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
Increasing evidence suggests that epigenetic dysfunction may influence the stability of normal pregnancy. The ten-eleven translocation （TET） family and 5-hydroxymethylcytosine （5-hmC） were found to be linked with ...Increasing evidence suggests that epigenetic dysfunction may influence the stability of normal pregnancy. The ten-eleven translocation （TET） family and 5-hydroxymethylcytosine （5-hmC） were found to be linked with epigenetic reprogramming. The present study aimed to examine the expression of the TET family and 5-hmC in the villi of human embryos and compared their expression between normal pregnancy and early pregnancy loss （EPL）. Embryonic villi were collected from normal pregnant women （control） experiencing medical abortion and from EPL patients at gestation ages of 6, 7 and 8 weeks. The mRNAs of TET family were analysed using quantitative polymerase chain reaction （qPCR）, and TET proteins using Western blotting and immunohistochemical analysis. The MethylFlashTM Kit was used to quantify the absolute amount of 5-methylcytosine （5-mC） and 5-hmC. Our results showed that the expression of the TETs and 5-hmC in the normal villus decreased with increasing gestational age. Immunohistochemistry revealed that the TET proteins were expressed in the cytoplasm of trophoblasts and their expression was the highest in the 6-week tissue samples, which was consistent with the qPCR and Western blot results. The expression of TET1, TET2, and TET3 was lower in the villi in EPL group than in normal pregnancy group （P〈0.05 for all）. It was concluded that the TET family and 5-hmC are critical in epigenetic reprogramming of human embryo. The findings also suggest that a deficiency of TETs in the villus might be associated with human EPL.展开更多
As a dioxygenase. Ten-Eleven Translocation 2 （TET2） catalyzes subsequent steps of 5-methylcytosine （5mC） oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hei-natopoi...As a dioxygenase. Ten-Eleven Translocation 2 （TET2） catalyzes subsequent steps of 5-methylcytosine （5mC） oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hei-natopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Dele- tion of Tet2 impairs the differentiation of osteoclast precursor cells （macrophages） and their matu- ration into bone-resorbing osteoclasts in vitro. Furthermore, Tet2 / mice exhibit mild osteopetrosis, accompanied by decreased number of osteoclasts in vivo. Tet2 loss in macrophages results in the altered expression of a set of genes implicated in osteoclast differentiation, such as Cehpa, Mafb, and Nfkbiz. Tet2 deletion also leads to a genome-wide alteration in the level of 5-hydroxymethylcytosine （ShmC） and altered expression of a specific subset of macrophage genes associated with osteoclast differentiation. Furthermore, Tet2 interacts with Runxl and negatively modulates its transcriptional activity. Our studies demonstrate a novel molecular mechanism controlling osteoclast differentiation and function by Tet2, that is, through interactions with Runxl and the maintenance of genomie 5hmC. Targeting Tet2 and its pathway could be a potential therapeutic strategy for the prevention and t,＇eatment of abnormal bone mass caused by the deregulation of osteoclast activities.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
Background： DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine （5mC） is catalyzed to 5-hydroxymethylcytosine （5hmC） by ten-eleven translocation （TET） family proteins. Rec...Background： DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine （5mC） is catalyzed to 5-hydroxymethylcytosine （5hmC） by ten-eleven translocation （TET） family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm^2 and 80 mJ/cm^2 doses of ultraviolet B （UVB） irradiation to HaCaT cells. Methods： To explore whether aberrant DNA hydroxymethylation is also related to skin photoaging, 40 mJ/cm^2 and 80 mJ/cm^2 doses of UVB were chosen to treat keratinocytes （HaCaT cells）. After 24 h of UVB irradiation, 5mC and 5hmC levels were determined by immunohistochemistry （IHC） and immunofluorescence （IF）, and at the same time, the expression levels of matrix metalloproteinase 1 （MMP-1） and TETs were assessed by reverse transcription-polymerase chain reaction or