1
|
Pommerenke C, Nagel S, Haake J, Koelz AL, Christgen M, Steenpass L, Eberth S. Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes. Cells 2024; 13:301. [PMID: 38391914 PMCID: PMC10886524 DOI: 10.3390/cells13040301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Continuous cell lines are important and commonly used in vitro models in breast cancer (BC) research. Selection of the appropriate model cell line is crucial and requires consideration of their molecular characteristics. To characterize BC cell line models in depth, we profiled a panel of 29 authenticated and publicly available BC cell lines by mRNA-sequencing, mutation analysis, and immunoblotting. Gene expression profiles separated BC cell lines in two major clusters that represent basal-like (mainly triple-negative BC) and luminal BC subtypes, respectively. HER2-positive cell lines were located within the luminal cluster. Mutation calling highlighted the frequent aberration of TP53 and BRCA2 in BC cell lines, which, therefore, share relevant characteristics with primary BC. Furthermore, we showed that the data can be used to find novel, potential oncogenic fusion transcripts, e.g., FGFR2::CRYBG1 and RTN4IP1::CRYBG1 in cell line MFM-223, and to elucidate the regulatory circuit of IRX genes and KLF15 as novel candidate tumor suppressor genes in BC. Our data indicated that KLF15 was activated by IRX1 and inhibited by IRX3. Moreover, KLF15 inhibited IRX1 in cell line HCC-1599. Each BC cell line carries unique molecular features. Therefore, the molecular characteristics of BC cell lines described here might serve as a valuable resource to improve the selection of appropriate models for BC research.
Collapse
Affiliation(s)
- Claudia Pommerenke
- Department of Bioinformatics, IT and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Josephine Haake
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Anne Leena Koelz
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Matthias Christgen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Laura Steenpass
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| |
Collapse
|
2
|
Schwermer M, Hiber M, Dreesmann S, Rieb A, Theißen J, Herold T, Schramm A, Temming P, Steenpass L. Corrigendum to “Comprehensive characterization of RB1 mutant and MYCN amplified retinoblastoma cell lines” [Exp. Cell Res. 375 (2019) 92–99]. Exp Cell Res 2023; 426:113569. [PMID: 36989729 DOI: 10.1016/j.yexcr.2023.113569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
3
|
Abstract
Human and animal cell lines serve as model systems in a wide range of life sciences such as cancer and infection research or drug screening. Reproducible data are highly dependent on authenticated, contaminant-free cell lines, no better delivered than by the official and certified biorepositories. Offering a web portal to high-throughput information on these model systems will facilitate working with and comparing to these references by data otherwise dispersed at different sources. We here provide DSMZCellDive to access a comprehensive data source on human and animal cell lines, freely available at celldive.dsmz.de. A wide variety of data sources are generated such as RNA-seq transcriptome data and STR (short tandem repeats) profiles. Several starting points ease entering the database via browsing, searching or visualising. This web tool is designed for further expansion on meta and high-throughput data to be generated in future. Explicated examples for the power of this novel tool include analysis of B-cell differentiation markers, homeo-oncogene expression, and measurement of genomic loss of heterozygosities by an enlarged STR panel of 17 loci. Sharing the data on cell lines by the biorepository itself will be of benefit to the scientific community since it (1) supports the selection of appropriate model cell lines, (2) ensures reliability, (3) avoids misleading data, (4) saves on additional experimentals, and (5) serves as reference for genomic and gene expression data.
