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Weigert M, Cui XL, West-Szymanski D, Yu X, Bilecz AJ, Zhang Z, Dhir R, Kehoe M, Zhang W, He C, Lengyel E. 5-Hydroxymethylcytosine signals in serum are a predictor of chemoresistance in high-grade serous ovarian cancer. Gynecol Oncol 2024; 182:82-90. [PMID: 38262243 DOI: 10.1016/j.ygyno.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024]
Abstract
OBJECTIVE The genome-wide profiling of 5-hydroxymethylcytosines (5hmC) on circulating cell-free DNA (cfDNA) has revealed promising biomarkers for various diseases. The purpose of this study was to investigate 5hmC signals in serum cfDNA and identify novel predictive biomarkers for the development of chemoresistance in high-grade serous ovarian cancer (HGSOC). We hypothesized that 5hmC profiles in cfDNA reflect the development of chemoresistance and elucidate pathways that may drive chemoresistance in HGSOC. Moreover, we sought to identify predictors that would better stratify outcomes for women with intermediate-sensitive HGSOC. METHODS Women diagnosed with HGSOC and known platinum sensitivity status were selected for this study. Nano-hmC-Seal was performed on cfDNA isolated from archived serum samples, and differential 5hmC features were identified using DESeq2 to establish a model predictive of chemoresistance. RESULTS A multivariate model consisting of three features (preoperative CA-125, largest residual implant after surgery, 5hmC level of OSGEPL), stratified samples from intermediate sensitive, chemo-naive women diagnosed with HGSOC into chemotherapy-resistant- and sensitive-like strata with a significant difference in overall survival (OS). Independent analysis of The Cancer Genome Atlas data further confirmed that high OSGEPL1 expression is a favorable prognostic factor for HGSOC. CONCLUSIONS We have developed a novel multivariate model based on clinico-pathologic data and a cfDNA-derived 5hmC modified gene, OSGEPL1, that predicted response to platinum-based chemotherapy in intermediate-sensitive HGSOC. Our multivariate model applies to chemo-naïve samples regardless if the patint was treated with adjuvant or neoadjuvant chemotherapy. These results merit further investigation of the predictive capability of our model in larger cohorts.
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Affiliation(s)
- Melanie Weigert
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Diana West-Szymanski
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Xianbin Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | | | - Zhou Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rohin Dhir
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA
| | - Mia Kehoe
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA
| | - Wei Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA.
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Yi Y, Wang Y, Wu Y, Liu Y. Targeting SIRT4/TET2 Signaling Alleviates Human Keratinocyte Senescence by Reducing 5-hydroxymethylcytosine Loss. J Transl Med 2024; 104:100268. [PMID: 37898292 DOI: 10.1016/j.labinv.2023.100268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
Skin aging is characterized by wrinkle formation and increased frailty and laxity, leading to the risk of age-related skin diseases. Keratinocyte is an important component of the epidermis in skin structure, and keratinocyte senescence has been identified as a pivotal factor in skin aging development. Because epigenetic pathways play a vital role in the regulation of skin aging, we evaluated human skin samples for DNA hydroxymethylation (5-hydroxymethylcytosine; 5-hmC) and SIRT4 expressions. Results found that both 5-hmC and SIRT4 showed a significant decrease in aged human skin samples. To test the results in vitro, human keratinocytes were cultured in H2O2, which modulates skin aging in vivo. However, H2O2-induced keratinocytes showed senescence-associated protein expression and significant downregulation of 5-hmC and SIRT4 expressions. Moreover, 5-hmC-converting enzymes ten eleven translocation 2 (TET2) showed a decrease and enhanced TET2 acetylation level in H2O2-induced keratinocytes. However, the overexpression of SIRT4 in keratinocytes alleviates the senescence phenotype, such as senescence-associated protein expression, decreases the TET2 acetylation, but increases TET2 and 5-hmC expressions. Our results provide a novel relevant mechanism whereby the epigenetic regulation of keratinocytes in skin aging may be correlated with SIRT4 expression and TET2 acetylation in 5-hmC alteration. Our study may provide a potential strategy for antiskin aging, which targets the SIRT4/TET2 axis involving epigenetic modification in keratinocyte senescence.
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Affiliation(s)
- Yi Yi
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yuchang Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yukun Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
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Duarte Hospital C, Tête A, Debizet K, Imler J, Tomkiewicz-Raulet C, Blanc EB, Barouki R, Coumoul X, Bortoli S. SDHi fungicides: An example of mitotoxic pesticides targeting the succinate dehydrogenase complex. ENVIRONMENT INTERNATIONAL 2023; 180:108219. [PMID: 37778286 DOI: 10.1016/j.envint.2023.108219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/15/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Succinate dehydrogenase inhibitors (SDHi) are fungicides used to control the proliferation of pathogenic fungi in crops. Their mode of action is based on blocking the activity of succinate dehydrogenase (SDH), a universal enzyme expressed by all species harboring mitochondria. The SDH is involved in two interconnected metabolic processes for energy production: the transfer of electrons in the mitochondrial respiratory chain and the oxidation of succinate to fumarate in the Krebs cycle. In humans, inherited SDH deficiencies may cause major pathologies including encephalopathies and cancers. The cellular and molecular mechanisms related to such genetic inactivation have been well described in neuroendocrine tumors, in which it induces an oxidative stress, a pseudohypoxic phenotype, a metabolic, epigenetic and transcriptomic remodeling, and alterations in the migration and invasion capacities of cancer cells, in connection with the accumulation of succinate, an oncometabolite, substrate of the SDH. We will discuss recent studies reporting toxic effects of SDHi in non-target organisms and their implications for risk assessment of pesticides. Recent data show that the SDH structure is highly conserved during evolution and that SDHi can inhibit SDH activity in mitochondria of non-target species, including humans. These observations suggest that SDHi are not specific inhibitors of fungal SDH. We hypothesize that SDHi could have toxic effects in other species, including humans. Moreover, the analysis of regulatory assessment reports shows that most SDHi induce tumors in animals without evidence of genotoxicity. Thus, these substances could have a non-genotoxic mechanism of carcinogenicity that still needs to be fully characterized and that could be related to SDH inhibition. The use of pesticides targeting mitochondrial enzymes encoded by tumor suppressor genes raises questions on the risk assessment framework of mitotoxic pesticides. The issue of SDHi fungicides is therefore a textbook case that highlights the urgent need for changes in regulatory assessment.
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Affiliation(s)
| | - Arnaud Tête
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Kloé Debizet
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Jules Imler
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | | | - Etienne B Blanc
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Robert Barouki
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Xavier Coumoul
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris.
| | - Sylvie Bortoli
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris.
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Zeng C, Song X, Zhang Z, Cai Q, Cai J, Horbinski C, Hu B, Cheng SY, Zhang W. Dissection of transcriptomic and epigenetic heterogeneity of grade 4 gliomas: implications for prognosis. Acta Neuropathol Commun 2023; 11:133. [PMID: 37580817 PMCID: PMC10426201 DOI: 10.1186/s40478-023-01619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Grade 4 glioma is the most aggressive and currently incurable brain tumor with a median survival of one year in adult patients. Elucidating novel transcriptomic and epigenetic contributors to the molecular heterogeneity underlying its aggressiveness may lead to improved clinical outcomes. METHODS To identify grade 4 glioma -associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with grade 4 gliomas and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms. RESULTS Despite global reduction, the majority of differential 5hmC features showed higher modification levels in grade 4 gliomas as compared to normal controls. In addition, the bi-directional correlations between 5hmC modifications over promoter regions or gene bodies and gene expression were greatly disturbed in grade 4 gliomas regardless of IDH1 mutation status. Phenotype-associated co-regulated 5hmC-5hmC modules and 5hmC-mRNA modules not only are enriched with different molecular pathways that are indicative of the pathogenesis of grade 4 gliomas, but also are of prognostic significance comparable to IDH1 mutation status. Lastly, the best-performing 5hmC model can predict patient survival at a much higher accuracy (c-index = 74%) when compared to conventional prognostic factor IDH1 (c-index = 57%), capturing the molecular characteristics of tumors that are independent of IDH1 mutation status and gene expression-based molecular subtypes. CONCLUSIONS The 5hmC-based prognostic model could offer a robust tool to predict survival in patients with grade 4 gliomas, potentially outperforming existing prognostic factors such as IDH1 mutations. The crosstalk between 5hmC and gene expression revealed another layer of complexity underlying the molecular heterogeneity in grade 4 gliomas, offering opportunities for identifying novel therapeutic targets.
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Affiliation(s)
- Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Xiao Song
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Qinyun Cai
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Jiajun Cai
- Huashan Hospital, Fudan University, 12 Wulumuqi Rd., Shanghai, 200040, China
| | - Craig Horbinski
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Bo Hu
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA.
