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Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov 2024; 14:683-689. [PMID: 38571435 DOI: 10.1158/2159-8290.cd-23-1550] [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] [Indexed: 04/05/2024]
Abstract
Research on precancers, as defined as at-risk tissues and early lesions, is of high significance given the effectiveness of early intervention. We discuss the need for risk stratification to prevent overtreatment, an emphasis on the role of genetic and epigenetic aging when considering risk, and the importance of integrating macroenvironmental risk factors with molecules and cells in lesions and at-risk normal tissues for developing effective intervention and health policy strategies.
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Affiliation(s)
- Mary M Stangis
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Zhengyi Chen
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jimin Min
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah E Glass
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jordan O Jackson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Megan D Radyk
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xen Ping Hoi
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - W Nathaniel Brennen
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins Medicine, Baltimore, Maryland
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, & Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keith S Chan
- Department of Urology, Houston Methodist Research Institute, Houston, Texas
- Neal Cancer Center, Houston Methodist Research Institute, Houston, Texas
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Srinivasan Yegnasubramanian
- Genitourinary Cancer Disease Division, Department of Oncology, Johns Hopkins Medicine, Baltimore, Maryland
- Molecular Radiation Science Division, Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland
- Kidney-Urologic Pathology Division, Department of Pathology, Johns Hopkins Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Gastroenterology, Internal Medicine, University of Washington, Seattle, Washington
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
- Gastroenterology Division, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ken S Lau
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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Hou Y, Khatri P, Rindy J, Schultz Z, Gao A, Chen Z, Gibson ALF, Huttenlocher A, Dinh HQ. Single-cell transcriptional landscape of temporal neutrophil response to burn wound in larval zebrafish. bioRxiv 2024:2024.04.01.587641. [PMID: 38617269 PMCID: PMC11014537 DOI: 10.1101/2024.04.01.587641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Neutrophils accumulate early in tissue injury. However, the cellular and functional heterogeneity of neutrophils during homeostasis and in response to tissue damage remains unclear. Here, we use larval zebrafish to understand neutrophil responses to thermal injury. Single-cell transcriptional mapping of myeloid cells during a 3-day time course in burn and control larvae revealed distinct neutrophil subsets and their cell-cell interactions with macrophages across time and conditions. The trajectory formed by three zebrafish neutrophil subsets resembles human neutrophil maturation, with varying transition patterns between conditions. Through ligand-receptor cell-cell interaction analysis, we found neutrophils communicate more in burns in a pathway and temporal manner. Finally, we identified the correlation between zebrafish myeloid signatures and human burn severity, establishing GPR84+ neutrophils as a potential marker of early innate immune response in burns. This work builds the molecular foundation and a comparative single-cell genomic framework to identify neutrophil markers of tissue damage using model organisms.
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Affiliation(s)
- Yiran Hou
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Parth Khatri
- McArdle Laboratory for Cancer Research;Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Julie Rindy
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Zachery Schultz
- McArdle Laboratory for Cancer Research;Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Anqi Gao
- McArdle Laboratory for Cancer Research;Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Zhili Chen
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
- McArdle Laboratory for Cancer Research;Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Angela LF Gibson
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research;Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
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3
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Brand J, Haro M, Lin X, Rimel B, McGregor SM, Lawrenson K, Dinh HQ. Fallopian tube single cell analysis reveals myeloid cell alterations in high-grade serous ovarian cancer. iScience 2024; 27:108990. [PMID: 38384837 PMCID: PMC10879678 DOI: 10.1016/j.isci.2024.108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Most high-grade serous ovarian cancers (HGSCs) likely initiate from fallopian tube (FT) epithelia. While epithelial subtypes have been characterized using single-cell RNA-sequencing (scRNA-Seq), heterogeneity of other compartments and their involvement in tumor progression are poorly defined. Integrated analysis of human FT scRNA-Seq and HGSC-related tissues, including tumors, revealed greater immune and stromal transcriptional diversity than previously reported. We identified abundant monocytes in FTs across two independent cohorts. The ratio of macrophages to monocytes is similar between benign FTs, ovaries, and adjacent normal tissues but significantly greater in tumors. FT-defined monocyte and macrophage signatures, cell-cell communication, and gene set enrichment analyses identified monocyte- and macrophage-specific interactions and functional pathways in paired tumors and adjacent normal tissues. Further reanalysis of HGSC scRNA-Seq identified monocyte and macrophage subsets associated with neoadjuvant chemotherapy. Taken together, our work provides data that an altered FT myeloid cell composition could inform the discovery of early detection markers for HGSC.
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Affiliation(s)
- Joshua Brand
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
| | - Marcela Haro
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- RNA Biology Group, Division of Natural and Applied Sciences and Global Health Research Center, Duke Kunshan University, Kunshan 215316, Jiangsu Province, China
| | - B.J. Rimel
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie M. McGregor
- Department of Pathology and Laboratory Medicine, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin – Madison, Madison, WI 53705, USA
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Giese MA, Bennin DA, Schoen TJ, Peterson AN, Schrope JH, Brand J, Jung HS, Keller NP, Beebe DJ, Dinh HQ, Slukvin II, Huttenlocher A. PTP1B phosphatase dampens iPSC-derived neutrophil motility and antimicrobial function. J Leukoc Biol 2024:qiae039. [PMID: 38417030 DOI: 10.1093/jleuko/qiae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
Neutrophils are rapidly recruited to sites of infection and are critical for pathogen clearance. Therapeutic use of primary neutrophils has been limited as they have a short lifespan and are not amenable to genetic manipulation. Human induced pluripotent stem cells (iPSCs) can provide a robust source of neutrophils for infusion and are genetically tractable. However, current work has indicated that dampened intracellular signaling limits iPSC-derived neutrophil (iNeutrophil) cellular activation and antimicrobial response. Here, we show that protein tyrosine phosphatase 1B (PTP1B) inhibits intracellular signaling and dampens iNeutrophil effector function. Deletion of the PTP1B phosphatase increased PI3K and ERK signaling and was associated with increased F-actin polymerization, cell migration and phagocytosis. In contrast, other effector functions like NETosis and ROS production were reduced. PTP1B-deficient neutrophils were more responsive to A. fumigatus and displayed rapid recruitment and control of hyphal growth. Accordingly, depletion of PTP1B increased production of inflammatory factors including the neutrophil chemokine IL-8. Taken together, these findings suggest that PTP1B limits iNeutrophil motility and antimicrobial function.
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Affiliation(s)
- Morgan A Giese
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - David A Bennin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Taylor J Schoen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ashley N Peterson
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan H Schrope
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Josh Brand
- Cell and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - Huy Q Dinh
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
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Alvarez-Breckenridge C, Anderson KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, Dunn GP, Evgin L, Goc J, Good Z, Hacohen N, Han P, Hanč P, Hickey J, Kersten K, Liu BC, Buque A, Miao Y‘P, Milner JJ, Pritykin Y, Pucci F, Scharping NE, Sudmeier L, Wang Y, Wieland A, Williams MM. Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer Immunol Res 2023; 11:1571-1577. [PMID: 37906619 PMCID: PMC10696930 DOI: 10.1158/2326-6066.cir-23-0522] [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: 07/03/2023] [Revised: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
The Arthur and Sandra Irving Cancer Immunology Symposium has been created as a platform for established cancer immunologists to mentor trainees and young investigators as they launch their research career in the field. By sharing their different paths to success, the senior faculty mentors provide an invaluable resource to support the development of the next generation of leaders in the cancer immunology community. This Commentary describes some of the key topics that were discussed during the 2022 symposium: scientific and career trajectory, leadership, mentoring, collaborations, and publishing. For each of these topics, established investigators discussed the elements that facilitate success in these areas as well as mistakes that can hinder progress. Herein, we outline the critical points raised in these discussions for establishing a successful independent research career. These points are highly relevant for the broader scientific community.
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Affiliation(s)
| | - Kristin G. Anderson
- Department of Microbiology, Immunology and Cancer Biology, Carter Center for Immunology Research, University of Virginia, Charlottesville, Virginia
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, Virginia
| | | | - Shadmehr Demehri
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research/Department of Oncology, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Karen Olivia Dixon
- Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Gavin P. Dunn
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Laura Evgin
- Michael Smith Genome Sciences Department, BC Cancer Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jeremy Goc
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, New York
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York
| | - Zinaida Good
- Stanford Cancer Institute and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Nir Hacohen
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Patrick Han
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Pavel Hanč
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - John Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly Kersten
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Beiyun C. Liu
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Aitziber Buque
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
| | | | - J. Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science, Princeton University, New Jersey
| | - Ferdinando Pucci
- Department of Otolaryngology and Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Nicole E. Scharping
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California
| | - Lisa Sudmeier
- Department of Radiation Oncology, Winship Cancer Institute and Emory University School of Medicine, Atlanta, Georgia
| | - Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andreas Wieland
- Department of Otolaryngology and Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Michelle M. Williams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Meyer MA, Dinh HQ, Alimadadi A, Araujo DJ, Chatterjee N, Gutierrez NA, Zhu YP, Hunter EL, Liang S, Seumois G, Kiosses WB, Catz SD, Vijayanand P, Ottensmeier C, Hedrick CC. Human CD79b + neutrophils in the blood are associated with early-stage melanoma. Front Immunol 2023; 14:1224045. [PMID: 38022639 PMCID: PMC10643866 DOI: 10.3389/fimmu.2023.1224045] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Due to their abundance in the blood, low RNA content, and short lifespan, neutrophils have been classically considered to be one homogenous pool. However, recent work has found that mature neutrophils and neutrophil progenitors are composed of unique subsets exhibiting context-dependent functions. In this study, we ask if neutrophil heterogeneity is associated with melanoma incidence and/or disease stage. Experimental design Using mass cytometry, we profiled melanoma patient blood for unique cell surface markers among neutrophils. Markers were tested for their predictiveness using flow cytometry data and random forest machine learning. Results We identified CD79b+ neutrophils (CD3-CD56-CD19-Siglec8-CD203c-CD86LoCD66b+CD79b+) that are normally restricted to the bone marrow in healthy humans but appear in the blood of subjects with early-stage melanoma. Further, we found CD79b+ neutrophils present in tumors of subjects with head and neck cancer. AI-mediated machine learning analysis of neutrophils from subjects with melanoma confirmed that CD79b expression among peripheral blood neutrophils is highly important in identifying melanoma incidence. We noted that CD79b+ neutrophils possessed a neutrophilic appearance but have transcriptional and surface-marker phenotypes reminiscent of B cells. Compared to remaining blood neutrophils, CD79b+ neutrophils are primed for NETosis, express higher levels of antigen presentation-related proteins, and have an increased capacity for phagocytosis. Conclusion Our work suggests that CD79b+ neutrophils are associated with early-stage melanoma.
