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Carlund O, Norberg A, Osterman P, Landfors M, Degerman S, Hultdin M. DNA methylation variations and epigenetic aging in telomere biology disorders. Sci Rep 2023; 13:7955. [PMID: 37193737 DOI: 10.1038/s41598-023-34922-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.
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Affiliation(s)
- Olivia Carlund
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Anna Norberg
- Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Pia Osterman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden.
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Sugino RP, Ohira M, Mansai SP, Kamijo T. Comparative epigenomics by machine learning approach for neuroblastoma. BMC Genomics 2022; 23:852. [PMID: 36572864 PMCID: PMC9793522 DOI: 10.1186/s12864-022-09061-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the second most common pediatric solid tumor. Because the number of genetic mutations found in tumors are small, even in some patients with unfavorable NB, epigenetic variation is expected to play an important role in NB progression. DNA methylation is a major epigenetic mechanism, and its relationship with NB prognosis has been a concern. One limitation with the analysis of variation in DNA methylation is the lack of a suitable analytical model. Therefore, in this study, we performed a random forest (RF) analysis of the DNA methylome data of NB from multiple databases. RESULTS RF is a popular machine learning model owing to its simplicity, intuitiveness, and computational cost. RF analysis identified novel intermediate-risk patient groups with characteristic DNA methylation patterns within the low-risk group. Feature selection analysis based on probe annotation revealed that enhancer-annotated regions had strong predictive power, particularly for MYCN-amplified NBs. We developed a gene-based analytical model to identify candidate genes related to disease progression, such as PRDM8 and FAM13A-AS1. RF analysis revealed sufficient predictive power compared to other machine learning models. CONCLUSIONS RF is a useful tool for DNA methylome analysis in cancer epigenetic studies, and has potential to identify a novel cancer-related genes.
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Affiliation(s)
- Ryuichi P. Sugino
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Miki Ohira
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Sayaka P. Mansai
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Takehiko Kamijo
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan ,grid.263023.60000 0001 0703 3735Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Kita-Urawa, Saitama, Japan
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3
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Vieri M, Brümmendorf TH, Beier F. Treatment of telomeropathies. Best Pract Res Clin Haematol 2021; 34:101282. [PMID: 34404536 DOI: 10.1016/j.beha.2021.101282] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 10/21/2022]
Abstract
Telomeropathies or telomere biology disorders (TBDs) are a group of rare diseases characterised by altered telomere maintenance. Most patients with TBDs show pathogenic variants of genes that encode factors involved in the prevention of telomere shortening. Particularly in adults, TBDs mostly present themselves with heterogeneous clinical features that often include bone marrow failure, hepatopathies, interstitial lung disease and other organ sites. Different degrees of severity are also observed among patients with TBDs, ranging from very severe syndromes manifesting themselves in early childhood, such as Revesz syndrome, Hoyeraal-Hreidarsson syndrome, and Coats plus disease, to dyskeratosis congenita (DKC) and adult-onset "cryptic" forms of TBD, which often affect fewer organ systems. Overall, the most relevant clinical complications of TBD are bone marrow failure, lung fibrosis, and liver cirrhosis. In this review, we summarise recent advances in the management and treatment of TBD and provide a brief overview of the various treatment approaches.
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Affiliation(s)
- Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology, Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Germany.
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology, Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Germany.
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology, Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Germany.
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AlSabbagh MM. Dyskeratosis congenita: ein Literaturüberblick. J Dtsch Dermatol Ges 2020; 18:943-968. [PMID: 32985809 DOI: 10.1111/ddg.14268_g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
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5
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AlSabbagh MM. Dyskeratosis congenita: a literature review. J Dtsch Dermatol Ges 2020; 18:943-967. [PMID: 32930426 DOI: 10.1111/ddg.14268] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/29/2020] [Indexed: 12/26/2022]
Abstract
Dyskeratosis congenita is a rare hereditary disease that occurs predominantly in males and manifests clinically as the classic triad of reticulate hyperpigmentation, nail dystrophy and leukoplakia. It increases the risk of malignancy and other potentially lethal complications such as bone marrow failure, lung and liver diseases. Mutations in 19 genes are associated with dyskeratosis congenita, and a fifth of the pathogenic mutations are found in DKC1, the gene coding for dyskerin. This review aims to address the clinical and genetic aspects of the disease.
