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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. Cell Genom 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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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.
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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
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Garancher A, Suzuki H, Haricharan S, Chau LQ, Masihi MB, Rusert JM, Norris PS, Carrette F, Romero MM, Morrissy SA, Skowron P, Cavalli FMG, Farooq H, Ramaswamy V, Jones SJM, Moore RA, Mungall AJ, Ma Y, Thiessen N, Li Y, Morcavallo A, Qi L, Kogiso M, Du Y, Baxter P, Henderson JJ, Crawford JR, Levy ML, Olson JM, Cho YJ, Deshpande AJ, Li XN, Chesler L, Marra MA, Wajant H, Becher OJ, Bradley LM, Ware CF, Taylor MD, Wechsler-Reya RJ. Retraction Note: Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma. Nat Neurosci 2021; 25:127. [PMID: 34907396 DOI: 10.1038/s41593-021-00994-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexandra Garancher
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hiromichi Suzuki
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Svasti Haricharan
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lianne Q Chau
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Meher Beigi Masihi
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jessica M Rusert
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paula S Norris
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Florent Carrette
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Megan M Romero
- Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Sorana A Morrissy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Dept. of Biochemistry and Molecular Biology, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Patryk Skowron
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Hamza Farooq
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology and Department of Paediatrics, Hospital for Sick Children, Toronto, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alaide Morcavallo
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Lin Qi
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Mari Kogiso
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yuchen Du
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Patricia Baxter
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jacob J Henderson
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - John R Crawford
- Departments of Pediatrics and Neurosciences, University of California, San Diego - Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yoon-Jae Cho
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Aniruddha J Deshpande
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Harald Wajant
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Oren J Becher
- Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Linda M Bradley
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Carl F Ware
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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5
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Garancher A, Suzuki H, Haricharan S, Chau LQ, Masihi MB, Rusert JM, Norris PS, Carrette F, Romero MM, Morrissy SA, Skowron P, Cavalli FMG, Farooq H, Ramaswamy V, Jones SJM, Moore RA, Mungall AJ, Ma Y, Thiessen N, Li Y, Morcavallo A, Qi L, Kogiso M, Du Y, Baxter P, Henderson JJ, Crawford JR, Levy ML, Olson JM, Cho YJ, Deshpande AJ, Li XN, Chesler L, Marra MA, Wajant H, Becher OJ, Bradley LM, Ware CF, Taylor MD, Wechsler-Reya RJ. Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma. Nat Neurosci 2020; 23:842-853. [PMID: 32424282 PMCID: PMC7456619 DOI: 10.1038/s41593-020-0628-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 01/23/2019] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
Abstract
Many immunotherapies act by enhancing the ability of cytotoxic T cells to kill tumor cells. Killing depends on T cell recognition of antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. In this study, we showed that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. In vitro, tumor necrosis factor (TNF) or lymphotoxin-β receptor agonist can rescue expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, low doses of TNF prolong survival and synergize with immune checkpoint inhibitors to promote tumor rejection. These studies identified p53 as a key regulator of immune evasion and suggest that TNF could be used to enhance sensitivity of tumors to immunotherapy.
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Affiliation(s)
- Alexandra Garancher
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hiromichi Suzuki
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Svasti Haricharan
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lianne Q Chau
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Meher Beigi Masihi
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jessica M Rusert
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paula S Norris
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Florent Carrette
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Megan M Romero
- Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Sorana A Morrissy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Dept. of Biochemistry and Molecular Biology, Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Patryk Skowron
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Hamza Farooq
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology and Department of Paediatrics, Hospital for Sick Children, Toronto, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alaide Morcavallo
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Lin Qi
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Mari Kogiso
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yuchen Du
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Patricia Baxter
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jacob J Henderson
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - John R Crawford
- Departments of Pediatrics and Neurosciences, University of California, San Diego - Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yoon-Jae Cho
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Aniruddha J Deshpande
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Harald Wajant
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Oren J Becher
- Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Linda M Bradley
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Carl F Ware
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center and the Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Tindale LC, Thiessen N, Leach S, Brooks-Wilson AR. Allele-Specific Transcript Abundance: A Pilot Study in Healthy Centenarians. J Gerontol A Biol Sci Med Sci 2020; 75:1068-1072. [PMID: 31504207 PMCID: PMC7243586 DOI: 10.1093/gerona/glz188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Indexed: 11/13/2022] Open
Abstract
The genetic basis of healthy aging and longevity remains largely unexplained. One hypothesis as to why long-lived individuals do not appear to have a lower number of common-complex disease variants, is that despite carrying risk variants, they express disease-linked alleles at a lower level than the wild-type alleles. Allele-specific abundance (ASA) is the different transcript abundance of the two haplotypes of a diploid individual. We sequenced the transcriptomes of four healthy centenarians and four mid-life controls. CIBERSORT was used to estimate blood cell fractions: neutrophils were the most abundant source of RNA, followed by CD8+ T cells, resting NK cells, and monocytes. ASA variants were more common in noncoding than coding regions. Centenarians and controls had a comparable distribution of ASA variants by predicted effect, and we did not observe an overall bias in expression toward major or minor alleles. Immune pathways were most highly represented among the gene set that showed ASA. Although we found evidence of ASA in disease-associated genes and transcription factors, we did not observe any differences in the pattern of expression between centenarians and controls in this small pilot study.
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Affiliation(s)
- Lauren C Tindale
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Stephen Leach
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, Canada
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7
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia HD, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2020; 52:464. [PMID: 32107479 DOI: 10.1038/s41588-020-0598-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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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 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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 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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 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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.
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9
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2019; 52:29-34. [PMID: 31844324 DOI: 10.1038/s41588-019-0547-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 01/25/2023]
Abstract
Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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10
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Wechsler-Reya R, Garancher A, Suzuki H, Haricharan S, Masihi MB, Rusert JM, Norris PS, Carrette F, Romero MM, Morrissy SA, Skowron P, Cavalli FM, Farooq H, Ramaswamy V, Jones SJ, Moore RA, Mungall AJ, Ma Y, Thiessen N, Li Y, Morcavallo A, Qi L, Henderson JJ, Crawford JR, Levy ML, Olson JM, Cho YJ, Deshpande A, Li XN, Chesler L, Marra MA, Becher OJ, Bradley LM, Ware CF, Taylor MD. TNF superfamily cytokines overcome immune evasion in medulloblastoma. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.194.41] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Many immunotherapies act by enhancing T cell killing of tumor cells. CD8+ cytotoxic T cells recognize antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. Here we show that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. Treatment with tumor necrosis factor (TNF) or lymphotoxin beta receptor agonist (LTβRag) rescues expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, TNF treatment prolongs survival and markedly augments the efficacy of the immune checkpoint inhibitor anti-PD-1. These studies identify p53 as a key regulator of immune evasion in vivo, and suggest that TNF could be used to enhance sensitivity of p53-mutant tumors to immunotherapy.
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Affiliation(s)
- Robert Wechsler-Reya
- 1Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandra Garancher
- 1Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Hiromichi Suzuki
- 2Division of Neurosurgery, Hospital For Sick Children, Toronto, Canada
| | - Svasti Haricharan
- 3Lester & Sue Smith Breast Center, Department of Medicine, Baylor College of Medicine
| | - Meher Beigi Masihi
- 1Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Jessica M. Rusert
- 1Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Paula S. Norris
- 4Immunity and Pathogenesis Program, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Florent Carrette
- 4Immunity and Pathogenesis Program, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute
| | | | - Sorana A. Morrissy
- 6Developmental and Stem Cell Biology Program, Hospital For Sick Children, Toronto, Canada
| | - Patryk Skowron
- 6Developmental and Stem Cell Biology Program, Hospital For Sick Children, Toronto, Canada
| | - Florence M.G. Cavalli
- 7Program in Developmental and Stem Cell Biology, Hospital For Sick Children, Toronto, Canada
| | - Hamza Farooq
- 6Developmental and Stem Cell Biology Program, Hospital For Sick Children, Toronto, Canada
| | - Vijay Ramaswamy
- 8Division of Haematology/Oncology and Division of Paediatrics, Hospital For Sick Children, Toronto, Canada
| | - Steven J.M. Jones
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Richard A. Moore
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Andrew J. Mungall
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Yussanne Ma
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Nina Thiessen
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Yisu Li
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | - Alaide Morcavallo
- 10Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Lin Qi
- 11Preclinical Neuro-Oncology Research Program, Texas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine
| | - Jacob J. Henderson
- 12Papé Family Pediatric Research Institute, Department of Pediatrics, Knight Cancer Institute, Oregon Health & Science University
| | - John R. Crawford
- 13Departments of Pediatrics and Neurosciences, University of California, San Diego, Rady Children’s Hospital San Diego
| | - Michael L. Levy
- 14Department of Neurosurgery, University of California, San Diego, Rady Children’s Hospital San Diego
| | - James M. Olson
- 15Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Yoon-Jae Cho
- 12Papé Family Pediatric Research Institute, Department of Pediatrics, Knight Cancer Institute, Oregon Health & Science University
| | - Ani Deshpande
- 1Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Xiao-Nan Li
- 11Preclinical Neuro-Oncology Research Program, Texas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine
| | - Louis Chesler
- 10Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Marco A. Marra
- 9Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada
| | | | - Linda M. Bradley
- 4Immunity and Pathogenesis Program, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Carl F. Ware
- 4Immunity and Pathogenesis Program, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute
| | - Michael D. Taylor
- 2Division of Neurosurgery, Hospital For Sick Children, Toronto, Canada
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11
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Garancher A, Suzuki H, Haricharan S, Masihi MB, Rusert JM, Norris PS, Carrette F, Romero MM, Morrissy SA, Skowron P, M.G. Cavalli F, Farooq H, Ramaswamy V, J.M. Jones S, Moore RA, Mungall AJ, Ma Y, Thiessen N, Li Y, Morcavallo A, Qi L, Henderson JJ, Crawford JR, Levy ML, Olson JM, Cho YJ, Deshpande A, Li XN, Chesler L, Marra MA, Becher OJ, Bradley LM, Ware CF, Taylor MD, Wechsler-Reya RJ. IMMU-03. TUMOR NECROSIS FACTOR OVERCOMES IMMUNE EVASION IN P53-MUTANT MEDULLOBLASTOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | | | | | | | - Jessica M Rusert
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paula S Norris
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Florent Carrette
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Yisu Li
- BC Cancer Agency, Vancouver, BC, Canada
| | | | - Lin Qi
- Baylor College of Medicine, Houston, TX, USA
| | | | - John R Crawford
- University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - Michael L Levy
- University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - James M Olson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yoon-Jae Cho
- Oregon Health & Science University, Portland, OR, USA
| | - Ani Deshpande
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiao-Nan Li
- Baylor College of Medicine, Houston, TX, USA
| | - Louis Chesler
- The Institute of Cancer Research, London, United Kingdom
| | | | | | - Linda M Bradley
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Carl F Ware
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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12
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Zhao EY, Shen Y, Pleasance E, Kasaian K, Leelakumari S, Jones M, Bose P, Ch'ng C, Reisle C, Eirew P, Corbett R, Mungall KL, Thiessen N, Ma Y, Schein JE, Mungall AJ, Zhao Y, Moore RA, Den Brok W, Wilson S, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Renouf D, Sun S, Schrader KA, Young S, Bosdet I, Karsan A, Laskin J, Marra MA, Jones SJM. Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer. Clin Cancer Res 2018; 23:7521-7530. [PMID: 29246904 DOI: 10.1158/1078-0432.ccr-17-1941] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/14/2017] [Accepted: 09/26/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas BRCA1/2 mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.Experimental Design: In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated). We computed a published metric called HRDetect, independently trained to predict BRCA1/2 status, and assessed its capacity to predict outcomes on platinum-based chemotherapies. Clinical endpoints were overall survival (OS), total duration on platinum-based therapy (TDT), and radiographic evidence of clinical improvement (CI).Results: HRDetect predicted BRCA1/2 status with an area under the curve (AUC) of 0.94 and optimal threshold of 0.7. Elevated HRDetect was also significantly associated with CI on platinum-based therapy (AUC = 0.89; P = 0.006) with the same optimal threshold, even after adjusting for BRCA1/2 mutation status and treatment timing. HRDetect scores over 0.7 were associated with a 3-month extended median TDT (P = 0.0003) and 1.3-year extended median OS (P = 0.04).Conclusions: Our findings not only independently validate HRDetect, but also provide the first evidence of its association with platinum response in advanced breast cancer. We demonstrate that HRD mutation signatures may offer clinically relevant information independently of BRCA1/2 mutation status and hope this work will guide the development of clinical trials. Clin Cancer Res; 23(24); 7521-30. ©2017 AACR.
