The critical importance of epigenetics in autoimmune-related skin diseases / 医学前沿

Autoimmune-related skin diseases are a group of disorders with diverse etiology and pathophysiology involved in autoimmunity. Genetics and environmental factors may contribute to the development of these autoimmune disorders. Although the etiology and pathogenesis of these disorders are poorly understood, environmental variables that induce aberrant epigenetic regulations may provide some insights. Epigenetics is the study of heritable mechanisms that regulate gene expression without changing DNA sequences. The most important epigenetic mechanisms are DNA methylation, histone modification, and noncoding RNAs. In this review, we discuss the most recent findings regarding the function of epigenetic mechanisms in autoimmune-related skin disorders, including systemic lupus erythematosus, bullous skin diseases, psoriasis, and systemic sclerosis. These findings will expand our understanding and highlight the possible clinical applications of precision epigenetics approaches.

Insights into epigenetic patterns in mammalian early embryos

Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.

Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders

Post-translational modification (PTM) in histone proteins is a covalent modification which mainly consists ofmethylation, phosphorylation, acetylation, ubiquitylation, SUMOylation, glycosylation, and ADP-ribosylation.PTMs have fundamental roles in chromatin structure and function. Histone modifications have also beenknown as epigenetic markers. The PTMs that have taken place in histone proteins can affect gene expressionby altering chromatin structure. Histone modifications act in varied biological processes such as transcriptionalactivation/inactivation, chromosome packaging, mitosis, meiosis, apoptosis, and DNA damage/repair. Defectsin the PTMs pathway have been associated with the occurrence and progression of various human diseases,such as cancer, heart failure, autoimmune diseases, and neurodegenerative disorders such as Parkinson’sdisease, Alzheimer’s disease, and Huntington’s disease. Histone modifications are reversible and used aspotential targets for cancer therapy and prevention. Recent different histone PTMs have key roles in cancercells since it has been shown that histone PTMs markers in cancers are acetylation, methylation, phosphorylation, and ubiquitylation. In this review, we have summarized the six most studied histone modifications andhave examined the role of these modifications in the development of cancer.

Elucidation and genetic intervention of CO2 concentration mechanism in Chlamydomonas reinhardtii for increased plant primary productivity

Post-translational modification (PTM) in histone proteins is a covalent modification which mainly consists ofmethylation, phosphorylation, acetylation, ubiquitylation, SUMOylation, glycosylation, and ADP-ribosylation.PTMs have fundamental roles in chromatin structure and function. Histone modifications have also beenknown as epigenetic markers. The PTMs that have taken place in histone proteins can affect gene expressionby altering chromatin structure. Histone modifications act in varied biological processes such as transcriptionalactivation/inactivation, chromosome packaging, mitosis, meiosis, apoptosis, and DNA damage/repair. Defectsin the PTMs pathway have been associated with the occurrence and progression of various human diseases,such as cancer, heart failure, autoimmune diseases, and neurodegenerative disorders such as Parkinson’sdisease, Alzheimer’s disease, and Huntington’s disease. Histone modifications are reversible and used aspotential targets for cancer therapy and prevention. Recent different histone PTMs have key roles in cancercells since it has been shown that histone PTMs markers in cancers are acetylation, methylation, phosphorylation, and ubiquitylation. In this review, we have summarized the six most studied histone modifications andhave examined the role of these modifications in the development of cancer.

Role of genomic imprinting in mammalian development

In mammals, DNA methyltransferases transfer a methyl group from S-adenosylmethionine to the 5 position ofcytosine in DNA. The product of this reaction, 5-methylcytosine (5mC), has many roles, particularly insuppressing transposable and repeat elements in DNA. Moreover, in many cellular systems, cell lineagespecification is accompanied by DNA demethylation at the promoters of genes expressed at high levels in thedifferentiated cells. However, since direct cleavage of the C-C bond connecting the methyl group to the 5position of cytosine is thermodynamically disfavoured, the question of whether DNA methylation wasreversible remained unclear for many decades. This puzzle was solved by our discovery of the TET (TenEleven Translocation) family of 5-methylcytosine oxidases, which use reduced iron, molecular oxygen and thetricarboxylic acid cycle metabolite 2-oxoglutarate (also known as a-ketoglutarate) to oxidise the methyl groupof 5mC to 5-hydroxymethylcytosine (5hmC) and beyond. TET-generated oxidised methylcytosines areintermediates in at least two pathways of DNA demethylation, which differ in their dependence on DNAreplication. In the decade since their discovery, TET enzymes have been shown to have important roles inembryonic development, cell lineage specification, neuronal function and cancer. We review these findings anddiscuss their implications here.

