1
|
Bai G, Dhillon N, Felton C, Meissner B, Saint-John B, Shelansky R, Meyerson E, Hrabeta-Robinson E, Hodjat B, Boeger H, Brooks AN. Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing. bioRxiv 2024:2024.03.20.585815. [PMID: 38562899 PMCID: PMC10983977 DOI: 10.1101/2024.03.20.585815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide identification of chromatin organization and structure has been generally probed by measuring accessibility of the underlying DNA to nucleases or methyltransferases. These methods either only observe the positioning of a single nucleosome or rely on large enzymes to modify or cleave the DNA. We developed adduct sequencing (Add-seq), a method to probe chromatin accessibility by treating chromatin with the small molecule angelicin, which preferentially intercalates into DNA not bound to core nucleosomes. We show that Nanopore sequencing of the angelicin-modified DNA is possible and allows visualization and analysis of long single molecules with distinct chromatin structure. The angelicin modification can be detected from the Nanopore current signal data using a neural network model trained on unmodified and modified chromatin-free DNA. Applying Add-seq to Saccharomyces cerevisiae nuclei, we identified expected patterns of accessibility around annotated gene loci in yeast. We also identify individual clusters of single molecule reads displaying different chromatin structure at specific yeast loci, which demonstrates heterogeneity in the chromatin structure of the yeast population. Thus, using Add-seq, we are able to profile DNA accessibility in the yeast genome across long molecules.
Collapse
Affiliation(s)
- Gali Bai
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Brett Meissner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Robert Shelansky
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Elliot Meyerson
- Cognizant AI Labs, San Francisco, California, 94105, United States of America
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Babak Hodjat
- Cognizant AI Labs, San Francisco, California, 94105, United States of America
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| |
Collapse
|
2
|
Soulette CM, Hrabeta-Robinson E, Arevalo C, Felton C, Tang AD, Marin MG, Brooks AN. Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations. Life Sci Alliance 2023; 6:e202000641. [PMID: 37487637 PMCID: PMC10366530 DOI: 10.26508/lsa.202000641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered mRNA isoforms associated with the mutation are largely unknown. To better understand the impact U2AF1 has on full-length isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without a U2AF1 S34F mutation. We identified 49,366 multi-exon transcript isoforms, more than half of which did not match GENCODE or short-read-assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes relative to WT, only 68% of which were assembled by short reads. Expression of isoforms from immune-related genes is largely down-regulated in mutant cells and without observed splicing changes. Finally, we reveal that isoforms likely targeted by nonsense-mediated decay are down-regulated in U2AF1 S34F cells, suggesting that isoform changes may alter the translational output of those affected genes. Altogether, our work provides a resource of full-length isoforms associated with U2AF1 S34F in lung cells.
Collapse
Affiliation(s)
- Cameron M Soulette
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Carlos Arevalo
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Maximillian G Marin
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| |
Collapse
|
3
|
Durham M, Vadde S, Brooks AN. MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples. MicroPubl Biol 2023; 2023:10.17912/micropub.biology.000957. [PMID: 37829573 PMCID: PMC10565573 DOI: 10.17912/micropub.biology.000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
MET exon 14 skipping ( METΔ14 ) is a well-characterized oncogene in the Ras-MAPK pathway driving lung adenocarcinoma (LUAD). Previous studies on METΔ14 revealed this aberrantly spliced oncogene is expressed in LUAD primary samples and is associated with heterozygous somatic mutations and deletions near exon 14 splice sites. Upon further examination of DNA and RNA sequencing data from primary samples, we highlight that METΔ14 is overexpressed in an allele-specific manner. These data suggest that dose-dependence of METΔ14 may be critical to oncogenesis.
Collapse
Affiliation(s)
- Megan Durham
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Swetha Vadde
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States
| |
Collapse
|
4
|
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
Collapse
Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| |
Collapse
|
5
|
Tang AD, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Detecting haplotype-specific transcript variation in long reads with FLAIR2. bioRxiv 2023:2023.06.09.544396. [PMID: 37398362 PMCID: PMC10312636 DOI: 10.1101/2023.06.09.544396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme which mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung ADC cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, short read RNA-Seq has limited the community's ability to interrogate both forms of RNA variation simultaneously. Results We employed long-read technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We have developed a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generated nanopore data with high sequence accuracy of H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We applied our workflow to identify key inosine-isoform associations to help clarify the prominence of ADAR in tumorigenesis. Conclusions Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
Collapse
Affiliation(s)
- Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | | | - Roger Volden
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | | | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz
| |
Collapse
|
6
|
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Thornton AM, Tumu M, Brooks AN. An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines. STAR Protoc 2022; 3:101651. [PMID: 36092819 PMCID: PMC9449654 DOI: 10.1016/j.xpro.2022.101651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We describe a bioinformatics protocol for eVIP2 (expression-based variant impact phenotyping). eVIP2 can predict a gene variant’s functional impact by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The predicted functional outcomes of the variants include gain-of-function, loss-of-function, change-of-function, or neutral. eVIP2 improves upon eVIP by being applicable to RNA-seq data and providing pathway-level functional predictions for each mutation. Here, we detail how to run eVIP2 on RNA-seq data from two RNF43 variants. For complete details on the use and execution of this protocol, please refer to Thornton et al. (2021). A user-friendly computational tool to predict variant impact Profiles many variants across multiple genes in a single run Identification of specific signaling pathways affected by each variant Static and interactive visualization of results
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Collapse
Affiliation(s)
- Alexis M Thornton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Manoj Tumu
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| |
Collapse
|
9
|
Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S. Cell Painting predicts impact of lung cancer variants. Mol Biol Cell 2022; 33:ar49. [PMID: 35353015 PMCID: PMC9265158 DOI: 10.1091/mbc.e21-11-0538] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/26/2022] [Accepted: 03/22/2022] [Indexed: 12/24/2022] Open
Abstract
Most variants in most genes across most organisms have an unknown impact on the function of the corresponding gene. This gap in knowledge is especially acute in cancer, where clinical sequencing of tumors now routinely reveals patient-specific variants whose functional impact on the corresponding genes is unknown, impeding clinical utility. Transcriptional profiling was able to systematically distinguish these variants of unknown significance as impactful vs. neutral in an approach called expression-based variant-impact phenotyping. We profiled a set of lung adenocarcinoma-associated somatic variants using Cell Painting, a morphological profiling assay that captures features of cells based on microscopy using six stains of cell and organelle components. Using deep-learning-extracted features from each cell's image, we found that cell morphological profiling (cmVIP) can predict variants' functional impact and, particularly at the single-cell level, reveals biological insights into variants that can be explored at our public online portal. Given its low cost, convenient implementation, and single-cell resolution, cmVIP profiling therefore seems promising as an avenue for using non-gene specific assays to systematically assess the impact of variants, including disease-associated alleles, on gene function.
Collapse
Affiliation(s)
| | - John Arevalo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | | | | | | | - Xiaoyun Wu
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | | | | | | | | | | |
Collapse
|
10
|
Yu T, Cazares O, Tang AD, Kim HY, Wald T, Verma A, Liu Q, Barcellos-Hoff MH, Floor SN, Jung HS, Brooks AN, Klein OD. SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal. Dev Cell 2022; 57:624-637.e4. [PMID: 35202586 PMCID: PMC8974236 DOI: 10.1016/j.devcel.2022.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/27/2020] [Revised: 11/04/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022]
Abstract
Alternative splicing generates distinct mRNA variants and is essential for development, homeostasis, and renewal. Proteins of the serine/arginine (SR)-rich splicing factor family are major splicing regulators that are broadly required for organ development as well as cell and organism viability. However, how these proteins support adult organ function remains largely unknown. Here, we used the continuously growing mouse incisor as a model to dissect the functions of the prototypical SR family protein SRSF1 during tissue homeostasis and renewal. We identified an SRSF1-governed alternative splicing network that is specifically required for dental proliferation and survival of progenitors but dispensable for the viability of differentiated cells. We also observed a similar progenitor-specific role of SRSF1 in the small intestinal epithelium, indicating a conserved function of SRSF1 across adult epithelial tissues. Thus, our findings define a regulatory mechanism by which SRSF1 specifically controls progenitor-specific alternative splicing events to support adult tissue homeostasis and renewal.
Collapse
Affiliation(s)
- Tingsheng Yu
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Oscar Cazares
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hyun-Yi Kim
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adya Verma
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Qi Liu
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Han-Sung Jung
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
11
|
Thornton AM, Fang L, Lo A, McSharry M, Haan D, O’Brien C, Berger AH, Giannakis M, Brooks AN. eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. PLoS Comput Biol 2021; 17:e1009132. [PMID: 34214079 PMCID: PMC8281988 DOI: 10.1371/journal.pcbi.1009132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/15/2021] [Accepted: 05/30/2021] [Indexed: 11/25/2022] Open
Abstract
While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type (WT) versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric, and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659 has been previously described as a passenger mutation that maintains the RNF43 WT function as a negative regulator of Wnt. Surprisingly, eVIP2 predicted G659fs to be a change-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF-α via NFκB signaling, KRAS signaling, and hypoxia, highlighting the benefit of a more comprehensive approach when determining the impact of gene variant function. To validate these predictions, we performed reporter assays and found that each pathway activated by expression of RNF43 G659fs, but not expression of RNF43 WT, was identified as impacted by eVIP2, supporting that RNF43 G659fs is a change-of-function mutation and its effect on the identified pathways. Pathway activation was further validated by Western blot analysis. Lastly, we show primary colon adenocarcinoma patient samples with R117fs and G659fs variants have transcriptional profiles similar to BRAF missense mutations with activated RAS/MAPK signaling, consistent with KRAS signaling pathways being GOF in both variants. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2.
