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Broghammer F, Korovina I, Gouda M, Celotti M, van Es J, Lange I, Brunner C, Mircetic J, Coppes RP, Gires O, Dahl A, Seifert M, Cordes N. Resistance of HNSCC cell models to pan-FGFR inhibition depends on the EMT phenotype associating with clinical outcome. Mol Cancer 2024; 23:39. [PMID: 38378518 PMCID: PMC10880239 DOI: 10.1186/s12943-024-01954-8] [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: 08/18/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Focal adhesion signaling involving receptor tyrosine kinases (RTK) and integrins co-controls cancer cell survival and therapy resistance. However, co-dependencies between these receptors and therapeutically exploitable vulnerabilities remain largely elusive in HPV-negative head and neck squamous cell carcinoma (HNSCC). METHODS The cytotoxic and radiochemosensitizing potential of targeting 10 RTK and β1 integrin was determined in up to 20 3D matrix-grown HNSCC cell models followed by drug screening and patient-derived organoid validation. RNA sequencing and protein-based biochemical assays were performed for molecular characterization. Bioinformatically identified transcriptomic signatures were applied to patient cohorts. RESULTS Fibroblast growth factor receptor (FGFR 1-4) targeting exhibited the strongest cytotoxic and radiosensitizing effects as monotherapy and combined with β1 integrin inhibition, exceeding the efficacy of the other RTK studied. Pharmacological pan-FGFR inhibition elicited responses ranging from cytotoxicity/radiochemosensitization to resistance/radiation protection. RNA sequence analysis revealed a mesenchymal-to-epithelial transition (MET) in sensitive cell models, whereas resistant cell models exhibited a partial epithelial-to-mesenchymal transition (EMT). Accordingly, inhibition of EMT-associated kinases such as EGFR caused reduced adaptive resistance and enhanced (radio)sensitization to FGFR inhibition cell model- and organoid-dependently. Transferring the EMT-associated transcriptomic profiles to HNSCC patient cohorts not only demonstrated their prognostic value but also provided a conclusive validation of the presence of EGFR-related vulnerabilities that can be strategically exploited for therapeutic interventions. CONCLUSIONS This study demonstrates that pan-FGFR inhibition elicits a beneficial radiochemosensitizing and a detrimental radioprotective potential in HNSCC cell models. Adaptive EMT-associated resistance appears to be of clinical importance, and we provide effective molecular approaches to exploit this therapeutically.
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Affiliation(s)
- Felix Broghammer
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Irina Korovina
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328, Dresden, Germany
| | - Mahesh Gouda
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwigs-Maximilians-University University Hospital, 81377, Munich, Germany
| | - Martina Celotti
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
| | - Johan van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
| | - Inga Lange
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Ulm University Medical Center, 89075, Ulm, Germany
| | - Jovan Mircetic
- German Cancer Consortium, Partner Site Dresden: German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Robert P Coppes
- Department of Biomedical Sciences of Cells and Systems, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9713, Groningen, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713, Groningen, The Netherlands
| | - Olivier Gires
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), 69192, Heidelberg, Germany
| | - Nils Cordes
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany.
- Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328, Dresden, Germany.
- German Cancer Consortium, Partner Site Dresden: German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), 69192, Heidelberg, Germany.
- Department of Radiotherapy and Radiation Oncology, University Hospital Carl Gustav Carus, 01307, Dresden, Germany.
