1
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Gologorsky MB, Mechler CM, Forgó E, Charville GW, Howitt MR. The abundance and morphology of human large intestinal goblet and tuft cells during chronic schistosomiasis. Parasite Immunol 2023; 45:e12981. [PMID: 37038837 DOI: 10.1111/pim.12981] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/23/2023] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
Schistosomiasis affects nearly 240 million people in predominately low- and middle-income countries and ranks second in the number of cases and socio-economic burden among all parasitic diseases. Despite the enormous burden posed by schistosomes, our understanding of how schistosomiasis impacts infected human tissues remains limited. Intestinal schistosomiasis in animal models leads to goblet cell hyperplasia, likely increasing mucus production and reflecting an intestinal type 2 immune response. However, it is unknown whether these same changes occur in schistosome-infected humans. Using immunofluorescence and light microscopy, we compared the abundance and morphology of goblet cells in patients diagnosed with schistosomiasis to uninfected controls. The mucin-containing vesicles in goblet cells from schistosome-infected patients were significantly larger (hypertrophic) than uninfected individuals, although goblet cell hyperplasia was absent in chronic human schistosomiasis. In addition, we examined tuft cells in the large intestinal epithelium of control and schistosome-infected patients. Tuft cell numbers expand during helminth infection in mice, but these cells have not been characterized in human parasite infections. We found no evidence of tuft cell hyperplasia during human schistosome infection. Thus, our study provides novel insight into schistosome-associated changes to the intestinal epithelium in humans, suggesting an increase in mucus production by large intestinal goblet cells but relatively minor effects on tuft cell numbers.
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Affiliation(s)
- Matthew B Gologorsky
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Claire M Mechler
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Gregory W Charville
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Palo Alto, California, USA
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2
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Jurmeister P, Glöß S, Roller R, Leitheiser M, Schmid S, Mochmann LH, Payá Capilla E, Fritz R, Dittmayer C, Friedrich C, Thieme A, Keyl P, Jarosch A, Schallenberg S, Bläker H, Hoffmann I, Vollbrecht C, Lehmann A, Hummel M, Heim D, Haji M, Harter P, Englert B, Frank S, Hench J, Paulus W, Hasselblatt M, Hartmann W, Dohmen H, Keber U, Jank P, Denkert C, Stadelmann C, Bremmer F, Richter A, Wefers A, Ribbat-Idel J, Perner S, Idel C, Chiariotti L, Della Monica R, Marinelli A, Schüller U, Bockmayr M, Liu J, Lund VJ, Forster M, Lechner M, Lorenzo-Guerra SL, Hermsen M, Johann PD, Agaimy A, Seegerer P, Koch A, Heppner F, Pfister SM, Jones DTW, Sill M, von Deimling A, Snuderl M, Müller KR, Forgó E, Howitt BE, Mertins P, Klauschen F, Capper D. DNA methylation-based classification of sinonasal tumors. Nat Commun 2022; 13:7148. [PMID: 36443295 PMCID: PMC9705411 DOI: 10.1038/s41467-022-34815-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent potentially previously misclassified adenoid cystic carcinomas. Our findings can aid in improving the diagnostic classification of sinonasal tumors and could help to change the current perception of SNUCs.
