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Seethy AA, Pethusamy K, Kushwaha T, Kumar G, Talukdar J, Chaubey R, Sundaram UD, Mahapatra M, Saxena R, Dhar R, Inampudi KK, Karmakar S. Alterations of the expression of TET2 and DNA 5-hmC predict poor prognosis in Myelodysplastic Neoplasms. BMC Cancer 2023; 23:1035. [PMID: 37884893 PMCID: PMC10601240 DOI: 10.1186/s12885-023-11449-2] [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: 05/15/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Myelodysplastic Neoplasms (MDS) are clonal stem cell disorders characterized by ineffective hematopoiesis and progression to acute myeloid leukemia, myelodysplasia-related (AML-MR). A major mechanism of pathogenesis of MDS is the aberration of the epigenetic landscape of the hematopoietic stem cells and/or progenitor cells, especially DNA cytosine methylation, and demethylation. Data on TET2, the predominant DNA demethylator of the hematopoietic system, is limited, particularly in the MDS patients from India, whose biology may differ since these patients present at a relatively younger age. We studied the expression and the variants of TET2 in Indian MDS and AML-MR patients and their effects on 5-hydroxymethyl cytosine (5-hmC, a product of TET2 catalysis) and on the prognosis of MDS patients. RESULTS Of the 42 MDS patients, cytogenetics was available for 31 sub-categorized according to the Revised International Prognostic Scoring System (IPSS-R). Their age resembled that of the previous studies from India. Bone marrow nucleated cells (BMNCs) were also obtained from 13 patients with AML-MR, 26 patients with de-novo AML, and 11 subjects with morphologically normal bone marrow. The patients had a significantly lower TET2 expression which was more pronounced in AML-MR and the IPSS-R higher-risk MDS categories. The 5-hmC levels in higher-risk MDS and AML-MR correlated with TET2 expression, suggesting a possible mechanistic role in the loss of TET2 expression. The findings on TET2 and 5-hmC were also confirmed at the tissue level using immunohistochemistry. Pathogenic variants of TET2 were found in 7 of 24 patient samples (29%), spanning across the IPSS-R prognostic categories. One of the variants - H1778R - was found to affect local and global TET2 structure when studied using structural predictions and molecular dynamics simulations. Thus, it is plausible that some pathogenic variants in TET2 can compromise the structure of TET2 and hence in the formation of 5-hmC. CONCLUSIONS IPSS-R higher-risk MDS categories and AML-MR showed a reduction in TET2 expression, which was not apparent in lower-risk MDS. DNA 5-hmC levels followed a similar pattern. Overall, a decreased TET2 expression and a low DNA 5-hmC level are predictors of advanced disease and adverse outcome in MDS in the population studied, i.e., MDS patients from India.
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Affiliation(s)
- Ashikh A Seethy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rekha Chaubey
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Udayakumar Dharmalingam Sundaram
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Renu Saxena
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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Zhang YY, Zhou JD, Yang DQ, He PF, Yao DM, Qian Z, Yang J, Xu WR, Lin J, Qian J. Intragenic hypomethylation of DNMT3A in patients with myelodysplastic syndrome. Clin Chem Lab Med 2018; 56:485-491. [PMID: 29031013 DOI: 10.1515/cclm-2016-0142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/07/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND DNMT3A is a DNA methyltransferase that acts in de novo methylation. Aberrant expression of DNMT3A has been reported in several human diseases, including myelodysplastic syndrome (MDS). However, the pattern of DNMT3A methylation remains unknown in MDS. METHODS The present study was aimed to investigate the methylation status of DNMT3A intragenic differentially methylated region 2 (DMR2) using real-time quantitative methylation-specific PCR and analyze its clinical significance in MDS. RESULTS Aberrant hypomethylation of DNMT3A was found in 57% (51/90) MDS cases. There were no significant differences in age, sex, white blood cell counts, platelet counts, hemoglobin counts and World Health Organization, International Prognostic Scoring System and karyotype classifications between DNMT3A hypomethylated and DNMT3A hypermethylated groups. However, the patients with DNMT3A hypomethylation had shorter overall survival time than those without DNMT3A hypomethylation (11 months vs. 36 months, p=0.033). Multivariate analysis confirmed the independent adverse impact of DNMT3A hypomethylation in MDS. CONCLUSIONS Our data suggest that DNMT3A DMR2 hypomethylation may be a negative prognostic hallmark in MDS.
