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Ismail JN, Mantash S, Hallal M, Jabado N, Khoueiry P, Shirinian M. Phenotypic and transcriptomic impact of expressing mammalian TET2 in the Drosophila melanogaster model. Epigenetics 2023; 18:2192375. [PMID: 36989121 PMCID: PMC10072067 DOI: 10.1080/15592294.2023.2192375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Ten-Eleven Translocation (TET) proteins have recently come to light as important epigenetic regulators conserved in multicellular organisms. TET knockdown studies in rodents have highlighted the critical role of these proteins for proper brain development and function. Mutations in mammalian mTET proteins and mTET2 specifically are frequent and deregulated in leukaemia and glioma respectively. Accordingly, we examined the role of mTET2 in tumorigenesis in larval haemocytes and adult heads in Drosophila melanogaster. Our findings showed that expression of mutant and wild type mTET2 resulted in general phenotypic defects in adult flies and accumulation of abdominal melanotic masses. Notably, flies with mTET2-R43G mutation at the N-terminus of mTET2 exhibited locomotor and circadian behavioural deficits, as well as reduced lifespan. Flies with mTET2-R1261C mutation in the catalytic domain, a common mutation in acute myeloid leukaemia (AML), displayed alterations affecting haemocyte haemostasis. Using transcriptomic approach, we identified upregulated immune genes in fly heads that were not exclusive to TET2 mutants but also found in wild type mTET2 flies. Furthermore, inhibiting expression of genes that were found to be deregulated in mTET2 mutants, such as those involved in immune pathways, autophagy, and transcriptional regulation, led to a rescue in fly survival, behaviour, and hemocyte number. This study identifies the transcriptomic profile of wild type mTET2 versus mTET2 mutants (catalytic versus non-catalytic) with indications of TET2 role in normal central nervous system (CNS) function and innate immunity.
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Affiliation(s)
- Joy N Ismail
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Sarah Mantash
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Mohammad Hallal
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Biomedical Engineering Program, American University of Beirut, Beirut, Lebanon
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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2
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Zhao A, Zhou H, Yang J, Li M, Niu T. Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Affiliation(s)
- Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Hui Zhou
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Jinrong Yang
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Meng Li
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China.
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3
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Elliott EK, Hopkins LN, Hensen R, Sutherland HG, Haupt LM, Griffiths LR. Epigenetic Regulation of miR-92a and TET2 and Their Association in Non-Hodgkin Lymphoma. Front Genet 2021; 12:768913. [PMID: 34899857 PMCID: PMC8661906 DOI: 10.3389/fgene.2021.768913] [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: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are well known for their ability to regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. In various cancers, miRNAs regulate gene expression by altering the epigenetic status of candidate genes that are implicated in various difficult to treat haematological malignancies such as non-Hodgkin lymphoma by acting as either oncogenes or tumour suppressor genes. Cellular and circulating miRNA biomarkers could also be directly utilised as disease markers for diagnosis and monitoring of non-Hodgkin lymphoma (NHL); however, the role of DNA methylation in miRNA expression regulation in NHL requires further scientific inquiry. In this study, we investigated the methylation levels of CpGs in CpG islands spanning the promoter regions of the miR-17–92 cluster host gene and the TET2 gene and correlated them with the expression levels of TET2 mRNA and miR-92a-3p and miR-92a-5p mature miRNAs in NHL cell lines, tumour samples, and the whole blood gDNA of an NHL case control cohort. Increased expression of both miR-92a-3p and miR-92a-5p and aberrant expression of TET2 was observed in NHL cell lines and tumour tissues, as well as disparate levels of dysfunctional promoter CGI methylation. Both miR-92a and TET2 may play a concerted role in NHL malignancy and disease pathogenesis.
