1
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Quail DF, Park M, Welm AL, Ekiz HA. Breast Cancer Immunity: It is TIME for the Next Chapter. Cold Spring Harb Perspect Med 2024; 14:a041324. [PMID: 37188526 PMCID: PMC10835621 DOI: 10.1101/cshperspect.a041324] [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: 05/17/2023]
Abstract
Our ability to interrogate the tumor immune microenvironment (TIME) at an ever-increasing granularity has uncovered critical determinants of disease progression. Not only do we now have a better understanding of the immune response in breast cancer, but it is becoming possible to leverage key mechanisms to effectively combat this disease. Almost every component of the immune system plays a role in enabling or inhibiting breast tumor growth. Building on early seminal work showing the involvement of T cells and macrophages in controlling breast cancer progression and metastasis, single-cell genomics and spatial proteomics approaches have recently expanded our view of the TIME. In this article, we provide a detailed description of the immune response against breast cancer and examine its heterogeneity in disease subtypes. We discuss preclinical models that enable dissecting the mechanisms responsible for tumor clearance or immune evasion and draw parallels and distinctions between human disease and murine counterparts. Last, as the cancer immunology field is moving toward the analysis of the TIME at the cellular and spatial levels, we highlight key studies that revealed previously unappreciated complexity in breast cancer using these technologies. Taken together, this article summarizes what is known in breast cancer immunology through the lens of translational research and identifies future directions to improve clinical outcomes.
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Affiliation(s)
- Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
- Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
- Departments of Biochemistry, Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Alana L Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, 35430 Urla, Izmir, Turkey
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2
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YV, Davies MA, Ekiz HA, Tay JK, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer. bioRxiv 2023:2023.09.29.560199. [PMID: 37873189 PMCID: PMC10592860 DOI: 10.1101/2023.09.29.560199] [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: 10/25/2023]
Abstract
Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFNγ)-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFNγ-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFNγR expression, tumor intrinsic IFNγ signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFNγ receptor influences outcomes of ICB.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
- current contact information: School of Dentistry, Taipei Medical University, Taiwan
| | - Junhua Wang
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
| | - Emily C. Wilson
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Coulson P. Rich
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir institute of Technology, Gulbahce, Urla, 35430, Izmir, Turkey
| | - Joshua K.H. Tay
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Kenneth M. Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Juan M. Oviedo
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Keke C. Fairfax
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Matthew A. Williams
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Sheri L. Holmen
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Roger K. Wolff
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Allie H. Grossmann
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Lead contact
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3
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Warde KM, Smith LJ, Liu L, Stubben CJ, Lohman BK, Willett PW, Ammer JL, Castaneda-Hernandez G, Imodoye SO, Zhang C, Jones KD, Converso-Baran K, Ekiz HA, Barry M, Clay MR, Kiseljak-Vassiliades K, Giordano TJ, Hammer GD, Basham KJ. Senescence-induced immune remodeling facilitates metastatic adrenal cancer in a sex-dimorphic manner. Nat Aging 2023; 3:846-865. [PMID: 37231196 DOI: 10.1038/s43587-023-00420-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Aging markedly increases cancer risk, yet our mechanistic understanding of how aging influences cancer initiation is limited. Here we demonstrate that the loss of ZNRF3, an inhibitor of Wnt signaling that is frequently mutated in adrenocortical carcinoma, leads to the induction of cellular senescence that remodels the tissue microenvironment and ultimately permits metastatic adrenal cancer in old animals. The effects are sexually dimorphic, with males exhibiting earlier senescence activation and a greater innate immune response, driven in part by androgens, resulting in high myeloid cell accumulation and lower incidence of malignancy. Conversely, females present a dampened immune response and increased susceptibility to metastatic cancer. Senescence-recruited myeloid cells become depleted as tumors progress, which is recapitulated in patients in whom a low myeloid signature is associated with worse outcomes. Our study uncovers a role for myeloid cells in restraining adrenal cancer with substantial prognostic value and provides a model for interrogating pleiotropic effects of cellular senescence in cancer.