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Cypris O, Eipel M, Franzen J, Rösseler C, Tharmapalan V, Kuo CC, Vieri M, Nikolić M, Kirschner M, Brümmendorf TH, Zenke M, Lampert A, Beier F, Wagner W. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. Clin Epigenetics 2020; 12:125. [PMID: 32819411 PMCID: PMC7439574 DOI: 10.1186/s13148-020-00914-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Dyskeratosis congenita (DKC) and idiopathic aplastic anemia (AA) are bone marrow failure syndromes that share characteristics of premature aging with severe telomere attrition. Aging is also reflected by DNA methylation changes, which can be utilized to predict donor age. There is evidence that such epigenetic age predictions are accelerated in premature aging syndromes, but it is yet unclear how this is related to telomere length. DNA methylation analysis may support diagnosis of DKC and AA, which still remains a challenge for these rare diseases. RESULTS In this study, we analyzed blood samples of 70 AA and 18 DKC patients to demonstrate that their epigenetic age predictions are overall increased, albeit not directly correlated with telomere length. Aberrant DNA methylation was observed in the gene PRDM8 in DKC and AA as well as in other diseases with premature aging phenotype, such as Down syndrome and Hutchinson-Gilford-Progeria syndrome. Aberrant DNA methylation patterns were particularly found within subsets of cell populations in DKC and AA samples as measured with barcoded bisulfite amplicon sequencing (BBA-seq). To gain insight into the functional relevance of PRDM8, we used CRISPR/Cas9 technology to generate induced pluripotent stem cells (iPSCs) with heterozygous and homozygous knockout. Loss of PRDM8 impaired hematopoietic and neuronal differentiation of iPSCs, even in the heterozygous knockout clone, but it did not impact on epigenetic age. CONCLUSION Taken together, our results demonstrate that epigenetic aging is accelerated in DKC and AA, independent from telomere attrition. Furthermore, aberrant DNA methylation in PRDM8 provides another biomarker for bone marrow failure syndromes and modulation of this gene in cellular subsets may be related to the hematopoietic and neuronal phenotypes observed in premature aging syndromes.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Corinna Rösseler
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Vithurithra Tharmapalan
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Tim H. Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
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7
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Ferreira MSV, Kirschner M, Halfmeyer I, Estrada N, Xicoy B, Isfort S, Vieri M, Zamora L, Abels A, Bouillon AS, Begemann M, Schemionek M, Maurer A, Koschmieder S, Wilop S, Panse J, Brümmendorf TH, Beier F. Comparison of flow-FISH and MM-qPCR telomere length assessment techniques for the screening of telomeropathies. Ann N Y Acad Sci 2019; 1466:93-103. [PMID: 31647584 DOI: 10.1111/nyas.14248] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/27/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Assessment of telomere length (TL) in peripheral blood leukocytes is part of the diagnostic algorithm applied to patients with acquired bone marrow failure syndromes (BMFSs) and dyskeratosis congenita (DKC). Monochrome multiplex-quantitative polymerase chain reaction (MM-qPCR) and fluorescence in situ hybridization (flow-FISH) are methodologies available for TL screening. Dependent on TL expressed in relation to percentiles of healthy controls, further genetic testing for inherited mutations in telomere maintenance genes is recommended. However, the correct threshold to trigger this genetic workup is still under debate. Here, we prospectively compared MM-qPCR and flow-FISH regarding their capacity for accurate identification of DKC patients. All patients (n = 105) underwent genetic testing by next-generation sequencing and in 16 patients, mutations in DKC-relevant genes were identified. Whole leukocyte TL of patients measured by MM-qPCR was found to be moderately correlated with lymphocyte TL measured by flow-FISH (r² = 0.34; P < 0.0001). The sensitivity of both methods was high, but the specificity of MM-qPCR (29%) was significantly lower compared with flow-FISH (58%). These results suggest that MM-qPCR of peripheral blood cells is inferior to flow-FISH for clinical routine screening for suspected DKC in adult patients with BMFS due to lower specificity and a higher rate of false-positive results.
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Affiliation(s)
- Monica S Ventura Ferreira
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Insa Halfmeyer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Natalia Estrada
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Blanca Xicoy
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Susanne Isfort
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Lurdes Zamora
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Anne Abels
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Anne-Sophie Bouillon
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Mirle Schemionek
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Angela Maurer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Stefan Wilop
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, University Hospital Aachen, Aachen, Germany
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Wagner W. The Link Between Epigenetic Clocks for Aging and Senescence. Front Genet 2019; 10:303. [PMID: 31001330 PMCID: PMC6456648 DOI: 10.3389/fgene.2019.00303] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023] Open
Abstract
Replicative senescence of cells in vitro is often considered as counterpart for aging of the organism in vivo. In fact, both processes are associated with functional decay and similar molecular modifications. On epigenetic level, replicative senescence and aging evoke characteristic modifications in the DNA methylation (DNAm) pattern, but at different sites in the genome. Various epigenetic signatures, which are often referred to as epigenetic clocks, provide useful biomarkers: Senescence-associated epigenetic modifications can be used for quality control of cell preparations or to elucidate effects of culture conditions on the state of cellular aging. Age-associated epigenetic modifications hold high expectations to determine chronological age in forensics or to identify parameters that impact on biological aging. Despite these differences, there are some striking similarities between senescence- and age-associated DNAm, such as complete rejuvenation during reprogramming into induced pluripotent stem cells (iPSCs). It is yet unclear what makes epigenetic clocks tick, but there is evidence that the underlying mechanisms of both processes are related to similar modifications in the histone code or higher order chromatin. Replicative senescence therefore appears to be a suitable model system to gain better insight into how organismal aging might be governed epigenetically.