Collapse
Affiliation(s)
- Alexis M. Thornton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lishan Fang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Department of Orthopedics, The Eight Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - April Lo
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Maria McSharry
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David Haan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Casey O’Brien
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Alice H. Berger
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| |
Collapse
|
12
|
Robinson EK, Jagannatha P, Covarrubias S, Cattle M, Smaliy V, Safavi R, Shapleigh B, Abu-Shumays R, Jain M, Cloonan SM, Akeson M, Brooks AN, Carpenter S. Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2. eLife 2021; 10:69431. [PMID: 34047695 PMCID: PMC8260223 DOI: 10.7554/elife.69431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/15/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to the isoforms produced. Of these AFE events, we identified 95 unannotated transcription start sites in mice using a de novo transcriptome generated by long-read native RNA-sequencing, one of which is in the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform expressed during inflammation and contains an iron-responsive element in its 5′UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.
Collapse
Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Pratibha Jagannatha
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States.,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Matthew Cattle
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Valeriya Smaliy
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Rojin Safavi
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Robin Abu-Shumays
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Miten Jain
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| |
Collapse
|
13
|
Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto RA, Herai RH, Huseynov A, Ferraz MSA, Borges FS, Kihara AH, Byrne A, Marin M, Vollmers C, Brooks AN, Lautz JD, Semendeferi K, Shapiro B, Yeo GW, Smith SEP, Green RE, Muotri AR. Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. Science 2021; 371:371/6530/eaax2537. [PMID: 33574182 DOI: 10.1126/science.aax2537] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/27/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.
Collapse
Affiliation(s)
- Cleber A Trujillo
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Edward S Rice
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nathan K Schaefer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Isaac A Chaim
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily C Wheeler
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Assael A Madrigal
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priscilla D Negraes
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ryan A Szeto
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Roberto H Herai
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Alik Huseynov
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Mariana S A Ferraz
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Fernando S Borges
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Alexandre H Kihara
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Ashley Byrne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximillian Marin
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics and Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Katerina Semendeferi
- Department of Anthropology, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gene W Yeo
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics and Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alysson R Muotri
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
14
|
Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol 2020; 38:675-678. [PMID: 32444850 DOI: 10.1038/s41587-020-0546-8] [Citation(s) in RCA: 1754] [Impact Index Per Article: 438.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mary J Goldman
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
| | - Brian Craft
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Akhil Kamath
- Birla Institute of Technology and Science, Goa, India
| | | | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Angela N Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.,Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jingchun Zhu
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| |
Collapse
|
15
|
Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell 2020; 178:1465-1477.e17. [PMID: 31491388 DOI: 10.1016/j.cell.2019.08.018] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [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: 10/15/2018] [Revised: 12/13/2018] [Accepted: 08/07/2019] [Indexed: 02/08/2023]
Abstract
Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. However, while a global change in transcription is recognized as a defining feature of cancer, the contribution of alternative promoters still remains largely unexplored. Here, we infer active promoters using RNA-seq data from 18,468 cancer and normal samples, demonstrating that alternative promoters are a major contributor to context-specific regulation of transcription. We find that promoters are deregulated across tissues, cancer types, and patients, affecting known cancer genes and novel candidates. For genes with independently regulated promoters, we demonstrate that promoter activity provides a more accurate predictor of patient survival than gene expression. Our study suggests that a dynamic landscape of active promoters shapes the cancer transcriptome, opening new diagnostic avenues and opportunities to further explore the interplay of regulatory mechanisms with transcriptional aberrations in cancer.
Collapse
Affiliation(s)
- Deniz Demircioğlu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Engin Cukuroglu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Martin Kindermans
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Tannistha Nandi
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Claudia Calabrese
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Genome Biology Unit, EMBL, Heidelberg, 69117, Germany
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão 4485-601, Portugal
| | - André Kahles
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Department of Biology, ETH Zurich, Zurich 8093, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland
| | - Kjong-Van Lehmann
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Genome Biology Unit, EMBL, Heidelberg, 69117, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gunnar Rätsch
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Department of Biology, ETH Zurich, Zurich 8093, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland; Weill Cornell Medical College, New York, NY 10065, USA
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore 169856, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore; Singapore Gastric Cancer Consortium, Singapore 119074, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore.
| |
Collapse
|
16
|
Huang HH, Ferguson ID, Thornton AM, Bastola P, Lam C, Lin YHT, Choudhry P, Mariano MC, Marcoulis MD, Teo CF, Malato J, Phojanakong PJ, Martin TG, Wolf JL, Wong SW, Shah N, Hann B, Brooks AN, Wiita AP. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Nat Commun 2020; 11:1931. [PMID: 32321912 PMCID: PMC7176739 DOI: 10.1038/s41467-020-15521-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 02/15/2019] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Enhancing the efficacy of proteasome inhibitors (PI) is a central goal in myeloma therapy. We proposed that signaling-level responses after PI may reveal new mechanisms of action that can be therapeutically exploited. Unbiased phosphoproteomics after treatment with the PI carfilzomib surprisingly demonstrates the most prominent phosphorylation changes on splicing related proteins. Spliceosome modulation is invisible to RNA or protein abundance alone. Transcriptome analysis after PI demonstrates broad-scale intron retention, suggestive of spliceosome interference, as well as specific alternative splicing of protein homeostasis machinery components. These findings lead us to evaluate direct spliceosome inhibition in myeloma, which synergizes with carfilzomib and shows potent anti-tumor activity. Functional genomics and exome sequencing further support the spliceosome as a specific vulnerability in myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.
Collapse
Affiliation(s)
- Hector H Huang
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Alexis M Thornton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Prabhakar Bastola
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Christine Lam
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Margarette C Mariano
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Makeba D Marcoulis
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Chin Fen Teo
- Department of Physiology, University of California, San Francisco, CA, USA
| | - Julia Malato
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Paul J Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Thomas G Martin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey L Wolf
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Sandy W Wong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Nina Shah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
| |
Collapse
|
17
|
Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN. Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Nat Commun 2020; 11:1438. [PMID: 32188845 PMCID: PMC7080807 DOI: 10.1038/s41467-020-15171-6] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [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: 09/24/2018] [Accepted: 02/06/2020] [Indexed: 01/01/2023] Open
Abstract
While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations. We report nanopore sequencing of full-length cDNA from CLL samples with and without SF3B1 mutation, as well as normal B cell samples, giving a total of 149 million pass reads. We present FLAIR (Full-Length Alternative Isoform analysis of RNA), a computational workflow to identify high-confidence transcripts, perform differential splicing event analysis, and differential isoform analysis. Using nanopore reads, we demonstrate differential 3' splice site changes associated with SF3B1 mutation, agreeing with previous studies. We also observe a strong downregulation of intron retention events associated with SF3B1 mutation. Full-length transcript analysis links multiple alternative splicing events together and allows for better estimates of the abundance of productive versus unproductive isoforms. Our work demonstrates the potential utility of nanopore sequencing for cancer and splicing research.
Collapse
Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Cameron M Soulette
- Department of Molecular Cell & Developmental Biology, University of California, Santa Cruz, CA, 95062, USA
| | - Marijke J van Baren
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Kevyn Hart
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institiute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA.
