1
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Kang M, Armenteros JJA, Gulati GS, Gleyzer R, Avagyan S, Brown EL, Zhang W, Usmani A, Earland N, Wu Z, Zou J, Fields RC, Chen DY, Chaudhuri AA, Newman AM. Mapping single-cell developmental potential in health and disease with interpretable deep learning. bioRxiv 2024:2024.03.19.585637. [PMID: 38562882 PMCID: PMC10983880 DOI: 10.1101/2024.03.19.585637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cell fate in developmental systems. However, identifying the molecular hallmarks of potency - the capacity of a cell to differentiate into other cell types - has remained challenging. Here, we introduce CytoTRACE 2, an interpretable deep learning framework for characterizing potency and differentiation states on an absolute scale from scRNA-seq data. Across 31 human and mouse scRNA-seq datasets encompassing 28 tissue types, CytoTRACE 2 outperformed existing methods for recovering experimentally determined potency levels and differentiation states covering the entire range of cellular ontogeny. Moreover, it reconstructed the temporal hierarchy of mouse embryogenesis across 62 timepoints; identified pan-tissue expression programs that discriminate major potency levels; and facilitated discovery of cellular phenotypes in cancer linked to survival and immunotherapy resistance. Our results illuminate a fundamental feature of cell biology and provide a broadly applicable platform for delineating single-cell differentiation landscapes in health and disease.
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2
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Subramanian A, Nemat-Gorgani N, Ellis-Caleo TJ, van IJzendoorn DGP, Sears TJ, Somani A, Luca BA, Zhou MY, Bradic M, Torres IA, Oladipo E, New C, Kenney DE, Avedian RS, Steffner RJ, Binkley MS, Mohler DG, Tap WD, D'Angelo SP, van de Rijn M, Ganjoo KN, Bui NQ, Charville GW, Newman AM, Moding EJ. Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy. Nat Cancer 2024:10.1038/s43018-024-00743-y. [PMID: 38429415 DOI: 10.1038/s43018-024-00743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we employed EcoTyper, a machine-learning framework, to identify the fundamental cell states and cellular ecosystems that make up sarcomas on a large scale using bulk transcriptomes with clinical annotations. We identified and validated 23 sarcoma-specific, transcriptionally defined cell states, many of which were highly prognostic of patient outcomes across independent datasets. We discovered three conserved cellular communities or ecotypes associated with underlying genomic alterations and distinct clinical outcomes. We show that one ecotype defined by tumor-associated macrophages and epithelial-like malignant cells predicts response to immune-checkpoint inhibition but not chemotherapy and validate our findings in an independent cohort. Our results may enable identification of patients with soft tissue sarcomas who could benefit from immunotherapy and help develop new therapeutic strategies.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Neda Nemat-Gorgani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | | | | | - Timothy J Sears
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Anish Somani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maggie Y Zhou
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Martina Bradic
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ileana A Torres
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Eniola Oladipo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christin New
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Deborah E Kenney
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Raffi S Avedian
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Robert J Steffner
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - David G Mohler
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | | | - Kristen N Ganjoo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Nam Q Bui
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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3
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Spasevska I, Sharma A, Steen CB, Josefsson SE, Blaker YN, Kolstad A, Rustad EH, Meyer S, Isaksen K, Chellappa S, Kushekhar K, Beiske K, Førsund MS, Spetalen S, Holte H, Østenstad B, Brodtkorb M, Kimby E, Olweus J, Taskén K, Newman AM, Lorenz S, Smeland EB, Alizadeh AA, Huse K, Myklebust JH. Diversity of intratumoral regulatory T cells in B-cell non-Hodgkin lymphoma. Blood Adv 2023; 7:7216-7230. [PMID: 37695745 PMCID: PMC10698546 DOI: 10.1182/bloodadvances.2023010158] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Tumor-infiltrating regulatory T cells (Tregs) contribute to an immunosuppressive tumor microenvironment. Despite extensive studies, the prognostic impact of tumor-infiltrating Tregs in B-cell non-Hodgkin lymphomas (B-NHLs) remains unclear. Emerging studies suggest substantial heterogeneity in the phenotypes and suppressive capacities of Tregs, emphasizing the importance of understanding Treg diversity and the need for additional markers to identify highly suppressive Tregs. Here, we applied single-cell RNA sequencing and T-cell receptor sequencing combined with high-dimensional cytometry to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma and follicular lymphoma (FL), compared with that in nonmalignant tonsillar tissue. We identified 3 distinct transcriptional states of Tregs: resting, activated, and unconventional LAG3+FOXP3- Tregs. Activated Tregs were enriched in B-NHL tumors, coexpressed several checkpoint receptors, and had stronger immunosuppressive activity compared with resting Tregs. In FL, activated Tregs were found in closer proximity to CD4+ and CD8+ T cells than other cell types. Furthermore, we used a computational approach to develop unique gene signature matrices, which were used to enumerate each Treg subset in cohorts with bulk gene expression data. In 2 independent FL cohorts, activated Tregs was the major subset, and high abundance was associated with adverse outcome. This study demonstrates that Tregs infiltrating B-NHL tumors are transcriptionally and functionally diverse. Highly immunosuppressive activated Tregs were enriched in tumor tissue but absent in the peripheral blood. Our data suggest that a deeper understanding of Treg heterogeneity in B-NHL could open new paths for rational drug design, facilitating selective targeting to improve antitumor immunity.
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Affiliation(s)
- Ivana Spasevska
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Ankush Sharma
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Chloé B. Steen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Sarah E. Josefsson
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
| | - Yngvild N. Blaker
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
| | - Arne Kolstad
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Department of Oncology, Innlandet Hospital Trust, Lillehammer, Norway
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Even H. Rustad
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Saskia Meyer
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Kathrine Isaksen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Stalin Chellappa
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kushi Kushekhar
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
| | - Klaus Beiske
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Division of Cancer Medicine, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Mette S. Førsund
- Division of Cancer Medicine, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Signe Spetalen
- Division of Cancer Medicine, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Harald Holte
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Bjørn Østenstad
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Marianne Brodtkorb
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Eva Kimby
- Department of Hematology, Karolinska Institute, Stockholm, Sweden
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Norway
| | - Kjetil Taskén
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
| | - Aaron M. Newman
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
- Divisions of Hematology & Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Susanne Lorenz
- Department of Core Facilities, Geonomics Core Facility, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Erlend B. Smeland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Ash A. Alizadeh
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
- Divisions of Hematology & Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Kanutte Huse
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - June H. Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
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4
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Rajbhandari N, Hamilton M, Quintero CM, Ferguson LP, Fox R, Schürch CM, Wang J, Nakamura M, Lytle NK, McDermott M, Diaz E, Pettit H, Kritzik M, Han H, Cridebring D, Wen KW, Tsai S, Goggins MG, Lowy AM, Wechsler-Reya RJ, Von Hoff DD, Newman AM, Reya T. Single-cell mapping identifies MSI + cells as a common origin for diverse subtypes of pancreatic cancer. Cancer Cell 2023; 41:1989-2005.e9. [PMID: 37802055 PMCID: PMC10836835 DOI: 10.1016/j.ccell.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/12/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Identifying the cells from which cancers arise is critical for understanding the molecular underpinnings of tumor evolution. To determine whether stem/progenitor cells can serve as cells of origin, we created a Msi2-CreERT2 knock-in mouse. When crossed to CAG-LSL-MycT58A mice, Msi2-CreERT2 mice developed multiple pancreatic cancer subtypes: ductal, acinar, adenosquamous, and rare anaplastic tumors. Combining single-cell genomics with computational analysis of developmental states and lineage trajectories, we demonstrate that MYC preferentially triggers transformation of the most immature MSI2+ pancreas cells into multi-lineage pre-cancer cells. These pre-cancer cells subsequently diverge to establish pancreatic cancer subtypes by activating distinct transcriptional programs and large-scale genomic changes, and enforced expression of specific signals like Ras can redirect subtype specification. This study shows that multiple pancreatic cancer subtypes can arise from a common pool of MSI2+ cells and provides a powerful model to understand and control the programs that shape divergent fates in pancreatic cancer.
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Affiliation(s)
- Nirakar Rajbhandari
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Hamilton
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Cynthia M Quintero
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York City, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA
| | - L Paige Ferguson
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Raymond Fox
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Jun Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mari Nakamura
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York City, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA
| | - Nikki K Lytle
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Matthew McDermott
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Emily Diaz
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah Pettit
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York City, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA
| | - Marcie Kritzik
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York City, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA
| | - Haiyong Han
- Molecular Medicine Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Derek Cridebring
- Molecular Medicine Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Kwun Wah Wen
- Department of Pathology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Susan Tsai
- Department of Surgery, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael G Goggins
- Departments of Pathology, Medicine and Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew M Lowy
- Department of Surgery, Division of Surgical Oncology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA; Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA; Department of Neurology, Columbia University Medical Center, New York City, NY, USA
| | - Daniel D Von Hoff
- Molecular Medicine Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tannishtha Reya
- Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York City, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York City, NY, USA.
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5
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Vahid MR, Brown EL, Steen CB, Zhang W, Jeon HS, Kang M, Gentles AJ, Newman AM. High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE. Nat Biotechnol 2023; 41:1543-1548. [PMID: 36879008 PMCID: PMC10635828 DOI: 10.1038/s41587-023-01697-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 01/25/2023] [Indexed: 03/08/2023]
Abstract
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.