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2
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Gorodetska I, Offermann A, Püschel J, Lukiyanchuk V, Gaete D, Kurzyukova A, Freytag V, Haider MT, Fjeldbo CS, Di Gaetano S, Schwarz FM, Patil S, Borkowetz A, Erb HHH, Baniahmad A, Mircetic J, Lyng H, Löck S, Linge A, Lange T, Knopf F, Wielockx B, Krause M, Perner S, Dubrovska A. ALDH1A1 drives prostate cancer metastases and radioresistance by interplay with AR- and RAR-dependent transcription. Theranostics 2024; 14:714-737. [PMID: 38169509 PMCID: PMC10758061 DOI: 10.7150/thno.88057] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/25/2023] [Indexed: 01/05/2024] Open
Abstract
Rationale: Current therapies for metastatic osseous disease frequently fail to provide a durable treatment response. To date, there are only limited therapeutic options for metastatic prostate cancer, the mechanisms that drive the survival of metastasis-initiating cells are poorly characterized, and reliable prognostic markers are missing. A high aldehyde dehydrogenase (ALDH) activity has been long considered a marker of cancer stem cells (CSC). Our study characterized a differential role of ALDH1A1 and ALDH1A3 genes as regulators of prostate cancer progression and metastatic growth. Methods: By genetic silencing of ALDH1A1 and ALDH1A3 in vitro, in xenografted zebrafish and murine models, and by comparative immunohistochemical analyses of benign, primary tumor, and metastatic specimens from patients with prostate cancer, we demonstrated that ALDH1A1 and ALDH1A3 maintain the CSC phenotype and radioresistance and regulate bone metastasis-initiating cells. We have validated ALDH1A1 and ALDH1A3 as potential biomarkers of clinical outcomes in the independent cohorts of patients with PCa. Furthermore, by RNAseq, chromatin immunoprecipitation (ChIP), and biostatistics analyses, we suggested the molecular mechanisms explaining the role of ALDH1A1 in PCa progression. Results: We found that aldehyde dehydrogenase protein ALDH1A1 positively regulates tumor cell survival in circulation, extravasation, and metastatic dissemination, whereas ALDH1A3 plays the opposite role. ALDH1A1 and ALDH1A3 are differentially expressed in metastatic tumors of patients with prostate cancer, and their expression levels oppositely correlate with clinical outcomes. Prostate cancer progression is associated with the increasing interplay of ALDH1A1 with androgen receptor (AR) and retinoid receptor (RAR) transcriptional programs. Polo-like kinase 3 (PLK3) was identified as a transcriptional target oppositely regulated by ALDH1A1 and ALDH1A3 genes in RAR and AR-dependent manner. PLK3 contributes to the control of prostate cancer cell proliferation, migration, DNA repair, and radioresistance. ALDH1A1 gain in prostate cancer bone metastases is associated with high PLK3 expression. Conclusion: This report provides the first evidence that ALDH1A1 and PLK3 could serve as biomarkers to predict metastatic dissemination and radiotherapy resistance in patients with prostate cancer and could be potential therapeutic targets to eliminate metastasis-initiating and radioresistant tumor cell populations.
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Affiliation(s)
- Ielizaveta Gorodetska
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Anne Offermann
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany; Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Jakob Püschel
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Vasyl Lukiyanchuk
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Diana Gaete
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
| | - Anastasia Kurzyukova
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies TU Dresden and Center for Healthy Aging, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Vera Freytag
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | - Marie-Therese Haider
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Simona Di Gaetano
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Franziska Maria Schwarz
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shivaprasad Patil
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Borkowetz
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Holger H H Erb
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Jovan Mircetic
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heidi Lyng
- Department of Radiation Biology, Oslo University Hospital, Oslo, Norway
- Department of Physics, University of Oslo, Oslo, Norway
| | - Steffen Löck
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), partner site Dresden: German Cancer Research Center (DKFZ), Heidelberg; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Annett Linge
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), partner site Dresden: German Cancer Research Center (DKFZ), Heidelberg; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Germany
- Institute of Anatomy I, Cancer Center Central Germany, Jena, University Hospital, Jena, Germany
| | - Franziska Knopf
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies TU Dresden and Center for Healthy Aging, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
| | - Mechthild Krause
