BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-posi...BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-positive carrier status or cirrhosis to liver cancer are unknown.The epigenetic modification of DNA hydroxymethylation is critical in tumor development.Further,5-hydroxymethylcytosine(5hmC)is an important base for DNA demethylation and epigenetic regulation.It is also involved in the assembly of chromosomes and the regulation of gene expression.However,the mechanism of action of 5hmC in HBsAgpositive carriers or patients with cirrhosis who develop liver cancer has not been fully elucidated.AIM To investigate the possible epigenetic mechanism of HBsAg-positive carriers and hepatocellular carcinoma(HCC)progression from cirrhosis.METHODS Forty HBsAg-positive carriers,forty patients with liver cirrhosis,and forty patients with liver cancer admitted to the First People's Hospital of Yongkang between March 2020 and November 2021 were selected as participants.Free DNA was extracted using a cf-DNA kit.cfDNA was extracted by 5hmC DNA sequencing for principal component analysis,the expression profiles of the three groups of samples were detected,and the differentially expressed genes(DEGs)modified by hydroxymethylation were screened.Bioinformatic analysis was used to enrich DEGs,such as in biological pathways.RESULTS A total of 16455 hydroxymethylated genes were identified.Sequencing results showed that 32 genes had significant 5hmC modification differences between HBsAg carriers and liver cancer patients,of which 30 were upregulated and 2 downregulated in patients with HCC compared with HBsAg-positive carriers.Significant 5hmC modification differences between liver cirrhosis and liver cancer patients were identified in 20 genes,of which 17 were upregulated and 3 were downregulated in patients with HCC compared with those with cirrhosis.These genes may have potential loci that are undiscovered or unelucidated,which contribute to the development and progression of liver cancer.Analysis of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes showed that the major signaling pathways involved in the differential genes were biliary secretion and insulin secretion.The analysis of protein interactions showed that the important genes in the protein-protein interaction network were phosphoenolpyruvate carboxykinase and solute carrier family 2.CONCLUSION The occurrence and development of liver cancer involves multiple genes and pathways,which may be potential targets for preventing hepatitis B carriers from developing liver cancer.展开更多
BACKGROUND Most gastric cancer(GC)patients are diagnosed at middle or late stage because the symptoms in early stage are obscure,which causes higher mortality rates of GC.Helicobacter pylori(H.pylori)was identified as...BACKGROUND Most gastric cancer(GC)patients are diagnosed at middle or late stage because the symptoms in early stage are obscure,which causes higher mortality rates of GC.Helicobacter pylori(H.pylori)was identified as a class I carcinogen and leads to aberrant DNA methylation/hydroxymethylation.5-hydroxymethylcytosine(5-hmC)plays complex roles in gene regulation of tumorigenesis and can be considered as an activating epigenetic mark of hydroxymethylation.AIM To explore the association between 5-hmC levels and the progression and prognosis of GC patients with or without H.pylori infection.METHODS A retrospective cohort study was conducted to estimate the predicted value of 5-hmC level in the progression and prognosis of GC patients with different H.pylori infection status.A total of 144 GC patients were recruited.RESULTS The levels of 5-hmC were significantly decreased in tumor tissues(0.076±0.048)compared with the matched control tissues(0.110±0.057,P=0.001).A high level of 5-hmC was an independent significant favorable predictor of overall survival in GC patients(hazard ratio=0.61,95% confidence interval:0.38-0.98,P=0.040),the H.pylori-negative GC subgroup(hazard ratio=0.30,95% confidence interval:0.13-0.68,P=0.004)and the GC patients with TNM stage Ⅰ or Ⅱ(hazard ratio=0.32,95% confidence interval:0.13-0.77,P=0.011).CONCLUSION Increased 5-hmC is a favorable prognostic factor in GC,especially for H.pylori-negative subgroups.展开更多