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Affiliation(s)
- Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Pinaki Bose
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard Corbett
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jacqueline E Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Wendie Den Brok
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sheridan Wilson
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Diego Villa
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Chia
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Gelmon
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Howard Lim
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Sun
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kasmintan A Schrader
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean Young
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
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13
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Thibodeau ML, Bonakdar M, Zhao E, Mungall KL, Reisle C, Zhang W, Bye MH, Thiessen N, Bleile D, Mungall AJ, Ma YP, Jones MR, Renouf DJ, Lim HJ, Yip S, Ng T, Ho C, Laskin J, Marra MA, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol 2018; 2:8. [PMID: 29872726 PMCID: PMC5871832 DOI: 10.1038/s41698-018-0050-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 07/05/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
Eccrine porocarcinomas (EPs) are rare malignant tumours of the intraepidermic sweat gland duct and most often arise from benign eccrine poromas. Some recurrent somatic genomic events have been identified in these malignancies, but very little is known about the complexity of their molecular pathophysiology. We describe the whole genome and whole transcriptome genomic profiling of a metastatic EP in a 66-year-old male patient with a previous history of localized porocarcinoma of the scalp. Whole genome and whole transcriptome genomic profiling was performed on the metastatic EP. Whole genome sequencing was performed on blood-derived DNA in order to allow a comparison between germline and somatic events. We found somatic copy losses of several tumour suppressor genes including APC, PTEN and CDKN2A, CDKN2B and CDKN1A. We identified a somatic hemizygous CDKN2A pathogenic splice site variant. De novo transcriptome assembly revealed abnormal splicing of CDKN2A p14ARF and p16INK4a. Elevated expression of oncogenes EGFR and NOTCH1 was noted and no somatic mutations were found in these genes. Wnt pathway somatic alterations were also observed. In conclusion, our results suggest that the molecular pathophysiology of malignant EP features high complexity and subtle interactions of multiple key genes. Cell cycle dysregulation and CDKN2A loss of function was found to be a new potential driver in EP tumourigenesis. Moreover, the combination of somatic copy number variants and abnormal gene expression perhaps partly related to epigenetic mechanisms, all likely contribute to the development of this rare malignancy in our patient.
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Melika Bonakdar
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Eric Zhao
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Karen L. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Caralyn Reisle
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Wei Zhang
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Morgan H. Bye
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Nina Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Dustin Bleile
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Yussanne P. Ma
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Martin R. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Daniel J. Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Howard J. Lim
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Tony Ng
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Cheryl Ho
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Janessa Laskin
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Marco A. Marra
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Kasmintan A. Schrader
- Hereditary Cancer Program, Department of Medical Genetics, British Columbia Cancer Agency, 614–750 West Broadway, Vancouver, BC V5Z 1H5 Canada
| | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
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14
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Shen Y, Jones MR, Pleasance E, Bonakdar M, Ch'ng C, Reisle C, Williamson L, Majounie E, Taylor G, Chan S, Pierce B, Zhang W, Muhammadzadeh A, Zhao EY, Bleile D, Mungall K, Thiessen N, Chuah E, Wong T, Corbett R, Ma Y, Moore RA, Mungall AJ, Zhao Y, Yip S, Lee AF, Rassekh R, Deyell R, Lim H, Renouf D, Roscoe R, Jones SJ, Laskin J, Marra MA. Abstract A184: Clinical application of whole genome and transcriptome sequencing in cancer care. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-a184] [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
Aim: To investigate feasibility and utility of whole genome and RNA sequencing in cancer care. The use of comprehensive personal genomic information to guide cancer treatment decisions has gained momentum in recent years. Here we present the Personalized Oncogenomics (POG) project launched at British Columbia Cancer Agency in 2012. This project uses paired tumor/normal whole genome and transcriptome sequencing to characterize a patient's tumor and inform treatment options within a clinically relevant time frame. In the past 5 years, around 600 patients with metastatic cancers (including 49 pediatric cases) have been sequenced and analyzed, representing over 50 cancer types. The breadth and depth of data in POG enable the detection of multiple types of alterations, from simple mutations, indels, and copy number changes, to more complex alterations such as gene fusion, mutation signatures, and homologous recombination deficiency score. Incorporation of gene expression data through transcriptome sequencing informs on the impact of observed genomic alterations, and provides information regarding specific diagnosis via expression comparison to other cancer subtypes. All genomic and transcriptomic variants are integrated to build a personalized tumor-specific molecular profile, identify actionable items supported by an in-house knowledgebase and publically available molecular oncology, and characterize each individual tumor by intensive pathway analysis and literature search. Such multidimensional data also impose challenges in interpretation and communication. We developed a pipeline to translate complex genomic data into clinically actionable and hypothetical recommendations for the treatment of individual patients. The pipeline produces two reports: a panel-like report that contains known SNVs and fusions with therapeutic relevance from a collection of more than 4000 events, and a second comprehensive and manually curated report to fully characterize the tumor using the whole genome and transcriptome datasets. Genomic data are presented and discussed at a multidisciplinary molecular tumor board consisting of medical oncologists, pathologists, bioinformaticians, geneticists, and biologists. This approach has enabled clinicians to make informed clinical decisions based on the genomic data integrated with other clinical features, as well as to form new treatment-related hypothesis. POG has shown that use of both whole genome and transcriptome sequencing allows identification of therapeutic targets in a significant proportion of patients. Almost 80% cases were found to have one or more actionable alterations (100% in pediatric cases), and almost one-third of these are defined only using RNA data. Based on molecular tumor board discussion, patients are directed to clinical trials, positioned to genomically informed standard-of-care options, or treated with off-label drugs. With demonstrated effectiveness, the integrative approach developed by POG not only provides molecular insight and treatment options into individual tumors, but also provides a rich resource of molecular data with matched clinical information that will aid our understanding of tumor biology and therapy response mechanisms to inform treatment strategies in the future.
Citation Format: Yaoqing Shen, Martin R. Jones, Erin Pleasance, Melika Bonakdar, Carolyn Ch'ng, Caralyn Reisle, Laura Williamson, Elisa Majounie, Greg Taylor, Simon Chan, Brandon Pierce, Wei Zhang, Amir Muhammadzadeh, Eric Y. Zhao, Dustin Bleile, Karen Mungall, Nina Thiessen, Eric Chuah, Tina Wong, Richard Corbett, Yussanne Ma, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Stephen Yip, Anna F. Lee, Rod Rassekh, Rebecca Deyell, Howard Lim, Daniel Renouf, Robyn Roscoe, Steven J.M Jones, Janessa Laskin, Marco A. Marra. Clinical application of whole genome and transcriptome sequencing in cancer care [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A184.
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Affiliation(s)
- Yaoqing Shen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Melika Bonakdar
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura Williamson
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Elisa Majounie
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Greg Taylor
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Simon Chan
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Brandon Pierce
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Wei Zhang
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Amir Muhammadzadeh
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Eric Y. Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Dustin Bleile
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Karen Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Eric Chuah
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Tina Wong
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Corbett
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard A. Moore
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Stephen Yip
- 2Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna F. Lee
- 2Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rod Rassekh
- 3Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca Deyell
- 3Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Howard Lim
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Renouf
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Robyn Roscoe
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J.M Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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15
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Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. The whole-genome landscape of medulloblastoma subtypes. Nature 2017; 547:311-317. [PMID: 28726821 PMCID: PMC5905700 DOI: 10.1038/nature22973] [Citation(s) in RCA: 667] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022]
Abstract
Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma. Genomic analysis of 491 medulloblastoma samples, including methylation profiling of 1,256 cases, effectively assigns candidate drivers to most tumours across all molecular subgroups. Medulloblastomas are highly malignant brain tumours that develop during childhood. Paul Northcott and colleagues analysed the whole-genome sequences of 491 medulloblastomas in order to characterize the genomic landscape across tumours and identify new drivers and mutational signatures. Their integrative genomic analyses, including methylation profiling of 1,256 medulloblastomas, identifies subgroup-specific driver mutations and suggests additional tumour subtypes. The authors assign driver mutations to a high proportion of the less well characterized Group 3 and Group 4, which together contribute to more than 60% of all medulloblastomas.
