1
|
Barrett J, Leysen S, Galmiche C, Al-Mossawi H, Bowness P, Edwards TE, Lawson AD. Chimeric antigens displaying GPR65 extracellular loops on a soluble scaffold enabled the discovery of antibodies, which recognized native receptor. Bioengineered 2024; 15:2299522. [PMID: 38184821 PMCID: PMC10773626 DOI: 10.1080/21655979.2023.2299522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024] Open
Abstract
GPR65 is a proton-sensing G-protein coupled receptor associated with multiple immune-mediated inflammatory diseases, whose function is relatively poorly understood. With few reagents commercially available to probe the biology of receptor, generation of an anti-GPR65 monoclonal antibody was desired. Using soluble chimeric scaffolds, such as ApoE3, displaying the extracellular loops of GPR65, together with established phage display technology, native GPR65 loop-specific antibodies were identified. Phage-derived loop-binding antibodies recognized the wild-type native receptor to which they had not previously been exposed, generating confidence in the use of chimeric soluble proteins to act as efficient surrogates for membrane protein extracellular loop antigens. This technique provides promise for the rational design of chimeric antigens in facilitating the discovery of specific antibodies to GPCRs.
Collapse
Affiliation(s)
- Janine Barrett
- UK Research Department, UCB Pharma, Slough, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | | | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | | |
Collapse
|
2
|
Schultheiß C, Paschold L, Mohebiany AN, Escher M, Kattimani YM, Müller M, Schmidt-Barbo P, Mensa-Vilaró A, Aróstegui JI, Boursier G, de Moreuil C, Hautala T, Willscher E, Jonas H, Chinchuluun N, Grosser B, Märkl B, Klapper W, Oommen PT, Gössling K, Hoffmann K, Tiegs G, Czernilofsky F, Dietrich S, Freeman A, Schwartz DM, Waisman A, Aksentijevich I, Binder M. A20 haploinsufficiency disturbs immune homeostasis and drives the transformation of lymphocytes with permissive antigen receptors. SCIENCE ADVANCES 2024; 10:eadl3975. [PMID: 39167656 DOI: 10.1126/sciadv.adl3975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 07/15/2024] [Indexed: 08/23/2024]
Abstract
Genetic TNFAIP3 (A20) inactivation is a classical somatic lymphoma lesion and the genomic trait in haploinsufficiency of A20 (HA20). In a cohort of 34 patients with HA20, we show that heterozygous TNFAIP3 loss skews immune repertoires toward lymphocytes with classical self-reactive antigen receptors typically found in B and T cell lymphomas. This skewing was mediated by a feed-forward tumor necrosis factor (TNF)/A20/nuclear factor κB (NF-κB) loop that shaped pre-lymphoma transcriptome signatures in clonally expanded B (CD81, BACH2, and NEAT1) or T (GATA3, TOX, and PDCD1) cells. The skewing was reversed by anti-TNF treatment but could also progress to overt lymphoma. Analysis of conditional TNFAIP3 knock-out mice reproduced the wiring of the TNF/A20/NF-κB signaling axis with permissive antigen receptors and suggested a distinct regulation in B and T cells. Together, patients with the genetic disorder HA20 provide an exceptional window into A20/TNF/NF-κB-mediated control of immune homeostasis and early steps of lymphomagenesis that remain clinically unrecognized.