Collapse
Affiliation(s)
- Julia Koblitz
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Wilhelm G. Dirks
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Sonja Eberth
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Stefan Nagel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Laura Steenpass
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Claudia Pommerenke
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| |
Collapse
|
4
|
Pohlmann A, Gerling T, Walter C, Melcher V, de Faria FW, Disch A, Kanber D, Wöstefeld J, Steenpass L, Lohmann D, Ryl T, Riedel N, Ketteler P, Schönberger S, Ting S, Bedzhov I, Kiefer T, Lever M, Schlüter S, Biewald E, Bechrakis N, Albert TK, Kerl K. OTHR-34. Identifying mechanisms of microglia-tumor cell interactions in retinoblastoma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND: Treatment-related long-term sequelae and chemotherapy resistance diminish the success of retinoblastoma (RB) treatment. To unravel the mechanisms leading to tumor progression and resistance we examined the intratumoral cellular heterogeneity of RB and its interactions with cells of the tumor microenvironment (TME). METHODS: We used single-cell RNA (scRNA-seq) and ATAC sequencing (scATAC-seq) as well as spatial transcriptomics to analyze and compare RB samples from patients with or without previous chemotherapy (chemo-treated vs. naïve). In addition, we developed a 3D model by injection of RB and TME cells into retinal organoids, which mimics the heterogeneous surrounding of the tumor in a spatially and functionally organized manner. RESULTS: ScRNA-seq revealed a high intratumoral heterogeneity of tumor cells representing distinct developmental stages from progenitors to more differentiated photoreceptor cells. The predominant cell type in the TME was M2-activated microglia (MG). M2-MG exerted multiple receptor-ligand interactions with RB tumor cells which were not found in non-diseased retinas. These tumor-specific cellular interactions regulate multiple signaling pathways (e. g. VEGF-, WNT-, BMP-, PGF- signaling) known to be involved in RB progression. By comparing chemo-treated and chemo-naïve RB samples we were able to identify treatment-resistant and -sensitive subpopulations of tumor cells. Finally, data from our RB-retina in vitro model highlighted the impact of RB cells on gene expression programs of normal retinal cells. CONCLUSION: In summary, we deciphered the intratumoral heterogeneity of RB, uncovered an intricate network of microglia-tumor cell interactions that connects numerous important signaling pathways, and further identified chemotherapy-resistant/sensitive tumor cell populations. The latter observation could prove to be very helpful in the development of novel therapeutic approaches in the treatment of RB.
Collapse
Affiliation(s)
- Anike Pohlmann
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Teresa Gerling
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Carolin Walter
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
- Institute of Medical Informatics , Münster , Germany
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Flavia W de Faria
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Alina Disch
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Julia Wöstefeld
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Dietmar Lohmann
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Tatsiana Ryl
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Nicole Riedel
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Petra Ketteler
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Stefan Schönberger
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Saskia Ting
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Ivan Bedzhov
- Max Planck Institute for Molecular Biomedicine , Münster , Germany
| | - Tobias Kiefer
- Department of Ophtalmology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Mael Lever
- Department of Ophtalmology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Sabrina Schlüter
- Department of Ophtalmology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Eva Biewald
- Department of Ophtalmology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Nikolaos Bechrakis
- Department of Ophtalmology, University Hospital Essen, University of Duisburg-Essen , Essen , Germany
| | - Thomas K Albert
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Münster , Münster , Germany
| |
Collapse
|
5
|
Wilk C, Effenberg L, Abberger H, Steenpass L, Hansen W, Zeschnigk M, Kirschning C, Buer J, Kehrmann J. CRISPR/Cas9-mediated demethylation of FOXP3-TSDR toward Treg-characteristic programming of Jurkat T cells. Cell Immunol 2022; 371:104471. [PMID: 34954490 DOI: 10.1016/j.cellimm.2021.104471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022]
Abstract
Demethylation of FOXP3-TSDR (Treg specific demethylated region) is a hallmark of stable differentiation and suppressive function of regulatory T (Treg) cells. Previous protocols aiming at human naïve T cell differentiation failed to implement a Treg cell specific epigenetic signature. Ten-eleven translocation (TET) enzymes catalyze DNA demethylation. Plasmids towardexpression of a fusion protein encompassing nonfunctional Cas9, the catalytic domain of TET1, blue fluorescent protein, and encoding single guide RNAs (sgRNAs) targeting specific segments of the FOXP3-TSDR were engineered and transfected into Jurkat T cells. FOXP3-TSDR methylation was analyzed by deep-amplicon bisulfite sequencing while cellular Foxp3, Tbet, Gata3, and Rorgt mRNA levels were determined by real-time PCR. Overexpression of dCas9TET1 significantly decreased Jurkat cell FOXP3-TSDR methylation and increased Foxp3 mRNA expression while expressions of master transcription factor mRNAs of other major T cell lineages remained largely unaffected. dCas9-TET1 construct transfection mediated Treg programming of patients' primary T cells might be feasible.