Robust and clinically convenient biomarkers for cancer diagnosis,early detection,and prognosis have great potential to improve patient survival and are the key to precision medicine.The advent of next-generation seque...Robust and clinically convenient biomarkers for cancer diagnosis,early detection,and prognosis have great potential to improve patient survival and are the key to precision medicine.The advent of next-generation sequencing technologies enables a more sensitive and comprehensive profiling of genetic and epigenetic information in tumor-derived materials.Researchers are now able to monitor the dynamics of tumorigenesis in new dimensions,such as using circulating cell-free DNA(cfDNA)and tumor DNA(ctDNA).Mutation-based assays in liquid biopsy cannot always provide consistent results across studies due partly to intra-and inter-tumoral heterogeneity as well as technical limitations.In contrast,epigenetic analysis of patient-derived cfDNA is a promising alternative,especially for early detection and disease surveillance,because epigenetic modifications are tissue-specific and reflect the dynamic process of cancer progression.Therefore,cfDNA-based epigenetic assays are emerging to be a highly sensitive,minimally invasive tool for cancer diagnosis and prognosis with great potential in future precise care of cancer patients.The major obstacle for applying epigenetic analysis of cfDNA,however,has been the lack of enabling techniques with high sensitivity and technical robustness.In this review,we summarized the advances in epigenome-wide profiling of 5-hydroxymethyl-cytosine(5hmC)in cfDNA,focusing on the detection approaches and potential role as biomarkers in different cancer types.展开更多
Although DNA 5-hydroxymethylcytosine(5 hmC)is recognized as an important epigenetic mark in cancer,its precise role in lymph node metastasis remains elusive.In this study,we investigated how 5 hmC associates with lymp...Although DNA 5-hydroxymethylcytosine(5 hmC)is recognized as an important epigenetic mark in cancer,its precise role in lymph node metastasis remains elusive.In this study,we investigated how 5 hmC associates with lymph node metastasis in breast cancer.Accompanying with high expression of TET1 and TET2 proteins,large numbers of genes in the metastasis-positive primary tumors exhibit higher 5 hmC levels than those in the metastasis-negative primary tumors.In contrast,the TET protein expression and DNA 5 hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors.Through genomewide analysis of 8 sets of primary tumors,we identified 100 high-confidence metastasis-associated5 hmC signatures,and it is found that increased levels of DNA 5 hmC and gene expression of MAP7 D1 associate with high risk of lymph node metastasis.Furthermore,we demonstrate that MAP7 D1,regulated by TET1,promotes tumor growth and metastasis.In conclusion,the dynamic5 hmC profiles during lymph node metastasis suggest a link between DNA 5 hmC and lymph node metastasis.Meanwhile,the role of MAP7 D1 in breast cancer progression suggests that the metastasis-associated 5 hmC signatures are potential biomarkers to predict the risk for lymph node metastasis,which may serve as diagnostic and therapeutic targets for metastatic breast cancer.展开更多
5-Hydroxymethylcytosine(5 hmC),an intermediate product of DNA demethylation,is important for the regulation of gene expression during development and even tumorigenesis.The challenges associated with determination of ...5-Hydroxymethylcytosine(5 hmC),an intermediate product of DNA demethylation,is important for the regulation of gene expression during development and even tumorigenesis.The challenges associated with determination of 5 hm C level include its extremely low abundance and high structural similarity with other cytosine derivatives,which resulted in sophisticated treatment with large amount of sample input.Herein,we developed a primer-initiated strand displacement amplification(PISDA)strategy to quantify the global 5 hm C in genomic DNA from mammalian tissues with high sensitivity/selectivity,low input and simple operation.This sensitive fluorescence method is based on 5 hmC-specific glucosylation,primer ligation and DNA amplification.After the primer was labeled on 5 hm C site,DNA polymerase and nicking enzyme will repeatedly act on each primer,causing a significant increase of fluorescence signal to magnify the minor difference of 5 hm C content from other cytosine derivatives.This method enables highly sensitive analysis of 5 hm C with a detection limit of 0.003%in DNA(13.6 fmol,S/N=3)from sample input of only 150 ng,which takes less than 15 min for determination.Further determination of 5 hmC in different tissues not only confirms the widespread presence of 5 hmC but also indicates its significant variation in different tissues and ages.Importantly,this PISDA strategy exhibits distinct advantages of bisulfite-free treatment,mild conditions and simple operation without the involvement of either expensive equipment or large amount of DNA sample.This method can be easily performed in almost all research and medical laboratories,and would provide a promising prospect to detect global 5 hmC in mammalian tissues.展开更多