Collapse
Affiliation(s)
- Christoph Schultheiß
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Lisa Paschold
- Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Alma Nazlie Mohebiany
- Institute for Molecular Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Moritz Escher
- Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Yogita Mallu Kattimani
- Institute for Molecular Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Melanie Müller
- Institute for Molecular Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Paul Schmidt-Barbo
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
- Collaborative Research Institute Intelligent Oncology (CRIION), Freiburg, Germany
| | - Anna Mensa-Vilaró
- Department of Immunology, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Juan Ignacio Aróstegui
- Department of Immunology, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, University of Barcelona, Barcelona, Spain
| | - Guilaine Boursier
- Department of molecular and cytogenomics, Rare and Autoinflammatory Diseases Laboratory, CHU Montpellier, IRMB, University of Montpellier, INSERM, CEREMAIA, Montpellier, France
| | - Claire de Moreuil
- Department of Internal Medicine, CHU Brest, Université de Bretagne Occidentale, Brest, France
| | - Timo Hautala
- Research Unit of Biomedicine, University of Oulu and Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Edith Willscher
- Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Hanna Jonas
- Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Namuun Chinchuluun
- Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Bianca Grosser
- Institute for Pathology, University Medical Center Augsburg, Augsburg, Germany
| | - Bruno Märkl
- Institute for Pathology, University Medical Center Augsburg, Augsburg, Germany
| | - Wolfram Klapper
- Institute of Pathology, Hematopathology Section, and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Prasad Thomas Oommen
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Center for Child and Adolescent Health, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katharina Gössling
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Center for Child and Adolescent Health, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Katrin Hoffmann
- Institute for Human Genetics and Molecular Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Gisa Tiegs
- Institute for Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Felix Czernilofsky
- Department of Medicine V, Hematology, Oncology, and Rheumatology, University of Heidelberg, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology, and Rheumatology, University of Heidelberg, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematolgy, Oncology, and Immunolgy, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Alexandra Freeman
- Laboratory of Clinical Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Daniella M Schwartz
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mascha Binder
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
- Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
- Collaborative Research Institute Intelligent Oncology (CRIION), Freiburg, Germany
| |
Collapse
|
3
|
Wang H, Torous W, Gong B, Purdom E. Visualizing scRNA-Seq Data at Population Scale with GloScope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.29.542786. [PMID: 37398321 PMCID: PMC10312527 DOI: 10.1101/2023.05.29.542786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism's phenotype. However, relatively few bioinformatic methods have been developed which adequately address the variation between samples for such population-level analyses. We propose a framework for representing the entire single-cell profile of a sample, which we call a GloScope representation. We implement GloScope on scRNA-Seq datasets from study designs ranging from 12 to over 300 samples and demonstrate how GloScope allows researchers to perform essential bioinformatic tasks at the sample-level, in particular visualization and quality control assessment.
Collapse
Affiliation(s)
- Hao Wang
- Division of Biostatistics, University of California, Berkeley, CA, USA
| | - William Torous
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Boying Gong
- Division of Biostatistics, University of California, Berkeley, CA, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| |
Collapse
|
4
|
García-Vega M, Llamas-Covarrubias MA, Loza M, Reséndiz-Sandoval M, Hinojosa-Trujillo D, Melgoza-González E, Valenzuela O, Mata-Haro V, Hernández-Oñate M, Soto-Gaxiola A, Chávez-Rueda K, Nakai K, Hernández J. Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19. J Med Virol 2024; 96:e29851. [PMID: 39132689 DOI: 10.1002/jmv.29851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Here, we performed single-cell RNA sequencing of S1 and receptor binding domain protein-specific B cells from convalescent COVID-19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pathway of atypical memory B cells (MBCs) in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The results revealed a proinflammatory signature across B cell subsets associated with disease severity, as evidenced by the upregulation of genes such as GADD45B, MAP3K8, and NFKBIA in critical and severe individuals. Furthermore, the analysis of atypical MBCs suggested a developmental pathway similar to that of conventional MBCs through germinal centers, as indicated by the expression of several genes involved in germinal center processes, including CXCR4, CXCR5, BCL2, and MYC. Additionally, the upregulation of genes characteristic of the immune response in COVID-19, such as ZFP36 and DUSP1, suggested that the differentiation and activation of atypical MBCs may be influenced by exposure to SARS-CoV-2 and that these genes may contribute to the immune response for COVID-19 recovery. Our study contributes to a better understanding of atypical MBCs in COVID-19 and the role of other B cell subsets across different clinical manifestations.
Collapse
Affiliation(s)
- Melissa García-Vega
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | | | - Martin Loza
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mónica Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Diana Hinojosa-Trujillo
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Edgar Melgoza-González
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Olivia Valenzuela
- Departamento de Ciencias Químico Biológicas, División de Ciencias Biológicas y de la Salud, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Verónica Mata-Haro
- Laboratorio de Microbiología e Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Miguel Hernández-Oñate
- CONAHCYT-Laboratorio de Fisiología y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Alan Soto-Gaxiola
- Hospital General del Estado de Sonora "Dr. Ernesto Ramos Bours", Secretaria de Salud del Estado de Sonora, Hermosillo, Sonora, Mexico
| | - Karina Chávez-Rueda
- Unidad de Investigación Médica en Inmunología, UMAE, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| |
Collapse
|
5
|
Yang X, Mann KK, Wu H, Ding J. scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration. Genome Biol 2024; 25:198. [PMID: 39075536 PMCID: PMC11285326 DOI: 10.1186/s13059-024-03338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or clarity of established transcriptomics. Coupled with data scarcity for less established modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross, a tool leveraging variational autoencoders, generative adversarial networks, and the mutual nearest neighbors (MNN) technique for modality alignment. By enabling single-cell cross-modal data generation, multi-omics data simulation, and in silico cellular perturbations, scCross enhances the utility of single-cell multi-omics studies.