Research progress on application of epigenetics and metabolomics in traditional Chinese medicine / 中草药

Traditional Chinese medicine has multi-component, multi-target, and multi-path action characteristics and complexity, which makes the task of modernizing traditional Chinese medicine arduous, and many medical researchers have made unremitting efforts to this end. The development of systems biology and omics has ushered in an opportunity for the integration of traditional Chinese medicine and modern science. In particular, the characteristics integrity, dynamics, personalization, and interaction with the environment of epigenetics and metabolomics are consistent with function concept of traditional Chinese medicine. The application of popular DNA methylation, histone modifications, miRNA regulation of epigenetic research, and the application of metabolomics in the substance basis, quality control, pharmacodynamic action mechanism in traditional Chinese medicine research are reviewed in this paper. This paper also puts forward the idea that combining the two and innovative application can clarify the scientific connotation of the whole action mechanism of traditional Chinese medicine and the mechanism of multi-component, multi-channel, and multi-target synergistic action at the micro level, and explore a new research model for the scientific connotation of the core thought of traditional Chinese medicine.

Transcriptional repression by androgen receptor: Roles in castration-resistant prostate cancer / 亚洲男科学杂志(英文版)

Androgen receptor (AR), a hormonal transcription factor, plays important roles during prostate cancer progression and is a key target for therapeutic interventions. While androgen-deprivation therapies are initially successful in regressing prostate tumors, the disease ultimately comes back as castration-resistant prostate cancer (CRPC) or at the late stage as neuroendocrine prostate cancer (NEPC). CRPC remains largely dependent on hyperactive AR signaling in the milieu of low androgen, while NEPC is negative of AR expression but positive of many AR-repressed genes. Recent technological advances in genome-wide analysis of transcription factor binding sites have revealed an unprecedented set of AR target genes. In addition to its well-known function in activating gene expression, AR is increasingly known to also act as a transcriptional repressor. Here, we review the molecular mechanisms by which AR represses gene expression. We also summarize AR-repressed genes that are aberrantly upregulated in CRPC and NEPC and represent promising targets for therapeutic intervention.

Alteraciones epigenéticas en leucemia linfoblástica aguda / Epigenetic alterations in acute lymphoblastic leukemia

Resumen: La leucemia linfoblástica aguda (LLA) es el tipo de cáncer más frecuente en niños. Aunque se sabe que las alteraciones genéticas constituyen la base de la etiología de la LLA, se ha demostrado que no son suficientes para el desarrollo leucémico; son necesarias alteraciones adicionales, como las modificaciones epigenéticas. En la LLA se han identificado alteraciones de este tipo, como la metilación del DNA, la modificación de histonas y la regulación por RNAs no codificantes. La hipermetilación del DNA en regiones promotoras es una de las alteraciones epigenéticas más frecuentes en LLA: y conlleva al silenciamiento de genes que generalmente son supresores de tumor y, en consecuencia, contribuye a la leucemogénesis. También se han detectado alteraciones en proteínas remodeladoras de histonas, como la sobreexpresión de enzimas desacetilasas de histonas, así como alteraciones en enzimas acetil transferasas y metil transferasas. En la LLA también se altera la expresión de miRNAs, lo cual produce desregulación en la expresión de sus genes blanco. Estas modificaciones epigenéticas son eventos clave en la transformación maligna, e involucran la desregulación de oncogenes como BLK, WNT5B y WISP1 y de supresores de tumor como FHIT, CDKN2A, CDKN2B y TP73, lo que afecta diversos procesos celulares fundamentales que conllevan al desarrollo de LLA. Las alteraciones epigenéticas y genéticas contribuyen en conjunto al desarrollo y evolución de la LLA.

Abstract: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. It is well-known that genetic alterations constitute the basis for the etiology of ALL. However, genetic abnormalities are not enough for the complete development of the disease, and additional alterations such as epigenetic modifications are required. Such alterations, like DNA methylation, histone modifications, and noncoding RNA regulation have been identified in ALL. DNA hypermethylation in promoter regions is one of the most frequent epigenetic modifications observed in ALL. This modification frequently leads to gene silencing in tumor suppressor genes, and in consequence, contributes to leukemogenesis. Alterations in histone remodeling proteins have also been detected in ALL, such as the overexpression of histone deacetylases enzymes, and alteration of acetyltransferases and methyltransferases. ALL also shows alteration in the expression of miRNAs, and in consequence, the modification in the expression of their target genes. All of these epigenetic modifications are key events in the malignant transformation since they lead to the deregulation of oncogenes as BLK, WNT5B and WISP1, and tumor suppressors such as FHIT, CDKN2A, CDKN2B, and TP53, which alter fundamental cellular processes and potentially lead to the development of ALL. Both genetic and epigenetic alterations contribute to the development and evolution of ALL.

