1
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Rao A, Zhang X, Cillo AR, Sussman JH, Sandlesh P, Tarbay AC, Mallela AN, Cardello C, Krueger K, Xu J, Li A, Xu J, Patterson J, Akca E, Angione A, Jaman E, Kim WJ, Allen J, Venketeswaran A, Zinn PO, Parise R, Beumer J, Duensing A, Holland EC, Ferris R, Bagley SJ, Bruno TC, Vignali DAA, Agnihotri S, Amankulor NM. All-trans retinoic acid induces durable tumor immunity in IDH-mutant gliomas by rescuing transcriptional repression of the CRBP1-retinoic acid axis. bioRxiv 2024:2024.04.09.588752. [PMID: 38645178 PMCID: PMC11030316 DOI: 10.1101/2024.04.09.588752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4 + T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.
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2
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Shan F, Cillo AR, Cardello C, Yuan DY, Kunning SR, Cui J, Lampenfeld C, Williams AM, McDonough AP, Pennathur A, Luketich JD, Kirkwood JM, Ferris RL, Bruno TC, Workman CJ, Benos PV, Vignali DAA. Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells. Sci Immunol 2023; 8:eadf6717. [PMID: 37713508 PMCID: PMC11045170 DOI: 10.1126/sciimmunol.adf6717] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Human regulatory T cells (Tregs) are crucial regulators of tissue repair, autoimmune diseases, and cancer. However, it is challenging to inhibit the suppressive function of Tregs for cancer therapy without affecting immune homeostasis. Identifying pathways that may distinguish tumor-restricted Tregs is important, yet the transcriptional programs that control intratumoral Treg gene expression, and that are distinct from Tregs in healthy tissues, remain largely unknown. We profiled single-cell transcriptomes of CD4+ T cells in tumors and peripheral blood from patients with head and neck squamous cell carcinomas (HNSCC) and those in nontumor tonsil tissues and peripheral blood from healthy donors. We identified a subpopulation of activated Tregs expressing multiple tumor necrosis factor receptor (TNFR) genes (TNFR+ Tregs) that is highly enriched in the tumor microenvironment (TME) compared with nontumor tissue and the periphery. TNFR+ Tregs are associated with worse prognosis in HNSCC and across multiple solid tumor types. Mechanistically, the transcription factor BATF is a central component of a gene regulatory network that governs key aspects of TNFR+ Tregs. CRISPR-Cas9-mediated BATF knockout in human activated Tregs in conjunction with bulk RNA sequencing, immunophenotyping, and in vitro functional assays corroborated the central role of BATF in limiting excessive activation and promoting the survival of human activated Tregs. Last, we identified a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral Tregs in patients with HNSCC. These findings uncover a primary transcriptional regulator of highly suppressive intratumoral Tregs, highlighting potential opportunities for therapeutic intervention in cancer without affecting immune homeostasis.
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Affiliation(s)
- Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R. Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Daniel Y. Yuan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sheryl R. Kunning
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Caleb Lampenfeld
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Asia M. Williams
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Alexandra P. McDonough
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Arjun Pennathur
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John M. Kirkwood
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert L. Ferris
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tullia C. Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Creg J. Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Dario A. A. Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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3
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Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile KL, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DAA. Publisher Correction: Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment. Nat Cancer 2023; 4:582. [PMID: 37012402 DOI: 10.1038/s43018-023-00549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Sayali Onkar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Graduate Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Mostofa Rafid Uddin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - April Sagan
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Marion Joy
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
| | - Hatice U Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Priscilla F McAuliffe
- Section of Breast Surgery, Division of Surgical Oncology, Department of Surgery, University of Pittsburgh College of Medicine, Magee Women's Hospital of UPMC, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter C Lucas
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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4
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Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile KL, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DAA. Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment. Nat Cancer 2023; 4:516-534. [PMID: 36927792 DOI: 10.1038/s43018-023-00527-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/10/2023] [Indexed: 03/18/2023]
Abstract
T cell-centric immunotherapies have shown modest clinical benefit thus far for estrogen receptor-positive (ER+) breast cancer. Despite accounting for 70% of all breast cancers, relatively little is known about the immunobiology of ER+ breast cancer in women with invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). To investigate this, we performed phenotypic, transcriptional and functional analyses for a cohort of treatment-naive IDC (n = 94) and ILC (n = 87) tumors. We show that macrophages, and not T cells, are the predominant immune cells infiltrating the tumor bed and the most transcriptionally diverse cell subset between IDC and ILC. Analysis of cellular neighborhoods revealed an interplay between macrophages and T cells associated with longer disease-free survival in IDC but not ILC. Our datasets provide a rich resource for further interrogation into immune cell dynamics in ER+ IDC and ILC and highlight macrophages as a potential target for ER+ breast cancer.
