is allergen immunotherapy. Unfortunately, apart from observations of drug use or the severity of symptoms, there is no direct method of determining the effectiveness or ineffectiveness of the medical intervention that has been provided. The hope of gaining insight into the adaptive processes occurring in the body during immunotherapy is offered by epigenetics. By observing such areas of biological activity as DNA methylation, modification of histone proteins, or studies of non-coding RNA fragments, physicians will gain reliable tools for determining the effectiveness of the undertaken therapy. They can link the data acquired to the expression levels of specific genes that activate or suppress the immune response, perhaps even before it is initiated. This paper describes the basic epigenetic mechanisms, their known links to specific diseases and therapies, and potential areas for further research.

Histone Deacetylases (HDACs) Roles in Inflammation-mediated Diseases; Current Knowledge

The histone acetyl transferases (HATs) and histone deacetylases (HDACs), which are mostly recognized for their involvement in regulating chromatin remodeling via histone acetylation/deacetylation, have been shown to also change several non-histone proteins to regulate other cellular processes. Acetylation affects the activity or function of cytokine receptors, nuclear hormone receptors, intracellular signaling molecules, and transcription factors in connection to inflammation. Some small-molecule HDAC inhibitors are utilized as anticancer medications in clinical settings due to their capability to regulate cellular growth arrest, differentiation, and death. Here, we summarize our present knowledge of the innate and adaptive immunological pathways that classical HDAC enzymes control. The aim is to justify the targeted (or non-targeted) use of inhibitors against certain HDAC enzymes in inflammatory diseases such as arthritis, inflammatory bowel diseases (IBD), airways inflammation and neurological diseases.

Epigenetic targets and their inhibitors in the treatment of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a deadly lung disease characterized by fibroblast proliferation, excessive extracellular matrix buildup, inflammation, and tissue damage, resulting in respiratory failure and death. Recent studies suggest that impaired interactions among epithelial, mesenchymal, immune, and endothelial cells play a key role in IPF development. Advances in bioinformatics have also linked epigenetics, which bridges gene expression and environmental factors, to IPF. Despite the incomplete understanding of the pathogenic mechanisms underlying IPF, recent preclinical studies have identified several novel epigenetic therapeutic targets, including DNMT, EZH2, G9a/GLP, PRMT1/7, KDM6B, HDAC, CBP/p300, BRD4, METTL3, FTO, and ALKBH5, along with potential small-molecule inhibitors relevant for its treatment. This review explores the pathogenesis of IPF, emphasizing epigenetic therapeutic targets and potential small molecule drugs. It also analyzes the structure-activity relationships of these epigenetic drugs and summarizes their biological activities. The objective is to advance the development of innovative epigenetic therapies for IPF.

Integrated Transcriptomic and Epigenomic Analysis Reveals Mechanisms Underlying Melanotic Spot Formation in Red Tilapia (Oreochromis spp.)

Red tilapia is highly valued as a premium variety in Asia due to its vibrant red skin coloration. However, during aquaculture production, irregular black pigmentation (melanotic spots) frequently appears on the skin of some individuals, significantly reducing their economic value. Although epigenetic regulation is suspected to play a role, its involvement remains poorly understood. To uncover the molecular mechanisms underlying black spot formation, we employed Cleavage Under Targets and Tagmentation (CUT&Tag) to compare four key histone modifications (H3K4me3, H3K4me1, H3K27me3, and H3K27ac) between red and black pigmented skin regions. Integrated with transcriptomic analysis, our data indicated that red skin regions exhibited high expression of genes suppressing melanin synthesis, whereas melanotic spots likely resulted from localized derepression, allowing upregulation of melanin biosynthetic genes. Furthermore, by combining epigenomic chromatin state analysis and transcriptome data, we identified critical genes consistently active in melanotic spots and their corresponding potential cis-regulatory elements. Motif analysis of transcription factor binding sites upstream of these regulatory elements revealed that Ehf, Klf9, and Egr1 might facilitate melanin production in black regions, while Prdm1 and Sp5 could inhibit melanogenesis in red regions by repressing the Wnt signaling pathway. These findings provide valuable epigenetic insights into the mechanisms driving melanotic spot formation in red tilapia.

Histone modifications and metabolic reprogramming in tumor-associated macrophages: a potential target of tumor immunotherapy

Histone modifications, including methylation, acetylation, lactylation, phosphorylation, ubiquitination, SUMOylation, ADP-ribosylation, and crotonylation, critically regulate tumor-associated macrophages (TAMs) polarization by modulating gene expression and functional states. Reprogramming TAMs from M2 to M1 phenotypes through epigenetic targeting has emerged as a promising strategy to enhance anti-tumor immunity and improve the efficacy of cancer immunotherapy. This review explores the role of histone modifications in TAM biology, their interplay with metabolic reprogramming, and the opportunities and challenges in developing epigenetic-based therapies to advance cancer immunotherapy.

Histone crotonylation in tumors (Review)

Lysine crotonylation (Kcr) refers to a type of modification in which crotonyl groups are transferred to lysine residues by histone crotonyltransferase (HCT) using crotonyl-coenzyme A (CoA) as a substrate. Kcr is distributed in core histones and in some nonhistone proteins. Histone crotonylation is a newly discovered epigenetic modification with a significant ability to regulate gene expression. Crotonylation occurs on the ε-amino group of lysine residues and results in a modification of the histone charge. Similar to acetylation, the substrate for crotonylation is a donor molecule, crotonyl-CoA, which is linked to the sulfhydryl group of CoA by a thioester bond. Crotonylation is involved in regulating a wide range of biological processes and diseases. With advances in detection technologies, the impact of histone crotonylation on tumors has been revealed. The present review examines the recent discoveries of histone crotonylation, its function in tumors and its regulatory mechanism, which will aid in elucidating the mechanisms of malignant tumor development and provide a theoretical foundation for the development of new targeted cancer therapies.

Treating human cancer by targeting EZH2

Enhancer of zeste homolog 2 (EZH2), an epigenetic regulator that primarily inhibits downstream gene expression by tri-methylating histone H3, which is usually overexpressed in tumors and participates in many processes such as tumor occurrence and development, invasion, migration, drug resistance, and anti-tumor immunity as an oncogene, making it an important biomarker in cancer therapy. Collectively, several transcription factors and RNAs cooperate to facilitate the elevated expression of EZH2 in cancer. Although the significance of blocking EZH2 in cancer for inhibiting cancer progression is widely recognized, the clinical application of EZH2 inhibitors continues to encounter numerous challenges. In this review, drawing upon our comprehensive understanding of the factual underpinnings of EZH2's role in cancer, we aim to clarify the crucial importance of targeting EZH2 in cancer treatment. Furthermore, we summarize the current research landscape surrounding targeted EZH2 inhibitors and offer insights into potential future applications of these inhibitors.