| |
Collapse
|
18
|
Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
Collapse
|
19
|
Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z. Genomic basis for RNA alterations in cancer. Nature 2020; 578:129-136. [PMID: 32025019 PMCID: PMC7054216 DOI: 10.1038/s41586-020-1970-0] [Citation(s) in RCA: 226] [Impact Index Per Article: 56.5] [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: 03/29/2018] [Accepted: 12/11/2019] [Indexed: 01/27/2023]
Abstract
Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
Collapse
Affiliation(s)
| | - Claudia Calabrese
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- 0000 0001 2156 2780grid.5801.cETH Zurich, Zurich, Switzerland ,0000 0001 2171 9952grid.51462.34Memorial Sloan Kettering Cancer Center, New York, NY USA ,000000041936877Xgrid.5386.8Weill Cornell Medical College, New York, NY USA ,0000 0001 2223 3006grid.419765.8SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,0000 0004 0478 9977grid.412004.3University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- 0000 0001 2180 6431grid.4280.eNational University of Singapore, Singapore, Singapore ,0000 0004 0620 715Xgrid.418377.eGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- 0000 0001 2256 9319grid.11135.37Peking University, Beijing, China
| | - André Kahles
- 0000 0001 2156 2780grid.5801.cETH Zurich, Zurich, Switzerland ,0000 0001 2171 9952grid.51462.34Memorial Sloan Kettering Cancer Center, New York, NY USA ,0000 0001 2223 3006grid.419765.8SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,0000 0004 0478 9977grid.412004.3University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- 0000 0001 2156 2780grid.5801.cETH Zurich, Zurich, Switzerland ,0000 0001 2171 9952grid.51462.34Memorial Sloan Kettering Cancer Center, New York, NY USA ,0000 0001 2223 3006grid.419765.8SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,0000 0004 0478 9977grid.412004.3University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- 0000 0001 2256 9319grid.11135.37Peking University, Beijing, China
| | - Yuichi Shiraishi
- 0000 0001 2151 536Xgrid.26999.3dThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- 0000 0001 0740 6917grid.205975.cUniversity of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- 0000 0004 0626 690Xgrid.419890.dOntario Institute for Cancer Research, Toronto, Ontario, Canada ,0000 0001 2297 6811grid.266102.1University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- 0000 0004 0626 690Xgrid.419890.dOntario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- 0000 0001 2256 9319grid.11135.37Peking University, Beijing, China
| | - Junjun Zhang
- 0000 0004 0626 690Xgrid.419890.dOntario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- 0000 0001 2193 314Xgrid.8756.cUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- 0000 0004 0495 846Xgrid.4709.aEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- 0000000122483208grid.10698.36The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- 0000 0001 1014 0849grid.419491.0Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- 0000000121901201grid.83440.3bUniversity College London, London, UK
| | - Jan O. Korbel
- 0000 0004 0495 846Xgrid.4709.aEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- 0000 0001 0740 6917grid.205975.cUniversity of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- 0000 0001 1014 0849grid.419491.0Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- 0000 0004 0620 715Xgrid.418377.eGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,0000 0004 1937 0626grid.4714.6Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.34Broad Institute, Cambridge, MA USA ,0000 0001 2106 9910grid.65499.37Dana-Farber Cancer Institute, Boston, MA USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.1Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- 0000 0001 2156 2780grid.5801.cETH Zurich, Zurich, Switzerland ,0000 0001 2171 9952grid.51462.34Memorial Sloan Kettering Cancer Center, New York, NY USA ,0000 0001 2223 3006grid.419765.8SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,0000 0004 0478 9977grid.412004.3University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- 0000 0004 0620 715Xgrid.418377.eGenome Institute of Singapore, Singapore, Singapore ,0000 0004 0385 0924grid.428397.3Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- 0000 0004 0495 846Xgrid.4709.aEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- 0000 0004 0626 690Xgrid.419890.dOntario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- 0000 0004 0626 690Xgrid.419890.dOntario Institute for Cancer Research, Toronto, Ontario, Canada ,0000 0001 2157 2938grid.17063.33University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- 0000 0001 2160 926Xgrid.39382.33Baylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.34Broad Institute, Cambridge, MA USA ,0000 0001 2106 9910grid.65499.37Dana-Farber Cancer Institute, Boston, MA USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China ,China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- 0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Angela N. Brooks
- 0000 0001 0740 6917grid.205975.cUniversity of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.34Broad Institute, Cambridge, MA USA ,0000 0001 2106 9910grid.65499.37Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- 0000 0004 0620 715Xgrid.418377.eGenome Institute of Singapore, Singapore, Singapore ,0000 0004 0620 9745grid.410724.4National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- 0000 0001 2156 2780grid.5801.cETH Zurich, Zurich, Switzerland ,0000 0001 2171 9952grid.51462.34Memorial Sloan Kettering Cancer Center, New York, NY USA ,000000041936877Xgrid.5386.8Weill Cornell Medical College, New York, NY USA ,0000 0001 2223 3006grid.419765.8SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,0000 0004 0478 9977grid.412004.3University Hospital Zurich, Zurich, Switzerland
| | - Roland F. Schwarz
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,0000 0001 1014 0849grid.419491.0Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,0000 0004 0492 0584grid.7497.dGerman Cancer Consortium (DKTK), partner site Berlin, Germany ,0000 0004 0492 0584grid.7497.dGerman Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,0000 0004 0495 846Xgrid.4709.aEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,0000 0004 0492 0584grid.7497.dGerman Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- 0000 0001 2256 9319grid.11135.37Peking University, Beijing, China
| | | |
Collapse
|
20
|
Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Ten Hacken E, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, DeCaprio JA, Getz G, Reed R, Carrasco RD, Wu CJ, Wang L. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell 2019; 35:283-296.e5. [PMID: 30712845 PMCID: PMC6372356 DOI: 10.1016/j.ccell.2018.12.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/24/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
Abstract
SF3B1 is recurrently mutated in chronic lymphocytic leukemia (CLL), but its role in the pathogenesis of CLL remains elusive. Here, we show that conditional expression of Sf3b1-K700E mutation in mouse B cells disrupts pre-mRNA splicing, alters cell development, and induces a state of cellular senescence. Combination with Atm deletion leads to the overcoming of cellular senescence and the development of CLL-like disease in elderly mice. These CLL-like cells show genome instability and dysregulation of multiple CLL-associated cellular processes, including deregulated B cell receptor signaling, which we also identified in human CLL cases. Notably, human CLLs harboring SF3B1 mutations exhibit altered response to BTK inhibition. Our murine model of CLL thus provides insights into human CLL disease mechanisms and treatment.
Collapse
MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Alternative Splicing
- Animals
- Antineoplastic Agents/pharmacology
- Ataxia Telangiectasia Mutated Proteins/deficiency
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/metabolism
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Cellular Senescence/drug effects
- DNA Damage
- Gene Deletion
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Mutant Strains
- Mutation
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/metabolism
- Phenotype
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Piperidines
- Protein Kinase Inhibitors/pharmacology
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- RNA Splicing Factors/genetics
- RNA Splicing Factors/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Rutendo G Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Zachary J Cartun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fara Faye D Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Youzhong Wan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Sarah E M Herman
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | | | | | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dean R Campagna
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ruben D Carrasco
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Systems Biology, Beckman Research Institute, City of Hope, Monrovia, CA, USA.
| |
Collapse
|
21
|
Hacken ET, Valentin R, Regis FFD, Sun J, Yin S, Werner L, Deng J, Gruber M, Wong J, Zheng M, Gill AL, Seiler M, Smith P, Thomas M, Buonamici S, Ghia EM, Kim E, Rassenti LZ, Burger JA, Kipps TJ, Meyerson ML, Bachireddy P, Wang L, Reed R, Neuberg D, Carrasco RD, Brooks AN, Letai A, Davids MS, Wu CJ. Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies. JCI Insight 2018; 3:121438. [PMID: 30282833 PMCID: PMC6237462 DOI: 10.1172/jci.insight.121438] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022] Open
Abstract
The identification of targetable vulnerabilities in the context of therapeutic resistance is a key challenge in cancer treatment. We detected pervasive aberrant splicing as a characteristic feature of chronic lymphocytic leukemia (CLL), irrespective of splicing factor mutation status, which was associated with sensitivity to the spliceosome modulator, E7107. Splicing modulation affected CLL survival pathways, including members of the B cell lymphoma-2 (BCL2) family of proteins, remodeling antiapoptotic dependencies of human and murine CLL cells. E7107 treatment decreased myeloid cell leukemia-1 (MCL1) dependence and increased BCL2 dependence, sensitizing primary human CLL cells and venetoclax-resistant CLL-like cells from an Eμ-TCL1-based adoptive transfer murine model to treatment with the BCL2 inhibitor venetoclax. Our data provide preclinical rationale to support the combination of venetoclax with splicing modulators to reprogram apoptotic dependencies in CLL for treating venetoclax-resistant CLL cases.
Collapse
Affiliation(s)
- Elisa ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Rebecca Valentin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Fara Faye D. Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lillian Werner
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jing Deng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jessica Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mei Zheng
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Amy L. Gill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Peter Smith
- H3 Biomedicine Inc., Cambridge, Massachusetts, USA
| | | | | | - Emanuela M. Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Ekaterina Kim
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Jan A. Burger
- University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Matthew L. Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Pavan Bachireddy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ruben D. Carrasco
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| |
Collapse
|
22
|
Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. eLife 2018; 7:37184. [PMID: 30059005 PMCID: PMC6103745 DOI: 10.7554/elife.37184] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [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] [Received: 04/01/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of mRNA precursors represents a key gene expression regulatory step and permits the generation of distinct protein products with diverse functions. In a genome-scale expression screen for inducers of the epithelial-to-mesenchymal transition (EMT), we found a striking enrichment of RNA-binding proteins. We validated that QKI and RBFOX1 were necessary and sufficient to induce an intermediate mesenchymal cell state and increased tumorigenicity. Using RNA-seq and eCLIP analysis, we found that QKI and RBFOX1 coordinately regulated the splicing and function of the actin-binding protein FLNB, which plays a causal role in the regulation of EMT. Specifically, the skipping of FLNB exon 30 induced EMT by releasing the FOXC1 transcription factor. Moreover, skipping of FLNB exon 30 is strongly associated with EMT gene signatures in basal-like breast cancer patient samples. These observations identify a specific dysregulation of splicing, which regulates tumor cell plasticity and is frequently observed in human cancer. As the human body develops, countless cells change from one state into another. Two important cell states are known as epithelial and mesenchymal. Cells in the epithelial state tend to be tightly connected and form barriers, like skin cells. Mesenchymal state cells are loosely organized, move around more and make up connective tissues. Some cells alternate between these states via an epithelial-to-mesenchymal transition (EMT for short) and back again. Without this transition, certain organs would not develop and wounds would not heal. Yet, cancer cells also use this transition to spread to distant sites of the body. Such cancers are often the most aggressive, and therefore the most deadly. The epithelial-to-mesenchymal transition is dynamically regulated in a reversible manner. For example, the genes for some proteins might only be active in the epithelial state and further reinforce this state by turning on other ‘epithelial genes’. Alternatively, there might be differences in the processing of mRNA molecules – the intermediate molecules between DNA and protein – that result in the production of different proteins in epithelial and mesenchymal cells. Li, Choi et al. wanted to know which of the thousands of human genes can endow epithelial state cells with mesenchymal characteristics. A better understanding of the switch could help to prevent cancers undergoing an epithelial-to-mesenchymal transition. From a large-scale experiment in human breast cancer cells, Li, Choi et al. found that a group of proteins that bind and modify mRNA molecules are important for the epithelial-to-mesenchymal transition. Two proteins in particular promoted the transition, most likely by binding to the mRNA of a third protein called FLNB and removing a small piece of it. FLNB normally works to prevent the epithelial-to-mesenchymal transition, but the smaller protein encoded by the shorter mRNA promoted the transition by turning on ‘mesenchymal genes’. This switching between different FLNB proteins happens in some of the more aggressive breast cancers, which also contain mesenchymal cells. Finding out which FLNB protein is made in a given cancer may provide an indication of its aggressiveness. Also, looking for drugs that can target the mRNA-binding proteins or FLNB may one day lead to new treatments for some of the most aggressive breast cancers.