Effects of suberoylanilide hydroxamic acidon proliferation and apoptosis of human hepatic stellate cells / 基础医学与临床

Objective To determine the effects of histone deacetylase inhibitor suberoylanilide hydroxamic acid(SAHA) on the cell proliferation and apoptosis of the human hepatic stellate cell line LX-2.The possible underlying mechanisms were also investigated.Methods The LX-2 cells were treated with SAHA in vitro.The morphology of LX-2 cells in different concentrations groups was observed by inverted microscope;the proliferation of LX-2 cells was measured by MTT assay;the Annexin V-FITC and PI staining was used to detect the apoptosis of LX-2 cells by flow cytometry and fluorescence microscope;the expression of α-SMA,collagen Ⅰ,acH3K9,acH3K14 and acH3K18 were detected by Western blot.Results The morphology change of LX-2 cells showed that SAHA inhibited the proliferation rate of LX-2 cells and in a dose dependent manner(P<0.05).The LX-2 cells were sensitive to SAHA along with time increasing,and in a time-dependent manner(P<0.05).Western blot showed that the expression levels of α-SMA and collagen-Ⅰ were significantly lower(P<0.05),on the contrary,the acetylation levels of acH3K9,acH3K14 and acH3K18 were significantly higher (P<0.05).Conclusions The increased acetylation of the histone acH3K9,acH3K14,acH3K18 and the lower expressed α-SMA and collagen-Ⅰ in LX-2 cells may be one of the mechanisms of SAHA.

The effects of arsenic on histone modifications / 中华地方病学杂志

Arsenic is one of the important metalloid elements, which is widely distributed in nature. Arsenic can cause many health hazards. However, the toxic mechanisms of arsenic have not yet been fully understood. In recent years, many studies have shown that epigenetic regulation and control mechanism is associated with arsenic toxicity. Histone modification is an important epigenetic regulation and control mechanism, changes in its patterns may be one of the mechanisms by which arsenic alters the gene expression. We reviewed the effects of arsenic on regulation of histone methylation, acetylation, phosphorylation and ubiquitination.

Levels of histone modifications in activated primarily cultured rat hepatic stellate cells / 中国病理生理杂志

AIM:To investigate the changes of histone modifications during the activation of primarily cultured rat hepatic stellate cells ( HSCs) and the relationship between histone modification patterns andα-smooth muscle actin (α-SMA) expression, and to explore the roles of histone modifications in the activation of HSCs.METHODS:The rat HSCs were isolated by in situ perfusion of collagenase combined with density gradient centrifugation, cultured in vitro and identi-fied by immunofluorescence staining.The morphological features of the cells were observed under inverted microscope.The changes of desmin and α-SMA during the activation of HSCs were detected by immunofluorescence staining and Western blotting.The levels of histone 3 lysine 4 dimethylation (H3K4me2), histone 3 lysine 9 dimethylation (H3K9me2), his-tone 3 lysine 9 acetylation (acH3K9) and histone 4 lysine 12 acetylation (acH4K12) in quiescent HSCs and activated HSCs were determined by Western blotting.RESULTS: The morphology of HSCs shifted from a quiescent phenotype to highly activated myofibroblast during the culture.Immunofluorescence staining and Western blotting showed that the expres-sion levels of α-SMA and desmin were increased over time and reached maximum at 15 d.According to the results of cell morphology and immunofluorescence staining, the cells cultured for 24 h and 15 d were quiescent and activated HSCs, re-spectively.Compared with quiescent HSCs, there were higher H3K4me2 and lower H3K9me2, acH3K9 and acH4K12 modification levels in activated HSCs ( P<0.01 ) .CONCLUSION: Histone modifications show anomalous expression during the activation of primarily cultured rat HSCs.Histone modifications may contribute to the transdifferentiation of HSCs and the development of hepatic fibrosis.