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Affiliation(s)
- Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - A Sorana Morrissy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Tobias Ehrenberger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Susanne Gröbner
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Maia Segura-Wang
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Zichner
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vasilisa A Rudneva
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hans-Jörg Warnatz
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Nikos Sidiropoulos
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Aaron H Phillips
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Serap Erkek
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Michael Heinold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Jäger-Schmidt
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alke Jugold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Risch
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | | | | | - Ursula D Weber
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xin Zhou
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David Finkelstein
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yanling Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Florence M G Cavalli
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Betty Luu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Vijay Ramaswamy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Xiaochong Wu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Jan Koster
- Department of Oncogenomics, Amsterdam Medical Center, Amsterdam, Netherlands
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Yoon-Jae Cho
- Department of Pediatrics, Papé Family Pediatric Research Institute, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christel Herold-Mende
- Department of Neurosurgery, University Clinic, Heidelberg University, Heidelberg Hospital, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Hematology and Oncology, Children's University Hospital Tübingen, Tübingen, Germany
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, North County, USA
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Eric Chuah
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Kane Tse
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tina Wong
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Richard Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael D Taylor
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario.,Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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16
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Cho SY, Park JW, Liu Y, Park YS, Kim JH, Yang H, Um H, Ko WR, Lee BI, Kwon SY, Ryu SW, Kwon CH, Park DY, Lee JH, Lee SI, Song KS, Hur H, Han SU, Chang H, Kim SJ, Kim BS, Yook JH, Yoo MW, Kim BS, Lee IS, Kook MC, Thiessen N, He A, Stewart C, Dunford A, Kim J, Shih J, Saksena G, Cherniack AD, Schumacher S, Weiner AT, Rosenberg M, Getz G, Yang EG, Ryu MH, Bass AJ, Kim HK. Sporadic Early-Onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations, but Low Frequency of Somatic RHOA Mutations Compared With Late-Onset Cancers. Gastroenterology 2017; 153:536-549.e26. [PMID: 28522256 PMCID: PMC6863080 DOI: 10.1053/j.gastro.2017.05.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/08/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Early-onset gastric cancer, which develops in patients younger than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea. Patients with pathogenic germline mutations in CDH1, TP53, and ATM were excluded from the onset of this analysis, given our focus on somatic alterations. We used MutSig2CV to evaluate the significance of mutated genes. We recruited 29 additional early-onset Korean DGC samples and performed SNP6.0 array and targeted sequencing analyses of these 109 early-onset DGC samples (54.1% female, median age, 38 years). We compared the SNP6.0 array and targeted sequencing data of the 109 early-onset DGC samples with those from diffuse-type stomach tumor samples collected from 115 patients in Korea who were 46 years or older (late onset) at the time of diagnosis (controls; 29.6% female, median age, 67 years). We compared patient survival times among tumors from different subgroups and with different somatic mutations. We performed gene silencing of RHOA or CDH1 in DGC cells with small interfering RNAs for cell-based assays. RESULTS We identified somatic mutations in the following genes in a significant number of early-onset DGCs: the cadherin 1 gene (CDH1), TP53, ARID1A, KRAS, PIK3CA, ERBB3, TGFBR1, FBXW7, RHOA, and MAP2K1. None of 109 early-onset DGC cases had pathogenic germline CDH1 mutations. A higher proportion of early-onset DGCs had mutations in CDH1 (42.2%) or TGFBR1 (7.3%) compared with control DGCs (17.4% and 0.9%, respectively) (P < .001 and P = .014 for CDH1 and TGFBR1, respectively). In contrast, a smaller proportion of early-onset DGCs contained mutations in RHOA (9.2%) than control DGCs (19.1%) (P = .033). Late-onset DGCs in The Cancer Genome Atlas also contained less frequent mutations in CDH1 and TGFBR1 and more frequent RHOA mutations, compared with early-onset DGCs. Early-onset DGCs from women contained significantly more mutations in CDH1 or TGFBR1 than early-onset DGCs from men. CDH1 alterations, but not RHOA mutations, were associated with shorter survival times in patients with early-onset DGCs (hazard ratio, 3.4; 95% confidence interval, 1.5-7.7). RHOA activity was reduced by an R5W substitution-the RHOA mutation most frequently detected in early-onset DGCs. Silencing of CDH1, but not RHOA, increased migratory activity of DGC cells. CONCLUSIONS In an integrative genomic analysis, we found higher proportions of early-onset DGCs to contain somatic mutations in CDH1 or TGFBR1 compared with late-onset DGCs. However, a smaller proportion of early-onset DGCs contained somatic mutations in RHOA than late-onset DGCs. CDH1 alterations, but not RHOA mutations, were associated with shorter survival times of patients, which might account for the aggressive clinical course of early-onset gastric cancer. Female predominance in early-onset gastric cancer may be related to relatively high rates of somatic CDH1 and TGFBR1 mutations in this population.
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Affiliation(s)
- Soo Young Cho
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Jun Won Park
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Yang Liu
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Young Soo Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ju Hee Kim
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Hanna Yang
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Hyejin Um
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Woo Ri Ko
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Byung Il Lee
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Seung Wan Ryu
- Department of Surgery, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Chae Hwa Kwon
- Department of Pathology and BioMedical Research Institute, Pusan National University Hospital and Pusan National University School of Medicine, Busan, Republic of Korea
| | - Do Youn Park
- Department of Pathology and BioMedical Research Institute, Pusan National University Hospital and Pusan National University School of Medicine, Busan, Republic of Korea
| | - Jae-Hyuk Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sang Il Lee
- Department of Surgery, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyu Sang Song
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hoon Hur
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Heekyung Chang
- Department of Pathology, Kosin University College of Medicine, Busan, Republic of Korea
| | - Su-Jin Kim
- Department of Pathology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Byung-Sik Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong-Hwan Yook
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Moon-Won Yoo
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom-Su Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - In-Seob Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Nina Thiessen
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - An He
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Chip Stewart
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew Dunford
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jaegil Kim
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Juliann Shih
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gordon Saksena
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew D. Cherniack
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven Schumacher
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Amaro-Taylor Weiner
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mara Rosenberg
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gad Getz
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eun Gyeong Yang
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Adam J. Bass
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hark Kyun Kim
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea; National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, Republic of Korea.
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17
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Zhao EY, Shen Y, Pleasance E, Kasaian K, Jones MR, Ch'ng C, Reisle C, Eirew P, Mungall K, Thiessen N, Ma Y, Fok A, Mungall AJ, Zhao Y, Moore R, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Sun S, Schrader KA, Young S, Karsan A, Roscoe R, Laskin J, Marra MA, Jones SJ. Abstract 2473: Breast cancer whole genomes link homologous recombination deficiency (HRD) with therapeutic outcomes. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2473] [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
Background: Homologous recombination deficiency (HRD) is common in cancer - germline BRCA1 & BRCA2 mutations account for 5-10% of breast cancers and confer 85% lifetime risk. HRD cancers exhibit genomic instability and sensitivity to platinum-based therapy and PARP inhibitors. While not all causes of HRD are known, recent sequencing efforts have revealed genome-wide somatic mutation signatures that characterize the HRD genomic instability phenotype, also known as “BRCA-ness”. This provides a promising new assay to predict sensitivity to platinum-based therapy. Here, we integrate two whole-genome sequencing metrics to assess their association with therapeutic outcomes in a breast cancer cohort.
Methods: Whole-genome sequencing of 47 breast cancer tumors (100x coverage) and matched normals (60x) was performed on an Illumina HiSeq. Alignment, assembly, SNV calling, and loss of heterozygosity (LOH) detection were performed with BWA, ABySS, Strelka, and APOLLOH respectively. SNV signatures were deciphered by non-negative matrix factorization with Monte Carlo resampling. An HRD score comprised of LOH, telomeric allelic imbalance (TAI), and large scale transition (LST) counts was computed. Clinical endpoints were obtained by retrospective review of treatment and imaging reports. Analysis is ongoing in an independent validation cohort of 62 sequenced cases.
Results: The HRD-linked SNV signature was significantly associated with radiographic clinical response (CR) to platinum-based therapy (p=0.015). Logistic regression demonstrated a 59% improved odds of CR to platinum-based therapy per 1000 somatic SNVs attributed to HRD (odds ratio 1.16-2.50). Tumors carried up to 10,246 such SNVs and all patients with CR were among the top quartile. The LOH-TAI-LST score was correlated with SNV signature (r=0.6, p=7×10-6) and associated with CR (p=0.025). Notably, elevated HRD signatures associated with CR were identified in tumors with wild-type BRCA1/BRCA2 or variants of unknown significance. Tumors with above median HRD signatures were associated with a 69-day longer time to treatment failure and an 18% daily decreased probability of treatment failure per 1000 HRD-attributed SNVs (hazard ratio 0.71-0.95, p = 0.007).
Discussion: We found that HRD mutation signatures are associated with clinical response and longer time to treatment failure with platinum-based therapy. While similar benefits were observed in patients with somatic bi-allelic loss of BRCA1/BRCA2, such cases are less common (8% of our cohort) compared to those with elevated HRD signature. Thus, mutation signature methods may identify patients who stand to benefit from platinum-based therapy missed by BRCA screening alone.
Citation Format: Eric Y. Zhao, Yaoqing Shen, Erin Pleasance, Katayoon Kasaian, Martin R. Jones, Carolyn Ch'ng, Caralyn Reisle, Peter Eirew, Karen Mungall, Nina Thiessen, Yussanne Ma, Alexandra Fok, Andrew J. Mungall, Yongjun Zhao, Richard Moore, Diego Villa, Tamara Shenkier, Caroline Lohrisch, Stephen Chia, Stephen Yip, Karen Gelmon, Howard Lim, Sophie Sun, Kasmintan A. Schrader, Sean Young, Aly Karsan, Robyn Roscoe, Janessa Laskin, Marco A. Marra, Steven J. Jones. Breast cancer whole genomes link homologous recombination deficiency (HRD) with therapeutic outcomes [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 2473. doi:10.1158/1538-7445.AM2017-2473
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Affiliation(s)
- Eric Y. Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Katayoon Kasaian
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Peter Eirew
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Alexandra Fok
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Moore
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Diego Villa
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Chia
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Yip
- 3The University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Gelmon
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Howard Lim
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Sun
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- 3The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Robyn Roscoe
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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18
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Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJM, Marra MA, Gunaratne PH. Correction: miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget 2017; 8:17406. [PMID: 28403581 PMCID: PMC5370050 DOI: 10.18632/oncotarget.15921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Chun HJE, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Palmquist DL, He A, Long W, Goya R, Ng M, LeBlanc VG, Pleasance E, Thiessen N, Wong T, Chuah E, Zhao YJ, Schein JE, Gerhard DS, Taylor MD, Mungall AJ, Moore RA, Ma Y, Jones SJM, Perlman EJ, Hirst M, Marra MA. Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways. Cancer Cell 2016; 29:394-406. [PMID: 26977886 PMCID: PMC5094835 DOI: 10.1016/j.ccell.2016.02.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [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] [Received: 07/17/2015] [Revised: 01/05/2016] [Accepted: 02/16/2016] [Indexed: 12/18/2022]
Abstract
Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.
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Affiliation(s)
- Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Saeed Saberi
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Mikhail Bilenky
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Annaick Carles
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kane Tse
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Inna Shlafman
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Kelsey Zhu
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jenny Q Qian
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Diana L Palmquist
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - An He
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - William Long
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Rodrigo Goya
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Michelle Ng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Veronique G LeBlanc
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Yong-Jun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Jacquie E Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
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20
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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.).
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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
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Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015; 372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2108] [Impact Index Per Article: 234.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).