Collapse
Affiliation(s)
- Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Peter S Choi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christine L Chaffer
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States.,Garvan Institute of Medical Research, Sydney, Australia
| | - Katherine Labella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jong Wook Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nina Ilic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Seav Huong Ly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Chao Dai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Kimberly Hagel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Ole Gjoerup
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Shom Goel
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, United States
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jean J Zhao
- Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Angela N Brooks
- University of California, Santa Cruz, Santa Cruz, United States
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research and MIT, Cambridge, United States
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| |
Collapse
|
23
|
Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell 2017; 32:884. [PMID: 29232558 DOI: 10.1016/j.ccell.2017.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
24
|
Beale H, Lam DL, Vivian J, Newton Y, Shah AT, Bjork I, Goldstein T, Brooks AN, Stuart J, Salama S, Sweet-Cordero EA, Haussler1 D, Morozova O. Abstract 2466: Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In the UC Santa Cruz Treehouse Childhood Cancer Initiative (treehousegenomics.soe.ucsc.edu), we are exploring the utility of using RNA-Seq analysis of tumor samples from children to identify potential novel therapeutic options for each individual. Within a single RNA-Seq data set, the gene expression measurements are not equally accurate. The identification of activated, druggable pathways requires accurate gene-level expression measurements.
We receive samples from a variety of clinical and research settings, and the quantity and complexity of the available input material and the depth of sequencing differ. These factors inspired us to develop a tool that will allow us to identify accurate measurements in most RNA-Seq samples we receive.
First, we characterized the relationship between depth of sequencing and the accuracy of the gene expression measurement. We analyzed subsets of reads in samples with more than 50 million Uniquely Mapped, Exonic, Non-duplicate (UMEND) reads. UMEND reads typically constitute over 80% of the reads in a high quality experiment with sufficient starting material. We compared gene expression across the subsets of reads to calculate how many UMEND reads are required to produce consistent measurements. We found that, on average, genes expressed at 1-5 TPM in our data require 30 million reads to be accurately measured. For this calculation, we define accuracy as the condition in which 75% of genes are measured to within 25% of the true value.
Secondly, we use these known relationships to identify genes that have been accurately measured in our tumor RNA-Seq samples. For a sample with 15 million UMEND reads, we find that genes expressed above 5 TPM can be accurately measured and are retained. In the first twelve samples analyzed, samples with more than 10 million UMEND reads retained at least 46% of the genes expressed above zero. We exclude as references those samples with fewer than 10 million UMEND reads due to the marked gene loss after thresholding for this group.
Using accurately measured genes allows us to more confidently assess similarity to other samples, identify enriched pathways, and confirm the expression of drug targets and related molecules under consideration. For example, we reconsidered the CDK4 inhibitor Palbociclib in one patient because the expression of RB1, downstream effector required for Palbociclib-mediated tumor cell death, was under our accuracy threshold. Accuracy thresholds can also be used in experiment planning.
Accuracy thresholding allows us to better assess the value of an RNA-Seq data set and, if necessary, identify the subset of genes whose expression can be confidently considered in a clinical setting. Our experience points to the importance of careful quality control in this process.
Citation Format: Holly Beale, Du Linh Lam, John Vivian, Yulia Newton, Avanthi Tayi Shah, Isabel Bjork, Ted Goldstein, Angela N. Brooks, Josh Stuart, Sofie Salama, E. Alejandro Sweet-Cordero, David Haussler1, Olena Morozova. Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2466. doi:10.1158/1538-7445.AM2017-2466
Collapse
|
25
|
Davidson NR, Brazma A, Brooks AN, Calabrese C, Fonseca NA, Goke J, He Y, Hu X, Kahles A, Lehmann KV, Liu F, Rätsch G, Li S, Schwarz RF, Yang M, Zhang Z, Zhang F, Zheng L. Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
We present a novel method to identify cancer driver genes that jointly examines any number of diverse transcriptomic alterations with the goal to uncover highly recurrent and heterogeneous patterns in 1190 samples across 26 cancer types as part of the PanCancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC).
Motivation:
Previous pan-cancer genomic studies have focused on the analysis of somatic mutations as the driver of phenotypic changes. Here, we propose a method to integrate a wide variety of RNA and DNA changes to redefine the concept of driver events and account for the transcriptome’s role in tumorigenesis. PTK2 provides a motivating example, since it has many RNA alterations that correlate with patient survival, such as overexpression, exon-skips, and alternative promoter usage.
In our analysis, we integrate an unprecedented amount of various alterations including gene fusions, RNA editing, alternative splicing, expression outliers, alternative promoters, allele specific expression, and somatic mutations. This enables us to also identify mutually exclusive (MutE) and co-occurring (CoO) patterns between different types of alterations within a gene.
Methods:
Our method has 3 main strengths: flexibility to handle any number or type of alteration, sensitivity to different frequencies of alterations so rare events are not lost in the recurrence analysis, and diversity of ranking such that genes with multiple alterations are prioritized. Our method is summarized in two steps:
1) Identify genes that are both recurrently and heterogeneously altered across many samples by calculating a rank-based score for each gene.
2) Identify MutE and CoO patterns between alteration types for the genes identified in the previous step.
To ensure that alterations were comparable, we applied a thresholding model to binarize all alterations for gene-sample pairs, allowing us to account for the properties of the different modalities involved.
Step 1 of our method calculates a score for each gene that takes into account: 1) the number of alterations to a gene across all samples, 2) the rarity of each alteration, and 3) how many types of alterations are observed per gene. The score is then used to rank the genes and top genes are considered for MutE and CoO analyses.
Results:
Our top 100 ranked genes were highly enriched for cancer census genes (adjusted p-value: 2.06e-9), indicating that we identify cancer relevant genes. Our top five ranked cancer census genes were IGF2, ERBB2, RARA, CREBBP, and ARID1A; all of which had at least 4 of 7 possible alterations, showing our scoring method prioritizes genes with diverse alterations. We also found that alternative promoter usage and alternative splicing were highly co-occurring alterations, with PTK2 having the highest co-occurrence between them. In summary, we propose a new method to analyze various RNA disruptions and show it can yield new insights beyond genomic variation.
Citation Format: Natalie R. Davidson, PanCancer Analysis of Whole Genomes 3 (PCAWG-3) for ICGC, Alvis Brazma, Angela N. Brooks, Claudia Calabrese, Nuno A. Fonseca, Jonathan Goke, Yao He, Xueda Hu, Andre Kahles, Kjong-Van Lehmann, Fenglin Liu, Gunnar Rätsch, Siliang Li, Roland F. Schwarz, Mingyu Yang, Zemin Zhang, Fan Zhang, Liangtao Zheng. Integrating diverse transcriptomic alterations to identify cancer-relevant genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 389. doi:10.1158/1538-7445.AM2017-389
Collapse
Affiliation(s)
| | - Alvis Brazma
- 2European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, United Kingdom
| | | | - Claudia Calabrese
- 2European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, United Kingdom
| | - Nuno A. Fonseca
- 2European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, United Kingdom
| | - Jonathan Goke
- 4Genome Institute of Singapore, Singapore, Singapore
| | - Yao He
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Xueda Hu
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | | | | | - Fenglin Liu
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | | | | | | | - Mingyu Yang
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Zemin Zhang
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Fan Zhang
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Liangtao Zheng
- 5Peking-Tsinghua Center for Life Sciences, Beijing, China
| | | |
Collapse
|
26
|
Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O. RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation. J Biol Chem 2017; 292:13381-13390. [PMID: 28655759 DOI: 10.1074/jbc.m117.784371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/14/2017] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, precursor mRNA (pre-mRNA) splicing removes non-coding intron sequences to produce mature mRNA. This removal is controlled in part by RNA-binding proteins that regulate alternative splicing decisions through interactions with the splicing machinery. RNA binding motif protein 25 (RBM25) is a putative splicing factor strongly conserved across eukaryotic lineages. However, the role of RBM25 in global splicing regulation and its cellular functions are unknown. Here we show that RBM25 is required for the viability of multiple human cell lines, suggesting that it could play a key role in pre-mRNA splicing. Indeed, transcriptome-wide analysis of splicing events demonstrated that RBM25 regulates a large fraction of alternatively spliced exons throughout the human genome. Moreover, proteomic analysis indicated that RBM25 interacts with components of the early spliceosome and regulators of alternative splicing. Previously, we identified an RBM25 species that is mono-methylated at lysine 77 (RBM25K77me1), and here we used quantitative mass spectrometry to show that RBM25K77me1 is abundant in multiple human cell lines. We also identified a region of RBM25 spanning Lys-77 that binds with high affinity to serine- and arginine-rich splicing factor 2 (SRSF2), a crucial protein in exon definition, but only when Lys-77 is unmethylated. Together, our findings uncover a pivotal role for RBM25 as an essential regulator of alternative splicing and reveal a new potential mechanism for regulation of pre-mRNA splicing by lysine methylation of a splicing factor.
Collapse
Affiliation(s)
- Scott M Carlson
- From the Department of Biology, Stanford University, Stanford, California 94305
| | | | - Ze Yang
- From the Department of Biology, Stanford University, Stanford, California 94305
| | - Joshua E Elias
- the Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California 94305, and
| | - Angela N Brooks
- Biomolecular Engineering, University of California, Santa Cruz, California 95060
| | - Or Gozani
- From the Department of Biology, Stanford University, Stanford, California 94305,
| |
Collapse
|
27
|
Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 2016; 30:750-763. [PMID: 27818134 PMCID: PMC5127278 DOI: 10.1016/j.ccell.2016.10.005] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/01/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022]
Abstract
Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.