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Affiliation(s)
- Kate M Warde
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lorenzo J Smith
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Lihua Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Chris J Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Brian K Lohman
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Parker W Willett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Julia L Ammer
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | | | - Sikiru O Imodoye
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Chenge Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kara D Jones
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Kimber Converso-Baran
- Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla Izmir, Turkey
| | - Marc Barry
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine at Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katja Kiseljak-Vassiliades
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas J Giordano
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Endocrine Oncology Program, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Gary D Hammer
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Endocrine Oncology Program, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Kaitlin J Basham
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Thompson JW, Hu R, Huffaker TB, Ramstead AG, Ekiz HA, Bauer KM, Tang WW, Ghazaryan A, Round JL, Fujinami RS, O’Connell RM. MicroRNA-155 Plays Selective Cell-Intrinsic Roles in Brain-Infiltrating Immune Cell Populations during Neuroinflammation. J Immunol 2023; 210:926-934. [PMID: 36883849 PMCID: PMC10305808 DOI: 10.4049/jimmunol.2200478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/27/2023] [Indexed: 03/09/2023]
Abstract
The proinflammatory microRNA-155 (miR-155) is highly expressed in the serum and CNS lesions of patients with multiple sclerosis (MS). Global knockout (KO) of miR-155 in mice confers resistance to a mouse model of MS, experimental autoimmune encephalomyelitis (EAE), by reducing the encephalogenic potential of CNS-infiltrating Th17 T cells. However, cell-intrinsic roles for miR-155 during EAE have not been formally determined. In this study, we use single-cell RNA sequencing and cell-specific conditional miR-155 KOs to determine the importance of miR-155 expression in distinct immune cell populations. Time-course single-cell sequencing revealed reductions in T cells, macrophages, and dendritic cells (DCs) in global miR-155 KO mice compared with wild-type controls at day 21 after EAE induction. Deletion of miR-155 in T cells, driven by CD4 Cre, significantly reduced disease severity similar to global miR-155 KOs. CD11c Cre-mediated deletion of miR-155 in DCs also resulted in a modest yet significant reduction in the development of EAE, with both T cell- and DC-specific KOs showing a reduction in Th17 T cell infiltration into the CNS. Although miR-155 is highly expressed in infiltrating macrophages during EAE, deletion of miR-155 using LysM Cre did not impact disease severity. Taken together, these data show that although miR-155 is highly expressed in most infiltrating immune cells, miR-155 has distinct roles and requirements depending on the cell type, and we have demonstrated this using the gold standard conditional KO approach. This provides insights into which functionally relevant cell types should be targeted by the next generation of miRNA therapeutics.
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Affiliation(s)
- Jacob W. Thompson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Ruozhen Hu
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Thomas B. Huffaker
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Andrew G. Ramstead
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - H. Atakan Ekiz
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Kaylyn M. Bauer
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - William W. Tang
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - June L. Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Robert S. Fujinami
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
| | - Ryan M. O’Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT 84112
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT 84112
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Lo WL, Kuhlmann M, Rizzuto G, Ekiz HA, Kolawole EM, Revelo MP, Andargachew R, Li Z, Tsai YL, Marson A, Evavold BD, Zehn D, Weiss A. A single-amino acid substitution in the adaptor LAT accelerates TCR proofreading kinetics and alters T-cell selection, maintenance and function. Nat Immunol 2023; 24:676-689. [PMID: 36914891 PMCID: PMC10063449 DOI: 10.1038/s41590-023-01444-x] [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: 09/01/2022] [Accepted: 01/25/2023] [Indexed: 03/14/2023]
Abstract
Mature T cells must discriminate between brief interactions with self-peptides and prolonged binding to agonists. The kinetic proofreading model posits that certain T-cell antigen receptor signaling nodes serve as molecular timers to facilitate such discrimination. However, the physiological significance of this regulatory mechanism and the pathological consequences of disrupting it are unknown. Here we report that accelerating the normally slow phosphorylation of the linker for activation of T cells (LAT) residue Y136 by introducing an adjacent Gly135Asp alteration (LATG135D) disrupts ligand discrimination in vivo. The enhanced self-reactivity of LATG135D T cells triggers excessive thymic negative selection and promotes T-cell anergy. During Listeria infection, LATG135D T cells expand more than wild-type counterparts in response to very weak stimuli but display an imbalance between effector and memory responses. Moreover, despite their enhanced engagement of central and peripheral tolerance mechanisms, mice bearing LATG135D show features associated with autoimmunity and immunopathology. Our data reveal the importance of kinetic proofreading in balancing tolerance and immunity.
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Affiliation(s)
- Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Miriam Kuhlmann
- Division of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Gabrielle Rizzuto
- Human Oncology and Pathogenesis Program, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, Turkey
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Monica P Revelo
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rakieb Andargachew
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan-Li Tsai
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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6
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Barba C, Ekiz HA, Tang WW, Ghazaryan A, Hansen M, Lee SH, Voth WP, O’Connell RM. Interferon Gamma-Inducible NAMPT in Melanoma Cells Serves as a Mechanism of Resistance to Enhance Tumor Growth. Cancers (Basel) 2023; 15:1411. [PMID: 36900204 PMCID: PMC10000695 DOI: 10.3390/cancers15051411] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
(1) Background: Immune cells infiltrate the tumor microenvironment and secrete inflammatory cytokines, including interferons (IFNs), to drive antitumor responses and promote tumor clearance. However, recent evidence suggests that sometimes, tumor cells can also harness IFNs to enhance growth and survival. The essential NAD+ salvage pathway enzyme nicotinamide phosphoribosyltransferase (NAMPT) gene is constitutively expressed in cells during normal homeostasis. However, melanoma cells have higher energetic demands and elevated NAMPT expression. We hypothesized that interferon gamma (IFNγ) regulates NAMPT in tumor cells as a mechanism of resistance that impedes the normal anti-tumorigenic effects of IFNγ. (2) Methods: Utilizing a variety of melanoma cells, mouse models, Crispr-Cas9, and molecular biology techniques, we explored the importance of IFNγ-inducible NAMPT during melanoma growth. (3) Results: We demonstrated that IFNγ mediates the metabolic reprogramming of melanoma cells by inducing Nampt through a Stat1 binding site in the Nampt gene, increasing cell proliferation and survival. Further, IFN/STAT1-inducible Nampt promotes melanoma in vivo. (4) Conclusions: We provided evidence that melanoma cells directly respond to IFNγ by increasing NAMPT levels, improving their fitness and growth in vivo (control n = 36, SBS KO n = 46). This discovery unveils a possible therapeutic target that may improve the efficacy of immunotherapies involving IFN responses in the clinic.