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Affiliation(s)
- Sayali Onkar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Graduate Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Mostofa Rafid Uddin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - April Sagan
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Marion Joy
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
| | - Hatice U Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Priscilla F McAuliffe
- Section of Breast Surgery, Division of Surgical Oncology, Department of Surgery, University of Pittsburgh College of Medicine, Magee Women's Hospital of UPMC, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter C Lucas
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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5
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Grebinoski S, Zhang Q, Cillo AR, Manne S, Xiao H, Brunazzi EA, Tabib T, Cardello C, Lian CG, Murphy GF, Lafyatis R, Wherry EJ, Das J, Workman CJ, Vignali DAA. Autoreactive CD8 + T cells are restrained by an exhaustion-like program that is maintained by LAG3. Nat Immunol 2022; 23:868-877. [PMID: 35618829 DOI: 10.1038/s41590-022-01210-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
Impaired chronic viral and tumor clearance has been attributed to CD8+ T cell exhaustion, a differentiation state in which T cells have reduced and altered effector function that can be partially reversed upon blockade of inhibitory receptors. The role of the exhaustion program and transcriptional networks that control CD8+ T cell function and fate in autoimmunity is not clear. Here we show that intra-islet CD8+ T cells phenotypically, transcriptionally, epigenetically and metabolically possess features of canonically exhausted T cells, yet maintain important differences. This 'restrained' phenotype can be perturbed and disease accelerated by CD8+ T cell-restricted deletion of the inhibitory receptor lymphocyte activating gene 3 (LAG3). Mechanistically, LAG3-deficient CD8+ T cells have enhanced effector-like functions, trafficking to the islets, and have a diminished exhausted phenotype, highlighting a physiological role for an exhaustion program in limiting autoimmunity and implicating LAG3 as a target for autoimmune therapy.
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Affiliation(s)
- Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Qianxia Zhang
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Sasikanth Manne
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,CMU-Pitt Joint Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin A Brunazzi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christine G Lian
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - George F Murphy
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy at University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA. .,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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6
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Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Ruffin AT, Kunning S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews LP, Duprex WP, Joglekar AV, Benos PV, Ray P, Ray A, McVerry BJ, Zhang Y, Lee JS, Das J, Singh H, Morris A, Bruno TC, Vignali DAA. People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden. Cell Rep Med 2021; 2:100476. [PMID: 34873589 PMCID: PMC8636386 DOI: 10.1016/j.xcrm.2021.100476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/27/2021] [Accepted: 11/23/2021] [Indexed: 01/08/2023]
Abstract
Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in people critically ill with COVID-19. Here, we present high-dimensional profiling of blood and respiratory samples from people with severe COVID-19 to examine the association between cell-linked molecular features and mortality outcomes. Peripheral transcriptional profiles by single-cell RNA sequencing (RNA-seq)-based deconvolution of immune states are associated with COVID-19 mortality. Further, persistently high levels of an interferon signaling module in monocytes over time lead to subsequent concerted upregulation of inflammatory cytokines. SARS-CoV-2-infected myeloid cells in the lower respiratory tract upregulate CXCL10, leading to a higher risk of death. Our analysis suggests a pivotal role for viral-infected myeloid cells and protracted interferon signaling in severe COVID-19.