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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6
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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Guo XJ, Huang XY, Yang X, Lu JC, Wei CY, Gao C, Pei YZ, Chen Y, Sun QM, Cai JB, Zhou J, Fan J, Ke AW, Shi YG, Shen YH, Zhang PF, Shi GM, Yang GH. Loss of 5-hydroxymethylcytosine induces chemotherapy resistance in hepatocellular carcinoma via the 5-hmC/PCAF/AKT axis. Cell Death Dis 2023; 14:79. [PMID: 36732324 PMCID: PMC9895048 DOI: 10.1038/s41419-022-05406-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 02/04/2023]
Abstract
Multidrug resistance is a major challenge in treating advanced hepatocellular carcinoma (HCC). Although recent studies have reported that the multidrug resistance phenotype is associated with abnormal DNA methylation in cancer cells, the epigenetic mechanism underlying multidrug resistance remains unknown. Here, we reported that the level of 5-hydroxymethylcytosine (5-hmC) in human HCC tissues was significantly lower than that in adjacent liver tissues, and reduced 5-hmC significantly correlated with malignant phenotypes, including poor differentiation and microvascular invasion; additionally, loss of 5-hmC was related to chemotherapy resistance in post-transplantation HCC patients. Further, the 5-hmC level was regulated by ten-eleven translocation 2 (TET2), and the reduction of TET2 in HCC contributes to chemotherapy resistance through histone acetyltransferase P300/CBP-associated factor (PCAF) inhibition and AKT signaling hyperactivation. In conclusion, loss of 5-hmC induces chemotherapy resistance through PCAF/AKT axis and is a promising chemosensitivity prediction biomarker and therapeutic target for HCC patients.
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Affiliation(s)
- Xiao-Jun Guo
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Xiao-Yong Huang
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Xuan Yang
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
- Department of General Surgery, Peking University Third Hospital, Beijing, PR China
| | - Jia-Cheng Lu
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Chuan-Yuan Wei
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Chao Gao
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Yan-Zi Pei
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Yi Chen
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Qi-Man Sun
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
| | - Jia-Bin Cai
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
| | - Jian Zhou
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Jia Fan
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Ai-Wu Ke
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China
| | - Yujiang G Shi
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, PR China.
| | - Ying-Hao Shen
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
| | - Peng-Fei Zhang
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China.
- Department of Medical Oncology, Zhongshan Hospital of Fudan University, Shanghai, 200032, PR China.
- Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, 200032, PR China.
| | - Guo-Ming Shi
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China.
- Clinical Research Unit, Institute of Clinical Science, Zhongshan Hospital of Fudan University, Shanghai, 200032, PR China.
| | - Guo-Huan Yang
- Department of Liver Surgery and Liver Transplantation, Liver Cancer Institute, Zhongshan Hospital of Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, 200032, PR China.
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Multi-Omics Approaches in Colorectal Cancer Screening and Diagnosis, Recent Updates and Future Perspectives. Cancers (Basel) 2022; 14:cancers14225545. [PMID: 36428637 PMCID: PMC9688479 DOI: 10.3390/cancers14225545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
Abstract
Colorectal cancer (CRC) is common Cancer as well as the third leading cause of mortality around the world; its exact molecular mechanism remains elusive. Although CRC risk is significantly correlated with genetic factors, the pathophysiology of CRC is also influenced by external and internal exposures and their interactions with genetic factors. The field of CRC research has recently benefited from significant advances through Omics technologies for screening biomarkers, including genes, transcripts, proteins, metabolites, microbiome, and lipidome unbiasedly. A promising application of omics technologies could enable new biomarkers to be found for the screening and diagnosis of CRC. Single-omics technologies cannot fully understand the molecular mechanisms of CRC. Therefore, this review article aims to summarize the multi-omics studies of Colorectal cancer, including genomics, transcriptomics, proteomics, microbiomics, metabolomics, and lipidomics that may shed new light on the discovery of novel biomarkers. It can contribute to identifying and validating new CRC biomarkers and better understanding colorectal carcinogenesis. Discovering biomarkers through multi-omics technologies could be difficult but valuable for disease genotyping and phenotyping. That can provide a better knowledge of CRC prognosis, diagnosis, and treatments.
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9
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Zhang C, Zhou W, Tan Y, Tian D, Zhong C. 5-Hydroxymethylcytosines in circulating cell-free DNA reveal a diagnostic biomarker for glioma. Heliyon 2022; 8:e11022. [PMID: 36281400 PMCID: PMC9587273 DOI: 10.1016/j.heliyon.2022.e11022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/12/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Gliomas typically have unfavorable prognosis, due to late detection and interventions. However, effective biomarkers for early glioma diagnosis based on 5-hydroxymethylcytosines (5 hm C) in circulating cell-free DNA (cfDNA) are not currently available. 5 hm C profiles in GSE132118 set were subjected for establishment of diagnostic model using the LASSO (least absolute shrinkage and selection operator) algorithm. The 5 hm C-based models demonstrated great potency in differentiating healthy subjects from gliomas, with area under the curves (AUCs) > 0.91 in the training and validation sets. Moreover, the indicator performed well in combination with clinicopathological characteristics to differentiate glioblastomas (GBMs) from lower grade glioma (LGGs). Enrichment analysis on 5 hm C profiles displayed great correlation with glioma pathophysiology. The 5 hm C-derived biomarker might act as an effective and non-invasive measure in glioma screening.
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Affiliation(s)
- Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200120, China,Department of Neurosurgery, Huzhou Central Hospital, Huzhou 313099, Zhejiang Province, China
| | - Wei Zhou
- Department of Anesthesiology, Huzhou Central Hospital, Huzhou 313099, Zhejiang Province, China
| | - Yinqiu Tan
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430060, Hubei Province, China
| | - Daofeng Tian
- Department of Neurosurgery, Wuhan University, Renmin Hospital, Wuhan 430060, Hubei Province, China,Corresponding author.
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai 200120, China,Corresponding author.
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10
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Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022; 12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g., methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.
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Moravveji SS, Khoshbakht S, Mokhtari M, Salimi M, Lanjanian H, Nematzadeh S, Torkamanian-Afshar M, Masoudi-Nejad A. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers. BMC Genom Data 2022; 23:49. [PMID: 35768769 PMCID: PMC9241275 DOI: 10.1186/s12863-022-01061-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aberrant levels of 5-hydroxymethylcytosine (5-hmC) can lead to cancer progression. Identification of 5-hmC-related biological pathways in cancer studies can produce better understanding of gastrointestinal (GI) cancers. We conducted a network-based analysis on 5-hmC levels extracted from circulating free DNAs (cfDNA) in GI cancers including colon, gastric, and pancreatic cancers, and from healthy donors. The co-5-hmC network was reconstructed using the weighted-gene co-expression network method. The cancer-related modules/subnetworks were detected. Preservation of three detected 5-hmC-related modules was assessed in an external dataset. The 5-hmC-related modules were functionally enriched, and biological pathways were identified. The relationship between modules was assessed using the Pearson correlation coefficient (p-value < 0.05). An elastic network classifier was used to assess the potential of the 5-hmC modules in distinguishing cancer patients from healthy individuals. To assess the efficiency of the model, the Area Under the Curve (AUC) was computed using five-fold cross-validation in an external dataset. RESULTS The main biological pathways were the cell cycle, apoptosis, and extracellular matrix (ECM) organization. Direct association between the cell cycle and apoptosis, inverse association between apoptosis and ECM organization, and inverse association between the cell cycle and ECM organization were detected for the 5-hmC modules in GI cancers. An AUC of 92% (0.73-1.00) was observed for the predictive model including 11 genes. CONCLUSION The intricate association between biological pathways of identified modules may reveal the hidden significance of 5-hmC in GI cancers. The identified predictive model and new biomarkers may be beneficial in cancer detection and precision medicine using liquid biopsy in the early stages.
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Affiliation(s)
- Sayyed Sajjad Moravveji
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Samane Khoshbakht
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Majid Mokhtari
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Lanjanian
- Molecular Biology and Genetics Department, Engineering and Natural Science Faculty, Istinye University, Istanbul, Turkey
| | - Sajjad Nematzadeh
- Computer Engineering Department, Architecture and Engineering Faculty, Nisantasi University, Istanbul, Turkey
| | - Mahsa Torkamanian-Afshar
- Computer Engineering Department, Architecture and Engineering Faculty, Nisantasi University, Istanbul, Turkey
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran.
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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12
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Shang Y, Jiang T, Ran L, Hu W, Wu Y, Ye J, Peng Z, Chen L, Wang R. TET2-BCLAF1 transcription repression complex epigenetically regulates the expression of colorectal cancer gene Ascl2 via methylation of its promoter. J Biol Chem 2022; 298:102095. [PMID: 35660018 PMCID: PMC9251787 DOI: 10.1016/j.jbc.2022.102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Ascl2 has been shown to be involved in tumorigenesis in colorectal cancer (CRC), although its epigenetic regulatory mechanism is largely unknown. Here, we found that methylation of the Ascl2 promoter (bp -1670 ∼ -1139) was significantly increased compared to the other regions of the Ascl2 locus in CRC cells and was associated with elevated Ascl2 mRNA expression. Furthermore, we found that promoter methylation was predictive of CRC patient survival after analyzing DNA methylation data, RNA-Seq data, and clinical data of 410 CRC patient samples from the MethHC database, the MEXPRESS database, and the Cbioportal website. Using the established TET methylcytosine dioxygenase 2 (TET2) knockdown and ectopic TET2 catalytic domain–expression cell models, we performed glucosylated hydroxymethyl–sensitive quatitative PCR (qPCR), real-time PCR, and Western blot assays to further confirm that hypermethylation of the Ascl2 promoter, and elevated Ascl2 expression in CRC cells was partly due to the decreased expression of TET2. Furthermore, BCLAF1 was identified as a TET2 interactor in CRC cells by LC-MS/MS, coimmunoprecipitation, immunofluorescence colocalization, and proximity ligation assays. Subsequently, we found the TET2–BCLAF1 complex bound to multiple elements around CCGG sites at the Ascl2 promoter and further restrained its hypermethylation by inducing its hydroxymethylation using chromatin immunoprecipitation-qPCR and glucosylated hydroxymethyl-qPCR assays. Finally, we demonstrate that TET2-modulated Ascl2-targeted stem gene expression in CRC cells was independent of Wnt signaling. Taken together, our data suggest an additional option for inhibiting Ascl2 expression in CRC cells through TET2–BCLAF1–mediated promoter methylation, Ascl2-dependent self-renewal of CRC progenitor cells, and TET2–BCLAF1–related CRC progression.