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Affiliation(s)
- Milad R Vahid
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Erin L Brown
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Chloé B Steen
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Wubing Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Hyun Soo Jeon
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Minji Kang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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6
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Earland N, Zhang W, Usmani A, Nene A, Bacchiocchi A, Chen DY, Sznol M, Halaban R, Chaudhuri AA, Newman AM. CD4 T cells and toxicity from immune checkpoint blockade. Immunol Rev 2023; 318:96-109. [PMID: 37491734 PMCID: PMC10838135 DOI: 10.1111/imr.13248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Immune-related toxicities, otherwise known as immune-related adverse events (irAEs), occur in a substantial fraction of cancer patients treated with immune checkpoint inhibitors (ICIs). Ranging from asymptomatic to life-threatening, ICI-induced irAEs can result in hospital admission, high-dose corticosteroid treatment, ICI discontinuation, and in some cases, death. A deeper understanding of the factors underpinning severe irAE development will be essential for improved irAE prediction and prevention, toward maximizing the benefits and safety profiles of ICIs. In recent work, we applied mass cytometry, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing, and bulk T-cell receptor (TCR) sequencing to identify pretreatment determinants of severe irAE development in patients with advanced melanoma. Across 71 patients separated into three cohorts, we found that two baseline features in circulation-elevated activated CD4 effector memory T-cell abundance and TCR diversity-are associated with severe irAE development, independent of the affected organ system within 3 months of ICI treatment initiation. Here, we provide an extended perspective on this work, synthesize and discuss related literature, and summarize practical considerations for clinical translation. Collectively, these findings lay a foundation for data-driven and mechanistic insights into irAE development, with the potential to reduce ICI morbidity and mortality in the future.
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Affiliation(s)
- Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Wubing Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Abul Usmani
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Antonella Bacchiocchi
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - David Y. Chen
- Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Mario Sznol
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
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7
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Kaiser AM, Gatto A, Hanson KJ, Zhao RL, Raj N, Ozawa MG, Seoane JA, Bieging-Rolett KT, Wang M, Li I, Trope WL, Liou DZ, Shrager JB, Plevritis SK, Newman AM, Van Rechem C, Attardi LD. p53 governs an AT1 differentiation programme in lung cancer suppression. Nature 2023:10.1038/s41586-023-06253-8. [PMID: 37468633 DOI: 10.1038/s41586-023-06253-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/24/2023] [Indexed: 07/21/2023]
Abstract
Lung cancer is the leading cause of cancer deaths worldwide1. Mutations in the tumour suppressor gene TP53 occur in 50% of lung adenocarcinomas (LUADs) and are linked to poor prognosis1-4, but how p53 suppresses LUAD development remains enigmatic. We show here that p53 suppresses LUAD by governing cell state, specifically by promoting alveolar type 1 (AT1) differentiation. Using mice that express oncogenic Kras and null, wild-type or hypermorphic Trp53 alleles in alveolar type 2 (AT2) cells, we observed graded effects of p53 on LUAD initiation and progression. RNA sequencing and ATAC sequencing of LUAD cells uncovered a p53-induced AT1 differentiation programme during tumour suppression in vivo through direct DNA binding, chromatin remodelling and induction of genes characteristic of AT1 cells. Single-cell transcriptomics analyses revealed that during LUAD evolution, p53 promotes AT1 differentiation through action in a transitional cell state analogous to a transient intermediary seen during AT2-to-AT1 cell differentiation in alveolar injury repair. Notably, p53 inactivation results in the inappropriate persistence of these transitional cancer cells accompanied by upregulated growth signalling and divergence from lung lineage identity, characteristics associated with LUAD progression. Analysis of Trp53 wild-type and Trp53-null mice showed that p53 also directs alveolar regeneration after injury by regulating AT2 cell self-renewal and promoting transitional cell differentiation into AT1 cells. Collectively, these findings illuminate mechanisms of p53-mediated LUAD suppression, in which p53 governs alveolar differentiation, and suggest that tumour suppression reflects a fundamental role of p53 in orchestrating tissue repair after injury.
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Affiliation(s)
- Alyssa M Kaiser
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alberto Gatto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn J Hanson
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard L Zhao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nitin Raj
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael G Ozawa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - José A Seoane
- Cancer Computational Biology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Kathryn T Bieging-Rolett
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mengxiong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Irene Li
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Winston L Trope
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Douglas Z Liou
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Capucine Van Rechem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Usmani A, Earland N, Zhang W, Harris PK, Bacchiocchi A, Nene A, Chen DY, Sznol M, Halaban R, Newman AM, Chaudhuri AA. Abstract 6670: Association between circulating CD4 memory T cell levels and severe immune-related adverse events in melanoma patients treated with immune checkpoint blockade. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6670] [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: 04/07/2023]
Abstract
Abstract
Introduction: Severe immune-related adverse events (irAEs) occur in up to 60% of melanoma patients treated with immune checkpoint inhibitors (ICIs), causing substantial treatment-related morbidity and in the most severe cases, death. There is no clinical assay to predict who will develop severe ICI-induced irAEs and who will not. Using single-cell profiling assays applied to a retrospective melanoma cohort treated with ICIs, we recently showed that higher baseline levels of circulating CD4 effector memory T (TEM) cells were associated with severe irAE development, independent of the affected organ system (Lozano et al. Nature Medicine, 2022). As part of a prospective validation study of 100 melanoma patients, here we report our initial findings on the first 24 patients accrued to date.
Methods: We prospectively collected pre-ICI blood from 24 metastatic melanoma patients from two academic medical centers from February 2021 onward. Peripheral blood was collected pre-treatment on the day of immunotherapy (cycle 1 day 1). We then isolated peripheral blood mononuclear cells (PBMCs) and applied mass cytometry by time of flight (CyTOF) to profile 38 leukocyte markers including markers specific to CD4 TEM cells. Cellular subpopulations were quantified using Cytobank v9. Patients underwent routine medical oncology follow-up during and after ICI treatment including grading of irAEs using the Common Terminology Criteria for Adverse Events v5.
Results: Median follow-up time after pre-ICI blood collection was 9.1 months (range 2.6-18.5). Fifteen (63%) patients received combination (anti-PD1/anti-CTLA4) ICIs while the remainder received anti-PD1 monotherapy. Eight patients developed severe (grade 3+) irAEs at a median of 8.5 weeks (range 4-21) after treatment initiation, including 4 who developed life-threatening (grade 4) irAEs. Severe and life-threatening irAE development spanned 9 separate organ systems, most commonly gastrointestinal, dermatological, and hepatic. Using CyTOF, we found that circulating CD4 TEM cells were more abundant in patients who developed severe irAEs compared to those who did not (P = 0.01; AUC = 0.81), irrespective of the involved organ systems. Moreover, median-splitting the patient cohort into two groups based on pretreatment CD4 TEM levels revealed that patients with low CD4 TEMs had significantly longer freedom from severe irAE than those with high CD4 TEMs (not reached vs. 4.6 months; P = 0.013; HR = 6.7). There was no significant difference in pretreatment CD4 TEM levels between patients with and without durable clinical benefit to ICIs (P = 0.75).
Conclusion: Circulating CD4 TEM levels measured by CyTOF were associated with severe irAE development, independent of response status, in patients with advanced melanoma. These findings could form the basis for pretreatment ICI risk stratification in the future.
Citation Format: Abul Usmani, Noah Earland, Wubing Zhang, Peter K. Harris, Antonietta Bacchiocchi, Aishwarya Nene, David Y. Chen, Mario Sznol, Ruth Halaban, Aaron M. Newman, Aadel A. Chaudhuri. Association between circulating CD4 memory T cell levels and severe immune-related adverse events in melanoma patients treated with immune checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6670.
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Affiliation(s)
- Abul Usmani
- 1Washington University in St. Louis, St. Louis, MO
| | - Noah Earland
- 1Washington University in St. Louis, St. Louis, MO
| | | | | | | | | | | | - Mario Sznol
- 3Yale University School of Medicine, New Haven, CT
| | - Ruth Halaban
- 3Yale University School of Medicine, New Haven, CT
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9
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Matusiak M, Hickey JW, Luca B, Lu G, Kidziński L, Zhu S, Colburg DRC, Phillips DJ, Brubaker SW, Charville GW, Shen J, Nolan GP, Newman AM, West RB, van de Rijn M. A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer. Res Sq 2023:rs.3.rs-2393443. [PMID: 36711732 PMCID: PMC9882614 DOI: 10.21203/rs.3.rs-2393443/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Tumor-associated macrophages (TAMs) display heterogeneous phenotypes. Yet the exact tissue cues that shape macrophage functional diversity are incompletely understood. Here we discriminate, spatially resolve and reveal the function of five distinct macrophage niches within malignant and benign breast and colon tissue. We found that SPP1 TAMs reside in hypoxic and necrotic tumor regions, and a novel subset of FOLR2 tissue resident macrophages (TRMs) supports the plasma cell tissue niche. We discover that IL4I1 macrophages populate niches with high cell turnover where they phagocytose dying cells. Significantly, IL4I1 TAMs abundance correlates with anti-PD1 treatment response in breast cancer. Furthermore, NLRP3 inflammasome activation in NLRP3 TAMs correlates with neutrophil infiltration in the tumors and is associated with poor outcome in breast cancer patients. This suggests the NLRP3 inflammasome as a novel cancer immunetherapy target. Our work uncovers context-dependent roles of macrophage subsets, and suggests novel predictive markers and macrophage subset-specific therapy targets.
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Affiliation(s)
| | - John W. Hickey
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Bogdan Luca
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Guolan Lu
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Lukasz Kidziński
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, California, USA
| | | | - Darci J. Phillips
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Jeanne Shen
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Garry P. Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Aaron M. Newman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Robert B. West
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, California, USA
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10
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Steen CB, Luca BA, Alizadeh AA, Gentles AJ, Newman AM. Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper. Methods Mol Biol 2023; 2629:43-71. [PMID: 36929073 DOI: 10.1007/978-1-0716-2986-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Tissues are composed of diverse cell types and cellular states that organize into distinct ecosystems with specialized functions. EcoTyper is a collection of machine learning tools for the large-scale delineation of cellular ecosystems and their constituent cell states from bulk, single-cell, and spatially resolved gene expression data. In this chapter, we provide a primer on EcoTyper and demonstrate its use for the discovery and recovery of cell states and ecosystems from healthy and diseased tissue specimens.