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Affiliation(s)
- Philipp Jurmeister
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany ,grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Glöß
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Renée Roller
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maximilian Leitheiser
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simone Schmid
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Liliana H. Mochmann
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Emma Payá Capilla
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Rebecca Fritz
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carsten Dittmayer
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Corinna Friedrich
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849MDC Graduate School, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Anne Thieme
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Philipp Keyl
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Armin Jarosch
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simon Schallenberg
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hendrik Bläker
- grid.411339.d0000 0000 8517 9062Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Inga Hoffmann
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Vollbrecht
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Lehmann
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Hummel
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Heim
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Patrick Harter
- grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7839.50000 0004 1936 9721Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Englert
- grid.411095.80000 0004 0477 2585Institute of Neuropathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Stephan Frank
- grid.410567.1Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Jürgen Hench
- grid.410567.1Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Werner Paulus
- grid.16149.3b0000 0004 0551 4246Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- grid.16149.3b0000 0004 0551 4246Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Wolfgang Hartmann
- grid.16149.3b0000 0004 0551 4246Division of Translational Pathology, Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Hildegard Dohmen
- grid.8664.c0000 0001 2165 8627Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Ursula Keber
- grid.10253.350000 0004 1936 9756Institute of Neuropathology, Philipps-University, Marburg, Germany
| | - Paul Jank
- grid.10253.350000 0004 1936 9756Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Carsten Denkert
- grid.10253.350000 0004 1936 9756Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, Marburg, Germany
| | - Christine Stadelmann
- grid.411984.10000 0001 0482 5331Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Felix Bremmer
- grid.411984.10000 0001 0482 5331Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Annika Richter
- grid.411984.10000 0001 0482 5331Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Annika Wefers
- grid.5253.10000 0001 0328 4908Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.13648.380000 0001 2180 3484Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julika Ribbat-Idel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany ,grid.418187.30000 0004 0493 9170Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany ,grid.452624.3German Center for Lung Research (DZL), Partner Site Luebeck, Luebeck, Germany
| | - Christian Idel
- grid.412468.d0000 0004 0646 2097Department of Otorhinolaryngology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Lorenzo Chiariotti
- grid.4691.a0000 0001 0790 385XDipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy ,grid.4691.a0000 0001 0790 385XCEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Rosa Della Monica
- grid.4691.a0000 0001 0790 385XCEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Alfredo Marinelli
- grid.4691.a0000 0001 0790 385XDepartment of Medicina Clinica e Chirurgia, University Federico II, Naples, Italy
| | - Ulrich Schüller
- grid.13648.380000 0001 2180 3484Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.470174.1Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Michael Bockmayr
- grid.6363.00000 0001 2218 4662Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany ,grid.13648.380000 0001 2180 3484Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.470174.1Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Jacklyn Liu
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Valerie J. Lund
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Martin Forster
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Matt Lechner
- grid.83440.3b0000000121901201UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK ,grid.83440.3b0000000121901201UCL Academic Head and Neck Centre, Division of Surgery and Interventional Science, University College London, London, UK
| | - Sara L. Lorenzo-Guerra
- grid.511562.4Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mario Hermsen
- grid.511562.4Department of Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pascal D. Johann
- Swabian Childrens’ Cancer Center, University Childrens’ Hospital Augsburg and EU-RHAB Registry, Augsburg, Germany
| | - Abbas Agaimy
- grid.411668.c0000 0000 9935 6525Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Philipp Seegerer
- grid.6734.60000 0001 2292 8254Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, Berlin, Germany
| | - Arend Koch
- grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Frank Heppner
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- grid.5253.10000 0001 0328 4908Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matija Snuderl
- grid.240324.30000 0001 2109 4251Division of Neuropathology, NYU Langone Health, New York, USA ,grid.240324.30000 0001 2109 4251Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, USA ,grid.240324.30000 0001 2109 4251Division of Molecular Pathology and Diagnostics, NYU Langone Health, New York, USA
| | - Klaus-Robert Müller
- grid.6734.60000 0001 2292 8254Machine-Learning Group, Department of Software Engineering and Theoretical Computer Science, Technical University of Berlin, Berlin, Germany ,grid.222754.40000 0001 0840 2678Department of Artificial Intelligence, Korea University, Seoul, South Korea ,grid.419528.30000 0004 0491 9823Max-Planck-Institute for Informatics, Saarbrücken, Germany ,BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Erna Forgó
- grid.168010.e0000000419368956Stanford University School of Medicine, Stanford, CA USA
| | - Brooke E. Howitt
- grid.168010.e0000000419368956Stanford University School of Medicine, Stanford, CA USA
| | - Philipp Mertins
- grid.484013.a0000 0004 6879 971XProteomics Platform, Berlin Institute of Health (BIH) and Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Frederick Klauschen
- grid.411095.80000 0004 0477 2585Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany ,grid.7497.d0000 0004 0492 0584 German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - David Capper
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.6363.00000 0001 2218 4662Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, Berlin, Germany
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3
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Lu G, Baertsch MA, Hickey JW, Goltsev Y, Rech AJ, Mani L, Forgó E, Kong C, Jiang S, Nolan GP, Rosenthal EL. A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data. Front Immunol 2022; 13:981825. [PMID: 36211386 PMCID: PMC9539451 DOI: 10.3389/fimmu.2022.981825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
Highly multiplexed, single-cell imaging has revolutionized our understanding of spatial cellular interactions associated with health and disease. With ever-increasing numbers of antigens, region sizes, and sample sizes, multiplexed fluorescence imaging experiments routinely produce terabytes of data. Fast and accurate processing of these large-scale, high-dimensional imaging data is essential to ensure reliable segmentation and identification of cell types and for characterization of cellular neighborhoods and inference of mechanistic insights. Here, we describe RAPID, a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data. RAPID deconvolves large-scale, high-dimensional fluorescence imaging data, stitches and registers images with axial and lateral drift correction, and minimizes tissue autofluorescence such as that introduced by erythrocytes. Incorporation of an open source CUDA-driven, GPU-assisted deconvolution produced results similar to fee-based commercial software. RAPID reduces data processing time and artifacts and improves image contrast and signal-to-noise compared to our previous image processing pipeline, thus providing a useful tool for accurate and robust analysis of large-scale, multiplexed, fluorescence imaging data.