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22
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Tindale LC, Zeng A, Bretherick KL, Leach S, Thiessen N, Brooks-Wilson AR. Burden of Common Complex Disease Variants in the Exomes of Two Healthy Centenarian Brothers. Gerontology 2015; 62:58-62. [PMID: 26066993 DOI: 10.1159/000430462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It is not understood whether long-term good health is promoted by the absence of disease risk variants, the presence of protective variants, or both. We characterized the exomes of two exceptionally healthy centenarian brothers aged 106 and 109 years who had never been diagnosed with cancer, cardiovascular disease, diabetes, Alzheimer's disease, or major pulmonary disease. OBJECTIVE The aim of this study was to gain insight into whether exceptional health and longevity are a result of carrying fewer disease-associated variants than typical individuals. METHODS We compared the number of disease-associated alleles, and the proportion of alleles predicted to be functionally damaging, between the centenarian brothers and published population data. Mitochondrial sequence reads were extracted from the exome data in order to analyze mitochondrial variants. RESULTS The brothers carry a similar number of common disease-associated variants and predicted damaging variants compared to reference groups. They did not carry any high-penetrance clinically actionable variants. They carry mitochondrial haplogroup T, and one brother has a single heteroplasmic variant. CONCLUSION Although our small sample size does not allow for definitive conclusions, a healthy aging and longevity phenotype is not necessarily due to a decreased burden of common disease-associated variants. Instead, it may be rare 'positive' variants that play a role in this desirable phenotype.
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Affiliation(s)
- Lauren C Tindale
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, B.C., Canada
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23
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Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Garside VC, Bilenky M, Griffith M, Morrissy AS, Robertson GA, Thiessen N, Zhao Y, Chen Q, Pan D, Jones SJM, Marra MA, Hoodless PA. Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep 2014; 9:261-271. [PMID: 25263553 PMCID: PMC4612615 DOI: 10.1016/j.celrep.2014.08.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [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: 01/29/2014] [Revised: 03/11/2014] [Accepted: 08/20/2014] [Indexed: 12/28/2022] Open
Abstract
Cell fate acquisition is heavily influenced by direct interactions between master regulators and tissue-specific enhancers. However, it remains unclear how lineage-specifying transcription factors, which are often expressed in both progenitor and mature cell populations, influence cell differentiation. Using in vivo mouse liver development as a model, we identified thousands of enhancers that are bound by the master regulators HNF4A and FOXA2 in a differentiation-dependent manner, subject to chromatin remodeling, and associated with differentially expressed target genes. Enhancers exclusively occupied in the embryo were found to be responsive to developmentally regulated TEAD2 and coactivator YAP1. Our data suggest that Hippo signaling may affect hepatocyte differentiation by influencing HNF4A and FOXA2 interactions with temporal enhancers. In summary, transcription factor-enhancer interactions are not only tissue specific but also differentiation dependent, which is an important consideration for researchers studying cancer biology or mammalian development and/or using transformed cell lines.
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Affiliation(s)
- Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Sam Lee
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Arohumam C Kan
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | | | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Malachi Griffith
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - A Sorana Morrissy
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gordon A Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Qian Chen
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Duojia Pan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada.
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Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJM, Birol İ. JAGuaR: junction alignments to genome for RNA-seq reads. PLoS One 2014; 9:e102398. [PMID: 25062255 PMCID: PMC4111418 DOI: 10.1371/journal.pone.0102398] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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: 09/19/2013] [Accepted: 06/19/2014] [Indexed: 01/06/2023] Open
Abstract
JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. Reads aligned to the transcript models are then re-mapped on to genomic coordinates, transforming alignments that span multiple exons into large-gapped alignments on the genome. While JAGuaR does not detect novel junctions, we demonstrate how JAGuaR generates fast and accurate transcriptome alignments, which allows for both sensitive and specific SNV calling.
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Affiliation(s)
| | - Maayan Kreitzman
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Johnson Pang
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yussanne P. Ma
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - İnanç Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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25
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Abstract
Oral lichen planus is a mucosal inflammatory disease whose pathogenesis is unclear. The chronic inflammation leads to development of a squamous cell carcinoma in 1-2% of the patients; we present an exemplary case.
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Affiliation(s)
- N Thiessen
- Hautklinik, Klinikum Stadt Ludwigshafen am Rhein gGmbH, Bremserstr. 79, 67063, Ludwigshafen, Deutschland,
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26
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Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJM. Complete genomic landscape of a recurring sporadic parathyroid carcinoma. J Pathol 2013; 230:249-60. [PMID: 23616356 DOI: 10.1002/path.4203] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/14/2013] [Accepted: 04/16/2013] [Indexed: 12/17/2022]
Abstract
Parathyroid carcinoma is a rare endocrine malignancy with an estimated incidence of less than 1 per million population. Excessive secretion of parathyroid hormone, extremely high serum calcium level, and the deleterious effects of hypercalcaemia are the clinical manifestations of the disease. Up to 60% of patients develop multiple disease recurrences and although long-term survival is possible with palliative surgery, permanent remission is rarely achieved. Molecular drivers of sporadic parathyroid carcinoma have remained largely unknown. Previous studies, mostly based on familial cases of the disease, suggested potential roles for the tumour suppressor MEN1 and proto-oncogene RET in benign parathyroid tumourigenesis, while the tumour suppressor HRPT2 and proto-oncogene CCND1 may also act as drivers in parathyroid cancer. Here, we report the complete genomic analysis of a sporadic and recurring parathyroid carcinoma. Mutational landscapes of the primary and recurrent tumour specimens were analysed using high-throughput sequencing technologies. Such molecular profiling allowed for identification of somatic mutations never previously identified in this malignancy. These included single nucleotide point mutations in well-characterized cancer genes such as mTOR, MLL2, CDKN2C, and PIK3CA. Comparison of acquired mutations in patient-matched primary and recurrent tumours revealed loss of PIK3CA activating mutation during the evolution of the tumour from the primary to the recurrence. Structural variations leading to gene fusions and regions of copy loss and gain were identified at a single-base resolution. Loss of the short arm of chromosome 1, along with somatic missense and truncating mutations in CDKN2C and THRAP3, respectively, provides new evidence for the potential role of these genes as tumour suppressors in parathyroid cancer. The key somatic mutations identified in this study can serve as novel diagnostic markers as well as therapeutic targets.
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Affiliation(s)
- Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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27
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Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JDK, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. BMC Genomics 2013; 14:550. [PMID: 23941359 PMCID: PMC3751903 DOI: 10.1186/1471-2164-14-550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022] Open
Abstract
Background Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. Results We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets. Conclusions Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.
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Affiliation(s)
- Lucas Swanson
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
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Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson AG, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MDM, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KRM, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013; 368:2059-74. [PMID: 23634996 PMCID: PMC3767041 DOI: 10.1056/nejmoa1301689] [Citation(s) in RCA: 3565] [Impact Index Per Article: 324.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories. CONCLUSIONS We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.).