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Affiliation(s)
- Melissa A. Meyer
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Huy Q. Dinh
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, United States
| | - Ahmad Alimadadi
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Daniel J. Araujo
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Nandini Chatterjee
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Norma A. Gutierrez
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Yanfang Peipei Zhu
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Pediatrics, School of Medicine, University of California, San Diego, San Diego, CA, United States
- School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Emma L. Hunter
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Shu Liang
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Gregory Seumois
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - William B. Kiosses
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sergio D. Catz
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Pandurangan Vijayanand
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Christian Ottensmeier
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
- School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- Institute of Translational Medicine, Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Catherine C. Hedrick
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
- Immunology Center of Georgia, Department of Medicine, Medical College of Georgia at Augusta University, Augusta, GA, United States
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7
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Lozar T, Laklouk I, Golfinos AE, Gavrielatou N, Xu J, Flynn C, Keske A, Yu M, Bruce JY, Wang W, Grasic Kuhar C, Bailey HH, Harari PM, Dinh HQ, Rimm DL, Hu R, Lambert PF, Fitzpatrick MB. Stress Keratin 17 Is a Predictive Biomarker Inversely Associated with Response to Immune Check-Point Blockade in Head and Neck Squamous Cell Carcinomas and Beyond. Cancers (Basel) 2023; 15:4905. [PMID: 37835599 PMCID: PMC10571921 DOI: 10.3390/cancers15194905] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Low response rates in immune check-point blockade (ICB)-treated head and neck squamous cell carcinoma (HNSCC) drive a critical need for robust, clinically validated predictive biomarkers. Our group previously showed that stress keratin 17 (CK17) suppresses macrophage-mediated CXCL9/CXCL10 chemokine signaling involved in attracting activated CD8+ T cells into tumors, correlating with decreased response rate to pembrolizumab-based therapy in a pilot cohort of ICB-treated HNSCC (n = 26). Here, we performed an expanded analysis of the predictive value of CK17 in ICB-treated HNSCC according to the REMARK criteria and investigated the gene expression profiles associated with high CK17 expression. Pretreatment samples from pembrolizumab-treated HNSCC patients were stained via immunohistochemistry using a CK17 monoclonal antibody (n = 48) and subjected to spatial transcriptomic profiling (n = 8). Our findings were validated in an independent retrospective cohort (n = 22). CK17 RNA expression in pembrolizumab-treated patients with various cancer types was investigated for predictive significance. Of the 48 patients (60% male, median age of 61.5 years), 21 (44%) were CK17 high, and 27 (56%) were CK17 low. A total of 17 patients (35%, 77% CK17 low) had disease control, while 31 patients (65%, 45% CK17 low) had progressive disease. High CK17 expression was associated with a lack of disease control (p = 0.037), shorter time to treatment failure (p = 0.025), and progression-free survival (PFS, p = 0.004), but not overall survival (OS, p = 0.06). A high CK17 expression was associated with lack of disease control in an independent validation cohort (p = 0.011). PD-L1 expression did not correlate with CK17 expression or clinical outcome. CK17 RNA expression was predictive of PFS and OS in 552 pembrolizumab-treated cancer patients. Our findings indicate that high CK17 expression may predict resistance to ICB in HNSCC patients and beyond.
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Affiliation(s)
- Taja Lozar
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Israa Laklouk
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Athena E Golfinos
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Christopher Flynn
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Aysenur Keske
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Justine Y Bruce
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Wei Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
| | - Cvetka Grasic Kuhar
- University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia
| | - Howard H Bailey
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Paul M Harari
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - David L Rimm
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Rong Hu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 6459 Wisconsin Institute for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705 WI, USA
| | - Megan B Fitzpatrick
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, MC 8550, 600 Highland Ave, Madison, WI 53792, USA
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8
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Kiss MG, Papac-Miličević N, Porsch F, Tsiantoulas D, Hendrikx T, Takaoka M, Dinh HQ, Narzt MS, Göderle L, Ozsvár-Kozma M, Schuster M, Fortelny N, Hladik A, Knapp S, Gruber F, Pickering MC, Bock C, Swirski FK, Ley K, Zernecke A, Cochain C, Kemper C, Mallat Z, Binder CJ. Cell-autonomous regulation of complement C3 by factor H limits macrophage efferocytosis and exacerbates atherosclerosis. Immunity 2023; 56:1809-1824.e10. [PMID: 37499656 PMCID: PMC10529786 DOI: 10.1016/j.immuni.2023.06.026] [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: 03/22/2021] [Revised: 10/21/2022] [Accepted: 06/30/2023] [Indexed: 07/29/2023]
Abstract
Complement factor H (CFH) negatively regulates consumption of complement component 3 (C3), thereby restricting complement activation. Genetic variants in CFH predispose to chronic inflammatory disease. Here, we examined the impact of CFH on atherosclerosis development. In a mouse model of atherosclerosis, CFH deficiency limited plaque necrosis in a C3-dependent manner. Deletion of CFH in monocyte-derived inflammatory macrophages propagated uncontrolled cell-autonomous C3 consumption without downstream C5 activation and heightened efferocytotic capacity. Among leukocytes, Cfh expression was restricted to monocytes and macrophages, increased during inflammation, and coincided with the accumulation of intracellular C3. Macrophage-derived CFH was sufficient to dampen resolution of inflammation, and hematopoietic deletion of CFH in atherosclerosis-prone mice promoted lesional efferocytosis and reduced plaque size. Furthermore, we identified monocyte-derived inflammatory macrophages expressing C3 and CFH in human atherosclerotic plaques. Our findings reveal a regulatory axis wherein CFH controls intracellular C3 levels of macrophages in a cell-autonomous manner, evidencing the importance of on-site complement regulation in the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Máté G Kiss
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | | | - Florentina Porsch
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Dimitrios Tsiantoulas
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Tim Hendrikx
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Minoru Takaoka
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Marie-Sophie Narzt
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Laura Göderle
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Mária Ozsvár-Kozma
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Anastasiya Hladik
- Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, Vienna, Austria
| | - Sylvia Knapp
- Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Filip K Swirski
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klaus Ley
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Clément Cochain
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany; Comprehensive Heart Failure Center Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Claudia Kemper
- Inflammation Research Section, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK; Institut National de la Santé et de la Recherche Médicale, Paris Cardiovascular Research Center, Paris, France
| | - Christoph J Binder
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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9
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Padgett LE, Marcovecchio PM, Olingy CE, Araujo DJ, Steel K, Dinh HQ, Alimadadi A, Zhu YP, Meyer MA, Kiosses WB, Thomas GD, Hedrick CC. Nonclassical monocytes potentiate anti-tumoral CD8 + T cell responses in the lungs. Front Immunol 2023; 14:1101497. [PMID: 37426658 PMCID: PMC10325638 DOI: 10.3389/fimmu.2023.1101497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
CD8+ T cells drive anti-cancer immunity in response to antigen-presenting cells such as dendritic cells and subpopulations of monocytes and macrophages. While CD14+ classical monocytes modulate CD8+ T cell responses, the contributions of CD16+ nonclassical monocytes to this process remain unclear. Herein we explored the role of nonclassical monocytes in CD8+ T cell activation by utilizing E2-deficient (E2-/-) mice that lack nonclassical monocytes. During early metastatic seeding, modeled by B16F10-OVA cancer cells injected into E2-/- mice, we noted lower CD8+ effector memory and effector T cell frequencies within the lungs as well as in lung-draining mediastinal lymph nodes in the E2-/- mice. Analysis of the myeloid compartment revealed that these changes were associated with depletion of MHC-IIloLy6Clo nonclassical monocytes within these tissues, with little change in other monocyte or macrophage populations. Additionally, nonclassical monocytes preferentially trafficked to primary tumor sites in the lungs, rather than to the lung-draining lymph nodes, and did not cross-present antigen to CD8+ T cells. Examination of the lung microenvironment in E2-/- mice revealed reduced CCL21 expression in endothelial cells, which is chemokine involved in T cell trafficking. Our results highlight the previously unappreciated importance of nonclassical monocytes in shaping the tumor microenvironment via CCL21 production and CD8+ T cell recruitment.
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Affiliation(s)
- Lindsey E. Padgett
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Paola M. Marcovecchio
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Claire E. Olingy
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Daniel J. Araujo
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Kathleen Steel
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Huy Q. Dinh
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Ahmad Alimadadi
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Yanfang Peipei Zhu
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Melissa A. Meyer
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - William B. Kiosses
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Graham D. Thomas
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Catherine C. Hedrick
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
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10
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Robertson TF, Hou Y, Schrope J, Shen S, Rindy J, Sauer JD, Dinh HQ, Huttenlocher A. A tessellated lymphoid network provides whole-body T cell surveillance in zebrafish. Proc Natl Acad Sci U S A 2023; 120:e2301137120. [PMID: 37155881 PMCID: PMC10193988 DOI: 10.1073/pnas.2301137120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 01/31/2023] [Accepted: 03/21/2023] [Indexed: 05/10/2023] Open
Abstract
Homeostatic trafficking to lymph nodes allows T cells to efficiently survey the host for cognate antigen. Nonmammalian jawed vertebrates lack lymph nodes but maintain diverse T cell pools. Here, we exploit in vivo imaging of transparent zebrafish to investigate how T cells organize and survey for antigen in an animal devoid of lymph nodes. We find that naïve-like T cells in zebrafish organize into a previously undescribed whole-body lymphoid network that supports streaming migration and coordinated trafficking through the host. This network has the cellular hallmarks of a mammalian lymph node, including naïve T cells and CCR7-ligand expressing nonhematopoietic cells, and facilitates rapid collective migration. During infection, T cells transition to a random walk that supports antigen-presenting cell interactions and subsequent activation. Our results reveal that T cells can toggle between collective migration and individual random walks to prioritize either large-scale trafficking or antigen search in situ. This lymphoid network thus facilitates whole-body T cell trafficking and antigen surveillance in the absence of a lymph node system.
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Affiliation(s)
- Tanner F. Robertson
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
| | - Yiran Hou
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
| | - Jonathan Schrope
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI53726
| | - Simone Shen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
| | - Julie Rindy
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI53705
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI53706
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI53792
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11
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Fonseca MAS, Haro M, Wright KN, Lin X, Abbasi F, Sun J, Hernandez L, Orr NL, Hong J, Choi-Kuaea Y, Maluf HM, Balzer BL, Fishburn A, Hickey R, Cass I, Goodridge HS, Truong M, Wang Y, Pisarska MD, Dinh HQ, El-Naggar A, Huntsman DG, Anglesio MS, Goodman MT, Medeiros F, Siedhoff M, Lawrenson K. Single-cell transcriptomic analysis of endometriosis. Nat Genet 2023; 55:255-267. [PMID: 36624343 PMCID: PMC10950360 DOI: 10.1038/s41588-022-01254-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2022] [Indexed: 01/11/2023]
Abstract
Endometriosis is a common condition in women that causes chronic pain and infertility and is associated with an elevated risk of ovarian cancer. We profiled transcriptomes of >370,000 individual cells from endometriomas (n = 8), endometriosis (n = 28), eutopic endometrium (n = 10), unaffected ovary (n = 4) and endometriosis-free peritoneum (n = 4), generating a cellular atlas of endometrial-type epithelial cells, stromal cells and microenvironmental cell populations across tissue sites. Cellular and molecular signatures of endometrial-type epithelium and stroma differed across tissue types, suggesting a role for cellular restructuring and transcriptional reprogramming in the disease. Epithelium, stroma and proximal mesothelial cells of endometriomas showed dysregulation of pro-inflammatory pathways and upregulation of complement proteins. Somatic ARID1A mutation in epithelial cells was associated with upregulation of pro-angiogenic and pro-lymphangiogenic factors and remodeling of the endothelial cell compartment, with enrichment of lymphatic endothelial cells. Finally, signatures of ciliated epithelial cells were enriched in ovarian cancers, reinforcing epidemiologic associations between these two diseases.