Regulatory mechanism of ABCB1 transcriptional repression by HDAC5 in rat hepatocytes under hypoxic environment

Objective

Previous research has demonstrated that the hypoxic environment at high altitudes significantly alters the pharmacokinetics of many drugs, reducing their efficacy and increasing adverse effects. A key factor in this altered drug metabolism is the inhibition of ATP-binding cassette subfamily B member 1 (ABCB1), an efflux transporter protein, in the liver tissues of plateau rats. Rat ABCB1, encoded by the ABCB1A and ABCB1B genes, has two isoforms functionally analogous to human ABCB1. Histone acetylation, an epigenetic mechanism, may regulate ABCB1 transcription in hypoxic conditions by modifying chromatin structure and interacting with signaling pathways. However, its role in ABCB1 transcriptional regulation under hypoxia remains unclear. Based on this, the present study employed the BRL cell line to establish a hypoxia model, aiming to investigate the histone acetylation-mediated regulatory mechanisms of ABCB1 expression under hypoxic conditions, with the ultimate goal of providing novel theoretical foundations for rational drug use in high-altitude regions.

Methods

Establishment of BRL hypoxia model: BRL cell viability was detected by CCK-8 assay, and HIF-1α expression was measured by RT-qPCR and Western blot. After treating the BRL hypoxia model with HDAC inhibitors, ABCB1 and HDAC5 expression were detected by RT-qPCR, Western blot, and immunofluorescence. Rhodamine 123 accumulation assay was performed to examine the effect of HDAC inhibitors on ABCB1 functional activity. HDAC5 was targeted by siRNA technology to detect ABCB1 and H3K9ac expression. CUT&Tag assay was used to measure H3K9ac levels at the ABCB1 promoter region. After SAHA treatment of the BRL hypoxia model, SP1 expression was detected by RT-qPCR and Western blot. Combined treatment with SAHA and siRNA targeting SP1 was performed to detect ABCB1 expression. Co-immunoprecipitation and fluorescence colocalization assays were conducted to examine interactions among SP1, HDAC5, and ABCB1.

Results

After hypoxic culture for different durations, cell viability decreased while HIF-1α expression increased, indicating the successful establishment of the BRL hypoxia model. In the BRL hypoxia model, ABCB1 and SP1 expression decreased while HDAC5 expression increased. After SAHA treatment, ABCB1 and SP1 expression were upregulated while HDAC5 was downregulated. Rhodamine 123 accumulation assay showed that SAHA could enhance ABCB1 functional activity by inducing its expression. After HDAC5 was knocked down using siRNA, ABCB1 and H3K9ac expression increased, and ABCB1 functional activity was enhanced. CUT&Tag assay demonstrated that H3K9ac levels at the ABCB1B promoter region decreased in the BRL hypoxia model, while HDAC5 inhibition increased H3K9ac levels at this region. After SP1 was knocked down using siRNA, the inductive effect of SAHA on ABCB1 was blocked. Co-immunoprecipitation and fluorescence colocalization showed interactions among SP1, HDAC5, and ABCB1.

Conclusion

In BRL cells, HDAC5 may be recruited by SP1 to form a complex, reducing free HDAC5, increasing H3K9ac at the ABCB1B promoter, and activating ABCB1 transcription. In the BRL hypoxia model, disruption of the SP1-HDAC5 complex increased free HDAC5, lowered H3K9ac at the ABCB1B promoter, and suppressed ABCB1 transcription. These results suggest that HDAC inhibitors enhance ABCB1 expression in hypoxic environments, indicating that combining HDAC inhibitors with therapeutic agents could mitigate reduced drug efficacy and adverse effects caused by ABCB1 suppression.

Development of a multiple reaction monitoring (MRM)-based LC-MS/MS method for the quantification of post-translational modifications on histone H3 variants in Arabidopsis thaliana

Background: although the canonical histone H3.1 and its variant H3.3 differ by only four amino acids, they exhibit distinct genome-wide binding patterns and regulate different biological pathways. Post-translational modifications (PTMs) on histone tails mediate diverse downstream regulatory processes, raising the question of whether H3.1 and H3.3 harbor variant-specific modifications. However, the minimal amino acid differences between H3.1 and H3.3 make it challenging to distinguish and quantify them using traditional methods. Results: in this study, we developed an integrated multiple reaction monitoring (MRM)-based LC-MS/MS method to accurately differentiate and quantify K27 and K36 modifications on H3.1 and H3.3 in Arabidopsis thaliana. Our findings show that H3.1 contains more K27 methylation marks, associated with gene silencing, whereas H3.3 is enriched in K36 methylation, a mark of active transcription. Additionally, we compared K36 methylation levels in wild-type and SDG8-depleted cells, revealing that the K36 methyltransferase SDG8 shows a strong preference for H3.3 in both in vitro and in vivo assays. By analyzing public datasets, we further identified a strong correlation between H3.3 and the regions where H3K36me3 levels were reduced in sdg8 knockout cells. Significance: the MRM-based LC-MS/MS method established in this study provides a reliable and robust tool for the quantification of histone H3.1 and H3.3 PTMs in Arabidopsis thaliana. We demonstrate that the methyltransferase SDG8 shows a strong substrate preference for H3.3. This discovery highlights the importance of histone variant-specific modifications and suggests new avenues for research into their regulatory roles.

Exploring epigenetic modifications as potential biomarkers and therapeutic targets in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. Whole-genome sequencing has identified many novel ALS-associated genes, but genetics alone cannot fully explain the onset of ALS and an effective treatment is still lacking. Moreover, we need more biomarkers for accurate diagnosis and assessment of disease prognosis. Epigenetics, which includes DNA methylation and hydroxymethylation, histone modifications, chromatin remodeling, and non-coding RNAs, influences gene transcription and expression by affecting chromatin accessibility and transcription factor binding without altering genetic information. These processes play a role in the onset and progression of ALS. Epigenetic targets can serve as potential biomarkers and more importantly, the reversibility of epigenetic changes supports their potential role as versatile therapeutic targets in ALS. This review summarized the alterations in different epigenetic modulations in ALS. Additionally, given the close association between aberrant metabolic profiles characterized by hypoxia and high glycolytic metabolism in ALS and epigenetic changes, we also integrate epigenetics with metabolomics. Finally, we discuss the application of therapies based on epigenetic mechanisms in ALS. Our data integration helps to identify potential diagnostic and prognostic biomarkers and support the development of new effective therapies.

Berberine inhibits prostate cancer progression by inducing ferroptosis: evidence from network pharmacology

The uncertain ferroptosis-related role of berberine in prostate cancer was explored using network pharmacology methodology. Integration of ferroptosis targets in prostate cancer from the Genecard database and berberine targets from the Traditional Chinese Medicine Systems Pharmacology and SwissTargetPrediction databases revealed 17 common targets. Among these, 10 hub genes, including CCNB1 , CDK1 , AURKA , AR , CDC42 , ICAM1 , TYMS , NTRK1 , PTGS 2, and SCD , were identified. Enrichment analyses yielded 799 Gene Ontology terms and 23 Kyoto Encyclopedia of Genes and Genomes pathways associated with berberine-related targets. Molecular docking simulations indicated berberine's binding capacity to all hub genes. In-vitro studies on LNCaP and PC3 cells demonstrated berberine's inhibition of cell proliferation and significant downregulation of TYMS , CCNB1 , AURKA , CDK1 , and SCD in both cell lines. Berberine exhibited cell line-specific effects by reducing AR expression in LNCaP cells and suppressing ICAM1 in PC3 cells. Overall, berberine shows promise in inhibiting prostate cancer progression through modulation of ferroptosis-related genes, including TYMS , AR , CCNB1 , AURKA , CDK1 , ICAM1 , NTRK1 , SCD , and CDC42 .

