1
|
Haertle L, Barrio S, Munawar U, Han S, Zhou X, Simicek M, Vogt C, Truger M, Fernandez RA, Steinhardt M, Weingart J, Snaurova R, Nerreter S, Teufel E, Garitano-Trojaola A, Da Viá M, Ruiz-Heredia Y, Rosenwald A, Bolli N, Hajek R, Raab P, Raab MS, Weinhold N, Haferlach C, Haaf T, Martinez-Lopez J, Einsele H, Rasche L, Kortüm KM. Single-Nucleotide Variants and Epimutations Induce Proteasome Inhibitor Resistance in Multiple Myeloma. Clin Cancer Res 2023; 29:279-288. [PMID: 36282272 DOI: 10.1158/1078-0432.ccr-22-1161] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/08/2022] [Accepted: 10/21/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Proteasome inhibitors (PI) are the backbone of various treatment regimens in multiple myeloma. We recently described the first in-patient point mutations affecting the 20S subunit PSMB5 underlying PI resistance. Notably, in vivo, the incidence of mutations in PSMB5 and other proteasome encoding genes is too low to explain the development of resistance in most of the affected patients. Thus, additional genetic and epigenetic alterations need to be explored. EXPERIMENTAL DESIGN We performed DNA methylation profiling by Deep Bisulfite Sequencing in PSMB5, PSMC2, PSMC5, PSMC6, PSMD1, and PSMD5, a subset of proteasome subunits that have hitherto been associated with PI resistance, recruited from our own previous research, the literature, or a meta-analysis on the frequency of somatic mutations. Methylation was followed up on gene expression level and by dual-luciferase reporter assay. The KMS11 cell line served as a model to functionally test the impact of demethylating agents. RESULTS We identified PSMD5 promoter hypermethylation and subsequent epigenetic gene silencing in 24% of PI refractory patients. Hypermethylation correlated with decreased expression and the regulatory impact of this region was functionally confirmed. In contrast, patients with newly diagnosed multiple myeloma, along with peripheral blood mononuclear cells and CD138+ plasma cells from healthy donors, generally show unmethylated profiles. CONCLUSIONS Under the selective pressure of PI treatment, multiple myeloma cells acquire methylation of the PSMD5 promoter silencing the PSMD5 gene expression. PSMD5 acts as a key orchestrator of proteasome assembly and its downregulation was described to increase the cell's proteolytic capacity. PSMD5 hypermethylation, therefore, represents a novel mechanism of PI tolerance in multiple myeloma.
Collapse
Affiliation(s)
- Larissa Haertle
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.,Department of Hematology, Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Complutense University Madrid, Madrid, Spain
| | - Santiago Barrio
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.,Department of Hematology, Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Complutense University Madrid, Madrid, Spain.,Altum Sequencing Co., Madrid, Spain
| | - Umair Munawar
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Seungbin Han
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Xiang Zhou
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Michal Simicek
- Haematology, Ostrava University Hospital, Ostrava, Czech Republic.,Faculty of Medicine, Ostrava University, Ostrava, Czech Republic
| | - Cornelia Vogt
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Rafael Alonso Fernandez
- Department of Hematology, Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Complutense University Madrid, Madrid, Spain
| | | | - Julia Weingart
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Renata Snaurova
- Haematology, Ostrava University Hospital, Ostrava, Czech Republic.,Faculty of Medicine, Ostrava University, Ostrava, Czech Republic
| | - Silvia Nerreter
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Eva Teufel
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Matteo Da Viá
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Yanira Ruiz-Heredia
- Department of Hematology, Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Complutense University Madrid, Madrid, Spain.,Altum Sequencing Co., Madrid, Spain
| | | | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Roman Hajek
- Haematology, Ostrava University Hospital, Ostrava, Czech Republic.,Faculty of Medicine, Ostrava University, Ostrava, Czech Republic
| | - Peter Raab
- Department of Orthopaedic Surgery, König Ludwig Haus, University of Würzburg, Würzburg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Molecular Hematology/Oncology, Department of Internal Medicine V, Heidelberg University Hospital, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Joaquin Martinez-Lopez