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Bie L, Ju Y, Jin Z, Donovan L, Birks S, Grunewald L, Zmuda F, Pilkington G, Kaul A, Chen YH, Dahiya S, Emnett R, Gianino S, Gutmann D, Poschl J, Bianchi E, Bockstaller M, Neumann P, Schuller U, Gevorgian A, Morozova E, Kazantsev I, Iukhta T, Safonova S, Punanov Y, Zheludkova O, Afanasyev B, Buss M, Remke M, Gandhi K, Kool M, Northcott P, Pfister S, Taylor M, Castellino R, Thompson J, Margraf L, Donahue D, Head H, Murray J, Burger P, Wortham M, Reitman Z, He Y, Bigner D, Yan H, Lee C, Triscott J, Foster C, Manoranjan B, Pambid MR, Fotovati A, Berns R, Venugopal C, O'Halloran K, Narendran A, Northcott P, Taylor MD, Singh SK, Singhal A, Rassekh R, Maxwell CA, Dunham C, Dunn SE, Pambid MR, Berns R, Hu K, Adomat H, Moniri M, Chin MY, Hessein M, Zisman N, Maurer N, Dunham C, Guns E, Dunn S, Koks C, De Vleeschouwer S, Graf N, Van Gool S, D'Asti E, Huang A, Korshunov A, Pfister S, Rak J, Gump W, Moriarty T, Gump W, Skjei K, Karkare S, Castelo-Branco P, Choufani S, Mack S, Gallagher D, Zhang C, Merino D, Wasserman J, Kool M, Jones DT, Croul S, Kreitzer F, Largaespada D, Conklin B, Taylor M, Weiss W, Garzia L, Morrissy S, Zayne K, Wu X, Dirks P, Hawkins C, Dick J, Stein L, Collier L, Largaespada D, Dupuy A, Taylor M, Rampazzo G, Moraes L, Paniago M, Oliveira I, Hitzler J, Silva N, Cappellano A, Cavalheiro S, Alves MT, Cerutti J, Toledo S, Liu Z, Zhao X, Mao H, Baxter P, Wang JCY, Huang Y, Yu L, Su J, Adekunle A, Perlaky L, Hurwitz M, Hurwitz R, Lau C, Chintagumpala M, Blaney S, Baruchel S, Li XN, Zhang J, Hariono S, Hashizume R, Fan Q, James CD, Weiss WA, Nicolaides T, Madsen PJ, Slaunwhite ES, Dirks PB, Ma JF, Henn RE, Hanno AG, Boucher KL, Storm PB, Resnick AC, Lourdusamy A, Rogers H, Ward J, Rahman R, Malkin D, Gilbertson R, Grundy R, Lourdusamy A, Rogers H, Ward J, Rahman R, Gilbertson R, Grundy R, Karajannis M, Fisher M, Pfister S, Milla S, Cohen K, Legault G, Wisoff J, Harter D, Merkelson A, Bloom M, Dhall G, Jones D, Korshunov A, Taylor MD, Pfister S, Eberhart C, Sievert A, Resnick A, Zagzag D, Allen J, Hankinson T, Gump J, Serrano-Almeida C, Torok M, Weksberg R, Handler M, Liu A, Foreman N, Garancher A, Rocques N, Miquel C, Sainte-Rose C, Delattre O, Bourdeaut F, Eychene A, Tabori U, Pouponnot C, Danielpour M, Levy R, Antonuk CD, Rodriguez J, Aravena JM, Kim GB, Gate D, Bannykh S, Svendsen C, Huang X, Town T, Breunig J, Amakye D, Robinson D, Rose K, Cho YJ, Ligon KL, Sharp T, Ando Y, Geoerger B, He Y, Doz F, Ashley D, Hargrave D, Casanova M, Tawbi H, Heath J, Bouffet E, Brandes AA, Chisholm J, Rodon J, Dubuc AM, Thomas A, Mita A, MacDonald T, Kieran M, Eisenstat D, Song X, Danielpour M, Levy R, Antonuk CD, Rodriguez J, Hashizume R, Aravena JM, Kim GB, Gate D, Bannykh S, Svendsen C, Town T, Breunig J, Morrissy AS, Mayoh C, Lo A, Zhang W, Thiessen N, Tse K, Moore R, Mungall A, Wu X, Van Meter TE, Cho YJ, Collins VP, MacDonald TJ, Li XN, Stehbens S, Fernandez-Lopez A, Malkin D, Marra MA, Taylor MD, Karajannis M, Legault G, Hagiwara M, Vega E, Merkelson A, Wisoff J, Younger S, Golfinos J, Roland JT, Allen J, Antonuk CD, Levy R, Kim GB, Town T, Danielpour M, Breunig J, Pak E, Barshow S, Zhao X, Ponomaryov T, Segal R, Levy R, Antonuk CD, Aravena JM, Kim GB, Svendsen C, Town T, Danielpour M, Zhu S, Breunig J, Chi S, Cohen K, Fisher M, Biegel J, Bowers D, Fangusaro J, Manley P, Janss A, Zimmerman MA, Wu X, Kieran M, Sayour E, Pham C, Sanchez-Perez L, Snyder D, Flores C, Kemeny H, Xie W, Cui X, Bigner D, Taylor MD, Sampson J, Mitchell D, Bandopadhayay P, Nguyen B, Masoud S, Vue N, Gholamin S, Yu F, Schubert S, Bergthold G, Weiss WA, Mitra S, Qi J, Bradner J, Kieran M, Beroukhim R, Cho YJ, Reddick W, Glass J, Ji Q, Paulus E, James CD, Gajjar A, Ogg R, Vanner R, Remke M, Aviv T, Lee L, Zhu X, Clarke I, Taylor M, Dirks P, Shuman MA, Hamilton R, Pollack I, Calligaris D, Liu X, Feldman D, Thompson C, Ide J, Buhrlage S, Gray N, Kieran M, Jan YN, Stiles C, Agar N, Remke M, Cavalli FMG, Northcott PA, Kool M, Pfister SM, Taylor MD, Project MAGIC, Rakopoulos P, Jan LY, Pajovic S, Buczkowicz P, Morrison A, Bouffet E, Bartels U, Becher O, Hawkins C, Truffaux N, Puget S, Philippe C, Gump W, Castel D, Taylor K, Mackay A, Le Dret L, Saulnier P, Calmon R, Boddaert N, Blauwblomme T, Sainte-Rose C, Jones C, Mutchnick I, Grill J, Liu X, Ebling M, Ide J, Wang L, Davis E, Marchionni M, Stuart D, Alberta J, Kieran M, Li KKW, Stiles C, Agar N, Remke M, Cavalli FMG, Northcott PA, Kool M, Pfister SM, Taylor MD, Project MAGIC, Tien AC, Pang JCS, Griveau A, Rowitch D, Ramkissoon L, Horowitz P, Craig J, Ramkissoon S, Rich B, Bergthold G, Tabori U, Taha H, Ng HK, Bowers D, Hawkins C, Packer R, Eberhart C, Goumnerova L, Chan J, Santagata S, Pomeroy S, Ligon A, Kieran M, Jackson S, Beroukhim R, Ligon K, Kuan CT, Chandramohan V, Keir S, Pastan I, Bigner D, Zhou Z, Ho S, Voss H, Patay Z, Souweidane M, Salloum R, DeWire M, Fouladi M, Goldman S, Chow L, Hummel T, Dorris K, Miles L, Sutton M, Howarth R, Stevenson C, Leach J, Griesinger A, Donson A, Hoffman L, Birks D, Amani V, Handler M, Foreman N, Sangar MC, Pai A, Pedro K, Ditzler SH, Girard E, Olson J, Gustafson WC, Meyerowitz J, Nekritz E, Charron E, Matthay K, Hertz N, Onar-Thomas A, Shokat K, Weiss W, Hanaford A, Raabe E, Eberhart C, Griesinger A, Donson A, Hoffman L, Amani V, Birks D, Gajjar A, Handler M, Mulcahy-Levy J, Foreman N, Olow AK, Dasgupta T, Yang X, Mueller S, Hashizume R, Kolkowitz I, Weiss W, Broniscer A, Resnick AC, Sievert AJ, Nicolaides T, Prados MD, Berger MS, Gupta N, James CD, Haas-Kogan DA, Flores C, Pham C, Dietl SM, Snyder D, Sanchez-Perez L, Bigner D, Sampson J, Mitchell D, Prakash V, Batanian J, Guzman M, Geller T, Pham CD, Wolfl M, Pei Y, Flores C, Snyder D, Bigner DD, Sampson JH, Wechsler-Reya RJ, Mitchell DA, Van Ommeren R, Venugopal C, Manoranjan B, Beilhack A, McFarlane N, Hallett R, Hassell J, Dunn S, Singh S, Dasgupta T, Olow A, Yang X, Hashizume R, Mueller S, Riedel S, Nicolaides T, Kolkowitz I, Weiss W, Prados M, Gupta N, James CD, Haas-Kogan D, Zhao H, Li L, Picotte K, Monoranu C, Stewart R, Modzelewska K, Boer E, Picard D, Huang A, Radiloff D, Lee C, Dunn S, Hutt M, Nazarian J, Dietl S, Price A, Lim KJ, Warren K, Chang H, Eberhart CG, Raabe EH, Persson A, Huang M, Chandler-Militello D, Li N, Vince GH, Berger M, James D, Goldman S, Weiss W, Lindquist R, Tate M, Rowitch D, Alvarez-Buylla A, Hoffman L, Donson A, Eyrich M, Birks D, Griesinger A, Amani V, Handler M, Foreman N, Meijer L, Walker D, Grundy R, O'Dowd S, Jaspan T, Schlegel PG, Dineen R, Fotovati A, Radiloff D, Coute N, Triscott J, Chen J, Yip S, Louis D, Toyota B, Hukin J, Weitzel D, Rassekh SR, Singhal A, Dunham C, Dunn S, Ahsan S, Hanaford A, Taylor I, Eberhart C, Raabe E, Sun YG, Ashcraft K, Stiles C, Han L, Zhang K, Chen L, Shi Z, Pu P, Dong L, Kang C, Cordero F, Lewis P, Liu C, Hoeman C, Schroeder K, Allis CD, Becher O, Gururangan S, Grant G, Driscoll T, Archer G, Herndon J, Friedman H, Li W, Kurtzberg J, Bigner D, Sampson J, Mitchell D, Yadavilli S, Kambhampati M, Becher O, MacDonald T, Bellamkonds R, Packer R, Buckley A, Nazarian J, DeWire M, Fouladi M, Stewart C, Wetmore C, Hawkins C, Jacobs C, Yuan Y, Goldman S, Fisher P, Rodriguez R, Rytting M, Bouffet E, Khakoo Y, Hwang E, Foreman N, Gilbert M, Gilbertson R, Gajjar A, Saratsis A, Yadavilli S, Wetzel W, Snyder K, Kambhampati M, Hall J, Raabe E, Warren K, Packer R, Nazarian J, Thompson J, Griesinger A, Foreman N, Spazojevic I, Rush S, Levy JM, Hutt M, Karajannis MA, Shah S, Eberhart CG, Raabe E, Rodriguez FJ, Gump J, Donson A, Tovmasyan A, Birks D, Handler M, Foreman N, Hankinson T, Torchia J, Khuong-Quang DA, Ho KC, Picard D, Letourneau L, Chan T, Peters K, Golbourn B, Morrissy S, Birks D, Faria C, Foreman N, Taylor M, Rutka J, Pfister S, Bouffet E, Hawkins C, Batinic-Haberle I, Majewski J, Kim SK, Jabado N, Huang A, Ladner T, Tomycz L, Watchmaker J, Yang T, Kaufman L, Pearson M, Dewhirst M, Ogg RJ, Scoggins MA, Zou P, Taherbhoy S, Jones MM, Li Y, Glass JO, Merchant TE, Reddick WE, Conklin HM, Gholamin S, Gajjar A, Khan A, Kumar A, Tye GW, Broaddus WC, Van Meter TE, Shih DJH, Northcott PA, Remke M, Korshunov A, Mitra S, Jones DTW, Kool M, Pfister SM, Taylor MD, Mille F, Levesque M, Remke M, Korshunov A, Izzi L, Kool M, Richard C, Northcott PA, Taylor MD, Pfister SM, Charron F, Yu F, Masoud S, Nguyen B, Vue N, Schubert S, Tolliday N, Kong DS, Sengupta S, Weeraratne D, Schreiber S, Cho YJ, Birks D, Jones K, Griesinger A, Amani V, Handler M, Vibhakar R, Achrol A, Foreman N, Brown R, Rangan K, Finlay J, Olch A, Freyer D, Bluml S, Gate D, Danielpour M, Rodriguez J, Shae JJ, Kim GB, Levy R, Bannykh S, Breunig JJ, Town T, Monje-Deisseroth M, Cho YJ, Weissman I, Cheshier S, Buczkowicz P, Rakopoulos P, Bouffet E, Morrison A, Bartels U, Becher O, Hawkins C, Dey A, Kenney A, Van Gool S, Pauwels F, De Vleeschouwer S, Barszczyk M, Buczkowicz P, Castelo-Branco P, Mack S, Nethery-Brokx K, Morrison A, Taylor M, Dirks P, Tabori U, Hawkins C, Chandramohan V, Keir ST, Bao X, Pastan IH, Kuan CT, Bigner DD, Bender S, Jones D, Kool M, Sturm D, Korshunov A, Lichter P, Pfister SM, Chen M, Lu J, Wang J, Keir S, Zhang M, Zhao S, Mook R, Barak L, Lyerly HK, Chen W, Ramachandran C, Nair S, Escalon E, Khatib Z, Quirrin KW, Melnick S, Kievit F, Stephen Z, Wang K, Silber J, Ellenbogen R, Zhang M, Hutzen B, Studebaker A, Bratasz A, Powell K, Raffel C, Guo C, Chang CC, Wortham M, Chen L, Kernagis D, Qin X, Cho YW, Chi JT, Grant G, McLendon R, Yan H, Ge K, Papadopoulos N, Bigner D, He Y, Cristiano B, Venkataraman S, Birks DK, Alimova I, Harris PS, Dubuc A, Taylor MD, Foreman NK, Vibhakar R, Ichimura K, Fukushima S, Totoki Y, Suzuki T, Mukasa A, Saito N, Kumabe T, Tominaga T, Kobayashi K, Nagane M, Iuchi T, Mizoguchi M, Sasaki T, Tamura K, Sugiyama K, Narita Y, Shibui S, Matsutani M, Shibata T, Nishikawa R, Northcott P, Zichner T, Jones D, Kool M, Jager N, Feychting M, Lannering B, Tynes T, Wesenberg F, Hauser P, Ra YS, Zitterbart K, Jabado N, Chan J, Fults D, Mueller S, Grajkowska