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Affiliation(s)
- Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kelly N Wright
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer Sun
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lourdes Hernandez
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Natasha L Orr
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Jooyoon Hong
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
| | - Yunhee Choi-Kuaea
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Horacio M Maluf
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bonnie L Balzer
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aaron Fishburn
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan Hickey
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ilana Cass
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mireille Truong
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yemin Wang
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Margareta D Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Amal El-Naggar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - David G Huntsman
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, UBC, Vancouver, British Columbia, Canada
- British Columbia's Gynecological Cancer Research (OVCARE) Program, University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, British Columbia, Canada
| | - Marc T Goodman
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabiola Medeiros
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew Siedhoff
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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12
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Robertson TF, Hou Y, Shen S, Rindy J, Sauer JD, Dinh HQ, Huttenlocher A. A tessellated lymphoid network provides whole-body T cell surveillance in zebrafish. bioRxiv 2023:2023.01.17.524414. [PMID: 36711463 PMCID: PMC9882119 DOI: 10.1101/2023.01.17.524414] [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: 01/21/2023]
Abstract
Homeostatic trafficking to lymph nodes allows T cells to efficiently survey the host for cognate antigen. Non-mammalian jawed vertebrates lack lymph nodes but maintain similarly diverse T cell pools. Here, we exploit in vivo imaging of transparent zebrafish to investigate how T cells organize and survey for antigen in an animal devoid of lymph nodes. We find that naïve-like T cells in zebrafish organize into a previously undescribed whole-body lymphoid network that supports streaming migration and coordinated trafficking through the host. This network has the cellular hallmarks of a mammalian lymph node, including naïve T cells and CCR7-ligand expressing non-hematopoietic cells, and facilitates rapid collective migration. During infection, T cells transition to a random walk that supports antigen presenting cell interactions and subsequent activation. Our results reveal that T cells can toggle between collective migration and individual random walks to prioritize either large-scale trafficking or antigen search in situ . This novel lymphoid network thus facilitates whole-body T cell trafficking and antigen surveillance in the absence of a lymph node system. Significance Statement In mammals, lymph nodes play a critical role in the initiation of adaptive immune responses by providing a dedicated place for T cells to scan antigen-presenting cells. Birds, reptiles, amphibians, and fish all maintain diverse repertoires of T cells but lack lymph nodes, raising questions about how adaptive immunity functions in lower jawed vertebrates. Here, we describe a novel network of lymphocytes in zebrafish that supports whole-body T cell trafficking and provides a site for antigen search, mirroring the function of mammalian lymph nodes. Within this network, T cells can prioritize large-scale trafficking or antigen scanning by toggling between two distinct modes of migration. This network provides valuable insights into the evolution of adaptive immunity.
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13
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, 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George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Pandori WJ, Padgett LE, Alimadadi A, Gutierrez NA, Araujo DJ, Huh CJ, Olingy CE, Dinh HQ, Wu R, Vijayanand P, Chee SJ, Ottensmeier CH, Hedrick CC. Single-cell immune profiling reveals long-term changes in myeloid cells and identifies a novel subset of CD9 + monocytes associated with COVID-19 hospitalization. J Leukoc Biol 2022; 112:1053-1063. [PMID: 35866369 PMCID: PMC9350203 DOI: 10.1002/jlb.4cova0122-076r] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in severe immune dysfunction, hospitalization, and death. Many patients also develop long-COVID-19, experiencing symptoms months after infection. Although significant progress has been made in understanding the immune response to acute SARS-CoV-2 infection, gaps remain in our knowledge of how innate immunity influences disease kinetics and severity. We hypothesized that cytometry by time-of-flight analysis of PBMCs from healthy and infected subjects would identify novel cell surface markers and innate immune cell subsets associated with COVID-19 severity. In this pursuit, we identified monocyte and dendritic cell subsets that changed in frequency during acute SARS-CoV-2 infection and correlated with clinical parameters of disease severity. Subsets of nonclassical monocytes decreased in frequency in hospitalized subjects, yet increased in the most severe patients and positively correlated with clinical values associated with worse disease severity. CD9, CD163, PDL1, and PDL2 expression significantly increased in hospitalized subjects, and CD9 and 6-Sulfo LacNac emerged as the markers that best distinguished monocyte subsets amongst all subjects. CD9+ monocytes remained elevated, whereas nonclassical monocytes remained decreased, in the blood of hospitalized subjects at 3-4 months postinfection. Finally, we found that CD9+ monocytes functionally released more IL-8 and MCP-1 after LPS stimulation. This study identifies new monocyte subsets present in the blood of COVID-19 patients that correlate with disease severity, and links CD9+ monocytes to COVID-19 progression.
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Affiliation(s)
- William J. Pandori
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Lindsey E. Padgett
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Ahmad Alimadadi
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Norma A. Gutierrez
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Daniel J. Araujo
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Christine J. Huh
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Claire E. Olingy
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Huy Q. Dinh
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Runpei Wu
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Pandurangan Vijayanand
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Serena J. Chee
- Institute of Systems, Molecular and Integrative Biology (ISMIB)University of LiverpoolLiverpoolUK
| | - Christian H. Ottensmeier
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
- Institute of Systems, Molecular and Integrative Biology (ISMIB)University of LiverpoolLiverpoolUK
| | - Catherine C. Hedrick
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
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16
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Wang W, Lozar T, Golfinos AE, Lee D, Gronski E, Ward-Shaw E, Hayes M, Bruce JY, Kimple RJ, Hu R, Harari PM, Xu J, Keske A, Sondel PM, Fitzpatrick MB, Dinh HQ, Lambert PF. Stress Keratin 17 Expression in Head and Neck Cancer Contributes to Immune Evasion and Resistance to Immune-Checkpoint Blockade. Clin Cancer Res 2022; 28:2953-2968. [PMID: 35621713 PMCID: PMC9250640 DOI: 10.1158/1078-0432.ccr-21-3039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 01/03/2023]
Abstract
PURPOSE We investigated whether in human head and neck squamous cell carcinoma (HNSCC) high levels of expression of stress keratin 17 (K17) are associated with poor survival and resistance to immunotherapy. EXPERIMENTAL DESIGN We investigated the role of K17 in regulating both the tumor microenvironment and immune responsiveness of HNSCC using a syngeneic mouse HNSCC model, MOC2. MOC2 gives rise to immunologically cold tumors that are resistant to immune-checkpoint blockade (ICB). We engineered multiple, independent K17 knockout (KO) MOC2 cell lines and monitored their growth and response to ICB. We also measured K17 expression in human HNSCC of patients undergoing ICB. RESULTS MOC2 tumors were found to express K17 at high levels. When knocked out for K17 (K17KO MOC2), these cells formed tumors that grew slowly or spontaneously regressed and had a high CD8+ T-cell infiltrate in immunocompetent syngeneic C57BL/6 mice compared with parental MOC2 tumors. This phenotype was reversed when we depleted mice for T cells. Whereas parental MOC2 tumors were resistant to ICB treatment, K17KO MOC2 tumors that did not spontaneously regress were eliminated upon ICB treatment. In a cohort of patients with HNSCC receiving pembrolizumab, high K17 expression correlated with poor response. Single-cell RNA-sequencing analysis revealed broad differences in the immune landscape of K17KO MOC2 tumors compared with parental MOC2 tumors, including differences in multiple lymphoid and myeloid cell types. CONCLUSIONS We demonstrate that K17 expression in HNSCC contributes to immune evasion and resistance to ICB treatment by broadly altering immune landscapes of tumors.
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Affiliation(s)
- Wei Wang
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Taja Lozar
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA,University of Ljubljana, Ljubljana, Slovenia
| | - Athena E. Golfinos
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Denis Lee
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Ellery Gronski
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Ella Ward-Shaw
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Mitchell Hayes
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Justine Y. Bruce
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Rong Hu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Paul M. Harari
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Jin Xu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Aysenur Keske
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Paul M. Sondel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA,University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison
| | - Megan B. Fitzpatrick
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA,University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison WI, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research/ Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison WI, USA,University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison
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Brand J, Harro M, Abbasi F, Lin X, Siedhoff M, Andrew L, Rimel BJ, Medeiros F, Lawrenson K, Dinh HQ. Abstract 5148: Immune landscapes and interactions in human fallopian tubes and their implications for early high-grade serous ovarian cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5148] [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 five-year survival rate of ovarian cancer (OC) dramatically rises from below 40% to 90% with patients who are diagnosed early (stage I), when the disease restricts to the ovary. Thus, the ultimate goals of our research are to learn how to detect ovarian cancer at its earliest stages of development and thereby improve patient survival and to learn how the immune microenvironment contributes to the development of OC. Achieving these goals requires us to better characterize the earliest steps in ovarian carcinogenesis. The human fallopian tube harbors the cell-of-origin for most high-grade serous 'ovarian' cancers (HGSOCs), but its cellular composition, particularly the immune component, is poorly characterized. Emerging evidence from several research groups using molecular sequencing technologies of fallopian tube epithelium strongly support this hypothesis. We recently described our use of single-cell transcriptome technology (scRNA-Seq) to profile the heterogeneity of non-malignant FT and define a novel transcriptional gene regulatory network of epithelial differentiation and tumorigenesis in the human FT. Here we present an in-depth characterization of the immune cell atlas for human fallopian tubes, which has not been reported. Our unpublished analyses of our FT dataset and the publicly available HGSOC scRNA-Seq dataset demonstrate a significant difference in the immune cell landscape. There are limited macrophages and a high abundance of monocytes in non-malignant FT and adjacent normal ovaries compared to those in HGSOC tumors. This finding leads us to hypothesize that the macrophage-to-monocyte ratio and their interactions with other immune cell types in human fallopian tubes create a permissive microenvironment allowing for the development of HGSOC and can provide a biomarker for early cancer detection. To test if those myeloid cells could be a marker for early HGSOC, we performed scRNA-seq on FT from women carrying mutant alleles of BRCA1 or BRCA2 who are at high risk of HGSOC. Intriguingly, the ratio of monocytes to macrophages in the FTs from half of these high-risk individuals is more like that found in HGSOC than in normal FT. Furthermore, computational analyses on myeloid cell types and their interactions with different epithelial cells, stromal fibroblast cells, and T and NK cells revealed the extended contribution of the non-epithelial microenvironment in FT, potentially driving early HGSOC development and progression. This cellular and molecular compendium of the human fallopian tube immune landscapes in cancer-free and cancer-high-risk women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.