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Affiliation(s)
- Esther K Elliott
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia.,Icon Cancer Centre, Brisbane, QLD, Australia
| | - Lloyd N Hopkins
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | | | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
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4
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CLL dedifferentiation to clonally related myeloid cells. Blood Adv 2021; 4:6169-6174. [PMID: 33351112 DOI: 10.1182/bloodadvances.2020002726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/14/2020] [Indexed: 02/07/2023] Open
Abstract
Key Points
Common progenitor cells exist in clonally related concomitant chronic lymphocytic leukemia and acute myeloid leukemias. CLL cells dedifferentiated to clonally related myeloid cells posttransplantation.
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Davis AR, Stone SL, Oran AR, Sussman RT, Bhattacharyya S, Morrissette JJD, Bagg A. Targeted massively parallel sequencing of mature lymphoid neoplasms: assessment of empirical application and diagnostic utility in routine clinical practice. Mod Pathol 2021; 34:904-921. [PMID: 33311649 DOI: 10.1038/s41379-020-00720-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Massively parallel sequencing (MPS) has become a viable diagnostic tool to interrogate genetic profiles of numerous tumors but has yet to be routinely adopted in the setting of lymphoma. Here, we report the empirical application of a targeted 40-gene panel developed for use in mature lymphoid neoplasms (MLNs) and report our experience on over 500 cases submitted for MPS during the first year of its clinical use. MPS was applied to both fresh and fixed specimens. The most frequent diagnoses were diffuse large B-cell lymphoma (116), chronic lymphocytic leukemia/small lymphocytic lymphoma (60), marginal zone lymphoma (52), and follicular lymphoma (43), followed by a spectrum of mature T-cell neoplasms (40). Of 534 cases submitted, 471 generated reportable results in MLNs, with disease-associated variants (DAVs) detected in 241 cases (51.2%). The most frequent DAVs affected TP53 (30%), CREBBP (14%), MYD88 (14%), TNFRSF14 (10%), TNFAIP3 (10%), B2M (7%), and NOTCH2 (7%). The bulk of our findings confirm what is reported in the scientific literature. While a substantial majority of mutations did not directly impact diagnosis, MPS results were utilized to either change, refine, or facilitate the final diagnosis in ~10.8% of cases with DAVs and 5.5% of cases overall. In addition, we identified preanalytic variables that significantly affect assay performance highlighting items for specimen triage. We demonstrate the technical viability and utility of the judicious use of a targeted MPS panel that may help to establish general guidelines for specimen selection and diagnostic application in MLNs in routine clinical practice.
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Affiliation(s)
- Adam R Davis
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sara L Stone
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda R Oran
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Robyn T Sussman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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6
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Li X, Ma J, Wang L, Yan S, Li F, Wang L, Wang L, Li G, Ma D, Li H. Multi Cytogenetic Changes in a Patient as Co-Existing MDS and CLL Progresses. Onco Targets Ther 2021; 14:177-186. [PMID: 33447059 PMCID: PMC7802771 DOI: 10.2147/ott.s281800] [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: 09/13/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) and myelodysplastic syndrome (MDS) existing simultaneously in untreated patients is extremely rare. There have only been nine cases of untreated CLL concurrent with or followed by the development of MDS. Of all nine cases, four patients exhibited results of cytogenetic phonotypes all showing more than one abnormal chromosome karyotype. It is unknown whether or not these abnormal chromosome karyotypes change during the development of the disease. Meanwhile, the optimal treatment for the concurrence of CLL with MDS has yet to be identified. Case Presentation A 69-year-old Chinese man diagnosed with co-existing CLL with MDS was observed from diagnosis, treatment, relapse to death during an admission period of a total of 158 days. Since being diagnosed with CLL and MDS, he was treated by decitabine and his condition went into remission for three months. Four laboratory tests showed an abnormal chromosome cytogenetic karyotype successively changed during the progression of the disease. Conclusion It is the first time the abnormal chromosome karyotype variation significantly associated with the change of the illness was discovered. In the relapse and deterioration stages of the disease, there was t(9;22)(q24; q11.2); add(11)(p15) and other chromosome translocation. Repeated occurrence of TET2 mutation is special at this stage of the disease. Furthermore, decitabine could be beneficial for the treatment of the disease.