Collapse
Affiliation(s)
- Camilla Wilk
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Laura Effenberg
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Hanna Abberger
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Germany; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Wiebke Hansen
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Carsten Kirschning
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Germany.
| |
Collapse
|
6
|
Döpper H, Menges J, Bozet M, Brenzel A, Lohmann D, Steenpass L, Kanber D. Differentiation Protocol for 3D Retinal Organoids, Immunostaining and Signal Quantitation. ACTA ACUST UNITED AC 2021; 55:e120. [PMID: 32956559 DOI: 10.1002/cpsc.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structures resembling whole organs, called organoids, are generated using pluripotent stem cells and 3D culturing methods. This relies on the ability of cells to self-reorganize after dissociation. In combination with certain supplemented factors, differentiation can be directed toward the formation of several organ-like structures. Here, a protocol for the generation of retinal organoids containing all seven retinal cell types is described. This protocol does not depend on Matrigel, and by keeping the organoids single and independent at all times, fusion is prevented and monitoring of differentiation is improved. Comprehensive phenotypic characterization of the in vitro-generated retinal organoids is achieved by the protocol for immunostaining outlined here. By comparing different stages of retinal organoids, the decrease and increase of certain cell populations can be determined. In order to be able to detect even small differences, it is necessary to quantify the immunofluorescent signals, for which we have provided a detailed protocol describing signal quantitation using the image-processing program Fiji. © 2020 The Authors. Basic Protocol 1: Differentiation protocol for 3D retinal organoids Basic Protocol 2: Immunostaining protocol for cryosections of retinal organoids Support Protocol: Embedding and sectioning protocol for 3D retinal organoids Basic Protocol 3: Quantitation protocol using Fiji.
Collapse
Affiliation(s)
- Hannah Döpper
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Julia Menges
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Morgane Bozet
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alexandra Brenzel
- Institute for Experimental Immunology and Imaging, Imaging Center Essen (LMU), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dietmar Lohmann
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Present address: Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
7
|
Pommerenke C, Rand U, Uphoff CC, Nagel S, Zaborski M, Hauer V, Kaufmann M, Meyer C, Denkmann SA, Riese P, Eschke K, Kim Y, Safranko ZM, Kurolt IC, Markotic A, Cicin-Sain L, Steenpass L. Identification of cell lines CL-14, CL-40 and CAL-51 as suitable models for SARS-CoV-2 infection studies. PLoS One 2021; 16:e0255622. [PMID: 34339474 PMCID: PMC8328321 DOI: 10.1371/journal.pone.0255622] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
The SARS-CoV-2 pandemic is a major global threat that sparked global research efforts. Pre-clinical and biochemical SARS-CoV-2 studies firstly rely on cell culture experiments where the importance of choosing an appropriate cell culture model is often underestimated. We here present a bottom-up approach to identify suitable permissive cancer cell lines for drug screening and virus research. Human cancer cell lines were screened for the SARS-CoV-2 cellular entry factors ACE2 and TMPRSS2 based on RNA-seq data of the Cancer Cell Line Encyclopedia (CCLE). However, experimentally testing permissiveness towards SARS-CoV-2 infection, we found limited correlation between receptor expression and permissiveness. This underlines that permissiveness of cells towards viral infection is determined not only by the presence of entry receptors but is defined by the availability of cellular resources, intrinsic immunity, and apoptosis. Aside from established cell culture infection models CACO-2 and CALU-3, three highly permissive human cell lines, colon cancer cell lines CL-14 and CL-40 and the breast cancer cell line CAL-51 and several low permissive cell lines were identified. Cell lines were characterised in more detail offering a broader choice of non-overexpression in vitro infection models to the scientific community. For some cell lines a truncated ACE2 mRNA and missense variants in TMPRSS2 might hint at disturbed host susceptibility towards viral entry.