- Department of Hematology, Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center, Complutense University Madrid, Madrid, Spain.,Altum Sequencing Co., Madrid, Spain
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Leo Rasche
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - K Martin Kortüm
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| |
Collapse
|
2
|
Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
Collapse
Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
| |
Collapse
|
3
|
Cereblon Enhancer Methylation and IMiD Resistance in Multiple Myeloma. Blood 2021; 138:1721-1726. [PMID: 34115836 DOI: 10.1182/blood.2020010452] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
Cereblon is the direct binding target of the immunomodulatory drugs that are commonly used to treat Multiple Myeloma, the second most frequent hematologic malignancy. Patients respond well to initial IMiD treatment but virtually all develop drug resistance over time with the underlying mechanisms poorly understood. We identified a yet undescribed DNA hypermethylation in an active intronic CRBN enhancer. Differential hypermethylation in this region was found increased in healthy plasma cells, but more pronounced in IMiD refractory MM. Methylation significantly correlated with decreased CRBN expression levels. DNTMi in vitro experiments induced CRBN enhancer demethylation and sensitizing effects on Lenalidomide treatment were observed in two MM cell lines. Thus, we provide first evidence that aberrant CRBN DNA methylation is a novel mechanism of IMiD resistance in Multiple Myeloma and may predict IMiD response prior treatment.
Collapse
|
4
|
Wu Z, Huang S, Zheng X, Gu S, Xu Q, Gong Y, Zhang J, Fu B, Tang L. Regulatory long non-coding RNAs of hepatic stellate cells in liver fibrosis (Review). Exp Ther Med 2021; 21:351. [PMID: 33732324 PMCID: PMC7903415 DOI: 10.3892/etm.2021.9782] [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: 10/06/2019] [Accepted: 04/29/2020] [Indexed: 12/11/2022] Open
Abstract
Liver fibrosis (LF) is a continuous wound healing process caused by numerous chronic hepatic diseases and poses a major threat to human health. Activation of hepatic stellate cells (HSCs) is a critical event in the development of hepatic fibrosis. Long non-coding RNAs (lncRNAs) that are involved in HSC activation, participate in the development of LF and are likely to be therapeutic targets for LF. In the present review, the cellular signaling pathways of LF with respect to HSCs were discussed. In particular, this present review highlighted the current knowledge on the role of lncRNAs in activating or inhibiting LF, revealing lncRNAs that are likely to be biomarkers or therapeutic targets for LF. Additional studies should be performed to elucidate the potential of lncRNAs in the diagnosis and prognosis of LF and to provide novel therapeutic approaches for the reversion of LF.
Collapse
Affiliation(s)
- Zhengjie Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Shunmei Huang
- Department of Geriatrics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Xiaoqin Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Yiwen Gong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Jiaying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Bin Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Lingling Tang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| |
Collapse
|
5
|
Abstract
Abstract
Genomic imprinting ensures the parent-specific expression of either the maternal or the paternal allele, by different epigenetic processes (DNA methylation and histone modifications) that confer parent-specific marks (imprints) in the paternal and maternal germline, respectively. Most protein-coding imprinted genes are involved in embryonic growth, development, and behavior. They are usually organized in genomic domains that are regulated by differentially methylated regions (DMRs). Genomic imprints are erased in the primordial germ cells and then reset in a gene-specific manner according to the sex of the germline. The imprinted genes regulate and interact with other genes, consistent with the existence of an imprinted gene network. Defects of genomic imprinting result in syndromal imprinting disorders. To date a dozen congenital imprinting disorders are known. Usually, a given imprinting disorder can be caused by different types of defects, including point mutations, deletions/duplications, uniparental disomy, and epimutations. Causative trans-acting factors in imprinting disorders, including ZFP57 and the subcortical maternal complex (SCMC), have the potential to affect multiple DMRs across the genome, resulting in a multi-locus imprinting disturbance. There is evidence that mutations in components of the SCMC can confer an increased risk for imprinting disorders.
