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Bassani S, Chrast J, Ambrosini G, Voisin N, Schütz F, Brusco A, Sirchia F, Turban L, Schubert S, Jamra RA, Schlump JU, DeMille D, Bayrak-Toydemir P, Nelson GR, Wong KN, Duncan L, Mosera M, Gilissen C, Vissers LE, Pfundt R, Kersseboom R, Yttervik H, Hansen GÅM, Falkenberg Smeland M, Butler KM, Lyons MJ, Carvalho CM, Zhang C, Lupski JR, Potocki L, Flores-Gallegos L, Morales-Toquero R, Petit F, Yalcin B, Tuttle A, Elloumi HZ, Mccormick L, Kukolich M, Klaas O, Horvath J, Scala M, Iacomino M, Operto F, Zara F, Writzl K, Maver A, Haanpää MK, Pohjola P, Arikka H, Iseli C, Guex N, Reymond A. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles. medRxiv 2024:2024.01.14.24301100. [PMID: 38293053 PMCID: PMC10827271 DOI: 10.1101/2024.01.14.24301100] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpression in zebrafish provided evidence for a dominant-negative (DN) mode-of-action, wherein an increased level of AFF3 resulted in pathological effects. Methods Evolutionary constraints suggest that other mode-of-inheritance could be at play. We challenged this hypothesis by screening ID cohorts for individuals with predicted-to-be deleterious variants in AFF3. We used both animal and cellular models to assess the deleteriousness of the identified variants. Results We identified an individual with a KINSSHIP-like phenotype carrying a de novo partial duplication of AFF3 further strengthening the hypothesis that an increased level of AFF3 is pathological. We also detected seventeen individuals displaying a milder syndrome with either heterozygous LoF or biallelic missense variants in AFF3. Consistent with semi-dominance, we discovered three patients with homozygous LoF and one compound heterozygote for a LoF and a missense variant, who presented more severe phenotypes than their heterozygous parents. Matching zebrafish knockdowns exhibit neurological defects that could be rescued by expressing human AFF3 mRNA, confirming their association with the ablation of aff3. Conversely, some of the human AFF3 mRNAs carrying missense variants identified in affected individuals did not complement. Overexpression of mutated AFF3 mRNAs in zebrafish embryos produced a significant increase of abnormal larvae compared to wild-type overexpression further demonstrating deleteriousness. To further assess the effect of AFF3 variation, we profiled the transcriptome of fibroblasts from affected individuals and engineered isogenic cells harboring +/+, DN/DN, LoF/+, LoF/LoF or DN/LoF AFF3 genotypes. The expression of more than a third of the AFF3 bound loci is modified in either the DN/DN or the LoF/LoF lines. While the same pathways are affected, only about one-third of the differentially expressed genes are common to these homozygote datasets, indicating that AFF3 LoF and DN variants largely modulate transcriptomes differently, e.g. the DNA repair pathway displayed opposite modulation. Conclusions Our results and the high pleiotropy shown by variation at this locus suggest that minute changes in AFF3 function are deleterious.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Ambrosini
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Biostatistics platform, University of Lausanne, Lausanne, Switzerland
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Fabio Sirchia
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Lydia Turban
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan-Ulrich Schlump
- Department of Pediatrics, Centre for Neuromedicine, Gemeinschaftskrankenhaus Herdecke Gerhard-Kienle-Weg, Herdecke, Germany
| | - Desiree DeMille
- Genomics Analysis 396, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Pinar Bayrak-Toydemir
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gary Rex Nelson
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kristen Nicole Wong
- Pediatric Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laura Duncan
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mackenzie Mosera
- Department of Pediatrics, Medical Center North, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rogier Kersseboom
- Center for genetic developmental disorders southwest, Zuidwester, Middelharnis, The Netherlands
| | - Hilde Yttervik
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
| | | | | | | | | | - Claudia M.B. Carvalho
- Pacific Northwest Research Institute (PNRI), Broadway, Seattle, Washington, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chaofan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | | | | | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy, 21000 Dijon, France
| | | | | | - Lane Mccormick
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Mary Kukolich
- Department of Genetics, Cook Children’s Medical Center, Cook Children’s Health Care System, Fort Worth, Texas, USA
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Operto
- Child and Adolescent Neuropsychiatry Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, Salerno, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maria K. Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Harri Arikka