Collapse
Affiliation(s)
- Claudia Pommerenke
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Ulfert Rand
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cord C. Uphoff
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Margarete Zaborski
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vivien Hauer
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine A. Denkmann
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peggy Riese
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kathrin Eschke
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | - Alemka Markotic
- Dr. Fran Mihaljević University Hospital for Infectious Diseases, Zagreb, Croatia
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, Hannover, Germany
| | - Laura Steenpass
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
8
|
Dirks WG, Capes-Davis A, Eberth S, Fähnrich S, Wilting J, Nagel S, Steenpass L, Becker J. Cross contamination meets misclassification: Awakening of CHP-100 from sleeping beauty sleep-A reviewed model for Ewing's sarcoma. Int J Cancer 2021; 148:2608-2613. [PMID: 33460449 DOI: 10.1002/ijc.33474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 11/11/2022]
Abstract
A human cell line of neuroblastic tissue, which was believed to have been lost to science due to its unavailability in public repositories, is revived and reclassified. In the 1970s, a triple set of neuroblastoma (NB) cell lines became available for research as MYCN-amplified vs nonamplified models (CHP-126/-134 and CHP-100, respectively). Confusingly, CHP-100 was used in subsequent years as a model for NB and, since the 1990s, as a model for neuroepithelioma and later as a model for Ewing's sarcoma (ES), which inevitably led to non-reproducible results. A deposit at a bioresource center revealed that globally available stocks of CHP-100 were identical to the prominent NB cell line IMR-32 and CHP-100 was included into the list of misidentified cell lines. Now we report on the rediscovery of an authentic CHP-100 cell line and provide evidence of incorrect classification during establishment. We show that CHP-100 cells carry a t(11;22)(q24;q12) type II EWSR1-FLI1 fusion and identify it as a classic ES. Although the question of whether CHP-100 was a virtual and never existing cell line from the beginning is now clarified, the results of all relevant publications should be considered questionable. Neither the time of the cross-contamination event with IMR-32 is known nor was the final classification as a model for Ewing family of tumors available with an associated short tandem repeat profile. After a long road of errors and confusion, authentic CHP-100 is now characterized as a type II EWSR1-FLI1 fusion model 44 years after its establishment.
Collapse
Affiliation(s)
- Wilhelm Gerhard Dirks
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Amanda Capes-Davis
- Cell Bank Australia, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Sonja Eberth
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Silke Fähnrich
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jörg Wilting
- Department of Anatomy and Cell Biology, University Medical School Göttingen, Göttingen, Germany
| | - Stefan Nagel
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Laura Steenpass
- Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jürgen Becker
- Department of Anatomy and Cell Biology, University Medical School Göttingen, Göttingen, Germany
| |
Collapse
|
9
|
Döpper H, Horstmann M, Menges J, Bozet M, Kanber D, Steenpass L. Biallelic and monoallelic deletion of the RB1 promoter in six isogenic clonal H9 hESC lines. Stem Cell Res 2020; 45:101779. [PMID: 32268247 DOI: 10.1016/j.scr.2020.101779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 11/15/2022] Open
Abstract
Retinoblastoma is a childhood tumor of the retina that is caused mostly by biallelic inactivation of the tumor suppressor gene RB1. To generate a research resource, we abrogated expression of RB1 in H9 hESCs by CRISPR/Cas9 induced deletion of the RB1 promoter, either on one or on both alleles. This enables studies on the role of RB1 loss during differentiation, for example in differentiation towards neural retina. The generation of three isogenic lines per deletion state enables validation of phenotypic results in independent clonal lines.
Collapse
Affiliation(s)
- Hannah Döpper
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Marius Horstmann
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Julia Menges
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Morgane Bozet
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany.
| |
Collapse
|
10
|
Kühnel T, Heinz HSB, Utz N, Božić T, Horsthemke B, Steenpass L. A human somatic cell culture system for modelling gene silencing by transcriptional interference. Heliyon 2020; 6:e03261. [PMID: 32021933 PMCID: PMC6994850 DOI: 10.1016/j.heliyon.2020.e03261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 11/30/2022] Open
Abstract
Transcriptional interference and transcription through regulatory elements (transcriptional read-through) are implicated in gene silencing and the establishment of DNA methylation. Transcriptional read-through is needed to seed DNA methylation at imprinted genes in the germ line and can lead to aberrant gene silencing by DNA methylation in human disease. To enable the study of parameters and factors influencing transcriptional interference and transcriptional read-through at human promoters, we established a somatic cell culture system. At two promoters of imprinted genes (UBE3A and SNRPN) and two promoters shown to be silenced by aberrant transcriptional read-through in human disease (MSH2 and HBA2) we tested, if transcriptional read-through is sufficient for gene repression and the acquisition of DNA methylation. Induction of transcriptional read-through from the doxycycline-inducible CMV promoter resulted in consistent repression of all downstream promoters, independent of promoter type and orientation. Repression was dependent on ongoing transcription, since withdrawal of induction resulted in reactivation. DNA methylation was not acquired at any of the promoters. Overexpression of DNMT3A and DNMT3L, factors needed for DNA methylation establishment in oocytes, was still not sufficient for the induction of DNA methylation. This indicates that induction of DNA methylation has more complex requirements than transcriptional read-through and the presence of de novo DNA methyltransferases.
