Redox and metabolic regulation of epigenetic modifications:an emerging toxic action mechanism

Epigenetic modifications modulate conformational structure of chromatin and consequently gene expression by enzyme-mediated chemical modifications of DNA and histones.The activities of epigenetic modifying enzymes depend on many co-substrates and cofactors,such as 2-oxoglutarate(2-OG),iron,S-adenosylmethionine(SAM),nicotinamide adenine dinucleotide(NAD+),flavin adenine dinucleotide(FAD),and acetyl-CoA.These factors are inter-connecting molecules that integrate cellular nutrient metabolism and redox homeostasis,two key regulators of cell proliferation,cell survival,and cell functions.Dysregulation of such delicate regulatory network has been implicated in many pathological conditions and also been increasingly recognized as an emerging mechanism responsible for environmental pollutant-induced adverse effects.In this review,we first summarize DNA and histone modifying enzymes and their essential factors,then discuss the metabolic sources and the redox regulatory roles of these enzymatic factors,and finally elaborate the mechanisms of how targeting such factors by environmental pollutants influences epigenetic regulation and perturbs cellular functions.

Evaluation of biomarkers, genetic mutations, and epigenetic modifications in early diagnosis of pancreatic cancer

BACKGROUND Pancreatic cancer(PC)is one of the deadliest malignancies with an alarming mortality rate.Despite significant advancement in diagnostics and therapeutics,early diagnosis remains elusive causing poor prognosis,marred by mutations and epigenetic modifications in key genes which contribute to disease progression.AIM To evaluate the various biological tumor markers collectively for early diagnosis which could act as prognostic biomarkers and helps in future therapeutics of PC in Kashmir valley.METHODS A total of 50 confirmed PC cases were included in the study to evaluate the levels of carbohydrate antigen 19-9(CA 19-9),tissue polypeptide specific antigen(TPS),carcinoembryonic antigen(CEA),vascular endothelial growth factor-A(VEGF-A),and epidermal growth factor receptor(EGFR).Mutational analysis was performed to evaluate the mutations in Kirsten rat sarcoma(KRAS),Breast cancer type 2(BRCA-2),and deleted in pancreatic cancer-4(DPC-4)genes.However,epigenetic modifications(methylation of CpG islands)were performed in the promoter regions of cyclin-dependent kinase inhibitor 2A(p16;CDKN2A),MutL homolog 1(hMLH1),and Ras association domain-containing protein 1(RASSF1A)genes.RESULTS We found significantly elevated levels of biological markers CA 19-9(P≤0.05),TPS(P≤0.05),CEA(P≤0.001),and VEGF(P≤0.001).Molecular genetic analysis revealed that KRAS gene mutation is predominant in codon 12(16 subjects,P≤0.05),and 13(12 subjects,P≤0.05).However,we did not find a mutation in DPC-4(1203G>T)and BRCA-2(617delT)genes.Furthermore,epigenetic modification revealed that CpG methylation in 21(P≤0.05)and 4 subjects in the promoter regions of the p16 and hMLH1 gene,respectively.CONCLUSION In conclusion,CA 19-9,TPS,CEA,and VEGF levels were significantly elevated and collectively have potential as diagnostic and prognostic markers in PC.Global data of mutation in the KRAS gene commonly in codon 12 and rare in codon 13 could augment the predisposition towards PC.Additionally,methylation of the p16 gene could also modulate transcription of genes thereby increasing the predisposition and susceptibility towards PC.

AB035. Lactate receptor GPR81 modulates epigenetic modification in the subretina

Background:Retinal pigment epithelium(RPE)is vital for the homeostasis of the subretina including photoreceptors and choroid.Interestingly,our previous results suggested that the recently discovered lactate receptor GPR81 is abundantly expressed in RPE.To date,only one previous study has shown that activating GPR81 could enhance DNA repair by activating HDAC1.Consequently,we investigated whether GPR81 exhibits epigenetic modification in the subretina by using GPR81−/−mice.Methods:GPR81−/−mice and wide type littermates were generated on a background of C57BL/6J mice.The thicknesses of their choroid were evaluated by immunohistochemistry.Meanwhile,Q-PCR,western blot and choroid sprout assay were performed.In vitro,primary retinal pigment epithelium(pRPE)cells were isolated from mice,and cultured for treatments.Results:The thickness of choroid was reduced in GPR81−/−mice compared to GPR81+/+mice,suggesting that GPR81 is important for the integrity of choroid.In the choroid sprout assay,lactate treated RPE/choroid complex showed a significant increase in angiogenesis compared to controls while lactate treated KO RPE/choroid complex showed no difference compared to their controls.For Q-PCR,most of the genes screened elevated their expression in GPR81−/−mice compared to WT mice,suggesting epigenetic modification may exist,which were confirmed by histone acetylation and HDACs activity assay.Conclusions:Taking together,the lactate receptor GPR81 in RPE is very important for maintaining homeostasis of the subretina.This novel discovery sheds new light on the relationship between metabolism and epigenetic modification.