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Affiliation(s)
- Yangyang Shang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Tao Jiang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Lijian Ran
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Wenjing Hu
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Yun Wu
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Jun Ye
- Department of Gastroenterology of 958 Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Zhihong Peng
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Lei Chen
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China
| | - Rongquan Wang
- Institute of Gastroenterology of PLA, Southwest Hospital, Army Medical University (Third Military Medical University) Chongqing 400038, China.
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Iacob R, Mandea M, Iacob S, Pietrosanu C, Paul D, Hainarosie R, Gheorghe C. Liquid Biopsy in Squamous Cell Carcinoma of the Esophagus and of the Head and Neck. Front Med (Lausanne) 2022; 9:827297. [PMID: 35572996 PMCID: PMC9098838 DOI: 10.3389/fmed.2022.827297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Squamous cell carcinomas of the esophagus (ESCC) and of the head and neck (HNSCC) are two neoplasms that share common risk factors and have the same embryological origin, but a very different prognosis, the 5-year survival of HNSCC being almost double (40–50%) compared to the 5-year survival of ESCC (20%). Current guidelines emphasize the importance of screening for ESCC in patients diagnosed with head and neck cancers. A liquid biopsy is a novel tool for diagnosis, prognostic stratification, and personalized therapy. Liquid biopsy biomarkers for these two malignancies could help both their early detection, facilitate residual disease identification, and provide prognosis information. The present systematic review of the literature was aimed at describing the liquid biopsy biomarkers present in these two malignancies, with an emphasis on potential clinical applications.
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Affiliation(s)
- Razvan Iacob
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Matei Mandea
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
| | - Speranta Iacob
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Catalina Pietrosanu
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Professor Doctor Dorin Hociota Institute of Phonoaudiology and Functional ENT Surgery, Bucharest, Romania
| | - Doru Paul
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Razvan Hainarosie
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Professor Doctor Dorin Hociota Institute of Phonoaudiology and Functional ENT Surgery, Bucharest, Romania
- *Correspondence: Razvan Hainarosie
| | - Cristian Gheorghe
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
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Lu MJ, Lu Y. 5-Hydroxymethylcytosine (5hmC) at or near cancer mutation hot spots as potential targets for early cancer detection. BMC Res Notes 2022; 15:143. [PMID: 35449110 PMCID: PMC9022237 DOI: 10.1186/s13104-022-06028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Universal noninvasive genomic screening to detect cancer and/or fetal DNA in plasma at all stages of development is highly warranted. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome. In the current study, we demonstrate that discrete 5hmC sites within 80 bp hotspot regions exist in a greater proportion of cancer versus normal cells. Result 5hmC was detected in 16 of 17 known hotspots having C to T or G to A mutations. The results show the presence of two characteristically distinct 5hmC groups: Tier 1 Group with 3 to eightfold more 5hmCs detected in tumor-cells than in normal-cell derived DNA (as observed in 6 of 11 CpG sites). Tier 2 group with equal allele frequency of 5hmC among normal and tumor-cell derived DNA at 5 CpG hotspot sites as well as 5 non-CpG hotspots. Thus, detection and quantification of the Tier 1 group of 5hmC sites or its prevalence at or near cancer mutation hot spots in cells may enable early detection, screening and potentially prediction of the likelihood of cancer occurrence or the severity of the cancer.
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Affiliation(s)
| | - Yabin Lu
- Anchor Molecular Inc., New York, USA.
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15
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Hu X, Luo K, Shi H, Yan X, Huang R, Zhao B, Zhang J, Xie D, Zhang W. Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer. Clin Epigenetics 2022; 14:15. [PMID: 35073982 PMCID: PMC8787948 DOI: 10.1186/s13148-022-01233-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Background Lung cancer is one of most common cancers worldwide, with a 5-year survival rate of less than 20%, which is mainly due to late-stage diagnosis. Noninvasive methods using 5-hydroxymethylation of cytosine (5hmC) modifications and fragmentation profiles from 5hmC cell-free DNA (cfDNA) sequencing provide an opportunity for lung cancer detection and management. Results A total of 157 lung cancer patients were recruited to generate the largest lung cancer cfDNA 5hmC dataset, which mainly consisted of 62 lung adenocarcinoma (LUAD), 48 lung squamous cell carcinoma (LUSC) and 25 small cell lung cancer (SCLC) patients, with most patients (131, 83.44%) at advanced tumor stages. A 37-feature 5hmC model was constructed and validated to distinguish lung cancer patients from healthy controls, with areas under the curve (AUCs) of 0.8938 and 0.8476 (sensitivity = 87.50% and 72.73%, specificity = 83.87% and 80.60%) in two distinct validation sets. Furthermore, fragment profiles of cfDNA 5hmC datasets were first explored to develop a 48-feature fragmentation model with good performance (AUC = 0.9257 and 0.822, sensitivity = 87.50% and 78.79%, specificity = 80.65% and 76.12%) in the two validation sets. Another diagnostic model integrating 5hmC signals and fragment profiles improved AUC to 0.9432 and 0.8639 (sensitivity = 87.50% and 83.33%, specificity = 90.30% and 77.61%) in the two validation sets, better than models based on either of them alone and performing well in different stages and lung cancer subtypes. Several 5hmC markers were found to be associated with overall survival (OS) and disease-free survival (DFS) based on gene expression data from The Cancer Genome Atlas (TCGA). Conclusions Both the 5hmC signal and fragmentation profiles in 5hmC cfDNA data are sensitive and effective in lung cancer detection and could be incorporated into the diagnostic model to achieve good performance, promoting research focused on clinical diagnostic models based on cfDNA 5hmC data. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01233-7.
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16
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Reverdatto S, Prasad A, Belrose JL, Zhang X, Sammons MA, Gibbs KM, Szaro BG. Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System. BMC Genomics 2022; 23:2. [PMID: 34979916 PMCID: PMC8725369 DOI: 10.1186/s12864-021-08247-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs, the South African claw-toed frog, Xenopus laevis, offers unique opportunities for exploring differences between regenerative and non-regenerative responses to CNS injury within the same organism. An earlier, three-way RNA-seq study (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) identified genes that regulate chromatin accessibility among those that were differentially expressed in regenerative vs non-regenerative CNS [11]. The current study used whole genome bisulfite sequencing (WGBS) of DNA collected from these same animals at the peak period of axon regeneration to study the extent to which DNA methylation could potentially underlie differences in chromatin accessibility between regenerative and non-regenerative CNS. RESULTS Consistent with the hypothesis that DNA of regenerative CNS is more accessible than that of non-regenerative CNS, DNA from both the regenerative tadpole hindbrain and frog eye was less methylated than that of the non-regenerative frog hindbrain. Also, consistent with observations of CNS injury in mammals, DNA methylation in non-regenerative frog hindbrain decreased after SCI. However, contrary to expectations that the level of DNA methylation would decrease even further with axotomy in regenerative CNS, DNA methylation in these regions instead increased with injury. Injury-induced differences in CpG methylation in regenerative CNS became especially enriched in gene promoter regions, whereas non-CpG methylation differences were more evenly distributed across promoter regions, intergenic, and intragenic regions. In non-regenerative CNS, tissue-related (i.e., regenerative vs. non-regenerative CNS) and injury-induced decreases in promoter region CpG methylation were significantly correlated with increased RNA expression, but the injury-induced, increased CpG methylation seen in regenerative CNS across promoter regions was not, suggesting it was associated with increased rather than decreased chromatin accessibility. This hypothesis received support from observations that in regenerative CNS, many genes exhibiting increased, injury-induced, promoter-associated CpG-methylation also exhibited increased RNA expression and association with histone markers for active promoters and enhancers. DNA immunoprecipitation for 5hmC in optic nerve regeneration found that the promoter-associated increases seen in CpG methylation were distinct from those exhibiting changes in 5hmC. CONCLUSIONS Although seemingly paradoxical, the increased injury-associated DNA methylation seen in regenerative CNS has many parallels in stem cells and cancer. Thus, these axotomy-induced changes in DNA methylation in regenerative CNS provide evidence for a novel epigenetic state favoring successful over unsuccessful CNS axon regeneration. The datasets described in this study should help lay the foundations for future studies of the molecular and cellular mechanisms involved. The insights gained should, in turn, help point the way to novel therapeutic approaches for treating CNS injury in mammals.
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Affiliation(s)
- Sergei Reverdatto
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology & Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA.