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Affiliation(s)
- Xiangxin Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Jiale Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Luqun Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Shuxin Yan
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Fanglin Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Lingling Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Lin Wang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Guosheng Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Hao Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
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7
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Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M. Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia. Epigenetics Chromatin 2019; 12:4. [PMID: 30616658 PMCID: PMC6322269 DOI: 10.1186/s13072-018-0252-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/23/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS We show that naïve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n = 15) compared to naïve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to naïve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.
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Affiliation(s)
- Sara Wernig-Zorc
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hallgerdur Lind Kristjansdottir
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden.,Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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8
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Wang X, Chen X, Yang Z, Dou H, Lu L, Bi J, Zou L, Yu J, Bao L. Correlation of TET2 SNP rs2454206 with improved survival in children with acute myeloid leukemia featuring intermediate-risk cytogenetics. Genes Chromosomes Cancer 2018; 57:379-386. [PMID: 29664232 DOI: 10.1002/gcc.22540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) may influence the disease course and outcome of hematologic neoplasms. SNP rs2454206 is common in the TET2 gene, which plays a role in epigenetic regulation of myelopoiesis. Few investigations examined the role of TET2 SNP rs2454206 in acute myeloid leukemia (AML) and none of those studies was performed in Chinese populations. Here, we report the prevalence and clinical relevance of TET2 SNP rs2454206 in 254 Chinese patients with childhood AML. Our data demonstrate that TET2 SNP rs2454206AG/GG is associated with improved overall survival and event-free survival in AML patients with intermediate-risk cytogenetics features. The prognostic impact of TET2 SNP rs2454206AG/GG was independent of other common AML risk factors, such as age, white blood cell count, and FLT3-ITD. No difference in TET2 expression levels in AML with TET2 SNP rs2454206AA and TET2 SNP rs2454206AG/GG was detected, indicating that TET2 SNP rs2454206 status does not affect TET2 expression in pediatric AML.
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Affiliation(s)
- Xingjuan Wang
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Chen
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenzhen Yang
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Dou
- Department of Clinical Laboratory, Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Lu
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Junqin Bi
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Yu
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Liming Bao
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire
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9
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Han X, Li W, He N, Feng P, Pang Y, Ji C, Ma D. Gene mutation patterns of Chinese acute myeloid leukemia patients by targeted next-generation sequencing and bioinformatic analysis. Clin Chim Acta 2018; 479:25-37. [PMID: 29309772 DOI: 10.1016/j.cca.2018.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/31/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
Abstract
PURPOSES The conventional risk stratification of acute myeloid leukemia (AML), based on cytogenetics, cannot meet the demand for accurate prognostic evaluations. In recent years, gene mutations are found to be potential markers for more accurate risk stratification, but reports on mutation screening of Chinese AML are limited. We aim to display the mutation patterns of Chinese AML patients, reveal the genotype-phenotype correlations and make a comparison with Caucasians patients. METHODS Genome DNA from 78 patients' bone marrow were extracted for targeted gene mutation panel by next-generation sequencing (NGS) technology. Statistics and bioinformatics were used to analyze the correlations between gene mutations and clinical features, as well as the comparison of our results with the Cancer Genome Atlas Research Network (TCGA) public AML dataset. RESULTS We found patients with mutations of FLT3 and TET2 had higher bone marrow blasts, peripheral blasts and white blood cell (WBC) count, mutations of SRSF2 were related with age, and mutations of FLT3-ITD, DNMT3A, IDH1, TET2 and SRSF2 were risk factors for overall survival. What's more, we discovered 15 novel mutations and difference of mutational incidence in 6 genes between Chinese and Caucasians AML. Bioinformatic analysis revealed some relationship between gene mutations and expressions as well as drug sensitivities. CONCLUSIONS We made an investigation on the mutation patterns of Chinese AML patients by NGS technique and revealed correlations between gene mutations and clinical features. Thus we recommend routine testing of suspected genes for better prognostic prediction and individualized treatment.
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Affiliation(s)
- Xiaoyu Han
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Wei Li
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Na He
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Panpan Feng
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Yihua Pang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China.
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, PR China.