Collapse
Affiliation(s)
- Xiuhui Yang
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Koren K Mann
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Hao Wu
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China.
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada.
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Mila-Quebec AI Institute, Montreal, QC, H2S 3H1, Canada.
| |
Collapse
|
6
|
Missarova A, Dann E, Rosen L, Satija R, Marioni J. Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biol 2024; 25:189. [PMID: 39026254 PMCID: PMC11256449 DOI: 10.1186/s13059-024-03334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
Collapse
Affiliation(s)
- Alsu Missarova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leah Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rahul Satija
- Center for Genomics and Systems Biology, NYU, New York, USA.
- New York Genome Center, New York, USA.
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
7
|
Wang J, Fonseca GJ, Ding J. scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning. Nat Commun 2024; 15:5989. [PMID: 39013867 PMCID: PMC11252419 DOI: 10.1038/s41467-024-50150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its application in expansive biomedical studies. Traditional cellular deconvolution approaches can infer cell type proportions from more affordable bulk sequencing data, yet they fall short in providing the detailed resolution required for single-cell-level analyses. To overcome this challenge, we introduce "scSemiProfiler", an innovative computational framework that marries deep generative models with active learning strategies. This method adeptly infers single-cell profiles across large cohorts by fusing bulk sequencing data with targeted single-cell sequencing from a few rigorously chosen representatives. Extensive validation across heterogeneous datasets verifies the precision of our semi-profiling approach, aligning closely with true single-cell profiling data and empowering refined cellular analyses. Originally developed for extensive disease cohorts, "scSemiProfiler" is adaptable for broad applications. It provides a scalable, cost-effective solution for single-cell profiling, facilitating in-depth cellular investigation in various biological domains.
Collapse
Affiliation(s)
- Jingtao Wang
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
| | - Gregory J Fonseca
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada
| | - Jun Ding
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada.
- School of Computer Science, McGill University, 3480 Rue University, Montreal, H3A 2A7, Quebec, Canada.
- Mila-Quebec AI Institute, 6666 Rue Saint-Urbain, Montreal, H2S 3H1, Quebec, Canada.
| |
Collapse
|
8
|
Ren L, Liu Y, Wang Y, Wu C, Guo L, Chen L, Wang X, Xiao Y, Huang L, Zhong J, Yao J, Liu L, Li H, Wang Y, Ma Y, Zhang Y, Di L, Dong T, Knight J, Wang J, Huang Y, Cao B, Ren X, Wang J. Longitudinal landscape of immune reconstitution after acute SARS-CoV-2 infection at single-cell resolution. Sci Bull (Beijing) 2024:S2095-9273(24)00488-2. [PMID: 39107149 DOI: 10.1016/j.scib.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/16/2024] [Accepted: 07/04/2024] [Indexed: 08/09/2024]
Affiliation(s)
- Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China.
| | - Yiwei Liu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yeming Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Chao Wu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lixue Huang
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingchuan Zhong
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Jiacheng Yao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lu Liu
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Li
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yongchao Ma
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yichunzi Zhang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Lin Di
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford OX3 9DS, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 9DS, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 9DS, UK
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology (ICSB), Tsinghua University, Beijing 100084, China; Chinese Institute for Brain Research (CIBR), Beijing 102206, China.
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518107, China.
| | - Bin Cao
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| |
Collapse
|
9
|
Tuong ZK, van der Merwe R, Canete PF, Roco JA. Computational estimation of clonal diversity in autoimmunity. Immunol Cell Biol 2024. [PMID: 39010261 DOI: 10.1111/imcb.12801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024]
Abstract
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single-cell T-cell receptor and B-cell receptor sequencing. We also discuss two case studies where single-cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
Collapse
Affiliation(s)
- Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rohan van der Merwe
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Canete
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
- Clinical Hub for Interventional Research, College of Health & Medicine, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
10
|
Pavlou A, Mulenge F, Gern OL, Busker LM, Greimel E, Waltl I, Kalinke U. Orchestration of antiviral responses within the infected central nervous system. Cell Mol Immunol 2024:10.1038/s41423-024-01181-7. [PMID: 38997413 DOI: 10.1038/s41423-024-01181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 07/14/2024] Open
Abstract
Many newly emerging and re-emerging viruses have neuroinvasive potential, underscoring viral encephalitis as a global research priority. Upon entry of the virus into the CNS, severe neurological life-threatening conditions may manifest that are associated with high morbidity and mortality. The currently available therapeutic arsenal against viral encephalitis is rather limited, emphasizing the need to better understand the conditions of local antiviral immunity within the infected CNS. In this review, we discuss new insights into the pathophysiology of viral encephalitis, with a focus on myeloid cells and CD8+ T cells, which critically contribute to protection against viral CNS infection. By illuminating the prerequisites of myeloid and T cell activation, discussing new discoveries regarding their transcriptional signatures, and dissecting the mechanisms of their recruitment to sites of viral replication within the CNS, we aim to further delineate the complexity of antiviral responses within the infected CNS. Moreover, we summarize the current knowledge in the field of virus infection and neurodegeneration and discuss the potential links of some neurotropic viruses with certain pathological hallmarks observed in neurodegeneration.