PIM1-HDAC2 axis modulates intestinal homeostasis through epigenetic modification

The mucosal barrier is crucial for intestinal homeostasis,and goblet cells are essential for maintaining the mucosal barrier integrity.The proviral integration site for Moloney murine leukemia virus-1(PIM1)kinase regulates multiple cellular functions,but its role in intestinal homeostasis during colitis is unknown.Here,we demonstrate that PIM1 is prominently elevated in the colonic epithelia of both ulcerative colitis patients and murine models,in the presence of intestinal microbiota.Epithelial PIM1 leads to decreased goblet cells,thus impairing resistance to colitis and colitis-associated colorectal cancer(CAC)in mice.Mechanistically,PIM1 modulates goblet cell differentiation through the Wnt and Notch signaling pathways.Interestingly,PIM1 interacts with histone deacetylase 2(HDAC2)and downregulates its level via phosphorylation,thereby altering the epigenetic profiles of Wnt signaling pathway genes.Collectively,these findings investigate the unknown function of the PIM1-HDAC2 axis in goblet cell differentiation and ulcerative colitis/CAC pathogenesis,which points to the potential for PIM1-targeted therapies of ulcerative colitis and CAC.

The research progress of epigenetics and metabolic memory in diabetic kidney disease

Diabetic kidney disease(DKD)is a clinical syndrome that is one of the major causes of end-stage renal disease(ESRD).The pathogenesis of DKD is complex and multifaceted,with most studies indicating its association with genetics,advanced glycosylation end-product deposition,polyol pathway and protein C activation,lipid metabolism abnormalities,microcirculatory dysfunction,oxidative stress,inflammatory factors,and the kallikrein-kinin system.Epigenetics is the science studying gene expression regulation without changes in the DNA sequence.In recent years,increasing evidence has shown that epigenetic mechanisms play a crucial role in the initiation and progression of DKD.For instance,epigenetic modifications such as DNA methylation,histone modifications,and non-coding RNAs can influence the expression of DKD-related genes,thereby regulating the development and progression of DKD.On the other hand,metabolic memory is an important concept in DKD research.Metabolic memory refers to the phenomenon where cells maintain a certain metabolic state even after the disappearance of metabolic stress factors.This state can influence cell function and fate.In DKD,metabolic stress factors such as hyperglycemia can lead to metabolic memory in renal cells,affecting their function and fate,ultimately leading to the development and progression of DKD.Therefore,to further explore the pathogenesis of DKD,research on epigenetics should be strengthened,aiming to provide new ideas and methods for the prevention and treatment of DKD.

Role of methionine on epigenetic modification of DNA methylation and gene expression in animals

DNA methylation is one of the main epigenetic phenomena affecting gene expression.It is an important mechanism for the development of embryo,growth and health of animals.As a key nutritional factor limiting the synthesis of protein,methionine serves as the precursor of S-adenosylmethionine(SAM) in the hepatic one-carbon metabolism.The dietary fluctuation of methionine content can alter the levels of metabolic substrates in one-carbon metabolism,e.g.,the SAM,S-adenosylhomocysteine(SAH),and change the expression of genes related to the growth and health of animals by DNA methylation reactions.The ratio of SAM to SAH is called ‘methylation index' but it should be carefully explained because the complexity of methylation reaction.Alterations of methylation in a specific cytosine-guanine(Cp G)site,rather than the whole promoter region,might be enough to change gene expression.Aberrant methionine cycle may provoke molecular changes of one-carbon metabolism that results in deregulation of cellular hemostasis and health problems.The importance of DNA methylation has been underscored but the mechanisms of methionine affecting DNA methylation are poorly understood.Nutritional epigenomics provides a promising insight into the targeting epigenetic changes in animals from a nutritional standpoint,which will deepen and expand our understanding of genes,molecules,tissues,and animals in which methionine alteration influences DNA methylation and gene expression.