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Affiliation(s)
- Guolan Lu
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Marc A. Baertsch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - John W. Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Andrew J. Rech
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Lucas Mani
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Christina Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Garry P. Nolan, ; Eben L. Rosenthal,
| | - Eben L. Rosenthal
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, CA, United States
- *Correspondence: Garry P. Nolan, ; Eben L. Rosenthal,
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4
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Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Pisco AO, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Crasta S, Culver RN, Cvijović I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kolluru S, Kong W, Kumar ME, Kuo AH, Leylek R, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Morri M, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Phansalkar R, Pisco AO, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Travaglini KJ, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Tan SY, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Detweiler AM, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, de Morree A, Olivieri JE, Park M, Pisco AO, Ravikumar N, Salzman J, Stanley G, Swift M, Tan M, Tan W, Tarashansky AJ, Vanheusden R, Vorperian SK, Wang P, Wang S, Xing G, Xu C, Yosef N, Alcántara-Hernández M, Antony J, Chan CKF, Chang CA, Colville A, Crasta S, Culver R, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Kershner AM, Kong W, Kumar ME, Kuo AH, Leylek R, Liu S, Loeb GB, Lu WJ, Maltzman JS, Metzger RJ, de Morree A, Neuhöfer P, Perez K, Phansalkar R, Qi Z, Rao P, Raquer-McKay H, Sasagawa K, Scott B, Sinha R, Song H, Spencer SP, Swarup A, Swift M, Travaglini KJ, Trimm E, Veizades S, Vijayakumar S, Wang B, Wang W, Winkler J, Xie J, Yung AR, Artandi SE, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Krasnow M, Kuo CS, Nguyen P, Quake SR, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wang B, Wu A, Wu SM, Wyss-Coray T. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 2022; 376:eabl4896. [PMID: 35549404 PMCID: PMC9812260 DOI: 10.1126/science.abl4896] [Citation(s) in RCA: 225] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.
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McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol 2022; 23:814. [PMID: 35277696 PMCID: PMC9098386 DOI: 10.1038/s41590-022-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sanjana Gupta
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratista K Ramdial
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Smriti Mehra
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert L Hunter
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Hsu D, Martin B, Forgó E, Greene E, Hassan M, Bass D. Tough to Swallow: Dysphagia in a Child with an Aberrant Left Subclavian Artery. Dig Dis Sci 2021; 66:2882-2887. [PMID: 33433797 DOI: 10.1007/s10620-020-06777-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 12/09/2022]
Affiliation(s)
- Diane Hsu
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, Stanford, CA, USA.
| | - Brock Martin
- Department of Surgical Pathology, Stanford University, Stanford, CA, USA
| | - Erna Forgó
- Department of Surgical Pathology, Stanford University, Stanford, CA, USA
| | - Elton Greene
- Department of Pediatric Radiology, Stanford University, Stanford, CA, USA
| | - Maheen Hassan
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, Stanford, CA, USA
| | - Dorsey Bass
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, Stanford, CA, USA
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Affiliation(s)
- Irmina A Elliott
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA.