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Affiliation(s)
- Wolfgang Wagner
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
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Zhang Y, Yan L, Yao W, Chen K, Xu H, Ye Z. Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. Med Sci Monit 2019; 25:193-239. [PMID: 30616239 PMCID: PMC6330996 DOI: 10.12659/msm.912294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The histone methyltransferase (HMT) family includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). The role of HMT gene variants in prostate cancer remains unknown. Therefore, this study aimed to evaluate HMT gene variants in the pathogenesis and prognosis of human prostate cancer, using in vitro cell studies and bioinformatics analysis. Material/Methods Integrative bioinformatics analysis of the expression of 51 HMT genes in human prostate cancer was based on datasets from the Cancer Genome Atlas (TCGA). Correlation and regression analysis were used to identify critical HMTs in prostate cancer. Kaplan-Meier and the area under the receiver operating characteristics curve (AUROC) were performed to evaluate the function of the HMTs on prognosis. Gene expression and function of 22Rv1 human prostate carcinoma cells were studied. Results The HMT genes identified to have a role in the pathogenesis of prostate cancer included the EZH2, SETD5, PRDM12, NSD1, SETD6, SMYD1, and the WHSC1L1 gene. The EZH2, SETD5, and SMYD1 genes were selected as a prognostic panel, with the SUV420H2 HMT gene. SETD2, NSD1, and ASH1L were identified as critical genes in the development of castration-resistant prostate cancer (CRPC), similar to mixed-lineage leukemia (MLL) complex family members. Knockdown of the SETD5 gene in 22Rv1 prostate carcinoma cells in vitro inhibited cancer cell growth and migration. Conclusions HMT gene variants may have a role in the pathogenesis of prostate cancer. Future studies may determine the role of HMT genes as prognostic biomarkers in patients with prostate cancer.
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Affiliation(s)
- Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Libin Yan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, AL, China (mainland).,Institute of Urology of Hubei Province, Wuhan, Hubei, China (mainland)
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Chen Z, Gao W, Pu L, Zhang L, Han G, Zuo X, Zhang Y, Li X, Shen H, Wu J, Wang X. PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1. Hepatology 2018; 68:994-1009. [PMID: 29572888 DOI: 10.1002/hep.29890] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/01/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major leading cause of cancer mortality worldwide. PRDI-BF1 and RIZ homology domain containing 8 (PRDM8) is a key regulator in neural development and testis steroidogenesis; however, its role in liver carcinogenesis remains to be investigated. In this study, PRDM8 was found to be down-regulated in HCC, which was linked with shorter recurrence-free survival. Lentiviral-based overexpression and knockdown approaches showed that PRDM8 inhibited HCC cell proliferation, migration, and invasion. PRDM8 caused G1/S cell cycle arrest and induced apoptosis. An in vivo tumor model confirmed the antitumor role of PRDM8 in HCC growth and metastasis. Mechanistic study showed that PRDM8 suppressed the PI3K/AKT/mTOR signaling cascade through the regulation of nucleosome assembly protein 1-like 1 (NAP1L1). Conclusion: PRDM8 as a functional tumor suppressor is frequently down-regulated in HCC. Through regulating NAP1L1, PRDM8 inhibits PI3K/AKT/mTOR signaling in HCC. PRDM8 is a potential target for therapies of HCC. (Hepatology 2018).
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Affiliation(s)
- Zhiqiang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liyong Pu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Long Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Guoyong Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xueliang Zuo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Yao Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Xiangcheng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jindao Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Key Laboratory on Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, China
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Kirschner M, Maurer A, Wlodarski MW, Ventura Ferreira MS, Bouillon AS, Halfmeyer I, Blau W, Kreuter M, Rosewich M, Corbacioglu S, Beck J, Schwarz M, Bittenbring J, Radsak MP, Wilk CM, Koschmieder S, Begemann M, Kurth I, Schemionek M, Brümmendorf TH, Beier F. Recurrent somatic mutations are rare in patients with cryptic dyskeratosis congenita. Leukemia 2018; 32:1762-1767. [PMID: 29749397 DOI: 10.1038/s41375-018-0125-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 12/22/2022]
Abstract
Dyskeratosis congenita (DKC) is a paradigmatic telomere disorder characterized by substantial and premature telomere shortening, bone marrow failure, and a dramatically increased risk of developing myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). DKC can occur as a late-onset, so-called cryptic form, with first manifestation in adults. Somatic MDS-related mutations are found in up to 35% of patients with acquired aplastic anemia (AA), especially in patients with short telomeres. The aim of our study was to investigate whether cryptic DKC is associated with an increased incidence of MDS-related somatic mutations, thereby linking the accelerated telomere shortening with the increased risk of MDS/AML. Samples from 15 adult patients (median age: 42 years, range: 23-60 years) with molecularly confirmed cryptic DKC were screened using next-generation gene panel sequencing to detect MDS-related somatic variants. Only one of the 15 patients (7%) demonstrated a clinically relevant MDS-related somatic variant. This incidence was dramatically lower than formerly described in acquired AA. Based on our data, we conclude that clonal evolution of subclones carrying MDS-related mutations is not the predominant mechanism for MDS/AML initiation in adult cryptic DKC patients.