Collapse
Affiliation(s)
- Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Angela N Brooks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; University of California, Santa Cruz, CA 95064, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Youzhong Wan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; National Engineering Laboratory of AIDS Vaccine, School of Life Science, Jilin University, Changchun, Jilin, PRC
| | - Rutendo Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shuqiang Li
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Sarah Hergert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Joshua Z Levin
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Lin Fan
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | | | | | | | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacey Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Donald B Bloch
- Center for Immunology and Inflammatory Disease, Massachusetts General Hospital, Boston, MA 02115, USA
| | | | - Dan A Landau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David S DeLuca
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Matthew M Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Dana 540, 44 Binney Street, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
28
|
Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell 2016; 30:214-228. [PMID: 27478040 PMCID: PMC5003022 DOI: 10.1016/j.ccell.2016.06.022] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 01/19/2023]
Abstract
Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas. We present an expression-based variant-impact phenotyping (eVIP) method that uses gene expression changes to distinguish impactful from neutral somatic mutations. eVIP identified 69% of mutations analyzed as impactful and 31% as functionally neutral. A subset of the impactful mutations induces xenograft tumor formation in mice and/or confers resistance to cellular EGFR inhibition. Among these impactful variants are rare somatic, clinically actionable variants including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and multiple BRAF variants, demonstrating that rare mutations can be functionally important in cancer.
Collapse
Affiliation(s)
- Alice H. Berger
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Angela N. Brooks
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
| | - Marcin Imielinski
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | | | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Sasha Pantel
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Jacqueline Watson
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Joshua D. Campbell
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | | | | | | | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
| | - Bang Wong
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Todd R. Golub
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Address correspondence to M.M. () or J.S.B. ()
| | - Jesse S. Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA
- Address correspondence to M.M. () or J.S.B. ()
| |
Collapse
|
29
|
Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Kaplan N, Root D, Narayan R, Natoli T, Lahr D, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. Abstract 4368: High-throughput phenotyping of lung cancer somatic mutations. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent cancer genome sequencing and analysis has identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood, limiting the use of this genetic knowledge for clinical decision-making. Here we describe a new high-throughput approach, expression-based variant impact phenotyping (eVIP), which uses gene expression changes to infer somatic mutation impact. We generated a lentiviral expression library representing 53 genes and 194 somatic mutations identified in primary lung adenocarcinomas. Next, we introduced this library into A549 lung adenocarcinoma cells and 96 hours later performed gene expression profiling using Luminex-based L1000 profiling. We built a computational pipeline, eVIP, to compare mutant and wild-type expression signatures to infer whether variants were gain-of-function, change-of-function, loss-of-function, or neutral. Overall, eVIP identified 69% of mutations as impactful whereas 31% appeared functionally neutral. A very high rate, 92%, of missense mutations in the KEAP1 and STK11 tumor suppressor genes were found to inactivate or diminish protein function. As a complementary approach, we assessed which mutations are epistatic to EGFR or capable of initiating xenograft tumor formation in vivo. A subset of the impactful mutations identified by eVIP could induce xenograft tumor formation in mice and/or confer resistance to cellular EGFR inhibition. Among these mutations were 20 rare or non-canonical somatic variants in clinically-actionable or -relevant oncogenes including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and PIK3CA E600K. eVIP can, in principle, characterize any genetic variant, independent of prior knowledge of gene function. Further application of eVIP should significantly advance the pace of functional characterization of mutations identified from genome sequencing.
Citation Format: Alice H. Berger, Angela N. Brooks, Xiaoyun Wu, Yashaswi Shrestha, Candace Chouinard, Federica Piccioni, Mukta Bagul, Atanas Kamburov, Marcin Imielinski, Larson Hogstrom, Cong Zhu, Xiaoping Yang, Sasha Pantel, Ryo Sakai, Nathan Kaplan, David Root, Rajiv Narayan, Ted Natoli, David Lahr, Itay Tirosh, Pablo Tamayo, Gad Getz, Bang Wong, John Doench, Aravind Subramanian, Todd R. Golub, Matthew Meyerson, Jesse S. Boehm. High-throughput phenotyping of lung cancer somatic mutations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4368.
Collapse
|
30
|
Wang L, Gambe R, Fan J, Brooks AN, Sun J, Neuberg D, Kharchenko P, Meyerson M, Fleming MD, Ebert BL, Carrasco R, Wu CJ. Abstract 669: Compound heterozygous Sf3b1-K700E mutation and Atm deletion in B cells leads to CLL in mice. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Unbiased next-generation sequencing using primary samples has identified SF3B1 as among the most frequently mutated genes in chronic lymphocytic leukemia (CLL). These mutations localize to a restricted gene region, with more than 50% at the K700E site. The presence of mutation is associated with poor clinical outcomes. These lines of evidence together emphasize the high priority for gaining an understanding of role of SF3B1 in CLL. However, the mechanistic basis for how mutated SF3B1 impacts CLL remains unknown. Prior transcriptomic studies using primary CLL samples have led to the appreciation of altered RNA splicing induced by this mutated gene, but studies of the functional impact of mutated SF3B1 in primary human samples have been complicated by its variable mutant allele frequency across samples as well as its common co-occurrence with other diverse gene mutations. We therefore generated a mouse line that conditionally expressed heterozygous Sf3b1-K700E mutation in B lineage cells.
We sought to characterize the effects of Sf3b1-K700E on RNA splicing and B cell function in this in vivo model. By RNA-sequencing of splenic B cells from wild-type and mutant mice (n = 3, each), we detected, classified, and quantified 54 differentially spliced transcripts (p10%) using the tool JuncBASE. Consistent with prior findings in human CLL samples, the splice variants in our mouse model were highly enriched with altered selection of 3’ splice sites (49 of 54 events, p<0.001), suggesting that Sf3b1-K700E mutation in the mouse lines cause altered RNA splicing in vivo and functions in a manner faithful to the human leukemia. B cell characterization of the mutant mice revealed that expression of Sf3b1-K700E caused subtle impairments in B cell development and function, and induced a state of cellular senescence based on gene expression and secretome characterization. Mice with heterozygous Sf3b1-K700E did not develop evidence of CLL-associated immunopathologic changes, even with prolonged aging to 24 months. Nevertheless, expression of Sf3b1-K700E with heterozygous deletion of Atm in B cells led to the overcoming of cellular senescence and resulted in the accumulation of clonal B220+CD5+ cells in peripheral blood, marrow, and spleen of elderly mice. We thus dissect the impact of mutated SF3B1 individually and in combination with Atm deletion on paving the path towards B cell leukemogenesis. This novel murine model faithfully recapitulates features of human CLL and has the potential to shed light on mechanisms of cooperation between Atm deletion and SF3B1 mutation in the pathogenesis of CLL.
Citation Format: Lili Wang, Rutendo Gambe, Jean Fan, Angela N. Brooks, Jing Sun, Donna Neuberg, Peter Kharchenko, Matthew Meyerson, Mark D. Fleming, Benjamin L. Ebert, Ruben Carrasco, Catherine J. Wu. Compound heterozygous Sf3b1-K700E mutation and Atm deletion in B cells leads to CLL in mice. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 669.
Collapse
Affiliation(s)
- Lili Wang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Jean Fan
- 2Harvard Medical School, Boston, MA
| | | | - Jing Sun
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AAM, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho T, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J(J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni H, Drummond J, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med 2016; 374:135-45. [PMID: 26536169 PMCID: PMC4775252 DOI: 10.1056/nejmoa1505917] [Citation(s) in RCA: 887] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
Collapse
Affiliation(s)
- W. Marston Linehan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | - Paul T. Spellman
- Oregon Health & Science University, Portland, OR
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | | | | | | | | | | | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Laura Schmidt
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Cathy D. Vocke
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Myron Peto
- Oregon Health & Science University, Portland, OR
| | | | | | | | - Samira Brooks
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Angela N. Brooks
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - A. Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Gordon Saksena
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Scott Haake
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jun Li
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Han Liang
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Yiling Lu
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rehan Akbani
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Pavana Anur
- Oregon Health & Science University, Portland, OR
| | - Donald Bottaro
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | | | | | | | - A. Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James Hsieh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - William Y. Kim
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Maria J. Merino
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Satish Tickoo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel Crain
- The International Genomics Consortium, Phoenix, AZ
| | | | - Kevin Lau
- The International Genomics Consortium, Phoenix, AZ
| | | | - Scott Morris
- The International Genomics Consortium, Phoenix, AZ
| | | | | | | | | | - Mark Sherman
- The International Genomics Consortium, Phoenix, AZ
| | | | - Peggy Yena
- The International Genomics Consortium, Phoenix, AZ
| | - Melissa T. Avedon
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Mark Gerken
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Kristen M. Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Nilsa C. Ramirez
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Tracie Santos
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Lisa Wise
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Erik Zmuda
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - John A. Demchok
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Carolyn M. Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Margi Sheth
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Roy Tarnuzzer
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Zhining Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Liming Yang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Brenda Ayala
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Julien Baboud
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Sudha Chudamani
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Jia Liu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Laxmi Lolla
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Rashi Naresh
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Todd Pihl
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Qiang Sun
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Yunhu Wan
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Ye Wu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Miruna Balasundaram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Saianand Balu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rameen Beroukhim
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Tom Bodenheimer
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Rebecca Carlsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Scott L. Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Hsu Chao
- Baylor College of Medicine, Houston, TX
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Amanda Clarke
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | | | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - Stacey B. Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Ranabir Guin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - D. Neil Hayes
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert A. Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Alan P. Hoyle
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven J.M. Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Corbin D. Jones
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Jie Li
- Baylor College of Medicine, Houston, TX
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Michael Mayo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Shaowu Meng
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Lisle E. Mose
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Joel S. Parker
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeffrey Roach
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven E. Schumacher
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Yan Shi
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Janae V. Simons
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Payal Sipahimalani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Tara Skelly
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Carrie Sougnez
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Donghui Tan
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Min Wang
- Baylor College of Medicine, Houston, TX
| | | | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Junyuan Wu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liu Xi
- Baylor College of Medicine, Houston, TX
| | - Jane Zhou
- Baylor College of Medicine, Houston, TX
| | | | | | - Yao Fu
- Yale University, New Haven, CT
| | | | - David Haussler
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Phillip Lai
- University of Southern California, Los Angeles, CA
| | - Shiyun Ling
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Amie Radenbaugh
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | | | | | - Jingchun Zhu
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Monique Albert
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - J. Todd Auman
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - John Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheldon Bastacky
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Julie Bergsten
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | - Lori Boice
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeff Boyd
- Fox Chase Cancer Center, Philadelphia, PA
| | | | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Erin Curley
- The International Genomics Consortium, Phoenix, AZ
| | - Benjamin Davies
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - April DeVolk
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Rajiv Dhir
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - John Eckman
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Jay Engel
- Kingston General Hospital, Kingston, Ontario, Canada
| | - Jodi Harr
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Ronald Hrebinko
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Mei Huang
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Mary Iacocca
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Bruce Jacobs
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Michael Lobis
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Jodi K. Maranchie
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Scott McMeekin
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jerome Myers
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Joel Nelson
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Anil Parwani
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Nicholas Petrelli
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Brenda Rabeno
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Somak Roy
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Joel Slaton
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | | | - Leigh Thorne
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelinda Tucker
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | | | | | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| |
Collapse
|
32
|
Brooks AN, Ge Y, Chau K, Freeman SS, Saksena G, Pedamallu CS, Meyerson M. Abstract B2-21: Identification of somatic RNA splicing alterations in human cancers. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent whole-exome sequencing studies have found that somatic mutations frequently occur in splicing factors across multiple cancer types, supporting the need to systematically and globally characterize splicing alterations across human cancers. Somatic alterations that affect RNA processing of cancer genes may be caused by multiple mechanisms, including mutations in splicing factors, mutations in cis-acting splice sites and other regulatory sequences, alterations in methylation, or alterations in chromatin structure. For a global look at somatic RNA splicing alterations, we are applying the Cancer Outlier Profile Analysis (COPA) approach on ~7,000 cancer transcriptomes from 12 tumor types in The Cancer Genome Atlas (TCGA) and investigating the underlying somatic mutations that cause these splicing alterations using matched whole-exome, whole-genome, and methylation data from these samples.