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10
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Bagacean C, Le Dantec C, Berthou C, Tempescul A, Saad H, Bordron A, Zdrenghea M, Cristea V, Douet-Guilbert N, Renaudineau Y. Combining cytogenetic and epigenetic approaches in chronic lymphocytic leukemia improves prognosis prediction for patients with isolated 13q deletion. Clin Epigenetics 2017; 9:122. [PMID: 29209431 PMCID: PMC5704505 DOI: 10.1186/s13148-017-0422-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Both defective DNA methylation and active DNA demethylation processes are emerging as important risk factors in chronic lymphocytic leukemia (CLL). However, associations between 5-cytosine epigenetic markers and the most frequent chromosomal abnormalities detected in CLL remain to be established. Methods CLL patients were retrospectively classified into a cytogenetic low-risk group (isolated 13q deletion), an intermediate-risk group (normal karyotype or trisomy 12), and a high-risk group (11q deletion, 17p deletion, or complex karyotype [≥ 3 breakpoints]). The two 5-cytosine derivatives, 5-methylcytosine (5-mCyt) and 5-hydroxymethylcytosine (5-hmCyt), were tested by ELISA (n = 60), while real-time quantitative PCR was used for determining transcriptional expression levels of DNMT and TET (n = 24). Results By using global DNA methylation/demethylation levels, in the low-risk disease group, two subgroups with significantly different clinical outcomes have been identified (median treatment-free survival [TFS] 45 versus > 120 months for 5-mCyt, p = 0.0008, and 63 versus > 120 months for 5-hmCyt, p = 0.04). A defective 5-mCyt status was further associated with a higher percentage of 13q deleted nuclei (> 80%), thus suggesting an acquired process. When considering the cytogenetic intermediate/high-risk disease groups, an association of 5-mCyt status with lymphocytosis (p = 0.0008) and the lymphocyte doubling time (p = 0.04) but not with TFS was observed, as well as a reduction of DNMT3A, TET1, and TET2 transcripts. Conclusions Combining cytogenetic studies with 5-mCyt assessment adds accuracy to CLL patients’ prognoses and particularly for those with 13q deletion as a sole cytogenetic abnormality.
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Affiliation(s)
- Cristina Bagacean
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France.,"Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Christelle Le Dantec
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Christian Berthou
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Adrian Tempescul
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Anne Bordron
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Mihnea Zdrenghea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Yves Renaudineau
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France
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Bagacean C, Tempescul A, Le Dantec C, Bordron A, Mohr A, Saad H, Olivier V, Zdrenghea M, Cristea V, Cartron PF, Douet-Guilbert N, Berthou C, Renaudineau Y. Alterations in DNA methylation/demethylation intermediates predict clinical outcome in chronic lymphocytic leukemia. Oncotarget 2017; 8:65699-65716. [PMID: 29029465 PMCID: PMC5630365 DOI: 10.18632/oncotarget.20081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
Cytosine derivative dysregulations represent important epigenetic modifications whose impact on the clinical outcome in chronic lymphocytic leukemia (CLL) is incompletely understood. Hence, global levels of 5-methylcytosine (5-mCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-CaCyt) and 5-hydroxymethyluracil were tested in purified B cells from CLL patients (n = 55) and controls (n = 17). The DNA methylation 'writers' (DNA methyltransferases [DNMT1/3A/3B]), 'readers' (methyl-CpG-binding domain [MBD2/4]), 'editors' (ten-eleven translocation [TET1/2/3]) and 'modulators' (SAT1) were also evaluated. Accordingly, patients were stratified into three subgroups. First, a subgroup with a global deficit in cytosine derivatives characterized by hyperlymphocytosis, reduced median progression free survival (PFS = 52 months) and shorter treatment free survival (TFS = 112 months) was identified. In this subgroup, major epigenetic modifications were highlighted including a reduction of 5-mCyt, 5-hmCyt, 5-CaCyt associated with DNMT3A, MBD2/4 and TET1/2 downregulation. Second, the cytosine derivative analysis revealed a subgroup with a partial deficit (PFS = 84, TFS = 120 months), mainly affecting DNA demethylation (5-hmCyt reduction, SAT1 induction). Third, a subgroup epigenetically similar to controls was identified (PFS and TFS > 120 months). The prognostic impact of stratifying CLL patients within three epigenetic subgroups was confirmed in a validation cohort. In conclusion, our results suggest that dysregulations of cytosine derivative regulators represent major events acquired during CLL progression and are independent from IGHV mutational status.