W, Lichter P, Korbel J, Pfister S, Kool M, Jones DTW, Jaeger N, Northcott PA, Pugh T, Hovestadt V, Markant SL, Esparza LA, Bourdeaut F, Remke M, Taylor MD, Cho YJ, Pomeroy SL, Schueller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, Keir S, Pegram C, Lipp E, Rasheed A, Chandramohan V, Kuan CT, Kwatra M, Yan H, Bigner D, Chornenkyy Y, Buczkowicz P, Agnihotri S, Becher O, Hawkins C, Rogers H, Mayne C, Kilday JP, Coyle B, Grundy R, Sun T, Warrington N, Luo J, Brooks M, Dahiya S, Sengupta R, Rubin J, Erdreich-Epstein A, Robison N, Ren X, Zhou H, Ji L, Margo A, Jones D, Pfister S, Kool M, Sposto R, Asgharzadeh S, Clifford S, Gustafsson G, Ellison D, Figarella-Branger D, Doz F, Rutkowski S, Lannering B, Pietsch T, Broniscer A, Tatevossian R, Sabin N, Klimo P, Dalton J, Lee R, Gajjar A, Ellison D, Garzia L, Dubuc A, Pitcher G, Northcott P, Mariampillai A, Chan T, Skowron P, Wu X, Yao Y, Hawkins C, Peacock J, Zayne K, Croul S, Rutka J, Kenney A, Huang A, Yang V, Baylin S, Salter M, Taylor M, Ward S, Sengupta R, Rubin J, Garzia L, Morrissy S, Skowron P, Jelveh S, Lindsay P, Largaespada D, Collier L, Dupuy A, Hill R, Taylor M, Lulla RR, Laskowski J, Fangusaro J, DiPatri AJ, Alden T, Vanin EF, Tomita T, Goldman S, Soares MB, Rajagopal MU, Lau LS, Hathout Y, Gordish-Dressman H, Rood B, Datar V, Bochare S, Singh A, Khatau S, Fangusaro J, Goldman S, Lulla R, Rajaram V, Gopalakrishnan V, Morfouace M, Shelat A, Jaccus M, Freeman B, Zindy F, Robinson G, Guy K, Stewart C, Gajjar A, Roussel M, Krebs S, Chow K, Yi Z, Brawley V, Ahmed N, Gottschalk S, Lerner R, Harness J, Yoshida Y, Santos R, Torre JDL, Nicolaides T, Ozawa T, James D, Petritsch C, Vitte J, Chareyre F, Stemmer-Rachamimov A, Giovannini M, Hashizume R, Yu-Jen L, Tom M, Ihara Y, Huang X, Waldman T, Mueller S, Gupta N, James D, Shevtsov M, Yakovleva L, Nikolaev B, Dobrodumov A, Onokhin K, Bychkova N, Mikhrina A, Khachatryan W, Guzhova I, Martynova M, Bystrova O, Ischenko A, Margulis B, Martin A, Nirschl C, Polanczyk M, Cohen K, Pardoll D, Drake C, Lim M, Crowther A, Chang S, Yuan H, Deshmukh M, Gershon T, Meyerowitz JG, Gustafson WC, Nekritz EA, Swartling F, Shokat KM, Ruggero D, Weiss WA, Bergthold G, Rich B, Bandopadhayay P, Chan J, Santaga S, Hoshida Y, Golub T, Tabak B, Ferrer-Luna R, Grill J, Wen PY, Stiles C, Kieran M, Ligon K, Beroukhim R, Lulla RR, Laskowski J, Gireud M, Fangusaro J, Goldman S, Gopalakrishnan V, Merino D, Shlien A, Pienkowska M, Tabori U, Gilbertson R, Malkin D, Mueller S, Hashizume R, Yang X, Kolkowitz I, Olow A, Phillips J, Smirnov I, Tom M, Prados M, Berger M, Gupta N, Haas-Kogan D, Beez T, Sarikaya-Seiwert S, Janssen G, Felsberg J, Steiger HJ, Hanggi D, Marino AM, Baryawno N, Johnsen JI, Ostman A, Wade A, Engler JR, Robinson AE, Phillips JJ, Witt H, Sill M, Mack SC, Wani KM, Lambert S, Tzaridis T, Bender S, Jones DT, Milde T, Northcott PA, Kool M, von Deimling A, Kulozik AE, Witt O, Lichter P, Collins VP, Aldape K, Taylor MD, Korshunov A, Pfister SM, Hatcher R, Das C, Datar V, Taylor P, Singh A, Lee D, Fuller G, Ji L, Fangusaro J, Rajaram V, Goldman S, Eberhart C, Gopalakrishnan V, Griveau A, Lerner R, Ihrie R, Sugiarto S, Ihara Y, Reichholf B, Huillard E, Mcmahon M, James D, Phillips J, Buylla AA, Rowitch D, Petritsch C, Snuderl M, Batista A, Kirkpatrick N, de Almodovar CR, Riedemann L, Knevels E, Schmidt T, Peterson T, Roberge S, Bais C, Yip S, Hasselblatt M, Rossig C, Ferrara N, Klagsbrun M, Duda D, Fukumura D, Xu L, Carmeliet P, Jain R, Nguyen A, Pencreach E, Lasthaus C, Lobstein V, Guerin E, Guenot D, Entz-Werle N, Diaz R, Golbourn B, Faria C, Shih D, MacKenzie D, Picard D, Bryant M, Smith C, Taylor M, Huang A, Rutka J, Gromeier M, Desjardins A, Sampson JH, Threatt SJE, Herndon JE, Friedman A, Friedman HS, Bigner DD, Cavalli FMG, Morrissy AS, Li Y, Chu A, Remke M, Thiessen N, Mungall AJ, Bader GD, Malkin D, Marra MA, Taylor MD, Manoranjan B, Wang X, Hallett R, Venugopal C, Mack S, McFarlane N, Nolte S, Scheinemann K, Gunnarsson T, Hassell J, Taylor M, Lee C, Triscott J, Foster C, Dunham C, Hawkins C, Dunn S, Singh S, McCrea HJ, Bander E, Venn RA, Reiner AS, Iorgulescu JB, Puchi LA, Schaefer PM, Cederquist G, Greenfield JP, Tsoli M, Luk P, Dilda P, Hogg P, Haber M, Ziegler D, Mack S, Agnihotri S, Witt H, Shih D, Wang X, Ramaswamy V, Zayne K, Bertrand K, Massimi L, Grajkowska W, Lach B, Gupta N, Weiss W, Guha A, Zadeh G, Rutka J, Korshunov A, Pfister S, Taylor M, Mack S, Witt H, Jager N, Zuyderduyn S, Nethery-Brokx K, Garzia L, Zayne K, Wang X, Barszczyk M, Wani K, Bouffet E, Weiss W, Hawkins C, Rutka J, Bader G, Aldape K, Dirks P, Pfister S, Korshunov A, Taylor M, Engler J, Robinson A, Wade A, Molinaro A, Phillips J, Ramaswamy V, Remke M, Bouffet E, Faria C, Shih D, Gururangan S, McLendon R, Schuller U, Ligon K, Pomeroy S, Jabado N, Dunn S, Fouladi M, Rutka J, Hawkins C, Tabori U, Packer R, Pfister S, Korshunov A, Taylor M, Faria C, Dubuc A, Golbourn B, Diaz R, Agnihotri S, Sabha N, Luck A, Leadly M, Reynaud D, Wu X, Remke M, Ramaswamy V, Northcott P, Pfister S, Croul S, Kool M, Korshunov A, Smith C, Taylor M, Rutka J, Pietsch T, Doerner E, Muehlen AZ, Velez-Char N, Warmuth-Metz M, Kortmann R, von Hoff K, Friedrich C, Rutkowski S, von Bueren A, Lu YJ, James CD, Hashizume R, Mueller S, Phillips J, Gupta N, Sturm D, Northcott PA, Jones DTW, Korshunov A, Picard D, Lichter P, Huang A, Pfister SM, Kool M, Ward J, Teague C, Shriyan B, Grundy R, Rahman R, Taylor K, Mackay A, Morozova O, Butterfield Y, Truffaux N, Philippe C, Vinci M, de Torres C, Cruz O, Mora J, Hargrave D, Puget S, Yip S, Jones C, Grill J, Smith S, Ward J, Tan C, Grundy R, Rahman R, Bjerke L, Mackay A, Nandhabalan M, Burford A, Jury A, Popov S, Bax D, Carvalho D, Taylor K, Vinci M, Bajrami I, McGonnell I, Lord C, Reis R, Hargrave D, Ashworth A, Workman P, Jones C, Carvalho D, Mackay A, Burford A, Bjerke L, Chen L, Kozarewa I, Lord C, Ashworth A, Hargrave D, Reis R, Jones C, Marigil M, Jauregui PJ, Alonso M, Chan TS, Hawkins C, Picard D, Henkin J, Huang A, Trubicka J, Kucharczyk M, Pelc M, Chrzanowska K, Ciara E, Perek-Polnik M, Grajkowska W, Piekutowska-Abramczuk D, Jurkiewicz D, Luczak S, Borucka-Mankiewicz M, Kowalski P, Krajewska-Walasek M, de Mola RML, Laskowski J, Fangusaro J, Costa FF, Vanin EF, Goldman S, Soares MB, Lulla RR, Mann A, Venugopal C, Vora P, Singh M, van Ommeren R, McFarlane N, Manoranjan B, Qazi M, Scheinemann K, MacDonald P, Delaney K, Whitton A, Dunn S, Singh S, Sievert A, Lang SS, Boucher K, Madsen P, Slaunwhite E, Choudhari N, Kellet M, Storm P, Resnick A, Agnihotri S, Burrell K, Fernandez N, Golbourn B, Clarke I, Barszczyk M, Sabha N, Dirks P, Jones C, Rutka J, Zadeh G, Hawkins C, Murphy B, Obad S, Bihannic L, Ayrault O, Zindy F, Kauppinen S, Roussel M, Golbourn B, Agnihotri S, Cairns R, Mischel P, Aldape K, Hawkins C, Zadeh G, Rutka J, Rush S, Donson A, Kleinschmidt-DeMasters B, Bemis L, Birks D, Chan M, Smith A, Handler M, Foreman N, Gronych J, Jones DTW, Zuckermann M, Hutter S, Korshunov A, Kool M, Ryzhova M, Reifenberger G, Pfister SM, Lichter P, Jones DTW, Hovestadt V, Picelli S, Wang W, Northcott PA, Kool M, Jager N, Reifenberger G, Rutkowski S, Pietsch T, Sultan M, Yaspo ML, Landgraf P, Eils R, Korshunov A, Zapatka M, Pfister SM, Radlwimmer B, Lichter P, Huang Y, Mao H, Wang Y, Kogiso M, Zhao X, Baxter P, Man C, Wang Z, Zhou Y, Li XN, Chung AH, Crabtree D, Schroeder K, Becher OJ, Panosyan E, Wang Y, Lasky J, Liu Z, Zhao X, Wang Y, Mao H, Huang Y, Kogiso M, Baxter P, Adesina A, Su J, Picard D, Huang A, Perlaky L, Chintagumpala M, Lau C, Blaney S, Li XN, Huang M, Persson A, Swartling F, Moriarity B. Abstracts. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tennant BR, Robertson AG, Kramer M, Li L, Zhang X, Beach M, Thiessen N, Chiu R, Mungall K, Whiting CJ, Sabatini PV, Kim A, Gottardo R, Marra MA, Lynn FC, Jones SJM, Hoodless PA, Hoffman BG. Identification and analysis of murine pancreatic islet enhancers. Diabetologia 2013; 56:542-52. [PMID: 23238790 PMCID: PMC4773896 DOI: 10.1007/s00125-012-2797-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/20/2012] [Indexed: 01/05/2023]
Abstract
AIMS/HYPOTHESIS The paucity of information on the epigenetic barriers that are blocking reprogramming protocols, and on what makes a beta cell unique, has hampered efforts to develop novel beta cell sources. Here, we aimed to identify enhancers in pancreatic islets, to understand their developmental ontologies, and to identify enhancers unique to islets to increase our understanding of islet-specific gene expression. METHODS We combined H3K4me1-based nucleosome predictions with pancreatic and duodenal homeobox 1 (PDX1), neurogenic differentiation 1 (NEUROD1), v-Maf musculoaponeurotic fibrosarcoma oncogene family, protein A (MAFA) and forkhead box A2 (FOXA2) occupancy data to identify enhancers in mouse islets. RESULTS We identified 22,223 putative enhancer loci in in vivo mouse islets. Our validation experiments suggest that nearly half of these loci are active in regulating islet gene expression, with the remaining regions probably poised for activity. We showed that these loci have at least nine developmental ontologies, and that islet enhancers predominately acquire H3K4me1 during differentiation. We next discriminated 1,799 enhancers unique to islets and showed that these islet-specific enhancers have reduced association with annotated genes, and identified a subset that are instead associated with novel islet-specific long non-coding RNAs (lncRNAs). CONCLUSIONS/INTERPRETATIONS Our results indicate that genes with islet-specific expression and function tend to have enhancers devoid of histone methylation marks or, less often, that are bivalent or repressed, in embryonic stem cells and liver. Further, we identify a subset of enhancers unique to islets that are associated with novel islet-specific genes and lncRNAs. We anticipate that these data will facilitate the development of novel sources of functional beta cell mass.