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natalie S Lui
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
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Abstract
AIMS Mucin 4 (MUC4) is a transmembrane glycoprotein normally expressed by several human epithelial surfaces, including those of the colon, vagina, and respiratory tract. Although MUC4 overexpression is seen in various carcinomas, its expression among mesenchymal neoplasms is fairly specific to low-grade fibromyxoid sarcoma and sclerosing epithelioid fibrosarcoma. Having observed unanticipated anti-MUC4 immunoreactivity in rhabdomyosarcoma, we aimed to further characterise its expression. METHODS AND RESULTS Expression of MUC4 was assessed by immunohistochemistry in a total of 97 rhabdomyosarcomas using formalin-fixed paraffin-embedded tissue sections. MUC4 was expressed by 21 of 26 PAX3/7-FOXO1 fusion-positive cases, wherein immunoreactivity, varying from weak to strong, was present in 20-100% of neoplastic cells. With the exception of one sclerosing rhabdomyosarcoma showing immunoreactivity in 20% of cells, MUC4 was not expressed by embryonal (n = 28), sclerosing (n = 20), or pleomorphic (n = 23) rhabdomyosarcomas. Analysing published gene expression microarray data from a separate cohort of 33 fusion-positive and 25 fusion-negative rhabdomyosarcomas, we found on average a 11.4-fold increased expression in fusion-positive tumours (P = 0.0004). CONCLUSIONS MUC4 is expressed to a variable extent in the majority of PAX3/7-FOXO1 fusion-positive (alveolar) rhabdomyosarcomas, while expression in other rhabdomyosarcoma subtypes is rare.
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Affiliation(s)
- Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gregory W Charville
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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9
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Affiliation(s)
- Ioana Baiu
- grid.168010.e0000000419368956Department of Surgery, Stanford University School of Medicine, 300 Pasteur Drive, H3563, Stanford, CA 94305 USA
| | - Erna Forgó
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, L235, Stanford, CA 94305 USA
| | - Cindy Kin
- grid.168010.e0000000419368956Department of Surgery, Stanford University School of Medicine, 300 Pasteur Drive, H3563, Stanford, CA 94305 USA
| | - Thomas G. Weiser
- grid.168010.e0000000419368956Department of Surgery, Stanford University School of Medicine, 300 Pasteur Drive, H3563, Stanford, CA 94305 USA
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10
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Forgó E, Gomez AJ, Steiner D, Zehnder J, Longacre TA. Morphological, immunophenotypical and molecular features of hypermutation in colorectal carcinomas with mutations in DNA polymerase ε (POLE). Histopathology 2019; 76:366-374. [PMID: 31479159 DOI: 10.1111/his.13984] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/16/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
Abstract
AIMS Colorectal carcinomas (CRC) with mismatch repair (MMR) deficiency have increased tumour mutation burden and respond to immune check-point inhibitor therapy. The Cancer Genome Atlas identified hypermutated CRCs with somatic mutations in DNA polymerase ε (POLE) with mutation burdens exceeding that of MMR-deficient CRCs. METHODS AND RESULTS To identify the morphological, immunophenotypical and molecular features of POLE-mutated CRCs, 63 consecutive MMR-intact CRCs were evaluated by Sanger sequencing for POLE exonuclease domain mutations in exons 9, 11, 13 and 14 and confirmed by next-generation sequencing. Tumour immune microenvironment and IMMUNOSCORE®1 were assessed in POLE-mutated CRCs using immunohistochemistry to detect CD3+ /CD8+ tumour-infiltrating lymphocytes and compared to 59 non-POLE mutated MMR-intact CRC, 10 non-POLE mutated MMR-deficient CRCs and 223 normal colonic mucosa. CONCLUSIONS A total of 4.8% CRC (four MMR-intact primary and one MMR-intact metastasis) harboured POLE mutations in amino acid 286 in exon 9 (p.P286R) or exon 13 (p.V411L). POLE-mutated CRCs arose in the transverse colon and rectum, were male-predominant, younger and showed increased tumour-infiltrating lymphocytes and immune cells at the tumour-stromal interface. The patient with metastatic POLE-mutated CRC was placed on PD-1 inhibitor treatment with marked and sustained response. These data indicate that POLE-mutated CRCs have hypermutated phenotypes despite MMR-intact status, with mutation burdens higher than that in microsatellite-unstable CRCs. Given the recent approval for treatment of microsatellite-unstable cancer with immune check-point inhibitors, assessment of POLE status may help to guide therapeutic decisions for hypermutated tumours with intact MMR that would otherwise be missed by routine testing.