- Department of Pediatric Neurology, Turku University Hospital, Turku, Finland; University of Turku, Turku, Finland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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Reijnders MRF, Seibt A, Brugger M, Lamers IJC, Ott T, Klaas O, Horváth J, Rose AMS, Craghill IM, Brunet T, Graf E, Mayerhanser K, Hellebrekers D, Pauck D, Neuen-Jacob E, Rodenburg RJT, Wieczorek D, Klee D, Mayatepek E, Driessen G, Bindermann R, Averdunk L, Lohmeier K, Sinnema M, Stegmann APA, Roepman R, Poulter JA, Distelmaier F. De novo missense variants in RRAGC lead to a fatal mTORopathy of early childhood. Genet Med 2023; 25:100838. [PMID: 37057673 DOI: 10.1016/j.gim.2023.100838] [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: 11/17/2022] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) regulates cell growth in response to nutritional status. Central to the mTORC1 function is the Rag-GTPase heterodimer. One component of the Rag heterodimer is RagC (Ras-related GTP-binding protein C), which is encoded by the RRAGC gene. METHODS Genetic testing via trio exome sequencing was applied to identify the underlying disease cause in 3 infants with dilated cardiomyopathy, hepatopathy, and brain abnormalities, including pachygyria, polymicrogyria, and septo-optic dysplasia. Studies in patient-derived skin fibroblasts and in a HEK293 cell model were performed to investigate the cellular consequences. RESULTS We identified 3 de novo missense variants in RRAGC (NM_022157.4: c.269C>A, p.(Thr90Asn), c.353C>T, p.(Pro118Leu), and c.343T>C, p.(Trp115Arg)), which were previously reported as occurring somatically in follicular lymphoma. Studies of patient-derived fibroblasts carrying the p.(Thr90Asn) variant revealed increased cell size, as well as dysregulation of mTOR-related p70S6K (ribosomal protein S6 kinase 1) and transcription factor EB signaling. Moreover, subcellular localization of mTOR was decoupled from metabolic state. We confirmed the key findings for all RRAGC variants described in this study in a HEK293 cell model. CONCLUSION The above results are in line with a constitutive overactivation of the mTORC1 pathway. Our study establishes de novo missense variants in RRAGC as cause of an early-onset mTORopathy with unfavorable prognosis.
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Affiliation(s)
- Margot R F Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Annette Seibt
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ideke J C Lamers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Torsten Ott
- University Children's Hospital, University Hospital Muenster, Münster, Germany
| | - Oliver Klaas
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Judit Horváth
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Ailsa M S Rose
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Isabel M Craghill
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - David Pauck
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eva Neuen-Jacob
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Richard J T Rodenburg
- Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, University Hospital, Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Gertjan Driessen
- Department of Paediatrics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Robert Bindermann
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Luisa Averdunk
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Klaus Lohmeier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Margje Sinnema
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
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Stinville JC, Hestroffer JM, Charpagne MA, Polonsky AT, Echlin MP, Torbet CJ, Valle V, Nygren KE, Miller MP, Klaas O, Loghin A, Beyerlein IJ, Pollock TM. Multi-modal Dataset of a Polycrystalline Metallic Material: 3D Microstructure and Deformation Fields. Sci Data 2022; 9:460. [PMID: 35915100 PMCID: PMC9343453 DOI: 10.1038/s41597-022-01525-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
The development of high-fidelity mechanical property prediction models for the design of polycrystalline materials relies on large volumes of microstructural feature data. Concurrently, at these same scales, the deformation fields that develop during mechanical loading can be highly heterogeneous. Spatially correlated measurements of 3D microstructure and the ensuing deformation fields at the micro-scale would provide highly valuable insight into the relationship between microstructure and macroscopic mechanical response. They would also provide direct validation for numerical simulations that can guide and speed up the design of new materials and microstructures. However, to date, such data have been rare. Here, a one-of-a-kind, multi-modal dataset is presented that combines recent state-of-the-art experimental developments in 3D tomography and high-resolution deformation field measurements.