Nutrigenetic and Epigenetic Mechanisms of Maternal Nutrition-Induced Glucolipid Metabolism Changes in the Offspring

Maternal nutrition during pregnancy regulates the offspring's metabolic homeostasis, including insulin sensitivity and the metabolism of glucose and lipids. The fetus undergoes a crucial period of plasticity in the uterus; metabolic changes in the fetus during pregnancy caused by maternal nutrition not only influence fetal growth and development but also have a long-term or even life-long impact for the offspring. Epigenetic modifications, such as DNA methylation, histone modification, and non-coding RNAs, play important roles in intergenerational and transgenerational effects. In this context, this narrative review comprehensively summarizes and analyzes the molecular mechanisms underlying how maternal nutrition, including a high-fat diet, polyunsaturated fatty acid diet, methyl donor nutrient supplementation, feed restriction, and protein restriction during pregnancy, impacts the genes involved in glucolipid metabolism in the liver, adipose tissue, hypothalamus, muscle, and oocytes of the offspring in terms of the epigenetic modifications. This will provide a foundation for the further exploration of nutrigenetic and epigenetic mechanisms for integrative mother-child nutrition and promotion of the offspring's health through the regulation of maternal nutrition during pregnancy. Note: This paper is part of the Nutrition Reviews Special Collection on Precision Nutrition.

HIF1A facilitates hypoxia-induced changes in H3K27ac modification to promote myometrial contractility

Prior studies have established that myometrial hypoxia during labor is pivotal in intensifying contractions, the alterations in gene expression and histone modifications in myometrial cells under hypoxia have yet to be documented. Here, hypoxia's enhancement of cellular contractility was confirmed, and RNA-seq identified 2,262 differentially expressed genes in human myometrial smooth muscle cells (hMSMCs) under hypoxia. Chromatin immunoprecipitation (ChIP), high-throughput chromosome conformation capture followed by ChIP (Hi-ChIP) were employed to investigate the epigenetic changes, specifically histone modifications (H3K27ac, H3K4me1, H3K27me3, and H3K4me3), in hMSMCs under hypoxia. We identified the enhancer and super-enhancer regions in hMSMCs and found HIF1A as the key mediator of these H3K27ac changes under hypoxia. Labor-associated genes regulated by HIF1A have been identified. Validation experiments on these genes such as CXCL8, RUNX1, IL-6, and PTGES3 demonstrated that HIF1A knockdown reduces their expression and associated H3K27ac modifications in peak regions of their promoters or enhancers. These findings indicate that HIF1A probably mediate changes in histone H3K27ac modifications to regulate myometrial cell contractions under hypoxia, providing potential therapeutic and intervention targets for disorders related to parturition.

Research on the regulation mechanism of drought tolerance in wheat

Wheat (Triticum aestivum L.) is one of the most important crops in arid and semi-arid areas of the world, and its sustainable and efficient production is essential for ensuring food security in China and globally. However, with the global climate change, wheat production is increasingly endangered by abiotic stress, and drought stress has become the main abiotic stress factor restricting wheat production efficiently. Therefore, investigating drought resistance genes and elucidating the mechanisms underlying drought resistance regulation is crucial for the genetic enhancement of drought resistance and the development of new drought-resistant wheat varieties. This paper reviews the majority of research conducted on wheat drought resistance over the past five years, focusing on aspects, such as transcriptional regulation, protein post-translational modifications, and other regulatory mechanisms related to drought resistance in wheat. Additionally, this paper discusses future directions for the genetic improvement of drought resistance and the breeding of new drought-resistant wheat varieties.

Lactylation: a promising therapeutic target in ischemia-reperfusion injury management

Ischemia-reperfusion injury (IRI) is a critical condition that poses a significant threat to patient safety. The production of lactate increases during the process of IRI, and lactate serves as a crucial indicator for assessing the severity of such injury. Lactylation, a newly discovered post-translational modification in 2019, is induced by lactic acid and predominantly occurs on lysine residues of histone or nonhistone proteins. Extensive studies have demonstrated the pivotal role of lactylation in the pathogenesis and progression of various diseases, including melanoma, myocardial infarction, hepatocellular carcinoma, Alzheimer's disease, and nonalcoholic fatty liver disease. Additionally, a marked correlation between lactylation and inflammation has been observed. This article provides a comprehensive review of the mechanism underlying lactylation in IRI to establish a theoretical foundation for better understanding the interplay between lactylation and IRI.

Appraising histone H4 lysine 5 lactylation as a novel biomarker in breast cancer

Background Posttranslational modifications of histone lysine (K) have integral connections with cell metabolism, and participate in the carcinogenesis of various cancers. This study focuses on evaluating the expression of histone H4 lys 5 lactylation (H4K5lac) and its clinical role in breast cancer (BC). Methods During this research, immunohistochemistry (IHC) and immunoblotting, utilizing a specific primary anti-L-lactyl-histone H4 (Lys 5) rabbit monoclonal antibody, were employed to assess H4K5lac expression in BC tissue chips. H4K5lac expression in the peripheral blood mononuclear cells (PBMCs) of BC patients was investigated through immunoblotting. Results IHC revealed upregulation of histone H4K5lac in both triple-negative breast cancer (TNBC) and non-TNBC tissues, with positive rate of 91.40% [170/(150 + 19 + 17)] and 93.64% (103/110) in TNBC and non-TNBC tissues, respectively. The expression of H4K5lac demonstrated positive correlations with lymph nodes (%), and Ki-67 expression. Survival analysis indicated a negative correlation between H4K5lac expression and overall survival (OS) time in both TNBC (HR [hazard ratio] = 2.773, 95%CI [confidence interval]: 1.128-6.851, P = 0.0384) and non-TNBC cases (HR = 2.156, 95%CI: 1.011-4.599, P = 0.0275). Furthermore, elevated levels of H4K5lac were observed in the PBMCs of BC cases, and H4K5lac expression is positively correlated with serum lactate and carcinoma embryonic antigen (CEA) levels. Conclusions Histone H4K5lac exhibits increased levels in both BC tissues and PBMCs, suggesting its potential as a promising biomarker for BC. This study might pave the way toward novel lactylation treatment strategies in BC.

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling

Mammalian pluripotent cells first segregate into neuroectoderm (NE), or mesoderm and endoderm (ME), characterized by lineage-specific transcriptional programs and chromatin states. To date, the relationship between transcription factor activities and dynamic chromatin changes that guide cell specification remains ill-defined. In this study, we employ mouse embryonic stem cell differentiation toward ME lineages to reveal crucial roles of the Tbx factor Eomes to globally establish ME enhancer accessibility as the prerequisite for ME lineage competence and ME-specific gene expression. EOMES cooperates with the SWItch/sucrose non-fermentable (SWI/SNF) complex to drive chromatin rewiring that is essential to overcome default NE differentiation, which is favored by asymmetries in chromatin accessibility at pluripotent state. Following global ME enhancer remodeling, ME-specific gene transcription is controlled by additional signals such as Wnt and transforming growth factor β (TGF-β)/NODAL, as a second layer of gene expression regulation, which can be mechanistically separated from initial chromatin remodeling activities.

Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers

Histone modifications play a crucial role in regulating chromatin architecture and gene expression. Here we develop a multiscale model for incorporating methylation in our nucleosome-resolution physics-based chromatin model to investigate the mechanisms by which H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3) influence chromatin structure and gene regulation. We apply three types of energy terms for this purpose: short-range potentials are derived from all-atom molecular dynamics simulations of wildtype and methylated chromatosomes, which revealed subtle local changes; medium-range potentials are derived by incorporating contacts between HP1 and nucleosomes modified by H3K9me3, to incorporate experimental results of enhanced contacts for short chromatin fibers (12 nucleosomes); for long-range interactions we identify H3K9me3- and H3K27me3-associated contacts based on Hi-C maps with a machine learning approach. These combined multiscale effects can model methylation as a first approximation in our mesoscale chromatin model, and applications to gene systems offer new insights into the epigenetic regulation of genomes mediated by H3K9me3 and H3K27me3.

Histone Phosphorylation in DNA Damage Response

The DNA damage response (DDR) is crucial for maintaining genomic stability and preventing the accumulation of mutations that can lead to various diseases, including cancer. The DDR is a complex cellular regulatory network that involves DNA damage sensing, signal transduction, repair, and cell cycle arrest. Modifications in histone phosphorylation play important roles in these processes, facilitating DNA repair factor recruitment, damage signal transduction, chromatin remodeling, and cell cycle regulation. The precise regulation of histone phosphorylation is critical for the effective repair of DNA damage, genomic integrity maintenance, and the prevention of diseases such as cancer, where DNA repair mechanisms are often compromised. Thus, understanding histone phosphorylation in the DDR provides insights into DDR mechanisms and offers potential therapeutic targets for diseases associated with genomic instability, including cancers.

Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells

To understand epigenetic inheritance in mammals, we investigate cell division modes and histone inheritance patterns in the mouse olfactory epithelium using an injury-induced regeneration model. Horizontal basal cells (HBCs), the adult stem cells in this tissue, undergo asymmetric division, coinciding with asymmetric histone H4 inheritance in vivo. Primary HBCs recapitulate both asymmetric cell division and asymmetric histone inheritance for H4, H3, and H3.3, but not H2A-H2B. Upon mitotic exit, asymmetric histone inheritance correlates with differential enrichment of a key 'stemness' transcription factor p63 and asynchronous transcription re-initiation. Single-cell RNA sequencing of paired daughter cells reveals their asymmetric cell fate priming in this multilineage stem cell system. Furthermore, disruption of asymmetric cell division abolishes these asymmetric cellular features, impairing olfactory epithelium regeneration and smell behavior in mice. Together, these findings reveal asymmetric histone inheritance in a mammalian adult stem cell lineage and highlight its biological significance in tissue regeneration and animal behavior.

The AaFoxA factor regulates female reproduction through chromatin remodeling in the mosquito vector Aedes aegypti

Female mosquitoes are vectors of many devastating human diseases because they require blood feeding to initiate reproduction. Thus, elucidation of molecular mechanisms managing female mosquito reproduction is essential. Although the regulation of gene expression during the mosquito gonadotrophic cycle has been studied in detail, how this process is controlled at the chromatin level remains unclear. Chromatin must be accessible for transcription factors (TFs) governing gene expression. A specialized class of TFs, called pioneer factors (PFs), binds and remodels closed chromatin, permitting other TFs to bind DNA and activate the gene expression. Here, we identified a homolog of the vertebrate PF FoxA in the mosquito Aedes aegypti and used the CRISPR-Cas9 system to generate mosquitoes deficient in AaFoxA. We found that ovary development was severely retarded in mutant females. Multiomics and molecular biology analyses have shown that AaFoxA increased histone acetylation and decreased methylation of H3K27 by controlling the chromatin accessibility of histone modification enzymes and chromatin remodelers. AaFoxA is bound to the loci of chromatin remodelers, changing their chromatin accessibility and modulating their temporal expression patterns. AaFoxA increased the accessibility of the ecdysone receptor (EcR) and E74 loci, indicating the important role of AaFoxA in the hormonal regulation of mosquito reproductive events. Further, the CUT&RUN and ATAC-seq analyses revealed that AaFoxA temporarily bound closed chromatin, making it differentially accessible during the mosquito gonadotrophic cycle. Hence, this study demonstrates that AaFoxA modulates chromatin dynamics throughout female mosquito reproduction.

SUV39H1 Regulates Gastric Cancer Progression via the H3K9me3/ALDOB Axis

Gastric cancer (GC) is a malignant tumor with high incidence rate. H3K9me3 is related to transcriptional suppression and modulated by histone methyltransferase suppressor of variegation 3-9 homolog 1 (SUV39H1). SUV39H1 is dysregulated in assorted cancers and exerts the regulatory function. Nevertheless, the specific biofunction of SUV39H1 in GC needs further confirmation. SUV39H1 and H3K9me3 expressions were tested through RT-qPCR and western blot. Colony formation, wound healing, and transwell assays were employed for testing cell behaviors. ChIP assay was utilized for assessing the interaction between H3K9me3 and aldolase B (ALDOB). Xenograft experiment was employed for measuring tumor growth. We found that SUV39H1 and H3K9me3 were overexpressed in GC tissues and cells. SUV39H1 knockdown notably suppressed GC cell proliferative, migratory, and invasive capabilities. The treatment of chaetocin or F5446 (inhibitors of SUV39H1 enzymatic activity) also restrained GC cell behaviors. In addition, we discovered that SUV39H1 could negatively regulate ALDOB expression. SUV39H1 depletion reduced H3K9me3 modification to ALDOB promoter region. In rescue assays, we proved that ALDOB reduction reversed the inhibitory functions of SUV39H1 silencing on GC progression. Furthermore, tumor growth of mice was suppressed by sh-SUV39H1 transfection, chaetocin treatment, or F5446 treatment. In conclusion, SUV39H1 promoted GC progression by modulating the H3K9me3/ALDOB axis.

Epigenetics and suicidal behavior in adolescents: a critical review

Suicide continues to be a significant public health issue globally, claiming over 700,000 lives annually. It is, therefore, important to assess the suicide risk properly and provide intervention in a timely fashion. While the heritability of suicidal behavior is around 50%, it does not explain the factors involved in causality. Recent evidence suggests that gene x environment interaction plays a vital role in suicidal behavior. In this paper, we critically evaluate the association between adolescent suicidal behavior and epigenetic modifications, including DNA methylation, histone modification, and non-coding RNAs, as well as epigenetic-based treatment options. It was noted that the prevalence of suicidal behavior in adolescents varied by age and sex and the presence of psychiatric disorders. Childhood adversity was closely associated with suicidal behavior. Studies show that alterations in epigenetic modifications may increase the risk of suicidal behavior independent of mental illnesses. Because epigenetic factors are reversible, environmental enrichment or the use of pharmacological agents that can target specific epigenetic modulation may be able to reduce suicidal behavior in this population.