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Affiliation(s)
- Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Gomez
- Department of Pathology, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - David Steiner
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Teri A Longacre
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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11
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Przybyl J, Spans L, Lum DA, Zhu S, Vennam S, Forgó E, Varma S, Ganjoo K, Hastie T, Bowen R, Debiec-Rychter M, van de Rijn M. Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas. JCO Precis Oncol 2019; 3. [PMID: 32232185 PMCID: PMC7105159 DOI: 10.1200/po.18.00409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/20/2022] Open
Abstract
PURPOSE The preoperative distinction between uterine leiomyoma (LM) and leiomyosarcoma (LMS) is difficult, which may result in dissemination of an unexpected malignancy during surgery for a presumed benign lesion. An assay based on circulating tumor DNA (ctDNA) could help in the preoperative distinction between LM and LMS. This study addresses the feasibility of applying the two most frequently used approaches for detection of ctDNA: profiling of copy number alterations (CNAs) and point mutations in the plasma of patients with LM. PATIENTS AND METHODS By shallow whole-genome sequencing, we prospectively examined whether LM-derived ctDNA could be detected in plasma specimens of 12 patients. Plasma levels of lactate dehydrogenase, a marker suggested for the distinction between LM and LMS by prior studies, were also determined. We also profiled 36 LM tumor specimens by exome sequencing to develop a panel for targeted detection of point mutations in ctDNA of patients with LM. RESULTS We identified tumor-derived CNAs in the plasma DNA of 50% (six of 12) of patients with LM. The lactate dehydrogenase levels did not allow for an accurate distinction between patients with LM and patients with LMS. We identified only two recurrently mutated genes in LM tumors (MED12 and ACLY). CONCLUSION Our results show that LMs do shed DNA into the circulation, which provides an opportunity for the development of ctDNA-based testing to distinguish LM from LMS. Although we could not design an LM-specific panel for ctDNA profiling, we propose that the detection of CNAs or point mutations in selected tumor suppressor genes in ctDNA may favor a diagnosis of LMS, since these genes are not affected in LM.
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Affiliation(s)
| | - Lien Spans
- KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Deirdre A Lum
- Stanford University School of Medicine, Stanford, CA
| | - Shirley Zhu
- Stanford University School of Medicine, Stanford, CA
| | - Sujay Vennam
- Stanford University School of Medicine, Stanford, CA
| | - Erna Forgó
- Stanford University School of Medicine, Stanford, CA
| | - Sushama Varma
- Stanford University School of Medicine, Stanford, CA
| | | | | | - Raffick Bowen
- Stanford University School of Medicine, Stanford, CA
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12
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Przybyl J, Chabon JJ, Spans L, Ganjoo KN, Vennam S, Newman AM, Forgó E, Varma S, Zhu S, Debiec-Rychter M, Alizadeh AA, Diehn M, van de Rijn M. Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma. Clin Cancer Res 2018; 24:2688-2699. [PMID: 29463554 DOI: 10.1158/1078-0432.ccr-17-3704] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/16/2018] [Accepted: 02/15/2018] [Indexed: 12/31/2022]
Abstract
Purpose: The clinical utility of circulating tumor DNA (ctDNA) monitoring has been shown in tumors that harbor highly recurrent mutations. Leiomyosarcoma represents a type of tumor with a wide spectrum of heterogeneous genomic abnormalities; thus, targeting hotspot mutations or a narrow genomic region for ctDNA detection may not be practical. Here, we demonstrate a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single-nucleotide variants (SNV), small indels, and copy-number alterations (CNA) in ctDNA.Experimental Design: We employed Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with leiomyosarcoma.Results: We detected ctDNA in 6 of 7 of these patients with >98% specificity for mutant allele fractions down to a level of 0.01%. We show that results from CAPP-Seq and GRP are highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. By analyzing multiple tumor specimens in individual patients obtained from different sites and at different times during treatment, we observed clonal evolution of these tumors that was reflected by ctDNA profiles.Conclusions: Our strategy allows for the comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma. Our approach may be clinically useful not only in leiomyosarcoma but also in other tumor types that lack recurrent genomic alterations. Clin Cancer Res; 24(11); 2688-99. ©2018 AACR.
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Affiliation(s)
- Joanna Przybyl
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| | - Jacob J Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Lien Spans
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Kristen N Ganjoo
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Shirley Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Maria Debiec-Rychter
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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13
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Przybyl J, Chabon JJ, Spans L, Ganjoo K, Vennam S, Newman AM, Forgó E, Varma S, Zhu S, Debiec-Rychter M, Alizadeh A, Diehn M, Rijn MVD. Abstract A05: Circulating tumor DNA levels correlate with response to treatment in LMS patients. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-a05] [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
Circulating tumor DNA (ctDNA) has significant potential for several clinical applications, including assessment of treatment response and monitoring of recurrent/residual disease. We performed a pilot study to explore the feasibility of ctDNA monitoring in patients with leiomyosarcoma (LMS).
