Roles of ten eleven translocation proteins family and 5-hydroxymethylcytosine in epigenetic regulation of stem cells and regenerative medicine / 北京大学学报(医学版)

The methylation of cytosine is one of the most fundamental epigenetic modifications in mammalian genomes, and is involved in multiple crucial processes including gene expression, cell differentiation, embryo development and oncogenesis. In the past, DNA methylation was thought to be an irreversible process, which could only be diluted passively through DNA replication. It is now becoming increa-singly obvious that DNA demethylation can be an active process and plays a crucial role in biological processes. Ten eleven translocation (TET) proteins are the key factors modulating DNA demethylation. This family contains three members: TET1, TET2 and TET3. Although three TET proteins have relatively conserved catalytic domains, their roles in organisms are not repeated, and their expression has significant cell/organ specificity. TET1 is mainly expressed in embryonic stem cells, TET2 is mainly expressed in hematopoietic system, and TET3 is widely expressed in cerebellum, cortex and hippocampus. This family catalyzes 5-methylcytosine to 5-hydroxymethylcytosine and other oxidative products, reactivates silenced-gene expression, in turn maintains stem cell pluripotency and regulates lineage specification. With the development of tissue engineering, organ transplantation, autologous tissue transplantation and artificial prosthesis have been widely used in clinical treatment, but these technologies have limitations. Regenerative medicine, which uses stem cells and stem cell related factors for treatment, may provide alternative therapeutic strategies for multiple diseases. Among all kinds of human stem cells, adipose-derived stem cells (ADSCs) are the most prospective stem cell lineage since they have no ethical issues and can be easily obtained with large quantities. To date, ADSCs have been shown to have strong proli-feration capacity, secrete numerous soluble factors and have multipotent differentiation ability. However, the underlying mechanism of the proliferation, secretion, acquired pluripotency, and lineage specific differentiation of ADSCs are still largely unknown. Some studies have explored the role of epigenetic regulation and TET protein in embryonic stem cells, but little is known about its role in ADSCs. By studying the roles of TET proteins and 5-hydroxymethylcytosine in ADSCs, we could provide new theoretical foundation for the clinical application of ADSCs and the stem cell-based therapy. In the future, combined with bioprinting technology, ADSCs may be used in tissue and organ regeneration, plastic surgery reconstruction and other broader fields.

TET methylcytosine oxidases: new insights from a decade of research

In primates, males compete for a mate, which is a non-sharable resource. This makes the conditions lessconducive for males to have stable relationships. One such special kind of relationship is a bond where theinteractions are reciprocated, equitable and differentiated. Bonds in macaque societies are based on the degreeof within-group contest competition for mates which is dependent on the synchronization of female fertilephase and reliability of fertility signals. Species of the Fascicularis group, including Nicobar subspecies, showintermediate reliability in the signals with mild peaks, and studies have shown reciprocity but no differentiation. We conducted a study on a group of wild Nicobar long-tailed macaques Macaca fascicularis umbrosusto understand the existing patterns of male-male relationships. We examined whether there is reciprocity inaffiliation among the individuals and whether the rate of affiliation is balanced. We also measured the dominance linearity and steepness in the group to understand the monopolizability of females. We used socialnetwork analysis to understand whether the relations are differentiated based on hierarchical position andwhether the high-ranking individuals are the most central individuals in the distribution of grooming in thegroup. We found that there is reciprocity among the males although that is not equitable. There was no rankrelated differentiation of affiliation among the males of the group. Instead, the identities of individualsinfluenced affiliation patterns. Our results correspond to the existent strong relationships but lack of social bondotherwise found in the Fascicularis group of macaques.

5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer / 基因组蛋白质组与生物信息学报·英文版

Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E-19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient's cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.