Collapse
Affiliation(s)
- Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Helena Sophie Barbara Heinz
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Nadja Utz
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
- Present address: Institute of Neuropathology, Justus Liebig University Giessen, Aulweg 128, 35392 Giessen, Germany
| | - Tanja Božić
- Helmholtz Institute for Biomedical Engineering, Division of Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
- Corresponding author.
| |
Collapse
|
11
|
Florian RT, Kraft F, Leitão E, Kaya S, Klebe S, Magnin E, van Rootselaar AF, Buratti J, Kühnel T, Schröder C, Giesselmann S, Tschernoster N, Altmueller J, Lamiral A, Keren B, Nava C, Bouteiller D, Forlani S, Jornea L, Kubica R, Ye T, Plassard D, Jost B, Meyer V, Deleuze JF, Delpu Y, Avarello MDM, Vijfhuizen LS, Rudolf G, Hirsch E, Kroes T, Reif PS, Rosenow F, Ganos C, Vidailhet M, Thivard L, Mathieu A, Bourgeron T, Kurth I, Rafehi H, Steenpass L, Horsthemke B, LeGuern E, Klein KM, Labauge P, Bennett MF, Bahlo M, Gecz J, Corbett MA, Tijssen MAJ, van den Maagdenberg AMJM, Depienne C. Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3. Nat Commun 2019; 10:4919. [PMID: 31664039 PMCID: PMC6820781 DOI: 10.1038/s41467-019-12763-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022] Open
Abstract
Familial Adult Myoclonic Epilepsy (FAME) is a genetically heterogeneous disorder characterized by cortical tremor and seizures. Intronic TTTTA/TTTCA repeat expansions in SAMD12 (FAME1) are the main cause of FAME in Asia. Using genome sequencing and repeat-primed PCR, we identify another site of this repeat expansion, in MARCH6 (FAME3) in four European families. Analysis of single DNA molecules with nanopore sequencing and molecular combing show that expansions range from 3.3 to 14 kb on average. However, we observe considerable variability in expansion length and structure, supporting the existence of multiple expansion configurations in blood cells and fibroblasts of the same individual. Moreover, the largest expansions are associated with micro-rearrangements occurring near the expansion in 20% of cells. This study provides further evidence that FAME is caused by intronic TTTTA/TTTCA expansions in distinct genes and reveals that expansions exhibit an unexpectedly high somatic instability that can ultimately result in genomic rearrangements.
Collapse
Affiliation(s)
- Rahel T Florian
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stephan Klebe
- Department of Neurology, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eloi Magnin
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Anne-Fleur van Rootselaar
- Departments of Neurology and Clinical Neurophysiology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sebastian Giesselmann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Nikolai Tschernoster
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Anaide Lamiral
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Caroline Nava
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Sylvie Forlani
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Ludmila Jornea
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Regina Kubica
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Tao Ye
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Damien Plassard
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Bernard Jost
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Yannick Delpu
- Genomic Vision, 80 Rue des Meuniers, 92220, Bagneux, France
| | | | - Lisanne S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Gabrielle Rudolf
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Edouard Hirsch
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Thessa Kroes
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Philipp S Reif
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Christos Ganos
- Department of Neurology, Charité University Medicine Berlin, 10117, Berlin, Germany
| | - Marie Vidailhet
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Lionel Thivard
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eric LeGuern
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Karl Martin Klein
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Pierre Labauge
- Department of Neurology, Gui de Chauliac University Hospital, 34295, Montpellier, France
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Jozef Gecz
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
- South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Mark A Corbett
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Marina A J Tijssen
- Department of Neurology, University Medical Center Groningen, University of Groningen, 9700, AB, Groningen, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France.