Epigenetic modifications and diabetic nephropathy

Diabetic nephropathy (DN) is a major complication associated with both type 1 and type 2 diabetes, and a leading cause of end-stage renal disease. Conventional therapeutic strategies are not fully efficacious in the treatment of DN, suggesting an incomplete understanding of the gene regulation mechanisms involved in its pathogenesis. Furthermore, evidence from clinical trials has demonstrated a "metabolic memory" of prior exposure to hyperglycemia that continues to persist despite subsequent glycemic control. This remains a major challenge in the treatment of DN and other vascular complications. Epigenetic mechanisms such as DNA methylation, nucleosomal histone modifications, and noncoding RNAs control gene expression through regulation of chromatin structure and function and post-transcriptional mechanisms without altering the underlying DNA sequence. Emerging evidence indicates that multiple factors involved in the etiology of diabetes can alter epigenetic mechanisms and regulate the susceptibility to diabetes complications. Recent studies have demonstrated the involvement of histone lysine methylation in the regulation of key fibrotic and inflammatory genes related to diabetes complications including DN. Interestingly, histone lysine methylation persisted in vascular cells even after withdrawal from the diabetic milieu, demonstrating a potential role of epigenetic modifications in metabolic memory. Rapid advances in high-throughput technologies in the fields of genomics and epigenomics can lead to the identification of genome-wide alterations in key epigenetic modifications in vascular and renal cells in diabetes. Altogether, these findings can lead to the identification of potential predictive biomarkers and development of novel epigenetic therapies for diabetes and its associated complications.

Epigenetic Regulation of DNA Repair / 生物化学与生物物理进展

Epigenetic changes are important etiological factors of human tumor. The integrity of the genome is frequently challenged by the damage of DNA. However, the highly condensed structure of chromatin imposes significant obstacles on the repair processes. Eukaryotes have developed intricate mechanisms to overcome this repressive barrier imposed by chromatin. Covalent histone modifications and ATP-dependent chromatin remodeling play important roles in the process of DNA repair. Recent advances of the epigenetic regulations in the repair process were summarized. New findings in the cellular responses to DNA double strand breaks and how histone modifications and chromatin remodeling contributes to DNA double strand break repair were introduced. Future challenges in this field are also discussed.

Metilación del ADN: un fenómeno epigenético de importancia médica / DNA methylation: an epigenetic process of medical importance

Methylation of CpG dinucleotides is an epigenetic mechanism involved in the regulation of gene expression in mammals. The patterns of CpG methylation are specie and tissue specific. The biological machinery of this system comprises a variety of regulatory proteins including DNA methyltransferases, putative demethylases, methyl-CpG binding proteins, histones modifying enzymes and chromatin remodeling complexes. DNA methylation maintains gene silencing and participates in normal development, genomic imprinting and X chromosome inactivation. In contrast, alterations in DNA methylation participate in the induction of some human diseases, especially those involving developmental defects and tumorigenesis. This review summarizes the molecular aspects of DNA methylation and its implications in cancer and other human diseases in which this epigenetic mechanism has been involved. Our understanding of the epigenetic changes that occur in human diseases will be very important for future management. Changes in the patterns of methylation can be used as markers in cancer and their potentially reversible state creates a target for therapeutic strategies involving specific gene re-activation or re-silencing.

La metilación del ADN en dinucleótidos CpG es uno de los mecanismos epigenéticos implicados en la regulación de la expresión génica en mamíferos. Los patrones de metilación son específicos para cada especie y tipo de tejido. La maquinaria implicada comprende diferentes proteínas reguladoras incluyendo a las ADN metiltransferasas, desmetilasas putativas, proteínas de unión a CpG metilados, enzimas modificadoras de histonas y complejos remodeladores de la cromatina. La metilación del ADN es de vital importancia para mantener el silenciamiento génico en el desarrollo normal, la impronta genómica y la inactivación del cromosoma X. En contraste, alteraciones en ella están implicadas en algunas enfermedades humanas, especialmente aquéllas relacionadas con defectos en el desarrollo y el proceso neoplásico. Esta revisión resume los aspectos moleculares de la metilación del ADN y su participación en el desarrollo normal, el cáncer y en algunas patologías humanas en las que los mecanismos epigenéticos han sido implicados. El conocimiento de las modificaciones epigenéticas que ocurren en las enfermedades humanas será importante para su manejo futuro. Los cambios en los patrones de metilación podrán ser empleados como marcadores en cáncer y el estado potencialmente reversible de este proceso constituye un blanco ideal para crear estrategias terapéuticas que impliquen la reactivación o el re-silenciamiento de genes específicos.