Epigenetic marvels: exploring the landscape of colorectal cancer treatment through cutting-edge epigenetic-based drug strategies

Epigenetics is currently considered the investigation of inheritable changes in gene expression that do not rely on DNA sequence alteration. Significant epigenetic procedures are involved, such as DNA methylations, histone modifications, and non-coding RNA actions. It is confirmed through several investigations that epigenetic changes are associated with the formation, development, and metastasis of various cancers, such as colorectal cancer (CRC). The difference between epigenetic changes and genetic mutations is that the former could be reversed or prevented; therefore, cancer treatment and prevention could be achieved by restoring abnormal epigenetic events within the neoplastic cells. These treatments, consequently, cause the anti-tumour effects augmentation, drug resistance reduction, and host immune response stimulation. In this article, we begin our survey by exploring basic epigenetic mechanisms to understand epigenetic tools and strategies for treating colorectal cancer in monotherapy and combination with chemotherapy or immunotherapy.

Acetylation of histone H2B on lysine 120 regulates BRD4 binding to intergenic enhancers

BRD4 is a bromodomain-containing transcriptional co-regulator that plays important roles in driving transcription by binding to histone acetyl-lysines at enhancers and promoters while recruiting additional transcriptional cofactors. While the mechanisms by which BRD4 regulates transcription have been explored, the critical acetylations primarily responsible for targeting it to chromatin remain unclear. Through a machine learning approach, we determined that distinct sets of histone acetylations dominate the prediction of chromatin accessibility and BRD4 binding in distinct chromatin contexts (e.g. intergenic enhancers, gene body enhancers and promoters). Using human fibroblasts engineered to predominantly express specific histones with lysine-to-arginine mutations, we demonstrate that one such acetylation, H2BK120ac, is required to recruit BRD4 specifically to intergenic enhancers, while not affecting chromatin accessibility. Loss of H2BK120ac did not affect BRD4 binding to either promoters or gene body enhancers, demonstrating that the rules governing BRD4 recruitment to regulatory regions depends on the specific genomic context. Highlighting the importance of H2BK120ac in directing BRD4 recruitment, we found that expression of the H2BK120R mutant significantly reduces the phenotypes driven by BRD4-NUT, an oncogenic fusion protein that drives NUT midline carcinoma. This work demonstrates the critical nature that genomic context plays in BRD4 recruitment to distinct classes of regulatory elements, and suggests that intergenic and gene body enhancers represent classes of functional distinct elements.

Short-chain fatty acids and cancer

Short-chain fatty acids (SCFAs), derived from the diet and the microbiota, serve as crucial links between the diet, gut microbiota, metabolism, immunity, and cancer. They function as energy sources through β-oxidation and regulate macromolecular synthesis, G protein-coupled receptor (GPCR) and histone deacetylase (HDAC) activities, protein modifications, signaling pathways, and gene expression in cells within the tumor microenvironment, particularly in tumor and immune cells. The critical role of SCFAs in maintaining normal homeostasis and influencing tumor progression highlights the potential of targeting SCFA-mediated cellular processes for cancer prevention and treatment.

Epigenetic regulation of macrophage function in kidney disease: New perspective on the interaction between epigenetics and immune modulation

The interaction between renal intrinsic cells and macrophages plays a crucial role in the onset and progression of kidney diseases. In recent years, epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA regulation have become essential windows for understanding these processes. This review focuses on how renal intrinsic cells (including tubular epithelial cells, podocytes, and endothelial cells), renal cancer cells, and mesenchymal stem cells influence the function and polarization status of macrophages through their own epigenetic alterations, and how the epigenetic regulation of macrophages themselves responds to kidney damage, thus participating in renal inflammation, fibrosis, and repair. Moreover, therapeutic studies targeting these epigenetic interaction mechanisms have found that the application of histone deacetylase inhibitors, histone methyltransferase inhibitors, various nanomaterials, and locked nucleic acids against non-coding RNA have positive effects on the treatment of multiple kidney diseases. This review summarizes the latest research advancements in these epigenetic regulatory mechanisms and therapies, providing a theoretical foundation for further elucidating the pathogenesis of kidney diseases and the development of novel therapeutic strategies.

Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis

Light and temperature are two key environmental factors that control plant growth and adaptation by influencing biomolecular events. This review highlights the latest milestones on the role of light and high temperatures in modulating the epigenetic and epitranscriptomic landscape of Arabidopsis to trigger developmental and adaptive responses to a changing environment. Recent discoveries on how light and high temperature signals are integrated in the nucleus to modulate gene expression are discussed, as well as highlighting research gaps and future perspectives in further understanding how to promote plant resilience in times of climate change.

The role of chromatin-related epigenetic modulations in CAKUT

Congenital anomalies of the kidney and urinary tract (CAKUT) represent a major health burden in humans. Phenotypes range from renal hypoplasia or renal agenesis, cystic renal dysplasia, duplicated or horseshoe kidneys to obstruction of the ureteropelvic junction, megaureters, duplicated ureters, urethral valves or bladder malformations. Over the past decade, next-generation sequencing has identified numerous causative genes; however, the genetic basis of most cases remains unexplained. It is assumed that environmental factors have a significant impact on the phenotype, but, overall, the pathogenesis has remained poorly understood. Interestingly however, CAKUT is a common phenotypic feature in two human syndromes, Kabuki and Koolen-de Vries syndrome, caused by dysfunction of genes encoding for KMT2D and KANSL1, both members of protein complexes playing an important role in histone modifications. In this chapter, we discuss current knowledge regarding epigenetic modulation in renal development and a putatively under-recognized role of epigenetics in CAKUT.

Melatonin Modulates ZAP70 and CD40 Transcripts via Histone Modifications in Canine Ileum Epithelial Cells

Melatonin (MLT), produced by the pineal gland and other tissues, is known for its anti-inflammatory effects, particularly in regulating inflammatory markers and cytokines in intestinal cells. Our study aimed to investigate how MLT influences the expression of inflammatory genes through histone modification in canine ileum epithelial cells (cIECs). In our experiment, cIECs were cultured and divided into a control group (CON) and an MLT-treatment group. MLT did not significantly affect cell growth or death in cIECs compared to the CON. However, MLT treatment led to an upregulation of CD40, ZAP70, and IL7R and a downregulation of LCK, RPL37, TNFRSF13B, CD4, CD40LG, BLNK, and CIITA at the mRNA expression level. Moreover, MLT significantly altered the NF-kappa B signaling pathway by upregulating genes, such as CD40, ZAP70, TICAM1, VCAMI, GADD45B, IRAK1, TRADD, RELA, RIPK1, and RELB, and downregulating PRKCB, LY96, CD40LG, ILIB, BLNK, and TNFRSF11A. Using ChIP-qPCR, we discovered that MLT treatment enhanced histone acetylation marks H3K9ac, H3K18ac, H3K27ac, and methylation marks H3K4me1 and H3K4me3 at the ZAP70 and CD40 gene loci (p < 0.05). Additionally, the enrichment of RNA polymerase II and phosphorylated Ser5 pol-II at these loci was increased in MLT-treated cells (p < 0.05), indicating heightened transcriptional activity. In conclusion, our findings suggest that MLT mitigates inflammation in cIECs by modulating the transcription of ZAP70 and CD40 through histone modifications, offering potential therapeutic insights for inflammatory bowel diseases.