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Affiliation(s)
- Chloé B Steen
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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11
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Wang J, Fite BZ, Kare AJ, Wu B, Raie M, Tumbale SK, Zhang N, Davis RR, Tepper CG, Aviran S, Newman AM, King DA, Ferrara KW. Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer. Am J Cancer Res 2022; 12:7884-7902. [PMID: 36451859 PMCID: PMC9706583 DOI: 10.7150/thno.73218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/24/2022] [Accepted: 10/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Although combination immunotherapies incorporating local and systemic components have shown promising results in treating solid tumors, varied tumor microenvironments (TMEs) can impact immunotherapeutic efficacy. Method: We designed and evaluated treatment strategies for breast and pancreatic cancer combining magnetic resonance-guided focused ultrasound (MRgFUS) ablation and antibody therapies. With a combination of single-cell sequencing, spectral flow cytometry, and histological analyses, we profiled an immune-suppressed KPC (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre) pancreatic adenocarcinoma (MT4) model and a dense epithelial neu deletion (NDL) HER2+ mammary adenocarcinoma model with a greater fraction of lymphocytes, natural killer cells and activated dendritic cells. We then performed gene ontology analysis, spectral and digital cytometry to assess the immune response to combination immunotherapies and correlation with survival studies. Result: Based on gene ontology analysis, adding ablation to immunotherapy enriched immune cell migration pathways in the pancreatic cancer model and extensively enriched wound healing pathways in the breast cancer model. With CIBERSORTx digital cytometry, aCD40 + aPD-1 immunotherapy combinations enhanced dendritic cell activation in both models. In the MT4 TME, adding the combination of aCD40 antibody and checkpoint inhibitors (aPD-1 and aCTLA-4) with ablation was synergistic, increasing activated natural killer cells and T cells in distant tumors. Furthermore, ablation with immunotherapy upregulated critical Ly6c myeloid remodeling phenotypes that enhance T-cell effector function and increased granzyme and protease encoding genes by as much as 100-fold. Ablation combined with immunotherapy then extended survival in the MT4 model to a greater extent than immunotherapy alone. Conclusion: In summary, TME profiling informed a successful multicomponent treatment protocol incorporating ablation and facilitated differentiation of TMEs in which ablation is most effective.
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Affiliation(s)
- James Wang
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
| | - Brett Z. Fite
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
| | - Aris J. Kare
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA,Department of Bioengineering, Stanford University, Palo Alto, CA 94305, USA
| | - Bo Wu
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
| | - Marina Raie
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
| | | | - Nisi Zhang
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
| | - Ryan R. Davis
- Department of Pathology and Laboratory Medicine, University of California Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Clifford G. Tepper
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Sharon Aviran
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Palo Alto, CA, 94305, USA,Department of Biomedical Data Science, Stanford University, Palo Alto, CA 94305, USA
| | - Daniel A. King
- Division of Medical Oncology/Hematology, Northwell Health Cancer Institute, New Hyde Park, NY 10042 USA
| | - Katherine W. Ferrara
- Department of Radiology, Stanford University, Palo Alto, CA 94305, USA,✉ Corresponding author: Katherine W. Ferrara PhD, Department of Radiology, Stanford University, 3165 Porter Dr, Palo Alto, CA 94305. E-mail:
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12
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Sikandar SS, Gulati GS, Antony J, Fetter I, Kuo AH, Ho WHD, Haro-Acosta V, Das S, Steen CB, Pereira TA, Qian D, Beachy PA, Dirbas FM, Red-Horse K, Rabbitts TH, Thiery JP, Newman AM, Clarke MF. Identification of a minority population of LMO2 + breast cancer cells that integrate into the vasculature and initiate metastasis. Sci Adv 2022; 8:eabm3548. [PMID: 36351009 PMCID: PMC10939096 DOI: 10.1126/sciadv.abm3548] [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] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Metastasis is responsible for most breast cancer-related deaths; however, identifying the cellular determinants of metastasis has remained challenging. Here, we identified a minority population of immature THY1+/VEGFA+ tumor epithelial cells in human breast tumor biopsies that display angiogenic features and are marked by the expression of the oncogene, LMO2. Higher abundance of LMO2+ basal cells correlated with tumor endothelial content and predicted poor distant recurrence-free survival in patients. Using MMTV-PyMT/Lmo2CreERT2 mice, we demonstrated that Lmo2 lineage-traced cells integrate into the vasculature and have a higher propensity to metastasize. LMO2 knockdown in human breast tumors reduced lung metastasis by impairing intravasation, leading to a reduced frequency of circulating tumor cells. Mechanistically, we find that LMO2 binds to STAT3 and is required for STAT3 activation by tumor necrosis factor-α and interleukin-6. Collectively, our study identifies a population of metastasis-initiating cells with angiogenic features and establishes the LMO2-STAT3 signaling axis as a therapeutic target in breast cancer metastasis.
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Affiliation(s)
- Shaheen S. Sikandar
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gunsagar S. Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Jane Antony
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Isobel Fetter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angera H. Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - William Hai Dang Ho
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Veronica Haro-Acosta
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Soumyashree Das
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chloé B. Steen
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Thiago Almeida Pereira
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Philip A. Beachy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
| | - Frederick M. Dirbas
- Department of Surgery, Stanford Cancer Institute, Stanford University School of Medicine, 875 Blake Wilbur Drive, Rm CC2235, Stanford, CA 94305, USA
| | - Kristy Red-Horse
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Terence H. Rabbitts
- Division of Cancer Therapeutics, Institute of Cancer Research, London SM2 5NG, UK
| | - Jean Paul Thiery
- Guangzhou Laboratory, International Biological Island, Guangzhou, Guangdong 510005, China
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Michael F. Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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13
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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14
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Farshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nat Commun 2022; 13:898. [PMID: 35197475 PMCID: PMC8866401 DOI: 10.1038/s41467-022-28566-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from 104 patients treated in North America (n = 37) or China (n = 67). We find that recurrent, late-arising focal amplifications of cytoband 22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 - a known tumor suppressor in other cancers - is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines causes apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiates processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and an increase in MAPK and SRC activities. Our results provide insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.
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Affiliation(s)
- Farshad Farshidfar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | | | - Cong Peng
- Xiangya Hospital, Central South University, Changsha, China
| | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06520, USA
| | | | - Juan Su
- Xiangya Hospital, Central South University, Changsha, China
| | - Mingzhu Yin
- Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Mario Sznol
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - James Clune
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Olino
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | | | - Joerg Nikolaus
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Meiling Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Shuang Zhao
- Xiangya Hospital, Central South University, Changsha, China
| | - Yan Wang
- Department of Dermatologic Surgery Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Gang Huang
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Miaojian Wan
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianan Li
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Jian Cao
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiang Chen
- Xiangya Hospital, Central South University, Changsha, China.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
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15
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Lozano AX, Chaudhuri AA, Nene A, Bacchiocchi A, Earland N, Vesely MD, Usmani A, Turner BE, Steen CB, Luca BA, Badri T, Gulati GS, Vahid MR, Khameneh F, Harris PK, Chen DY, Dhodapkar K, Sznol M, Halaban R, Newman AM. T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:353-362. [PMID: 35027754 DOI: 10.1038/s41591-021-01623-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Severe immune-related adverse events (irAEs) occur in up to 60% of patients with melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether a common baseline immunological state precedes irAE development. Here we applied mass cytometry by time of flight, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing and bulk T cell receptor (TCR) sequencing to study peripheral blood samples from patients with melanoma treated with anti-PD-1 monotherapy or anti-PD-1 and anti-CTLA-4 combination ICIs. By analyzing 93 pre- and early on-ICI blood samples and 3 patient cohorts (n = 27, 26 and 18), we found that 2 pretreatment factors in circulation-activated CD4 memory T cell abundance and TCR diversity-are associated with severe irAE development regardless of organ system involvement. We also explored on-treatment changes in TCR clonality among patients receiving combination therapy and linked our findings to the severity and timing of irAE onset. These results demonstrate circulating T cell characteristics associated with ICI-induced toxicity, with implications for improved diagnostics and clinical management.
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Affiliation(s)
- Alexander X Lozano
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Computer Science & Engineering, Washington University, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Aishwarya Nene
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Noah Earland
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Vesely
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brandon E Turner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Chloé B Steen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Ti Badri
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Milad R Vahid
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Farnaz Khameneh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kavita Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Mario Sznol
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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16
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Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell 2021; 184:5482-5496.e28. [PMID: 34597583 DOI: 10.1016/j.cell.2021.09.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [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: 11/19/2020] [Revised: 06/21/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.
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Affiliation(s)
- Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Chloé B Steen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Armon Azizi
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Joanna Przybyl
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
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17
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Foster DS, Januszyk M, Yost KE, Chinta MS, Gulati GS, Nguyen AT, Burcham AR, Salhotra A, Ransom RC, Henn D, Chen K, Mascharak S, Tolentino K, Titan AL, Jones RE, da Silva O, Leavitt WT, Marshall CD, des Jardins-Park HE, Hu MS, Wan DC, Wernig G, Wagh D, Coller J, Norton JA, Gurtner GC, Newman AM, Chang HY, Longaker MT. Integrated spatial multiomics reveals fibroblast fate during tissue repair. Proc Natl Acad Sci U S A 2021; 118:e2110025118. [PMID: 34620713 PMCID: PMC8521719 DOI: 10.1073/pnas.2110025118] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive, in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing across both time and space. We employ a stented wound model that recapitulates human tissue repair kinetics and multiple Rainbow transgenic lines to precisely track fibroblast fate during the physiologic response to skin injury. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to reveal potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems.