To identify and quantify alternative splicing in RNA-Seq data, including unannotated splicing events, we have further developed a computational pipeline called JuncBASE. To distinguish between cancer-specific splicing alterations and normal transcriptome variation, we are utilizing ~700 RNA-Seq libraries from healthy individuals from the Genotype-Tissue Expression (GTEx) project.
COPA analysis of outlier splicing events in lung adenocarcinomas and glioblastomas successfully identified known altered splicing events in MET and EGFR, respectively, that are caused by DNA level somatic mutations. The genomic mechanisms for novel somatic splicing events in known cancer genes such as FGFR3, as well as genes previously uncharacterized in cancer genomes, are currently being investigated.
To identify splicing events that may be novel somatic driver alterations, these events have been profiled using RNA-Seq data from the Cancer Cell Line Encyclopedia and are being used as biomarkers to identify genetic vulnerabilities in high-throughput shRNA screens. This work will have a significant impact on the identification of somatic splicing events that contribute to cancer pathogenesis.
Citation Format: Angela N. Brooks, Yawei Ge, Kevin Chau, Samuel S. Freeman, Gordon Saksena, Chandra Sekhar Pedamallu, Matthew Meyerson. Identification of somatic RNA splicing alterations in human cancers. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-21.
Collapse
Affiliation(s)
| | - Yawei Ge
- 2Harvard Medical School, Boston, MA,
| | | | | | | | | | | |
Collapse
|
33
|
Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Booth BW, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res 2015; 25:1771-80. [PMID: 26294686 PMCID: PMC4617972 DOI: 10.1101/gr.192518.115] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [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: 03/26/2015] [Accepted: 08/19/2015] [Indexed: 12/26/2022]
Abstract
Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence elements and activate or repress adjacent exons. Here, we used RNA interference and RNA-seq to identify splicing events regulated by 56 Drosophila proteins, some previously unknown to regulate splicing. Nearly all proteins affected alternative first exons, suggesting that RBPs play important roles in first exon choice. Half of the splicing events were regulated by multiple proteins, demonstrating extensive combinatorial regulation. We observed that SR and hnRNP proteins tend to act coordinately with each other, not antagonistically. We also identified a cross-regulatory network where splicing regulators affected the splicing of pre-mRNAs encoding other splicing regulators. This large-scale study substantially enhances our understanding of recent models of splicing regulation and provides a resource of thousands of exons that are regulated by 56 diverse RBPs.
Collapse
Affiliation(s)
- Angela N Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Broad Institute, Cambridge, Massachusetts 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Michael O Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Gemma May
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Li Yang
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Mohan Bolisetty
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Jane Landolin
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ken Wan
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Sandler
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Benjamin W Booth
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan E Celniker
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Steven E Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| |
Collapse
|
34
|
Berger AH, Brooks AN, Imielinski M, Cherniack A, Duke F, Kaplan N, Wala J, Meyerson M. Abstract PR08: NF1, MET, and RIT1 mutations are RAS-pathway driver events in lung adenocarcinoma. Mol Cancer Res 2014. [DOI: 10.1158/1557-3125.rasonc14-pr08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung adenocarcinoma is comprised of distinct mutational subtypes characterized by mutually exclusive oncogenic alterations such as EGFR and KRAS mutations. Identification of these oncogenic events has transformed treatment strategies and drug development for lung adenocarcinoma. However, such mutations have been identified in only 50-60% of lung adenocarcinoma cases in the United States.
We analyzed SNP array, exome, and RNA sequencing data from 230 primary lung adenocarcinomas to identify known and novel mutually exclusive driver events. MET exon 14 skipping was present in 10/230 tumors (4.3%) and only RNA sequencing data allowed robust detection of this event. To identify novel driver events, we performed a focused statistical analysis of the 87/230 tumors (38%) that lacked a mutation in MET or other known oncogenes. Copy number analysis revealed rare, focal amplifications of MET and ERBB2 that were enriched in this subset. Exome analysis revealed significant enrichment of TP53, KEAP1, NF1, and RIT1 mutations in the previously oncogene-negative subset. Of these mutated genes, only NF1 and RIT1 displayed mutual exclusivity with the other known and candidate driver events.
Whereas TP53, KEAP1, and NF1 are well-documented cancer genes, little is known about the role of RIT1 in human cancer. RIT1 is a RAS-subfamily small GTPase with significant homology to HRAS, NRAS, and KRAS. Mutations in RIT1 were present in ∼2% of cases and clustered in the switch II domain. Ectopic expression of mutated RIT1 in murine fibroblasts and human immortalized lung epithelial cells conferred anchorage-independent growth and tumor forming capability. cDNA sequencing identified a p.M90I missense mutation in the NCI-H2110 cell line. Knockdown of RIT1 in NCI-H2110 cells revealed the role of RIT1 in regulation of PI3K and MEK signaling. Consistently, combination PI3K/mTOR/MEK inhibition could inhibit cellular transformation induced by ectopic expression of mutated RIT1, and PI3K/mTOR inhibition suppressed in vivo tumor growth of NCI-H2110 cells.
Recently, RIT1 mutations were described in myeloid malignancies and Noonan syndrome. Our data, together with these reported observations, indicate that RIT1 is a RAS-pathway oncogene in lung adenocarcinoma. In addition, PI3K/mTOR inhibition with or without MEK inhibition should be explored as a therapeutic strategy for RIT1-mutated lung or other RIT1-mutated cancers. This work expands the number of U.S. lung adenocarcinoma tumors with identified driver events from 62% to 75% and nominates these additional alterations as candidate therapeutic targets.
This abstract is also presented as Poster B26.
Citation Format: Alice H. Berger, Angela N. Brooks, Marcin Imielinski, Andrew Cherniack, Fujiko Duke, Nathan Kaplan, Jeremiah Wala, Matthew Meyerson. NF1, MET, and RIT1 mutations are RAS-pathway driver events in lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr PR08. doi: 10.1158/1557-3125.RASONC14-PR08
Collapse
|
35
|
Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, Deluca DS, Brooks AN, Que J, Rustgi AK, Wong KK, Ligon KL, Liu XS, Marto JA, Meyerson M, Bass AJ. Abstract 1391: SOX2-p63 interaction and genomic co-localization in squamous cell carcinomas. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-1391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
SOX2 is a transcription factor essential for pluripotent stem cells and the development and maintenance of squamous epithelium. We previously reported SOX2 to be an oncogene subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs). Here, we aim to further characterize SOX2's function in SCC. We demonstrate that SOX2 binds to distinct genomic loci in SCCs than in embryonic stem (ES) cells through comparative ChIP-seq analysis. Through mass-spectrometric analysis following tandem-affinity immunopurification in SCCs we identify SOX2 interacts with another master squamous transcription factor, p63, instead of its partner in ES cells, OCT4. We find that genomic occupancy of SOX2 in SCC overlaps with that of p63 at a large number of loci and this SOX2-p63 coordinate binding is absent in ES cells. We further demonstrate that SOX2 and p63 jointly regulate gene expression, including the oncogene ETV4, which we find essential for SOX2-amplified SCC cell survival. Together, these findings demonstrate that SOX2's actions in SCC differ substantially from its role in pluripotency. The identification of novel SOX2-p63 interaction enables deeper characterization of SOX2's function in SCC and normal squamous epithelial physiology.