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Affiliation(s)
- Ying-Ying Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,Department of Hematology and Oncology, Yizheng People's Hospital, Yangzhou, Jiangsu, P.R. China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Dong-Qin Yang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Pin-Fang He
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Dong-Ming Yao
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Zhen Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Jing Yang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China
| | - Wen-Rong Xu
- Key Laboratory of Laboratory Medicine of Jiangsu Province, Medical Key Talent Project of Zhenjiang, Zhenjiang, P.R. China
| | - Jiang Lin
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., 212002 Zhenjiang, P.R. China, Fax: +86.511.85234387
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, P.R. China.,The Key Laboratory of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, P.R. China.,Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., 212002 Zhenjiang, P.R. China, Fax: +86.511.85234387
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DNA Methylation Events as Markers for Diagnosis and Management of Acute Myeloid Leukemia and Myelodysplastic Syndrome. DISEASE MARKERS 2017; 2017:5472893. [PMID: 29038614 PMCID: PMC5606093 DOI: 10.1155/2017/5472893] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/17/2017] [Accepted: 07/30/2017] [Indexed: 01/18/2023]
Abstract
During the onset and progression of hematological malignancies, many changes occur in cellular epigenome, such as hypo- or hypermethylation of CpG islands in promoter regions. DNA methylation is an epigenetic modification that regulates gene expression and is a key event for tumorigenesis. The continuous search for biomarkers that signal early disease, indicate prognosis, and act as therapeutic targets has led to studies investigating the role of DNA in cancer onset and progression. This review focuses on DNA methylation changes as potential biomarkers for diagnosis, prognosis, response to treatment, and early toxicity in acute myeloid leukemia and myelodysplastic syndrome. Here, we report that distinct changes in DNA methylation may alter gene function and drive malignant cellular transformation during several stages of leukemogenesis. Most of these modifications occur at an early stage of disease and may predict myeloid/lymphoid transformation or response to therapy, which justifies its use as a biomarker for disease onset and progression. Methylation patterns, or its dynamic change during treatment, may also be used as markers for patient stratification, disease prognosis, and response to treatment. Further investigations of methylation modifications as therapeutic biomarkers, which may correlate with therapeutic response and/or predict treatment toxicity, are still warranted.
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Zhou L, Wang N, Li H, Tong G, Yang J, Lai L, Pan H, Ye X, Huang J. SOCS1 gene promoter methylation status is associated with in-stent restenosis after percutaneous coronary intervention. Oncotarget 2017; 8:56959-56967. [PMID: 28915645 PMCID: PMC5593616 DOI: 10.18632/oncotarget.18398] [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: 02/20/2017] [Accepted: 05/02/2017] [Indexed: 11/25/2022] Open
Abstract
Background Inflammation is involved in the development of In-stent restenosis (ISR) after percutaneous coronary intervention. We aimed to investigate the association between of suppressor of cytokine signaling-1 (SOCS1), a major negative regulator for inflammation, and the occurrence of ISR in Chinese patients. Methods We enrolled patients with coronary artery disease who underwent PCI with stenting. PCI procedures were performed successfully and a follow-up angiography was repeated 1 year later to determine ISR presence. Real-time quantitative reverse transcription polymerase chain reaction and methylation-specific polymerase chain reaction (MSP) was used for SOCS1 methylation status determination. Results There are a total of 187 patients had SOCS1 methylation while there are 275 had no methylated SOCS1. Patients with SOCS1 methylation have a higher inflammatory status. Of note, patients with SOCS1 methylation had a significantly lower SOCS1 mRNA levels compared to those without. Patients with ISR tend to have a significantly higher percentage of SOCS1 gene methylation (P<0.001). We next conducted the Binary logistic regression analyses to determine the correlation of SOCS1 with ISR, using demographic and clinical characteristics. Our data show that SOCS1 methylation is the only factors which are closely associated with ISR incidence. Patients with SOCS1 methylation are 5 times more likely to have ISR after successful PCI as opposed to those without SOCS1 methylation (P<0.001). Conclusion Our data suggest that blood SOCS1 gene promoter methylation status is closely associated with ISR occurrence, thus may be used as a marker to predict ISR.
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Affiliation(s)
- Liang Zhou
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Ningfu Wang
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Hong Li
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Guoxin Tong
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Jianmin Yang
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Lei Lai
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Hao Pan
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Xianhua Ye
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
| | - Jinyu Huang
- Department of Cardiology, Hangzhou First People's Hospital, Nanjing Medical University Hangzhou Hospital, Hangzhou, 310006 China
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Chaubey R, Sazawal S, Mahapatra M, Chhikara S, Saxena R. Does Indian Myelodysplastic Syndrome Have a Biology Different from That in the West ? Asian Pac J Cancer Prev 2016; 17:2341-2. [PMID: 27221942 DOI: 10.7314/apjcp.2016.17.4.2341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
abstract.
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Affiliation(s)
- Rekha Chaubey
- Department of Hematology, All India Institute of Medical Sciences, New Delhi E-mail : drrekhacgupta@ gmail.com
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