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J 2022; 20:26-39. [PMID: 34976309 PMCID: PMC8669313 DOI: 10.1016/j.csbj.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
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Key Words
- Cancer heterogeneity
- Cell free DNA
- Computation
- DMP, Differentially methylated base position
- DMR, Differentially methylated regions
- Diagnosis
- HELP-seq, HpaII-tiny fragment Enrichment by Ligation-mediated PCR sequencing
- MBD-seq, Methyl-CpG Binding Domain Protein Capture Sequencing
- MCTA-seq, Methylated CpG tandems amplification and sequencing
- MSCC, Methylation Sensitive Cut Counting
- MSRE, methylation sensitive restriction enzymes
- MeDIP-seq, Methylated DNA Immunoprecipitation Sequencing
- RRBS, Reduced-Representation Bisulfite Sequencing
- WGBS, Whole Genome Bisulfite Sequencing
- cfDNA, cell free DNA
- ctDNA, circulating tumor DNA
- dPCR, digital polymerase chain reaction
- ddMCP, droplet digital methylation-specific PCR
- ddPCR, droplet digital polymerase chain reaction
- scCGI, methylated CGIs at single cell level
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Liu H, Wang Y, Zhou X. Labeling and sequencing nucleic acid modifications using bio-orthogonal tools. RSC Chem Biol 2022; 3:994-1007. [PMID: 35975003 PMCID: PMC9347354 DOI: 10.1039/d2cb00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
The bio-orthogonal reaction is a type of reaction that can occur within a cell without interfering with the active components of the cell. Bio-orthogonal reaction techniques have been used to label and track the synthesis, metabolism, and interactions of distinct biomacromolecules in cells. Thus, it is a handy tool for analyzing biological macromolecules within cells. Nucleic acid modifications are widely distributed in DNA and RNA in cells and play a critical role in regulating physiological and pathological cellular activities. Utilizing bio-orthogonal tools to study modified bases is a critical and worthwhile research direction. The development of bio-orthogonal reactions focusing on nucleic acid modifications has enabled the mapping of nucleic acid modifications in DNA and RNA. This review discusses the recent advances in bio-orthogonal labeling and sequencing nucleic acid modifications in DNA and RNA. Labeling nucleic acid modifications using bio-orthogonal tools, then sequencing and imaging the labeled modifications in DNA and RNA.![]()
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Affiliation(s)
- Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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19
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Gutiérrez JR, Salgadoa ARM, Arias MDÁ, Vergara HSJ, Rada WR, Gómez CMM. Epigenetic Modulators as Treatment Alternative to Diverse Types of Cancer. Curr Med Chem 2021; 29:1503-1542. [PMID: 34963430 DOI: 10.2174/0929867329666211228111036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/17/2021] [Accepted: 10/21/2021] [Indexed: 01/10/2023]
Abstract
DNA is packaged in rolls in an octamer of histones forming a complex of DNA and proteins called chromatin. Chromatin as a structural matrix of a chromosome and its modifications are nowadays considered relevant aspects for regulating gene expression, which has become of high interest in understanding genetic mechanisms regulating various diseases, including cancer. In various types of cancer, the main modifications are found to be DNA methylation in the CpG dinucleotide as a silencing mechanism in transcription, post-translational histone modifications such as acetylation, methylation and others that affect the chromatin structure, the ATP-dependent chromatin remodeling and miRNA-mediated gene silencing. In this review we analyze the main alterations in gene expression, the epigenetic modification patterns that cancer cells present, as well as the main modulators and inhibitors of each epigenetic mechanism and the molecular evolution of the most representative inhibitors, which have opened a promising future in the study of HAT, HDAC, non-glycoside DNMT inhibitors and domain inhibitors.
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Affiliation(s)
- Jorseth Rodelo Gutiérrez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Arturo René Mendoza Salgadoa
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
| | - Marcio De Ávila Arias
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Homero San- Juan- Vergara
- Department of Medicine, Biotechnology Research Group, Health Sciences Division, Universidad del Norte, Barranquilla, Colombia
| | - Wendy Rosales Rada
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
- Advanced Biomedicine Research Group. Faculty of Exact and Natural Sciences, Universidad Libre Seccional, Barranquilla, Colombia
| | - Carlos Mario Meléndez Gómez
- Organic and Biomedical Chemistry Research Group, Faculty of Basic Sciences, Universidad del Atlántico, Barranquilla, Colombia
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Du Y, Lai Y, Liu JY, Diao J. Epigenetic Quantification of DNA 5-Hydroxymethylcytosine Using DNA Hybridization-Based Single-Molecule Immunofluorescent Imaging. SMALL METHODS 2021; 5:e2100061. [PMID: 34928080 DOI: 10.1002/smtd.202100061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/15/2021] [Indexed: 02/05/2023]
Abstract
5-Hydroxymethylcytosine (5hmC) is a deoxyribonucleic acid (DNA) epigenetic modification that has an important function in embryonic development and human diseases. However, the numerous methods that have been developed to detect and quantify 5hmC, require large amounts of DNA sample to be modified via chemical reactions, which considerably limits their application with cell-free DNA (cfDNA). Meanwhile, other antibody-based methods of detecting 5hmC do not offer information about the DNA sequence. Here, in this article DNA hybridization-based single-molecule immunofluorescent imaging is presented, an ultrasensitive method of detecting 5hmC modification in DNA. Via using the probe DNA to capture the DNA fragment of interest and the 5hmC antibody to detect the 5hmC modification in DNA, the fluorescent response signal of the 5hmC modification from the secondary antibody at the single-molecule level is successfully detected. Using the method, one could determine the quantity of 5hmC in the gene of interest within 6 h. In addition, it requires only 3 pg of the DNA sample and minimal experience and training for operation and analysis.
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Affiliation(s)
- Yang Du
- Department of Biotherapy, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ying Lai
- State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, The Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ji-Yan Liu
- Department of Biotherapy, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
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21
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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22
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Genetics of Myelodysplastic Syndromes. Cancers (Basel) 2021; 13:cancers13143380. [PMID: 34298596 PMCID: PMC8304604 DOI: 10.3390/cancers13143380] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Myelodysplastic syndrome (MDS) describes a heterogeneous group of bone marrow diseases, now understood to reflect numerous germline and somatic drivers, characterized by recurrent cytogenetic abnormalities and gene mutations. Precursor conditions including clonal hematopoiesis of indeterminate potential and clonal cytopenia of undetermined significance confer risk for MDS as well as other hematopoietic malignancies and cardiovascular complications. The future is likely to bring an understanding of those individuals who are at the highest risk of progression to MDS and preventive strategies to prevent malignant transformation.
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23
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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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24
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Dong ZR, Ke AW, Li T, Cai JB, Yang YF, Zhou W, Shi GM, Fan J. CircMEMO1 modulates the promoter methylation and expression of TCF21 to regulate hepatocellular carcinoma progression and sorafenib treatment sensitivity. Mol Cancer 2021; 20:75. [PMID: 33985545 PMCID: PMC8117652 DOI: 10.1186/s12943-021-01361-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background Cirrhosis is a recognized risk factor for developing hepatocellular carcinoma (HCC). Few studies have reported the expression profile of circRNAs in HCC samples compared to paratumour dysplastic nodule (DN) samples. Methods The Arraystar Human circRNA Array combined with laser capture microdissection (LCM) was used to analyse the expression profile of circRNAs in HCC samples compared to paratumour DN samples. Then, both in vitro and in vivo HCC models were used to determine the role and mechanism of key circRNA in HCC progression and treatment sensitivity. Results We found that circMEMO1 was significantly downregulated in HCC samples and that the level of circMEMO1 was closely related to the OS and disease-free survival (DFS) of HCC patients. Mechanistic analysis revealed that circMEMO1 can modulate the promoter methylation and gene expression of TCF21 to regulate HCC progression by acting as a sponge for miR-106b-5p, which targets the TET family of genes and increases the 5hmC level. More importantly, circMEMO1 can increase the sensitivity of HCC cells to sorafenib treatment. Conclusion Our study determined that circMEMO1 can promote the demethylation and expression of TCF21 and can be considered a crucial epigenetic modifier in HCC progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01361-3.
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Affiliation(s)
- Zhao-Ru Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China.,Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Ai-Wu Ke
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Jia-Bing Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Ya-Fei Yang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Wei Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Guo-Ming Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China.
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 YiXue Yuan Road, Shanghai, 200032, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China. .,Cancer Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200031, China.
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25
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Zhao F, Zhang ZW, Zhang J, Zhang S, Zhang H, Zhao C, Chen Y, Luo L, Tong WM, Li C, Niu Y, Liu P. Loss of 5-Hydroxymethylcytosine as an Epigenetic Signature That Correlates With Poor Outcomes in Patients With Medulloblastoma. Front Oncol 2021; 11:603686. [PMID: 33718152 PMCID: PMC7945595 DOI: 10.3389/fonc.2021.603686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
Medulloblastoma, as the most common malignant brain tumor in children, exhibits highly dysregulated DNA methylation. The novel epigenetic marker—5-hydroxymethylcytosine (5hmC) plays essential role in gene regulation during brain development and in brain tumors. However, the biological and clinical implications of 5hmC in medulloblastoma are still unclear. Here, we detected global 5hmC levels in two independent medulloblastoma patient cohorts (discovery cohort: n = 81; validation cohort: n = 171) using ultra-high performance liquid chromatography-tandem mass spectrometry analysis. Immunohistochemistry was used to identify the cell proliferation and expression of Ten-eleven translocation 1 and 2 (TET1/2). The prognostic impacts of covariates on progression-free survival (PFS) and overall survival (OS) were evaluated using multivariate Cox hazards regression models. We observed that global 5hmC levels were decreased in medulloblastomas compared to normal cerebellums (P < 0.001). Multivariate analysis showed that low global 5hmC levels correlated with poor PFS and OS rates (discovery cohort: PFS: P = 0.003, OS: P = 0.002; validation cohort: PFS: P = 0.0002, OS: P = 0.001). Immunohistochemistry showed an inverse correlation between 5hmC score and Ki-67 index (r = -0.747, P < 0.0001). Moreover, 5hmC score in MB samples was associated with nuclear expression of TET1 (r = -0.419, P = 0.003) and TET2 (r = -0.399, P = 0.005) proteins. Our study demonstrates that loss of 5hmC is an epigenetic biomarker in medulloblastomas. Our results indicate that 5hmC could be a candidate prognostic indicator for improving survival prediction of risk stratification in patients with medulloblastoma.