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Affiliation(s)
- Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305
| | - Malini S Chinta
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Alan T Nguyen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Austin R Burcham
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Ankit Salhotra
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - R Chase Ransom
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dominic Henn
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Kellen Chen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Shamik Mascharak
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305
| | - Ashley L Titan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - R Ellen Jones
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Oscar da Silva
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - W Tripp Leavitt
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Clement D Marshall
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Heather E des Jardins-Park
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael S Hu
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Derrick C Wan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dhananjay Wagh
- Stanford Functional Genomics Facility, Stanford University, Stanford, CA 94305
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University, Stanford, CA 94305
| | - Jeffrey A Norton
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Geoffrey C Gurtner
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305;
- HHMI, Stanford University, Stanford, CA 94305
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305;
- Department of Surgery, Stanford University School of Medicine, Stanford CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
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18
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Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell 2021; 39:1422-1437.e10. [PMID: 34597589 PMCID: PMC9205168 DOI: 10.1016/j.ccell.2021.08.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [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: 11/19/2020] [Revised: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).
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Affiliation(s)
- Chloé B Steen
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mohammad S Esfahani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Armon Azizi
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - David M Kurtz
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Farnaz Khameneh
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
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19
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Nabet BY, Esfahani MS, Moding EJ, Hamilton EG, Chabon JJ, Rizvi H, Steen CB, Chaudhuri AA, Liu CL, Hui AB, Almanza D, Stehr H, Gojenola L, Bonilla RF, Jin MC, Jeon YJ, Tseng D, Liu C, Merghoub T, Neal JW, Wakelee HA, Padda SK, Ramchandran KJ, Das M, Plodkowski AJ, Yoo C, Chen EL, Ko RB, Newman AM, Hellmann MD, Alizadeh AA, Diehn M. Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition. Cell 2020; 183:363-376.e13. [PMID: 33007267 PMCID: PMC7572899 DOI: 10.1016/j.cell.2020.09.001] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/18/2020] [Accepted: 08/28/2020] [Indexed: 12/30/2022]
Abstract
Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICIs) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we demonstrate that pre-treatment circulating tumor DNA (ctDNA) and peripheral CD8 T cell levels are independently associated with DCB. We further show that ctDNA dynamics after a single infusion can aid in identification of patients who will achieve DCB. Integrating these determinants, we developed and validated an entirely noninvasive multiparameter assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA-On-treatment) that robustly predicts which patients will achieve DCB with higher accuracy than any individual feature. Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICIs.
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Affiliation(s)
- Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chloe B Steen
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Diego Almanza
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Young-Jun Jeon
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Diane Tseng
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Cailian Liu
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell School of Medicine, New York, NY, USA; Parker Institute for Cancer Immunotherapy at MSK, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel W Neal
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Sukhmani K Padda
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Kavitha J Ramchandran
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Millie Das
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Yoo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily L Chen
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Matthew D Hellmann
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell School of Medicine, New York, NY, USA; Parker Institute for Cancer Immunotherapy at MSK, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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20
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Accomando WP, Rao AR, Hogan DJ, Newman AM, Nakao A, Alizadeh AA, Diehn M, Diago OR, Gammon D, Haghighi A, Gruber HE, Jolly DJ, Ostertag D. Molecular and Immunologic Signatures are Related to Clinical Benefit from Treatment with Vocimagene Amiretrorepvec (Toca 511) and 5-Fluorocytosine (Toca FC) in Patients with Glioma. Clin Cancer Res 2020; 26:6176-6186. [PMID: 32816892 DOI: 10.1158/1078-0432.ccr-20-0536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE High-grade gliomas (HGGs) are central nervous system tumors with poor prognoses and limited treatment options. Vocimagene amiretrorepvec (Toca 511) is a retroviral replicating vector encoding cytosine deaminase, which converts extended release 5-fluorocytosine (Toca FC) into the anticancer agent, 5-fluorouracil. According to preclinical studies, this therapy kills cancer cells and immunosuppressive myeloid cells in the tumor microenvironment, leading to T-cell-mediated antitumor immune activity. Therefore, we sought to elucidate this immune-related mechanism of action in humans, and to investigate potential molecular and immunologic indicators of clinical benefit from therapy. PATIENTS AND METHODS In a phase I clinical trial (NCT01470794), patients with recurrent HGG treated with Toca 511 and Toca FC showed improved survival relative to historical controls, and some had durable complete responses to therapy. As a part of this trial, we performed whole-exome DNA sequencing, RNA-sequencing, and multiplex digital ELISA measurements on tumor and blood samples. RESULTS Genetic analyses suggest mutations, copy-number variations, and neoantigens are linked to survival. Quantities of tumor immune infiltrates estimated by transcript abundance may potentially predict clinical outcomes. Peak values of cytokines in peripheral blood samples collected during and after therapy could indicate response. CONCLUSIONS These results support an immune-related mechanism of action for Toca 511 and Toca FC, and suggest that molecular and immunologic signatures are related to clinical benefit from treatment.
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Affiliation(s)
| | | | | | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Aki Nakao
- CiberMed Inc., Palo Alto, California
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford University, Stanford, California.,Division of Hematology, Department of Medicine, 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.,Department of Radiation Oncology, Stanford University, Stanford, California
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Luca BA, Steen CB, Azizi A, Matusiak M, Przybyl J, Neishaboori N, Pérez AE, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Abstract 3443: Atlas of clinically-distinct cell states and cellular ecosystems across human solid tumors. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3443] [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
Tumors are complex ecosystems consisting of malignant, immune, and stromal elements whose dynamic interactions drive patient survival and response to therapy. A comprehensive understanding of the diversity of cellular states within the tumor microenvironment (TME), and their patterns of co-occurrence, could provide new diagnostic tools for improved disease management and novel targets for therapeutic intervention. To address this challenge, we developed EcoTyper, a novel machine learning framework for large-scale identification of TME cell states and their co-association patterns from bulk, single-cell, and spatially resolved tumor expression data. EcoTyper starts by “purifying” cell type-specific gene expression profiles of epithelial cells, immune, and stromal cell types from bulk tissue transcriptomes using CIBERSORTx (Newman et al., Nat Biotechnol 2019). It then identifies transcriptional states for each cell type, validates them in scRNA-seq data, and uncovers co-occurrence patterns between cell states in order to define tumor cellular ecosystems. Applied to 6,475 tumor and adjacent normal samples from solid tumor types profiled by The Cancer Genome Atlas (TCGA), EcoTyper identified robust transcriptional states across 12 major cell types, including epithelial, fibroblast, endothelial, and 9 immune subsets. These states included both known and novel cellular phenotypes, nearly all of which could be validated in a compendium of scRNA-seq tumor atlases spanning ~140,000 cells. Most cell states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly associated with overall survival, both in TCGA and in 9,062 held-out tumor specimens (Gentles/Newman et al., Nat Medicine 2015). We found that specific cell states co-occur in distinct cellular communities with characteristic patterns of ligand-receptor interactions, genomic features, clinical outcomes, and spatial organization. One such ecosystem defined a normal-like state that was strongly enriched in non-malignant samples. Others delineated novel pro- and anti-tumor inflammatory environments involving specific fibroblast, endothelial, and immune cell transcriptional programs. In summary, large-scale deconvolution of cell type-specific transcriptomes across thousands of solid tumors revealed a comprehensive atlas of TME cell states and cellular ecosystems. Our results provide a high-resolution portrait of cellular heterogeneity in the TME across multiple solid tumor types, with implications for novel diagnostics and immunotherapeutic targets.
References:
1. Newman, A.M., et al., Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol, 2019. 37(7): p. 773-782.
2. Gentles, A.J., et al., The prognostic landscape of genes and infiltrating immune cells across human cancers. Nature medicine, 2015. 21(8): p. 938.
Citation Format: Bogdan A. Luca, Chloé B. Steen, Armon Azizi, Magdalena Matusiak, Joanna Przybyl, Nastaran Neishaboori, Almudena Espín Pérez, Maximilian Diehn, Ash A. Alizadeh, Matt van de Rijn, Andrew J. Gentles, Aaron M. Newman. Atlas of clinically-distinct cell states and cellular ecosystems across human solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3443.
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Steen CB, Luca B, Esfahani MS, Nabet BY, Sworder B, Farshidfar F, Kurtz D, Liu CL, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles A, Alizadeh A, Newman AM. Abstract 1557: Landscape of tumor cell states and cellular ecosystems in diffuse large B cell lymphoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1557] [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
The tumor microenvironment (TME) plays critical roles in cancer development, tumor progression, and susceptibility to therapy. However, the phenotypic states and interaction patterns of its underlying cell types remain poorly understood. To address this challenge, we developed a new computational framework, EcoTyper, for large-scale dissection of cell states and cellular communities (i.e., ecosystems) from tumor genomic profiles. EcoTyper integrates single-cell RNA sequencing (scRNA-seq) with CIBERSORTx, an algorithm for bulk RNA-seq deconvolution (Newman et al., Nat Biotechnol, 2019), to identify and validate cellular states and ecosystems that reflect fundamental distinctions in TME biology. Here we applied EcoTyper to diffuse large B cell lymphoma (DLBCL), an aggressive B cell malignancy with clinically distinct molecular subtypes and several immunologically-active therapies. We sought to determine whether EcoTyper could reveal novel biological variation in the DLBCL TME linked to tumor subtypes and genotypes, therapeutic responses, and clinical outcomes. We applied our approach to define transcriptional states from 13 cell types, including malignant, immune, and stromal cells, in over 1,500 DLBCL tumors. Remarkably, nearly all cell states identified by EcoTyper were validated in independent scRNA-seq and bulk RNA-seq datasets. Moreover, many cells states reflected novel phenotypic groupings, and the majority showed strong associations with overall survival, specific mutational profiles, and tumor molecular subtypes. Additionally, by identifying DLBCL tumors with similar communities of cellular states, we defined novel cellular ecosystems, or “ecotypes”, with distinct biological characteristics and clinical outcomes. Several ecotypes showed significant enrichments in canonical or novel tumor genotypes, suggesting an evolutionary interplay between the tumor and host TME. In summary, we developed a novel computational framework to dissect the TME at scale and present the most comprehensive atlas to date of cell states and cellular communities in DLBCL. Our approach is extensible to nearly any cancer type and may lead to the development of novel diagnostics and individualized immunotherapies.