Collapse
Affiliation(s)
- Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
| | - Felix Mulenge
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
| | - Olivia Luise Gern
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
| | - Lena Mareike Busker
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany
| | - Elisabeth Greimel
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625, Hannover, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany.
| |
Collapse
|
11
|
Zheng Y, Caron DP, Kim JY, Jun SH, Tian Y, Florian M, Stuart KD, Sims PA, Gottardo R. ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets. RESEARCH SQUARE 2024:rs.3.rs-4572811. [PMID: 39041028 PMCID: PMC11261982 DOI: 10.21203/rs.3.rs-4572811/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
CITE-seq enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. Due to the high copy number of surface protein molecules, sequencing antibody-derived tags (ADTs) allows for robust protein detection, improving cell-type identification. However, variability in antibody staining leads to batch effects in the ADT expression, obscuring biological variation, reducing interpretability, and obstructing cross-study analyses. Here, we present ADTnorm (https://github.com/yezhengSTAT/ADTnorm), a normalization and integration method designed explicitly for ADT abundance. Benchmarking against 14 existing scaling and normalization methods, we show that ADTnorm accurately aligns populations with negative- and positive-expression of surface protein markers across 13 public datasets, effectively removing technical variation across batches and improving cell-type separation. ADTnorm enables efficient integration of public CITE-seq datasets, each with unique experimental designs, paving the way for atlas-level analyses. Beyond normalization, ADTnorm includes built-in utilities to aid in automated threshold-gating as well as assessment of antibody staining quality for titration optimization and antibody panel selection. Applying ADTnorm to a published COVID-19 CITE-seq dataset allowed for identifying previously undetected disease-associated markers, illustrating a broad utility in biological applications.
Collapse
Affiliation(s)
- Ye Zheng
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daniel P. Caron
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Ju Yeong Kim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Seong-Hwan Jun
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yuan Tian
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mair Florian
- Department of Biology, ETH Zürich, Zürich 8093, Switzerland
| | - Kenneth D. Stuart
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Peter A. Sims
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne 1005, Switzerland
| |
Collapse
|
12
|
Agamah FE, Ederveen THA, Skelton M, Martin DP, Chimusa ER, ’t Hoen PAC. Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases. Front Mol Biosci 2024; 11:1393240. [PMID: 39040605 PMCID: PMC11260748 DOI: 10.3389/fmolb.2024.1393240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/24/2024] Open
Abstract
Background COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. Aim To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. Method We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Results Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state. Conclusion This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.
Collapse
Affiliation(s)
- Francis E. Agamah
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Science, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| |
Collapse
|
13
|
Gong Q, Fu M, Wang J, Zhao S, Wang H. Potential Immune-Inflammatory Proteome Biomarkers for Guiding the Treatment of Patients with Primary Acute Angle-Closure Glaucoma Caused by COVID-19. J Proteome Res 2024; 23:2587-2597. [PMID: 38836775 PMCID: PMC11232099 DOI: 10.1021/acs.jproteome.4c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Primary acute angle-closure glaucoma (PAACG) is a sight-threatening condition that can lead to blindness. With the increasing incidence of COVID-19, a multitude of people are experiencing acute vision loss and severe swelling of the eyes and head. These patients were then diagnosed with acute angle closure, with or without a history of PACG. However, the mechanism by which viral infection causes PACG has not been clarified. This is the first study to explore the specific inflammatory proteomic landscape in SARS-CoV-2-induced PAACG. The expression of 92 inflammation-related proteins in 19 aqueous humor samples from PAACGs or cataract patients was detected using the Olink Target 96 Inflammation Panel based on a highly sensitive and specific proximity extension assay technology. The results showed that 76 proteins were significantly more abundant in the PAACG group than in the cataract group. Notably, the top eight differentially expressed proteins were IL-8, MCP-1, TNFRSF9, DNER, CCL4, Flt3L, CXCL10, and CD40. Generally, immune markers are related to inflammation, macrophage activation, and viral infection, revealing the crucial role of macrophages in the occurrence of PAACGs caused by SARS-CoV-2.