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Affiliation(s)
- Fu Zhao
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhi-Wei Zhang
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Zhang
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Shun Zhang
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Heng Zhang
- Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Chi Zhao
- Department of Neuro-Oncology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Luo
- Department of Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Pinan Liu
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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26
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Sharma A, Liu H, Herwig-Carl MC, Chand Dakal T, Schmidt-Wolf IGH. Epigenetic Regulatory Enzymes: mutation Prevalence and Coexistence in Cancers. Cancer Invest 2021; 39:257-273. [PMID: 33411587 DOI: 10.1080/07357907.2021.1872593] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation is an important layer of transcriptional control with the particularity to affect the broad spectrum of genome. Over the years, largely due to the substantial number of recurrent mutations, there have been hundreds of novel driver genes characterized in various cancers. Additionally, the relative contribution of two dysregulated epigenomic entities (DNA methylation and histone modifications) that gradually drive the cancer phenotype remains in the research focus. However, a complex scenario arises when the disease phenotype does not harbor any relevant mutation or an abnormal transcription level. Although the cancer landscape involves the contribution of multiple genetic and non-genetic factors, herein, we discuss specifically the mutation spectrum of epigenetically-related enzymes in cancer. In addition, we address the coexistence of these two epigenetic entities in malignant human diseases, especially cancer. We suggest that the study of epigenetically-related somatic mutations in the early cellular differentiation stage of embryonic development might help to understand their later-staged footprints in the cancer genome. Furthermore, understanding the co-occurrence and/or inverse association of different disease types and redefining the general definition of "healthy" controls could provide insights into the genome reorganization.
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Affiliation(s)
- Amit Sharma
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany.,Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | | | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Rajasthan, India
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany
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27
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Li CC, Dong YH, Zou X, Luo X, Shen D, Hu J, Zhang CY. Label-Free and Template-Free Chemiluminescent Biosensor for Sensitive Detection of 5-Hydroxymethylcytosine in Genomic DNA. Anal Chem 2021; 93:1939-1943. [PMID: 33427439 DOI: 10.1021/acs.analchem.0c05419] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
5-Hydroxymethylcytosine (5hmC) is a modified base present at low levels in various mammalian cells, and it plays essential roles in gene expression, DNA demethylation, and genomic reprogramming. Herein, we develop a label-free and template-free chemiluminescent biosensor for sensitive detection of 5hmC in genomic DNAs based on 5hmC-specific glucosylation, periodate (IO4+) oxidation, biotinylation, and terminal deoxynucleotidyl transferase (TdT)-assisted isothermal amplification strategy, which we term hmC-GLIB-IAS. This hmC-GLIB-IAS exhibits distinct advantages of bisulfite-free, improved sensitivity, and genome-wide analysis of 5hmC at constant reaction temperature without the involvement of either specially labeled nucleic acid probes or specific templates for signal amplification. This method can sensitively detect 5hmC with a detection limit of 2.07 × 10-13 M, and it can detect 5hmC in the whole genome DNA with a detection limit of 3.92 × 10-5 ng/μL. Moreover, this method can distinguish 5hmC from 5-methylcytosine (5mC) and cytosine (C) and even discriminate 0.1% 5hmC in the mixture of 5hmC-DNA and 5mC-DNA. Importantly, this hmC-GLIB-IAS strategy enables genome-wide analysis without the involvement of either isotope-labeled substrates or specific antibodies, providing a powerful platform to detect 5hmC in real genomic DNA with high reproducibility and accuracy.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China.,Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, P. R. China
| | - Yue-Hong Dong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, P. R. China
| | - Dazhong Shen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Juan Hu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
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28
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The Separation of Benign and Malignant Mesothelial Proliferations: New Markers and How to Use Them. Am J Surg Pathol 2020; 44:e100-e112. [PMID: 32826526 DOI: 10.1097/pas.0000000000001565] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The separation of benign from malignant mesothelial proliferations is an important clinical but often a difficult morphologic problem. Over the last roughly 10 years a variety of new markers that aid in this separation have been published and some older recommended markers reconsidered. Unlike previous, and largely unusable, empiric immunohistochemical (IHC) stains, these new markers, some using IHC and some using fluourescent in situ hybridization (FISH), are largely based on documented genomic abnormalities in malignant mesotheliomas. However, no marker works in all situations; rather, markers need to be chosen by the morphology of the process in question (epithelial vs. spindled) and the body cavity of interest (pleural vs. peritoneal). It is also important to be familiar with the exact pattern, for example nuclear versus cytoplasmic loss, that indicates a positive test. Furthermore, no single marker is 100% sensitive even with the optimal morphology/location, so that combinations of markers are essential. This review covers the various new markers in the literature, highlights their advantages and limitations, and suggests morphology/site specific combinations that can produce sensitivities in the 80% to 90% (and perhaps higher) range. At present only BRCA-1 related protein-1 and methylthioadenosine phosphorylase IHC, and cyclin-dependent kinase inhibitor 2A (p16) FISH have sufficient publications and reproducibility of results to be considered as established markers. 5-Hydroxymethyl cytosine, enhancer of zeste homolog 2, cyclin D1, and programmed death-ligand 1 IHC, and NF2 FISH are all potentially useful but need further study. The newly described entity of malignant mesothelioma in situ sits at the interface of benign and malignant mesothelial process; criteria for this diagnosis are reviewed.
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29
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Yuan Z, Wang X, Geng X, Li Y, Mu J, Tan F, Xue Q, Gao S, He J. Liquid biopsy for esophageal cancer: Is detection of circulating cell-free DNA as a biomarker feasible? Cancer Commun (Lond) 2020; 41:3-15. [PMID: 33264481 PMCID: PMC7819547 DOI: 10.1002/cac2.12118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
Esophageal cancer (EC) is a common cancer and is histopathologically classified into esophageal squamous cell carcinoma and esophageal adenocarcinoma. EC is a worldwide public health issue because of late diagnosis and lack of effective therapy. In contrast to standard tumor biopsies, liquid biopsies are emerging as a tool which is minimally invasive that can complement or even substitute more classical approaches. Specifically, cell-free DNA (cfDNA) has shown promise in cancer-related clinical applications. Indeed, cfDNA has been shown to be an effective circulating biomarker for non-invasive cancer diagnosis and monitoring of cancer patients. Although the clinical application of cfDNA has been reported on other cancers, few studies have evaluated its use in EC. Here, we review this relevant literature and discuss limitations and advantages of its application in the diagnosis and monitoring of EC.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xinfeng Wang
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiao Geng
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yin Li
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Juwei Mu
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Fengwei Tan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Qi Xue
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Shugeng Gao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Jie He
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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30
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Kato M, Onoyama I, Kawakami M, Yoshida S, Kawamura K, Kodama K, Hori E, Cui L, Matsumura Y, Yagi H, Asanoma K, Yahata H, Itakura A, Takeda S, Kato K. Downregulation of 5-hydroxymethylcytosine is associated with the progression of cervical intraepithelial neoplasia. PLoS One 2020; 15:e0241482. [PMID: 33141854 PMCID: PMC7608920 DOI: 10.1371/journal.pone.0241482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Around the world, cervical cancer is one of the most common neoplastic diseases among women, and the prognosis of patients in an advanced stage remains poor. To reduce the mortality rate of cervical cancer, early diagnosis and treatment are essential. DNA methylation is an important aspect of gene regulation, and aberrant DNA methylation contributes to carcinogenesis and cancer progression in various cancers. Although 5-methylcytosine (5mC) has been analyzed intensively, the function of 5-hydroxymethylcytosine (5hmC) has not been clarified. The purpose of our study was to identify the molecular biomarkers for early diagnosis of cervical tumors due to epigenetic alterations. To assess the clinical relevance of DNA methylation, we used immunohistochemistry (IHC) to characterize the level of 5hmC in 102 archived human cervical intraepithelial neoplasia (CIN) samples and cervical cancer specimens. The level of 5hmC was significantly decreased between CIN2 and CIN3. The progression of cervical tumors is caused by a reduction of TP53 and RB1 because of HPV infection. We observed that Tp53 and Rb1 were knocked down in mouse embryonic fibroblasts (MEF), a model of normal cells. The level of 5hmC was reduced in Tp53-knockdown cells, and the expression levels of DNA methyltransferase 1 (DNMT1) and ten-eleven translocation methylcytosine dioxygenase 1 (TET1) were induced. In contrast, there was no significant change in Rb1-knockdown cells. Mechanistically, we focused on apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) 3B (A3B) as a cause of 5hmC reduction after TP53 knockdown. In the human cell line HHUA with a wild-type TP53 gene, A3B was induced in TP53-knockdown cells, and A3B knockdown recovered 5hmC levels in TP53-knockdown cells. These data indicate that TP53 suppression leads to 5hmC reduction in part through A3B induction. Moreover, IHC showed that expression levels of A3B in CIN3 were significantly higher than those in both normal epithelium and in CIN2. In conclusion, 5hmC levels are decreased between CIN2 and CIN3 through the TP53-A3B pathway. Since A3B could impair genome stability, 5hmC loss might increase the chances of accumulating mutations and of progressing from CIN3 to cervical cancer. Thus, these epigenetic changes could predict whether CINs are progressing to cancer or disappearing.
