1
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Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J. Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans. JCI Insight 2023; 8:e164672. [PMID: 37856221 PMCID: PMC10721317 DOI: 10.1172/jci.insight.164672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
The development of human prenatal adaptive immunity progresses faster than previously appreciated, with the emergence of memory CD4+ T cells alongside regulatory T cells by midgestation. We previously identified a prenatal specific population of promyelocytic leukemia zinc finger-positive (PLZF+) CD4+ T cells with heightened effector potential that were enriched in the developing intestine and accumulated in the cord blood of infants exposed to prenatal inflammation. However, the signals that drive their tissue distribution and effector maturation are unknown. Here, we define the transcriptional and functional heterogeneity of human prenatal PLZF+CD4+ T cells and identify the compartmentalization of T helper-like (Th-like) effector function across the small intestine (SI) and mesenteric lymph nodes (MLNs). IL-7 was more abundant in the SI relative to the MLNs and drove the preferential expansion of naive PLZF+CD4+ T cells via enhanced STAT5 and MEK/ERK signaling. Exposure to IL-7 was sufficient to induce the acquisition of CD45RO expression and rapid effector function in a subset of PLZF+CD4+ T cells, identifying a human analog of memory phenotype CD4+ T cells. Further, IL-7 modulated the differentiation of Th1- and Th17-like PLZF+CD4+ T cells and thus likely contributes to the anatomic compartmentalization of human prenatal CD4+ T cell effector function.
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Affiliation(s)
- Veronica Locher
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Sara Park
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Daniel G. Bunis
- Bakar ImmunoX Initiative and
- CoLabs, UCSF, San Francisco, California, USA
| | - Stephanie Makredes
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Margareta Mayer
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Trevor D. Burt
- Division of Neonatology and the Children’s Health & Discovery Initiative, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gabriela K. Fragiadakis
- Bakar ImmunoX Initiative and
- CoLabs, UCSF, San Francisco, California, USA
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Joanna Halkias
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
- Bakar ImmunoX Initiative and
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2
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Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards AW, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron JL, Combes AJ, Fragiadakis GK. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Front Immunol 2023; 14:1167241. [PMID: 37731497 PMCID: PMC10507399 DOI: 10.3389/fimmu.2023.1167241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/04/2023] [Indexed: 09/22/2023] Open
Abstract
In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.
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Affiliation(s)
- Ravi K. Patel
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca G. Jaszczak
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Kwok Im
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas D. Carey
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Tristan Courau
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Daniel G. Bunis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Bushra Samad
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Lia Avanesyan
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
| | - Nayvin W. Chew
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Sarah Stenske
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Jillian M. Jespersen
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Jean Publicover
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Austin W. Edwards
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Mohammad Naser
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Arjun A. Rao
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Leonard Lupin-Jimenez
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Stewart Cooper
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
| | - Jody L. Baron
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
| | - Alexis J. Combes
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Gabriela K. Fragiadakis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
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3
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Clark IC, Mudvari P, Thaploo S, Smith S, Abu-Laban M, Hamouda M, Theberge M, Shah S, Ko SH, Pérez L, Bunis DG, Lee JS, Kilam D, Zakaria S, Choi S, Darko S, Henry AR, Wheeler MA, Hoh R, Butrus S, Deeks SG, Quintana FJ, Douek DC, Abate AR, Boritz EA. HIV silencing and cell survival signatures in infected T cell reservoirs. Nature 2023; 614:318-325. [PMID: 36599978 PMCID: PMC9908556 DOI: 10.1038/s41586-022-05556-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel Smith
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mohammad Abu-Laban
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Hamouda
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marc Theberge
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sakshi Shah
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Sung Hee Ko
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel G Bunis
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James S Lee
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Divya Kilam
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saami Zakaria
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sally Choi
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA.