Citation Format: Josh Brand, Marcela Harro, Forough Abbasi, Xianzhi Lin, Matthew Siedhoff, Li Andrew, Bobbie J. Rimel, Fabiola Medeiros, Kate Lawrenson, Huy Q. Dinh. Immune landscapes and interactions in human fallopian tubes and their implications for early high-grade serous ovarian cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5148.
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Affiliation(s)
- Josh Brand
- 1University of Wisconsin - Madison, Madison, WI
| | | | | | - Xianzhi Lin
- 2Cedars Sinai Medical Center, Los Angeles, CA
| | | | - Li Andrew
- 2Cedars Sinai Medical Center, Los Angeles, CA
| | | | | | | | - Huy Q. Dinh
- 1University of Wisconsin - Madison, Madison, WI
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Golfinos AE, Wang W, Mergaert A, Lambert PF, Dinh HQ. Abstract 1994: Defining tumor infiltrating myeloid microenvironment landscapes in HPV+ and HPV- head and neck cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1994] [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
Head and neck cancer (HNC) has a <20% response rate to immunotherapy, making it imperative to learn what causes high treatment resistance and how to overcome these challenges. One way to generate a holistic view of both human papillomavirus positive (HPV+) and negative (HPV-) HNC is to study the tumor immune microenvironment (TIME). Since HPV+ HNC often results in more favorable outcomes than HPV- HNC, assessing differences between these two disease states may provide critical mechanistic insight into what causes discrepancies in treatment response. This study uses publicly available and in-house collected single-cell transcriptome (scRNA-seq) data from preclinical murine models and human HNC to assess the differences between HPV+ and HPV- HNC TIME. Recent scRNA-Seq data showed extensive characterization of infiltrating T and B cells between HPV+ and HPV- HNC, but little is known about the myeloid compartment. As myeloid cells with both pro- and anti-tumoral functions make up a bulk of the HNC TIME, we sought to identify the differences in myeloid cells between HPV+ vs. HPV- HNC and their roles in response to immune checkpoint inhibitor (ICI) therapy. We identified higher myeloid heterogeneity than previously reported from both published and our generated scRNA-Seq. In human HNC patients, we identified four macrophage, seven monocyte, and five dendritic cell subsets. One macrophage subset expressed high levels of CXCL9 in both humans and our murine HNC model. Interestingly, recent studies identified CXCL9 as a biomarker for immunotherapy response. Observing conserved Cxcl9-expressing macrophages between murine and human HNC could help assess treatment response in cancer patients. We will assess the translational value of murine HPV+ and HPV- HNC models compared to their human counterparts. To this end, we are generating scRNA-Seq data from different HNC murine models: MOC1, MOC2, mEERL. The MOC2 and MOC1 cell lines recapitulate a responsive and non-responsive HPV- HNC tumor phenotype, respectively. The mEERL cell line recapitulates an HPV+ HNC phenotype. Our analysis shows high concordance between mouse models with immunological cold TIME (MOC2) and a proportion of human HNCs. We also identified changes in myeloid landscapes between immunological cold-to-hot TIME mice receiving ICI (anti-PD1 + anti-CTL4) therapies. We will present an in-depth comparative analysis to provide mechanistic insights into observed differences in the TIME between mice and humans. We will also present a novel bioinformatics analysis to interrogate how cell-cell signaling interactions between myeloid and T cell subsets influence their downstream gene regulatory network and tumor immune phenotypes. This analysis provides a reference for future studies in HNC immunology.
Citation Format: Athena E. Golfinos, Wei Wang, Aisha Mergaert, Paul F. Lambert, Huy Q. Dinh. Defining tumor infiltrating myeloid microenvironment landscapes in HPV+ and HPV- head and neck cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1994.
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Affiliation(s)
| | - Wei Wang
- 1University of Wisconsin-Madison, Madison, WI
| | | | | | - Huy Q. Dinh
- 1University of Wisconsin-Madison, Madison, WI
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Olingy C, Alimadadi A, Araujo DJ, Barry D, Gutierrez NA, Werbin MH, Arriola E, Patel SP, Ottensmeier CH, Dinh HQ, Hedrick CC. CD33 Expression on Peripheral Blood Monocytes Predicts Efficacy of Anti-PD-1 Immunotherapy Against Non-Small Cell Lung Cancer. Front Immunol 2022; 13:842653. [PMID: 35493454 PMCID: PMC9046782 DOI: 10.3389/fimmu.2022.842653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/02/2022] [Indexed: 12/25/2022] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related deaths globally. Immune checkpoint blockade (ICB) has transformed cancer medicine, with anti-programmed cell death protein 1 (anti-PD-1) therapy now well-utilized for treating NSCLC. Still, not all patients with NSCLC respond positively to anti-PD-1 therapy, and some patients acquire resistance to treatment. There remains an urgent need to find markers predictive of anti-PD-1 responsiveness. To this end, we performed mass cytometry on peripheral blood mononuclear cells from 26 patients with NSCLC during anti-PD-1 treatment. Patients who responded to anti-PD-1 ICB displayed significantly higher levels of antigen-presenting myeloid cells, including CD9+ nonclassical monocytes, and CD33hi classical monocytes. Using matched pre-post treatment samples, we found that the baseline pre-treatment frequencies of CD33hi monocytes predicted patient responsiveness to anti-PD-1 therapy. Moreover, some of these classical and nonclassical monocyte subsets were associated with reduced immunosuppression by T regulatory (CD4+FOXP3+CD25+) cells in the same patients. Our use of machine learning corroborated the association of specific monocyte markers with responsiveness to ICB. Our work provides a high-dimensional profile of monocytes in NSCLC and links CD33 expression on monocytes with anti-PD-1 effectiveness in patients with NSCLC.
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Affiliation(s)
- Claire Olingy
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Ahmad Alimadadi
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Daniel J. Araujo
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - David Barry
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Norma A. Gutierrez
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Max Hardy Werbin
- Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
| | - Edurne Arriola
- Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar-Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Barcelona, Spain
| | - Sandip Pravin Patel
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
| | - Christian H. Ottensmeier
- Institute of Translational Medicine, Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Catherine C. Hedrick
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, United States
- *Correspondence: Catherine C. Hedrick,
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20
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Dinh HQ, Pan F, Wang G, Huang QF, Olingy CE, Wu ZY, Wang SH, Xu X, Xu XE, He JZ, Yang Q, Orsulic S, Haro M, Li LY, Huang GW, Breunig JJ, Koeffler HP, Hedrick CC, Xu LY, Lin DC, Li EM. Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Nat Commun 2021; 12:7335. [PMID: 34921160 PMCID: PMC8683407 DOI: 10.1038/s41467-021-27599-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 06/09/2020] [Accepted: 11/29/2021] [Indexed: 02/05/2023] Open
Abstract
The tumor microenvironment is a highly complex ecosystem of diverse cell types, which shape cancer biology and impact the responsiveness to therapy. Here, we analyze the microenvironment of esophageal squamous cell carcinoma (ESCC) using single-cell transcriptome sequencing in 62,161 cells from blood, adjacent nonmalignant and matched tumor samples from 11 ESCC patients. We uncover heterogeneity in most cell types of the ESCC stroma, particularly in the fibroblast and immune cell compartments. We identify a tumor-specific subset of CST1+ myofibroblasts with prognostic values and potential biological significance. CST1+ myofibroblasts are also highly tumor-specific in other cancer types. Additionally, a subset of antigen-presenting fibroblasts is revealed and validated. Analyses of myeloid and T lymphoid lineages highlight the immunosuppressive nature of the ESCC microenvironment, and identify cancer-specific expression of immune checkpoint inhibitors. This work establishes a rich resource of stromal cell types of the ESCC microenvironment for further understanding of ESCC biology.
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Affiliation(s)
- Huy Q Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Feng Pan
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
| | - Geng Wang
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
- Department of Thoracic Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Qing-Feng Huang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
| | - Claire E Olingy
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | | | - Xin Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
| | - Xiu-E Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
| | - Jian-Zhong He
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China
| | - Qian Yang
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandra Orsulic
- Department of Obstetrics and Gynecology and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marcela Haro
- Department of Obstetrics and Gynecology and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Li-Yan Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Guo-Wei Huang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Catherine C Hedrick
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Li-Yan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China.
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - En-Min Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
- Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Shantou, China.
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21
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Pan L, Dinh HQ, Pawitan Y, Vu TN. Isoform-level quantification for single-cell RNA sequencing. Bioinformatics 2021; 38:1287-1294. [PMID: 34864849 PMCID: PMC8826380 DOI: 10.1093/bioinformatics/btab807] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3' bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3' 10× Genomics is currently performed at the gene level. RESULTS We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-level expression. The reanalysis of a CITE-Seq dataset with isoform-based Scasa reveals a subgroup of CD14 monocytes missed by gene-based methods. AVAILABILITY AND IMPLEMENTATION Implementation of Scasa including source code, documentation, tutorials and test data supporting this study is available at Github: https://github.com/eudoraleer/scasa and Zenodo: https://doi.org/10.5281/zenodo.5712503. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lu Pan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Huy Q Dinh
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53705-227, USA,Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden,To whom correspondence should be addressed.
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22
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Gaddis DE, Padgett LE, Wu R, Nguyen A, McSkimming C, Dinh HQ, Araujo DJ, Taylor AM, McNamara CA, Hedrick CC. Atherosclerosis Impairs Naive CD4 T-Cell Responses via Disruption of Glycolysis. Arterioscler Thromb Vasc Biol 2021; 41:2387-2398. [PMID: 34320835 PMCID: PMC10206822 DOI: 10.1161/atvbaha.120.314189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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] [Indexed: 11/16/2022]
Abstract
Objective CD4 T cells are important regulators of atherosclerotic progression. The metabolic profile of CD4 T cells controls their signaling and function, but how atherosclerosis affects T-cell metabolism is unknown. Here, we sought to determine the impact of atherosclerosis on CD4 T-cell metabolism and the contribution of such metabolic alterations to atheroprogression. Approach and Results Using PCR arrays, we profiled the expression of metabolism genes in CD4 T cells from atherosclerotic apolipoprotein-E knockout mice fed a Western diet. These cells exhibited dysregulated expression of genes critically involved in glycolysis and fatty acid degradation, compared with those from animals fed a standard laboratory diet. We examined how T-cell metabolism was changed in either Western diet–fed apolipoprotein-E knockout mice or samples from patients with cardiovascular disease by measuring glucose uptake, activation, and proliferation in CD4 T cells. We found that naive CD4 T cells from Western diet–fed apolipoprotein-E knockout mice failed to uptake glucose and displayed impaired proliferation and activation, compared with CD4 T cells from standard laboratory diet–fed animals. Similarly, we observed that naive CD4 T-cell frequencies were reduced in the circulation of human subjects with high cardiovascular disease compared with low cardiovascular disease. Naive T cells from high cardiovascular disease subjects also showed reduced proliferative capacity. Conclusions These results highlight the dysfunction that occurs in CD4 T-cell metabolism and immune responses during atherosclerosis. Targeting metabolic pathways within naive CD4 T cells could thus yield novel therapeutic approaches for improving CD4 T-cell responses against atheroprogression.