The effect of DNA hydroxymethylase Tet2 on γ globin activation in the treatment of β-thalassemia / 中华内科杂志

Objective To study the function of ten-eleven translocation 2 (Tet2) in γglobin gene expression in patients with β-thalassemia.Methods Gamma globin expression was induced by 5-azacytidine and Tet2 gene expression was knocked down by short hairpin RNA (shRNA) in a human immortalized myelogenous leukemia K562 cell line.The global 5-hydroxymethylcytosine (5hmC) level was measured by an ELISA kit.5hmC level of γglobin gene was quantified by sulfite sequencing.The mRNA level of Tet2,γglobin,and related transcription factors Nfe4 and Klfl were quantified by real-time PCR.Results Tet2 knockdown resulted in a decreased global 5hmC level from 0.14％ to 0.03％ as of the control group in K562 cells.The expression of γ globin was enhanced after 5-azacytidine treatment in vitro.However,γglobin mRNA level in Tet2 knockdown cells was only 55％ as that in control group.The CG sites on γ globin gene were unmethylated.As Tet2 was down-regulated,the expression levels of Nfe4 and Klf1 decreased by about 80％ and increased to 3.5 folds,respectively.Conclusions Tet2 appears to maintain 5hmC level and facilitates γ globin gene activation.Moreover,Tet2 more likely regulates γglobin expression via affecting transcription factors rather than the gene itself.Thus,Tet2 could be a potential therapeutic target for β thalassemias.

Expression of TET and 5-HmC in Trophoblast Villi of Women with Normal Pregnancy and with Early Pregnancy Loss / 华中科技大学学报（医学）（英德文版）

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.

Expression of TET and 5-HmC in Trophoblast Villi of Women with Normal Pregnancy and with Early Pregnancy Loss / 华中科技大学学报（医学）（英德文版）

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.

Tet: novel anti-tumor drug target based on DNA demethylation / 上海交通大学学报（医学版）

Tet (ten-eleven translocation) proteins belong to α-ketoglutaric acid (α-KG or 2-OG) and Fe2+ dependent dioxygenases. Tets are found to be involved in the unique mammalian DNA active demethylation process by specifically oxidizing the methyl group of 5-methylcytosine (5mC) in mammalian genome, and play critical roles in gene regulation in early embryonic development and stem cell differentiation via regulating the dynamic balance distribution of 5mC. Abnormal expression and function of Tets are closely associated with various hematological malignances, including myelodysplastic syndrome, chronic myelomonocytic leukemia, and acute lymphoblastic leukemia, as well as solid tumors. Hence, Tets and Tets-mediated DNA demethylation are novel anti-tumor drug targets. Investigation of biological function and catalytic mechanism of Tets is helpful for further understanding mechanisms of tumor incidence and development relevant to DNA demethylation pathway and can provide reference for developing new anti-tumor targeted drugs.

Progress in TET enzymes and their intermediate products / 中国病理生理杂志

DNA methylation is an important epigenetic modification mode , which plays a crucial role in gene expression , genome stability and development .DNA methylation is catalyzed and maintained in cell proliferation by the family of DNA methyltransferases.The ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC).Here, we briefly describe the TET enzymes and their role in cancer , and the distribution , the role and detection method of those three oxidation products of cytosine in genome .

Genome-wide analysis of DNA 5-hydroxymethylcytosine in uremia patients using hMeDIP-chip / 中华风湿病学杂志

Objective To investigate the role of the 5-hydroxymethylcytosine (5-hmC) DNA modification in the onset of systemic lupus erythemosus (SLE),we compared tihe levels 5-hmC between SLE patients and normal controls.Methods With informed consent,whole blood was obtained from patients,and genomic DNA was extracted.Using hMeDIP-seq analysis and validation by quantitative real-time quantitative polymerase chain reaction (RT-PCR),we identified the differentially hydroxymethylated regions that were associated with SLE.Results There were 1 701 genes with significantly different 5-hmC levels at the promoter region in the SLE patients compared with the normal controls.The CpG islands of 3 826 genes showed significant difference at 5-hmC levels in SLE patients compared with the normal controls.Out of the differentially hydroxymethylated genes,three were selected for validation,including TREX1,CDKN1A,and CDKN1B.The hydroxymethylation levels of these three genes were confirmed by quantitative RT-PCR.Conclusion Our studies indicate that there are significant alterations of 5-hmC in SLE patients;these differentially hydroxymethylated genes may contribute to the pathogenesis of SLE.Such novel findings show the significance of 5-hmC as a potential biomarker or promising target for epigenetic-based SLE therapies.