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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4
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Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer’s Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Front Aging Neurosci 2022; 14:749991. [PMID: 35572130 PMCID: PMC9093608 DOI: 10.3389/fnagi.2022.749991] [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: 07/30/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s Disease (AD) is a complex neurodegenerative disease that gravely affects patients and imposes an immense burden on caregivers. Apolipoprotein E4 (APOE4) has been identified as the most common genetic risk factor for AD, yet the molecular mechanisms connecting APOE4 to AD are not well understood. Past transcriptomic analyses in AD have revealed APOE genotype-specific transcriptomic differences; however, these differences have not been explored at a single-cell level. To elucidate more complex APOE genotype-specific disease-relevant changes masked by the bulk analysis, we leverage the first two single-nucleus RNA sequencing AD datasets from human brain samples, including nearly 55,000 cells from the prefrontal and entorhinal cortices. In each brain region, we performed a case versus control APOE genotype-stratified differential gene expression analysis and pathway network enrichment in astrocytes, microglia, neurons, oligodendrocytes, and oligodendrocyte progenitor cells. We observed more global transcriptomic changes in APOE4 positive AD cells and identified differences across APOE genotypes primarily in glial cell types. Our findings highlight the differential transcriptomic perturbations of APOE isoforms at a single-cell level in AD pathogenesis and have implications for precision medicine development in the diagnosis and treatment of AD.
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Affiliation(s)
- Stella A. Belonwu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
| | - Arjun Arkal Rao
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Caroline Warly Solsberg
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Alice L. Taubes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Brian Grone
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Kelly A. Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Gabriela K. Fragiadakis
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Yadong Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Marina Sirota,
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5
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Bunis DG, Wang W, Vallvé-Juanico J, Houshdaran S, Sen S, Ben Soltane I, Kosti I, Vo KC, Irwin JC, Giudice LC, Sirota M. Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis. Front Immunol 2022; 12:788315. [PMID: 35069565 PMCID: PMC8766492 DOI: 10.3389/fimmu.2021.788315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be identified, as most studies have focused on bulk tissue or select cell populations. Herein, through integrating whole-tissue deconvolution and single-cell RNAseq, we comprehensively characterized immune and nonimmune cell types in the endometrium of women with or without disease and their dynamic changes across the menstrual cycle. We designed metrics to evaluate specificity of deconvolution signatures that resulted in single-cell identification of 13 novel signatures for immune cell subtypes in healthy endometrium. Guided by statistical metrics, we identified contributions of endometrial epithelial, endothelial, plasmacytoid dendritic cells, classical dendritic cells, monocytes, macrophages, and granulocytes to the endometrial pro-inflammatory phenotype, underscoring roles for nonimmune as well as immune cells to the dysfunctionality of this tissue.
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Affiliation(s)
- Daniel G Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Wanxin Wang
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Júlia Vallvé-Juanico
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Sahar Houshdaran
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Sushmita Sen
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Isam Ben Soltane
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Kim Chi Vo
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Juan C Irwin
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Linda C Giudice
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.,Department of Pediatrics, Division of Neonatology, University of California, San Francisco, San Francisco, CA, United States
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6
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Le BL, Andreoletti G, Oskotsky T, Vallejo-Gracia A, Rosales R, Yu K, Kosti I, Leon KE, Bunis DG, Li C, Kumar GR, White KM, García-Sastre A, Ott M, Sirota M. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. Sci Rep 2021; 11:12310. [PMID: 34112877 PMCID: PMC8192542 DOI: 10.1038/s41598-021-91625-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated 16 of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.
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Affiliation(s)
- Brian L Le
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Gaia Andreoletti
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Tomiko Oskotsky
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | | | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katharine Yu
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, UCSF, San Francisco, CA, USA
| | - Idit Kosti
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Kristoffer E Leon
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Daniel G Bunis
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, UCSF, San Francisco, CA, USA
| | - Christine Li
- Department of Pediatrics, UCSF, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Shanghai American School, Shanghai, China
| | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, UCSF, San Francisco, CA, USA
| | - Marina Sirota
- Department of Pediatrics, UCSF, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.
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7
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Le BL, Andreoletti G, Oskotsky T, Vallejo-Gracia A, Rosales R, Yu K, Kosti I, Leon KE, Bunis DG, Li C, Kumar GR, White KM, García-Sastre A, Ott M, Sirota M. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. Res Sq 2021:rs.3.rs-333578. [PMID: 33821262 PMCID: PMC8020993 DOI: 10.21203/rs.3.rs-333578/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated sixteen of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.