Epigenetic Mechanisms Underlying Sex Differences in Neurodegenerative Diseases

Neurodegenerative diseases are characterized by profound differences between females and males in terms of incidence, clinical presentation, and disease progression. Furthermore, there is evidence suggesting that differences in sensitivity to medical treatments may exist between the two sexes. Although the role of sex hormones and sex chromosomes in driving differential susceptibility to these diseases is well-established, the molecular alterations underlying these differences remain poorly understood. Epigenetic mechanisms, including DNA methylation, histone tail modifications, and the activity of non-coding RNAs, are strongly implicated in the pathogenesis of neurodegenerative diseases. While it is known that epigenetic mechanisms play a crucial role in sexual differentiation and that distinct epigenetic patterns characterize females and males, sex-specific epigenetic patterns have been largely overlooked in studies aiming to identify epigenetic alterations associated with neurodegenerative diseases. This review aims to provide an overview of sex differences in epigenetic mechanisms, the role of sex-specific epigenetic processes in the central nervous system, and the main evidence of sex-specific epigenetic alterations in three neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Understanding the sex-related differences of these diseases is essential for developing personalized treatments and interventions that account for the unique epigenetic landscapes of each sex.

Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)

Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.

The Role of Chronic Inflammation in Pediatric Cancer

Inflammation plays a crucial role in wound healing and the host immune response following pathogenic invasion. However, unresolved chronic inflammation can result in tissue fibrosis and genetic alterations that contribute to the pathogenesis of human diseases such as cancer. Recent scientific advancements exploring the underlying mechanisms of malignant cellular transformations and cancer progression have exposed significant disparities between pediatric and adult-onset cancers. For instance, pediatric cancers tend to have lower mutational burdens and arise in actively developing tissues, where cell-cycle dysregulation leads to gene, chromosomal, and fusion gene development not seen in adult-onset counterparts. As such, scientific findings in adult cancers cannot be directly applied to pediatric cancers, where unique mutations and inherent etiologies remain poorly understood. Here, we review the role of chronic inflammation in processes of genetic and chromosomal instability, the tumor microenvironment, and immune response that result in pediatric tumorigenesis transformation and explore current and developing therapeutic interventions to maintain and/or restore inflammatory homeostasis.

Epigenetic Regulation of Stromal and Immune Cells and Therapeutic Targets in the Tumor Microenvironment

The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation and progression. Epigenetic machinery, governing the expression of core oncogenes and tumor suppressor genes in transformed cells, significantly contributes to tumor development at both primary and distant sites. Recent studies have illuminated how epigenetic mechanisms integrate external cues and downstream signals, altering the phenotype of stromal cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering an immunosuppressive microenvironment. Therefore, correcting the TME by targeting the epigenetic modifications holds substantial promise for cancer treatment. This review synthesizes recent research that elucidates the impact of specific epigenetic regulations-ranging from DNA methylation to histone modifications and chromatin remodeling-on stromal and immune cells within the TME. Notably, we highlight their functional roles in either promoting or restricting tumor progression. We also discuss the potential applications of epigenetic agents for cancer treatment, envisaging their ability to normalize the ecosystem. This review aims to assist researchers in understanding the dynamic interplay between epigenetics and the TME, paving the way for better epigenetic therapy.

Autoimmune Thyroid Disease and Pregnancy: The Interaction Between Genetics, Epigenetics and Environmental Factors

Autoimmune thyroid disease (AITD) is the leading cause of thyroid dysfunction globally, characterized primarily by two distinct clinical manifestations: Hashimoto's thyroiditis (HT) and Graves' disease (GD). The prevalence of AITD is approximately twice as high in women compared to men, with a particularly pronounced risk during the reproductive years. Pregnancy exerts profound effects on thyroid physiology and immune regulation due to hormonal fluctuations and immune adaptations aimed at fostering maternal-fetal tolerance, potentially triggering or exacerbating AITD. The impact of AITD on pregnancy outcomes is multifaceted. Both HT and GD have been associated with adverse obstetric and neonatal outcomes, including miscarriage, preterm delivery, preeclampsia and fetal growth restriction. Inadequately managed AITD can also affect fetal neurodevelopment due to disrupted maternal thyroid hormone availability during critical periods of brain maturation. This review explores the complex interplay between the genetic, epigenetic and environmental factors that drive AITD during pregnancy, highlighting their roles in disease development and impacts on pregnancy outcomes. Gaining a deeper understanding of these mechanisms is crucial for improving diagnostic tools, treatment options and preventive measures to enhance the health and well-being of both the mother and the newborn.

Covalent inhibitors meet epigenetics: New opportunities

Epigenetic intervention has become an important therapeutic strategy for a variety of diseases, such as cancer. Although a small number of epigenetic drugs have been marketed, most of these inhibitors are limited by their poor efficacy, dose-dependent toxicity, poor selectivity, and drug resistance. The development of covalent inhibitors has progressed from questioning to resurgence. Its slow dissociation is expected to inject new vitality into epigenetic drugs. In this review, more than 40 covalent inhibitors of 29 epigenetic targets were collated, focusing on their design strategies, reaction mechanisms, covalent warheads and targeted amino acids, and covalent verification methods. Furthermore, this review presented new opportunities based on the current development of covalent inhibitors targeting epigenetic regulators. It is believed that epigenetic covalent inhibitors will lead to more breakthroughs.

PFKP Lactylation Promotes the Ovarian Cancer Progression Through Targeting PTEN

Ovarian cancer (OC) ranks among the most prevalent malignancies affecting females globally and is a leading cause of cancer-related mortality in women. This study sought to elucidate the influence of phosphofructokinase P (PFKP) on the progression of OC. A cohort of sixty OC patients was enrolled. OC cells were exposed to both normoxic and hypoxic conditions. Expression levels of PFKP and phosphatase and tensin homolog (PTEN) were quantified using real time quantitative polymerase chain reaction (RT-qPCR) and Western blot analyses. Immunofluorescence confirmed these protein expression patterns. Glycolysis-related parameters, encompassing glucose uptake, extracellular lactate levels, extracellular acidification rates, and oxygen consumption rates, were assessed using commercially available kits. Lactylation status of PFKP was evaluated via immunoprecipitation followed by Western blot analysis. An OC xenograft mouse model was also established. Findings indicated elevated PFKP expression in OC tissues and cells. Additionally, PFKP knockdown attenuated glycolysis and counteracted the hypoxia-induced enhancement of glycolytic activity in OC cells. Mutation of the lysine (K) residue at position 392 diminished PFKP lactylation. Further investigations revealed that PFKP depletion upregulated PTEN expression in hypoxia-treated OC cells. Besides, PTEN suppression increased the glycolysis in hypoxia-treated OC cells. Animal study results demonstrated that PFKP inhibition curtailed OC tumor growth by modulating PTEN expression. Collectively, these results suggested that lactylation of PFKP at the K392 residue promoted glycolysis in OC cells by regulating PTEN, thereby facilitating the disease's progression.