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Affiliation(s)
- Cindy Barba
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - H. Atakan Ekiz
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
- Izmir Institute of Technology, Molecular Biology and Genetics Department, Gulbahce, Izmir 35430, Turkey
| | - William Weihao Tang
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Arevik Ghazaryan
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mason Hansen
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Soh-Hyun Lee
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Warren Peter Voth
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Michael O’Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
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7
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Ma WF, Turner AW, Gancayco C, Wong D, Song Y, Mosquera JV, Auguste G, Hodonsky CJ, Prabhakar A, Ekiz HA, van der Laan SW, Miller CL. PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics. Front Cardiovasc Med 2022; 9:969421. [PMID: 36003902 PMCID: PMC9393487 DOI: 10.3389/fcvm.2022.969421] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
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Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, United States
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Computer Engineering, University of Virginia, Charlottesville, VA, United States
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Research Computing, University of Virginia, Charlottesville, VA, United States
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Chani J. Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Ajay Prabhakar
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gülbahçe, Turkey
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- *Correspondence: Clint L. Miller
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8
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Lai SCA, Gundlapalli H, Ekiz HA, Jiang A, Fernandez E, Welm AL. Blocking Short-Form Ron Eliminates Breast Cancer Metastases through Accumulation of Stem-Like CD4+ T Cells That Subvert Immunosuppression. Cancer Discov 2021; 11:3178-3197. [PMID: 34330779 PMCID: PMC8800951 DOI: 10.1158/2159-8290.cd-20-1172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/07/2020] [Revised: 04/26/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Immunotherapy has potential to prevent and treat metastatic breast cancer, but strategies to enhance immune-mediated killing of metastatic tumors are urgently needed. We report that a ligand-independent isoform of Ron kinase (SF-Ron) is a key target to enhance immune infiltration and eradicate metastatic tumors. Host-specific deletion of SF-Ron caused recruitment of lymphocytes to micrometastases, augmented tumor-specific T-cell responses, and nearly eliminated breast cancer metastasis in mice. Lack of host SF-Ron caused stem-like TCF1+ CD4+ T cells with type I differentiation potential to accumulate in metastases and prevent metastatic outgrowth. There was a corresponding increase in tumor-specific CD8+ T cells, which were also required to eliminate lung metastases. Treatment of mice with a Ron kinase inhibitor increased tumor-specific CD8+ T cells and protected from metastatic outgrowth. These data provide a strong preclinical rationale to pursue small-molecule Ron kinase inhibitors for the prevention and treatment of metastatic breast cancer. SIGNIFICANCE The discovery that SF-Ron promotes antitumor immune responses has significant clinical implications. Therapeutic antibodies targeting full-length Ron may not be effective for immunotherapy; poor efficacy of such antibodies in trials may be due to their inability to block SF-Ron. Our data warrant trials with inhibitors targeting SF-Ron in combination with immunotherapy. This article is highlighted in the In This Issue feature, p. 2945.