Collapse
Affiliation(s)
- Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine , University Medical Centre Johannes Gutenberg University Mainz , Obere Zahlbacher Str. 63 , Mainz , Germany
| | - Thomas Haaf
- Institute of Human Genetics , Julius Maximilians University , Würzburg , Germany
| |
Collapse
|
6
|
Yu F, Geng W, Dong P, Huang Z, Zheng J. LncRNA-MEG3 inhibits activation of hepatic stellate cells through SMO protein and miR-212. Cell Death Dis 2018; 9:1014. [PMID: 30282972 PMCID: PMC6170498 DOI: 10.1038/s41419-018-1068-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/15/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022]
Abstract
Activation of hepatic stellate cells (HSCs), a pivotal event in liver fibrosis, is considered as an epithelial–mesenchymal transition (EMT) process. Deregulation of long noncoding RNAs (lncRNAs) has been reported to be involved in a series of human diseases. LncRNA-maternally expressed gene 3 (MEG3) functions as a tumor suppressor in cancers and has been shown to play a vital role in EMT process. However, the biological role of MEG3 in liver fibrosis is largely unknown. In this study, MEG3 was reduced in vivo and in vitro during liver fibrosis. Restoring of MEG3 expression led to the suppression of liver fibrosis, with a reduction in α-SMA and type I collagen. Notably, MEG3 overexpression inhibited HSC activation through EMT, associated with an increase in epithelial markers and a reduction in mesenchymal markers. Further studies showed that Hedgehog (Hh) pathway-mediated EMT process was involved in the effects of MEG3 on HSC activation. Smoothened (SMO) is a member of Hh pathway. Using bioinformatic analysis, an interaction between MEG3 and SMO protein was predicted. This interaction was confirmed by the results of RNA immunoprecipitation and deletion-mapping analysis. Furthermore, MEG3 was confirmed as a target of microRNA-212 (miR-212). miR-212 was partly responsible for the effects of MEG3 on EMT process. Interestingly, MEG3 was also reduced in chronic hepatitis B (CHB) patients with liver fibrosis when compared with healthy controls. MEG3 negatively correlated with fibrosis stage in CHB patients. In conclusion, we demonstrate that MEG3 inhibits Hh-mediated EMT process in liver fibrosis via SMO protein and miR-212.
Collapse
Affiliation(s)
- Fujun Yu
- Departments of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wujun Geng
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Peihong Dong
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Zhiming Huang
- Departments of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Jianjian Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| |
Collapse
|
7
|
Potabattula R, Dittrich M, Böck J, Haertle L, Müller T, Hahn T, Schorsch M, Hajj NE, Haaf T. Allele-specific methylation of imprinted genes in fetal cord blood is influenced by cis-acting genetic variants and parental factors. Epigenomics 2018; 10:1315-1326. [PMID: 30238782 PMCID: PMC6240887 DOI: 10.2217/epi-2018-0059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To examine the effects of genetic variation, parental age and BMI on parental allele-specific methylation of imprinted genes in fetal cord blood samples. Methodology: We have developed SNP genotyping and deep bisulphite sequencing assays for six imprinted genes to determine parental allele-specific methylation patterns in diploid somatic tissues. Results: Multivariate linear regression analyses revealed a negative correlation of paternal age with paternal MEG3 allele methylation in fetal cord blood. Methylation of the maternal PEG3 allele showed a positive correlation with maternal age. Paternal BMI was positively correlated with paternal MEST allele methylation. In addition to parental origin, allele-specific methylation of most imprinted genes was largely dependent on the underlying SNP haplotype. Conclusion: Our study supports the idea that parental factors can have an impact, although of small effect size, on the epigenome of the next generation, providing an additional layer of complexity to phenotypic diversity.