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), partner site Dresden: German Cancer Research Center (DKFZ), Heidelberg; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Luebeck, Germany; Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Anna Dubrovska
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), partner site Dresden: German Cancer Research Center (DKFZ), Heidelberg; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
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Mircetic J, Camgöz A, Abohawya M, Ding L, Dietzel J, Tobar SG, Paszkowski-Rogacz M, Seidlitz T, Schmäche T, Mehnert MC, Sidorova O, Weitz J, Buchholz F, Stange DE. CRISPR/Cas9 Screen in Gastric Cancer Patient-Derived Organoids Reveals KDM1A-NDRG1 Axis as a Targetable Vulnerability. Small Methods 2023; 7:e2201605. [PMID: 36908010 DOI: 10.1002/smtd.202201605] [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] [Received: 12/03/2022] [Revised: 02/01/2023] [Indexed: 06/09/2023]
Abstract
Viability CRISPR screens have proven indispensable in parsing genome function. However, their application in new, more physiologically relevant culturing systems like patient-derived organoids (PDOs) has been much slower. To probe epigenetic contribution to gastric cancer (GC), the third leading cause of cancer-related deaths worldwide, the first negative selection CRISPR screen in GC PDOs that faithfully preserve primary tumor characteristics is performed. Extensive quality control measurements showing feasibility of CRISPR screens in primary organoid culture are provided. The screen reveals the histone lysine demethylase-1A (KDM1A) to constitute a GC vulnerability. Both genetic and pharmacological inhibition of KDM1A cause organoid growth retardation. Further, it is shown that most of KDM1A cancer-supporting functions center on repression of N-myc downstream regulates gene-1 (NDRG1). De-repression of NDRG1 by KDM1A inhibitors (KDM1Ai) causes inhibition of Wnt signaling and a strong G1 cell cycle arrest. Finally, by profiling 20 GC PDOs, it is shown that NDRG1 upregulation predicts KDM1Ai response with 100% sensitivity and 82% specificity in the tested cohort. Thus, this work pioneers the use of negative selection CRISPR screens in patient-derived organoids, identifies a marker of KDM1Ai response, and accordingly a cohort of patients who may benefit from such therapy.
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Affiliation(s)
- Jovan Mircetic
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Aylin Camgöz
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
| | - Moustafa Abohawya
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
| | - Li Ding
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Julia Dietzel
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Sebastián García Tobar
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Tim Schmäche
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Marie-Christin Mehnert
- Mildred Scheel Early Career Center (MSNZ) P2, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Olga Sidorova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité Berlin, 10117, Berlin, Germany
| | - Jürgen Weitz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Daniel E Stange
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), 01309, Dresden, Germany
- National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), 01307, Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf (HZDR), 01307, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
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4
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Sayed S, Sidorova OA, Hennig A, Augsburg M, Cortés Vesga CP, Abohawya M, Schmitt LT, Sürün D, Stange DE, Mircetic J, Buchholz F. Efficient Correction of Oncogenic KRAS and TP53 Mutations through CRISPR Base Editing. Cancer Res 2022; 82:3002-3015. [PMID: 35802645 PMCID: PMC9437569 DOI: 10.1158/0008-5472.can-21-2519] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 08/02/2021] [Revised: 08/19/2021] [Accepted: 06/29/2022] [Indexed: 01/07/2023]
Abstract
KRAS is the most frequently mutated oncogene in human cancer, and its activating mutations represent long-sought therapeutic targets. Programmable nucleases, particularly the CRISPR-Cas9 system, provide an attractive tool for genetically targeting KRAS mutations in cancer cells. Here, we show that cleavage of a panel of KRAS driver mutations suppresses growth in various human cancer cell lines, revealing their dependence on mutant KRAS. However, analysis of the remaining cell population after long-term Cas9 expression unmasked the occurence of oncogenic KRAS escape variants that were resistant to Cas9-cleavage. In contrast, the use of an adenine base editor to correct oncogenic KRAS mutations progressively depleted the targeted cells without the appearance of escape variants and allowed efficient and simultaneous correction of a cancer-associated TP53 mutation. Oncogenic KRAS and TP53 base editing was possible in patient-derived cancer organoids, suggesting that base editor approaches to correct oncogenic mutations could be developed for functional interrogation of vulnerabilities in a personalized manner for future precision oncology applications. SIGNIFICANCE Repairing KRAS mutations with base editors can be used for providing a better understanding of RAS biology and may lay the foundation for improved treatments for KRAS-mutant cancers.