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Affiliation(s)
- Brian L. Le
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
| | - Gaia Andreoletti
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
| | - Tomiko Oskotsky
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
| | | | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katharine Yu
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
- Biomedical Sciences Graduate Program, UCSF, SF, CA, USA
| | - Idit Kosti
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
| | | | - Daniel G. Bunis
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
- Biomedical Sciences Graduate Program, UCSF, SF, CA, USA
| | - Christine Li
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
- Shanghai American School, Shanghai, China
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, SF, CA, USA
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, SF, CA, USA
- Department of Medicine, UCSF, SF, CA, USA
| | - Marina Sirota
- Department of Pediatrics, UCSF, SF, CA, USA
- Bakar Computational Health Sciences Institute, UCSF, SF, CA, USA
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Bunis DG, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. Cell Rep 2021; 34:108573. [PMID: 33406429 PMCID: PMC10263444 DOI: 10.1016/j.celrep.2020.108573] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Whereas the human fetal immune system is poised to generate immune tolerance and suppress inflammation in utero, an adult-like immune system emerges to orchestrate anti-pathogen immune responses in post-natal life. It has been posited that cells of the adult immune system arise as a discrete ontological "layer" of hematopoietic stem-progenitor cells (HSPCs) and their progeny; evidence supporting this model in humans has, however, been inconclusive. Here, we combine bulk and single-cell transcriptional profiling of lymphoid cells, myeloid cells, and HSPCs from fetal, perinatal, and adult developmental stages to demonstrate that the fetal-to-adult transition occurs progressively along a continuum of maturity-with a substantial degree of inter-individual variation at the time of birth-rather than via a transition between discrete waves. These findings have important implications for the design of strategies for prophylaxis against infection in the newborn and for the use of umbilical cord blood (UCB) in the setting of transplantation.
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Affiliation(s)
- Daniel G Bunis
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Yelena Bronevetsky
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elisabeth Krow-Lucal
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nirav R Bhakta
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles C Kim
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Srilaxmi Nerella
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Norman Jones
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ventura F Mendoza
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yvonne J Bryson
- Division of Pediatric Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Mattel Children's Hospital UCLA, Los Angeles, CA, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Rachel L Rutishauser
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA.
| | - Joseph M McCune
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Trevor D Burt
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA.
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9
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Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. Bioinformatics 2020; 36:5535-5536. [PMID: 33313640 PMCID: PMC8016464 DOI: 10.1093/bioinformatics/btaa1011] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use, and allows highly customizable generation of both daily-use and publication-quality figures. AVAILABILITY AND IMPLEMENTATION dittoSeq is an R package available through Bioconductor via an open source MIT license. SUPPLEMENTARY INFORMATION Supplementary Code and figures are available at Bioinformatics online. Full vignettes are available through Bioconductor, https://bioconductor.org/packages/dittoSeq/, and github, github.com/dtm2451/dittoSeq/.
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Affiliation(s)
- Daniel G Bunis
- San Francisco, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California, San Francisco, CA, USA.,Bakar Computational Health Sciences Institute University of California, San Francisco, San Francisco, CA, USA
| | - Jared Andrews
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gabriela K Fragiadakis
- Department of Medicine Division of Rheumatology, University of California, San Francisco, San Francisco, CA, USA
| | - Trevor D Burt
- San Francisco, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California, San Francisco, CA, USA.,Department of Pediatrics Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics, Division of Neonatology and the Children's Health and Discovery Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA
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Abstract
Over the last several years, next-generation sequencing and its recent push toward single-cell resolution have transformed the landscape of immunology research by revealing novel complexities about all components of the immune system. With the vast amounts of diverse data currently being generated, and with the methods of analyzing and combining diverse data improving as well, integrative systems approaches are becoming more powerful. Previous integrative approaches have combined multiple data types and revealed ways that the immune system, both as a whole and as individual parts, is affected by genetics, the microbiome, and other factors. In this review, we explore the data types that are available for studying immunology with an integrative systems approach, as well as the current strategies and challenges for conducting such analyses.
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, 28029 Madrid, Spain
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California 94158, USA
- Department of Pediatrics, University of California, San Francisco, California 94143, USA
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