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Robinson N, Casement J, Gunter MJ, Huybrechts I, Agudo A, Barranco MR, Eichelmann F, Johnson T, Kaaks R, Pala V, Panico S, Sandanger TM, Schultze MB, Travis RC, Tumino R, Vineis P, Weiderpass E, Skinner R, Sharp L, McKay JA, Strathdee G. Anti-cancer therapy is associated with long-term epigenomic changes in childhood cancer survivors. Br J Cancer 2022; 127:288-300. [PMID: 35354948 PMCID: PMC9296636 DOI: 10.1038/s41416-022-01792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Childhood cancer survivors (CCS) exhibit significantly increased chronic diseases and premature death. Abnormalities in DNA methylation are associated with development of chronic diseases and reduced life expectancy. We investigated the hypothesis that anti-cancer treatments are associated with long-term DNA methylation changes that could be key drivers of adverse late health effects. METHODS Genome-wide DNA methylation was assessed using MethylationEPIC arrays in paired samples (before/after therapy) from 32 childhood cancer patients. Separately, methylation was determined in 32 samples from different adult CCS (mean 22-years post-diagnosis) and compared with cancer-free controls (n = 284). RESULTS Widespread DNA methylation changes were identified post-treatment in childhood cancer patients, including 146 differentially methylated regions (DMRs), which were consistently altered in the 32 post-treatment samples. Analysis of adult CCS identified matching methylation changes at 107/146 of the DMRs, suggesting potential long-term retention of post-therapy changes. Adult survivors also exhibited epigenetic age acceleration, independent of DMR methylation. Furthermore, altered methylation at the DUSP6 DMR was significantly associated with early mortality, suggesting altered methylation may be prognostic for some late adverse health effects in CCS. CONCLUSIONS These novel methylation changes could serve as biomarkers for assessing normal cell toxicity in ongoing treatments and predicting long-term health outcomes in CCS.
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Affiliation(s)
- Natassia Robinson
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Casement
- Bioinformatic Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Marc J Gunter
- Section of Nutrition and Metabolism, IARC, Lyon, France
| | | | - Antonio Agudo
- Unit of Nutrition and Cancer, Catalan Institute of Oncology - ICO, Nutrition and Cancer Group, Bellvitge Biomedical Research Institute - IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
| | | | - Fabian Eichelmann
- German Institute of Human Nutrition Potsdam-Rehbrücke, Heidelberg, Germany
| | - Theron Johnson
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valeria Pala
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | | | | | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Rosario Tumino
- Cancer Registry and Histopathology Department Azienda Sanitaria Provinciale (ASP), Ragusa, Italy
| | - Paolo Vineis
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | | | - Roderick Skinner
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Paediatric and Adolescent Haematology/Oncology, Great North Children's Hospital, Newcastle, UK
| | - Linda Sharp
- Newcastle University Centre for Cancer, Population Health Sciences Institute, Newcastle upon Tyne, UK
| | - Jill A McKay
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Gordon Strathdee
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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2
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Rahmani M, Fardi M, Farshdousti Hagh M, Hosseinpour Feizi AA, Talebi M, Solali S. An investigation of methylation pattern changes in the IKZF1 promoter in patients with childhood B-cell acute lymphoblastic leukemia. Blood Res 2019; 54:144-148. [PMID: 31309094 PMCID: PMC6614096 DOI: 10.5045/br.2019.54.2.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/09/2019] [Accepted: 04/04/2019] [Indexed: 11/29/2022] Open
Abstract
Background Ikaros family zinc finger 1 (IKZF1) is a transcription factor with an important role in controlling hematopoietic proliferation and function, particularly lymphoid cell differentiation. It was previously shown that various mechanisms and expression patterns of Ikaros are linked to a variety of cancers. We hypothesized that aberrant methylation (hypomethylation) of the IKZF1 promoter region might be one of the causes of B-cell acute lymphoblastic leukemia (B-ALL). In B-ALL patients, an increased expression of this gene is a potential cause of B-cell differentiation arrest and proliferation induction. Therefore, as more than 90% of patients with ALL are <15 years old, we investigated the methylation pattern of the IKZF1 promoter in childhood B-ALL. Methods Twenty-five newly diagnosed B-ALL cases were included (all younger than 15 yr). In addition, we selected 25 healthy age- and sex-matched children as the control group. We collected the blood samples in EDTA-containing tubes and isolated lymphocytes from whole blood using Ficoll 1.077 Lymphosep. Next, we extracted genomic DNA with the phenol/chloroform method. Two microgram of DNA per sample was treated with sodium bisulfite using the EpiTect Bisulfite Kit, followed by an assessment of DNA methylation by polymerase chain reaction (PCR) analysis of the bisulfite-modified genomic DNA. Results Our data highlighted a hypomethylated status of the IKZF1 promoter in the ALL cases (96% of the cases were unmethylated). In contrast, the control group samples were partially methylated (68%). Conclusion This study demonstrated a hypomethylated pattern of the IKZF1 promoter region in childhood B-ALL, which might underlie the aberrant Ikaros expression patterns that were previously linked to this malignancy.