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Affiliation(s)
- Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Angela Maurer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Marcin W Wlodarski
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University of Hospital Freiburg, Freiburg, Germany
| | - Monica S Ventura Ferreira
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Anne-Sophie Bouillon
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Insa Halfmeyer
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Blau
- Department of Hematology and Oncology, Justus-Liebig University, Giessen, Germany
| | - Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Pneumology and Respiratory Critical Care Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Martin Rosewich
- Department of Paediatric Pulmonology, Allergy and Cystic Fibrosis, Children's Hospital, Goethe-University, Frankfurt, Germany
| | - Selim Corbacioglu
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Regensburg, Germany
| | - Joachim Beck
- Department of Hematology, Medical Oncology, & Pneumology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Michaela Schwarz
- Department of Hematology and Oncology, University Hospital Charité, Berlin, Germany
| | - Jörg Bittenbring
- Department of Hematology and Oncology, University Hospital Saarland, Homburg, Germany
| | - Markus P Radsak
- Department of Hematology, Medical Oncology, & Pneumology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | | | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Mirle Schemionek
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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Guastafierro T, Bacalini MG, Marcoccia A, Gentilini D, Pisoni S, Di Blasio AM, Corsi A, Franceschi C, Raimondo D, Spanò A, Garagnani P, Bondanini F. Genome-wide DNA methylation analysis in blood cells from patients with Werner syndrome. Clin Epigenetics 2017; 9:92. [PMID: 28861129 PMCID: PMC5577832 DOI: 10.1186/s13148-017-0389-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/15/2017] [Indexed: 12/15/2022] Open
Abstract
Background Werner syndrome is a progeroid disorder characterized by premature age-related phenotypes. Although it is well established that autosomal recessive mutations in the WRN gene is responsible for Werner syndrome, the molecular alterations that lead to disease phenotype remain still unidentified. Results To address whether epigenetic changes can be associated with Werner syndrome phenotype, we analysed genome-wide DNA methylation profile using the Infinium MethylationEPIC BeadChip in the whole blood from three patients affected by Werner syndrome compared with three age- and sex-matched healthy controls. Hypermethylated probes were enriched in glycosphingolipid biosynthesis, FoxO signalling and insulin signalling pathways, while hypomethylated probes were enriched in PI3K-Akt signalling and focal adhesion pathways. Twenty-two out of 47 of the differentially methylated genes belonging to the enriched pathways resulted differentially expressed in a publicly available dataset on Werner syndrome fibroblasts. Interestingly, differentially methylated regions identified CERS1 and CERS3, two members of the ceramide synthase family. Moreover, we found differentially methylated probes within ITGA9 and ADAM12 genes, whose methylation is altered in systemic sclerosis, and within the PRDM8 gene, whose methylation is affected in dyskeratosis congenita and Down syndrome. Conclusions DNA methylation changes in the peripheral blood from Werner syndrome patients provide new insight in the pathogenesis of the disease, highlighting in some cases a functional correlation of gene expression and methylation status. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0389-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Guastafierro
- UOC of Clinical Biochemistry, Sandro Pertini Hospital, Rome, Italy.,CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy
| | - M G Bacalini
- IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - A Marcoccia
- CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy.,UOSD Ischemic Microangiopathy and Sclerodermic Ulcers, Sandro Pertini Hospital, Rome, Italy
| | - D Gentilini
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - S Pisoni
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - A M Di Blasio
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - A Corsi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - C Franceschi
- IRCCS Institute of Neurological Sciences, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - D Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - A Spanò
- UOC of Clinical Biochemistry, Sandro Pertini Hospital, Rome, Italy
| | - P Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute at Huddinge University Hospital, S-141 86 Stockholm, Sweden.,CNR Institute for Molecular Genetics, Unit of Bologna, Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy
| | - F Bondanini
- CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy.,UOC of Clinical Pathology, Saint' Eugenio Hospital, Rome, Italy
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