Collapse
Affiliation(s)
- Qiaoyun Gong
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Mingshui Fu
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Jingyi Wang
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Shuzhi Zhao
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Haiyan Wang
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| |
Collapse
|
14
|
Drost F, An Y, Bonafonte-Pardàs I, Dratva LM, Lindeboom RGH, Haniffa M, Teichmann SA, Theis F, Lotfollahi M, Schubert B. Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nat Commun 2024; 15:5577. [PMID: 38956082 PMCID: PMC11220149 DOI: 10.1038/s41467-024-49806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advances in single-cell immune profiling have enabled the simultaneous measurement of transcriptome and T cell receptor (TCR) sequences, offering great potential for studying immune responses at the cellular level. However, integrating these diverse modalities across datasets is challenging due to their unique data characteristics and technical variations. Here, to address this, we develop the multimodal generative model mvTCR to fuse modality-specific information across transcriptome and TCR into a shared representation. Our analysis demonstrates the added value of multimodal over unimodal approaches to capture antigen specificity. Notably, we use mvTCR to distinguish T cell subpopulations binding to SARS-CoV-2 antigens from bystander cells. Furthermore, when combined with reference mapping approaches, mvTCR can map newly generated datasets to extensive T cell references, facilitating knowledge transfer. In summary, we envision mvTCR to enable a scalable analysis of multimodal immune profiling data and advance our understanding of immune responses.
Collapse
Affiliation(s)
- Felix Drost
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Yang An
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Irene Bonafonte-Pardàs
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rik G H Lindeboom
- The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge, UK
| | - Fabian Theis
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Mohammad Lotfollahi
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Benjamin Schubert
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany.
| |
Collapse
|
15
|
Otto DJ, Jordan C, Dury B, Dien C, Setty M. Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon. Nat Methods 2024; 21:1185-1195. [PMID: 38890426 DOI: 10.1038/s41592-024-02302-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Cell-state density characterizes the distribution of cells along phenotypic landscapes and is crucial for unraveling the mechanisms that drive diverse biological processes. Here, we present Mellon, an algorithm for estimation of cell-state densities from high-dimensional representations of single-cell data. We demonstrate Mellon's efficacy by dissecting the density landscape of differentiating systems, revealing a consistent pattern of high-density regions corresponding to major cell types intertwined with low-density, rare transitory states. We present evidence implicating enhancer priming and the activation of master regulators in emergence of these transitory states. Mellon offers the flexibility to perform temporal interpolation of time-series data, providing a detailed view of cell-state dynamics during developmental processes. Mellon facilitates density estimation across various single-cell data modalities, scaling linearly with the number of cells. Our work underscores the importance of cell-state density in understanding the differentiation processes, and the potential of Mellon to provide insights into mechanisms guiding biological trajectories.
Collapse
Affiliation(s)
- Dominik J Otto
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cailin Jordan
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Brennan Dury
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christine Dien
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
16
|
Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature 2024; 631:189-198. [PMID: 38898278 PMCID: PMC11222146 DOI: 10.1038/s41586-024-07575-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection.
Collapse
Affiliation(s)
- Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - David Scobie
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Helen R Wagstaffe
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | | | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Microbiology, Faculty of Science, and Integrative Computational BioScience Center, Mahidol University, Bangkok, Thailand
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Ensocell Therapeutics, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rakesh Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ben Killingley
- Department of Infectious Diseases, University College London Hospital, London, UK
| | | | | | | | | | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Samuel Ellis
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Robert Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Andreas Mayer
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
17
|
Wei X, Ma W, Wu Z, Wu H. Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq. RESEARCH SQUARE 2024:rs.3.rs-4559348. [PMID: 38978578 PMCID: PMC11230472 DOI: 10.21203/rs.3.rs-4559348/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cell-type identification is the most crucial step in single cell RNA-seq (scRNA-seq) data analysis, for which the supervised cell-type identification method is a desired solution due to the accuracy and efficiency. The performance of such methods is highly dependent on the quality of the reference data. Even though there are many supervised cell-type identification tools, there is no method for selecting and constructing reference data. Here we develop Target-Oriented Reference Construction (TORC), a widely applicable strategy for constructing reference given target dataset in scRNA-seq supervised cell-type identification. TORC alleviates the differences in data distribution and cell-type composition between reference and target. Extensive benchmarks on simulated and real data analyses demonstrate consistent improvements in cell-type identification from TORC. TORC is freely available at https://github.com/weix21/TORC.