Citation Format: Hideo Watanabe, Qiuping Ma, Shouyong Peng, Guillaume Adelmant, Danielle Swain, Wenyu Song, Cameron Fox, Joshua M. Francis, Chandra Sekhar Pedamallu, David S. Deluca, Angela N. Brooks, Jianwen Que, Anil K. Rustgi, Kwok-kin Wong, Keith L. Ligon, X. Shirley Liu, Jarrod A. Marto, Matthew Meyerson, Adam J. Bass. SOX2-p63 interaction and genomic co-localization in squamous cell carcinomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1391. doi:10.1158/1538-7445.AM2014-1391
Collapse
Affiliation(s)
| | - Qiuping Ma
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - Wenyu Song
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | - Anil K. Rustgi
- 4University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | | | | | | | | | | |
Collapse
|
36
|
Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, DeLuca DS, Brooks AN, Wang S, Que J, Rustgi AK, Wong KK, Ligon KL, Liu XS, Marto JA, Meyerson M, Bass AJ. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. J Clin Invest 2014; 124:1636-45. [PMID: 24590290 DOI: 10.1172/jci71545] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022] Open
Abstract
The transcription factor SOX2 is an essential regulator of pluripotent stem cells and promotes development and maintenance of squamous epithelia. We previously reported that SOX2 is an oncogene and subject to highly recurrent genomic amplification in squamous cell carcinomas (SCCs). Here, we have further characterized the function of SOX2 in SCC. Using ChIP-seq analysis, we compared SOX2-regulated gene profiles in multiple SCC cell lines to ES cell profiles and determined that SOX2 binds to distinct genomic loci in SCCs. In SCCs, SOX2 preferentially interacts with the transcription factor p63, as opposed to the transcription factor OCT4, which is the preferred SOX2 binding partner in ES cells. SOX2 and p63 exhibited overlapping genomic occupancy at a large number of loci in SCCs; however, coordinate binding of SOX2 and p63 was absent in ES cells. We further demonstrated that SOX2 and p63 jointly regulate gene expression, including the oncogene ETV4, which was essential for SOX2-amplified SCC cell survival. Together, these findings demonstrate that the action of SOX2 in SCC differs substantially from its role in pluripotency. The identification of the SCC-associated interaction between SOX2 and p63 will enable deeper characterization the downstream targets of this interaction in SCC and normal squamous epithelial physiology.
Collapse
|
37
|
Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One 2014; 9:e87361. [PMID: 24498085 PMCID: PMC3909098 DOI: 10.1371/journal.pone.0087361] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [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: 06/28/2013] [Accepted: 12/20/2013] [Indexed: 01/23/2023] Open
Abstract
Although recurrent somatic mutations in the splicing factor U2AF1 (also known as U2AF35) have been identified in multiple cancer types, the effects of these mutations on the cancer transcriptome have yet to be fully elucidated. Here, we identified splicing alterations associated with U2AF1 mutations across distinct cancers using DNA and RNA sequencing data from The Cancer Genome Atlas (TCGA). Using RNA-Seq data from 182 lung adenocarcinomas and 167 acute myeloid leukemias (AML), in which U2AF1 is somatically mutated in 3-4% of cases, we identified 131 and 369 splicing alterations, respectively, that were significantly associated with U2AF1 mutation. Of these, 30 splicing alterations were statistically significant in both lung adenocarcinoma and AML, including three genes in the Cancer Gene Census, CTNNB1, CHCHD7, and PICALM. Cell line experiments expressing U2AF1 S34F in HeLa cells and in 293T cells provide further support that these altered splicing events are caused by U2AF1 mutation. Consistent with the function of U2AF1 in 3' splice site recognition, we found that S34F/Y mutations cause preferences for CAG over UAG 3' splice site sequences. This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types.
Collapse
Affiliation(s)
- Angela N. Brooks
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter S. Choi
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Luc de Waal
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tanaz Sharifnia
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marcin Imielinski
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gordon Saksena
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Chandra Sekhar Pedamallu
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrey Sivachenko
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mara Rosenberg
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Juliann Chmielecki
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Michael S. Lawrence
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David S. DeLuca
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Gad Getz
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
38
|
Brooks AN, Wan Y, Choi P, Jing R, DeLuca DS, Sougnez C, Chmielecki J, Imielinski M, Getz G, Wu CJ, Meyerson M. Abstract 3150: Characterizing the effects of somatic mutations in splice factors on the transcriptome. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies have identified recurrent somatic mutations in splice factors, including SF3B1 and U2AF1, in myelodysplastic syndromes, chronic lymphocytic leukemias, breast cancer, and lung adenocarcinoma. In one study, 91 tumor and matched normal whole-exomes were sequenced from patients with CLL and the second most frequently mutated gene was SF3B1. Analysis of 187 whole-exomes in lung adenocarcinoma and matched normals revealed recurrent somatic mutations in the splice factor U2AF1 in 3% of cases. In addition to U2AF1 mutations, recurrent truncating mutations were observed in a putative splice factor, RBM10, in 4% of lung adenocarcinomas. The recurrence of somatic mutations in splice factors in multiple tumor types suggests that alterations in RNA splicing may play an important role in tumorigenesis.
Although these mutations have been identified in cancer genomes, the effect on the cancer transcriptome has yet to be fully explored; therefore, we do not understand how mutations in splice factors can contribute to tumorigenesis. We hypothesize that somatic mutations in splice factors cause alterations in mRNA splicing of important cancer genes.
We are using a computational tool called JuncBASE to identify alternative splicing in tumor transcriptomes from RNA-Seq data. We are then associating somatic mutations in splice factors, found from whole-exome sequencing, with splicing signatures identified through RNA-Seq.
Preliminary results on the identification of splice events associated with SF3B1 mutations in CLL reveal novel isoforms of multiple genes specifically expressed in SF3B1 mutant samples. Additionally, we examined the effects of SF3B1, U2AF1, and RBM10 mutations on tumor transcriptomes using RNA-Seq data from The Cancer Genome Atlas.
Citation Format: Angela N. Brooks, Youzhong Wan, Peter Choi, Rui Jing, David S. DeLuca, Carrie Sougnez, Juliann Chmielecki, Marcin Imielinski, Gad Getz, Catherine J. Wu, Matthew Meyerson. Characterizing the effects of somatic mutations in splice factors on the transcriptome. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3150. doi:10.1158/1538-7445.AM2013-3150
Collapse
Affiliation(s)
| | | | - Peter Choi
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA 2011; 17:1884-94. [PMID: 21865603 PMCID: PMC3185920 DOI: 10.1261/rna.2696311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/08/2011] [Indexed: 05/22/2023]
Abstract
RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5' and 3' splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes.
Collapse
Affiliation(s)
- Angela N. Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Julie L. Aspden
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Anna I. Podgornaia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Donald C. Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Corresponding author.E-mail .
| |
Collapse
|
40
|
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SCR, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010; 330:1787-97. [PMID: 21177974 DOI: 10.1126/science.1198374] [Citation(s) in RCA: 899] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
Collapse
Affiliation(s)
-
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 2010; 21:193-202. [PMID: 20921232 DOI: 10.1101/gr.108662.110] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing is generally controlled by proteins that bind directly to regulatory sequence elements and either activate or repress splicing of adjacent splice sites in a target pre-mRNA. Here, we have combined RNAi and mRNA-seq to identify exons that are regulated by Pasilla (PS), the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2. We identified 405 splicing events in 323 genes that are significantly affected upon depletion of ps, many of which were annotated as being constitutively spliced. The sequence regions upstream and within PS-repressed exons and downstream from PS-activated exons are enriched for YCAY repeats, and these are consistent with the location of these motifs near NOVA-regulated exons in mammals. Thus, the RNA regulatory map of PS and NOVA1/2 is highly conserved between insects and mammals despite the fact that the target gene orthologs regulated by PS and NOVA1/2 are almost entirely nonoverlapping. This observation suggests that the regulatory codes of individual RNA binding proteins may be nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable.
Collapse
Affiliation(s)
- Angela N Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell 2009; 33:438-49. [PMID: 19250905 DOI: 10.1016/j.molcel.2009.01.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 12/17/2008] [Accepted: 01/09/2009] [Indexed: 01/11/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been traditionally seen as proteins packaging RNA nonspecifically into ribonucleoprotein particles (RNPs), but evidence suggests specific cellular functions on discrete target pre-mRNAs. Here we report genome-wide analysis of alternative splicing patterns regulated by four Drosophila homologs of the mammalian hnRNP A/B family (hrp36, hrp38, hrp40, and hrp48). Analysis of the global RNA-binding distributions of each protein revealed both small and extensively bound regions on target transcripts. A significant subset of RNAs were bound and regulated by more than one hnRNP protein, revealing a combinatorial network of interactions. In vitro RNA-binding site selection experiments (SELEX) identified distinct binding motif specificities for each protein, which were overrepresented in their respective regulated and bound transcripts. These results indicate that individual heterogeneous ribonucleoproteins have specific affinities for overlapping, but distinct, populations of target pre-mRNAs controlling their patterns of RNA processing.
Collapse
Affiliation(s)
- Marco Blanchette
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | |
Collapse
|
43
|
Hyatt MA, Gopalakrishnan GS, Bispham J, Gentili S, McMillen IC, Rhind SM, Rae MT, Kyle CE, Brooks AN, Jones C, Budge H, Walker D, Stephenson T, Symonds ME. Maternal nutrient restriction in early pregnancy programs hepatic mRNA expression of growth-related genes and liver size in adult male sheep. J Endocrinol 2007; 192:87-97. [PMID: 17210746 DOI: 10.1677/joe.1.06801] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The liver is a major metabolic and endocrine organ of critical importance in the regulation of growth and metabolism. Its function is determined by a complex interaction of nutritionally regulated counter-regulatory hormones. The extent to which hepatic endocrine sensitivity can be programed in utero and whether the resultant adaptations persist into adulthood is unknown and was therefore the subject of this study. Young adult male sheep born to mothers that were fed either a control diet (i.e.100% of total live weight-maintenance requirements) throughout gestation or 50% of that intake (i.e. nutrient restricted (NR)) from 0 to 95 days gestation and thereafter 100% of requirements (taking into account increasing fetal mass) were entered into the study. All mothers gave birth normally at term, the singleton offspring were weaned at 16 weeks, and then reared at pasture until 3 years of age when their livers were sampled. NR offspring were of similar birth and body weights at 3 years of age when they had disproportionately smaller livers than controls. The abundance of mRNA for GH, prolactin, and IGF-II receptors, plus hepatocyte growth factor and suppressor of cytokine signaling-3 were all lower in livers of NR offspring. In contrast, the abundance of the mitochondrial protein voltage-dependent anion channel and the pro-apoptotic factor Bax were up regulated relative to controls. In conclusion, maternal nutrient restriction in early gestation results in adult offspring with smaller livers. This may be mediated by alterations in both hepatic mitogenic and apoptotic factors.