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Affiliation(s)
- Shady Sayed
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Olga A. Sidorova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Alexander Hennig
- National Center for Tumor Diseases (NCT), Dresden, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.,Mildred Scheel Early Career Center (MSNZ) P2, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martina Augsburg
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Catherine P. Cortés Vesga
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Moustafa Abohawya
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
| | - Lukas T. Schmitt
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Duran Sürün
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Daniel E. Stange
- National Center for Tumor Diseases (NCT), Dresden, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.,Mildred Scheel Early Career Center (MSNZ) P2, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.,Mildred Scheel Early Career Center (MSNZ) P2, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany.,Corresponding Author: Frank Buchholz, Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany. E-mail:
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5
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Ding L, Schmitt LT, Brux M, Sürün D, Augsburg M, Lansing F, Mircetic J, Theis M, Buchholz F. DNA methylation-independent long-term epigenetic silencing with dCRISPR/Cas9 fusion proteins. Life Sci Alliance 2022; 5:e202101321. [PMID: 35288457 PMCID: PMC8921183 DOI: 10.26508/lsa.202101321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/27/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/03/2023] Open
Abstract
The programmable CRISPR/Cas9 DNA nuclease is a versatile genome editing tool, but it requires the host cell DNA repair machinery to alter genomic sequences. This fact leads to unpredictable changes of the genome at the cut sites. Genome editing tools that can alter the genome without causing DNA double-strand breaks are therefore in high demand. Here, we show that expression of promoter-associated short guide (sg)RNAs together with dead Cas9 (dCas9) fused to a Krüppel-associated box domains (KRABd) in combination with the transcription repression domain of methyl CpG-binding protein 2 (MeCP2) can lead to persistent gene silencing in mouse embryonic stem cells and in human embryonic kidney (HEK) 293 cells. Surprisingly, this effect is achievable and even enhanced in DNA (cytosine-5)-methyltransferase 3A and 3B (Dnmt3A-/-, Dnmt3b-/-) depleted cells. Our results suggest that dCas9-KRABd-MeCP2 fusions are useful for long-term epigenetic gene silencing with utility in cell biology and potentially in therapeutical settings.
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Affiliation(s)
- Li Ding
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Melanie Brux
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC) Dresden, German Cancer Research Center (DKFZ), University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Duran Sürün
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martina Augsburg
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Felix Lansing
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- Mildred Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Mirko Theis
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC) Dresden, German Cancer Research Center (DKFZ), University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT/UCC) Dresden, German Cancer Research Center (DKFZ), University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
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6
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Sayed S, Sürün D, Mircetic J, Sidorova OA, Buchholz F. Using CRISPR-Cas9 to Dissect Cancer Mutations in Cell Lines. Methods Mol Biol 2022; 2508:235-260. [PMID: 35737245 DOI: 10.1007/978-1-0716-2376-3_18] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The CRISPR-Cas9 technology has revolutionized the scope and pace of biomedical research, enabling the targeting of specific genomic sequences for a wide spectrum of applications. Here we describe assays to functionally interrogate mutations identified in cancer cells utilizing both CRISPR-Cas9 nuclease and base editors. We provide guidelines to interrogate known cancer driver mutations or functionally screen for novel vulnerability mutations with these systems in characterized human cancer cell lines. The proposed platform should be transferable to primary cancer cells, opening up a path for precision oncology on a functional level.
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Affiliation(s)
- Shady Sayed
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Duran Sürün
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Jovan Mircetic
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Olga Alexandra Sidorova
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany.
- National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany.
- German Cancer Consortium (DKTK), Dresden, Germany.
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7
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Ding L, Paszkowski-Rogacz M, Mircetic J, Chakraborty D, Buchholz F. The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells. Life Sci Alliance 2020; 4:4/3/e202000792. [PMID: 33376128 PMCID: PMC7772781 DOI: 10.26508/lsa.202000792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 05/25/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Using ChIP-seq and functional genomic analyses, the study shows that the Paf1 complex occupies transcriptional enhancers and positively regulates their activity. The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines, opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here, we show that the Paf1C positively regulates enhancer activity in mouse embryonic stem cells. In particular, our analyses reveal extensive Paf1C occupancy and function at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity, improving the predictive power to classify enhancers in genomic sequences. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that Paf1C-mediated positive regulation of pluripotency enhancers is crucial to maintain mouse embryonic stem cell self-renewal.