Collapse
Affiliation(s)
| | | | | | - Hao Wu
- Shenzhen University of Advanced Technology
| |
Collapse
|
18
|
Zhou M, Zhang H, Bai Z, Mann-Krzisnik D, Wang F, Li Y. Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique. STAR Protoc 2024; 5:103066. [PMID: 38748882 PMCID: PMC11109308 DOI: 10.1016/j.xpro.2024.103066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/21/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.
Collapse
Affiliation(s)
- Manqi Zhou
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA; Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hao Zhang
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zilong Bai
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA; Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Fei Wang
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA; Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yue Li
- Quantitative Life Science, McGill University, Montréal, QC H3A 0G4, Canada; School of Computer Science, McGill University, Montréal, QC H3A 0G4, Canada; Mila - Quebec AI Institute, Montréal, QC H2S 3H1, Canada.
| |
Collapse
|
19
|
Murphy SL, Balzer NR, Ranheim T, Sagen EL, Huse C, Bjerkeli V, Michelsen AE, Finbråten AK, Heggelund L, Dyrhol-Riise AM, Tveita A, Holten AR, Trøseid M, Ueland T, Ulas T, Aukrust P, Barratt-Due A, Halvorsen B, Dahl TB. Extracellular matrix remodelling pathway in peripheral blood mononuclear cells from severe COVID-19 patients: an explorative study. Front Immunol 2024; 15:1379570. [PMID: 38957465 PMCID: PMC11217192 DOI: 10.3389/fimmu.2024.1379570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
There is a reciprocal relationship between extracellular matrix (ECM) remodelling and inflammation that could be operating in the progression of severe COVID-19. To explore the immune-driven ECM remodelling in COVID-19, we in this explorative study analysed these interactions in hospitalised COVID-19 patients. RNA sequencing and flow analysis were performed on peripheral blood mononuclear cells. Inflammatory mediators in plasma were measured by ELISA and MSD, and clinical information from hospitalised COVID-19 patients (N=15) at admission was included in the analysis. Further, we reanalysed two publicly available datasets: (1) lung tissue RNA-sequencing dataset (N=5) and (2) proteomics dataset from PBCM. ECM remodelling pathways were enriched in PBMC from COVID-19 patients compared to healthy controls. Patients treated at the intensive care unit (ICU) expressed distinct ECM remodelling gene profiles compared to patients in the hospital ward. Several markers were strongly correlated to immune cell subsets, and the dysregulation in the ICU patients was positively associated with plasma levels of inflammatory cytokines and negatively associated with B-cell activating factors. Finally, our analysis of publicly accessible datasets revealed (i) an augmented ECM remodelling signature in inflamed lung tissue compared to non-inflamed tissue and (ii) proteomics analysis of PBMC from severe COVID-19 patients demonstrated an up-regulation in an ECM remodelling pathway. Our results may suggest the presence of an interaction between ECM remodelling, inflammation, and immune cells, potentially initiating or perpetuating pulmonary pathology in severe COVID-19.
Collapse
Affiliation(s)
- Sarah Louise Murphy
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nora Reka Balzer
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Trine Ranheim
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ellen Lund Sagen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Camilla Huse
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Vigdis Bjerkeli
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Annika E. Michelsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Lars Heggelund
- Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Anne Ma Dyrhol-Riise
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Infectious Diseases, Oslo University Hospital Ullevål, Oslo, Norway
| | - Anders Tveita
- Department of Internal Medicine, Bærum Hospital, Vestre Viken Hospital Trust, Gjettum, Norway
- Division of Laboratory Medicine, Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Aleksander Rygh Holten
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Acute Medicine, Oslo University Hospital, Oslo, Norway
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Thrombosis Research Center (TREC), Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Thomas Ulas
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andreas Barratt-Due
- Division of Laboratory Medicine, Department of Immunology, Oslo University Hospital, Oslo, Norway
- Department of Anesthesia and Intensive Care Medicine, Oslo University Hospital, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| |
Collapse
|
20
|