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Affiliation(s)
- J C Stinville
- University of Illinois at Urbana-Champaign, Urbana, 61801, USA.
| | - J M Hestroffer
- University of California Santa Barbara, Santa Barbara, 93106-5050, USA
| | - M A Charpagne
- University of Illinois at Urbana-Champaign, Urbana, 61801, USA
| | - A T Polonsky
- Materials Mechanics & Tribology Department, Sandia National Laboratories, Albuquerque, NM, 87185, USA
| | - M P Echlin
- University of California Santa Barbara, Santa Barbara, 93106-5050, USA.
| | - C J Torbet
- University of California Santa Barbara, Santa Barbara, 93106-5050, USA
| | - V Valle
- Institut PPRIME, Université de Poitiers, CNRS, ENSMA, UPR 3346, 86962, Chasseneuil Cedex, France
| | - K E Nygren
- Cornell High Energy Synchrotron Source, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - M P Miller
- Cornell High Energy Synchrotron Source, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - O Klaas
- Simmetrix, Clifton Park, NY, 12065, USA
| | - A Loghin
- Simmetrix, Clifton Park, NY, 12065, USA
| | - I J Beyerlein
- University of California Santa Barbara, Santa Barbara, 93106-5050, USA
| | - T M Pollock
- University of California Santa Barbara, Santa Barbara, 93106-5050, USA
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Rose M, Huth S, Wiesehöfer M, Ehling J, Henkel C, Steitz J, Lammers T, Kistermann J, Klaas O, Koch M, Rushrush S, Knüchel R, Dahl E. ITIH5-Derived Polypeptides Covering the VIT Domain Suppress the Growth of Human Cancer Cells In Vitro. Cancers (Basel) 2022; 14:cancers14030488. [PMID: 35158755 PMCID: PMC8833355 DOI: 10.3390/cancers14030488] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 01/27/2023] Open
Abstract
Oncogenic drivers such as mutated EGFR are the preferred targets in modern drug development. However, restoring the lost function of tumor suppressor proteins could also be a valid approach to combatting cancer. ITIH5 has been revealed as a potent metastasis suppressor in both breast and pancreatic cancer. Here, we show that ITIH5 overexpression in MDA-MB-231 breast cancer cells can also locally suppress tumor growth by 85%, when transplanted into the mammary fat pad of nude mice. For a potential drug development approach, we further aimed to define downsized ITIH5 polypeptides that still are capable of mediating growth inhibitory effects. By cloning truncated and His-tagged ITIH5 fragments, we synthesized two recombinant N-terminal polypeptides (ITIH5681aa and ITIH5161aa), both covering the ITI heavy chain specific “vault protein inter-alpha-trypsin” (VIT) domain. Truncated ITIH5 variants caused dose-dependent cell growth inhibition by up to 50% when applied to various cancer cell lines (e.g., MDA-MB-231, SCaBER, A549) reflecting breast, bladder and lung cancer in vitro. Thus, our data suggest the substantial role of the ITIH5-specific VIT domain in ITIH5-mediated suppression of tumor cell proliferation. As extracellularly administered ITIH5 peptides mimic the growth-inhibitory effects of the full-length ITIH5 tumor suppressor protein, they may constitute the basis for developing anticancer drugs in the future.
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Affiliation(s)
- Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-80-89715 (M.R.); +49-241-80-88431 (E.D.); Fax: +49-241-8082439 (M.R. & E.D.)
| | - Sebastian Huth
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
- Department of Dermatology and Allergology, RWTH Aachen University, 52074 Aachen, Germany
| | - Marc Wiesehöfer
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
| | - Josef Ehling
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging, Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany; (J.E.); (T.L.)
| | - Corinna Henkel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
- Bruker Daltonik GmbH, 28359 Bremen, Germany
| | - Julia Steitz
- Institute for Laboratory Animal Science, University Hospital, RWTH Aachen University, 52074 Aachen, Germany;
| | - Twan Lammers
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging, Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany; (J.E.); (T.L.)
| | - Jennifer Kistermann
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
| | - Oliver Klaas
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
| | - Maximilian Koch
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
| | - Sandra Rushrush
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Edgar Dahl
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.H.); (M.W.); (C.H.); (J.K.); (O.K.); (M.K.); (S.R.); (R.K.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-80-89715 (M.R.); +49-241-80-88431 (E.D.); Fax: +49-241-8082439 (M.R. & E.D.)
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5
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Jürgens L, Manske F, Hubert E, Kischka T, Flötotto L, Klaas O, Shabardina V, Schliemann C, Makalowski W, Wethmar K. Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer. Biomedicines 2021; 9:biomedicines9060618. [PMID: 34072580 PMCID: PMC8227997 DOI: 10.3390/biomedicines9060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer.