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Affiliation(s)
- Shu-Chin Alicia Lai
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Harika Gundlapalli
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - H. Atakan Ekiz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Amanda Jiang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Elvelyn Fernandez
- Genomics Summer Research for Minorities (GSRM) Program, University of Utah, Salt Lake City, Utah
| | - Alana L. Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.,Corresponding Author: Alana L. Welm, University of Utah, 2000 Circle of Hope, Room 2515, Salt Lake City, UT 84112. Phone: 801-587-4622; E-mail:
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9
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Stephens WZ, Kubinak JL, Ghazaryan A, Bauer KM, Bell R, Buhrke K, Chiaro TR, Weis AM, Tang WW, Monts JK, Soto R, Ekiz HA, O'Connell RM, Round JL. Epithelial-myeloid exchange of MHC class II constrains immunity and microbiota composition. Cell Rep 2021; 37:109916. [PMID: 34731608 PMCID: PMC9012449 DOI: 10.1016/j.celrep.2021.109916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 06/01/2020] [Revised: 08/13/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Intestinal epithelial cells (IECs) have long been understood to express high levels of major histocompatibility complex class II (MHC class II) molecules but are not considered canonical antigen-presenting cells, and the impact of IEC-MHC class II signaling on gut homeostasis remains enigmatic. As IECs serve as the primary barrier between underlying host immune cells, we reasoned that IEC-intrinsic antigen presentation may play a role in responses toward the microbiota. Mice with an IEC-intrinsic deletion of MHC class II (IECΔMHC class II) are healthy but have fewer microbial-bound IgA, regulatory T cells (Tregs), and immune repertoire selection. This was associated with increased interindividual microbiota variation and altered proportions of two taxa in the ileum where MHC class II on IECs is highest. Intestinal mononuclear phagocytes (MNPs) have similar MHC class II transcription but less surface MHC class II and are capable of acquiring MHC class II from IECs. Thus, epithelial-myeloid interactions mediate development of adaptive responses to microbial antigens within the gastrointestinal tract.
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Affiliation(s)
- W Zac Stephens
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Jason L Kubinak
- University of South Carolina School of Medicine, Department of Pathology, Microbiology and Immunology, Columbia, SC 29209, USA
| | - Arevik Ghazaryan
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Kaylyn M Bauer
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Rickesha Bell
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Kate Buhrke
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Tyson R Chiaro
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Allison M Weis
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - William W Tang
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - Josh K Monts
- University of Utah School of Medicine, Flow Cytometry Core, Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Ray Soto
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - H Atakan Ekiz
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA; Izmir Institute of Technology, Molecular Biology and Genetics Department, Gulbahce, Izmir 35430, Turkey
| | - Ryan M O'Connell
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA.
| | - June L Round
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA.
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10
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Scherer SD, Riggio AI, Haroun F, DeRose YS, Ekiz HA, Fujita M, Toner J, Zhao L, Li Z, Oesterreich S, Samatar AA, Welm AL. An immune-humanized patient-derived xenograft model of estrogen-independent, hormone receptor positive metastatic breast cancer. Breast Cancer Res 2021; 23:100. [PMID: 34717714 PMCID: PMC8556932 DOI: 10.1186/s13058-021-01476-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Metastatic breast cancer (MBC) is incurable, with a 5-year survival rate of 28%. In the USA, more than 42,000 patients die from MBC every year. The most common type of breast cancer is estrogen receptor-positive (ER+), and more patients die from ER+ breast cancer than from any other subtype. ER+ tumors can be successfully treated with hormone therapy, but many tumors acquire endocrine resistance, at which point treatment options are limited. There is an urgent need for model systems that better represent human ER+ MBC in vivo, where tumors can metastasize. Patient-derived xenografts (PDX) made from MBC spontaneously metastasize, but the immunodeficient host is a caveat, given the known role of the immune system in tumor progression and response to therapy. Thus, we attempted to develop an immune-humanized PDX model of ER+ MBC. METHODS NSG-SGM3 mice were immune-humanized with CD34+ hematopoietic stem cells, followed by engraftment of human ER+ endocrine resistant MBC tumor fragments. Strategies for exogenous estrogen supplementation were compared, and immune-humanization in blood, bone marrow, spleen, and tumors was assessed by flow cytometry and tissue immunostaining. Characterization of the new model includes assessment of the human tumor microenvironment performed by immunostaining. RESULTS We describe the development of an immune-humanized PDX model of estrogen-independent endocrine resistant ER+ MBC. Importantly, our model harbors a naturally occurring ESR1 mutation, and immune-humanization recapitulates the lymphocyte-excluded and myeloid-rich tumor microenvironment of human ER+ breast tumors. CONCLUSION This model sets the stage for development of other clinically relevant models of human breast cancer and should allow future studies on mechanisms of endocrine resistance and tumor-immune interactions in an immune-humanized in vivo setting.
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Affiliation(s)
- Sandra D Scherer
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Alessandra I Riggio
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Fadi Haroun
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Yoko S DeRose
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - H Atakan Ekiz
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Maihi Fujita
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Jennifer Toner
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Ling Zhao
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA
| | - Zheqi Li
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Women's Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Ahmed A Samatar
- Zentalis Pharmaceuticals, Inc., 10835 Road to the Cure, Suite 205, San Diego, CA, 92121, USA
| | - Alana L Welm
- Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA.
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT, 84112, USA.