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France.
| |
Collapse
|
12
|
Schipper L, Kanber D, Steenpass L. Generation of heterozygous and homozygous hESC H9 sublines carrying inactivating mutations in RB1. Stem Cell Res 2018; 33:41-45. [PMID: 30312872 DOI: 10.1016/j.scr.2018.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Inactivation of the tumor suppressor gene RB1 is causal for development of retinoblastoma, a tumor of the neural retina arising in children under the age of five. In addition, secondary RB1 mutations are found in many other tumor types. To investigate retinoblastoma formation in vitro, stem cells with inactivated RB1 can be differentiated into neural retina. To enable such studies, two sublines of hESC line H9 carrying mutations in RB1 exon 3 in heterozygous or homozygous state were generated and characterized. Homozygous mutation led to loss of RB1 protein expression. Resource table.
Collapse
Affiliation(s)
- Leonie Schipper
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany.
| |
Collapse
|
13
|
Neureiter A, Brändl B, Hiber M, Tandon R, Müller FJ, Steenpass L. Generation of an iPSC line of a patient with Angelman syndrome due to an imprinting defect. Stem Cell Res 2018; 33:20-24. [PMID: 30296670 DOI: 10.1016/j.scr.2018.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Angelman syndrome (AS) is a neurodevelopmental disorder with leading symptoms of happy demeanor, intellectual disability, ataxia and seizures. AS can be caused by genetic and epigenetic aberrations, resulting in the absence of functional UBE3A protein in the brain. UBE3A is an imprinted gene, which is, in neurons of the brain, expressed exclusively from maternal chromosome 15. The generated iPSC line was derived from skin fibroblasts of a patient with AS, who, due to an imprinting defect, lacked DNA methylation at the chromosome 15 imprinting center, which controls maternal-specific expression of UBE3A. Resource table.
Collapse
Affiliation(s)
- Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Björn Brändl
- Zentrum für integrative Psychiatrie, University Hospital Kiel, Kiel, Germany
| | - Michaela Hiber
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Rashmi Tandon
- Zentrum für integrative Psychiatrie, University Hospital Kiel, Kiel, Germany
| | - Franz-Josef Müller
- Zentrum für integrative Psychiatrie, University Hospital Kiel, Kiel, Germany; Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, Essen, Germany.
| |
Collapse
|
14
|
Stanurova J, Neureiter A, Hiber M, de Oliveira Kessler H, Stolp K, Goetzke R, Klein D, Bankfalvi A, Klump H, Steenpass L. Corrigendum: Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing. Sci Rep 2018. [PMID: 29516994 PMCID: PMC5842440 DOI: 10.1038/srep46952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Steenpass L. Generation of two H1 hESC sublines carrying a heterozygous and homozygous knock-out of RB1. Stem Cell Res 2017; 25:270-273. [PMID: 29246572 DOI: 10.1016/j.scr.2017.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 10/19/2022] Open
Abstract
Retinoblastoma is a childhood cancer of the retina caused by biallelic inactivation of the tumor suppressor gene RB1. In heritable retinoblastoma, one allele is inherited in mutant form via one of the parental germ cells. To study molecular mechanisms in retinoblastoma, two sublines of H1 hESCs were generated, carrying a knock-out allele of RB1 in the heterozygous or homozygous state. Exon 3 of RB1 was targeted and modified by nucleotide deletions using the CRISPR/Cas9 nuclease system. Based on a nearby single nucleotide polymorphism, the modification could be assigned to one allele.
Collapse
Affiliation(s)
- Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany.