Overview of PRMT1 modulators: Inhibitors and degraders

Protein arginine methyltransferase 1 (PRMT1) is pivotal in executing normal cellular functions through its catalytic action on the methylation of arginine side chains on protein substrates. Emerging research has revealed a correlation between the dysregulation of PRMT1 expression and the initiation and progression of tumors, significantly influence on patient prognostication, attributed to the essential role played by PRMT1 in a number of biological processes, including transcriptional regulation, signal transduction or DNA repair. Therefore, PRMT1 emerged as a promising therapeutic target for anticancer drug discovery in the past decade. In this review, we first summarize the structure and biological functions of PRMT1 and its association with cancer. Next, we focus on the recent advances in the design and development of PRMT1 modulators, including isoform-selective PRMT1 inhibitors, pan type I PRMT inhibitors, PRMT1-based dual-target inhibitors, and PRMT1-targeting PROTAC degraders, from the perspectives of rational design, pharmacodynamics, pharmacokinetics, and clinical status. Finally, we discuss the challenges and future directions for PRMT1-based drug discovery for cancer therapy.

Ionotropic purinergic receptor 7 (P2X7) channel structure and pharmacology provides insight regarding non-nucleotide agonism

P2X7 is a member of the Ionotropic Purinergic Receptor (P2X) family. The P2X family of receptors is composed of seven (P2X1-7), ligand-gated, nonselective cation channels. Changes in P2X expression have been reported in multiple disease models. P2Xs have large complex extracellular domains that function as receptors for a variety of ligands, including endogenous and synthetic agonists and antagonists. ATP is the canonical agonist. ATP affinity ranges from nanomolar to micromolar for most P2XRs, but P2X7 has uniquely poor ATP affinity. In many physiological settings, it may be difficult to achieve the millimolar extracellular ATP concentrations needed for P2X7 channel activation; however, channel function is implicated in pain sensation, immune cell function, cardiovascular disease, cancer, and osteoporosis. Multiple high-resolution P2X7 structures have been solved in apo-, ATP-, and antagonist-bound states. P2X7 structural data reveal distinct allosteric and orthosteric antagonist-binding sites. Both allosteric and orthosteric P2X7 antagonists are well documented to inhibit ATP-evoked channel current. However, a growing body of evidence supports P2X7 activation by non-nucleotide agonists, including extracellular histone proteins and human cathelicidin-derived peptides (LL-37). Interestingly, P2X7 non-nucleotide agonism is not inhibited by allosteric antagonists, but is inhibited by orthosteric antagonists. Herein, we review P2X7 function with a focus on the efficacy of available pharmacology on P2X7 channel current activation by non-nucleotide agonists in effort to understand agonist/antagonist efficacy, and consider the impact of these data on the current understanding of P2X7 in physiology and disease given these limitations of P2X7-selective antagonists and incomplete knockout mouse models.

Design and synthesis of triazolopyridine derivatives as potent JAK/HDAC dual inhibitors with broad-spectrum antiproliferative activity

A series of triazolopyridine-based dual JAK/HDAC inhibitors were rationally designed and synthesised by merging different pharmacophores into one molecule. All triazolopyridine derivatives exhibited potent inhibitory activities against both targets and the best compound 4-(((5-(benzo[d][1, 3]dioxol-5-yl)-[1, 2, 4]triazolo[1, 5-a]pyridin-2-yl)amino)methyl)-N-hydroxybenzamide (19) was dug out. 19 was proved to be a pan-HDAC and JAK1/2 dual inhibitor and displayed high cytotoxicity against two cancer cell lines MDA-MB-231 and RPMI-8226 with IC50 values in submicromolar range. Docking simulation revealed that 19 fitted well into the active sites of HDAC and JAK proteins. Moreover, 19 exhibited better metabolic stability in vitro than SAHA. Our study demonstrated that compound 19 was a promising candidate for further preclinical studies.

Epigenetic modifications involving ncRNAs in digestive system cancers: focus on histone modification

In recent years, epigenetic modifications have been strongly linked to tumor development, with histone modifications representing a key epigenetic mechanism. In addition, non-coding RNAs (ncRNAs) play a critical role in regulating cancer-related pathways. The abnormal interaction between histone modifications and ncRNAs, both pivotal epigenetic regulators, has been widely observed across various cancer types. Here, we systematically explore the molecular mechanisms through which histone modifications and ncRNAs contribute in the pathogenesis of digestive system cancers, and aberrant ncRNA-mediated histone modifications manipulate various biological behaviors of tumor cells including proliferation, migration, angiogenesis, etc. In addition, we provide new insights into diagnostic, prognostic markers, therapeutic targets and chemoradiation resistance for digestive system cancers from the epigenetic perspective.

Crosstalk between adipogenesis and aging: role of polyphenols in combating adipogenic-associated aging

In the last forty years, the number of people over 60 years of age has increased significantly owing to better nutrition and lower rates of infectious diseases in developing countries. Aging significantly impacts adipose tissue, which plays crucial role in hormone regulation and energy storage. This can lead to imbalances in glucose, and overall energy homeostasis within the body. Aging is irreversible phenomena and potentially causing lipid infiltration in other organs, leading to systemic inflammation, metabolic disorders. This review investigates various pathways contributing to aging-related defects in adipogenesis, such as changes in adipose tissue function and distribution. Polyphenols, a diverse group of natural compounds, can mitigate aging effects via free radicals, oxidative stress, inflammation, senescence, and age-related diseases. Polyphenols like resveratrol, quercetin and EGCG exhibit distinct mechanisms and regulate crucial pathways, such as the TGF-β, AMPK, Wnt, PPAR-γ, and C/EBP transcription factors, and influence epigenetic modifications, such as DNA methylation and histone modification. This review highlights the critical importance of understanding the intricate relationship between aging and adipogenesis for optimizing well-being with increasing age. These findings highlight the therapeutic potential of polyphenols like quercetin and resveratrol in enhancing adipose tissue function and promoting healthy aging.

Influence of Nutrition on Growth and Development of Metabolic Syndrome in Children

Obesity is currently an increasing public health burden due to its related metabolic and cardiovascular complications. In Western countries, a significant number of people are overweight or obese, and this trend is, unfortunately, becoming increasingly common even among the pediatric population. In this narrative review, we analyzed the role of nutrition during growth and its impact on the risk of developing metabolic syndrome and cardiovascular complications later in life. An impactful role in determining the phenotypic characteristics of the offspring is the parental diet carried out before conception. During intrauterine growth, the main risk factors are represented by an unbalanced maternal diet, excessive gestational weight gain, and impaired glycemic status. Breastfeeding, on the other hand, has many beneficial effects, but at the same time the quality of breast milk may be modified if maternal overweight or obesity subsists. Complementary feeding is likewise pivotal because an early introduction before 4 months of age and a high protein intake contribute to weight gain later. Knowledge of these mechanisms may allow early modification of risk factors by implementing targeted preventive strategies.