We profiled matching plasma and FFPE tumor specimens from 9 LMS patients. We analyzed between 2 to 6 longitudinal plasma samples (median of 5) and between 1 to 7 tumor specimens (median of 2) per patient. ctDNA analysis was performed on plasma samples collected pre-/post-surgery, throughout chemo-/radiotherapy and during follow-up. We used two separate approaches in our study: 1) targeted deep sequencing of ctDNA, tumor DNA and germline DNA to detect single nucleotide variants and indels using Cancer Personalized Profiling by deep Sequencing with integrated digital error suppression (CAPP-Seq; with a median deduplicated depth of sequencing of 2,136x); 2) copy number variant analysis in ctDNA by genome representation profiling (GRP; median coverage across the whole genome 0.23x) and in the matched tumors by SNP arrays. One patient was excluded from the analysis due to inadequate sequencing coverage in tumor specimen.
For CAPP-Seq analysis, we designed a custom 184kb capture panel targeting 89 genes that are recurrently mutated in LMS. Using strict variant calling criteria (requiring that variants be present on each strand of the original DNA “duplex” molecule) our panel identified a median of one nonsynonymous coding/splicing variant per tumor. We detected the same variants in TP53, RB1 and ATRX genes in ctDNA of 6/8 patients (with a baseline sensitivity of 87.5% and overall specificity of 98.96% calculated using plasma from 24 healthy donors). These six patients presented with advanced disease at the time of the first blood collection and were progressing throughout multiple lines of therapy. Two patients who did not have any variants detectable by CAPP-Seq in plasma had localized disease at the time of the first blood collection and/or responded well to the therapy. We found that changes in ctDNA levels appear to correspond with the extent of disease and response to treatment. Specifically, ctDNA levels decreased in a subset of patients after surgery or at the time of temporary response to chemo- and/or radiotherapy. Congruently, increases in ctDNA levels correlated with progression in most of the patients. There was a high correlation between ctDNA levels detected by CAPP-Seq (quantified as mutant molecules/mL plasma) and GRP (quantified as percent of genome showing copy number aberrations) across all plasma samples (Pearson's r= 0.88, p < 0.0001), but in a few samples ctDNA was detected by only one of the two assays.
Our results suggest that serial analysis of ctDNA is a promising approach for evaluation of treatment response in LMS patients. Validation of these findings in a prospective study on a larger group of patients will be required to determine the use of this approach in a clinical setting.
References:
CAPP-Seq: PMIDs 24705333, 27018799
GRP: PMIDs 25585704, 26687610
Citation Format: Joanna Przybyl, Jacob J. Chabon, Lien Spans, Kristen Ganjoo, Sujay Vennam, Aaron M. Newman, Erna Forgó, Sushama Varma, Shirley Zhu, Maria Debiec-Rychter, Ash Alizadeh, Maximilian Diehn, Matt van de Rijn. Circulating tumor DNA levels correlate with response to treatment in LMS patients [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A05.
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Affiliation(s)
| | | | - Lien Spans
- 2KU Leuven and University Hospitals, Leuven, Belgium
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14
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Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF. CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med 2016; 374:211-22. [PMID: 26789870 PMCID: PMC4784450 DOI: 10.1056/nejmoa1506597] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [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: 12/15/2022]
Abstract
Background The identification of high-risk stage II colon cancers is key to the selection of patients who require adjuvant treatment after surgery. Microarray-based multigene-expression signatures derived from stem cells and progenitor cells hold promise, but they are difficult to use in clinical practice. Methods We used a new bioinformatics approach to search for biomarkers of colon epithelial differentiation across gene-expression arrays and then ranked candidate genes according to the availability of clinical-grade diagnostic assays. With the use of subgroup analysis involving independent and retrospective cohorts of patients with stage II or stage III colon cancer, the top candidate gene was tested for its association with disease-free survival and a benefit from adjuvant chemotherapy. Results The transcription factor CDX2 ranked first in our screening test. A group of 87 of 2115 tumor samples (4.1%) lacked CDX2 expression. In the discovery data set, which included 466 patients, the rate of 5-year disease-free survival was lower among the 32 patients (6.9%) with CDX2-negative colon cancers than among the 434 (93.1%) with CDX2-positive colon cancers (hazard ratio for disease recurrence, 3.44; 95% confidence interval [CI], 1.60 to 7.38; P=0.002). In the validation data set, which included 314 patients, the rate of 5-year disease-free survival was lower among the 38 patients (12.1%) with CDX2 protein-negative colon cancers than among the 276 (87.9%) with CDX2 protein-positive colon cancers (hazard ratio, 2.42; 95% CI, 1.36 to 4.29; P=0.003). In both these groups, these findings were independent of the patient's age, sex, and tumor stage and grade. Among patients with stage II cancer, the difference in 5-year disease-free survival was significant both in the discovery data set (49% among 15 patients with CDX2-negative tumors vs. 87% among 191 patients with CDX2-positive tumors, P=0.003) and in the validation data set (51% among 15 patients with CDX2-negative tumors vs. 80% among 106 patients with CDX2-positive tumors, P=0.004). In a pooled database of all patient cohorts, the rate of 5-year disease-free survival was higher among 23 patients with stage II CDX2-negative tumors who were treated with adjuvant chemotherapy than among 25 who were not treated with adjuvant chemotherapy (91% vs. 56%, P=0.006). Conclusions Lack of CDX2 expression identified a subgroup of patients with high-risk stage II colon cancer who appeared to benefit from adjuvant chemotherapy. (Funded by the National Comprehensive Cancer Network, the National Institutes of Health, and others.).