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11
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Fix DK, Ekiz HA, Petrocelli JJ, Mckenzie AM, Mahmassani ZS, O'Connell RM, Drummond MJ. Disrupted macrophage metabolic reprogramming in aged soleus muscle during early recovery following disuse atrophy. Aging Cell 2021; 20:e13448. [PMID: 34365717 PMCID: PMC8441489 DOI: 10.1111/acel.13448] [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: 10/01/2020] [Revised: 06/22/2021] [Accepted: 07/20/2021] [Indexed: 10/25/2022] Open
Abstract
Aged skeletal muscle is characterized by poor muscle recovery following disuse coinciding with an impaired muscle pro-inflammatory macrophage response. Macrophage inflammatory status is regulated by its metabolic state, but little is understood of macrophage metabolism and its relation to macrophage inflammation in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and inflammation in aged muscle during early recovery following disuse atrophy using single cell transcriptomics and functional assays. Young (4-5 months) and old (20-22 months) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery. CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing. We found that aged pro-inflammatory macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome, and this dysregulation was accompanied by a suppression of HIF-1α and its immediate downstream target, Glut1. As a follow-up, bone marrow-derived macrophages were isolated from a separate cohort of young and old mice at 4-d recovery and were polarized to a pro-inflammatory phenotype and used for glycolysis stress test, phagocytosis activity assay, and targeted GC-MS metabolomics. Aged bone marrow-derived pro-inflammatory macrophages were characterized with impaired glycolysis and phagocytosis function, decreased succinate and an accumulation of glycolytic metabolic intermediates overall supporting reduced glycolytic flux and macrophage function. Our results indicate that the metabolic reprograming and function of aged skeletal muscle pro-inflammatory macrophages are dysfunctional during early recovery from disuse atrophy possibly attributing to attenuated regrowth.
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Affiliation(s)
- Dennis K. Fix
- Molecular Medicine ProgramDepartment of Integrative Physiology and NutritionDepartment of Physical Therapy and Athletic TrainingUniversity of UtahSalt Lake CityUtahUSA
| | - H. Atakan Ekiz
- Department of PathologyDivision of Microbiology and ImmunologyUniversity of UtahSalt Lake CityUtahUSA
| | - Jonathan J. Petrocelli
- Molecular Medicine ProgramDepartment of Integrative Physiology and NutritionDepartment of Physical Therapy and Athletic TrainingUniversity of UtahSalt Lake CityUtahUSA
| | - Alec M. Mckenzie
- Molecular Medicine ProgramDepartment of Integrative Physiology and NutritionDepartment of Physical Therapy and Athletic TrainingUniversity of UtahSalt Lake CityUtahUSA
| | - Ziad S. Mahmassani
- Molecular Medicine ProgramDepartment of Integrative Physiology and NutritionDepartment of Physical Therapy and Athletic TrainingUniversity of UtahSalt Lake CityUtahUSA
| | - Ryan M. O'Connell
- Department of PathologyDivision of Microbiology and ImmunologyUniversity of UtahSalt Lake CityUtahUSA
| | - Micah J. Drummond
- Molecular Medicine ProgramDepartment of Integrative Physiology and NutritionDepartment of Physical Therapy and Athletic TrainingUniversity of UtahSalt Lake CityUtahUSA
- Department of PathologyDivision of Microbiology and ImmunologyUniversity of UtahSalt Lake CityUtahUSA
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12
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Huffaker TB, Ekiz HA, Barba C, Lee SH, Runtsch MC, Nelson MC, Bauer KM, Tang WW, Mosbruger TL, Cox JE, Round JL, Voth WP, O'Connell RM. A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages. Nat Commun 2021; 12:2620. [PMID: 33976173 PMCID: PMC8113251 DOI: 10.1038/s41467-021-22923-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 05/05/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Tumor associated macrophage responses are regulated by distinct metabolic states that affect their function. However, the ability of specific signals in the local tumor microenvironment to program macrophage metabolism remains under investigation. Here, we identify NAMPT, the rate limiting enzyme in NAD salvage synthesis, as a target of STAT1 during cellular activation by interferon gamma, an important driver of macrophage polarization and antitumor responses. We demonstrate that STAT1 occupies a conserved element within the first intron of Nampt, termed Nampt-Regulatory Element-1 (NRE1). Through disruption of NRE1 or pharmacological inhibition, a subset of M1 genes is sensitive to NAMPT activity through its impact on glycolytic processes. scRNAseq is used to profile in vivo responses by NRE1-deficient, tumor-associated leukocytes in melanoma tumors through the creation of a unique mouse strain. Reduced Nampt and inflammatory gene expression are present in specific myeloid and APC populations; moreover, targeted ablation of NRE1 in macrophage lineages results in greater tumor burden. Finally, elevated NAMPT expression correlates with IFNγ responses and melanoma patient survival. This study identifies IFN and STAT1-inducible Nampt as an important factor that shapes the metabolic program and function of tumor associated macrophages.