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Affiliation(s)
- Dalia E. Gaddis
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Lindsey E. Padgett
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Runpei Wu
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Anh Nguyen
- Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville, VA 22908
| | - Chantel McSkimming
- Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville, VA 22908
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705
| | - Daniel J. Araujo
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Angela M. Taylor
- Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville, VA 22908
| | - Coleen A. McNamara
- Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville, VA 22908
| | - Catherine C. Hedrick
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA 92037
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23
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Dinh HQ, Eggert T, Meyer MA, Zhu YP, Olingy CE, Llewellyn R, Wu R, Hedrick CC. Coexpression of CD71 and CD117 Identifies an Early Unipotent Neutrophil Progenitor Population in Human Bone Marrow. Immunity 2021; 53:319-334.e6. [PMID: 32814027 DOI: 10.1016/j.immuni.2020.07.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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: 01/04/2020] [Revised: 04/18/2020] [Accepted: 07/23/2020] [Indexed: 12/30/2022]
Abstract
Neutrophils are the most abundant peripheral immune cells and thus, are continually replenished by bone marrow-derived progenitors. Still, how newly identified neutrophil subsets fit into the bone marrow neutrophil lineage remains unclear. Here, we use mass cytometry to show that two recently defined human neutrophil progenitor populations contain a homogeneous progenitor subset we term "early neutrophil progenitors" (eNePs) (Lin-CD66b+CD117+CD71+). Surface marker- and RNA-expression analyses, together with in vitro colony formation and in vivo adoptive humanized mouse transfers, indicate that eNePs are the earliest human neutrophil progenitors. Furthermore, we identified CD71 as a marker associated with the earliest neutrophil developmental stages. Expression of CD71 marks proliferating neutrophils, which were expanded in the blood of melanoma patients and detectable in blood and tumors from lung cancer patients. In summary, we establish CD117+CD71+ eNeP as the inceptive human neutrophil progenitor and propose a refined model of the neutrophil developmental lineage in bone marrow.
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Affiliation(s)
- Huy Q Dinh
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Tobias Eggert
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Melissa A Meyer
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Yanfang Peipei Zhu
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Claire E Olingy
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ryan Llewellyn
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Runpei Wu
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Catherine C Hedrick
- Center for Cancer Immunotherapy & Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
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24
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Dinh HQ, Lin X, Abbasi F, Nameki R, Haro M, Olingy CE, Chang H, Hernandez L, Gayther SA, Wright KN, Aspuria PJ, Karlan BY, Corona RI, Li A, Rimel BJ, Siedhoff MT, Medeiros F, Lawrenson K. Single-cell transcriptomics identifies gene expression networks driving differentiation and tumorigenesis in the human fallopian tube. Cell Rep 2021; 35:108978. [PMID: 33852846 PMCID: PMC10108902 DOI: 10.1016/j.celrep.2021.108978] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 05/27/2020] [Revised: 09/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
The human fallopian tube harbors the cell of origin for the majority of high-grade serous "ovarian" cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We perform single-cell transcriptomic profiling of around 53,000 individual cells from 12 primary fallopian specimens to map their major cell types. We identify 10 epithelial subpopulations with diverse transcriptional programs. Based on transcriptional signatures, we reconstruct a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of advanced HGSCs identifies the "early secretory" population as a likely precursor state for the majority of HGSCs. Its signature comprises both epithelial and mesenchymal features and is enriched in mesenchymal-type HGSCs (p = 6.7 × 10-27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.
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Affiliation(s)
- Huy Q Dinh
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Claire E Olingy
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Heidi Chang
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lourdes Hernandez
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kelly N Wright
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul-Joseph Aspuria
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Beth Y Karlan
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Li
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - B J Rimel
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew T Siedhoff
- Division of Minimally Invasive Gynecologic Surgery, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Fabiola Medeiros
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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25
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Padgett LE, Dinh HQ, Wu R, Gaddis DE, Araujo DJ, Winkels H, Nguyen A, McNamara CA, Hedrick CC. Naive CD8 + T Cells Expressing CD95 Increase Human Cardiovascular Disease Severity. Arterioscler Thromb Vasc Biol 2020; 40:2845-2859. [PMID: 33054398 DOI: 10.1161/atvbaha.120.315106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Cardiovascular disease (CVD) remains a significant global health concern with a high degree of mortality. While CD4+ T cells have been extensively studied in CVD, the importance of CD8+ T cells in this disease, despite their abundance and increased activation in human atherosclerotic plaques, remains largely unknown. Thus, the objective of this study was to compare peripheral T-cell signatures between humans with a high (severe) risk of CVD (including myocardial infarction or stroke) and those with a low risk of CVD. Approach and Results: Using mass cytometry, we uncovered a naive CD8+ T (TN) cell population expressing CD95 (termed CD95+CD8+ stem cell memory T [CD8 TSCM] cells) that was enriched in patients with high compared with low CVD. This T-cell subset enrichment within individuals with high CVD was a relative increase and resulted from the loss of CD95lo cells within the TN compartment. We found that CD8 TSCM cells positively correlated with CVD risk in humans, while CD8+ TN cells were inversely correlated. Atherosclerotic apolipoprotein E-deficient (ApoE-/-) mice also displayed respective 7- and 2-fold increases in CD8+ TSCM frequencies within the peripheral blood and aorta-draining paraaortic lymph nodes compared with C57BL/6J mice. CD8+ TSCM cells were 1.7-fold increased in aortas from western diet fed ApoE-/- mice compared with normal laboratory diet-fed ApoE-/- mice. Importantly, transfer of TSCM cells into immune-deficient Rag.Ldlr recipient mice that lacked T cells increased atherosclerosis, illustrating the importance of these cells in atherogenesis. CONCLUSIONS CD8+ TSCM cells are increased in humans with high CVD. As these TSCM cells promote atherosclerosis, targeting them may attenuate atherosclerotic plaque progression.
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Affiliation(s)
- Lindsey E Padgett
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Huy Q Dinh
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Runpei Wu
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Dalia E Gaddis
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Daniel J Araujo
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Holger Winkels
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
| | - Anh Nguyen
- Cardiovascular Research Center and Division of Cardiovascular Medicine, University of Virginia, Charlottesville (A.N., C.A.M.)
| | - Coleen A McNamara
- Cardiovascular Research Center and Division of Cardiovascular Medicine, University of Virginia, Charlottesville (A.N., C.A.M.)
| | - Catherine C Hedrick
- Division of Inflammation Biology, La Jolla Institute for Immunology, CA (L.E.P., H.Q.D., R.W., D.E.G., D.J.A., H.W., C.C.H.)
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26
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Zernecke A, Winkels H, Cochain C, Williams JW, Wolf D, Soehnlein O, Robbins CS, Monaco C, Park I, McNamara CA, Binder CJ, Cybulsky MI, Scipione CA, Hedrick CC, Galkina EV, Kyaw T, Ghosheh Y, Dinh HQ, Ley K. Meta-Analysis of Leukocyte Diversity in Atherosclerotic Mouse Aortas. Circ Res 2020; 127:402-426. [PMID: 32673538 PMCID: PMC7371244 DOI: 10.1161/circresaha.120.316903] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [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] [Indexed: 12/11/2022]
Abstract
The diverse leukocyte infiltrate in atherosclerotic mouse aortas was recently analyzed in 9 single-cell RNA sequencing and 2 mass cytometry studies. In a comprehensive meta-analysis, we confirm 4 known macrophage subsets-resident, inflammatory, interferon-inducible cell, and Trem2 (triggering receptor expressed on myeloid cells-2) foamy macrophages-and identify a new macrophage subset resembling cavity macrophages. We also find that monocytes, neutrophils, dendritic cells, natural killer cells, innate lymphoid cells-2, and CD (cluster of differentiation)-8 T cells form prominent and separate immune cell populations in atherosclerotic aortas. Many CD4 T cells express IL (interleukin)-17 and the chemokine receptor CXCR (C-X-C chemokine receptor)-6. A small number of regulatory T cells and T helper 1 cells is also identified. Immature and naive T cells are present in both healthy and atherosclerotic aortas. Our meta-analysis overcomes limitations of individual studies that, because of their experimental approach, over- or underrepresent certain cell populations. Mass cytometry studies demonstrate that cell surface phenotype provides valuable information beyond the cell transcriptomes. The present analysis helps resolve some long-standing controversies in the field. First, Trem2+ foamy macrophages are not proinflammatory but interferon-inducible cell and inflammatory macrophages are. Second, about half of all foam cells are smooth muscle cell-derived, retaining smooth muscle cell transcripts rather than transdifferentiating to macrophages. Third, Pf4, which had been considered specific for platelets and megakaryocytes, is also prominently expressed in the main population of resident vascular macrophages. Fourth, a new type of resident macrophage shares transcripts with cavity macrophages. Finally, the discovery of a prominent innate lymphoid cell-2 cluster links the single-cell RNA sequencing work to recent flow cytometry data suggesting a strong atheroprotective role of innate lymphoid cells-2. This resolves apparent discrepancies regarding the role of T helper 2 cells in atherosclerosis based on studies that predated the discovery of innate lymphoid cells-2 cells.
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Affiliation(s)
- Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Holger Winkels
- Heart Center, University Hospital Cologne, Cologne, Germany
- Clinic III for Internal Medicine, Department of Cardiology, University of Cologne, Cologne, Germany
| | - Clément Cochain
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Center, University Hospital Würzburg, Wüzburg, Germany
| | - Jesse W. Williams
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN USA
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN USA
| | - Dennis Wolf
- Department of Cardiology and Angiology I, University Heart Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention (IPEK), Klinikum LMU Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Physiology and Pharmacology (FyFa), Karolinska Institute, Stockholm, Sweden
| | - Clint S. Robbins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S1A1, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S1A1, Canada
- Toronto General Research Institute, University Health Network, Toronto, ON, Canada
- Peter Munk Cardiac Centre, Toronto, ON M5G1L7, Canada
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Inhye Park
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Coleen A. McNamara
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, USA
- Division of Cardioascular Medicine, University of Virginia School of Medicine, Charlottesville, USA
| | - Christoph J. Binder
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Myron I. Cybulsky
- Toronto General Research Institute, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Corey A. Scipione
- Toronto General Research Institute, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - Elena V. Galkina
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, 700 West Olney Road, Norfolk, VA USA
| | - Tin Kyaw
- Vascular Biology and Atherosclerosis Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Centre for Inflammatory Diseases, Department of Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | | | - Huy Q. Dinh
- La Jolla Institute for Immunology, La Jolla, CA USA
| | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA USA
- Department of Bioengineering, University of California San Diego, CA, USA
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27
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Marcovecchio PM, Zhu YP, Hanna RN, Dinh HQ, Tacke R, Wu R, McArdle S, Reynolds S, Araujo DJ, Ley K, Hedrick CC. Frontline Science: Kindlin-3 is essential for patrolling and phagocytosis functions of nonclassical monocytes during metastatic cancer surveillance. J Leukoc Biol 2020; 107:883-892. [PMID: 32386455 DOI: 10.1002/jlb.4hi0420-098r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/02/2020] [Revised: 04/18/2020] [Accepted: 04/19/2020] [Indexed: 01/03/2023] Open
Abstract
Nonclassical monocytes maintain vascular homeostasis by patrolling the vascular endothelium, responding to inflammatory signals, and scavenging cellular debris. Nonclassical monocytes also prevent metastatic tumor cells from seeding new tissues, but whether the patrolling function of nonclassical monocytes is required for this process is unknown. To answer this question, we utilized an inducible-knockout mouse that exhibits loss of the integrin-adaptor protein Kindlin-3 specifically in nonclassical monocytes. We show that Kindlin-3-deficient nonclassical monocytes are unable to patrol the vascular endothelium in either the lungs or periphery. We also find that Kindlin-3-deficient nonclassical monocytes cannot firmly adhere to, and instead "slip" along, the vascular endothelium. Loss of patrolling activity by nonclassical monocytes was phenocopied by ablation of LFA-1, an integrin-binding partner of Kindlin-3. When B16F10 murine melanoma tumor cells were introduced into Kindlin-3-deficient mice, nonclassical monocytes showed defective patrolling towards tumor cells and failure to ingest tumor particles in vivo. Consequently, we observed a significant, 4-fold increase in lung tumor metastases in mice possessing Kindlin-3-deficient nonclassical monocytes. Thus, we conclude that the patrolling function of nonclassical monocytes is mediated by Kindlin-3 and essential for these cells to maintain vascular endothelial homeostasis and prevent tumor metastasis to the lung.