Hopkins G, Gomez N, Tucis D, Bartlett L, Steers G, Burns E, Brown M, Harvey-Cowlishaw T, Santos R, Lauder SN, Scurr M, Capitani L, Burnell S, Rees T, Smart K, Somerville M, Gallimore A, Perera M, Potts M, Metaxaki M, Krishna B, Jackson H, Tighe P, Onion D, Godkin A, Wills M, Fairclough L. Lower Humoral and Cellular Immunity Following Asymptomatic SARS-CoV-2 Infection Compared to Symptomatic Infection in Education (The ACE Cohort). J Clin Immunol 2024; 44:147. [PMID: 38856804 PMCID: PMC11164737 DOI: 10.1007/s10875-024-01739-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/20/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE Asymptomatic SARS-CoV-2 infections were widely reported during the COVID-19 pandemic, acting as a hidden source of infection. Many existing studies investigating asymptomatic immunity failed to recruit true asymptomatic individuals. Thus, we conducted a longitudinal cohort study to evaluate humoral- and cell-mediated responses to infection and vaccination in well-defined asymptomatic young adults (the Asymptomatic COVID-19 in Education [ACE] cohort). METHODS Asymptomatic testing services located at three UK universities identified asymptomatic young adults who were subsequently recruited with age- and sex-matched symptomatic and uninfected controls. Blood and saliva samples were collected after SARS-CoV-2 Wuhan infection, and again after vaccination. 51 participant's anti-spike antibody titres, neutralizing antibodies, and spike-specific T-cell responses were measured, against both Wuhan and Omicron B.1.1.529.1. RESULTS Asymptomatic participants exhibited reduced Wuhan-specific neutralization antibodies pre- and post-vaccination, as well as fewer Omicron-specific neutralization antibodies post-vaccination, compared to symptomatic participants. Lower Wuhan and Omicron-specific IgG titres in asymptomatic individuals were also observed pre- and post-vaccination, compared to symptomatic participants. There were no differences in salivary IgA levels. Conventional flow cytometry analysis and multi-dimensional clustering analysis indicated unvaccinated asymptomatic participants had significantly fewer Wuhan-specific IL-2 secreting CD4+ CD45RA+ T cells and activated CD8+ T cells than symptomatic participants, though these differences dissipated after vaccination. CONCLUSIONS Asymptomatic infection results in decreased antibody and T cell responses to further exposure to SARS-CoV-2 variants, compared to symptomatic infection. Post-vaccination, antibody responses are still inferior, but T cell immunity increases to match symptomatic subjects, emphasising the importance of vaccination to help protect asymptomatic individuals against future variants.
Collapse
Affiliation(s)
- Georgina Hopkins
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nancy Gomez
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Davis Tucis
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Laura Bartlett
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Graham Steers
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ellie Burns
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michaela Brown
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Rute Santos
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Martin Scurr
- School of Medicine, Cardiff University, Cardiff, UK
- ImmunoServ Ltd, Cardiff, UK
| | | | | | - Tara Rees
- School of Medicine, Cardiff University, Cardiff, UK
| | | | | | | | - Marianne Perera
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Potts
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marina Metaxaki
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Hannah Jackson
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paddy Tighe
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - David Onion
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Andrew Godkin
- School of Medicine, Cardiff University, Cardiff, UK
- ImmunoServ Ltd, Cardiff, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lucy Fairclough
- School of Life Sciences, University of Nottingham, Nottingham, UK.
| |
Collapse
|
21
|
Haviv D, Kunes RZ, Dougherty T, Burdziak C, Nawy T, Gilbert A, Pe'er D. Wasserstein Wormhole: Scalable Optimal Transport Distance with Transformers. ARXIV 2024:arXiv:2404.09411v4. [PMID: 38827453 PMCID: PMC11142316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Optimal transport (OT) and the related Wasserstein metric ( W ) are powerful and ubiquitous tools for comparing distributions. However, computing pairwise Wasserstein distances rapidly becomes intractable as cohort size grows. An attractive alternative would be to find an embedding space in which pairwise Euclidean distances map to OT distances, akin to standard multidimensional scaling (MDS). We present Wasserstein Wormhole, a transformer-based autoencoder that embeds empirical distributions into a latent space wherein Euclidean distances approximate OT distances. Extending MDS theory, we show that our objective function implies a bound on the error incurred when embedding non-Euclidean distances. Empirically, distances between Wormhole embeddings closely match Wasserstein distances, enabling linear time computation of OT distances. Along with an encoder that maps distributions to embeddings, Wasserstein Wormhole includes a decoder that maps embeddings back to distributions, allowing for operations in the embedding space to generalize to OT spaces, such as Wasserstein barycenter estimation and OT interpolation. By lending scalability and interpretability to OT approaches, Wasserstein Wormhole unlocks new avenues for data analysis in the fields of computational geometry and single-cell biology. Software is available at http://wassersteinwormhole.readthedocs.io/en/latest/.