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Affiliation(s)
- Masaya Kato
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Obstetrics and Gynecology, School of Medical Sciences, Juntendo University, Tokyo, Japan
| | - Ichiro Onoyama
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
| | - Minoru Kawakami
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sachiko Yoshida
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiko Kawamura
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Kodama
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Emiko Hori
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Lin Cui
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yumiko Matsumura
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Yagi
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuo Asanoma
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideaki Yahata
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, School of Medical Sciences, Juntendo University, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, School of Medical Sciences, Juntendo University, Tokyo, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, School of Medical Sciences, Kyushu University, Fukuoka, Japan
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31
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Ke Q, Wang K, Fan M, Li M, Luo G, Wang D. Prognostic role of high TET1 expression in patients with solid tumors: A meta-analysis. Medicine (Baltimore) 2020; 99:e22863. [PMID: 33126331 PMCID: PMC7598857 DOI: 10.1097/md.0000000000022863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recently, increased expression of TET1 has been shown to inhibit tumor development in many studies. Therefore, a meta-analysis was conducted to assess the prognostic role of TET1 in solid tumors. METHODS PubMed, Embase, and the Web of Science (last updated on June 13, 2019) were searched and 16 eligible studies involving 3100 patients were eventually taken forward into the meta-analysis. RESULTS Pooled results indicated that higher TET1 expression in cancer tissues was associated with improved overall survival (OS) [hazard ratio (HR) = 0.736, 95% confidence interval (95% CI) = 0.542-0.998, P = .049]. In the subgroup analysis, higher TET1 expression in respiratory tumors (HR = 0.778, 95% CI = 0.639-0.946, P = .012) and breast cancer in Asian patients (HR = 0.326, 95% CI = 0.199-0.533, P < .001) were significantly associated with better OS. In addition, the association between high TET1 expression and prolonged OS was also statistically significant in the following subgroups; data source from samples (HR = 0.561, 95% CI = 0.384-0.819, P = .003), reported in text (HR = 0.539, 95% CI = 0.312-0.931, P = .027), TET1 protein (HR = 0.635, 95% CI = 0.409-0.984, P = .042), Asians (HR = 0.563, 95% CI = 0.376-0.844, P = .005). CONCLUSION This meta-analysis displays that high expression levels of TET1 in tissues is significantly associated with better survival in patients with solid tumors. This finding can be used as evidence to the tone that TET1 may be a useful target for the treatment of patients with solid tumors in the future.
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Affiliation(s)
- Qiwei Ke
- Department of Emergency, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou 213003
| | - Kai Wang
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Road, Jiangning District, Nanjing 211100
| | | | - Mengchao Li
- Department of Emergency, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou 213003
| | - Guanghua Luo
- Comprehensive Laboratory, Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou 213003, Jiangsu Province, China
| | - Daming Wang
- Department of Emergency, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou 213003
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Pol β gap filling, DNA ligation and substrate-product channeling during base excision repair opposite oxidized 5-methylcytosine modifications. DNA Repair (Amst) 2020; 95:102945. [PMID: 32853828 DOI: 10.1016/j.dnarep.2020.102945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/07/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation on cytosine in CpG islands generates 5-methylcytosine (5mC), and further modification of 5mC can result in the oxidized variants 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxy (5caC). Base excision repair (BER) is crucial for both genome maintenance and active DNA demethylation of modified cytosine products and involves substrate-product channeling from nucleotide insertion by DNA polymerase (pol) β to the subsequent ligation step. Here, we report that, in contrast to the pol β mismatch insertion products (dCTP, dATP, and dTTP), the nicked products after pol β dGTP insertion can be ligated by DNA ligase I or DNA ligase III/XRCC1 complex when a 5mC oxidation modification is present opposite in the template position in vitro. A Pol β K280A mutation, which perturbates the stabilization of these base modifications within the active site, hinders the BER ligases. Moreover, the nicked repair intermediates that mimic pol β mismatch insertion products, i.e., with 3'-preinserted dGMP or dTMP opposite templating 5hmC, 5fC or 5caC, can be efficiently ligated, whereas preinserted 3'-dAMP or dCMP mismatches result in failed ligation reactions. These findings herein contribute to our understanding of the insertion tendencies of pol β opposite different cytosine base forms, the ligation properties of DNA ligase I and DNA ligase III/XRCC1 complex in the context of gapped and nicked damage-containing repair intermediates, and the efficiency and fidelity of substrate channeling during the final steps of BER in situations involving oxidative 5mC base modifications in the template strand.
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33
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Dang Y, Hu D, Xu J, Li C, Tang Y, Yang Z, Liu Y, Zhou W, Zhang L, Xu H, Xu Y, Ji G. Comprehensive analysis of 5-hydroxymethylcytosine in zw10 kinetochore protein as a promising biomarker for screening and diagnosis of early colorectal cancer. Clin Transl Med 2020; 10:e125. [PMID: 32628818 PMCID: PMC7418801 DOI: 10.1002/ctm2.125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND As a new epigenetic biomarker, 5-hydroxymethylcytosine (5hmC) is broadly involved in various diseases including cancers. However, the function and diagnostic performance of 5hmC in colorectal cancer (CRC) remain unclear. RESULTS High-throughput sequencing was used to profile 5hmC levels in adjacent normal colon, advanced adenomas, and CRC. The expression and 5hmC levels in zw10 kinetochore protein (ZW10) were significantly increased in the tissues and blood samples for patients with advanced adenoma and CRC, and were much higher in the early stages of CRC (I and II). The receiver operating characteristic analysis had potential diagnostic value for CRC. The area under the curve (AUC) of ZW10 5hmC levels in tissue samples of CRC was 0.901. In blood samples, the AUC was 0.748 for CRC. In addition, the ZW10 5hmC level had much higher diagnostic performance in early stages of CRC (AUC = 0.857) than it did in advanced stages (AUC = 0.594). Compared with FHC cell, ZW10 expression in HT29 cell was significantly increased. The ZW10 knockdown could inhibit cell proliferation and the ZW10 overexpression could promote cell proliferation in HT-29 cell. Furthermore, ZW10 knockdown inhibited AKT and mTOR phosphorylation, and ZW10 overexpression promoted AKT and mTOR phosphorylation. CONCLUSIONS The ZW10 5hmC level may serve as an effective epigenetic biomarker for minimally invasive screening and diagnosis of CRC, and it has higher diagnostic performance in early stages of CRC than it does in advanced stages. In addition, ZW10 could regulate CRC progression through the AKT-mTOR signaling.
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Affiliation(s)
- Yanqi Dang
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Dan Hu
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
- Department of Traditional Chinese MedicineSeventh People's Hospital of Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Jingjuan Xu
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Chunlin Li
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yingjue Tang
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Zhenhua Yang
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
- Digestive Endoscopy DepartmentLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yang Liu
- Department of General SurgeryLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Wenjun Zhou
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Li Zhang
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Hanchen Xu
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yangxian Xu
- Department of General SurgeryLonghua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang Ji
- Institute of Digestive DiseasesLonghua HospitalChina‐Canada Center of Research for Digestive Diseases (ccCRDD)Shanghai University of Traditional Chinese MedicineShanghaiChina
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Chapel DB, Schulte JJ, Husain AN, Krausz T. Application of immunohistochemistry in diagnosis and management of malignant mesothelioma. Transl Lung Cancer Res 2020; 9:S3-S27. [PMID: 32206567 PMCID: PMC7082260 DOI: 10.21037/tlcr.2019.11.29] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Immunohistochemistry plays an indispensable role in accurate diagnosis of malignant mesothelioma, particularly in morphologically challenging cases and in biopsy and cytology specimens, where tumor architecture is difficult or impossible to evaluate. Application of a targeted panel of mesothelial- and epithelial-specific markers permits correct identification of tumor lineage in the vast majority of cases. An immunopanel including two mesothelial markers (calretinin, CK5/6, WT-1, or D2-40) and two epithelial markers (MOC-31 and claudin-4) offers good sensitivity and specificity, with adjustments as appropriate for the differential diagnosis. Once mesothelial lineage is established, malignancy-specific studies can help verify a diagnosis of malignant mesothelioma. BAP1 loss, CDKN2A homozygous deletion, and MTAP loss are highly specific markers of malignancy in a mesothelial lesion, and they attain acceptable diagnostic sensitivity when applied as a diagnostic panel. Novel markers of malignancy, such as 5-hmC loss and increased EZH2 expression, are promising, but have not yet achieved widespread clinical adoption. Some diagnostic markers also have prognostic significance, and PD-L1 immunohistochemistry may predict tumor response to immunotherapy. Application and interpretation of these immnuomarkers should always be guided by clinical history, radiographic findings, and above all histomorphology.