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Affiliation(s)
- Paola M Marcovecchio
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA.,Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Yanfang Peipei Zhu
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Huy Q Dinh
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Runpei Wu
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Sara McArdle
- Microscopy Core Facility, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Sophia Reynolds
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Daniel J Araujo
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Klaus Ley
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Catherine C Hedrick
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, California, USA.,Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
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28
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Joshi S, Liu KX, Zulcic M, Singh AR, Skola D, Glass CK, Sanders PD, Sharabi AB, Pham TV, Tamayo P, Shiang D, Dinh HQ, Hedrick CC, Morales GA, Garlich JR, Durden DL. Macrophage Syk-PI3Kγ Inhibits Antitumor Immunity: SRX3207, a Novel Dual Syk-PI3K Inhibitory Chemotype Relieves Tumor Immunosuppression. Mol Cancer Ther 2020; 19:755-764. [PMID: 31974273 PMCID: PMC7450492 DOI: 10.1158/1535-7163.mct-19-0947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 10/02/2019] [Revised: 12/05/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022]
Abstract
Macrophages (MΦ) play a critical role in tumor growth, immunosuppression, and inhibition of adaptive immune responses in cancer. Hence, targeting signaling pathways in MΦs that promote tumor immunosuppression will provide therapeutic benefit. PI3Kγ has been recently established by our group and others as a novel immuno-oncology target. Herein, we report that an MΦ Syk-PI3K axis drives polarization of immunosuppressive MΦs that establish an immunosuppressive tumor microenvironment in in vivo syngeneic tumor models. Genetic or pharmacologic inhibition of Syk and/or PI3Kγ in MΦs promotes a proinflammatory MΦ phenotype, restores CD8+ T-cell activity, destabilizes HIF under hypoxia, and stimulates an antitumor immune response. Assay for transposase-accessible Chromatin using Sequencing (ATAC-seq) analyses on the bone marrow-derived macrophages (BMDM) show that inhibition of Syk kinase promotes activation and binding of NF-κB motif in SykMC-KO BMDMs, thus stimulating immunostimulatory transcriptional programming in MΦs to suppress tumor growth. Finally, we have developed in silico the "first-in-class" dual Syk/PI3K inhibitor, SRX3207, for the combinatorial inhibition of Syk and PI3K in one small molecule. This chemotype demonstrates efficacy in multiple tumor models and represents a novel combinatorial approach to activate antitumor immunity.
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MESH Headings
- Animals
- Apoptosis
- Carcinoma, Lewis Lung/drug therapy
- Carcinoma, Lewis Lung/enzymology
- Carcinoma, Lewis Lung/immunology
- Carcinoma, Lewis Lung/pathology
- Cell Proliferation
- Class Ib Phosphatidylinositol 3-Kinase/chemistry
- Colonic Neoplasms/drug therapy
- Colonic Neoplasms/enzymology
- Colonic Neoplasms/immunology
- Colonic Neoplasms/pathology
- Cytokines/metabolism
- Humans
- Immune Tolerance
- Immunosuppression Therapy
- Macrophages/drug effects
- Macrophages/immunology
- Macrophages/metabolism
- Melanoma, Experimental/drug therapy
- Melanoma, Experimental/enzymology
- Melanoma, Experimental/immunology
- Melanoma, Experimental/pathology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Phosphoinositide-3 Kinase Inhibitors/pharmacology
- Signal Transduction
- Syk Kinase/antagonists & inhibitors
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Shweta Joshi
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California.
| | - Kevin X Liu
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California
| | - Muamera Zulcic
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California
| | - Alok R Singh
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California
| | - Dylan Skola
- UCSD School of Medicine, University of California, San Diego, San Diego, California
| | - Christopher K Glass
- UCSD School of Medicine, University of California, San Diego, San Diego, California
| | - P Dominick Sanders
- Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, University of California, San Diego, San Diego, California
| | - Andrew B Sharabi
- Moores Cancer Center, Department of Radiation Medicine and Applied Sciences, University of California, San Diego, San Diego, California
| | - Timothy V Pham
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California
- Office of Cancer Genomics, University of California, San Diego, San Diego, California
| | - Pablo Tamayo
- Office of Cancer Genomics, University of California, San Diego, San Diego, California
| | - Daniel Shiang
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California
| | - Huy Q Dinh
- La Jolla Institute of Allergy and Immunology, La Jolla, California
| | | | | | | | - Donald L Durden
- UCSD Department of Pediatrics, University of California, San Diego, San Diego, California.
- SignalRx Pharmaceuticals, Omaha, Nebraska
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, 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Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, 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Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Zhu YP, Padgett L, Dinh HQ, Marcovecchio P, Blatchley A, Wu R, Ehinger E, Kim C, Mikulski Z, Seumois G, Madrigal A, Vijayanand P, Hedrick CC. Identification of an Early Unipotent Neutrophil Progenitor with Pro-tumoral Activity in Mouse and Human Bone Marrow. Cell Rep 2020; 24:2329-2341.e8. [PMID: 30157427 DOI: 10.1016/j.celrep.2018.07.097] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [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: 03/03/2018] [Revised: 06/18/2018] [Accepted: 07/27/2018] [Indexed: 12/31/2022] Open
Abstract
Neutrophils are short-lived cells that play important roles in both health and disease. Neutrophils and monocytes originate from the granulocyte monocyte progenitor (GMP) in bone marrow; however, unipotent neutrophil progenitors are not well defined. Here, we use cytometry by time of flight (CyTOF) and single-cell RNA sequencing (scRNA-seq) methodologies to identify a committed unipotent early-stage neutrophil progenitor (NeP) in adult mouse bone marrow. Importantly, we found a similar unipotent NeP (hNeP) in human bone marrow. Both NeP and hNeP generate only neutrophils. NeP and hNeP both significantly increase tumor growth when transferred into murine cancer models, including a humanized mouse model. hNeP are present in the blood of treatment-naive melanoma patients but not of healthy subjects. hNeP can be readily identified by flow cytometry and could be used as a biomarker for early cancer discovery. Understanding the biology of hNeP should allow the development of new therapeutic targets for neutrophil-related diseases, including cancer.
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Affiliation(s)
- Yanfang Peipei Zhu
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
| | - Lindsey Padgett
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Huy Q Dinh
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Paola Marcovecchio
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Amy Blatchley
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Runpei Wu
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Erik Ehinger
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Zbigniew Mikulski
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Gregory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Ariel Madrigal
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Catherine C Hedrick
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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Hamers AAJ, Dinh HQ, Thomas GD, Marcovecchio P, Blatchley A, Nakao CS, Kim C, McSkimming C, Taylor AM, Nguyen AT, McNamara CA, Hedrick CC. Human Monocyte Heterogeneity as Revealed by High-Dimensional Mass Cytometry. Arterioscler Thromb Vasc Biol 2019; 39:25-36. [PMID: 30580568 DOI: 10.1161/atvbaha.118.311022] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Objective- Three distinct human monocyte subsets have been identified based on the surface marker expression of CD14 and CD16. We hypothesized that monocytes were likely more heterogeneous in composition. Approach and Results- We used the high dimensionality of mass cytometry together with the FlowSOM clustering algorithm to accurately identify and define monocyte subsets in blood of healthy human subjects and those with coronary artery disease (CAD). To study the behavior and functionality of the newly defined monocyte subsets, we performed RNA sequencing, transwell migration, and efferocytosis assays. Here, we identify 8 human monocyte subsets based on their surface marker phenotype. We found that 3 of these subsets fall within the CD16+ nonclassical monocyte population and 4 subsets belong to the CD14+ classical monocytes, illustrating significant monocyte heterogeneity in humans. As nonclassical monocytes are important in modulating atherosclerosis in mice, we studied the functions of our 3 newly identified nonclassical monocytes in subjects with CAD. We found a marked expansion of a Slan+CXCR6+ nonclassical monocyte subset in CAD subjects, which was positively correlated with CAD severity. This nonclassical subset can migrate towards CXCL16 and shows an increased efferocytosis capacity, indicating it may play an atheroprotective role. Conclusions- Our data demonstrate that human nonclassical monocytes are a heterogeneous population, existing of several subsets with functional differences. These subsets have changed frequencies in the setting of severe CAD. Understanding how these newly identified subsets modulate CAD will be important for CAD-based therapies that target myeloid cells.
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Affiliation(s)
- Anouk A J Hamers
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Huy Q Dinh
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Graham D Thomas
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Paola Marcovecchio
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Amy Blatchley
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Catherine S Nakao
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Allergy and Immunology, CA (C.K.)
| | - Chantel McSkimming
- Robert M. Berne Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville (C.M., A.M.T., A.T.N., C.A.M.)
| | - Angela M Taylor
- Robert M. Berne Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville (C.M., A.M.T., A.T.N., C.A.M.)
| | - Anh T Nguyen
- Robert M. Berne Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville (C.M., A.M.T., A.T.N., C.A.M.)
| | - Coleen A McNamara
- Robert M. Berne Cardiovascular Research Center and Division of Cardiology, University of Virginia, Charlottesville (C.M., A.M.T., A.T.N., C.A.M.)
| | - Catherine C Hedrick
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA (A.A.J.H., H.Q.D., G.D.T., P.M., A.B., C.S.N., C.C.H.)