Western blot analysis. Results： After 40 mJ/cm^2 and 80 mJ/cm^2 doses of UVB exposure, both IHC and IF results showed that 5hmC levels increased significantly, while the 5mC levels did not exhibit significant changes in HaCaT cells, compared with HaCat cells without UVB exposure. Moreover, compared with HaCat cells without UVB exposure, the levels ofTET1, TET2, and TET3 mRNA and protein expression were significantly upregulated （mRNA： P = 0.0022 and 0.0043 for TET1; all P 〈 0.0001 for TET2; all P = 0.0006 for TET3; protein： P = 0.0012 and 0.0006 tbr TET 1 ; all P = 0.0022 for TET2; and all P = 0.0002 for TET3）, and the levels of MMP- 1 mRNA expression increased dose dependently in 40 mJ/cm^2 and 80 mJ/cm^2 UVB-irradiated groups. Conclusion： UVB radiation could cause increased 5hmC and TET expression, which might become a novel biomarker in UVB-related skin aging.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
Aberrant DNA methylation has raised widespread attention in tumorigenesis. In this study, we aimed to investigate the changes of global DNA methylation and hydroxymethylation from normal to tumor tissues in colorectal...Aberrant DNA methylation has raised widespread attention in tumorigenesis. In this study, we aimed to investigate the changes of global DNA methylation and hydroxymethylation from normal to tumor tissues in colorectal cancer(CRC) and their association with the prognosis. The levels of genomic 5-hydroxymethylcytosine(5hmC) and 5-methylcytosine(5mC) in cancerous tissues were significantly lower than those in corresponding adjacent normal tissues. The genomic levels of 5mC were significantly positively correlated with 5hmC in normal and cancerous tissues(all P<0.05). The ratio of 5mC in cancerous tissues to matched normal tissues(C/N-5mC) was also significantly positively correlated with the ratio of 5hmC in cancerous tissues to matched normal tissues(C/N-5hmC)(P=0.01). The 5mC levels and C/N-5mC ratios decreased with age(all P<0.05). Higher 5mC and 5hmC levels were found in rectal than in colon tissues(all P<0.05). High levels of 5mC in cancerous tissues and high C/N-5hmC ratios were each associated with lymph node metastasis(all P<0.05). Survival analysis indicated that the C/N-5mC ratio(P=0.04) is an independent protective factor for overall survival. The data showed that patients with a combination of high C/N-5hmC and low C/N-5mC ratios tended to have a worse prognosis(P<0.01). Our findings showed that the C/N-5mC ratio may be an independent prognostic factor for CRC outcome. Patients with both a high C/N-5hmC ratio and a low C/N-5mC ratio exhibited the worst survival, suggesting that 5mC and 5hmC can be used as critical markers in tumorigenesis and prognosis estimation.展开更多
5-hydroxymethylcytosine （5-hmC） is an important epigenetic derivative of cytosine and quantitative detection of 5-hmC could be used as a reliable biomarker for a variety of human diseases. Current technologies used ...5-hydroxymethylcytosine （5-hmC） is an important epigenetic derivative of cytosine and quantitative detection of 5-hmC could be used as a reliable biomarker for a variety of human diseases. Current technologies used in 5-hmC detection are complicated and time/cost inefficient. In this work, we report the first application of antibody-functionalized carbon nanotube field-effect transistors （CNT-FETs） in quantitative detection of 5-hmC from mouse tissues. This method achieves facile and ultra-sensitive 5-hmC detection based on electrical performance device and avoids complicated processing for DNA samples. The 5-hmC content percentages of normal mouse cerebrum, cerebellum, spleen, lung, liver, and heart samples presented in the genomic DNA were measured as 0.653, 0.573, 0.002, 0.020, 0.076, and 0.009, respectively, which is consistent with previous reports. This technology could be developed into fadle routine 5-hmC monitoring devices for clinic human disease diagnoses.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
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 study was supported by National Natural Science Foundation of China （No. 81601280, No. 31371517）, Foundation of Nanfang Hospital, Southern Medical University, and Science and Technology Project of Guangdong Province （No. 2013B051000086）.