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Affiliation(s)
- David B Chapel
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jefree J Schulte
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Aliya N Husain
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Krausz
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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35
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Wu T, Zhang ZW, Li S, Wang B, Yang Z, Li P, Zhang J, Tong WM, Li C, Zhao F, Niu Y, Liu P. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma. Clin Epigenetics 2020; 12:19. [PMID: 31992357 PMCID: PMC6988368 DOI: 10.1186/s13148-020-0809-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/06/2020] [Indexed: 12/16/2022] Open
Abstract
Background 5-Hydroxymethylcytosine (5hmC) is a novel epigenetic mark and may be involved in the mechanisms of tumorigenesis and malignant transformation. However, the role of 5hmC in ependymoma, the third most common brain tumor in children, remains unclear. The aim of this study sought to identify the characterization of 5hmC levels in pediatric posterior fossa ependymoma and to evaluate whether 5hmC levels could be a potential factor to predict clinical outcomes. Results Our results showed that 5hmC levels were globally decreased in posterior fossa ependymoma compared with normal cerebellum tissues (P < 0.001). Group A posterior fossa ependymomas had higher 5hmC levels than group B tumors (P = 0.007). Moreover, 5hmC levels positively correlated with Ki-67 index in posterior fossa ependymoma (r = 0.428, P = 0.003). Multivariate Cox hazards model revealed that patients with high 5hmC levels (> 0.102%) had worse PFS and OS than patients with lower 5hmC levels (< 0.102%) (PFS: HR = 3.014; 95% CI, 1.040–8.738; P = 0.042; OS: HR = 2.788; 95% CI, 0.974–7.982; P = 0.047). Conclusions Our findings suggest that loss of 5hmC is an epigenetic hallmark for pediatric posterior fossa ependymoma. 5hmC levels may represent a potential biomarker to predict prognosis in children with posterior fossa ependymoma.
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Affiliation(s)
- Tao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Zhi-Wei Zhang
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Shiwei Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Bo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Zhijun Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Peng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Jing Zhang
- Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Fu Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - Pinan Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China. .,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China.
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36
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Dong C, Chen J, Zheng J, Liang Y, Yu T, Liu Y, Gao F, Long J, Chen H, Zhu Q, He Z, Hu S, He C, Lin J, Tang Y, Zhu H. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease. Clin Epigenetics 2020; 12:17. [PMID: 31964422 PMCID: PMC6974971 DOI: 10.1186/s13148-020-0810-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023] Open
Abstract
Background The 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes. Its function has been studied extensively in tumors, neurodegenerative diseases, and atherosclerosis. Studies have reported that 5hmC modification is closely related to the phenotype transformation of vascular smooth muscle cells and endothelial dysfunction. However, its role in coronary artery disease (CAD) has not been fully studied. Results To investigate whether 5hmC modification correlates with CAD pathogenesis and whether 5hmC can be used as a biomarker, we used a low-input whole-genome sequencing technology based on selective chemical capture (hmC-Seal) to firstly generate the 5hmC profiles in the circulating cell-free DNA(cfDNA) of CAD patients, including stable coronary artery disease (sCAD) patients and acute myocardial infarction (AMI) patients. We detected a significant difference of 5hmC enrichment in gene bodies from CAD patients compared with normal coronary artery (NCA) individuals. Our results showed that CAD patients can be well separated from NCA individuals by 5hmC markers. The prediction performance of the model established by differentially regulated 5hmc modified genes were superior to common clinical indicators for the diagnosis of CAD (AUC = 0.93) and sCAD (AUC = 0.93). Specially, we found that 5hmC markers in cfDNA showed prediction potential for AMI (AUC = 0.95), which was superior to that of cardiac troponin I, muscle/brain creatine kinase, and myoglobin. Conclusions Our results suggest that 5hmC markers derived from cfDNA can serve as effective epigenetic biomarkers for minimally noninvasive diagnosis and prediction of CAD.
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Affiliation(s)
- Chaoran Dong
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China
| | - Jiemei Chen
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China
| | - Jilin Zheng
- Department of Cardiology, Coronary Heart Disease Center, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Road, Beijing, 100037, China
| | - Yiming Liang
- College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, No. 5 Yiheyuan Road Haidian District, Beijing, 100871, China
| | - Tao Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yupeng Liu
- Department of Cardiology, Coronary Heart Disease Center, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Road, Beijing, 100037, China
| | - Feng Gao
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China
| | - Jie Long
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China
| | - Hangyu Chen
- College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, No. 5 Yiheyuan Road Haidian District, Beijing, 100871, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zilong He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuan He
- College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, No. 5 Yiheyuan Road Haidian District, Beijing, 100871, China.,Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Jian Lin
- College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, No. 5 Yiheyuan Road Haidian District, Beijing, 100871, China.
| | - Yida Tang
- Department of Cardiology, Coronary Heart Disease Center, State Key Laboratory of Cardiovascular Disease, Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Road, Beijing, 100037, China.
| | - Haibo Zhu
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Xian Nong Tan Street 1, Xicheng District, Beijing, 100050, China.
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37
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Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019; 15:398-418. [PMID: 31842685 PMCID: PMC7153548 DOI: 10.1080/15592294.2019.1695332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - E Andres Houseman
- Department of Biostatistics, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Jessica E King
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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38
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Yuan F, Yu Y, Zhou YL, Zhang XX. 5hmC-MIQuant: Ultrasensitive Quantitative Detection of 5-Hydroxymethylcytosine in Low-Input Cell-Free DNA Samples. Anal Chem 2019; 92:1605-1610. [DOI: 10.1021/acs.analchem.9b04920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Fang Yuan
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yue Yu
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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39
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Huang J, Wang L. Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. Cancers (Basel) 2019; 11:cancers11111741. [PMID: 31698791 PMCID: PMC6896050 DOI: 10.3390/cancers11111741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.
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40
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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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Wang X, Yu Y, Zhou Z, Liu Y, Yang Y, Xu J, Chen J. Ultrafast Intersystem Crossing in Epigenetic DNA Nucleoside 2′-Deoxy-5-formylcytidine. J Phys Chem B 2019; 123:5782-5790. [DOI: 10.1021/acs.jpcb.9b04361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yang Yu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Youjun Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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42
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Applebaum MA, Barr EK, Karpus J, Nie J, Zhang Z, Armstrong AE, Uppal S, Sukhanova M, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman R, Godley LA, Stranger BE, He C, Cohn SL. 5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype. JCO Precis Oncol 2019; 3. [PMID: 31179414 PMCID: PMC6553657 DOI: 10.1200/po.18.00402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Whole-genome profiles of the epigenetic modification 5-hydroxymethylcytosine (5-hmC) are robust diagnostic biomarkers in adult patients with cancer. We investigated if 5-hmC profiles would serve as novel prognostic markers in neuroblastoma, a clinically heterogeneous pediatric cancer. Because this DNA modification facilitates active gene expression, we hypothesized that 5-hmC profiles would identify transcriptomic networks driving the clinical behavior of neuroblastoma. PATIENTS AND METHODS Nano-hmC-Seal sequencing was performed on DNA from Discovery (n = 51), Validation (n = 38), and Children’s Oncology Group (n = 20) cohorts of neuroblastoma tumors. RNA was isolated from 48 tumors for RNA sequencing. Genes with differential 5-hmC or expression between clusters were identified using DESeq2. A 5-hmC model predicting outcome in high-risk patients was established using linear discriminant analysis. RESULTS Comparison of low- versus high-risk tumors in the Discovery cohort revealed 577 genes with differential 5-hmC. Hierarchical clustering of tumors from the Discovery and Validation cohorts using these genes identified two main clusters highly associated with established prognostic markers, clinical risk group, and outcome. Genes with increased 5-hmC and expression in the favorable cluster were enriched for pathways of neuronal differentiation and KRAS activation, whereas genes involved in inflammation and the PRC2 complex were identified in the unfavorable cluster. The linear discriminant analysis model trained on high-risk Discovery cohort tumors was prognostic of outcome when applied to high-risk tumors from the Validation and Children’s Oncology Group cohorts (hazard ratio, 3.8). CONCLUSION 5-hmC profiles may be optimal DNA-based biomarkers in neuroblastoma. Analysis of transcriptional networks regulated by these epigenomic modifications may lead to a deeper understanding of drivers of neuroblastoma phenotype.
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Affiliation(s)
| | - Erin K Barr
- Texas Tech University Health Sciences, Lubbock, TX
| | | | - Ji Nie
- University of Chicago, Chicago, IL
| | | | | | | | | | - Wei Zhang
- Northwestern University, Chicago, IL
| | | | | | | | | | | | | | | | - Chuan He
- University of Chicago, Chicago, IL.,Howard Hughes Medical Institute, Chevy Chase, MD
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Liu Y, Siejka-Zielińska P, Velikova G, Bi Y, Yuan F, Tomkova M, Bai C, Chen L, Schuster-Böckler B, Song CX. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol 2019; 37:424-429. [PMID: 30804537 DOI: 10.1038/s41587-019-0041-2] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/22/2019] [Indexed: 02/07/2023]
Abstract
Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades1-4. However, this harsh chemical treatment degrades the majority of the DNA and generates sequencing libraries with low complexity2,5,6. Here, we present a bisulfite-free and base-level-resolution sequencing method, TET-assisted pyridine borane sequencing (TAPS), for detection of 5mC and 5hmC. TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). Subsequent PCR converts DHU to thymine, enabling a C-to-T transition of 5mC and 5hmC. TAPS detects modifications directly with high sensitivity and specificity, without affecting unmodified cytosines. This method is nondestructive, preserving DNA fragments over 10 kilobases long. We applied TAPS to the whole-genome mapping of 5mC and 5hmC in mouse embryonic stem cells and show that, compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, thus enabling higher quality, more comprehensive and cheaper methylome analyses.