| |
Collapse
|
16
|
Schwermer M, Dreesmann S, Eggert A, Althoff K, Steenpass L, Schramm A, Schulte JH, Temming P. Pharmaceutically inhibiting polo-like kinase 1 exerts a broad anti-tumour activity in retinoblastoma cell lines. Clin Exp Ophthalmol 2017; 45:288-296. [PMID: 27647547 DOI: 10.1111/ceo.12838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/16/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Retinoblastoma is the most common malignant cancer of the eye in children. Although metastatic retinoblastoma is rare, cure rates for this advanced disease remain below 50%. High-level polo-like kinase 1 expression in retinoblastomas has previously been shown to be correlated with adverse outcome parameters. Polo-like kinase 1 is a serine/threonine kinase involved in cell cycle regulation at the G2/M transition. Polo-like kinase 1 inhibition has been demonstrated to have anti-tumour effects in preclinical models of several paediatric tumours. Here, we assessed its efficacy against retinoblastoma cell lines. METHODS Expression of polo-like kinase 1 was determined in a panel of retinoblastoma cell lines by polymerase chain reaction and western blot analysis. We analysed viability (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) (MTT assay), proliferation (5-bromo-2'-deoxyuridine enzyme-linked immunosorbent assay), cell cycle progression (propidium iodid staining) and apoptosis (cell death enzyme-linked immunosorbent assay) in three retinoblastoma cell lines after treatment with two adenosine triphosphate-competitive polo-like kinase 1 inhibitors, BI6727 or GSK461364. Activation of polo-like kinase 1 downstream signalling components including TP53 were assessed. RESULTS Treatment of retinoblastoma cells with either BI6727 or GSK461364 reduced cell viability and proliferative capacity and induced both cell cycle arrest and apoptosis. Polo-like kinase 1 inhibition also induced the p53 signalling pathway. Analysis of key players in cell cycle control revealed that low nanomolar concentrations of either polo-like kinase 1 inhibitor upregulated cyclin B1 and increased activated cyclin-dependent kinase 1 (phosphorylated at Y15) in retinoblastoma cell lines. CONCLUSIONS These preclinical data indicate that polo-like kinase 1 inhibitors could be useful as components in rationally designed chemotherapy protocols to treat patients with metastasized retinoblastoma in early phase clinical trials.
Collapse
Affiliation(s)
- Melanie Schwermer
- Department of Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Sabine Dreesmann
- Department of Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité University Medicine Berlin, Berlin, Germany
| | - Kristina Althoff
- Department of Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité University Medicine Berlin, Berlin, Germany
| | - Petra Temming
- Department of Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
- Eye Oncogenetics Research Group, Institute of Human Genetics, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| |
Collapse
|
17
|
Stanurova J, Neureiter A, Hiber M, de Oliveira Kessler H, Stolp K, Goetzke R, Klein D, Bankfalvi A, Klump H, Steenpass L. Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing. Sci Rep 2016; 6:30792. [PMID: 27484051 PMCID: PMC4971516 DOI: 10.1038/srep30792] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/02/2016] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin-specific gene expression that is regulated by a differentially methylated region. Gene mutations or failures in the imprinting process lead to the development of imprinting disorders, such as Angelman syndrome. The symptoms of Angelman syndrome are caused by the absence of functional UBE3A protein in neurons of the brain. To create a human neuronal model for Angelman syndrome, we reprogrammed dermal fibroblasts of a patient carrying a defined three-base pair deletion in UBE3A into induced pluripotent stem cells (iPSCs). In these iPSCs, both parental alleles are present, distinguishable by the mutation, and express UBE3A. Detailed characterization of these iPSCs demonstrated their pluripotency and exceptional stability of the differentially methylated region regulating imprinted UBE3A expression. We observed strong induction of SNHG14 and silencing of paternal UBE3A expression only late during neuronal differentiation, in vitro. This new Angelman syndrome iPSC line allows to study imprinted gene regulation on both parental alleles and to dissect molecular pathways affected by the absence of UBE3A protein.
Collapse
Affiliation(s)
- Jana Stanurova
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Michaela Hiber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannah de Oliveira Kessler
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Kristin Stolp
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Diana Klein
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| |
Collapse
|
18
|
Steenpass L, Kanber D, Hiber M, Buiting K, Horsthemke B, Lohmann D. Human PPP1R26P1 functions as cis-repressive element in mouse Rb1. PLoS One 2013; 8:e74159. [PMID: 24019952 PMCID: PMC3760807 DOI: 10.1371/journal.pone.0074159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 07/26/2013] [Indexed: 01/26/2023] Open
Abstract
The human retinoblastoma gene (RB1) is imprinted; the mouse Rb1 gene is not. Imprinted expression of RB1 is due to differential methylation of a CpG island (CpG85), which is located in the pseudogene PPP1R26P1 in intron 2 of RB1. CpG85 serves as promoter for an alternative RB1 transcript, which is expressed from the unmethylated paternal allele only and is thought to suppress expression of the full-length RB1 transcript in cis. PPP1R26P1 contains another CpG island (CpG42), which is biallelically methylated. To determine the influence of PPP1R26P1 on RB1 expression, we generated an in vitro murine embryonic stem cell model by introducing human PPP1R26P1 into mouse Rb1. Next generation bisulfite sequencing of CpG85 and CpG42 revealed differences in their susceptibility to DNA methylation, gaining methylation at a median level of 4% and 18%, respectively. We showed binding of RNA polymerase II at and transcription from the unmethylated CpG85 in PPP1R26P1 and observed reduced expression of full-length Rb1 from the targeted allele. Our results identify human PPP1R26P1 as a cis-repressive element and support a connection between retrotransposition of PPP1R26P1 into human RB1 and the reduced expression of RB1 on the paternal allele.