文摘Increasing evidence suggests that epigenetic dysfunction may influence the stability of normal pregnancy. The ten-eleven translocation （TET） family and 5-hydroxymethylcytosine （5-hmC） were found to be linked with epigenetic reprogramming. The present study aimed to examine the expression of the TET family and 5-hmC in the villi of human embryos and compared their expression between normal pregnancy and early pregnancy loss （EPL）. Embryonic villi were collected from normal pregnant women （control） experiencing medical abortion and from EPL patients at gestation ages of 6, 7 and 8 weeks. The mRNAs of TET family were analysed using quantitative polymerase chain reaction （qPCR）, and TET proteins using Western blotting and immunohistochemical analysis. The MethylFlashTM Kit was used to quantify the absolute amount of 5-methylcytosine （5-mC） and 5-hmC. Our results showed that the expression of the TETs and 5-hmC in the normal villus decreased with increasing gestational age. Immunohistochemistry revealed that the TET proteins were expressed in the cytoplasm of trophoblasts and their expression was the highest in the 6-week tissue samples, which was consistent with the qPCR and Western blot results. The expression of TET1, TET2, and TET3 was lower in the villi in EPL group than in normal pregnancy group （P〈0.05 for all）. It was concluded that the TET family and 5-hmC are critical in epigenetic reprogramming of human embryo. The findings also suggest that a deficiency of TETs in the villus might be associated with human EPL.
基金supported by grants from the National Institutes of Health (Grant No. CA172408 to MX and FCY, Grant No. HL112294 to MX)the Leukemia & Lymphoma Society (LLS) (SCOR program to SN, FCY, and MX+7 种基金 translational grant to SN)University of Miami Sylvester Comprehensive Cancer Center (SCCC to MX and FCY), the United Statessupported by the Ministry of Science and Technology of China (Grant Nos. 2017YFA0103402to WY)National Natural Science Foundation of China (Grant Nos. 81629001 to MX, 81670102 to ZZ, 81600136 to YC, and 81421002 to WY)CAMS Innovation Fund for Medical Sciences (Grant Nos. 2017-I2M-3-015 to WY and 2016-I2M-1-017 to YC)Tianjin Application Foundation and Advanced Technology Research Program (Grant Nos. 16JCYBJC25200 to ZZ and 17JCQNJC09800 to YC)SKLEH-Pilot Research Grand (Grant No. ZK16-3 to ZZ)Peking Union Medical College Youth Fund (Grant No. 3332016092 to YC), China
文摘As a dioxygenase. Ten-Eleven Translocation 2 （TET2） catalyzes subsequent steps of 5-methylcytosine （5mC） oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hei-natopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Dele- tion of Tet2 impairs the differentiation of osteoclast precursor cells （macrophages） and their matu- ration into bone-resorbing osteoclasts in vitro. Furthermore, Tet2 / mice exhibit mild osteopetrosis, accompanied by decreased number of osteoclasts in vivo. Tet2 loss in macrophages results in the altered expression of a set of genes implicated in osteoclast differentiation, such as Cehpa, Mafb, and Nfkbiz. Tet2 deletion also leads to a genome-wide alteration in the level of 5-hydroxymethylcytosine （ShmC） and altered expression of a specific subset of macrophage genes associated with osteoclast differentiation. Furthermore, Tet2 interacts with Runxl and negatively modulates its transcriptional activity. Our studies demonstrate a novel molecular mechanism controlling osteoclast differentiation and function by Tet2, that is, through interactions with Runxl and the maintenance of genomie 5hmC. Targeting Tet2 and its pathway could be a potential therapeutic strategy for the prevention and t,＇eatment of abnormal bone mass caused by the deregulation of osteoclast activities.
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.