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Affiliation(s)
- Thomas B Huffaker
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - H Atakan Ekiz
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Cindy Barba
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Soh-Hyun Lee
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Marah C Runtsch
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Morgan C Nelson
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kaylyn M Bauer
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - William W Tang
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT, USA
| | - June L Round
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Warren P Voth
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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13
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Syage AR, Ekiz HA, Skinner DD, Stone C, O'Connell RM, Lane TE. Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus. J Virol 2020; 94:e01295-20. [PMID: 32999036 PMCID: PMC7925182 DOI: 10.1128/jvi.01295-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/16/2020] [Indexed: 01/12/2023] Open
Abstract
Intracranial (i.c.) infection of susceptible C57BL/6 mice with the neurotropic JHM strain of mouse hepatitis virus (JHMV) (a member of the Coronaviridae family) results in acute encephalomyelitis and viral persistence associated with an immune-mediated demyelinating disease. The present study was undertaken to better understand the molecular pathways evoked during innate and adaptive immune responses as well as the chronic demyelinating stage of disease in response to JHMV infection of the central nervous system (CNS). Using single-cell RNA sequencing analysis (scRNAseq) on flow-sorted CD45-positive (CD45+) cells enriched from brains and spinal cords of experimental mice, we demonstrate the heterogeneity of the immune response as determined by the presence of unique molecular signatures and pathways involved in effective antiviral host defense. Furthermore, we identify potential genes involved in contributing to demyelination as well as remyelination being expressed by both microglia and macrophages. Collectively, these findings emphasize the diversity of the immune responses and molecular networks at defined stages following viral infection of the CNS.IMPORTANCE Understanding the immunological mechanisms contributing to both host defense and disease following viral infection of the CNS is of critical importance given the increasing number of viruses that are capable of infecting and replicating within the nervous system. With this in mind, the present study was undertaken to evaluate the molecular signatures of immune cells within the CNS at defined times following infection with a neuroadapted murine coronavirus using scRNAseq. This approach has revealed that the immunological landscape is diverse, with numerous immune cell subsets expressing distinct mRNA expression profiles that are, in part, dictated by the stage of infection. In addition, these findings reveal new insight into cellular pathways contributing to control of viral replication as well as to neurologic disease.
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Affiliation(s)
- Amber R Syage
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - H Atakan Ekiz
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Dominic D Skinner
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Colleen Stone
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Ryan M O'Connell
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Thomas E Lane
- Division of Microbiology & Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
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14
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Mangale V, Syage AR, Ekiz HA, Skinner DD, Cheng Y, Stone CL, Brown RM, O'Connell RM, Green KN, Lane TE. Microglia influence host defense, disease, and repair following murine coronavirus infection of the central nervous system. Glia 2020; 68:2345-2360. [PMID: 32449994 PMCID: PMC7280614 DOI: 10.1002/glia.23844] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022]
Abstract
The present study examines functional contributions of microglia in host defense, demyelination, and remyelination following infection of susceptible mice with a neurotropic coronavirus. Treatment with PLX5622, an inhibitor of colony stimulating factor 1 receptor (CSF1R) that efficiently depletes microglia, prior to infection of the central nervous system (CNS) with the neurotropic JHM strain of mouse hepatitis virus (JHMV) resulted in increased mortality compared with control mice that correlated with impaired control of viral replication. Single cell RNA sequencing (scRNASeq) of CD45+ cells isolated from the CNS revealed that PLX5622 treatment resulted in muted CD4+ T cell activation profile that was associated with decreased expression of transcripts encoding MHC class II and CD86 in macrophages but not dendritic cells. Evaluation of spinal cord demyelination revealed a marked increase in white matter damage in PLX5622-treated mice that corresponded with elevated expression of transcripts encoding disease-associated proteins Osteopontin (Spp1), Apolipoprotein E (Apoe), and Triggering receptor expressed on myeloid cells 2 (Trem2) that were enriched within macrophages. In addition, PLX5622 treatment dampened expression of Cystatin F (Cst7), Insulin growth factor 1 (Igf1), and lipoprotein lipase (Lpl) within macrophage populations which have been implicated in promoting repair of damaged nerve tissue and this was associated with impaired remyelination. Collectively, these findings argue that microglia tailor the CNS microenvironment to enhance control of coronavirus replication as well as dampen the severity of demyelination and influence repair.