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Affiliation(s)
- Mina Rahmani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoumeh Fardi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Talebi
- Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Rahmani T, Azad M, Chahardouli B, Nasiri H, Vatanmakanian M, Kaviani S. Patterns of DNMT1 Promoter Methylation in Patients with Acute Lymphoblastic Leukemia. Int J Hematol Oncol Stem Cell Res 2017; 11:172-177. [PMID: 28989582 PMCID: PMC5625466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Background: Acute lymphoblastic leukemia (ALL) is a clonal malignant disorder characterized by an uncontrolled proliferation of immature T or B lymphocytes. Extensive studies have shown that the epigenetic changes, especially modified DNA methylation patterns in the regulatory regions through the DNA methyltransferase (DNMTs), play an important role in the development of genetic disorders and abnormal growth and maturation capacity of leukemic stem cells (LSCs).The aim of this study was to evaluate the changes in DNMT1 promoter methylation and its expression pattern in patients with ALL. Materials and Methods: In this experimental study, methylation specific PCR (MSP) was used to assess the methylation status of DNMT1 promoter regions in samples collected from ALL patients (n=45) and healthy control subjects. According to this method, un-methylated cytosine nucleotides are converted to uracil by sodium bisulfite and the proliferation of methylated and un-methylated regions are performed using specific primers for target sequences. Results: None of the patients with B and T-ALL showed methylated promoter regions of the DNMT1 gene, while the methylation pattern of both pre-B ALL patients and the control group showed a relative promoter methylation. Conclusion: Analysis of promoter methylation patterns in various subgroups of ALL has revealed the importance of DNMT1 in the regulation of gene expression. Likewise, extensive data have also highlighted the methylation-based mechanisms exerted by DNAM1 as one of the main participants regulating gene expression in B-ALL and T-ALL patients. Investigation of the overall DNA methylation pattern offers significant improvements in the prediction of disease prognosis and treatment response.
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Affiliation(s)
- Tirdad Rahmani
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Bahram Chahardouli
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hajar Nasiri
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran,Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mousa Vatanmakanian
- Department of Hematology, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeid Kaviani
- Department of Hematology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Chromatin states modify network motifs contributing to cell-specific functions. Sci Rep 2015; 5:11938. [PMID: 26169043 PMCID: PMC4500950 DOI: 10.1038/srep11938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/11/2015] [Indexed: 01/06/2023] Open
Abstract
Epigenetic modification can affect many important biological processes, such as cell proliferation and apoptosis. It can alter chromatin conformation and contribute to gene regulation. To investigate how chromatin states associated with network motifs, we assembled chromatin state-modified regulatory networks by combining 269 ChIP-seq data and chromatin states in four cell types. We found that many chromatin states were significantly associated with network motifs, especially for feedforward loops (FFLs). These distinct chromatin state compositions contribute to different expression levels and translational control of targets in FFLs. Strikingly, the chromatin state-modified FFLs were highly cell-specific and, to a large extent, determined cell-selective functions, such as the embryonic stem cell-specific bivalent modification-related FFL with an important role in poising developmentally important genes for expression. Besides, comparisons of chromatin state-modified FFLs between cancerous/stem and primary cell lines revealed specific type of chromatin state alterations that may act together with motif structural changes cooperatively contribute to cell-to-cell functional differences. Combination of these alterations could be helpful in prioritizing candidate genes. Together, this work highlights that a dynamic epigenetic dimension can help network motifs to control cell-specific functions.