Collapse
Affiliation(s)
- M A Hyatt
- Institute of Clinical Research, Centre for Reproduction and Early Life, The University of Nottingham, Nottingham, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.
Collapse
Affiliation(s)
- Ian J Macrae
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively.
Collapse
Affiliation(s)
- Peter Schattner
- Department of Biomolecular Engineering and the UCSC RNA Center, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | | | | |
Collapse
|
46
|
Brennan KA, Gopalakrishnan GS, Kurlak L, Rhind SM, Kyle CE, Brooks AN, Rae MT, Olson DM, Stephenson T, Symonds ME. Impact of maternal undernutrition and fetal number on glucocorticoid, growth hormone and insulin-like growth factor receptor mRNA abundance in the ovine fetal kidney. Reproduction 2005; 129:151-9. [PMID: 15695609 DOI: 10.1530/rep.1.00229] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Epidemiological and animal studies strongly indicate that the environment experienced in utero determines, in part, an individual's likelihood of developing cardiovascular disease in later life. This risk has been further linked to impaired kidney function, as a result of compromised development during fetal life. The present study therefore examined the influence of maternal nutrient restriction (NR), targeted at specific periods of kidney development during early to mid gestation, on the mRNA abundance of receptors for glucocorticoid (GCR), growth hormone (GHR) and insulin-like growth factors-I (IGF-IR) and -II (IGF-IIR), and the IGF-I and -II ligands. This was undertaken in both singleton and twin fetuses. At conception ewes were randomly allocated to either an adequately fed control group or one of four nutrient-restricted groups that were fed half the control amount from 0 to 30, 31 to 65, 66 to 110 or 0 to 110 days gestation. At 110 days gestation all ewes were humanely euthanased and fetal kidneys and surrounding adipose tissue sampled. There was no effect of NR or fetal number on kidney weight, shape or nephron number, but the surrounding fat mass was increased in singleton fetuses exposed to NR for 110 days. An increase in kidney mRNA abundance with NR only occurred in singleton fetuses where IGF-IR mRNA was enhanced with NR from 66-110 days gestation. In twin fetuses, NR had no effect on mRNA abundance. However, for all genes examined mRNA expression was lower in the kidneys of twin compared with singleton fetuses following NR, and the magnitude of the effect was dependent on the timing of NR. In conclusion, the abundance of mRNA for receptors which regulate fetal kidney development are lower in twin animals compared with singletons following periods of nutrient deficiency. This may impact on later kidney development and function.
Collapse
Affiliation(s)
- K A Brennan
- Centre for Reproduction and Early Life, Institute of Clinical Research, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Gopalakrishnan GS, Gardner DS, Rhind SM, Rae MT, Kyle CE, Brooks AN, Walker RM, Ramsay MM, Keisler DH, Stephenson T, Symonds ME. Programming of adult cardiovascular function after early maternal undernutrition in sheep. Am J Physiol Regul Integr Comp Physiol 2004; 287:R12-20. [PMID: 14975924 DOI: 10.1152/ajpregu.00687.2003] [Citation(s) in RCA: 82] [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] [Indexed: 11/22/2022]
Abstract
The prenatal nutritional environment influences the subsequent risk of hypertension in adulthood. Animal studies have used, generally, the rat as a model species to illustrate the association between maternal nutrient intake and blood pressure in the resulting adult offspring. No study to date has shown programming of adult cardiovascular function in the sheep through maternal dietary intervention. We therefore fed pregnant sheep to either 100% recommended intake from day 0 of gestation to term [ approximately 147 days gestational age (dGA); controls n = 8] or to 50% recommended intake from day 0 to 95 dGA and thereafter to 100% intake (NR; n = 9). Sheep lambed naturally, offspring were weaned at 16 wk, and the male offspring were reared on pasture until 3 yr of age. At this time, cardiovascular catheters were inserted under halothane anesthesia and sheep were allowed 2-4 days recovery. Basal cardiovascular status and pressor responses to infusion of norepinephrine, angiotensin II, and captopril were then assessed alongside basal plasma concentrations of glucose, cortisol, and leptin. NR sheep were of similar birth weight to controls but at 3 yr of age had higher blood pressure before, but not after, feeding. Peripheral sensitivity to vasoconstrictor infusion was similar between dietary groups, although a reflex bradycardia was not apparent in NR sheep during norepinephrine infusion. Circulating leptin correlated well with fat mass and increased more after vasoconstrictor infusion in NR sheep. In conclusion, early NR has been shown to program aspects of cardiovascular control and adipocyte function in adult sheep.
Collapse
Affiliation(s)
- G S Gopalakrishnan
- Academic Division of Child Health, School of Human Development, Univ. Hospital, Nottingham NG7 2UH, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
Environmental influences on fetal and neonatal development can affect neural, reproductive, immune and cardiovascular function in adult humans and animals. The effects can be exerted at many different stages of development from before conception to after birth. Effects may even be exerted during a preceding generation. Some known and some possible mechanisms are reviewed. Systems likely to be affected include the brain, hypothalamus, pituitary and adrenal glands and the gonads. The effects may be exerted through altered gene expression at any stage of development or through changes in organ structure or physiology.
Collapse
Affiliation(s)
- S M Rhind
- Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, UK.
| | | | | |
Collapse
|
49
|
Rae MT, Kyle CE, Miller DW, Hammond AJ, Brooks AN, Rhind SM. The effects of undernutrition, in utero, on reproductive function in adult male and female sheep. Anim Reprod Sci 2002; 72:63-71. [PMID: 12106966 DOI: 10.1016/s0378-4320(02)00068-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The aim of this study was to determine the effects of maternal undernutrition during pregnancy on adult reproductive function in male and female offspring. Groups of ewes were fed rations providing either 100% (High, H) or 50% (Low, L) of estimated metabolisable energy (ME) requirements for pregnancy, from mating until day 95 of gestation, and thereafter were conventionally managed. At 20 months of age, LH and FSH profiles, and LH responses to exogenous GnRH were measured in male and female offspring and, in males, testicular responses to exogenous LH (as measured by testosterone concentrations) were also measured. Undernutrition had no effect on the mean birth weights of lambs of either sex, or on testicular size in male animals at either 6 weeks or 20 months of age. L males exhibited significantly higher FSH concentrations than H males (P < 0.05) but there were no differences with treatment in FSH profiles in females, basal LH profiles or gonadotrophin responses to GnRH in offspring of either sex, and no difference in basal testosterone concentrations or in the testosterone response to exogenous LH administration in males. Semen quality at 20 months of age was unaffected by pre-natal undernutrition but ovulation rate was significantly reduced in L compared to H female offspring (P < 0.05). It is concluded that pre-natal undernutrition had no effect on male reproductive development and adult function, but reduced ovulation rate in female progeny. This effect was not associated with a change in gonadotrophin profiles or pituitary responsiveness.
Collapse
Affiliation(s)
- M T Rae
- Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | | | | | | | | | | |
Collapse
|
50
|
Rae MT, Rhind SM, Fowler PA, Miller DW, Kyle CE, Brooks AN. Effect of maternal undernutrition on fetal testicular steroidogenesis during the CNS androgen-responsive period in male sheep fetuses. Reproduction 2002; 124:33-9. [PMID: 12090916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The aim of this study was to determine the effects of maternal undernutrition, applied during physiologically relevant stages of development of the reproductive system, on reproductive development in male sheep fetuses. Groups of ewes (n = 11-19) were fed rations providing either 100% (high; H) or 50% (low; L) of metabolizable energy requirements for live weight maintenance during selected 'windows', bounded by days 0, 30, 50, 65 and 110 after mating. Ewes of control groups (HH (Expts 1 and 2) and HHH (Expt 3)) were fed the H ration from mating until they were killed at day 50 (Expt 1), day 65 (Expt 2) or day 110 (Expt 3) of gestation, whereas ewes of other groups were fed the L ration for the periods days 0-30 of gestation (LH and LHH), days 31-50 or days 31-65 of gestation (HL and HLH), days 65-110 of gestation (HHL), or day 0 to day 50, day 65 or day 110 of gestation (LL and LLL) when the animals were killed. At day 50 of gestation, there was no effect of nutritional treatment on mean fetal mass or fetal testicular mass, but there was increased expression of mRNA for steroidogenic acute regulatory protein (StAR) in the testes of LL animals (P < 0.05) compared with HH controls. Compared with HH animals, the mean plasma testosterone concentrations of LL fetuses tended to be higher, but this result did not reach significance. At day 65 of gestation there were no significant differences between treatments in mean fetal masses, testicular masses, mean plasma testosterone concentrations or StAR mRNA content. At day 110 of gestation, fetal masses in the LLL group were lower (P < 0.01) than those of control fetuses, although no differences in testicular size or fetal plasma testosterone concentrations were recorded. It is concluded that the effects of undernutrition on reproductive development of male sheep fetuses are dependent on the timing of the period of undernutrition.
Collapse
Affiliation(s)
- M T Rae
- Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | | | | | | | | | | |
Collapse
|