Citation Format: Chloe B. Steen, Bogdan Luca, Mohammad S. Esfahani, Barzin Y. Nabet, Brian Sworder, Farshad Farshidfar, David Kurtz, Chih Long Liu, Ranjana H. Advani, Yasodha Natkunam, June H. Myklebust, Maximilian Diehn, Andrew Gentles, Ash Alizadeh, Aaron M. Newman. Landscape of tumor cell states and cellular ecosystems in diffuse large B cell lymphoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1557.
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Nabet BY, Esfahani MS, Hamilton EG, Chabon JJ, Moding EJ, Rizvi H, Steen CB, Chaudhuri AA, Liu CL, Hui AB, Stehr H, Goljenola L, Jin MC, Jeon YJ, Tseng D, Merghoub T, Neal JW, Wakelee HA, Padda SK, Ramchandran KJ, Das M, Bonilla RF, Yoo C, Chen EL, Ko RB, Newman AM, Hellmann MD, Alizadeh AA, Diehn M. Abstract 5666: A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5666] [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
Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICI) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we analyze 211 samples from 99 patients and demonstrate that pre-treatment circulating tumor DNA (ctDNA) and circulating immune profiles are independently associated with DCB. We further show that ctDNA dynamics after a single ICI infusion can identify the majority of patients who will achieve DCB. Integrating these determinants, we describe an entirely noninvasive multi-analyte assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA- On-treatment) that robustly predicted DCB, and that was validated in two independent cohorts (AUC = 0.89-0.93, PPV = 92-100%, HR = 0.04-0.11). Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICI.
Citation Format: Barzin Y. Nabet, Mohammad S. Esfahani, Emily G. Hamilton, Jacob J. Chabon, Everett J. Moding, Hira Rizvi, Chloe B. Steen, Aadel A. Chaudhuri, Chih Long Liu, Angela B. Hui, Henning Stehr, Linda Goljenola, Michael C. Jin, Young-Jun Jeon, Diane Tseng, Taha Merghoub, Joel W. Neal, Heather A. Wakelee, Sukhmani K. Padda, Kavitha J. Ramchandran, Millie Das, Rene F. Bonilla, Christopher Yoo, Emily L. Chen, Ryan B. Ko, Aaron M. Newman, Matthew D. Hellmann, Ash A. Alizadeh, Maximilian Diehn. A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5666.
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Affiliation(s)
| | | | | | | | | | - Hira Rizvi
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | | | - Taha Merghoub
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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Newman AM, Nakao A, Li K, Liu CL, Mathi K, Sigal N, Maecker H, Diehn M, Alizadeh AA. Analytical validation of digital cytometry (iSort) for leukocyte enumeration using stored blood. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3542] [Citation(s) in RCA: 1] [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] [Indexed: 11/20/2022] Open
Abstract
3542 Background: Blood leukocyte enumeration is a cornerstone for clinical diagnosis and immune monitoring of diverse cancers and immunotherapies. Existing methods rely on intact/living cells and can thus be limiting due to handling time constraints and need for predefined antibody panels. While indirect cytometry methods including digital cytometry can overcome this limitation on archival specimens, their clinical performance has not been extensively characterized. We developed iSort, a novel transcriptome deconvolution method based on CIBERSORTx. Here, we comprehensively evaluated iSort and validated it against established diagnostic standards. Methods: We recruited 36 healthy adult blood donors and characterized their blood leukocyte profiles. We used several established clinical cytometry methods requiring intact cells in a CLIA laboratory including Complete Blood Count [CBC] and 6-color TBNK [TBNK]. We also immunophenotyped leukocytes by a research flow cytometry panel (FACS) and by mass cytometry (CyTOF). We then used these techniques as standards for validating leukocyte populations enumerated by iSort. iSort was performed on whole blood through deconvolution of 22 subsets from RNA-Seq. We assessed iSort’s analytical detection performance by spiking purified lymphocyte subsets into lymphodepleted human blood and by simulating blood mixtures using defined leukocyte mixtures within latin square designs. We assessed iSort concordance with an FDA approved IVD assay (TBNK) comparing distinct RNA-Seq library preparation chemistries. Results: iSort was highly correlated with TBNK/CBC across CD4 T, CD8 T, B cells, NK cells, monocytes, and neutrophils (r≥0.95). When comparing correlations to TBNK/CBC, we found no significant differences between iSort, CyTOF, and FACS, nor between RNA-Seq library chemistries. iSort demonstrated high linearity at low abundance levels (0.1 - 1%, r = 0.99, B-cells spiked into lymphodepleted blood samples after Rituximab) and at higher abundance levels (0.5 - 90%, r > 0.99) across lymphoid and myeloid subsets. iSort also showed high reproducibility among triplicate blood tubes for each population (median CV = 11%). Conclusions: iSort digital cytometry achieves highly accurate and robust leukocyte enumeration for diverse hematopoietic subsets. Given its favorable performance against existing clinical standards that require intact/living cells, iSort is a promising approach for the development of immunotherapy biomarkers.
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Affiliation(s)
| | | | | | | | | | | | - Holden Maecker
- Institute for Immunity, Transplantation and Infection, Stanford School of Medicine, Stanford, CA
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Newman AM, Nakao A, Li K, Wilson DC, Liu CL, Diehn M, Alizadeh AA. Analytical validation of iSort digital cytometry for leukocyte enumeration in clinical tumor specimens. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e15243] [Citation(s) in RCA: 1] [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] [Indexed: 11/20/2022] Open
Abstract
e15243 Background: Tumor infiltrating leukocytes (TILs) are major determinants of anti-tumor immune responses and mediate effector functions for diverse immunotherapies. Techniques relying on intact cells such as flow cytometry (FACS), immunohistochemistry (IHC), and scRNA-Seq can be powerful for measuring TIL heterogeneity. However, such methods are often impractical on large patient cohorts, can be poorly quantitative, and some cannot be applied to formalin-fixed paraffin embedded (FFPE) specimens. We developed iSort, a transcriptome deconvolution method based on CIBERSORTx for TIL enumeration. We evaluated iSort by comparing its performance in FFPE and fresh frozen (FF) human tumor tissues to established methods. Methods: We profiled human tumors for diverse TIL subsets, as quantified by iSort, FACS, and IHC. iSort was performed on RNA-Seq libraries derived from bulk human tumors, including FF tumor tissue samples, tumor cell suspensions obtained after dissociation, and FFPE specimens. We assessed the influence of tissue fixation on common TIL subsets enumerated by iSort, by comparing matched pairs of FF and FFPE lung tumor specimens (NSCLC). Finally, we compared iSort with automated microscopic enumeration of CD8 TILs by IHC on primary human lung tumors (FFPE/NSCLC). Results: iSort TIL enumeration was highly correlated with FACS across primary human tumors (CRC = 3, HNSCC = 1) for common TIL subsets (B cells, CD8 T, CD4 T, monocytes/macrophages, dendritic cells, PMNs/MDSCs) and total immune content (median r = 0.91 [0.71 - 0.99]). Tissue dissociation caused significant depletion of monocytes/macrophages (p < 0.01), when comparing bulk tumor specimens with cell suspensions after sample digestion. iSort showed high correlation across 12 TIL subsets when comparing 9 pairs of FF and FFPE specimens (r = 0.90). Finally, we observed high linearity between iSort and microscopic enumeration of CD8 TILs from IHC (r = 0.87, n = 5). Conclusions: iSort digital cytometry achieves accurate and robust TIL enumeration as compared with FACS and IHC, showing comparable performance in fixed and frozen primary human tumors. Importantly, iSort is directly applicable to bulk tumors and is unaffected by tissue dissociation artifacts, unlike methods requiring cell suspensions for TIL enumeration (FACS, scRNA-seq). Therefore, iSort is a promising approach for development and measurement of immunotherapy biomarkers.
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Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 2020; 367:405-411. [PMID: 31974247 PMCID: PMC7694873 DOI: 10.1126/science.aax0249] [Citation(s) in RCA: 377] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/03/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential-the number of expressed genes per cell-and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.
