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Sánchez-Rivera FJ, Diaz BJ, Kastenhuber ER, Schmidt H, Katti A, Kennedy M, Tem V, Ho YJ, Leibold J, Paffenholz SV, Barriga FM, Chu K, Goswami S, Wuest AN, Simon JM, Tsanov KM, Chakravarty D, Zhang H, Leslie CS, Lowe SW, Dow LE. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nat Biotechnol 2022; 40:862-873. [PMID: 35165384 PMCID: PMC9232935 DOI: 10.1038/s41587-021-01172-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
Base editing can be applied to characterize single nucleotide variants of unknown function, yet defining effective combinations of single guide RNAs (sgRNAs) and base editors remains challenging. Here, we describe modular base-editing-activity 'sensors' that link sgRNAs and cognate target sites in cis and use them to systematically measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. By quantifying sensor editing across >200,000 editor-sgRNA combinations, we provide a comprehensive resource of sgRNAs for introducing and interrogating cancer-associated single nucleotide variants in multiple model systems. We demonstrate that sensor-validated tools streamline production of in vivo cancer models and that integrating sensor modules in pooled sgRNA libraries can aid interpretation of high-throughput base editing screens. Using this approach, we identify several previously uncharacterized mutant TP53 alleles as drivers of cancer cell proliferation and in vivo tumor development. We anticipate that the framework described here will facilitate the functional interrogation of cancer variants in cell and animal models.
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Affiliation(s)
- Francisco J Sánchez-Rivera
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bianca J Diaz
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Edward R Kastenhuber
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Henri Schmidt
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alyna Katti
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Margaret Kennedy
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Vincent Tem
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Josef Leibold
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Oncology and Pneumology, University Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Stella V Paffenholz
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Francisco M Barriga
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle M Simon
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongxin Zhang
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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Paffenholz P, Peine A, Hellmich M, Paffenholz SV, Martin L, Luedde M, Haverkamp M, Roderburg C, Marx G, Heidenreich A, Trautwein C, Luedde T, Loosen SH. Perception of the 2020 SARS-CoV-2 pandemic among medical professionals in Germany: results from a nationwide online survey. Emerg Microbes Infect 2020; 9:1590-1599. [PMID: 32573350 PMCID: PMC7473195 DOI: 10.1080/22221751.2020.1785951] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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] [Indexed: 01/08/2023]
Abstract
Background: The COVID-19 pandemic represents an unprecedented global challenge and implicates a wide range of burden on medical professionals. Here, we evaluated the perception of the COVID-19 pandemic among medical professionals in Germany. Methods: A total of n = 2827 medical professionals participated in an online survey between 27 March and 11 April. Results: While most participants stated that Germany was well prepared and rated the measures taken by their employer as positive, subgroup analyses revealed decisive differences. The preventive measures were rated significantly worse by nurses compared to doctors (p < 0.001) and by participants from ambulatory healthcare centres compared to participants from maximum-care hospitals (p < 0.001). Importantly, shortage of protective medical equipment was reported more commonly in the ambulatory sector (p < 0.001) and in East German federal states (p = 0.004). Moreover, the majority of health care professionals (72.4%) reported significant restrictions of daily work routine. Finally, over 60% of medical professionals had concerns regarding their own health, which were more pronounced among female participants (p = 0.024). Conclusion: This survey may indicate starting points on how medical professionals could be supported in carrying out their important activities during the ongoing and future healthcare challenges.
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Affiliation(s)
- Pia Paffenholz
- Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, Cologne, Germany
| | - Arne Peine
- Department of Intensive Care Medicine and Intermediate Care, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin Hellmich
- Faculty of Medicine, Institute for Medical Statistics and Computational Biology (IMSB), University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Stella V Paffenholz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lukas Martin
- Department of Intensive Care Medicine and Intermediate Care, University Hospital RWTH Aachen, Aachen, Germany
| | | | - Miriam Haverkamp
- Department of Infection Control and Infectious Diseases, University Hospital RWTH Aachen, Aachen, Germany
| | - Christoph Roderburg
- Department of Gastroenterology/Hepatology, Charité University Medicine Berlin, Berlin, Germany
| | - Gernot Marx
- Department of Intensive Care Medicine and Intermediate Care, University Hospital RWTH Aachen, Aachen, Germany
| | - Axel Heidenreich
- Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, Cologne, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Tom Luedde
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany.,Clinic for Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sven H Loosen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.,Clinic for Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
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Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 2016; 8:442-57. [PMID: 26992833 PMCID: PMC5126213 DOI: 10.15252/emmm.201506055] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [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] [Indexed: 12/21/2022] Open
Abstract
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor‐specific mutations not only in protein‐coding sequences but also in non‐coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this “dark matter” of the genome. Malignancy‐driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5′‐UTR and 3′‐UTR. Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non‐coding RNA, such as microRNA, lncRNA, and lincRNA. A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR‐21 as well as tumor suppressor genes such as TP53/p53,APC,BRCA1, or RB1 can be affected by these alterations. In summary, coding‐independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non‐coding or allegedly silent mutations in tumorigenesis.
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Affiliation(s)
- Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany
| | - Lorenz Bartsch
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Julia C Berkmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Karin Fröse
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jana Heitmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Caroline Hoppe
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Deetje Iggena
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Danny Jazmati
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Philipp Karschnia
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Miriam Linsenmeier
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Thomas Maulhardt
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Lino Möhrmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Johannes Morstein
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Stella V Paffenholz
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Paula Röpenack
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Timo Rückert
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ludger Sandig
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maximilian Schell
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Anna Steinmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Gjendine Voss
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jacqueline Wasmuth
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maria E Weinberger
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ramona Wullenkord
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
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