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Affiliation(s)
- Anthony R Cillo
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Ashwin Somasundaram
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Feng Shan
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Integrative Systems Biology (ISB) Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carly Cardello
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Creg J Workman
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ayana T Ruffin
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sheryl Kunning
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Caleb Lampenfeld
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Sayali Onkar
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Stephanie Grebinoski
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Gaurav Deshmukh
- Meso Scale Discovery, A division of Meso Scale Diagnostics, LLC, 1601 Research Boulevard, Rockville, MD 20850-3173, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Chang Liu
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence P Andrews
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Panayiotis V Benos
- Department of Computer Science, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, PA 15260, USA.,Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anuradha Ray
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Harinder Singh
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alison Morris
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Tullia C Bruno
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Dario A A Vignali
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
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7
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Hensley MK, Bain WG, Jacobs J, Nambulli S, Parikh U, Cillo A, Staines B, Heaps A, Sobolewski MD, Rennick LJ, Macatangay BJC, Klamar-Blain C, Kitsios GD, Methé B, Somasundaram A, Bruno TC, Cardello C, Shan F, Workman C, Ray P, Ray A, Lee J, Sethi R, Schwarzmann WE, Ladinsky MS, Bjorkman PJ, Vignali DA, Duprex WP, Agha ME, Mellors JW, McCormick KD, Morris A, Haidar G. Intractable Coronavirus Disease 2019 (COVID-19) and Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Replication in a Chimeric Antigen Receptor-Modified T-Cell Therapy Recipient: A Case Study. Clin Infect Dis 2021; 73:e815-e821. [PMID: 33507235 PMCID: PMC7929077 DOI: 10.1093/cid/ciab072] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
A chimeric antigen receptor-modified T-cell therapy recipient developed severe coronavirus disease 2019, intractable RNAemia, and viral replication lasting >2 months. Premortem endotracheal aspirate contained >2 × 1010 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies/mL and infectious virus. Deep sequencing revealed multiple sequence variants consistent with intrahost virus evolution. SARS-CoV-2 humoral and cell-mediated immunity were minimal. Prolonged transmission from immunosuppressed patients is possible.
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Affiliation(s)
- Matthew K Hensley
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William G Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Jana Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvi Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anthony Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michele D Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ashwin Somasundaram
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Creg Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rahil Sethi
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William E Schwarzmann
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dario A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mounzer E Agha
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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8
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Bain W, Yang H, Shah FA, Suber T, Drohan C, Al-Yousif N, DeSensi RS, Bensen N, Schaefer C, Rosborough BR, Somasundaram A, Workman CJ, Lampenfeld C, Cillo AR, Cardello C, Shan F, Bruno TC, Vignali DAA, Ray P, Ray A, Zhang Y, Lee JS, Methé B, McVerry BJ, Morris A, Kitsios GD. COVID-19 versus Non-COVID-19 Acute Respiratory Distress Syndrome: Comparison of Demographics, Physiologic Parameters, Inflammatory Biomarkers, and Clinical Outcomes. Ann Am Thorac Soc 2021; 18:1202-1210. [PMID: 33544045 PMCID: PMC8328355 DOI: 10.1513/annalsats.202008-1026oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 01/14/2023] Open
Abstract
Rationale: There is an urgent need for improved understanding of the mechanisms and clinical characteristics of acute respiratory distress syndrome (ARDS) due to coronavirus disease (COVID-19).Objectives: To compare key demographic and physiologic parameters, biomarkers, and clinical outcomes of COVID-19 ARDS and ARDS secondary to direct lung injury from other etiologies of pneumonia.Methods: We enrolled 27 patients with COVID-19 ARDS in a prospective, observational cohort study and compared them with a historical, pre-COVID-19 cohort of patients with viral ARDS (n = 14), bacterial ARDS (n = 21), and ARDS due to culture-negative pneumonia (n = 30). We recorded clinical demographics; measured respiratory mechanical parameters; collected serial peripheral blood specimens for measurement of plasma interleukin (IL)-6, IL-8, and IL-10; and followed patients prospectively for patient-centered outcomes. We conducted between-group comparisons with nonparametric tests and analyzed time-to-event outcomes with Kaplan-Meier and Cox proportional hazards models.Results: Patients with COVID-19 ARDS had higher body mass index and were more likely to be Black, or residents of skilled nursing facilities, compared with those with non-COVID-19 ARDS (P < 0.05). Patients with COVID-19 had lower delivered minute ventilation compared with bacterial and culture-negative ARDS (post hoc P < 0.01) but not compared with viral ARDS. We found no differences in static compliance, hypoxemic indices, or carbon dioxide clearance between groups. Patients with COVID-19 had lower IL-6 levels compared with bacterial and culture-negative ARDS at early time points after intubation but no differences in IL-6 levels compared with viral ARDS. Patients with COVID-19 had longer duration of mechanical ventilation but similar 60-day mortality in both unadjusted and adjusted analyses.Conclusions: COVID-19 ARDS bears several similarities to viral ARDS but demonstrates lower minute ventilation and lower systemic levels of IL-6 compared with bacterial and culture-negative ARDS. COVID-19 ARDS was associated with longer dependence on mechanical ventilation compared with non-COVID-19 ARDS. Such detectable differences of COVID-19 do not merit deviation from evidence-based management of ARDS but suggest priorities for clinical research to better characterize and treat this new clinical entity.