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Affiliation(s)
- Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shaheen S Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anoop Manjunath
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anjan Bharadwaj
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark J Berger
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Francisco Ilagan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angera H Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert W Hsieh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shang Cai
- School of Life Sciences, Westlake University, Zhejiang Province, China
| | - Maider Zabala
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ferenc A Scheeren
- Department of Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Neethan A Lobo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94305, USA
| | - Frederick M Dirbas
- Department of Surgery, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael F Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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Azad TD, Chaudhuri AA, Fang P, Qiao Y, Esfahani MS, Chabon JJ, Hamilton EG, Yang YD, Lovejoy A, Newman AM, Kurtz DM, Jin M, Schroers-Martin J, Stehr H, Liu CL, Hui ABY, Patel V, Maru D, Lin SH, Alizadeh AA, Diehn M. Circulating Tumor DNA Analysis for Detection of Minimal Residual Disease After Chemoradiotherapy for Localized Esophageal Cancer. Gastroenterology 2020; 158:494-505.e6. [PMID: 31711920 PMCID: PMC7010551 DOI: 10.1053/j.gastro.2019.10.039] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Biomarkers are needed to risk stratify after chemoradiotherapy for localized esophageal cancer. These could improve identification of patients at risk for cancer progression and selection of additional therapy. METHODS We performed deep sequencing (CAncer Personalized Profiling by deep Sequencing, [CAPP-Seq]) analyses of plasma cell-free DNA collected from 45 patients before and after chemoradiotherapy for esophageal cancer, as well as DNA from leukocytes and fixed esophageal tumor biopsy samples collected during esophagogastroduodenoscopy. Patients were treated from May 2010 through October 2015; 23 patients subsequently underwent esophagectomy, and 22 did not undergo surgery. We also sequenced DNA from blood samples from 40 healthy control individuals. We analyzed 802 regions of 607 genes for single-nucleotide variants previously associated with esophageal adenocarcinoma or squamous cell carcinoma. Patients underwent imaging analyses 6-8 weeks after chemoradiotherapy and were followed for 5 years. Our primary aim was to determine whether detection of circulating tumor DNA (ctDNA) after chemoradiotherapy is associated with risk of tumor progression (growth of local, regional, or distant tumors, detected by imaging or biopsy). RESULTS The median proportion of tumor-derived DNA in total cell-free DNA before treatment was 0.07%, indicating that ultrasensitive assays are needed for quantification and analysis of ctDNA from localized esophageal tumors. Detection of ctDNA after chemoradiotherapy was associated with tumor progression (hazard ratio, 18.7; P < .0001), formation of distant metastases (hazard ratio, 32.1; P < .0001), and shorter disease-specific survival times (hazard ratio, 23.1; P < .0001). A higher proportion of patients with tumor progression had new mutations detected in plasma samples collected after chemoradiotherapy than patients without progression (P = .03). Detection of ctDNA after chemoradiotherapy preceded radiographic evidence of tumor progression by an average of 2.8 months. Among patients who received chemoradiotherapy without surgery, combined ctDNA and metabolic imaging analysis predicted progression in 100% of patients with tumor progression, compared with 71% for only ctDNA detection and 57% for only metabolic imaging analysis (P < .001 for comparison of either technique to combined analysis). CONCLUSIONS In an analysis of cell-free DNA in blood samples from patients who underwent chemoradiotherapy for esophageal cancer, detection of ctDNA was associated with tumor progression, metastasis, and disease-specific survival. Analysis of ctDNA might be used to identify patients at highest risk for tumor progression.
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Affiliation(s)
- Tej D. Azad
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Aadel A. Chaudhuri
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | - Penny Fang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yawei Qiao
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mohammad S. Esfahani
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Emily G. Hamilton
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Yi D. Yang
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Alex Lovejoy
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Aaron M. Newman
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - David M. Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Michael Jin
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Joseph Schroers-Martin
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Henning Stehr
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Viren Patel
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dipen Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California; Stanford Cancer Institute, Stanford University, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.
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Abstract
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cell or bulk-sorted RNA sequencing data can be used to learn molecular signatures of distinct cell types from a small collection of biospecimens. These signatures can then be repeatedly applied to characterize cellular heterogeneity from bulk tissue transcriptomes without physical cell isolation. In this chapter, we provide a detailed primer on CIBERSORTx and demonstrate its capabilities for high-throughput profiling of cell types and cellular states in normal and neoplastic tissues.
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Affiliation(s)
- Chloé B Steen
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA. .,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun 2019; 10:5712. [PMID: 31836708 PMCID: PMC6911043 DOI: 10.1038/s41467-019-13392-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/07/2019] [Indexed: 12/23/2022] Open
Abstract
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.
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Affiliation(s)
- Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Luke J Lee
- Stanford Cancer Institute, Stanford University, Stanford, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Noriko Ishisoko
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Eric Kildebeck
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Scott V Bratman
- Department of Radiation Oncology, Stanford University, Stanford, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, University of Toronto, Toronto, CA, USA
| | | | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Department of Radiation Oncology, Stanford University, Stanford, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA.
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Liu CC, Steen CB, Newman AM. Computational approaches for characterizing the tumor immune microenvironment. Immunology 2019; 158:70-84. [PMID: 31347163 PMCID: PMC6742767 DOI: 10.1111/imm.13101] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput molecular profiling technologies and multiplexed imaging platforms have revolutionized our ability to characterize the tumor immune microenvironment. As a result, studies of tumor-associated immune cells increasingly involve complex data sets that require sophisticated methods of computational analysis. In this review, we present an overview of key assays and related bioinformatics tools for analyzing the tumor-associated immune system in bulk tissues and at the single-cell level. In parallel, we describe how data science strategies and novel technologies have advanced tumor immunology and opened the door for new opportunities to exploit host immunity to improve cancer clinical outcomes.
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Affiliation(s)
- Candace C. Liu
- Immunology Graduate ProgramSchool of MedicineStanford UniversityStanfordCAUSA
| | - Chloé B. Steen
- Division of OncologyDepartment of MedicineStanford Cancer InstituteStanford UniversityStanfordCAUSA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative MedicineStanford UniversityStanfordCAUSA
- Department of Biomedical Data ScienceStanford UniversityStanfordCAUSA
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2019; 51:411-412. [PMID: 31433971 DOI: 10.1016/j.immuni.2019.08.004] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | | | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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32
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2019. [PMID: 31433971 DOI: 10.1016/j.immuni.2019.08.004.erratumfor:immunity.2018;48(4),812-830.e14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | | | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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Kurtz DM, Esfahani MS, Scherer F, Soo J, Jin MC, Liu CL, Newman AM, Dührsen U, Hüttmann A, Casasnovas O, Westin JR, Ritgen M, Böttcher S, Langerak AW, Roschewski M, Wilson WH, Gaidano G, Rossi D, Bahlo J, Hallek M, Tibshirani R, Diehn M, Alizadeh AA. Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction. Cell 2019; 178:699-713.e19. [PMID: 31280963 DOI: 10.1016/j.cell.2019.06.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [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: 12/06/2018] [Revised: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
Abstract
Accurate prediction of long-term outcomes remains a challenge in the care of cancer patients. Due to the difficulty of serial tumor sampling, previous prediction tools have focused on pretreatment factors. However, emerging non-invasive diagnostics have increased opportunities for serial tumor assessments. We describe the Continuous Individualized Risk Index (CIRI), a method to dynamically determine outcome probabilities for individual patients utilizing risk predictors acquired over time. Similar to "win probability" models in other fields, CIRI provides a real-time probability by integrating risk assessments throughout a patient's course. Applying CIRI to patients with diffuse large B cell lymphoma, we demonstrate improved outcome prediction compared to conventional risk models. We demonstrate CIRI's broader utility in analogous models of chronic lymphocytic leukemia and breast adenocarcinoma and perform a proof-of-concept analysis demonstrating how CIRI could be used to develop predictive biomarkers for therapy selection. We envision that dynamic risk assessment will facilitate personalized medicine and enable innovative therapeutic paradigms.
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Scherer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Joanne Soo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ulrich Dührsen
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Andreas Hüttmann
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Olivier Casasnovas
- Department of Hematology, Hopital F. Mitterrand, CHU Dijon and INSERM 1231, Dijon, France
| | - Jason R Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthais Ritgen
- Department II of Internal Medicine, Campus Kiel, University of Schleswig-Holstein, Kiel, Germany
| | - Sebastian Böttcher
- Department III of Internal Medicine, University Hospital Rostock, Rostock, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jasmin Bahlo
- German CLL Study Group, Department I of Internal Medicine and Center of Integrated Oncology Cologne Bonn, University Hospital of Cologne, Cologne, Germany
| | - Michael Hallek
- German CLL Study Group, Department I of Internal Medicine and Center of Integrated Oncology Cologne Bonn, University Hospital of Cologne, Cologne, Germany; Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Related Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Robert Tibshirani
- Department Statistics, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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34
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Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol 2019; 37:773-782. [PMID: 31061481 PMCID: PMC6610714 DOI: 10.1038/s41587-019-0114-2] [Citation(s) in RCA: 1884] [Impact Index Per Article: 376.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. We previously developed an approach for digital cytometry, called CIBERSORT, that enables estimation of cell type abundances from bulk tissue transcriptomes. We now introduce CIBERSORTx, a machine learning method that extends this framework to infer cell-type-specific gene expression profiles without physical cell isolation. By minimizing platform-specific variation, CIBERSORTx also allows the use of single-cell RNA-sequencing data for large-scale tissue dissection. We evaluated the utility of CIBERSORTx in multiple tumor types, including melanoma, where single-cell reference profiles were used to dissect bulk clinical specimens, revealing cell-type-specific phenotypic states linked to distinct driver mutations and response to immune checkpoint blockade. We anticipate that digital cytometry will augment single-cell profiling efforts, enabling cost-effective, high-throughput tissue characterization without the need for antibodies, disaggregation or viable cells.
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Affiliation(s)
- Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Chloé B Steen
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Chih Long Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA.,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Florian Scherer
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Michael S Khodadoust
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Steiner
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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35
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Myers LM, Tal MC, Torrez Dulgeroff LB, Carmody AB, Messer RJ, Gulati G, Yiu YY, Staron MM, Angel CL, Sinha R, Markovic M, Pham EA, Fram B, Ahmed A, Newman AM, Glenn JS, Davis MM, Kaech SM, Weissman IL, Hasenkrug KJ. A functional subset of CD8 + T cells during chronic exhaustion is defined by SIRPα expression. Nat Commun 2019; 10:794. [PMID: 30770827 PMCID: PMC6377614 DOI: 10.1038/s41467-019-08637-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 04/18/2018] [Accepted: 01/09/2019] [Indexed: 12/21/2022] Open
Abstract
Prolonged exposure of CD8+ T cells to antigenic stimulation, as in chronic viral infections, leads to a state of diminished function termed exhaustion. We now demonstrate that even during exhaustion there is a subset of functional CD8+ T cells defined by surface expression of SIRPα, a protein not previously reported on lymphocytes. On SIRPα+ CD8+ T cells, expression of co-inhibitory receptors is counterbalanced by expression of co-stimulatory receptors and it is only SIRPα+ cells that actively proliferate, transcribe IFNγ and show cytolytic activity. Furthermore, target cells that express the ligand for SIRPα, CD47, are more susceptible to CD8+ T cell-killing in vivo. SIRPα+ CD8+ T cells are evident in mice infected with Friend retrovirus, LCMV Clone 13, and in patients with chronic HCV infections. Furthermore, therapeutic blockade of PD-L1 to reinvigorate CD8+ T cells during chronic infection expands the cytotoxic subset of SIRPα+ CD8+ T cells.