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Affiliation(s)
- Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Felix Manske
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Elvira Hubert
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Tabea Kischka
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Lea Flötotto
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Oliver Klaas
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Victoria Shabardina
- Institute of Evolutionary Biology, CSIC-Unversitat Pompeu Frabra, 08002 Barcelona, Spain;
| | - Christoph Schliemann
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, University of Münster, 48149 Münster, Germany; (F.M.); (T.K.); (W.M.)
| | - Klaus Wethmar
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, 48149 Münster, Germany; (L.J.); (E.H.); (L.F.); (O.K.); (C.S.)
- Correspondence: ; Tel.: +49-251-8347587; Fax: +49-251-8347588
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Schulz J, Mah N, Neuenschwander M, Kischka T, Ratei R, Schlag PM, Castaños-Vélez E, Fichtner I, Tunn PU, Denkert C, Klaas O, Berdel WE, von Kries JP, Makalowski W, Andrade-Navarro MA, Leutz A, Wethmar K. Loss-of-function uORF mutations in human malignancies. Sci Rep 2018; 8:2395. [PMID: 29402903 PMCID: PMC5799362 DOI: 10.1038/s41598-018-19201-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 03/07/2017] [Accepted: 12/27/2017] [Indexed: 11/09/2022] Open
Abstract
Ribosome profiling revealed widespread translational activity at upstream open reading frames (uORFs) and validated uORF-mediated translational control as a commonly repressive mechanism of gene expression. Translational activation of proto-oncogenes through loss-of-uORF mutations has been demonstrated, yet a systematic search for cancer-associated genetic alterations in uORFs is lacking. Here, we applied a PCR-based, multiplex identifier-tagged deep sequencing approach to screen 404 uORF translation initiation sites of 83 human tyrosine kinases and 49 other proto-oncogenes in 308 human malignancies. We identified loss-of-function uORF mutations in EPHB1 in two samples derived from breast and colon cancer, and in MAP2K6 in a sample of colon adenocarcinoma. Both mutations were associated with enhanced translation, suggesting that loss-of-uORF-mediated translational induction of the downstream main protein coding sequence may have contributed to carcinogenesis. Computational analysis of whole exome sequencing datasets of 464 colon adenocarcinomas subsequently revealed another 53 non-recurrent somatic mutations functionally deleting 22 uORF initiation and 31 uORF termination codons, respectively. These data provide evidence for somatic mutations affecting uORF initiation and termination codons in human cancer. The insufficient coverage of uORF regions in current whole exome sequencing datasets demands for future genome-wide analyses to ultimately define the contribution of uORF-mediated translational deregulation in oncogenesis.
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Affiliation(s)
- Julia Schulz
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Nancy Mah
- Charité University Medicine Berlin, Campus Virchow-Klinikum, Berlin-Brandenburg Center for Regenerative Therapies, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Martin Neuenschwander
- Leibniz Institute fuer Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Tabea Kischka
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Straße 14, 48149, Muenster, Germany
| | - Richard Ratei
- Carl-Thiem-Klinikum, 2. Medizinische Klinik, Thiemstr. 111, 03048, Cottbus, Germany.,Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125, Berlin, Germany
| | - Peter M Schlag
- Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Iduna Fichtner
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Per-Ulf Tunn
- Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125, Berlin, Germany
| | - Carsten Denkert
- Charité University Medicine Berlin, Institute of Pathology, Chariteplatz 1, 10117, Berlin, Germany
| | - Oliver Klaas
- University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany
| | - Wolfgang E Berdel
- University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany
| | - Jens P von Kries
- Leibniz Institute fuer Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Wojciech Makalowski
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Straße 14, 48149, Muenster, Germany
| | - Miguel A Andrade-Navarro
- Johannes-Gutenberg University of Mainz, Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Achim Leutz
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany. .,Humboldt-University, Department of Biology, Invalidenstr. 43, 10115, Berlin, Germany.
| | - Klaus Wethmar
- Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125, Berlin, Germany. .,University Hospital Muenster, Department of Medicine A, Hematology, Oncology and Pneumology, Albert-Schweitzer-Campus 1, 48149, Muenster, Germany.