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Zhu YP, Padgett L, Dinh HQ, Marcovecchio P, Wu R, Hinz D, Kim C, Hedrick CC. Preparation of Whole Bone Marrow for Mass Cytometry Analysis of Neutrophil-lineage Cells. J Vis Exp 2019. [PMID: 31282876 DOI: 10.3791/59617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In this article, we present a protocol that is optimized to preserve neutrophil-lineage cells in fresh BM for whole BM CyTOF analysis. We utilized a myeloid-biased 39-antibody CyTOF panel to evaluate the hematopoietic system with a focus on the neutrophil-lineage cells by using this protocol. The CyTOF result was analyzed with an open-resource dimensional reduction algorithm, viSNE, and the data was presented to demonstrate the outcome of this protocol. We have discovered new neutrophil-lineage cell populations based on this protocol. This protocol of fresh whole BM preparation may be used for 1), CyTOF analysis to discover unidentified cell populations from whole BM, 2), investigating whole BM defects for patients with blood disorders such as leukemia, 3), assisting optimization of fluorescence-activated flow cytometry protocols that utilize fresh whole BM.
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Affiliation(s)
| | - Lindsey Padgett
- Division of Inflammation Biology, La Jolla Institute for Immunology
| | - Huy Q Dinh
- Division of Inflammation Biology, La Jolla Institute for Immunology
| | | | - Runpei Wu
- Division of Inflammation Biology, La Jolla Institute for Immunology
| | - Denise Hinz
- Flow Cytometry Core Facility, La Jolla Institute for Immunology
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Immunology
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Olingy CE, Dinh HQ, Hedrick CC. Monocyte heterogeneity and functions in cancer. J Leukoc Biol 2019; 106:309-322. [PMID: 30776148 PMCID: PMC6658332 DOI: 10.1002/jlb.4ri0818-311r] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/11/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
Monocytes are innate immune cells of the mononuclear phagocyte system that have emerged as important regulators of cancer development and progression. Our understanding of monocytes has advanced from viewing these cells as a homogenous population to a heterogeneous system of cells that display diverse responses to different stimuli. During cancer, different monocyte subsets perform functions that contribute to both pro‐ and antitumoral immunity, including phagocytosis, secretion of tumoricidal mediators, promotion of angiogenesis, remodeling of the extracellular matrix, recruitment of lymphocytes, and differentiation into tumor‐associated macrophages and dendritic cells. The ability of cancer to evade immune recognition and clearance requires protumoral signals to outweigh ongoing attempts by the host immune system to prevent tumor growth. This review discusses current understanding of monocyte heterogeneity during homeostasis, highlights monocyte functions in cancer progression, and describes monocyte‐targeted therapeutic strategies for cancer treatment.
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Affiliation(s)
- Claire E Olingy
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Huy Q Dinh
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
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Lin DC, Dinh HQ, Xie JJ, Mayakonda A, Silva TC, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Li C, Xu LY, Li EM, Berman BP, Phillip Koeffler H. Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut 2018; 67:1769-1779. [PMID: 28860350 PMCID: PMC5980794 DOI: 10.1136/gutjnl-2017-314607] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. DESIGN Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (ChIP)-seq to characterise epigenetic alterations. RESULTS OSCC and OAC displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to Catalogue Of Somatic Mutations In Cancer (COSMIC)signature 16, which has prognostic value in OSCC. Two newly discovered SMGs, CUL3 and ZFP36L2, were validated as important tumour-suppressors specific to the OSCC subtype. We further identified their additional loss-of-function mechanisms. CUL3 was homozygously deleted specifically in OSCC and other squamous cell cancers (SCCs). Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated SCC suppressor. CONCLUSIONS These data comprehensively contrast differences between OSCC and OAC at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.
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Affiliation(s)
- De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jian-Jun Xie
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA,Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tiago Chedraoui Silva
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jian-Zhong He
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Xiu-E Xu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunquan Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Li-Yan Xu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA,Cancer Science Institute of Singapore, National University of Singapore, Singapore,National University Cancer Institute, National University Hospital Singapore, Singapore
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35
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Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat Genet 2018; 50:591-602. [PMID: 29610480 PMCID: PMC5893360 DOI: 10.1038/s41588-018-0073-4] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 01/24/2018] [Indexed: 12/31/2022]
Abstract
DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed Partially Methylated Domains (PMDs). We profiled 39 diverse primary tumors and 8 matched adjacent tissues using Whole-Genome Bisulfite Sequencing (WGBS), and analyzed them alongside 343 additional human and 206 mouse WGBS datasets. We identified a local CpG sequence context associated with preferential hypomethylation in PMDs. Analysis of CpGs in this context (“Solo-WCGWs”) revealed previously undetected PMD hypomethylation in almost all healthy tissue types. PMD hypomethylation increased with age, beginning during fetal development, and appeared to track the accumulation of cell divisions. In cancer, PMD hypomethylation depth correlated with somatic mutation density and cell-cycle gene expression, consistent with its reflection of mitotic history, and suggesting its application as a mitotic clock. We propose that late replication leads to lifelong progressive methylation loss, which acts as a biomarker for cellular aging and which may contribute to oncogenesis.
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Affiliation(s)
- Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Daniel J Weisenberger
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Charles M Nicolet
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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36
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Winkels H, Ehinger E, Vassallo M, Buscher K, Dinh HQ, Kobiyama K, Hamers AAJ, Cochain C, Vafadarnejad E, Saliba AE, Zernecke A, Pramod AB, Ghosh AK, Anto Michel N, Hoppe N, Hilgendorf I, Zirlik A, Hedrick CC, Ley K, Wolf D. Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry. Circ Res 2018; 122:1675-1688. [PMID: 29545366 DOI: 10.1161/circresaha.117.312513] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [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: 12/06/2017] [Revised: 03/04/2018] [Accepted: 03/14/2018] [Indexed: 12/24/2022]
Abstract
RATIONALE Atherosclerosis is a chronic inflammatory disease that is driven by the interplay of pro- and anti-inflammatory leukocytes in the aorta. Yet, the phenotypic and transcriptional diversity of aortic leukocytes is poorly understood. OBJECTIVE We characterized leukocytes from healthy and atherosclerotic mouse aortas in-depth by single-cell RNA-sequencing and mass cytometry (cytometry by time of flight) to define an atlas of the immune cell landscape in atherosclerosis. METHODS AND RESULTS Using single-cell RNA-sequencing of aortic leukocytes from chow diet- and Western diet-fed Apoe-/- and Ldlr-/- mice, we detected 11 principal leukocyte clusters with distinct phenotypic and spatial characteristics while the cellular repertoire in healthy aortas was less diverse. Gene set enrichment analysis on the single-cell level established that multiple pathways, such as for lipid metabolism, proliferation, and cytokine secretion, were confined to particular leukocyte clusters. Leukocyte populations were differentially regulated in atherosclerotic Apoe-/- and Ldlr-/- mice. We confirmed the phenotypic diversity of these clusters with a novel mass cytometry 35-marker panel with metal-labeled antibodies and conventional flow cytometry. Cell populations retrieved by these protein-based approaches were highly correlated to transcriptionally defined clusters. In an integrated screening strategy of single-cell RNA-sequencing, mass cytometry, and fluorescence-activated cell sorting, we detected 3 principal B-cell subsets with alterations in surface markers, functional pathways, and in vitro cytokine secretion. Leukocyte cluster gene signatures revealed leukocyte frequencies in 126 human plaques by a genetic deconvolution strategy. This approach revealed that human carotid plaques and microdissected mouse plaques were mostly populated by macrophages, T-cells, and monocytes. In addition, the frequency of genetically defined leukocyte populations in carotid plaques predicted cardiovascular events in patients. CONCLUSIONS The definition of leukocyte diversity by high-dimensional analyses enables a fine-grained analysis of aortic leukocyte subsets, reveals new immunologic mechanisms and cell-type-specific pathways, and establishes a functional relevance for lesional leukocytes in human atherosclerosis.
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Affiliation(s)
- Holger Winkels
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Erik Ehinger
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Melanie Vassallo
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Konrad Buscher
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Huy Q Dinh
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Kouji Kobiyama
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Anouk A J Hamers
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Clément Cochain
- Institute of Experimental Biomedicine, University Hospital Würzburg, Germany (C.C., A.Z.)
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany (E.V., A.-E.S.)
| | | | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Germany (C.C., A.Z.)
| | - Akula Bala Pramod
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Amlan K Ghosh
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Nathaly Anto Michel
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.).,the Faculty of Medicine, University of Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.)
| | - Natalie Hoppe
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.).,the Faculty of Medicine, University of Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.)
| | - Ingo Hilgendorf
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.).,the Faculty of Medicine, University of Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.)
| | - Andreas Zirlik
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.).,the Faculty of Medicine, University of Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.)
| | - Catherine C Hedrick
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.)
| | - Klaus Ley
- From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.).,Department of Bioengineering, University of California, San Diego (K.L.)
| | - Dennis Wolf
- Institute of Experimental Biomedicine, University Hospital Würzburg, Germany (C.C., A.Z.) .,From the Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, CA (H.W., E.E., M.V., K.B., H.Q.D., K.K., A.A.J.H., A.B.P., A.K.G., C.C.H., K.L., D.W.).,Department of Cardiology and Angiology I, University Heart Center Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.).,the Faculty of Medicine, University of Freiburg, Germany (N.A.M., N.H., I.H., A.Z., D.W.)
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Lin DC, Mayakonda A, Dinh HQ, Huang P, Lin L, Liu X, Ding LW, Wang J, Berman BP, Song EW, Yin D, Koeffler HP. Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma. Cancer Res 2017; 77:2255-2265. [PMID: 28302680 DOI: 10.1158/0008-5472.can-16-2822] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/14/2016] [Accepted: 02/04/2017] [Indexed: 02/06/2023]
Abstract
Understanding the intratumoral heterogeneity of hepatocellular carcinoma is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 hepatocellular carcinoma cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions, that is, located on the "trunk" of the evolutionary tree. In addition, we found that variants within several drug targets such as KIT, SYK, and PIK3CA were mutated in a fully clonal manner, indicating their therapeutic potentials for hepatocellular carcinoma. Temporal dissection of mutational signatures suggested that mutagenic processes associated with exposure to aristolochic acid and aflatoxin might play a more important role in early, as opposed to late, stages of hepatocellular carcinoma development. Moreover, we observed extensive intratumoral epigenetic heterogeneity in hepatocellular carcinoma based on multiple independent analytical methods and showed that intratumoral methylation heterogeneity might play important roles in the biology of hepatocellular carcinoma cells. Our results also demonstrated prominent heterogeneity of intratumoral methylation even in a stable hepatocellular carcinoma genome. Together, these findings highlight widespread intratumoral heterogeneity at both the genomic and epigenomic levels in hepatocellular carcinoma and provide an important molecular foundation for better understanding the pathogenesis of this malignancy. Cancer Res; 77(9); 2255-65. ©2017 AACR.