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Affiliation(s)
- Lara M Myers
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA
| | - Michal Caspi Tal
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laughing Bear Torrez Dulgeroff
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aaron B Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, 59840, USA
| | - Ronald J Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA
| | - Gunsagar Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ying Ying Yiu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew M Staron
- Research Technologies Branch, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, 59840, USA
- Foundational Immunology, AbbVie Bioresearch Center, Worcester, MA, 01605, USA
| | - Cesar Lopez Angel
- Deparment of Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maxim Markovic
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Edward A Pham
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Benjamin Fram
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aijaz Ahmed
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jeffrey S Glenn
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Deparment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark M Davis
- Deparment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Susan M Kaech
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06520, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute, La Jolla, CA, 92037, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA.
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36
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Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas O, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA. Reply to J. Wang et al. J Clin Oncol 2019; 37:755-757. [PMID: 30753108 DOI: 10.1200/jco.18.01907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- David M Kurtz
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Florian Scherer
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michael C Jin
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Joanne Soo
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Alexander F M Craig
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Mohammad S Esfahani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Jacob J Chabon
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Henning Stehr
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Chih Long Liu
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Robert Tibshirani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Lauren S Maeda
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Neel K Gupta
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michael S Khodadoust
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ranjana H Advani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Aaron M Newman
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ulrich Dührsen
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Andreas Hüttmann
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michel Meignan
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Olivier Casasnovas
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Jason R Westin
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Mark Roschewski
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Wyndham H Wilson
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Gianluca Gaidano
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Davide Rossi
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Maximilian Diehn
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ash A Alizadeh
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
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Rosental B, Kowarsky M, Seita J, Corey DM, Ishizuka KJ, Palmeri KJ, Chen SY, Sinha R, Okamoto J, Mantalas G, Manni L, Raveh T, Clarke DN, Tsai JM, Newman AM, Neff NF, Nolan GP, Quake SR, Weissman IL, Voskoboynik A. Complex mammalian-like haematopoietic system found in a colonial chordate. Nature 2018; 564:425-429. [PMID: 30518860 PMCID: PMC6347970 DOI: 10.1038/s41586-018-0783-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 10/15/2018] [Indexed: 12/11/2022]
Abstract
Haematopoiesis is an essential process that evolved in multicellular animals. At the heart of this process are haematopoietic stem cells (HSCs), which are multipotent and self-renewing, and generate the entire repertoire of blood and immune cells throughout an animal's life1. Although there have been comprehensive studies on self-renewal, differentiation, physiological regulation and niche occupation in vertebrate HSCs, relatively little is known about the evolutionary origin and niches of these cells. Here we describe the haematopoietic system of Botryllus schlosseri, a colonial tunicate that has a vasculature and circulating blood cells, and interesting stem-cell biology and immunity characteristics2-8. Self-recognition between genetically compatible B. schlosseri colonies leads to the formation of natural parabionts with shared circulation, whereas incompatible colonies reject each other3,4,7. Using flow cytometry, whole-transcriptome sequencing of defined cell populations and diverse functional assays, we identify HSCs, progenitors, immune effector cells and an HSC niche, and demonstrate that self-recognition inhibits allospecific cytotoxic reactions. Our results show that HSC and myeloid lineage immune cells emerged in a common ancestor of tunicates and vertebrates, and also suggest that haematopoietic bone marrow and the B. schlosseri endostyle niche evolved from a common origin.
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Affiliation(s)
- Benyamin Rosental
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
| | - Mark Kowarsky
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Jun Seita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- AI based Healthcare and Medical Data Analysis Standardization Unit, Medical Sciences Innovation Hub Program, RIKEN, Tokyo, Japan
| | - Daniel M Corey
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine J Ishizuka
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Karla J Palmeri
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gary Mantalas
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Molecular Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy
| | - Tal Raveh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - D Nathaniel Clarke
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA
| | - Jonathan M Tsai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
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38
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Abstract
We introduce a novel data reduction technique whereby we select a subset of tiles to "cover" maximally events of interest in large-scale biological datasets (e.g., genetic mutations), while minimizing the number of tiles. A tile is a genomic unit capturing one or more biological events, such as a sequence of base pairs that can be sequenced and observed simultaneously. The goal is to reduce significantly the number of tiles considered to those with areas of dense events in a cohort, thus saving on cost and enhancing interpretability. However, the reduction should not come at the cost of too much information, allowing for sensible statistical analysis after its application. We envisage application of our methods to a variety of high throughput data types, particularly those produced by next generation sequencing (NGS) experiments. The procedure is cast as a convex optimization problem, which is presented, along with methods of its solution. The method is demonstrated on a large dataset of somatic mutations spanning 5000+ patients, each having one of 29 cancer types. Applied to these data, our method dramatically reduces the number of gene locations required for broad coverage of patients and their mutations, giving subject specialists a more easily interpretable snapshot of recurrent mutational profiles in these cancers. The locations identified coincide with previously identified cancer genes. Finally, despite considerable data reduction, we show that our covering designs preserve the cancer discrimination ability of multinomial logistic regression models trained on all of the locations (> 1M).
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Affiliation(s)
- Stephen Reid
- Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA, USA
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39
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Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Levy R, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas RO, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA. Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma. J Clin Oncol 2018; 36:2845-2853. [PMID: 30125215 DOI: 10.1200/jco.2018.78.5246] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Outcomes for patients with diffuse large B-cell lymphoma remain heterogeneous, with existing methods failing to consistently predict treatment failure. We examined the additional prognostic value of circulating tumor DNA (ctDNA) before and during therapy for predicting patient outcomes. PATIENTS AND METHODS We studied the dynamics of ctDNA from 217 patients treated at six centers, using a training and validation framework. We densely characterized early ctDNA dynamics during therapy using cancer personalized profiling by deep sequencing to define response-associated thresholds within a discovery set. These thresholds were assessed in two independent validation sets. Finally, we assessed the prognostic value of ctDNA in the context of established risk factors, including the International Prognostic Index and interim positron emission tomography/computed tomography scans. RESULTS Before therapy, ctDNA was detectable in 98% of patients; pretreatment levels were prognostic in both front-line and salvage settings. In the discovery set, ctDNA levels changed rapidly, with a 2-log decrease after one cycle (early molecular response [EMR]) and a 2.5-log decrease after two cycles (major molecular response [MMR]) stratifying outcomes. In the first validation set, patients receiving front-line therapy achieving EMR or MMR had superior outcomes at 24 months (EMR: EFS, 83% v 50%; P = .0015; MMR: EFS, 82% v 46%; P < .001). EMR also predicted superior 24-month outcomes in patients receiving salvage therapy in the first validation set (EFS, 100% v 13%; P = .011). The prognostic value of EMR and MMR was further confirmed in the second validation set. In multivariable analyses including International Prognostic Index and interim positron emission tomography/computed tomography scans across both cohorts, molecular response was independently prognostic of outcomes, including event-free and overall survival. CONCLUSION Pretreatment ctDNA levels and molecular responses are independently prognostic of outcomes in aggressive lymphomas. These risk factors could potentially guide future personalized risk-directed approaches.
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Affiliation(s)
- David M Kurtz
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Florian Scherer
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michael C Jin
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Joanne Soo
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Alexander F M Craig
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Mohammad Shahrokh Esfahani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jacob J Chabon
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Henning Stehr
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Chih Long Liu
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Robert Tibshirani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Lauren S Maeda
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Neel K Gupta
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michael S Khodadoust
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ranjana H Advani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ronald Levy
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Aaron M Newman
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ulrich Dührsen
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Andreas Hüttmann
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michel Meignan
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - René-Olivier Casasnovas
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jason R Westin
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Mark Roschewski
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Wyndham H Wilson
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Gianluca Gaidano
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Davide Rossi
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Maximilian Diehn
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ash A Alizadeh
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2018; 48:812-830.e14. [PMID: 29628290 PMCID: PMC5982584 DOI: 10.1016/j.immuni.2018.03.023] [Citation(s) in RCA: 3110] [Impact Index Per Article: 518.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/23/2018] [Accepted: 03/21/2018] [Indexed: 02/08/2023]
Abstract
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.
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Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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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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42
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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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43
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Das R, Bar N, Ferreira M, Newman AM, Zhang L, Bailur JK, Bacchiocchi A, Kluger H, Wei W, Halaban R, Sznol M, Dhodapkar MV, Dhodapkar KM. Early B cell changes predict autoimmunity following combination immune checkpoint blockade. J Clin Invest 2018; 128:715-720. [PMID: 29309048 DOI: 10.1172/jci96798] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Combination checkpoint blockade (CCB) targeting inhibitory CTLA4 and PD1 receptors holds promise for cancer therapy. Immune-related adverse events (IRAEs) remain a major obstacle for the optimal application of CCB in cancer. Here, we analyzed B cell changes in patients with melanoma following treatment with either anti-CTLA4 or anti-PD1, or in combination. CCB therapy led to changes in circulating B cells that were detectable after the first cycle of therapy and characterized by a decline in circulating B cells and an increase in CD21lo B cells and plasmablasts. PD1 expression was higher in the CD21lo B cells, and B cell receptor sequencing of these cells demonstrated greater clonality and a higher frequency of clones compared with CD21hi cells. CCB induced proliferation in the CD21lo compartment, and single-cell RNA sequencing identified B cell activation in cells with genomic profiles of CD21lo B cells in vivo. Increased clonality of circulating B cells following CCB occurred in some patients. Treatment-induced changes in B cells preceded and correlated with both the frequency and timing of IRAEs. Patients with early B cell changes experienced higher rates of grade 3 or higher IRAEs 6 months after CCB. Thus, early changes in B cells following CCB may identify patients who are at increased risk of IRAEs, and preemptive strategies targeting B cells may reduce toxicities in these patients.