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Affiliation(s)
- Piero Dalerba
- From the Herbert Irving Comprehensive Cancer Center and the Departments of Pathology and Cell Biology and Medicine, Columbia University, New York (P.D.); Institute for Stem Cell Biology and Regenerative Medicine (P.D., D.S., P.S.R., S.P.M., S.H., J.H., D.Q., M.F.C.) and the Departments of Pathology (X.G., E.F., M.R.), and Medicine, Division of Oncology (N.W.-F., G.A.F., M.F.C.), Stanford University, Stanford, and the Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego (D.S.) - both in California; Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel (T.K.); the National Surgical Adjuvant Breast and Bowel Project, NRG Oncology (S.P., G.Y., N.S., N.W.) and the Allegheny Cancer Center at Allegheny General Hospital (N.W.) - both in Pittsburgh; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea (S.P.); and the Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng, China (X.G.)
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15
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Abstract
Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation. Little is known about its molecular heterogeneity and no targeted therapy currently exists for LMS. We performed expression profiling on 99 cases of LMS with 3'end RNA sequencing (3SEQ) and demonstrated the existence of 3 molecular subtypes in this cohort. We consequently showed that these molecular subtypes are reproducible using an independent cohort of 82 LMS cases from TCGA. Two new formalin-fixed, paraffin-embedded (FFPE) tissue-compatible diagnostic immunohistochemical markers were identified for two of the three subtypes: LMOD1 for subtype I LMS and ARL4C for subtype II LMS. Subtype I and subtype II LMS were associated with good and poor prognosis, respectively. Here, we describe the details of LMS diagnosis, RNA isolation, 3SEQ library construction, 3SEQ sequencing data analysis and molecular subtype determination. The 3SEQ data produced in this study was deposited into Gene Expression Omnibus (GEO) under GSE45510.
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Affiliation(s)
- Xiangqian Guo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305 USA ; Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng, Henan, 475004 China
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305 USA
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16
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Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB. Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer. Breast Cancer Res 2015; 17:108. [PMID: 26265211 PMCID: PMC4534146 DOI: 10.1186/s13058-015-0623-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 03/24/2015] [Accepted: 07/24/2015] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Screening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from lineage evolution analysis, we examined whether measuring genomic features of DCIS would predict association with invasive breast carcinoma (IBC). The long-term goal is to enhance standard clinicopathologic measures of low- versus high-risk DCIS and to enable risk-appropriate treatment. METHODS We studied three common chromosomal copy number alterations (CNA) in IBC and designed fluorescence in situ hybridization-based assay to measure copy number at these loci in DCIS samples. Clinicopathologic data were extracted from the electronic medical records of Stanford Cancer Institute and linked to demographic data from the population-based California Cancer Registry; results were integrated with data from tissue microarrays of specimens containing DCIS that did not develop IBC versus DCIS with concurrent IBC. Multivariable logistic regression analysis was performed to describe associations of CNAs with these two groups of DCIS. RESULTS We examined 271 patients with DCIS (120 that did not develop IBC and 151 with concurrent IBC) for the presence of 1q, 8q24 and 11q13 copy number gains. Compared to DCIS-only patients, patients with concurrent IBC had higher frequencies of CNAs in their DCIS samples. On multivariable analysis with conventional clinicopathologic features, the copy number gains were significantly associated with concurrent IBC. The state of two of the three copy number gains in DCIS was associated with a risk of IBC that was 9.07 times that of no copy number gains, and the presence of gains at all three genomic loci in DCIS was associated with a more than 17-fold risk (P = 0.0013). CONCLUSIONS CNAs have the potential to improve the identification of high-risk DCIS, defined by presence of concurrent IBC. Expanding and validating this approach in both additional cross-sectional and longitudinal cohorts may enable improved risk stratification and risk-appropriate treatment in DCIS.