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Affiliation(s)
- De-Chen Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California
| | - Pinbo Huang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Hepatobiliary Surgery, Sun-Yat-Sen Memorial Hospital, Sun-Yat-Sen University, Guangzhou, China
| | - Lehang Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoping Liu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jie Wang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Hepatobiliary Surgery, Sun-Yat-Sen Memorial Hospital, Sun-Yat-Sen University, Guangzhou, China
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Biomedical Sciences, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California.
| | - Er-Wei Song
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Dong Yin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - H Phillip Koeffler
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,National University Cancer Institute, National University Hospital Singapore, Singapore
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Popova OV, Dinh HQ, Aufsatz W, Jonak C. The RdDM pathway is required for basal heat tolerance in Arabidopsis. Mol Plant 2013; 6:396-410. [PMID: 23376771 PMCID: PMC3603006 DOI: 10.1093/mp/sst023] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/20/2013] [Indexed: 05/19/2023]
Abstract
Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epigenetic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methylation, histone modifications, chromatin-remodeling, or siRNA-based silencing pathways. Plants deficient in NRPD2, the common second-largest subunit of RNA polymerases IV and V, and in the Rpd3-type histone deacetylase HDA6 were hypersensitive to heat exposure. Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress. The misexpression of protein-coding genes in nrpd2 mutants recovering from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription. We provide evidence that the transcriptional response to temperature stress, at least partially, relies on the integrity of the RNA-dependent DNA methylation pathway.
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Affiliation(s)
| | | | | | - Claudia Jonak
- To whom correspondence should be addressed. E-mail , tel. +43 1 790449850, fax +43 1 790449001
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40
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Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One 2012; 7:e41528. [PMID: 22911809 PMCID: PMC3401099 DOI: 10.1371/journal.pone.0041528] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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: 12/01/2011] [Accepted: 06/27/2012] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing after bisulfite conversion (BS-Seq) is the method of choice to generate whole genome maps of cytosine methylation at single base-pair resolution. Its application to genomic DNA of Arabidopsis flower bud tissue resulted in the first complete methylome, determining a methylation rate of 6.7% in this tissue. BS-Seq reads were mapped onto an in silico converted reference genome, applying the so-called 3-letter genome method. Here, we present BiSS (Bisufite Sequencing Scorer), a new method applying Smith-Waterman alignment to map bisulfite-converted reads to a reference genome. In addition, we introduce a comprehensive adaptive error estimate that accounts for sequencing errors, erroneous bisulfite conversion and also wrongly mapped reads. The re-analysis of the Arabidopsis methylome data with BiSS mapped substantially more reads to the genome. As a result, it determines the methylation status of an extra 10% of cytosines and estimates the methylation rate to be 7.7%. We validated the results by individual traditional bisulfite sequencing for selected genomic regions. In addition to predicting the methylation status of each cytosine, BiSS also provides an estimate of the methylation degree at each genomic site. Thus, BiSS explores BS-Seq data more extensively and provides more information for downstream analysis.
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Affiliation(s)
- Huy Q. Dinh
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna and Medical University Vienna, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Manu Dubin
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Fritz J. Sedlazeck
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna and Medical University Vienna, Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (OMS); or (AvH)
| | - Arndt von Haeseler
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna and Medical University Vienna, Vienna, Austria
- * E-mail: (OMS); or (AvH)
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41
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Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res 2012; 22:2018-30. [PMID: 22534400 PMCID: PMC3460196 DOI: 10.1101/gr.132811.111] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is encoded in the cis-regulatory DNA sequence has, however, remained unclear. We computationally dissect context-specific TF binding sites in Drosophila, Caenorhabditis elegans, mouse, and human and find distinct combinations of sequence motifs for partner factors, which are predictive and reveal specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself depend on Vielfaltig motifs, suggesting that Vielfaltig is more generally important for early transcription. Our finding that the motif content can predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes (cis-regulatory signatures), which appear to be conserved during evolution. Taken together, this study establishes a novel approach to derive predictive cis-regulatory motif requirements for individual TF binding sites and enhancers. Importantly, the method is generally applicable across different cell types and organisms to elucidate cis-regulatory sequence determinants and the corresponding trans-acting factors from the increasing number of tissue- and cell-type-specific TF binding studies.
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Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JWS. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 2012; 40:2454-69. [PMID: 22127866 PMCID: PMC3315328 DOI: 10.1093/nar/gkr932] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/22/2011] [Accepted: 10/10/2011] [Indexed: 11/26/2022] Open
Abstract
Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5' or 3'UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3'-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.
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Affiliation(s)
- Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Craig G. Simpson
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Naeem H. Syed
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Dominika Lewandowska
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Branislav Kusenda
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Jacqueline Marshall
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - John Fuller
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Linda Cardle
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Jim McNicol
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Huy Q. Dinh
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - John W. S. Brown
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
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Foerster AM, Dinh HQ, Sedman L, Wohlrab B, Mittelsten Scheid O. Genetic rearrangements can modify chromatin features at epialleles. PLoS Genet 2011; 7:e1002331. [PMID: 22028669 PMCID: PMC3197671 DOI: 10.1371/journal.pgen.1002331] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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: 05/13/2011] [Accepted: 08/18/2011] [Indexed: 12/22/2022] Open
Abstract
Analogous to genetically distinct alleles, epialleles represent heritable states of different gene expression from sequence-identical genes. Alleles and epialleles both contribute to phenotypic heterogeneity. While alleles originate from mutation and recombination, the source of epialleles is less well understood. We analyze active and inactive epialleles that were found at a transgenic insert with a selectable marker gene in Arabidopsis. Both converse expression states are stably transmitted to progeny. The silent epiallele was previously shown to change its state upon loss-of-function of trans-acting regulators and drug treatments. We analyzed the composition of the epialleles, their chromatin features, their nuclear localization, transcripts, and homologous small RNA. After mutagenesis by T-DNA transformation of plants carrying the silent epiallele, we found new active alleles. These switches were associated with different, larger or smaller, and non-overlapping deletions or rearrangements in the 3' regions of the epiallele. These cis-mutations caused different degrees of gene expression stability depending on the nature of the sequence alteration, the consequences for transcription and transcripts, and the resulting chromatin organization upstream. This illustrates a tight dependence of epigenetic regulation on local structures and indicates that sequence alterations can cause epigenetic changes at some distance in regions not directly affected by the mutation. Similar effects may also be involved in gene expression and chromatin changes in the vicinity of transposon insertions or excisions, recombination events, or DNA repair processes and could contribute to the origin of new epialleles.
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Affiliation(s)
- Andrea M. Foerster
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna, Austria
| | - Huy Q. Dinh
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories (MFPL), Vienna, Austria
| | - Laura Sedman
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna, Austria
| | - Bonnie Wohlrab
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna, Austria
- * E-mail:
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Brini F, Yamamoto A, Jlaiel L, Takeda S, Hobo T, Dinh HQ, Hattori T, Masmoudi K, Hanin M. Pleiotropic effects of the wheat dehydrin DHN-5 on stress responses in Arabidopsis. Plant Cell Physiol 2011; 52:676-88. [PMID: 21421569 DOI: 10.1093/pcp/pcr030] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We have previously reported that transgenic Arabidopsis plants overexpressing the wheat dehydrin DHN-5 show enhanced tolerance to osmotic stresses. In order to understand the mechanisms through which DHN-5 exerts this effect, we performed transcriptome profiling using the Affymetrix ATH1 microarray. Our data show an altered expression of 77 genes involved mainly in transcriptional regulation, cellular metabolism, stress tolerance and signaling. Among the up-regulated genes, we identified those which are known to be stress-related genes. Several late embryogenesis abundant (LEA) genes, ABA/stress-related genes (such as RD29B) and those involved in pathogen responses (PR genes) are among the most up-regulated genes. In addition, the MDHAR gene involved in the ascorbate biosynthetic pathway was also up-regulated. This up-regulation was correlated with higher ascorbate content in two dehydrin transgenic lines. In agreement with this result and as ascorbate is known to be an antioxidant, we found that both transgenic lines show enhanced tolerance to oxidative stress caused by H₂O₂. On the other hand, multiple types of transcription factors constitute the largest group of the down-regulated genes. Moreover, three members of the jasmonate-ZIM domain (JAZ) proteins which are negative regulators of jasmonate signaling were severely down-regulated. Interestingly, the dehydrin-overexpressing lines exhibit less sensitivity to jasmonate than wild-type plants and changes in regulation of jasmonate-responsive genes, in a manner similar to that in the jasmonate-insensitive jai3-1 mutant. Altogether, our data unravel the potential pleiotropic effects of DHN-5 on both abiotic and biotic stress responses in Arabidopsis.
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Affiliation(s)
- Faïçal Brini
- Laboratory of Plant Protection and Improvement, Centre of Biotechnology of Sfax/University of Sfax, BP '1177' 3018 Sfax-Tunisia
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Pecinka A, Dinh HQ, Baubec T, Rosa M, Lettner N, Scheid OM. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 2010; 22:3118-29. [PMID: 20876829 PMCID: PMC2965555 DOI: 10.1105/tpc.110.078493] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 08/02/2010] [Accepted: 09/06/2010] [Indexed: 05/18/2023]
Abstract
Epigenetic factors determine responses to internal and external stimuli in eukaryotic organisms. Whether and how environmental conditions feed back to the epigenetic landscape is more a matter of suggestion than of substantiation. Plants are suitable organisms with which to address this question due to their sessile lifestyle and diversification of epigenetic regulators. We show that several repetitive elements of Arabidopsis thaliana that are under epigenetic regulation by transcriptional gene silencing at ambient temperatures and upon short term heat exposure become activated by prolonged heat stress. Activation can occur without loss of DNA methylation and with only minor changes to histone modifications but is accompanied by loss of nucleosomes and by heterochromatin decondensation. Whereas decondensation persists, nucleosome loading and transcriptional silencing are restored upon recovery from heat stress but are delayed in mutants with impaired chromatin assembly functions. The results provide evidence that environmental conditions can override epigenetic regulation, at least transiently, which might open a window for more permanent epigenetic changes.
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Affiliation(s)
- Ales Pecinka
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Huy Q. Dinh
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, 1030 Vienna, Austria
| | - Tuncay Baubec
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Marisa Rosa
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
- Address correspondence to
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Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, Wohlrab B, von Haeseler A, Scheid OM. Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis. Plant Cell 2010; 22:34-47. [PMID: 20097869 PMCID: PMC2828703 DOI: 10.1105/tpc.109.072819] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 12/15/2009] [Accepted: 12/29/2009] [Indexed: 05/18/2023]
Abstract
Epigenetic changes of gene expression can potentially be reversed by developmental programs, genetic manipulation, or pharmacological interference. However, a case of transcriptional gene silencing, originally observed in tetraploid Arabidopsis thaliana plants, created an epiallele resistant to many mutations or inhibitor treatments that activate many other suppressed genes. This raised the question about the molecular basis of this extreme stability. A combination of forward and reverse genetics and drug application provides evidence for an epigenetic double lock that is only alleviated upon the simultaneous removal of both DNA methylation and histone methylation. Therefore, the cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states and contributes to heritable diversity of gene expression patterns.
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Affiliation(s)
- Tuncay Baubec
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Huy Q. Dinh
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Ales Pecinka
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Branislava Rakic
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Wilfried Rozhon
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Bonnie Wohlrab
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
- Address correspondence to
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