Collapse
Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | | | | | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| |
Collapse
|
8
|
Veron V, Marandel L, Liu J, Vélez EJ, Lepais O, Panserat S, Skiba S, Seiliez I. DNA methylation of the promoter region of bnip3 and bnip3l genes induced by metabolic programming. BMC Genomics 2018; 19:677. [PMID: 30223788 PMCID: PMC6142374 DOI: 10.1186/s12864-018-5048-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Environmental changes of biotic or abiotic nature during critical periods of early development may exert a profound influence on physiological functions later in life. This process, named developmental programming can also be driven through parental nutrition. At molecular level, epigenetic modifications are the most likely candidate for persistent modulation of genes expression in later life. RESULTS In order to investigate epigenetic modifications induced by programming in rainbow trout, we focused on bnip3 and bnip3l paralogous genes known to be sensitive to environmental changes but also regulated by epigenetic modifications. Two specific stimuli were used: (i) early acute hypoxia applied at embryo stage and (ii) broodstock and fry methionine deficient diet, considering methionine as one of the main methyl-group donor needed for DNA methylation. We observed a programming effect of hypoxia with an increase of bnip3a and the four paralogs of bnip3l expression level in fry. In addition, parental methionine nutrition was correlated to bnip3a and bnip3lb1 expression showing evidence for early fry programming. We highlighted that both stimuli modified DNA methylation levels at some specific loci of bnip3a and bnip3lb1. CONCLUSION Overall, these data demonstrate that methionine level and hypoxia stimulus can be of critical importance in metabolic programming. Both stimuli affected DNA methylation of specific loci, among them, an interesting CpG site have been identified, namely - 884 bp site of bnip3a, and may be positively related with mRNA levels.
Collapse
Affiliation(s)
- Vincent Veron
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Jingwei Liu
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Emilio J Vélez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Olivier Lepais
- INRA, Univ Pau & Pays de l'Adour, UMR Ecobiop, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Stéphane Panserat
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Sandrine Skiba
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France
| | - Iban Seiliez
- INRA, Univ Pau & Pays de l'Adour, E2S UPPA, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310, Saint-Pée-sur-Nivelle, France.
| |
Collapse
|
9
|
Lu Z, Ma Y, Gao L, Li Y, Li Q, Qiang M. Urine mercury levels correlate with DNA methylation of imprinting gene H19 in the sperm of reproductive-aged men. PLoS One 2018; 13:e0196314. [PMID: 29698523 PMCID: PMC5919660 DOI: 10.1371/journal.pone.0196314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/10/2018] [Indexed: 12/31/2022] Open
Abstract
Background Mercury (Hg) is a well-recognized environmental pollutant known by its toxicity of development and neurotoxicity, which results in adverse health outcomes. However, the mechanisms underlying the teratogenic effects of Hg are not well understood. Imprinting genes are emerging regulators for fetal development subjecting to environmental pollutants impacts. In this study, we examined the association between preconceptional Hg exposure and the alteration of DNA methylation of imprinting genes H19, Meg3, and Peg3 in human sperm DNA. Methods A total of 616 men, aged from 22 to 59, were recruited from Reproductive Medicine Clinic of Maternal and Child Care Service Center and the Urologic Surgery Clinic of Shanxi Academy of Medical Sciences during April 2015 and March 2016. Demographic information was collected through questionnaires. Urine was collected and urinary Hg concentrations were measured using a fully-automatic double-channel hydride generation atomic fluorescence spectrometer. Methylation of imprinting genes H19, Meg3 and Peg3 of sperm DNA from 242 participants were examined by bisulfite pyrosequencing. Spearman’s rank and multivariate regression analysis were used for correlation analysis between sperm DNA methylation status of imprinting genes and urinary Hg levels. Results The median concentration of Hg for 616 participants was 9.14μg/l (IQR: 5.56–12.52 μg/l; ranging 0.16–71.35μg/l). A total of 42.7% of the participants are beyond normal level for non-occupational exposure according to the criterion of Hg poisoning (≥10 μg/L). Spearman’s rank analysis indicated a negative correlation between urinary Hg concentrations and average DNA methylation levels of imprinted genes H19 (rs = −0.346, p <0.05), but there was no such a correlation for Peg3 and Meg3. Further, we analyzed the correlation between methylation level at individual CpG site of H19 and urinary Hg level. The results showed a negative correlation between urinary Hg concentrations and three out of seven CpG sites on H19 DMR, namely CpG2 (rs = −0.137, p <0.05), CpG4 (rs = −0.380, p <0.05) and CpG6 (rs = −0.228, p <0.05). After adjusting age, smoking, drinking, intake of aquatic products and education by multivariate regression analysis, the results have confirmed the correlation as mentioned above. Conclusions Mercury non-occupational environmental exposure in reproductive-aged men was associated with altered DNA methylation outcomes at imprinting gene H19 in sperm, implicating the susceptibility of the developing sperm for environmental insults.