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Affiliation(s)
| | | | - Michelle Ferreira
- Department of Medicine.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, and.,Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | | | | | - Wei Wei
- Yale Center for Analytic Sciences
| | | | - Mario Sznol
- Department of Medicine.,Yale Cancer Center, and
| | - Madhav V Dhodapkar
- Department of Medicine.,Yale Cancer Center, and.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kavita M Dhodapkar
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Cancer Center, and
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Abstract
Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as immunohistochemistry or flow cytometry suffer from limitations in phenotypic markers and can be challenging to practically implement and standardize. An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally. We recently described CIBERSORT, a versatile computational method for quantifying cell fractions from bulk tissue gene expression profiles (GEPs). Combining support vector regression with prior knowledge of expression profiles from purified leukocyte subsets, CIBERSORT can accurately estimate the immune composition of a tumor biopsy. In this chapter, we provide a primer on the CIBERSORT method and illustrate its use for characterizing TILs in tumor samples profiled by microarray or RNA-Seq.
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Affiliation(s)
- Binbin Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA.,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, 875 Blake Wilbur Drive, Stanford, CA, 94305, USA. .,Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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45
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Zarnegar MA, Reinitz F, Newman AM, Clarke MF. Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers. Nucleic Acids Res 2017; 45:e153. [PMID: 28973448 PMCID: PMC5622369 DOI: 10.1093/nar/gkx648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/27/2017] [Accepted: 07/19/2017] [Indexed: 01/20/2023] Open
Abstract
The complexity and inefficiency of chromatin immunoprecipitation strategies restrict their sensitivity and application when examining rare cell populations. We developed a new technique that replaces immunoprecipitation with a simplified chromatin fragmentation and proximity ligation step that eliminates bead purification and washing steps. We present a simple single tube proximity ligation technique, targeted chromatin ligation, that captures histone modification patterns with only 200 cells. Our technique eliminates loss of material and sensitivity due to multiple inefficient steps, while simplifying the workflow to enhance sensitivity and create the potential for novel applications.
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Affiliation(s)
- Mark A. Zarnegar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Felicia Reinitz
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael F. Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
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46
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh AA, Diehn M. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discov 2017; 7:1394-1403. [PMID: 28899864 DOI: 10.1158/2159-8290.cd-17-0716] [Citation(s) in RCA: 602] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/07/2017] [Accepted: 08/31/2017] [Indexed: 12/15/2022]
Abstract
Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant therapies. Here, we apply cancer personalized profiling by deep sequencing (CAPP-seq) circulating tumor DNA (ctDNA) analysis to 255 samples from 40 patients treated with curative intent for stage I-III lung cancer and 54 healthy adults. In 94% of evaluable patients experiencing recurrence, ctDNA was detectable in the first posttreatment blood sample, indicating reliable identification of MRD. Posttreatment ctDNA detection preceded radiographic progression in 72% of patients by a median of 5.2 months, and 53% of patients harbored ctDNA mutation profiles associated with favorable responses to tyrosine kinase inhibitors or immune checkpoint blockade. Collectively, these results indicate that ctDNA MRD in patients with lung cancer can be accurately detected using CAPP-seq and may allow personalized adjuvant treatment while disease burden is lowest.Significance: This study shows that ctDNA analysis can robustly identify posttreatment MRD in patients with localized lung cancer, identifying residual/recurrent disease earlier than standard-of-care radiologic imaging, and thus could facilitate personalized adjuvant treatment at early time points when disease burden is lowest. Cancer Discov; 7(12); 1394-403. ©2017 AACR.See related commentary by Comino-Mendez and Turner, p. 1368This article is highlighted in the In This Issue feature, p. 1355.
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Affiliation(s)
- Aadel A Chaudhuri
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Alexander F Lovejoy
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Tej D Azad
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Michael S Khodadoust
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Florian Scherer
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - David M Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Bioengineering, Stanford University, Stanford, California
| | - Carmen Say
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Justin N Carter
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - David J Merriott
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Jonathan C Dudley
- Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Pathology, Stanford University, Stanford, California
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Leslie Modlin
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Robert B West
- Department of Pathology, Stanford University, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford School of Medicine, Stanford University, Stanford, California
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, California. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California. .,Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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Abstract
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The Cancer Genome Atlas. Methods to characterize TIL biology are increasingly important, and the authors offer several arguments in favor of their strategy. Several of these claims warrant further discussion and highlight the critical importance of data normalization in gene expression deconvolution applications.Please see related Li et al correspondence: www.dx.doi.org/10.1186/s13059-017-1256-5 and Zheng correspondence: www.dx.doi.org/10.1186/s13059-017-1258-3.
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Affiliation(s)
- Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA.
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
| | - Andrew J Gentles
- Center for Cancer Systems Biology, Stanford University, Stanford, California, 94305, USA
- Department of Radiology, Stanford University, Stanford, California, 94305, USA
| | - Chih Long Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, California, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, 94305, USA.
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
- Center for Cancer Systems Biology, Stanford University, Stanford, California, 94305, USA.
- Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
- Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, 94305, USA.
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Przybyl J, Kowalewska M, Quattrone A, Dewaele B, Vanspauwen V, Varma S, Vennam S, Newman AM, Swierniak M, Bakuła-Zalewska E, Siedlecki JA, Bidzinski M, Cools J, van de Rijn M, Debiec-Rychter M. Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas. JCI Insight 2017; 2:94033. [PMID: 28570276 DOI: 10.1172/jci.insight.94033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Endometrial stromal tumors include translocation-associated low- and high-grade endometrial stromal sarcomas (ESS) and highly malignant undifferentiated uterine sarcomas (UUS). UUS is considered a poorly defined group of aggressive tumors and is often seen as a diagnosis of exclusion after ESS and leiomyosarcoma (LMS) have been ruled out. We performed a comprehensive analysis of gene expression, copy number variation, point mutations, and immune cell infiltrates in the largest series to date of all major types of uterine sarcomas to shed light on the biology of UUS and to identify potential novel therapeutic targets. We show that UUS tumors have a distinct molecular profile from LMS and ESS. Gene expression and immunohistochemical analyses revealed the presence of high numbers of tumor-associated macrophages (TAMs) in UUS, which makes UUS patients suitable candidates for therapies targeting TAMs. Our results show a high genomic instability of UUS and downregulation of several TP53-mediated tumor suppressor genes, such as NDN, CDH11, and NDRG4. Moreover, we demonstrate that UUS carry somatic mutations in several oncogenes and tumor suppressor genes implicated in RAS/PI3K/AKT/mTOR, ERBB3, and Hedgehog signaling.
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Affiliation(s)
- Joanna Przybyl
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Magdalena Kowalewska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,Department of Immunology, Biochemistry and Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Anna Quattrone
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Vanessa Vanspauwen
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine.,Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Michal Swierniak
- Human Cancer Genetics, Center of New Technologies, CENT, University of Warsaw, Warsaw, Poland
| | | | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Mariusz Bidzinski
- Department of Gynecologic Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,The Faculty of Medicine and Health Sciences, Jan Kochanowski University, Kielce, Poland
| | - Jan Cools
- KU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB), Leuven, Belgium
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maria Debiec-Rychter
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Zhou L, Liu CL, Scherer F, Kurtz DM, Esfahani MS, Say C, Carter JN, Merriott D, Dudley J, Binkley MS, Modlin L, Padda SK, Gensheimer M, West RB, Shrager JB, Neal JW, Wakelee HA, Billy, Loo W, Alizadeh AA, Diehn M. (S012) Circulating Tumor DNA Detects Residual Disease and Anticipates Tumor Progression Earlier Than CT Imaging. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.02.048] [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: 10/19/2022]
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50
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Chaudhuri A, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Carter JN, Merriott DJ, Liu CL, Kurtz DM, Dudley JC, Padda SK, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh AA, Diehn M. Analysis of circulating tumor DNA in localized lung cancer for detection of molecular residual disease and personalization of adjuvant strategies. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.8519] [Citation(s) in RCA: 2] [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] [Indexed: 11/20/2022] Open
Abstract
8519 Background: Identifying localized non-small cell lung cancer (NSCLC) patients with residual disease following curative intent therapy is difficult due to normal tissue changes caused by surgery or radiation and an inability to detect microscopic disease. Analysis of circulating tumor DNA (ctDNA) might enable identification of molecular residual disease (MRD) and personalization of adjuvant treatment approaches but has not been explored in lung cancer. Methods: We applied CAPP-Seq, an ultra-sensitive next-generation sequencing based ctDNA quantitation method, to pre- and post-treatment blood samples from a cohort of 41 patients treated with chemoradiation, radiotherapy or surgery for stage I-III primary lung cancer. Detection of ctDNA at a single MRD time-point within 4 months of treatment completion was compared with surveillance by cross-sectional imaging. Furthermore, we developed an approach for identification of tumor mutation burden based on mutations detected in plasma, leveraging whole exome sequencing data from 1,177 NSCLCs sequenced by TCGA. Results: Median follow-up time was 35 months. Pre-treatment ctDNA was detected in 38 (93%) patients and 19 (46%) had detectable post-treatment ctDNA MRD. MRD+ patients displayed significantly inferior 3-year freedom from progression (0% vs. 92%; HR 38; P < 0.0001) and 3-year overall survival (8% vs. 75%; HR 12; P < 0.0001) than MRD- patients. Detection of ctDNA MRD had positive and negative predictive values for disease progression of 100% and 93%, respectively. Furthermore, we non-invasively identified activating EGFR mutations or high mutational burden (≥5 CAPP-Seq non-synonymous mutations, corresponding to > 200 non-synonymous mutations per exome or > 4 single nucleotide variants per megabase of exome) in 47% of patients with detectable ctDNA MRD, suggesting potentially favorable responses to TKIs and immune checkpoint inhibitors, respectively. Conclusions: Our results indicate that ctDNA analysis accurately detects MRD in localized lung cancer patients and could facilitate personalized adjuvant treatment at early time-points when disease burden is minimal.
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