RECENT ADVANCES IN THE REGULATION OF CLIMACTERIC FRUIT RIPENING:HORMONE,TRANSCRIPTION FACTOR AND EPIGENETIC MODIFICATIONS

Fruit ripening is a complex developmental process made up of genetically programmed physiological and biochemical activities.It culminates in desirable changes in the structural and textural properties and is governed by a complex regulatory network.Much is known about ethylene,one of the most important metabolites promoting the ripening of climacteric fruits.However,the dynamic interplay between phytohormones also plays an important part.Additional regulatory factors such as transcription factors(TFs)and epigenetic modifications also play vital role in the regulation of climacteric fruit ripening.Here,we review and evaluate the complex regulatory network comprising interactions between hormones and the action of TFs and epigenetic modifications during climacteric fruit ripening.

Epigenetic modification enzymes: catalytic mechanisms and inhibitors

Epigenetic modifications alter chromatin structures and consequently affect transcription and cellular functions.Major epigenetic markers include DNA methylation and histone acetylation and methylation.The modifications are reversible and are achieved in aid of relative enzymes.Much effort has been directed at the understanding of the chemical mechanisms of individual catalytic reactions,which can serve as a foundation for inhibitor development.Among the many methods deployed,structural studies have proven the most effective for understanding enzyme-mediated modifications and have provided support for the development of lead-candidate drug inhibitors.This review briefly summarizes the existing knowledge on the catalytic mechanisms of the major epigenetic modification enzymes,with an emphasis on the structural information and inhibitors of these enzymes.

Epigenetic modifications of chronic hypoxiamediated neurodegeneration in Alzheimer’s disease

Alzheimer’s disease(AD)is the most common neurodegenerative disorder affecting the elderly people.AD is characterized by progressive and gradual decline in cognitive function and memory loss.While familial early-onset AD is usually associated with gene mutations,the etiology of sporadic late-onset form of AD is largely unknown.It has been reported that environmental factors and epigenetic alterations significantly contribute to the process of AD.Our previous studies have documented that chronic hypoxia is one of the environmental factors that may trigger the AD development and aggravate the disease progression.In this review,we will summarize the pathological effects of chronic hypoxia on the onset and development of AD and put forward the possible molecule mechanisms underlying the chronic hypoxia mediated AD pathogenesis.Finally,we propose that epigenetic regulations may represent new opportunity for the therapeutic intervention of this disease.

Connections between metabolism and epigenetic modifications in cancer

How cells sense and respond to environmental changes is still a key question.It has been identified that cellular metabolism is an important modifier of various epigenetic modifications,such as DNA methylation,histone methylation and acetylation and RNA N6-methyladenosine(m6A)methylation.This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression,and is crucial to regulate cellular homeostasis,cell growth and differentiation.Cancer metabolic reprogramming and epigenetic alterations are widely observed,and facilitate cancer development and progression.In cancer cells,oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the keymetabolite levels.In this review,we briefly summarized the current evidence that the abundance of key metabolites,such as S-adenosyl methionine(SAM),acetyl-CoA,α-ketoglutarate(α-KG),2-hydroxyglutarate(2-HG),uridine diphospho-N-acetylglucosamine(UDP-GlcNAc)and lactate,affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer.An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.

Optical Imaging of Epigenetic Modifications in Cancer:A Systematic Review

Increasing evidence has demonstrated that abnormal epigenetic modifications are strongly related to cancer initiation.Thus,sensitive and specific detection of epigenetic modifications could markedly improve biological investigations and cancer precision medicine.A rapid development of molecular imaging approaches for the diagnosis and prognosis of cancer has been observed during the past few years.Various biomarkers unique to epigenetic modifications and targeted imaging probes have been characterized and used to discriminate cancer from healthy tissues,as well as evaluate therapeutic responses.In this study,we summarize the latest studies associated with optical molecular imaging of epigenetic modification targets,such as those involving DNA methylation,histone modification,noncoding RNA regulation,and chromosome remodeling,and further review their clinical application on cancer diagnosis and treatment.Lastly,we further propose the future direc-tions for precision imaging of epigenetic modification in cancer.Supported by promising clinical and preclinical studies associated with optical molecular imaging technology and epigenetic drugs,the central role of epigenetics in cancer should be increasingly recognized and accepted.

Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs

Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and growth.Recent studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth.Methods:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis underneath.Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig myogenesis.Whole-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 myoblasts.The protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast cells.Further,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs.Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of pigs.Last,we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m^(6)A modifications in postnatal skeletal muscle growth in pigs.Conclusions:Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.

Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease

Non-alcoholic fatty liver disease(NAFLD)poses a significant health challenge in modern societies due to shifts in lifestyle and dietary habits.Its complexity stems from genetic predisposition,environmental influences,and metabolic factors.Epigenetic processes govern various cellular functions such as transcription,chromatin structure,and cell division.In NAFLD,these epigenetic tendencies,especially the process of histone methylation,are intricately intertwined with fat accumulation in the liver.Histone methylation is regulated by different enzymes like methyltransferases and demethylases and influences the expression of genes related to adipogenesis.While early-stage NAFLD is reversible,its progression to severe stages becomes almost irreversible.Therefore,early detection and intervention in NAFLD are crucial,and understanding the precise role of histone methylation in the early stages of NAFLD could be vital in halting or potentially reversing the progression of this disease.

The Investigation into Intrinsic Elements Influencing the Onset of Lung Cancer

Lung cancer is a highly heterogeneous malignancy with a complex pathogenesis, involving a series of endogenous alterations such as genetic mutations, epigenetic modifications, and oxidative stress. Recent advancements in lung cancer research, especially at the genomic and molecular biology levels, have continuously provided new potential targets and perspectives for the diagnosis and treatment of lung cancer. Therefore, this article summarizes the recent progress in the study of endogenous factors related to the pathogenesis of lung cancer, aiming to enhance the understanding of intrinsic factors in lung cancer and to organize ideas for subsequent related research.

Histone modifications and alcohol-induced liver disease:Are altered nutrients the missing link?

Alcoholism is a major health problem in the United States and worldwide,and alcohol remains the single most significant cause of liver-related diseases and deaths.Alcohol is known to influence nutritional status at many levels including nutrient intake,absorption,utilization,and excretion,and can lead to many nutritional disturbances and deficiencies.Nutrients can dramatically affect gene expression and alcohol-induced nutrient imbalance may be a major contributor to pathogenic gene expression in alcohol-induced liver disease(ALD).There is growing interest regarding epigenetic changes,including histone modifications that regulate gene expression during disease pathogenesis.Notably,modifications of core histones in the nucleosome regulate chromatin structure and DNA methylation,and control gene transcription.This review highlights the role of nutrient disturbances brought about during alcohol metabolism and their impact on epigenetic histone modifications that may contribute to ALD.The review is focused on four critical metabolites,namely,acetate,S-adenosylmethionine,nicotinamide adenine dinucleotide and zinc that are particularly relevant to alcohol metabolism and ALD.

Targeting histone deacetylases： perspectives for epigenetic-based therapy in cardio-cerebrovascular disease

Although the pathogenesis of cardio-cerebrovascular disease （CCVD） is multifactorial, an increasing number of experimental and clinical studies have highlighted the importance of histone deacetylase （HDAC）-mediated epigenetic processes in the development of cardio-cerebrovascular injury. HDACs are a family of enzymes to balance the acetylation activities of histone acetyltransferases on chromatin remodeling and play essential roles in regulating gene transcription. To date, 18 mammalian HDACs are identified and grouped into four classes based on similarity to yeast orthologs. The zinc-dependent HDAC family currently consists of 11 members divided into three classes （class I, II, and IV） on the basis of structure, sequence homology, and domain organization. In comparison, class III HDACs （also known as the sirtuins） are composed of a family of NAD＋-dependent protein-modifying enzymes related to the Sir2 gene. HDAC inhibitors are a group of compounds that block HDAC activities typically by binding to the zinc-containing catalytic domain of HDACs and have displayed an- ti-inflammatory and antifibrotic effects in the cardio-cerebrovascular system. In this review, we summarize the current knowledge about classifications, functions of HDACs and their roles and regulatory mechanisms in the cardio-cerebrovascular system. Pharmacological tar- geting of HDAC-mediated epigenetic processes may open new therapeutic avenues for the treatment of CCVD.