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Affiliation(s)
- Cristina Bagacean
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adrian Tempescul
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Christelle Le Dantec
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Anne Bordron
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Audrey Mohr
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Valerie Olivier
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
| | - Mihnea Zdrenghea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, ‘Ion Chiricuta’ Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | | | - Christian Berthou
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Yves Renaudineau
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
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Van Damme M, Crompot E, Meuleman N, Maerevoet M, Mineur P, Bron D, Lagneaux L, Stamatopoulos B. Characterization of TET and IDH gene expression in chronic lymphocytic leukemia: comparison with normal B cells and prognostic significance. Clin Epigenetics 2016; 8:132. [PMID: 27980696 PMCID: PMC5141649 DOI: 10.1186/s13148-016-0298-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/24/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) is the most common hematological malignancy in western countries, characterized by a heterogeneous clinical course. Although genetic studies have identified chromosomal aberrations or specific mutations, epigenetic changes have been poorly characterized in CLL. METHODS We assessed ten-eleven translocations (TET) 1, 2, and 3, isocitrate dehydrogenase (IDH) 1, and 2 messenger RNA (mRNA) expression using real-time PCR on purified leukemic B cells from 214 CLL patients (median follow-up = 75 months, range 1-380), normal peripheral blood B cells (n = 20), and umbilical cord blood B cells (n = 21). The microenvironment influence was assessed after 24 h co-culture of CLL cells with bone marrow mesenchymal stromal cells (BMSC). Finally, 5-hydroxymethylcytosine level (%5-hmC) was assessed by ELISA in CLL cells alone or with microenvironment stimuli. RESULTS TET 1 and 3 and IDH2 were decreased in CLL cells compared with healthy B cells (P = 0.0221, 0.0013, <0.0001, respectively), while IDH1 was overexpressed (P = 0.0037). TET2 and IDH1 were significantly correlated with treatment-free survival (TFS); patients with high TET2/IDH1 expression had a higher median TFS (111 months) than patients with low expression (78 months, P = 0.0071/0.0123). Moreover, TET1 expression decreased (P = 0.0371), while TET3 and IDH2 expression increased (P = 0.0273/0.0039) in co-cultures. However, %5-hmC was not correlated with clinical data and was unchanged following microenvironment stimuli. CONCLUSIONS Despite a slight deregulation in CLL cells compared with normal B cells, we identified a significant association between TET/IDH gene expression and prognosis, suggesting that epigenetic changes could potentially be associated with disease progression. Moreover, despite an identical %5-hmC, TET gene expression was influenced by contact with BMSC confirming the crucial role of the microenvironment in CLL pathogenesis.
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Affiliation(s)
- Michaël Van Damme
- Laboratory of Clinical Cell Therapy, ULB Cancer Research Center (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Route de Lennik, 808, 1070 Brussels, Belgium
| | - Emerence Crompot
- Laboratory of Clinical Cell Therapy, ULB Cancer Research Center (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Route de Lennik, 808, 1070 Brussels, Belgium
| | - Nathalie Meuleman
- Department of Hematology (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marie Maerevoet
- Department of Hematology (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Philippe Mineur
- Department of Hemato-Oncology, Grand Hôpital de Charleroi, Gilly, Belgium
| | - Dominique Bron
- Department of Hematology (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Laurence Lagneaux
- Laboratory of Clinical Cell Therapy, ULB Cancer Research Center (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Route de Lennik, 808, 1070 Brussels, Belgium
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, ULB Cancer Research Center (U-CRC), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Route de Lennik, 808, 1070 Brussels, Belgium
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