文摘Background： DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine （5mC） is catalyzed to 5-hydroxymethylcytosine （5hmC） by ten-eleven translocation （TET） family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm^2 and 80 mJ/cm^2 doses of ultraviolet B （UVB） irradiation to HaCaT cells. Methods： To explore whether aberrant DNA hydroxymethylation is also related to skin photoaging, 40 mJ/cm^2 and 80 mJ/cm^2 doses of UVB were chosen to treat keratinocytes （HaCaT cells）. After 24 h of UVB irradiation, 5mC and 5hmC levels were determined by immunohistochemistry （IHC） and immunofluorescence （IF）, and at the same time, the expression levels of matrix metalloproteinase 1 （MMP-1） and TETs were assessed by reverse transcription-polymerase chain reaction or Western blot analysis. Results： After 40 mJ/cm^2 and 80 mJ/cm^2 doses of UVB exposure, both IHC and IF results showed that 5hmC levels increased significantly, while the 5mC levels did not exhibit significant changes in HaCaT cells, compared with HaCat cells without UVB exposure. Moreover, compared with HaCat cells without UVB exposure, the levels ofTET1, TET2, and TET3 mRNA and protein expression were significantly upregulated （mRNA： P = 0.0022 and 0.0043 for TET1; all P 〈 0.0001 for TET2; all P = 0.0006 for TET3; protein： P = 0.0012 and 0.0006 tbr TET 1 ; all P = 0.0022 for TET2; and all P = 0.0002 for TET3）, and the levels of MMP- 1 mRNA expression increased dose dependently in 40 mJ/cm^2 and 80 mJ/cm^2 UVB-irradiated groups. Conclusion： UVB radiation could cause increased 5hmC and TET expression, which might become a novel biomarker in UVB-related skin aging.
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Project supported by the 111 Project(No.B13026)the National High-Tech R&D Program(863)of China(No.2012AA02A601)+1 种基金the Fundamental Research Funds for the Central Universitiesthe Zhejiang Provincial Program for the Cultivation of High-Level Innovative Health Talents
文摘Aberrant DNA methylation has raised widespread attention in tumorigenesis. In this study, we aimed to investigate the changes of global DNA methylation and hydroxymethylation from normal to tumor tissues in colorectal cancer(CRC) and their association with the prognosis. The levels of genomic 5-hydroxymethylcytosine(5hmC) and 5-methylcytosine(5mC) in cancerous tissues were significantly lower than those in corresponding adjacent normal tissues. The genomic levels of 5mC were significantly positively correlated with 5hmC in normal and cancerous tissues(all P<0.05). The ratio of 5mC in cancerous tissues to matched normal tissues(C/N-5mC) was also significantly positively correlated with the ratio of 5hmC in cancerous tissues to matched normal tissues(C/N-5hmC)(P=0.01). The 5mC levels and C/N-5mC ratios decreased with age(all P<0.05). Higher 5mC and 5hmC levels were found in rectal than in colon tissues(all P<0.05). High levels of 5mC in cancerous tissues and high C/N-5hmC ratios were each associated with lymph node metastasis(all P<0.05). Survival analysis indicated that the C/N-5mC ratio(P=0.04) is an independent protective factor for overall survival. The data showed that patients with a combination of high C/N-5hmC and low C/N-5mC ratios tended to have a worse prognosis(P<0.01). Our findings showed that the C/N-5mC ratio may be an independent prognostic factor for CRC outcome. Patients with both a high C/N-5hmC ratio and a low C/N-5mC ratio exhibited the worst survival, suggesting that 5mC and 5hmC can be used as critical markers in tumorigenesis and prognosis estimation.
文摘5-hydroxymethylcytosine （5-hmC） is an important epigenetic derivative of cytosine and quantitative detection of 5-hmC could be used as a reliable biomarker for a variety of human diseases. Current technologies used in 5-hmC detection are complicated and time/cost inefficient. In this work, we report the first application of antibody-functionalized carbon nanotube field-effect transistors （CNT-FETs） in quantitative detection of 5-hmC from mouse tissues. This method achieves facile and ultra-sensitive 5-hmC detection based on electrical performance device and avoids complicated processing for DNA samples. The 5-hmC content percentages of normal mouse cerebrum, cerebellum, spleen, lung, liver, and heart samples presented in the genomic DNA were measured as 0.653, 0.573, 0.002, 0.020, 0.076, and 0.009, respectively, which is consistent with previous reports. This technology could be developed into fadle routine 5-hmC monitoring devices for clinic human disease diagnoses.
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.