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Affiliation(s)
- B. R. Tennant
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - A. G. Robertson
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - M. Kramer
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - L. Li
- Biostatistics Branch, National Institute of Environmental Health Sciences/NIH, Research Triangle Park, NC, USA
| | - X. Zhang
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - M. Beach
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - N. Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - R. Chiu
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - K. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - C. J. Whiting
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - P. V. Sabatini
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - A. Kim
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - R. Gottardo
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M. A. Marra
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - F. C. Lynn
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - S. J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - P. A. Hoodless
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - B. G. Hoffman
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
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Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Guidry Auvil JM, Gerhard DS, Hogarty MD, Jones SJM, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet 2013; 45:279-84. [PMID: 23334666 PMCID: PMC3682833 DOI: 10.1038/ng.2529] [Citation(s) in RCA: 813] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/20/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers.
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Affiliation(s)
- Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Zhang W, Prakash C, Sum C, Gong Y, Li Y, Kwok JJT, Thiessen N, Pettersson S, Jones SJM, Knapp S, Yang H, Chin KC. Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells. J Biol Chem 2012; 287:43137-55. [PMID: 23086925 DOI: 10.1074/jbc.m112.413047] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transcriptional elongation by RNA polymerase II (Pol II) is regulated by positive transcription elongation factor b (P-TEFb) in association with bromodomain-containing protein 4 (BRD4). We used genome-wide chromatin immunoprecipitation sequencing in primary human CD4+ T cells to reveal that BRD4 co-localizes with Ser-2-phosphorylated Pol II (Pol II Ser-2) at both enhancers and promoters of active genes. Disruption of bromodomain-histone acetylation interactions by JQ1, a small-molecule bromodomain inhibitor, resulted in decreased BRD4 binding, reduced Pol II Ser-2, and reduced expression of lineage-specific genes in primary human CD4+ T cells. A large number of JQ1-disrupted BRD4 binding regions exhibited diacetylated H4 (lysine 5 and -8) and H3K27 acetylation (H3K27ac), which correlated with the presence of histone acetyltransferases and deacetylases. Genes associated with BRD4/H3K27ac co-occupancy exhibited significantly higher activity than those associated with H3K27ac or BRD4 binding alone. Comparison of BRD4 binding in T cells and in human embryonic stem cells revealed that enhancer BRD4 binding sites were predominantly lineage-specific. Our findings suggest that BRD4-driven Pol II phosphorylation at serine 2 plays an important role in regulating lineage-specific gene transcription in human CD4+ T cells.
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Affiliation(s)
- Weishi Zhang
- Laboratory of Gene Regulation and Inflammation, SIgN (Singapore Immunology Network), A*STAR (Agency for Science, Technology and Research), Biopolis, Immunos 04-00, 8A Biomedical Grove, Singapore
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Wittmann M, Boehm O, Thiessen N, Hoeft A, Knuefermann P, Baumgarten G. Studentische Evaluation der anästhesiologischen Lehre. Anaesthesist 2012; 61:588-90, 592-6. [DOI: 10.1007/s00101-012-2030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/29/2012] [Accepted: 04/10/2012] [Indexed: 11/30/2022]
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Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, Perizzolo M, Qian J, Roldan G, Smith EE, Tamura-Wells J, Thiessen N, Varhol R, Weiss S, Wu W, Young S, Zhao Y, Mungall AJ, Jones SJM, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol 2011; 226:7-16. [PMID: 22072542 DOI: 10.1002/path.2995] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 11/06/2022]
Abstract
Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of the identity and function of the genes affected by these alterations is limited. We performed exome sequencing on a discovery set of 16 oligodendrogliomas with 1p/19q co-deletion to identify new molecular features at base-pair resolution. As anticipated, there was a high rate of IDH mutations: all cases had mutations in either IDH1 (14/16) or IDH2 (2/16). In addition, we discovered somatic mutations and insertions/deletions in the CIC gene on chromosome 19q13.2 in 13/16 tumours. These discovery set mutations were validated by deep sequencing of 13 additional tumours, which revealed seven others with CIC mutations, thus bringing the overall mutation rate in oligodendrogliomas in this study to 20/29 (69%). In contrast, deep sequencing of astrocytomas and oligoastrocytomas without 1p/19q loss revealed that CIC alterations were otherwise rare (1/60; 2%). Of the 21 non-synonymous somatic mutations in 20 CIC-mutant oligodendrogliomas, nine were in exon 5 within an annotated DNA-interacting domain and three were in exon 20 within an annotated protein-interacting domain. The remaining nine were found in other exons and frequently included truncations. CIC mutations were highly associated with oligodendroglioma histology, 1p/19q co-deletion, and IDH1/2 mutation (p < 0.001). Although we observed no differences in the clinical outcomes of CIC mutant versus wild-type tumours, in a background of 1p/19q co-deletion, hemizygous CIC mutations are likely important. We hypothesize that the mutant CIC on the single retained 19q allele is linked to the pathogenesis of oligodendrogliomas with IDH mutation. Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co-deletion.
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Affiliation(s)
- Stephen Yip
- Department of Pathology and Laboratory Medicine, BC Cancer Agency, BC, Canada
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35
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Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK. Cell of origin in AML: susceptibility to MN1-induced transformation is regulated by the MEIS1/AbdB-like HOX protein complex. Cancer Cell 2011; 20:39-52. [PMID: 21741595 PMCID: PMC3951989 DOI: 10.1016/j.ccr.2011.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [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: 06/22/2010] [Revised: 04/03/2011] [Accepted: 06/06/2011] [Indexed: 12/14/2022]
Abstract
Pathways defining susceptibility of normal cells to oncogenic transformation may be valuable therapeutic targets. We characterized the cell of origin and its critical pathways in MN1-induced leukemias. Common myeloid (CMP) but not granulocyte-macrophage progenitors (GMP) could be transformed by MN1. Complementation studies of CMP-signature genes in GMPs demonstrated that MN1-leukemogenicity required the MEIS1/AbdB-like HOX-protein complex. ChIP-sequencing identified common target genes of MN1 and MEIS1 and demonstrated identical binding sites for a large proportion of their chromatin targets. Transcriptional repression of MEIS1 targets in established MN1 leukemias demonstrated antileukemic activity. As MN1 relies on but cannot activate expression of MEIS1/AbdB-like HOX proteins, transcriptional activity of these genes determines cellular susceptibility to MN1-induced transformation and may represent a promising therapeutic target.
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MESH Headings
- Animals
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genes, Dominant/genetics
- Granulocyte-Macrophage Progenitor Cells/metabolism
- Granulocyte-Macrophage Progenitor Cells/pathology
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Models, Biological
- Multiprotein Complexes/metabolism
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Michael Heuser
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Haiyang Yun
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Tobias Berg
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Bob Argiropoulos
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Florian Kuchenbauer
- Department of Internal Medicine III, University Hospital Medical Center, 89075 Ulm, Germany
| | - Gyeongsin Park
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Iyas Hamwi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Lars Palmqvist
- Institute of Biomedicine, Sahlgrenska University Hospital, 413 45 Göteborg, Sweden
| | - Courteney K. Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Malina Leung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Grace Lin
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Basant Kumar Thakur
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Masayuki Iwasaki
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mikhail Bilenky
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nina Thiessen
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Gordon Robertson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Martin Hirst
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - David Kent
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Bertie Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Connie Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Michael L. Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - R. Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
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Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 2011; 11 Suppl 1:81-92. [PMID: 21429165 DOI: 10.1111/j.1755-0998.2010.02960.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26,595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.
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Affiliation(s)
- Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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Indio V, Pantaleo MA, Astolfi A, Casadio R, Paterini P, Formica S, Martelli P, Moore R, Thiessen N, di Battista M, Catena F, Santini D, Heinrich MC, Gnocchi C, Dei Tos AP, Biasco G. Identification of single nucleotide variants in gastrointestinal stromal tumor KIT/PDGFRA wild-type (WT GISTs) by massively parallel sequencing. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.10046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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38
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Pantaleo MA, Astolfi A, Indio V, Paterini P, Formica S, Casadio R, Martelli P, Maleddu A, Nannini M, Dei Tos AP, Heinrich MC, Santini D, Catena F, Ceccarelli C, Fiorentino M, di Battista M, Moore R, Thiessen N, Gnocchi C, Biasco G. Identification of SDHA (subunit A of the succinate dehydrogenase) mutations in KIT/PDGFRA WT gastrointestinal stromal tumors (GISTs). J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.10045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Somorjai RL, Dolenko B, Nikulin A, Roberson W, Thiessen N. Class proximity measures--dissimilarity-based classification and display of high-dimensional data. J Biomed Inform 2011; 44:775-88. [PMID: 21545844 DOI: 10.1016/j.jbi.2011.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 04/11/2011] [Accepted: 04/16/2011] [Indexed: 11/16/2022]
Abstract
For two-class problems, we introduce and construct mappings of high-dimensional instances into dissimilarity (distance)-based Class-Proximity Planes. The Class Proximity Projections are extensions of our earlier relative distance plane mapping, and thus provide a more general and unified approach to the simultaneous classification and visualization of many-feature datasets. The mappings display all L-dimensional instances in two-dimensional coordinate systems, whose two axes represent the two distances of the instances to various pre-defined proximity measures of the two classes. The Class Proximity mappings provide a variety of different perspectives of the dataset to be classified and visualized. We report and compare the classification and visualization results obtained with various Class Proximity Projections and their combinations on four datasets from the UCI data base, as well as on a particular high-dimensional biomedical dataset.
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Affiliation(s)
- R L Somorjai
- Institute for Biodiagnostics, National Research Council Canada, 435 Ellice Avenue, Winnipeg, MB R3B1Y6, Canada.