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Affiliation(s)
- Vrushali Mangale
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Amber R. Syage
- Department of Neurobiology & Behavior, School of Biological SciencesUniversity of CaliforniaIrvineCaliforniaUSA
| | - H. Atakan Ekiz
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Dominic D. Skinner
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Yuting Cheng
- Department of Neurobiology & Behavior, School of Biological SciencesUniversity of CaliforniaIrvineCaliforniaUSA
| | - Colleen L. Stone
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - R. Marshall Brown
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Ryan M. O'Connell
- Division of Microbiology & Immunology, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Kim N. Green
- Department of Neurobiology & Behavior, School of Biological SciencesUniversity of CaliforniaIrvineCaliforniaUSA
| | - Thomas E. Lane
- Department of Neurobiology & Behavior, School of Biological SciencesUniversity of CaliforniaIrvineCaliforniaUSA
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15
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Petersen C, Bell R, Klag KA, Lee SH, Soto R, Ghazaryan A, Buhrke K, Ekiz HA, Ost KS, Boudina S, O'Connell RM, Cox JE, Villanueva CJ, Stephens WZ, Round JL. T cell-mediated regulation of the microbiota protects against obesity. Science 2020; 365:365/6451/eaat9351. [PMID: 31346040 DOI: 10.1126/science.aat9351] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 02/22/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022]
Abstract
The microbiota influences obesity, yet organisms that protect from disease remain unknown. During studies interrogating host-microbiota interactions, we observed the development of age-associated metabolic syndrome (MetS). Expansion of Desulfovibrio and loss of Clostridia were key features associated with obesity in this model and are present in humans with MetS. T cell-dependent events were required to prevent disease, and replacement of Clostridia rescued obesity. Inappropriate immunoglobulin A targeting of Clostridia and increased Desulfovibrio antagonized the colonization of beneficial Clostridia. Transcriptional and metabolic analysis revealed enhanced lipid absorption in the obese host. Colonization of germ-free mice with Clostridia, but not Desulfovibrio, down-regulated genes that control lipid absorption and reduced adiposity. Thus, immune control of the microbiota maintains beneficial microbial populations that constrain lipid metabolism to prevent MetS.
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Affiliation(s)
- Charisse Petersen
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rickesha Bell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kendra A Klag
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Soh-Hyun Lee
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Raymond Soto
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin Buhrke
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - H Atakan Ekiz
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kyla S Ost
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sihem Boudina
- Department of Nutrition and Integrative Physiology, College of Health, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan M O'Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Claudio J Villanueva
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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16
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Ekiz HA, Ramstead AG, Lee SH, Nelson MC, Bauer KM, Wallace JA, Hu R, Round JL, Rutter J, Drummond MJ, Rao DS, O'Connell RM. T Cell-Expressed microRNA-155 Reduces Lifespan in a Mouse Model of Age-Related Chronic Inflammation. J Immunol 2020; 204:2064-2075. [PMID: 32161096 DOI: 10.4049/jimmunol.1901484] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/31/2020] [Indexed: 01/13/2023]
Abstract
Aging-related chronic inflammation is a risk factor for many human disorders through incompletely understood mechanisms. Aged mice deficient in microRNA (miRNA/miR)-146a succumb to life-shortening chronic inflammation. In this study, we report that miR-155 in T cells contributes to shortened lifespan of miR-146a-/- mice. Using single-cell RNA sequencing and flow cytometry, we found that miR-155 promotes the activation of effector T cell populations, including T follicular helper cells, and increases germinal center B cells and autoantibodies in mice aged over 15 months. Mechanistically, aerobic glycolysis genes are elevated in T cells during aging, and upon deletion of miR-146a, in a T cell miR-155-dependent manner. Finally, skewing T cell metabolism toward aerobic glycolysis by deleting mitochondrial pyruvate carrier recapitulates age-dependent T cell phenotypes observed in miR-146a-/- mice, revealing the sufficiency of metabolic reprogramming to influence immune cell functions during aging. Altogether, these data indicate that T cell-specific miRNAs play pivotal roles in regulating lifespan through their influences on inflammaging.
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Affiliation(s)
- H Atakan Ekiz
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Andrew G Ramstead
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Soh-Hyun Lee
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Morgan C Nelson
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Kaylyn M Bauer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Jared A Wallace
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Ruozhen Hu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - June L Round
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Jared Rutter
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Micah J Drummond
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112.,Department of Physical Therapy and Athletic Training, University of Utah, Salt Lake City, UT 84112.,Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT 84112; and
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095
| | - Ryan M O'Connell
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112; .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
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17
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Ramstead AG, Wallace JA, Lee SH, Bauer KM, Tang WW, Ekiz HA, Lane TE, Cluntun AA, Bettini ML, Round JL, Rutter J, O'Connell RM. Mitochondrial Pyruvate Carrier 1 Promotes Peripheral T Cell Homeostasis through Metabolic Regulation of Thymic Development. Cell Rep 2020; 30:2889-2899.e6. [PMID: 32130894 PMCID: PMC7170217 DOI: 10.1016/j.celrep.2020.02.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/10/2019] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolic pathways regulate T cell development and function, but many remain understudied. Recently, the mitochondrial pyruvate carrier (MPC) was identified as the transporter that mediates pyruvate entry into mitochondria, promoting pyruvate oxidation. Here we find that deleting Mpc1, an obligate MPC subunit, in the hematopoietic system results in a specific reduction in peripheral αβ T cell numbers. MPC1-deficient T cells have defective thymic development at the β-selection, intermediate single positive (ISP)-to-double-positive (DP), and positive selection steps. We find that early thymocytes deficient in MPC1 display alterations to multiple pathways involved in T cell development. This results in preferred escape of more activated T cells. Finally, mice with hematopoietic deletion of Mpc1 are more susceptible to experimental autoimmune encephalomyelitis. Altogether, our study demonstrates that pyruvate oxidation by T cell precursors is necessary for optimal αβ T cell development and that its deficiency results in reduced but activated peripheral T cell populations.