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7
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Rose M, Kloten V, Noetzel E, Gola L, Ehling J, Heide T, Meurer SK, Gaiko-Shcherbak A, Sechi AS, Huth S, Weiskirchen R, Klaas O, Antonopoulos W, Lin Q, Wagner W, Veeck J, Gremse F, Steitz J, Knüchel R, Dahl E. ITIH5 mediates epigenetic reprogramming of breast cancer cells. Mol Cancer 2017; 16:44. [PMID: 28231808 PMCID: PMC5322623 DOI: 10.1186/s12943-017-0610-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 10/21/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023] Open
Abstract
Background Extracellular matrix (ECM) is known to maintain epithelial integrity. In carcinogenesis ECM degradation triggers metastasis by controlling migration and differentiation including cancer stem cell (CSC) characteristics. The ECM-modulator inter- α-trypsin inhibitor heavy chain family member five (ITIH5) was recently identified as tumor suppressor potentially involved in impairing breast cancer progression but molecular mechanisms underlying its function are still elusive. Methods ITIH5 expression was analyzed using the public TCGA portal. ITIH5-overexpressing single-cell clones were established based on T47D and MDA-MB-231 cell lines. Colony formation, growth, apoptosis, migration, matrix adhesion, traction force analyses and polarization of tumor cells were studied in vitro. Tumor-initiating characteristics were analyzed by generating a metastasis mouse model. To identify ITIH5-affected pathways we utilized genome wide gene expression and DNA methylation profiles. RNA-interference targeting the ITIH5-downstream regulated gene DAPK1 was used to confirm functional involvement. Results ITIH5 loss was pronounced in breast cancer subtypes with unfavorable prognosis like basal-type tumors. Functionally, cell and colony formation was impaired after ITIH5 re-expression in both cell lines. In a metastasis mouse model, ITIH5 expressing MDA-MB-231 cells almost completely failed to initiate lung metastases. In these metastatic cells ITIH5 modulated cell-matrix adhesion dynamics and altered biomechanical cues. The profile of integrin receptors was shifted towards β1-integrin accompanied by decreased Rac1 and increased RhoA activity in ITIH5-expressing clones while cell polarization and single-cell migration was impaired. Instead ITIH5 expression triggered the formation of epithelial-like cell clusters that underwent an epigenetic reprogramming. 214 promoter regions potentially marked with either H3K4 and /or H3K27 methylation showed a hyper- or hypomethylated DNA configuration due to ITIH5 expression finally leading to re-expression of the tumor suppressor DAPK1. In turn, RNAi-mediated knockdown of DAPK1 in ITIH5-expressing MDA-MB-231 single-cell clones clearly restored cell motility. Conclusions Our results provide evidence that ITIH5 triggers a reprogramming of breast cancer cells with known stem CSC properties towards an epithelial-like phenotype through global epigenetic changes effecting known tumor suppressor genes like DAPK1. Therewith, ITIH5 may represent an ECM modulator in epithelial breast tissue mediating suppression of tumor initiating cancer cell characteristics which are thought being responsible for the metastasis of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0610-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Rose
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Vera Kloten
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Erik Noetzel
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Lukas Gola
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Josef Ehling
- Department of Experimental Molecular Imaging (ExMI), Helmholtz Institute for Biomedical Engineering, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Timon Heide
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Steffen K Meurer
- Experimental Gene Therapy and Clinical Chemistry, Institute of Molecular Pathobiochemistry, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Aljona Gaiko-Shcherbak
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Antonio S Sechi
- Institute for Biomedical Engineering-Cell Biology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Sebastian Huth
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Ralf Weiskirchen
- Experimental Gene Therapy and Clinical Chemistry, Institute of Molecular Pathobiochemistry, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Oliver Klaas
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Wiebke Antonopoulos
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Qiong Lin
- Institute for Biomedical Engineering-Cell Biology, Medical Faculty of the RWTH Aachen University, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering-Stem Cell Biology and Cellular Engineering, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Biomedical Engineering-Cell Biology, Medical Faculty of the RWTH Aachen University, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering-Stem Cell Biology and Cellular Engineering, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Jürgen Veeck
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany.,Division of Medical Oncology, Department of Internal Medicine, Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Felix Gremse
- Department of Experimental Molecular Imaging (ExMI), Helmholtz Institute for Biomedical Engineering, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Julia Steitz
- Institute for Laboratory Animal Science, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Ruth Knüchel
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Edgar Dahl
- Institute of Pathology, Medical Faculty of the RWTH Aachen University, Aachen, Germany.
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Hohmann L, Gorny R, Klaas O, Ahlert J, Wohlgemuth K, Kockmann N. Design of a Continuous Tubular Cooling Crystallizer for Process Development on Lab-Scale. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201600072] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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