Brain development and aging are associated with alterations in multiple epigenetic systems,including DNA methylation and demethylation patterns.Here,we observed that the levels of the 5-hydroxymethylcytosine(5hmC)ten-...Brain development and aging are associated with alterations in multiple epigenetic systems,including DNA methylation and demethylation patterns.Here,we observed that the levels of the 5-hydroxymethylcytosine(5hmC)ten-eleven translocation(TET)enzyme-mediated active DNA demethylation products were dynamically changed and involved in postnatal brain development and aging in tree shrews(Tupaia belangeri chinensis).The levels of5hm C in multiple anatomic structures showed a gradual increase throughout postnatal development,whereas a significant decrease in 5hmC was found in several brain regions in aged tree shrews,including in the prefrontal cortex and hippocampus,but not the cerebellum.Active changes in Tet mR NA levels indicated that TET2 and TET3 predominantly contributed to the changes in 5hmC levels.Our findings provide new insight into the dynamic changes in 5hm C levels in tree shrew brains during postnatal development and aging processes.展开更多
BACKGROUND As the third most abundant element,aluminum is widespread in the environment.Previous studies have shown that aluminum has a neurotoxic effect and its exposure can impair neuronal development and cognitive ...BACKGROUND As the third most abundant element,aluminum is widespread in the environment.Previous studies have shown that aluminum has a neurotoxic effect and its exposure can impair neuronal development and cognitive function.AIM To study the effects of aluminum on epigenetic modification in neural stem cells and neurons.METHODS Neural stem cells were isolated from the forebrain of adult mice.Neurons were isolated from the hippocampi tissues of embryonic day 16-18 mice.AlCl3 at 100 and 200μmol/L was applied to stem cells and neurons.RESULTS Aluminum altered the differentiation of adult neural stem cells and caused apoptosis of newborn neurons while having no significant effects on the proliferation of neural stem cells.Aluminum application also significantly inhibited the dendritic development of hippocampal neurons.Mechanistically,aluminum exposure significantly affected the levels of DNA 5-hydroxy methylcytosine,5-methylcytosine,and N6-methyladenine in stem cells and neurons.CONCLUSION Our findings indicate that aluminum may regulate neuronal development by modulating DNA modifications.展开更多
Background:Function of epigenetic modifications is one of the most competitive fields in life science.Over the past several decades,it has been revealed that epigenetic modifications play essential roles in developmen...Background:Function of epigenetic modifications is one of the most competitive fields in life science.Over the past several decades,it has been revealed that epigenetic modifications play essential roles in development and diseases including developmental diseases.In the present review,we summarize the recent progress about the function of epigenetic regulation,especially DNA and RNA modifi cations in developmental diseases.Data sources:Original research articles and literature reviews published in PubMed-indexed journals.Results:DNA modifications including methylation and demethylation can regulate gene expression,and are involved in development and multiple diseases including Rett syndrome,Autism spectrum disorders,congenital heart disease and cancer,etc.RNA methylation and demethylation play important roles in RNA processing,reprogramming,circadian,and neuronal activity,and then modulate development.Conclusions:DNA and RNA modifications play important roles in development and diseases through regulating gene expression.Epigenetic components could serve as novel targets for the treatment of developmental diseases.展开更多
基金Supported by Science and Technology Planning Project of Zhejiang Province,No.LGF20H160001.