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Affiliation(s)
- Li Ding
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Mildred Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Debojyoti Chakraborty
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany .,National Center for Tumor Diseases (NCT), Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
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8
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Sürün D, Schneider A, Mircetic J, Neumann K, Lansing F, Paszkowski-Rogacz M, Hänchen V, Lee-Kirsch MA, Buchholz F. Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors. Genes (Basel) 2020; 11:E511. [PMID: 32384610 PMCID: PMC7288465 DOI: 10.3390/genes11050511] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human induced pluripotent stem cells (iPSC). Whereas we were unable to correct a disease-causing mutation in patient derived iPSCs using a CRISPR/Cas9 nuclease approach, we corrected the mutation back to wild type with high efficiency utilizing an adenine BE. We also used adenine and cytosine BEs to introduce nine different cancer associated TP53 mutations into human iPSCs with up to 90% efficiency, generating a panel of cell lines to investigate the biology of these mutations in an isogenic background. Finally, we pioneered the use of prime editing in human iPSCs, opening this important cell type for the precise modification of nucleotides not addressable by BEs and to multiple nucleotide exchanges. These approaches eliminate the necessity of deriving disease specific iPSCs from human donors and allows the comparison of different disease-causing mutations in isogenic genetic backgrounds.
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Affiliation(s)
- Duran Sürün
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Aksana Schneider
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Jovan Mircetic
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
- Mildred Scheel Early Career Center, National Center for Tumor Diseases Dresden (NCT/UCC), Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Katrin Neumann
- Stem Cell Engineering Facility, Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden, 01307 Dresden, Germany;
| | - Felix Lansing
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
| | - Vanessa Hänchen
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (V.H.); (M.A.L.-K.)
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (V.H.); (M.A.L.-K.)
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (D.S.); (A.S.); (J.M.); (F.L.); (M.P.-R.)
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9
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Chakraborty D, Paszkowski-Rogacz M, Berger N, Ding L, Mircetic J, Fu J, Iesmantavicius V, Choudhary C, Anastassiadis K, Stewart AF, Buchholz F. lncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1. Cell Rep 2018; 21:3012-3021. [PMID: 29241531 DOI: 10.1016/j.celrep.2017.11.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 05/24/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in diverse biological processes, including embryonic stem cell (ESC) maintenance. However, their functional mechanisms remain largely undefined. Here, we show that the lncRNA Panct1 regulates the transient recruitment of a putative X-chromosome-encoded protein A830080D01Rik, hereafter referred to as transient octamer binding factor 1 (TOBF1), to genomic sites resembling the canonical Oct-Sox motif. TOBF1 physically interacts with Panct1 and exhibits a cell-cycle-specific punctate localization in ESCs. At the chromatin level, this correlates with its recruitment to promoters of pluripotency genes. Strikingly, mutating an octamer-like motif in Panct1 RNA abrogates the strength of TOBF1 localization and recruitment to its targets. Taken together, our data reveal a tightly controlled spatial and temporal pattern of lncRNA-mediated gene regulation in a cell-cycle-dependent manner and suggest that lncRNAs might function as barcodes for identifying genomic addresses for maintaining cellular states.
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Affiliation(s)
- Debojyoti Chakraborty
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nicolas Berger
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.