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Affiliation(s)
- William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Veterans Affairs Pittsburgh Health System, Pittsburgh, Pennsylvania
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- School of Medicine, Tsinghua University, Beijing, China
| | - Faraaz Ali Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Veterans Affairs Pittsburgh Health System, Pittsburgh, Pennsylvania
| | - Tomeka Suber
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Rebecca S. DeSensi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Nicole Bensen
- Department of Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Brian R. Rosborough
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Ashwin Somasundaram
- Division of Hematology-Oncology, Department of Medicine
- Tumor Microenvironment Center, and
- Department of Immunology and
| | - Creg J. Workman
- Tumor Microenvironment Center, and
- Department of Immunology and
| | | | | | - Carly Cardello
- Tumor Microenvironment Center, and
- Department of Immunology and
| | - Feng Shan
- Tumor Microenvironment Center, and
- Department of Immunology and
| | - Tullia C. Bruno
- Tumor Microenvironment Center, and
- Cancer Immunology and Immunotherapy Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania; and
- Department of Immunology and
| | - Dario A. A. Vignali
- Tumor Microenvironment Center, and
- Cancer Immunology and Immunotherapy Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania; and
- Department of Immunology and
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Department of Immunology and
| | - Anuradha Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Department of Immunology and
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Janet S. Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
- Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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9
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Cillo AR, Somasundaram A, Shan F, Cardello C, Workman CJ, Kitsios GD, Ruffin A, Kunning S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews L, Duprex WP, Joglekar AV, Benos PV, Ray P, Ray A, McVerry BJ, Zhang Y, Lee JS, Das J, Singh H, Morris A, Bruno TC, Vignali DAA. Bifurcated monocyte states are predictive of mortality in severe COVID-19. bioRxiv 2021:2021.02.10.430499. [PMID: 33594364 PMCID: PMC7885916 DOI: 10.1101/2021.02.10.430499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection presents with varied clinical manifestations1, ranging from mild symptoms to acute respiratory distress syndrome (ARDS) with high mortality2,3. Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in severe COVID-19. We performed high-dimensional cellular and molecular profiling of blood and respiratory samples from critically ill COVID-19 patients to define immune cell genomic states that are predictive of outcome in severe COVID-19 disease. Critically ill patients admitted to the intensive care unit (ICU) manifested increased frequencies of inflammatory monocytes and plasmablasts that were also associated with ARDS not due to COVID-19. Single-cell RNAseq (scRNAseq)-based deconvolution of genomic states of peripheral immune cells revealed distinct gene modules that were associated with COVID-19 outcome. Notably, monocytes exhibited bifurcated genomic states, with expression of a cytokine gene module exemplified by CCL4 (MIP-1β) associated with survival and an interferon signaling module associated with death. These gene modules were correlated with higher levels of MIP-1β and CXCL10 levels in plasma, respectively. Monocytes expressing genes reflective of these divergent modules were also detectable in endotracheal aspirates. Machine learning algorithms identified the distinctive monocyte modules as part of a multivariate peripheral immune system state that was predictive of COVID-19 mortality. Follow-up analysis of the monocyte modules on ICU day 5 was consistent with bifurcated states that correlated with distinct inflammatory cytokines. Our data suggests a pivotal role for monocytes and their specific inflammatory genomic states in contributing to mortality in life-threatening COVID-19 disease and may facilitate discovery of new diagnostics and therapeutics.
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Affiliation(s)
- Anthony R Cillo
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Ashwin Somasundaram
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Feng Shan
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Integrative Systems Biology (ISB) Graduate Program, University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Carly Cardello
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Creg J Workman
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Ayana Ruffin
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Sheryl Kunning
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Caleb Lampenfeld
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Sayali Onkar
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Stephanie Grebinoski
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Graduate Program of Microbiology and Immunology (PMI), University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA 15213, USA
| | - Gaurav Deshmukh
- Meso Scale Discovery, A division of Meso Scale Diagnostics, LLC, 1601 Research Boulevard, Rockville, MD 20850-3173, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Chang Liu
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence Andrews
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Panayiotis V Benos
- Department of Computer Science, University of Pittsburgh, 4200 Fifth Avenue, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anuradha Ray
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- University of Pittsburgh Asthma Institute at the University of Pittsburgh Medical Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Harinder Singh
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Center for Systems Immunology, Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Alison Morris
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15213, USA
| | - Tullia C Bruno
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Dario A A Vignali
- Department of Immunology, School of Medicine, University of Pittsburgh. Pittsburgh, PA 15260, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center. Pittsburgh, PA 15232, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
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