文摘BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-positive carrier status or cirrhosis to liver cancer are unknown.The epigenetic modification of DNA hydroxymethylation is critical in tumor development.Further,5-hydroxymethylcytosine(5hmC)is an important base for DNA demethylation and epigenetic regulation.It is also involved in the assembly of chromosomes and the regulation of gene expression.However,the mechanism of action of 5hmC in HBsAgpositive carriers or patients with cirrhosis who develop liver cancer has not been fully elucidated.AIM To investigate the possible epigenetic mechanism of HBsAg-positive carriers and hepatocellular carcinoma(HCC)progression from cirrhosis.METHODS Forty HBsAg-positive carriers,forty patients with liver cirrhosis,and forty patients with liver cancer admitted to the First People's Hospital of Yongkang between March 2020 and November 2021 were selected as participants.Free DNA was extracted using a cf-DNA kit.cfDNA was extracted by 5hmC DNA sequencing for principal component analysis,the expression profiles of the three groups of samples were detected,and the differentially expressed genes(DEGs)modified by hydroxymethylation were screened.Bioinformatic analysis was used to enrich DEGs,such as in biological pathways.RESULTS A total of 16455 hydroxymethylated genes were identified.Sequencing results showed that 32 genes had significant 5hmC modification differences between HBsAg carriers and liver cancer patients,of which 30 were upregulated and 2 downregulated in patients with HCC compared with HBsAg-positive carriers.Significant 5hmC modification differences between liver cirrhosis and liver cancer patients were identified in 20 genes,of which 17 were upregulated and 3 were downregulated in patients with HCC compared with those with cirrhosis.These genes may have potential loci that are undiscovered or unelucidated,which contribute to the development and progression of liver cancer.Analysis of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes showed that the major signaling pathways involved in the differential genes were biliary secretion and insulin secretion.The analysis of protein interactions showed that the important genes in the protein-protein interaction network were phosphoenolpyruvate carboxykinase and solute carrier family 2.CONCLUSION The occurrence and development of liver cancer involves multiple genes and pathways,which may be potential targets for preventing hepatitis B carriers from developing liver cancer.
基金Supported by National Natural Science Foundation of China,No.81874279Scientific and Technological Development Program of Jilin Province,No.20190201093JC and No.20200201326JC+1 种基金Jilin Province Department of Finance,No.JLSWSRCZX2020-010Youth Development Fund from First Hospital of Jilin University,No.JDYY11202021.
文摘BACKGROUND Most gastric cancer(GC)patients are diagnosed at middle or late stage because the symptoms in early stage are obscure,which causes higher mortality rates of GC.Helicobacter pylori(H.pylori)was identified as a class I carcinogen and leads to aberrant DNA methylation/hydroxymethylation.5-hydroxymethylcytosine(5-hmC)plays complex roles in gene regulation of tumorigenesis and can be considered as an activating epigenetic mark of hydroxymethylation.AIM To explore the association between 5-hmC levels and the progression and prognosis of GC patients with or without H.pylori infection.METHODS A retrospective cohort study was conducted to estimate the predicted value of 5-hmC level in the progression and prognosis of GC patients with different H.pylori infection status.A total of 144 GC patients were recruited.RESULTS The levels of 5-hmC were significantly decreased in tumor tissues(0.076±0.048)compared with the matched control tissues(0.110±0.057,P=0.001).A high level of 5-hmC was an independent significant favorable predictor of overall survival in GC patients(hazard ratio=0.61,95% confidence interval:0.38-0.98,P=0.040),the H.pylori-negative GC subgroup(hazard ratio=0.30,95% confidence interval:0.13-0.68,P=0.004)and the GC patients with TNM stage Ⅰ or Ⅱ(hazard ratio=0.32,95% confidence interval:0.13-0.77,P=0.011).CONCLUSION Increased 5-hmC is a favorable prognostic factor in GC,especially for H.pylori-negative subgroups.
基金This work was partly supported by a grant from the National Institutes of Health P30 C060553 Career Development Fund(to W.Z.)