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Affiliation(s)
- Anosheh Afghahi
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Aya A Mitani
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Tina Seto
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Joseph Rigdon
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Kristin C Jensen
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
- Pathology and Laboratory Medicine, Palo Alto Veterans Affairs Health Care System, 795 Willow Road, Palo Alto, CA, 94025, USA.
| | - Megan L Troxell
- Department of Pathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
| | - Scarlett Lin Gomez
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
- Cancer Prevention Institute of California (CPIC), 2201 Walnut Avenue, Fremont, CA, 94538, USA.
| | - Amar K Das
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Psychiatry and The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine, 1 Rope Ferry Road, Lebanon, NH, 03755, USA.
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA.
| | - Allison W Kurian
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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Guo X, Jo VY, Mills AM, Zhu SX, Lee CH, Espinosa I, Nucci MR, Varma S, Forgó E, Hastie T, Anderson S, Ganjoo K, Beck AH, West RB, Fletcher CD, van de Rijn M. Clinically Relevant Molecular Subtypes in Leiomyosarcoma. Clin Cancer Res 2015; 21:3501-11. [PMID: 25896974 DOI: 10.1158/1078-0432.ccr-14-3141] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/11/2015] [Indexed: 01/23/2023]
Abstract
PURPOSE Leiomyosarcoma is a malignant neoplasm with smooth muscle differentiation. Little is known about its molecular heterogeneity and no targeted therapy currently exists for leiomyosarcoma. Recognition of different molecular subtypes is necessary to evaluate novel therapeutic options. In a previous study on 51 leiomyosarcomas, we identified three molecular subtypes in leiomyosarcoma. The current study was performed to determine whether the existence of these subtypes could be confirmed in independent cohorts. EXPERIMENTAL DESIGN Ninety-nine cases of leiomyosarcoma were expression profiled with 3'end RNA-Sequencing (3SEQ). Consensus clustering was conducted to determine the optimal number of subtypes. RESULTS We identified 3 leiomyosarcoma molecular subtypes and confirmed this finding by analyzing publically available data on 82 leiomyosarcoma from The Cancer Genome Atlas (TCGA). We identified two new formalin-fixed, paraffin-embedded tissue-compatible diagnostic immunohistochemical markers; LMOD1 for subtype I leiomyosarcoma and ARL4C for subtype II leiomyosarcoma. A leiomyosarcoma tissue microarray with known clinical outcome was used to show that subtype I leiomyosarcoma is associated with good outcome in extrauterine leiomyosarcoma while subtype II leiomyosarcoma is associated with poor prognosis in both uterine and extrauterine leiomyosarcoma. The leiomyosarcoma subtypes showed significant differences in expression levels for genes for which novel targeted therapies are being developed, suggesting that leiomyosarcoma subtypes may respond differentially to these targeted therapies. CONCLUSIONS We confirm the existence of 3 molecular subtypes in leiomyosarcoma using two independent datasets and show that the different molecular subtypes are associated with distinct clinical outcomes. The findings offer an opportunity for treating leiomyosarcoma in a subtype-specific targeted approach.
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Affiliation(s)
- Xiangqian Guo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Vickie Y Jo
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Anne M Mills
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Shirley X Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Cheng-Han Lee
- Division of Anatomical Pathology, Royal Alexandra Hospital, Edmonton, Alberta, Canada
| | - Inigo Espinosa
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Marisa R Nucci
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Trevor Hastie
- Department of Statistics, Stanford University, Stanford, California
| | - Sharon Anderson
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kristen Ganjoo
- Stanford Comprehensive Cancer Center, Stanford University, Stanford, California
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christopher D Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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