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10
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Sőnksen PH, Bavington LD, Boehning T, Cowan D, Guha N, Holt R, Karkazis K, Ferguson-Smith MA, Mircetic J, Bőhning D. Hyperandrogenism controversy in elite women's sport: an examination and critique of recent evidence. Br J Sports Med 2018; 52:1481-1482. [PMID: 29351951 DOI: 10.1136/bjsports-2017-098446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2017] [Indexed: 11/03/2022]
Affiliation(s)
- Peter H Sőnksen
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK.,Department of Endocrinology, St Thomas' Hospital and King's College, London, UK
| | - L Dawn Bavington
- School of Physical Education, University of Otago, Dunedin, New Zealand
| | - Tan Boehning
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - David Cowan
- Department of Pharmacy and Forensic Science, Drug Control Centre, King's College London, London, UK
| | - Nishan Guha
- Clinical Biochemistry, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Richard Holt
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Katrina Karkazis
- Center for Biomedical Ethics, Stanford University, Stanford, California, USA
| | | | - Jovan Mircetic
- Medical Faculty Carl Gustav Carus, Technical University, Dresden, Saxony, Germany
| | - Dankmar Bőhning
- Southampton Statistical Sciences Research Institute, University of Southampton, Southampton, UK
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11
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Mircetic J, Dietrich A, Paszkowski-Rogacz M, Krause M, Buchholz F. Development of a genetic sensor that eliminates p53 deficient cells. Nat Commun 2017; 8:1463. [PMID: 29133879 PMCID: PMC5684360 DOI: 10.1038/s41467-017-01688-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 09/24/2015] [Accepted: 10/09/2017] [Indexed: 01/22/2023] Open
Abstract
The TP53 gene fulfills a central role in protecting cells from genetic insult. Given this crucial role it might be surprising that p53 itself is not essential for cell survival. Indeed, TP53 is the single most mutated gene across different cancer types. Thus, both a theoretical and a question of significant practical applicability arise: can cells be programmed to make TP53 an essential gene? Here we present a genetic p53 sensor, in which the loss of p53 is coupled to the rise of HSV-TK expression. We show that the sensor can distinguish both p53 knockout and cells expressing a common TP53 cancer mutation from otherwise isogenic TP53 wild-type cells. Importantly, the system is sensitive enough to specifically target TP53 loss-of-function cells with the HSV-TK pro-drug Ganciclovir both in vitro and in vivo. Our work opens new ways to programming cell intrinsic transformation protection systems that rely on endogenous components. TP53 is mutated in many cancers, a system to detect and selectively eliminate p53 mutant cells is an attractive therapeutic strategy. Here, the authors present a genetic sensor that can detect p53 activity and is coupled to the thymidine kinase gene, which can activate the drug Ganciclovir, resulting in cell death.
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Affiliation(s)
- Jovan Mircetic
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany
| | - Antje Dietrich
- German Cancer Consortium (DKTK), OncoRay-National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany
| | - Mechthild Krause
- German Cancer Consortium (DKTK), OncoRay-National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, Dresden and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Radiation Oncology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany.,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology, 01328, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, 01307, Dresden, Germany.,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307, Dresden, Germany. .,German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, 01307, Dresden, Germany. .,National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
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12
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Gebler C, Lohoff T, Paszkowski-Rogacz M, Mircetic J, Chakraborty D, Camgoz A, Hamann MV, Theis M, Thiede C, Buchholz F. Inactivation of Cancer Mutations Utilizing CRISPR/Cas9. J Natl Cancer Inst 2017; 109:2905662. [PMID: 27576906 PMCID: PMC6284257 DOI: 10.1093/jnci/djw183] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/06/2016] [Accepted: 06/24/2016] [Indexed: 12/26/2022] Open
Abstract
Although whole-genome sequencing has uncovered a large number of mutations that drive tumorigenesis, functional ratification for most mutations remains sparse. Here, we present an approach to test functional relevance of tumor mutations employing CRISPR/Cas9. Combining comprehensive sgRNA design and an efficient reporter assay to nominate efficient and selective sgRNAs, we establish a pipeline to dissect roles of cancer mutations with potential applicability to personalized medicine and future therapeutic use.
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Affiliation(s)
- Christina Gebler
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Tim Lohoff
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Jovan Mircetic
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Debojyoti Chakraborty
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Aylin Camgoz
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Martin V Hamann
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Mirko Theis
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
| | - Christian Thiede
- Medical Faculty Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
- German Cancer Research Center, Heidelberg and German Cancer Consortium partner site Dresden, Germany
| | - Frank Buchholz
- Affiliations of author: Medical Systems Biology, Medical Faculty Carl Gustav Carus, University cancer center, Technische Universitat Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- German Cancer Research Center, Heidelberg and German Cancer Consortium partner site Dresden, Germany
- National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
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