文摘Robust and clinically convenient biomarkers for cancer diagnosis,early detection,and prognosis have great potential to improve patient survival and are the key to precision medicine.The advent of next-generation sequencing technologies enables a more sensitive and comprehensive profiling of genetic and epigenetic information in tumor-derived materials.Researchers are now able to monitor the dynamics of tumorigenesis in new dimensions,such as using circulating cell-free DNA(cfDNA)and tumor DNA(ctDNA).Mutation-based assays in liquid biopsy cannot always provide consistent results across studies due partly to intra-and inter-tumoral heterogeneity as well as technical limitations.In contrast,epigenetic analysis of patient-derived cfDNA is a promising alternative,especially for early detection and disease surveillance,because epigenetic modifications are tissue-specific and reflect the dynamic process of cancer progression.Therefore,cfDNA-based epigenetic assays are emerging to be a highly sensitive,minimally invasive tool for cancer diagnosis and prognosis with great potential in future precise care of cancer patients.The major obstacle for applying epigenetic analysis of cfDNA,however,has been the lack of enabling techniques with high sensitivity and technical robustness.In this review,we summarized the advances in epigenome-wide profiling of 5-hydroxymethyl-cytosine(5hmC)in cfDNA,focusing on the detection approaches and potential role as biomarkers in different cancer types.
基金supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(Grant Nos.2016ZX310182-2 and 2016ZX310176-6 to NY)the Medical Epigenetics Research Center,Chinese Academy of Medical Sciences(Grant Nos.2017PT31035 and 2018PT31035 to NY)the National Natural Science Foundation of China(Grant No.81773163 to JF)
文摘Although DNA 5-hydroxymethylcytosine(5 hmC)is recognized as an important epigenetic mark in cancer,its precise role in lymph node metastasis remains elusive.In this study,we investigated how 5 hmC associates with lymph node metastasis in breast cancer.Accompanying with high expression of TET1 and TET2 proteins,large numbers of genes in the metastasis-positive primary tumors exhibit higher 5 hmC levels than those in the metastasis-negative primary tumors.In contrast,the TET protein expression and DNA 5 hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors.Through genomewide analysis of 8 sets of primary tumors,we identified 100 high-confidence metastasis-associated5 hmC signatures,and it is found that increased levels of DNA 5 hmC and gene expression of MAP7 D1 associate with high risk of lymph node metastasis.Furthermore,we demonstrate that MAP7 D1,regulated by TET1,promotes tumor growth and metastasis.In conclusion,the dynamic5 hmC profiles during lymph node metastasis suggest a link between DNA 5 hmC and lymph node metastasis.Meanwhile,the role of MAP7 D1 in breast cancer progression suggests that the metastasis-associated 5 hmC signatures are potential biomarkers to predict the risk for lymph node metastasis,which may serve as diagnostic and therapeutic targets for metastatic breast cancer.
基金supported by the Scientific Technology Project of Shenzhen City(Nos.JCYJ20200109142410170,JCYJ20210324120601004 and JCYJ20210324124003008)the National Natural Science Foundations of China(Nos.21775169,21801259 and 21974153)+2 种基金the Scientific Technology Project of Guangzhou City(No.202103000003)the Guangdong Natural Science Foundation(No.2019A1515010587)the Guangdong Science and Technology Plan Project(No.2020B1212060077)。
文摘5-Hydroxymethylcytosine(5 hmC),an intermediate product of DNA demethylation,is important for the regulation of gene expression during development and even tumorigenesis.The challenges associated with determination of 5 hm C level include its extremely low abundance and high structural similarity with other cytosine derivatives,which resulted in sophisticated treatment with large amount of sample input.Herein,we developed a primer-initiated strand displacement amplification(PISDA)strategy to quantify the global 5 hm C in genomic DNA from mammalian tissues with high sensitivity/selectivity,low input and simple operation.This sensitive fluorescence method is based on 5 hmC-specific glucosylation,primer ligation and DNA amplification.After the primer was labeled on 5 hm C site,DNA polymerase and nicking enzyme will repeatedly act on each primer,causing a significant increase of fluorescence signal to magnify the minor difference of 5 hm C content from other cytosine derivatives.This method enables highly sensitive analysis of 5 hm C with a detection limit of 0.003%in DNA(13.6 fmol,S/N=3)from sample input of only 150 ng,which takes less than 15 min for determination.Further determination of 5 hmC in different tissues not only confirms the widespread presence of 5 hmC but also indicates its significant variation in different tissues and ages.Importantly,this PISDA strategy exhibits distinct advantages of bisulfite-free treatment,mild conditions and simple operation without the involvement of either expensive equipment or large amount of DNA sample.This method can be easily performed in almost all research and medical laboratories,and would provide a promising prospect to detect global 5 hmC in mammalian tissues.