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Parikh K, Cang S, Sekhri A, Liu D. Selective inhibitors of nuclear export (SINE)--a novel class of anti-cancer agents. J Hematol Oncol 2014; 7:78. [PMID: 25316614 PMCID: PMC4200201 DOI: 10.1186/s13045-014-0078-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/09/2014] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of the nucleo-cytoplasmic transport of proteins plays an important role in carcinogenesis. The nuclear export of proteins depends on the activity of transport proteins, exportins. Exportins belong to the karyopherin β superfamily. Exportin-1 (XPO1), also known as chromosomal region maintenance 1 (CRM1), mediates transport of around 220 proteins. In this review, we summarized the development of a new class of antitumor drugs, collectively known as selective inhibitors of nuclear export (SINE). KPT-330 (selinexor) as an oral agent is showing activities in early clinical trials in both solid tumors and hematological malignancies.
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Affiliation(s)
| | | | | | - Delong Liu
- Henan Tumor Hospital, Zhengzhou University, Zhengzhou, China.
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Edwards SKE, Baron J, Moore CR, Liu Y, Perlman DH, Hart RP, Xie P. Mutated in colorectal cancer (MCC) is a novel oncogene in B lymphocytes. J Hematol Oncol 2014; 7:56. [PMID: 25200342 PMCID: PMC4172902 DOI: 10.1186/s13045-014-0056-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 07/24/2014] [Indexed: 01/04/2023] Open
Abstract
Background Identification of novel genetic risk factors is imperative for a better understanding of B lymphomagenesis and for the development of novel therapeutic strategies. TRAF3, a critical regulator of B cell survival, was recently recognized as a tumor suppressor gene in B lymphocytes. The present study aimed to identify novel oncogenes involved in malignant transformation of TRAF3-deficient B cells. Methods We used microarray analysis to identify genes differentially expressed in TRAF3−/− mouse splenic B lymphomas. We employed lentiviral vector-mediated knockdown or overexpression to manipulate gene expression in human multiple myeloma (MM) cell lines. We analyzed cell apoptosis and proliferation using flow cytometry, and performed biochemical studies to investigate signaling mechanisms. To delineate protein-protein interactions, we applied affinity purification followed by mass spectrometry-based sequencing. Results We identified mutated in colorectal cancer (MCC) as a gene strikingly up-regulated in TRAF3-deficient mouse B lymphomas and human MM cell lines. Aberrant up-regulation of MCC also occurs in a variety of primary human B cell malignancies, including non-Hodgkin lymphoma (NHL) and MM. In contrast, MCC expression was not detected in normal or premalignant TRAF3−/− B cells even after treatment with B cell stimuli, suggesting that aberrant up-regulation of MCC is specifically associated with malignant transformation of B cells. In elucidating the functional roles of MCC in malignant B cells, we found that lentiviral shRNA vector-mediated knockdown of MCC induced apoptosis and inhibited proliferation in human MM cells. Experiments of knockdown and overexpression of MCC allowed us to identify several downstream targets of MCC in human MM cells, including phospho-ERK, c-Myc, p27, cyclin B1, Mcl-1, caspases 8 and 3. Furthermore, we identified 365 proteins (including 326 novel MCC-interactors) in the MCC interactome, among which PARP1 and PHB2 were two hubs of MCC signaling pathways in human MM cells. Conclusions Our results indicate that in sharp contrast to its tumor suppressive role in colorectal cancer, MCC functions as an oncogene in B cells. Our findings suggest that MCC may serve as a diagnostic marker and therapeutic target in B cell malignancies, including NHL and MM. Electronic supplementary material The online version of this article (doi:10.1186/s13045-014-0056-6) contains supplementary material, which is available to authorized users.
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