Transcriptional changes in epigenetic modifiers associated with gene silencing in the intestine of the sea cucumber,Apostichopus japonicus(Selenka),during aestivation

The sea cucumber, Apostichopusjaponicus, undergoes aestivation to improve survival during periods of high-temperature. During aestivation, the metabolic rate is depressed to reduce the consumption of reserved energy. We evaluated the role of epigenetic modification on global gene silencing during metabolic rate depression in the sea cucumber. We compared the expression of epigenetic modifiers in active and aestivating sea cucumbers. The expression of three genes involved in DNA methylation and chromatin remodeling （DNA （cytosine-5）-methyltransferase l, Methyl-CpG-binding domain protein 2）, and Chromodomain-helicase-DNA-binding protein 5） was significantly higher during aestivation （Days 20 and 40）. Similarly, we observed an increase in the expression of genes involved in histone acetylation （Histone deacetylase 3） and Histone-binding protein RBBP4） during the early （Days 5 and 10） and late phases （Days 20 and 40） of aestivation. There was no change in the expression of KAT2B, a histone acetyltransferase. However, the expression of histone methylation associated modifiers （Histone-arginine methyltransferase CARMER and Histone-lysine N-methyltransferase MLL5） was significantly higher after 5 d in the aestivating group. The results suggest that the expression of epigenetic modifiers involved in DNA methylation, chromatin remodeling, histone acetylation, and histone methylation is upregulated during aestivation. We hypothesize that these changes regulate global gene silencing during aestivation in A. japonicus.

Decoding epigenetic codes: new frontiers in exploring recovery from spinal cord injury

Spinal cord injury that results in severe neurological disability is often incurable.The poor clinical outcome of spinal cord injury is mainly caused by the failure to reconstruct the injured neural circuits.Several intrinsic and extrinsic determinants contribute to this inability to reconnect.Epigenetic regulation acts as the driving force for multiple pathological and physiological processes in the central nervous system by modulating the expression of certain critical genes.Recent studies have demonstrated that post-SCI alteration of epigenetic landmarks is strongly associated with axon regeneration,glial activation and neurogenesis.These findings not only establish a theoretical foundation for further exploration of spinal cord injury,but also provide new avenues for the clinical treatment of spinal cord injury.This review focuses on the epigenetic regulation in axon regeneration and secondary spinal cord injury.Together,these discoveries are a selection of epigenetic-based prognosis biomarkers and attractive therapeutic targets in the treatment of spinal cord injury.

Streptavidin-Biotin Complexes as Tools for Modulating an Important DNA Episgenetic Modification

DNA 5-formylcytosine(5fC)is a prominent epigenetic modification within biological systems.Recent investigations have shed light on its pivotal role in governing cell fate,gene expression,and disease pathways.However,our comprehension of the precise control of the 5f site structure to influence its functionality remains limited.In this study,we have successfully achieved precise control over 5fc activity by harnessing the interaction between streptavidin and biotin.This research underscores the potential application of interactions between biomacromolecules and small molecules in advancing the field of DNA epigenetic functional regulation.

Id2 epigenetically controls CD8^(+)T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex

CD8^(+)T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6^(+)progenitor exhausted(Tex^(prog))and Tim-^(3+)terminally exhausted(Tex^(term))subpopulations.Inhibitor of DNA binding protein 2(Id2)has been shown to play important roles in T-cell development and CD8^(+)T-cell immunity.However,the role of Id2 in CD8^(+)T-cell exhaustion is unclear.Here,we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm cells.Genetic deletion of Id2 dampens CD8^(+)T-cell-mediated immune responses and the maintenance of stem-like CD8^(+)T-cell subpopulations,suppresses PD-1 blockade and increases tumor susceptibility.Mechanistically,through its HLH domain,Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex,and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase LSD1.Therefore,Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter,modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+Texprog cells.An LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing mice.Inhibition of LSD1 increases the abundance of Slamf6^(+)Tim-3^(−)Tex^(prog) cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+T cells.This study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8^(+)T-cell exhaustion,and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.