Collapse
Affiliation(s)
- Zhaoxu Lu
- Department of Child and Adolescence Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan, China
| | - Yufeng Ma
- Department of Child and Adolescence Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan, China
| | - Linying Gao
- Department of Sanitary Inspection, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan, China
| | - Yingjun Li
- Department of Child and Adolescence Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan, China
| | - Qiang Li
- Department of Andrology, Children’s Hospital and Women Health Center of Shanxi, Shanxi, Taiyuan, China
| | - Mei Qiang
- Department of Child and Adolescence Health, School of Public Health, Shanxi Medical University, Shanxi, Taiyuan, China
- * E-mail:
| |
Collapse
|
10
|
Böck J, Appenzeller S, Haertle L, Schneider T, Gehrig A, Schröder J, Rost S, Wolf B, Bartram CR, Sutter C, Haaf T. Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation-negative early-onset and high-risk breast cancer patients. Int J Cancer 2018; 143:1416-1425. [PMID: 29659014 PMCID: PMC6099327 DOI: 10.1002/ijc.31526] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/28/2018] [Indexed: 01/01/2023]
Abstract
To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2-mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in tumor progression. We analyzed blood samples of two breast cancer (BC) cohorts with early onset (EO) and high risk (HR) for a heterozygous mutation, respectively, along with age-matched controls. Methylation analysis of up to 50,000 individual DNA molecules per gene and sample allowed quantification of epimutations (alleles with >50% methylated CpGs), which are associated with epigenetic silencing. Compared to ESR1, which is representative for an average promoter, TS genes were characterized by a very low (< 1%) average methylation level and a very low mean epimutation rate (EMR; < 0.0001% to 0.1%). With exception of BRCA1, which showed an increased EMR in BC (0.31% vs. 0.06%), there was no significant difference between patients and controls. One of 36 HR BC patients exhibited a dramatically increased EMR (14.7%) in BRCA1, consistent with a disease-causing epimutation. Approximately one third (15 of 44) EO BC patients exhibited increased rates of single CpG methylation errors in multiple TS genes. Both EO and HR BC patients exhibited global underexpression of blood TS genes. We propose that epigenetic abnormalities in normal body cells are indicative of disturbed mechanisms for maintaining low methylation and appropriate expression levels and may be associated with an increased BC risk.
Collapse
Affiliation(s)
- Julia Böck
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | | | - Larissa Haertle
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Tamara Schneider
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Jörg Schröder
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Beat Wolf
- University of Applied Sciences Western Switzerland, Fribourg, Switzerland.,Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| |
Collapse
|
11
|
Long Non-Coding RNAs in Multiple Myeloma. Genes (Basel) 2018; 9:genes9020069. [PMID: 29389884 PMCID: PMC5852565 DOI: 10.3390/genes9020069] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 12/30/2022] Open
Abstract
Multiple myeloma (MM) is an incurable disease caused by the malignant proliferation of bone marrow plasma cells, whose pathogenesis remains largely unknown. Although a large fraction of the genome is actively transcribed, most of the transcripts do not serve as templates for proteins and are referred to as non-coding RNAs (ncRNAs), broadly divided into short and long transcripts on the basis of a 200-nucleotide threshold. Short ncRNAs, especially microRNAs, have crucial roles in virtually all types of cancer, including MM, and have gained importance in cancer diagnosis and prognosis, predicting the response to therapy and, notably, as innovative therapeutic targets. Long ncRNAs (lncRNAs) are a very heterogeneous group, involved in many physiological cellular and genomic processes as well as in carcinogenesis, cancer metastasis, and invasion. LncRNAs are aberrantly expressed in various types of cancers, including hematological malignancies, showing either oncogenic or tumor suppressive functions. However, the mechanisms of the related disease-causing events are not yet revealed in most cases. Besides emerging as key players in cancer initiation and progression, lncRNAs own many interesting features as biomarkers with diagnostic and prognostic importance and, possibly, for their utility in therapeutic terms as druggable molecules. This review focuses on the role of lncRNAs in the pathogenesis of MM and summarizes the recent literature.
Collapse
|