Collapse
Affiliation(s)
- Laura Steenpass
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- * E-mail:
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Michaela Hiber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Dietmar Lohmann
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| |
Collapse
|
19
|
Latos PA, Stricker SH, Steenpass L, Pauler FM, Huang R, Senergin BH, Regha K, Koerner MV, Warczok KE, Unger C, Barlow DP. An in vitro ES cell imprinting model shows that imprinted expression of the Igf2r gene arises from an allele-specific expression bias. Development 2009; 136:437-48. [PMID: 19141673 DOI: 10.1242/dev.032060] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genomic imprinting is an epigenetic process that results in parental-specific gene expression. Advances in understanding the mechanism that regulates imprinted gene expression in mammals have largely depended on generating targeted manipulations in embryonic stem (ES) cells that are analysed in vivo in mice. However, genomic imprinting consists of distinct developmental steps, some of which occur in post-implantation embryos, indicating that they could be studied in vitro in ES cells. The mouse Igf2r gene shows imprinted expression only in post-implantation stages, when repression of the paternal allele has been shown to require cis-expression of the Airn non-coding (nc) RNA and to correlate with gain of DNA methylation and repressive histone modifications. Here we follow the gain of imprinted expression of Igf2r during in vitro ES cell differentiation and show that it coincides with the onset of paternal-specific expression of the Airn ncRNA. Notably, although Airn ncRNA expression leads, as predicted, to gain of repressive epigenetic marks on the paternal Igf2r promoter, we unexpectedly find that the paternal Igf2r promoter is expressed at similar low levels throughout ES cell differentiation. Our results further show that the maternal and paternal Igf2r promoters are expressed equally in undifferentiated ES cells, but during differentiation expression of the maternal Igf2r promoter increases up to 10-fold, while expression from the paternal Igf2r promoter remains constant. This indicates, contrary to expectation, that the Airn ncRNA induces imprinted Igf2r expression not by silencing the paternal Igf2r promoter, but by generating an expression bias between the two parental alleles.
Collapse
Affiliation(s)
- Paulina A Latos
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Dr Bohr-Gasse 9/4, Vienna Biocenter, A-1030 Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Stricker SH, Steenpass L, Pauler FM, Santoro F, Latos PA, Huang R, Koerner MV, Sloane MA, Warczok KE, Barlow DP. Silencing and transcriptional properties of the imprinted Airn ncRNA are independent of the endogenous promoter. EMBO J 2008; 27:3116-28. [PMID: 19008856 DOI: 10.1038/emboj.2008.239] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 10/17/2008] [Indexed: 01/09/2023] Open
Abstract
The Airn macro ncRNA is the master regulator of imprinted expression in the Igf2r imprinted gene cluster where it silences three flanking genes in cis. Airn transcription shows unusual features normally viewed as promoter specific, such as impaired post-transcriptional processing and a macro size. The Airn transcript is 108 kb long, predominantly unspliced and nuclear localized, with only a minority being variably spliced and exported. Here, we show by deletion of the Airn ncRNA promoter and replacement with a constitutive strong or weak promoter that splicing suppression and termination, as well as silencing activity, are maintained by strong Airn expression from an exogenous promoter. This indicates that all functional regions are located within the Airn transcript. DNA methylation of the maternal imprint control element (ICE) restricts Airn expression to the paternal allele and we also show that a strong active promoter is required to maintain the unmethylated state of the paternal ICE. Thus, Airn expression not only induces silencing of flanking mRNA genes but also protects the paternal copy of the ICE from de novo methylation.
Collapse
Affiliation(s)
- Stefan H Stricker
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | | | | | | | | | | | | | | |
Collapse
|