Histone lactylation facilitates hepatocellular carcinoma progression by upregulating endothelial cell-specific molecule 1 expression

Hepatocellular carcinoma (HCC) is a common malignant tumor. Histone lactylation, a novel epigenetic modification, plays a crucial role in various cancers. However, the functional role and underlying mechanism of histone lactylation in HCC progression have not yet been investigated. Histone lactylation levels in HCC tissues and cells were assessed using a densitometric kit and western blot analysis. The role of histone lactylation in cell malignant phenotypes was determined through functional assays in vitro, and a xenograft tumor model was established to verify the function of histone lactylation in vivo. ChIP assay was performed to explore the interaction between histone lactylation and endothelial cell-specific molecule 1 (ESM1). Additionally, gain-and-loss-of-function assays were conducted to investigate the regulatory role of ESM1 in HCC pathogenesis. Histone lactylation levels were increased in HCC tissues and cells, and H3K9 lactylation (H3K9la) and H3K56 lactylation (H3K56la) were identified as the histone modification sites. We observed that H3K9la and H3K56la caused abnormal histone lactylation and were associated with poor prognosis. Functionally, histone lactylation was found to promote HCC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) process in vitro. However, histone lactylation inhibition with 2-deoxy-d-glucose (2-DG) reduced the malignant phenotypes of HCC cells. In vivo, 2-DG treatment reduced tumor growth and metastasis in the HCC mouse model. Mechanistically, it was revealed that histone lactylation activated ESM1 transcription in HCC cells. ESM1 was expressed at a high level in HCC and exerted a carcinogenic role. Histone lactylation facilitates cell malignant phenotypes, tumor growth, and metastasis by upregulating ESM1 expression in HCC, which reveals the downstream molecular mechanism of histone lactylation and might provide a novel therapeutic target for HCC therapy.

Overview of chromatin regulatory processes during surface ectodermal development and homeostasis

The ectoderm is the outermost of the three germ layers of the early embryo that arise during gastrulation. Once the germ layers are established, the complex interplay of cellular proliferation, differentiation, and migration results in organogenesis. The ectoderm is the progenitor of both the surface ectoderm and the neural ectoderm. Notably, the surface ectoderm develops into the epidermis and its associated appendages, nails, external exocrine glands, olfactory epithelium, and the anterior pituitary. Specification, development, and homeostasis of these organs demand a tightly orchestrated gene expression program that is often dictated by epigenetic regulation. In this review, we discuss the recent discoveries that have highlighted the importance of chromatin regulatory mechanisms mediated by transcription factors, histone and DNA modifications that aid in the development of surface ectodermal organs and maintain their homeostasis post-development.

Multifaceted paternal exposures before conception and their epigenetic impact on offspring

As scientific research progresses, there is an increasing understanding of the importance of paternal epigenetics in influencing the health and developmental path of offspring. Prior to conception, the environmental exposures and lifestyle choices of fathers can significantly influence the epigenetic state of sperm, including DNA methylation and histone changes, among other factors. These alterations in epigenetic patterns have the potential for transgenerational transmission potential and may exert profound effects on the biological characteristics of descendants. Paternal epigenetic changes not only affect the regulation of gene expression patterns in offspring but also increase the risk to certain diseases. It is crucial to comprehend the conditions that fathers are exposed to before conception and the potential outcomes of these conditions. This understanding is essential for assessing personal reproductive decisions and anticipating health risks for future generations. This review article systematically summarizes and analyzes current research findings regarding how paternal pre-pregnancy exposures influence offspring as well as elucidates underlying mechanisms, aiming to provide a comprehensive perspective for an enhanced understanding of the impact that paternal factors have on offspring health.

Histone demethylases in neurodevelopment and neurodegenerative diseases

Neurodevelopment can be precisely regulated by epigenetic mechanisms, including DNA methylations, noncoding RNAs, and histone modifications. Histone methylation was a reversible modification, catalyzed by histone methyltransferases and demethylases. So far, dozens of histone lysine demethylases (KDMs) have been discovered, and they (members from KDM1 to KDM7 family) are important for neurodevelopment by regulating cellular processes, such as chromatin structure and gene transcription. The role of KDM5C and KDM7B in neural development is particularly important, and mutations in both genes are frequently found in human X-linked mental retardation (XLMR). Functional disorders of specific KDMs, such as KDM1A can lead to the development of neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD). Several KDMs can serve as potential therapeutic targets in the treatment of neurodegenerative diseases. At present, the function of KDMs in neurodegenerative diseases is not fully understood, so more comprehensive and profound studies are needed. Here, the role and mechanism of histone demethylases were summarized in neurodevelopment, and the potential of them was introduced in the treatment of neurodegenerative diseases.

New insights into the roles of lactylation in cancer

Lactylation, a novel discovered posttranslational modification, is a vital component of lactate function and is prevalent in a wide range of cells, interacting with both histone and non-histone proteins. Recent studies have confirmed that lactylation as a new contributor to epigenetic landscape is involved in multiple pathological processes. Accumulating evidence reveals that lactylation exists in different pathophysiological states and leads to inflammation and cancer; however, few mechanisms of lactylation have been elaborated. This review summarizes the biological processes and pathophysiological roles of lactylation in cancer, as well as discusses the relevant mechanisms and potential therapeutic targets, aiming to provide new insights for targeted cancer therapy.

Oxygen Glucose Deprivation-Induced Lactylation of H3K9 Contributes to M1 Polarization and Inflammation of Microglia Through TNF Pathway

BACKGROUND

Hypoxia-induced M1 polarization of microglia and resultant inflammation take part in the damage caused by hypoxic-ischemic encephalopathy (HIE). Histone lactylation, a novel epigenetic modification where lactate is added to lysine residues, may play a role in HIE pathogenesis. This study investigates the role of histone lactylation in hypoxia-induced M1 microglial polarization and inflammation, aiming to provide insights for HIE treatment.

METHODS

In this study, we assessed the effects of hypoxia on microglial polarization using both an HIE animal model and an oxygen-glucose deprivation cell model. Histone lactylation at various lysine residues was detected by Western blotting. Microglial polarization and inflammatory cytokines were analyzed by immunofluorescence, qPCR, and Western blotting. RNA sequencing, ChIP-qPCR, and siRNA were used to elucidate mechanisms of H3K9 lactylation.

RESULTS

H3K9 lactylation increased due to cytoplasmic lactate during M1 polarization. Inhibiting P300 or reducing lactate dehydrogenase A expression decreased H3K9 lactylation, suppressing M1 polarization. Transcriptomic analysis indicated that H3K9 lactylation regulated M1 polarization via the TNF signaling pathway. ChIP-qPCR confirmed H3K9 lactylation enrichment at the TNFα locus, promoting OGD-induced M1 polarization and inflammation.

CONCLUSIONS

H3K9 lactylation promotes M1 polarization and inflammation via the TNF pathway, identifying it as a potential therapeutic target for neonatal HIE.

Dysregulation of epigenetic modifications in inborn errors of immunity

Inborn errors of immunity (IEIs) are a group of typically monogenic disorders characterized by dysfunction in the immune system. Individuals with these disorders experience increased susceptibility to infections, autoimmunity and malignancies due to abnormal immune responses. Epigenetic modifications, including DNA methylation, histone modifications and chromatin remodeling, have been well explored in the regulation of immune cell development and effector function. Aberrant epigenetic modifications can disrupt gene expression profiles crucial for immune responses, resulting in impaired immune cell differentiation and function. Dysregulation of these processes caused by mutations in genes involving in epigenetic modifications has been associated with various IEIs. In this review article, we focus on IEIs that are caused by mutations in 13 genes involved in the regulation of DNA methylation, histone modification and chromatin remodeling.