基金supported by the Hundred-Talent Program of Chinese Academy of Sciences(Y4065411411100050210)to J.L.+3 种基金the National Natural Science Foundation of China(8147131391649119)to J.L.the National Natural Science Foundation of China(31260242 to)F.Lthe National Science and Technology Infrastructure Program(2014BAI01B01-04)to S.L.
文摘Brain development and aging are associated with alterations in multiple epigenetic systems,including DNA methylation and demethylation patterns.Here,we observed that the levels of the 5-hydroxymethylcytosine(5hmC)ten-eleven translocation(TET)enzyme-mediated active DNA demethylation products were dynamically changed and involved in postnatal brain development and aging in tree shrews(Tupaia belangeri chinensis).The levels of5hm C in multiple anatomic structures showed a gradual increase throughout postnatal development,whereas a significant decrease in 5hmC was found in several brain regions in aged tree shrews,including in the prefrontal cortex and hippocampus,but not the cerebellum.Active changes in Tet mR NA levels indicated that TET2 and TET3 predominantly contributed to the changes in 5hmC levels.Our findings provide new insight into the dynamic changes in 5hm C levels in tree shrew brains during postnatal development and aging processes.
文摘BACKGROUND As the third most abundant element,aluminum is widespread in the environment.Previous studies have shown that aluminum has a neurotoxic effect and its exposure can impair neuronal development and cognitive function.AIM To study the effects of aluminum on epigenetic modification in neural stem cells and neurons.METHODS Neural stem cells were isolated from the forebrain of adult mice.Neurons were isolated from the hippocampi tissues of embryonic day 16-18 mice.AlCl3 at 100 and 200μmol/L was applied to stem cells and neurons.RESULTS Aluminum altered the differentiation of adult neural stem cells and caused apoptosis of newborn neurons while having no significant effects on the proliferation of neural stem cells.Aluminum application also significantly inhibited the dendritic development of hippocampal neurons.Mechanistically,aluminum exposure significantly affected the levels of DNA 5-hydroxy methylcytosine,5-methylcytosine,and N6-methyladenine in stem cells and neurons.CONCLUSION Our findings indicate that aluminum may regulate neuronal development by modulating DNA modifications.
基金This work was supported by the International Collaboration Program of Science Technology Department of Zhejiang Province(2015C340012016C34004)to Shu Q and Li XQ+2 种基金Zhejiang Provincial Program for the Cultivation of Highlevel Innovative Health talents to Shu Qthe National Key Basic Research Program of China(No.2014CB943001)National Natural Science Foundation of China(No.31371309)to Li XQ.
文摘Background:Function of epigenetic modifications is one of the most competitive fields in life science.Over the past several decades,it has been revealed that epigenetic modifications play essential roles in development and diseases including developmental diseases.In the present review,we summarize the recent progress about the function of epigenetic regulation,especially DNA and RNA modifi cations in developmental diseases.Data sources:Original research articles and literature reviews published in PubMed-indexed journals.Results:DNA modifications including methylation and demethylation can regulate gene expression,and are involved in development and multiple diseases including Rett syndrome,Autism spectrum disorders,congenital heart disease and cancer,etc.RNA methylation and demethylation play important roles in RNA processing,reprogramming,circadian,and neuronal activity,and then modulate development.Conclusions:DNA and RNA modifications play important roles in development and diseases through regulating gene expression.Epigenetic components could serve as novel targets for the treatment of developmental diseases.