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40
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Pantaleo MA, Astolfi A, Indio V, Moore R, Thiessen N, Heinrich MC, Gnocchi C, Santini D, Catena F, Formica S, Martelli PL, Casadio R, Pession A, Biasco G. SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst 2011; 103:983-7. [PMID: 21505157 DOI: 10.1093/jnci/djr130] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Approximately 10%-15% of gastrointestinal stromal tumors (GISTs) in adults do not harbor any mutation in the KIT or PDGFRA genes (ie, KIT/PDGFRA wild-type GISTs). Recently, mutations in SDHB and SDHC (which encode succinate dehydrogenase subunits B and C, respectively) but not in SDHA and SDHD (which encode subunits A and D, respectively) were identified in KIT/PDGFRA wild-type GISTs. To search for novel pathogenic mutations, we sequenced the tumor transcriptome of two young adult patients who developed sporadic KIT/PDGFRA wild-type GISTs by using a massively parallel sequencing approach. The only variants identified as disease related by computational analysis were in SDHA. One patient carried the homozygous nonsense mutation p.Ser384X, the other patient was a compound heterozygote harboring a p.Arg31X nonsense mutation and a p.Arg589Trp missense mutation. The heterozygous nonsense mutations in both patients were present in germline DNA isolated from peripheral blood. Protein structure analysis indicates that all three mutations lead to functional inactivation of the protein. This is the first report, to our knowle dge, that identifies SDHA inactivation as a common oncogenic event in GISTs that lack a mutation in KIT and PDGFRA.
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Affiliation(s)
- Maria A Pantaleo
- Department of Hematology and Oncological Sciences "L.A.Seragnoli," Sant'Orsola-Malpighi Hospital, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
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41
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Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods 2010; 7:909-12. [PMID: 20935650 DOI: 10.1038/nmeth.1517] [Citation(s) in RCA: 595] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/13/2010] [Indexed: 12/20/2022]
Abstract
We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.
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Affiliation(s)
- Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
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Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJM, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010; 466:253-7. [PMID: 20613842 PMCID: PMC3998662 DOI: 10.1038/nature09165] [Citation(s) in RCA: 1218] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 05/06/2010] [Indexed: 12/18/2022]
Abstract
While the methylation of DNA in 5′ promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear1–5. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5′ CpG island (CGI) promoters, while a far greater proportion occurs across gene bodies, coinciding with highly conserved sequences5–10. Tissue-specific intragenic methylation might reduce,3 or, paradoxically, enhance transcription elongation efficiency1,2,4,5. Capped analysis of gene expression (CAGE) experiments also indicate that transcription commonly initiates within and between genes11–15. To investigate the role of intragenic methylation, we generated a map of DNA methylation from human brain encompassing 24.7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were revealed to be in intragenic and intergenic regions, while less than 3% of CpG islands in 5′ promoters were methylated. The CpG islands in all three locations overlapped with RNA markers of transcription initiation, and unmethylated CpG islands also overlapped significantly with trimethylation of H3K4, a histone modification enriched at promoters16. The general and CpG-island-specific patterns of methylation are conserved in mouse tissues. An in-depth investigation of the human SHANK3 locus17,18 and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo. These methylation-regulated, alternative transcripts are expressed in a tissue and cell type-specific manner, and are expressed differentially within a single cell type from distinct brain regions. These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies.
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Affiliation(s)
- Alika K Maunakea
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
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Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol 2010; 11:R82. [PMID: 20696054 PMCID: PMC2945784 DOI: 10.1186/gb-2010-11-8-r82] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [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: 04/12/2010] [Revised: 07/08/2010] [Accepted: 08/09/2010] [Indexed: 01/26/2023] Open
Abstract
Background Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment. Results In the pre-treatment tumor we identified 7,629 genes within regions of copy number gain. There were 1,078 genes that exhibited increased expression relative to the blood and unrelated tumors and four genes contained somatic protein-coding mutations. Our analysis suggested the tumor cells were driven by the RET oncogene. Genes whose protein products are targeted by the RET inhibitors sunitinib and sorafenib correlated with being amplified and or highly expressed. Consistent with our observations, administration of sunitinib was associated with stable disease lasting 4 months, after which the lung lesions began to grow. Administration of sorafenib and sulindac provided disease stabilization for an additional 3 months after which the cancer progressed and new lesions appeared. A recurring metastasis possessed 7,288 genes within copy number amplicons, 385 genes exhibiting increased expression relative to other tumors and 9 new somatic protein coding mutations. The observed mutations and amplifications were consistent with therapeutic resistance arising through activation of the MAPK and AKT pathways. Conclusions We conclude that complete genomic characterization of a rare tumor has the potential to aid in clinical decision making and identifying therapeutic approaches where no established treatment protocols exist. These results also provide direct in vivo genomic evidence for mutational evolution within a tumor under drug selection and potential mechanisms of drug resistance accrual.
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Affiliation(s)
- Steven Jm Jones
- Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada.
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Morozova O, Vojvodic M, Grinshtein N, Hansford LM, Blakely KM, Maslova A, Hirst M, Cezard T, Morin RD, Moore R, Smith KM, Miller F, Taylor P, Thiessen N, Varhol R, Zhao Y, Jones S, Moffat J, Kislinger T, Moran MF, Kaplan DR, Marra MA. System-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma. Clin Cancer Res 2010; 16:4572-82. [PMID: 20651058 DOI: 10.1158/1078-0432.ccr-10-0627] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Neuroblastoma (NB) is an aggressive tumor of the developing peripheral nervous system that remains difficult to cure in the advanced stages. The poor prognosis for high-risk NB patients is associated with common disease recurrences that fail to respond to available therapies. NB tumor-initiating cells (TICs), isolated from metastases and primary tumors, may escape treatment and contribute to tumor relapse. New therapies that target the TICs may therefore prevent or treat tumor recurrences. EXPERIMENTAL DESIGN We undertook a system-level characterization of NB TICs to identify potential drug targets against recurrent NB. We used next-generation RNA sequencing and/or human exon arrays to profile the transcriptomes of 11 NB TIC lines from six NB patients, revealing genes that are highly expressed in the TICs compared with normal neural crest-like cells and unrelated cancer tissues. We used gel-free two-dimensional liquid chromatography coupled to shotgun tandem mass spectrometry to confirm the presence of proteins corresponding to the most abundant TIC-enriched transcripts, thereby providing validation to the gene expression result. RESULTS Our study revealed that genes in the BRCA1 signaling pathway are frequently misexpressed in NB TICs and implicated Aurora B kinase as a potential drug target for NB therapy. Treatment with a selective AURKB inhibitor was cytotoxic to NB TICs but not to the normal neural crest-like cells. CONCLUSION This work provides the first high-resolution system-level analysis of the transcriptomes of 11 primary human NB TICs and identifies a set of candidate NB TIC-enriched transcripts for further development as therapeutic targets.
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Affiliation(s)
- Olena Morozova
- Genome Sciences Centre, BC Cancer Agency, University of British Columbia, Vancouver, British Columbia, Canada.
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Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Genomic analysis of a rare human tumor. BMC Bioinformatics 2010. [PMCID: PMC3290057 DOI: 10.1186/1471-2105-11-s4-o3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJM, Hoodless PA. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res 2010; 20:1037-51. [PMID: 20551221 DOI: 10.1101/gr.104356.109] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The liver and pancreas share a common origin and coexpress several transcription factors. To gain insight into the transcriptional networks regulating the function of these tissues, we globally identify binding sites for FOXA2 in adult mouse islets and liver, PDX1 in islets, and HNF4A in liver. Because most eukaryotic transcription factors bind thousands of loci, many of which are thought to be inactive, methods that can discriminate functionally active binding events are essential for the interpretation of genome-wide transcription factor binding data. To develop such a method, we also generated genome-wide H3K4me1 and H3K4me3 localization data in these tissues. By analyzing our binding and histone methylation data in combination with comprehensive gene expression data, we show that H3K4me1 enrichment profiles discriminate transcription factor occupied loci into three classes: those that are functionally active, those that are poised for activation, and those that reflect pioneer-like transcription factor activity. Furthermore, we demonstrate that the regulated presence of H3K4me1-marked nucleosomes at transcription factor occupied promoters and enhancers controls their activity, implicating both tissue-specific transcription factor binding and nucleosome remodeling complex recruitment in determining tissue-specific gene expression. Finally, we apply these approaches to generate novel insights into how FOXA2, PDX1, and HNF4A cooperate to drive islet- and liver-specific gene expression.
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Affiliation(s)
- Brad G Hoffman
- Department of Cancer Endocrinology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.
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Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Chuah E, Corbett R, Fejes A, Chan S, Liao N, Kasaian K, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Personalized oncogenomics. Genome Biol 2010. [PMCID: PMC3026219 DOI: 10.1186/gb-2010-11-s1-i5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Sleumer MC, Bilenky M, He A, Robertson G, Thiessen N, Jones SJM. Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. Nucleic Acids Res 2009; 37:1323-34. [PMID: 19151087 PMCID: PMC2651782 DOI: 10.1093/nar/gkn1041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The availability of completely sequenced genomes from eight species of nematodes has provided an opportunity to identify novel cis-regulatory elements in the promoter regions of Caenorhabditis elegans transcripts using comparative genomics. We determined orthologues for C. elegans transcripts in C. briggsae, C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Brugia malayi and Trichinella spiralis using the WABA alignment algorithm. We pooled the upstream region of each transcript in C. elegans with the upstream regions of its orthologues and identified conserved DNA sequence elements by de novo motif discovery. In total, we discovered 158 017 novel conserved motifs upstream of 3847 C. elegans transcripts for which three or more orthologues were available, and identified 82% of 44 experimentally proven regulatory elements from ORegAnno. We annotated 26% of the motifs as similar to known binding sequences of transcription factors from ORegAnno, TRANSFAC and JASPAR. This is the first catalogue of annotated conserved upstream elements for nematodes and can be used to find putative regulatory elements, improve gene models, discover novel RNA genes, and understand the evolution of transcription factors and their binding sites in phylum Nematoda. The annotated motifs provide novel binding site candidates for both characterized transcription factors and orthologues of characterized mammalian transcription factors.
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Affiliation(s)
- Monica C Sleumer
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
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Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 2008; 18:1906-17. [PMID: 18787082 DOI: 10.1101/gr.078519.108] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined approximately 270,000 and approximately 301,000 H3K4me1-enriched regions, and approximately 54,500 and approximately 76,100 H3K4me3-enriched regions. In mouse adult liver, we determined approximately 227,000 and approximately 34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the approximately 70,300 STAT1 binding sites in stimulated HeLa cells and 87% of the approximately 11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, approximately 83% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96% of marked distal sites. After filtering against predicted transcription start sites, 50% of approximately 26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95% of approximately 5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding.
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Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res 2008; 36:4549-64. [PMID: 18611952 PMCID: PMC2504304 DOI: 10.1093/nar/gkn382] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP–Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the ∼11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function.
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