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Affiliation(s)
- Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paulina Siejka-Zielińska
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gergana Velikova
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ying Bi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fang Yuan
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chunsen Bai
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- College of Chemistry, Nankai University, Tianjin, China
| | - Lei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Mitochondrial Biology and Medicine and Center for Translational Medicine, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Zeng C, Stroup EK, Zhang Z, Chiu BCH, Zhang W. Towards precision medicine: advances in 5-hydroxymethylcytosine cancer biomarker discovery in liquid biopsy. Cancer Commun (Lond) 2019; 39:12. [PMID: 30922396 PMCID: PMC6440138 DOI: 10.1186/s40880-019-0356-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
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-hydroxymethylcytosine (5hmC) in cfDNA, focusing on the detection approaches and potential role as biomarkers in different cancer types.
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Affiliation(s)
- Chang Zeng
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Emily Kunce Stroup
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Brian C-H Chiu
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA. .,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Institute of Precision Medicine, Jining Medical University, Jining, 272067, Shandong, P. R. China.
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45
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Immunohistochemical evaluation of nuclear 5-hydroxymethylcytosine (5-hmC) accurately distinguishes malignant pleural mesothelioma from benign mesothelial proliferations. Mod Pathol 2019; 32:376-386. [PMID: 30315275 DOI: 10.1038/s41379-018-0159-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/10/2018] [Accepted: 09/16/2018] [Indexed: 12/22/2022]
Abstract
Accurate distinction of benign mesothelial proliferations from malignant mesothelioma remains a diagnostic challenge. Sequential use of BAP1 immunohistochemistry and CDKN2A fluorescence in situ hybridization is specific for diagnosis of mesothelioma, but fluorescence in situ hybridization is both costly and time-consuming. Early data indicate that mesothelioma shows extensive loss of nuclear 5-hydroxymethylcytosine (5-hmC). We studied 49 cases of mesothelioma (17 epithelioid mesothelioma, 22 biphasic mesothelioma, and 10 sarcomatoid mesothelioma) and 23 benign mesothelial proliferations using a 5-hmC single immunohistochemical stain, CAM5.2/5-hmC double immunohistochemical stain, and BAP1 immunohistochemistry. Estimations of extent of 5-hmC loss were made using the 5-hmC single stain and CAM5.2/5-hmC double stain, and extent of nuclear 5-hmC loss was definitively quantitated in at least 1000 cells per case. Mean nuclear 5-hmC loss in mesothelioma (84%) was significantly greater than in benign mesothelial proliferations (4%) (p < 0.0001). Using 5-hmC loss in > 50% of tumor nuclei to define the diagnosis of mesothelioma, 5-hmC immunohistochemistry showed sensitivity of 92% and specificity of 100%. An immunopanel including 5-hmC and BAP1 immunohistochemistry achieved sensitivity of 98% and specificity of 100%. Extensive nuclear 5-hmC loss is sensitive and specific for mesothelioma in the differential diagnosis with benign mesothelial proliferations. In challenging mesothelial lesions, immunohistochemical studies showing either extensive 5-hmC loss or BAP1 loss indicate a diagnosis of mesothelioma, precluding the need for CDKN2A fluorescence in situ hybridization in a considerable number of cases.
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46
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The effects of 2-hydroxyglutarate on the tumorigenesis of gliomas. Contemp Oncol (Pozn) 2018; 22:215-222. [PMID: 30783384 PMCID: PMC6377424 DOI: 10.5114/wo.2018.82642] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022] Open
Abstract
Mutation of the isocitrate-dehydrogenase (IDH) enzymes is one of the central research topics regarding gliomagenesis. Indeed, 70% of gliomas are associated with a gain-of-function IDH mutation and consequently synthesize the oncometabolite, 2-hydroxyglutarate (2-HG). This review aims to elucidate the effects of 2-HG on gliomagenesis. 2-HG promotes tumorigenesis by impacting metabolism, vascularization and altering the epigenome of glioma cells. Glioma metabolism and vascularization is altered by 2-HG's effect on the stability of hypoxia-inducible factor (HIF) and inhibition of endostatin. However, 2-HG's impacts on epigenetic mechanisms are more profound to gliomagenesis. Through competitive inhibition of JHDMs and TET proteins, 2-HG orchestrates histone and DNA hypermethylation, which is associated with gene silencing and dedifferentiation of cells. The hypermethylator phenotype induced by 2-HG also results in alterations of the interaction of the immune system with the tumour. Additionally, this study reviews 2-HG promotion of tumorigenesis by inhibiting repair of DNA alkylation damage through competitive inhibition of AlkB proteins.
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Zeng H, He B, Xia B, Bai D, Lu X, Cai J, Chen L, Zhou A, Zhu C, Meng H, Gao Y, Guo H, He C, Dai Q, Yi C. Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution. J Am Chem Soc 2018; 140:13190-13194. [PMID: 30278133 DOI: 10.1021/jacs.8b08297] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC-CATCH enabled us to detect genome-wide hydroxymethylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Bo He
- Peking-Tsinghua Center for Life Sciences , Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871 , China
| | - Bo Xia
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Dongsheng Bai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Xingyu Lu
- Shanghai Epican Genetech, Co. Ltd., Zhangjiang Hi-Tech Park , Shanghai 201203 , China
| | - Jiabin Cai
- Department of Liver Surgery , Liver Cancer Institute, Zhongshan Hospital, Fudan University , Shanghai 200032 , China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction , Eastern Hepatobiliary Surgery Institute, Second Military Medical University , Shanghai 200438 , China
| | - Ankun Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China
| | - Yun Gao
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics , School of Life Sciences, Peking University , Beijing 100871 , China
| | - Hongshan Guo
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics , School of Life Sciences, Peking University , Beijing 100871 , China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology , Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago , Chicago , Illinois 60637 , United States.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center , College of Chemistry and Molecular Engineering, Peking University , Beijing 100871 , China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology , Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871 , China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center , College of Chemistry and Molecular Engineering, Peking University , Beijing 100871 , China
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Vitamin C promotes decitabine or azacytidine induced DNA hydroxymethylation and subsequent reactivation of the epigenetically silenced tumour suppressor CDKN1A in colon cancer cells. Oncotarget 2018; 9:32822-32840. [PMID: 30214687 PMCID: PMC6132357 DOI: 10.18632/oncotarget.25999] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic silencing of tumour suppressor genes is a key hallmark of colorectal carcinogenesis. Despite this, the therapeutic potential of epigenetic agents capable of reactivating these silenced genes remains relatively unexplored. Evidence has shown the dietary antioxidant vitamin C (ascorbate) acts as an inducer of the ten-eleven translocation (TET) dioxygenases, an enzyme family that catalyses a recently described mechanism of DNA demethylation linked to gene re-expression. In this study, we set out to determine whether vitamin C can enhance the known anti-neoplastic actions of the DNA-demethylating agents decitabine (DAC) and azacytidine (AZA) in colorectal cancer cells. Administration of vitamin C alone significantly enhanced global levels of 5-hydroxymethyl-2’-deoxycytidine (5-hmdC), without altering 5-methyl-2’-deoxycytidine (5-mdC), as would be expected upon the activation of TET dioxygenases. Concomitant treatment of vitamin C with either AZA or DAC resulted in an unexpectedly high increase of global 5-hmdC levels, one that administration of any these compounds alone could not achieve. Notably, this was also accompanied by increased expression of the tumour suppressor p21 (CDKN1A), and a significant increase in apoptotic cell induction. Our in vitro data leads us to hypothesize that the reactivation of genes in colorectal cancer cells by AZA or DAC can be improved when the 5-hmdC levels are simultaneously increased by the TET activator vitamin C. The dual administration of demethylating agents and vitamin C to colorectal cancer patients, a demographic in which vitamin C deficiencies are common, may improve responses to epigenetic therapies.
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Koivunen P, Laukka T. The TET enzymes. Cell Mol Life Sci 2018; 75:1339-1348. [PMID: 29184981 PMCID: PMC11105636 DOI: 10.1007/s00018-017-2721-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 12/19/2022]
Abstract
During the past decade, we have learnt that the most common DNA modification, 5-methylcytosine (5mC), playing crucial roles in development and disease, is not stable but can be actively reversed to its unmodified form via enzymatic catalysis involving the TET enzymes. These ground-breaking discoveries have been achieved thanks to technological advances in the detection of the oxidized forms of 5mC and to the boldness of individual scientists. The TET enzymes require molecular oxygen for their catalysis, making them important targets for hypoxia research. They also require special cofactors which enable additional levels of regulation. Moreover, mutations and other genetic alterations in TETs are found, especially in myeloid malignances. This review focuses on the kinetic and inhibitory properties of the TET enzymes and the role of TETs in cellular differentiation and transformation and in cancer.
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Affiliation(s)
- Peppi Koivunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, 90014, Oulu, Finland.
| | - Tuomas Laukka
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Oulu Center for Cell-Matrix Research, University of Oulu, 90014, Oulu, Finland
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