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Affiliation(s)
- Andrew G Ramstead
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Jared A Wallace
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Soh-Hyun Lee
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Kaylyn M Bauer
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - William W Tang
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - H Atakan Ekiz
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Lane
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Matthew L Bettini
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - June L Round
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan M O'Connell
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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18
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Snook JP, Soedel AJ, Ekiz HA, O'Connell RM, Williams MA. Inhibition of SHP-1 Expands the Repertoire of Antitumor T Cells Available to Respond to Immune Checkpoint Blockade. Cancer Immunol Res 2020; 8:506-517. [PMID: 32075800 DOI: 10.1158/2326-6066.cir-19-0690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/12/2019] [Accepted: 02/11/2020] [Indexed: 12/13/2022]
Abstract
The presence and activity of CD8+ T cells within the tumor microenvironment are essential for the control of tumor growth. Utilizing B16-F10 melanoma tumors that express altered peptide ligands of chicken ovalbumin, OVA257-264, we measured high- and low-affinity OVA-specific responses following adoptive transfer of OT-I CD8+ T cell into mice subsequently challenged with tumors. T-cell receptor (TCR) affinity positively correlated with the frequency of OT-I tumor-infiltrating lymphocytes (TIL). Differences in TCR affinity inversely corresponded to in vivo tumor growth rate. Blockade of the PD-1 and CTLA-4 checkpoints preferentially increased the frequency and antitumor function of TIL responding to high-affinity antigens, while failing to enhance the antitumor activity of low-affinity T cells. To determine whether lowering the TCR activation threshold could enhance the breadth and magnitude of the antitumor T-cell response, we inhibited Src homology region 2 domain-containing phosphatase 1 (SHP-1) in OT-I T cells prior to tumor antigen exposure. SHP-1 knockdown increased the cytokine-producing potential of high- and low-affinity T cells but failed to enhance control of tumor growth. In contrast, when SHP-1 knockdown of OT-I T cells was combined with immunotherapy, we observed a significant and long-lasting suppression of tumor growth mediated by low-affinity T cells. We conclude that lowering the TCR activation threshold by targeting SHP-1 expands the repertoire of T cells available to respond to conventional checkpoint blockade, leading to enhanced control of tumor growth.
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Affiliation(s)
- Jeremy P Snook
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.,Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah
| | - Ashleigh J Soedel
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.,Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah
| | - H Atakan Ekiz
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.,Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah
| | - Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah.,Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah
| | - Matthew A Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah. .,Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah
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19
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Ekiz HA, Huffaker TB, Grossmann AH, Stephens WZ, Williams MA, Round JL, O'Connell RM. MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in human cancers. JCI Insight 2019; 4:126543. [PMID: 30721153 DOI: 10.1172/jci.insight.126543] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/31/2019] [Indexed: 12/27/2022] Open
Abstract
miR-155 has recently emerged as an important promoter of antitumor immunity through its functions in T lymphocytes. However, the impact of T cell-expressed miR-155 on immune cell dynamics in solid tumors remains unclear. In the present study, we used single-cell RNA sequencing to define the CD45+ immune cell populations at different time points within B16F10 murine melanoma tumors growing in either wild-type or miR-155 T cell conditional knockout (TCKO) mice. miR-155 was required for optimal T cell activation and reinforced the T cell response at the expense of infiltrating myeloid cells. Further, myeloid cells from tumors growing in TCKO mice were defined by an increase in wound healing genes and a decreased IFN-γ-response gene signature. Finally, we found that miR-155 expression predicted a favorable outcome in human melanoma patients and was associated with a strong immune signature. Moreover, gene expression analysis of The Cancer Genome Atlas (TCGA) data revealed that miR-155 expression also correlates with an immune-enriched subtype in 29 other human solid tumors. Together, our study provides an unprecedented analysis of the cell types and gene expression signatures of immune cells within experimental melanoma tumors and elucidates the role of miR-155 in coordinating antitumor immune responses in mammalian tumors.
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Affiliation(s)
| | | | - Allie H Grossmann
- Division of Anatomic Pathology, Department of Pathology, University of Utah.,Huntsman Cancer Institute, University of Utah Health Sciences Center, and.,ARUP Laboratories, University of Utah, Salt Lake City, Utah, USA
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