Collapse
Affiliation(s)
- Doron Haviv
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine
| | - Russell Zhang Kunes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Department of Statistics, Columbia University
| | - Thomas Dougherty
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine
| | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Anna Gilbert
- Department of Mathematics and Statistics, Yale University
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Howard Hughes Medical Institute
| |
Collapse
|
22
|
Menéndez R, Méndez R, González-Jiménez P, Latorre A, Reyes S, Zalacain R, Ruiz LA, Serrano L, España PP, Uranga A, Cillóniz C, Gaetano-Gil A, Fernández-Félix BM, Pérez-de-Llano L, Golpe R, Torres A. Basic host response parameters to classify mortality risk in COVID-19 and community-acquired pneumonia. Sci Rep 2024; 14:12726. [PMID: 38830925 PMCID: PMC11148180 DOI: 10.1038/s41598-024-62718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Improved phenotyping in pneumonia is necessary to strengthen risk assessment. Via a feasible and multidimensional approach with basic parameters, we aimed to evaluate the effect of host response at admission on severity stratification in COVID-19 and community-acquired pneumonia (CAP). Three COVID-19 and one CAP multicenter cohorts including hospitalized patients were recruited. Three easily available variables reflecting different pathophysiologic mechanisms-immune, inflammation, and respiratory-were selected (absolute lymphocyte count [ALC], C-reactive protein [CRP] and, SpO2/FiO2). In-hospital mortality and intensive care unit (ICU) admission were analyzed as outcomes. A multivariable, penalized maximum likelihood logistic regression was performed with ALC (< 724 lymphocytes/mm3), CRP (> 60 mg/L), and, SpO2/FiO2 (< 450). A total of 1452, 1222 and 462 patients were included in the three COVID-19 and 1292 in the CAP cohort for the analysis. Mortality ranged between 4 and 32% (0 to 3 abnormal biomarkers) and 0-9% in SARS-CoV-2 pneumonia and CAP, respectively. In the first COVID-19 cohort, adjusted for age and sex, we observed an increased odds ratio for in-hospital mortality in COVID-19 with elevated biomarkers altered (OR 1.8, 3, and 6.3 with 1, 2, and 3 abnormal biomarkers, respectively). The model had an AUROC of 0.83. Comparable findings were found for ICU admission, with an AUROC of 0.76. These results were confirmed in the other COVID-19 cohorts Similar OR trends were reported in the CAP cohort; however, results were not statistically significant. Assessing the host response via accessible biomarkers is a simple and rapidly applicable approach for pneumonia.
Collapse
Affiliation(s)
- Rosario Menéndez
- Pneumology Department, La Fe University and Polytechnic Hospital, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Respiratory Infections, Health Research Institute La Fe (IISLAFE), Valencia, Spain
- University of Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Raúl Méndez
- Pneumology Department, La Fe University and Polytechnic Hospital, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain.
- Respiratory Infections, Health Research Institute La Fe (IISLAFE), Valencia, Spain.
- University of Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
| | - Paula González-Jiménez
- Pneumology Department, La Fe University and Polytechnic Hospital, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Respiratory Infections, Health Research Institute La Fe (IISLAFE), Valencia, Spain
- University of Valencia, Valencia, Spain
| | - Ana Latorre
- Respiratory Infections, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Soledad Reyes
- Pneumology Department, La Fe University and Polytechnic Hospital, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Respiratory Infections, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Rafael Zalacain
- Pneumology Department, Cruces University Hospital, Barakaldo, Spain
| | - Luis A Ruiz
- Pneumology Department, Cruces University Hospital, Barakaldo, Spain
- Department of Immunology, Microbiology and Parasitology, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Leioa, Spain
| | - Leyre Serrano
- Pneumology Department, Cruces University Hospital, Barakaldo, Spain
- Department of Immunology, Microbiology and Parasitology, Facultad de Medicina y Enfermería, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Leioa, Spain
| | - Pedro P España
- Pneumology Department, Galdakao-Usansolo Hospital, Galdacano, Spain
| | - Ane Uranga
- Pneumology Department, Galdakao-Usansolo Hospital, Galdacano, Spain
| | - Catia Cillóniz
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- University of Barcelona, Barcelona, Spain
- Pneumology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Andrea Gaetano-Gil
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Borja M Fernández-Félix
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Rafael Golpe
- Pneumology Department, Lucus Augusti University Hospital, Lugo, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- University of Barcelona, Barcelona, Spain
- Pneumology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| |
Collapse
|
23
|
Li X, Mara AB, Musial SC, Kolling FW, Gibbings SL, Gerebtsov N, Jakubzick CV. Coordinated chemokine expression defines macrophage subsets across tissues. Nat Immunol 2024; 25:1110-1122. [PMID: 38698086 DOI: 10.1038/s41590-024-01826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
Lung-resident macrophages, which include alveolar macrophages and interstitial macrophages (IMs), exhibit a high degree of diversity, generally attributed to different activation states, and often complicated by the influx of monocytes into the pool of tissue-resident macrophages. To gain a deeper insight into the functional diversity of IMs, here we perform comprehensive transcriptional profiling of resident IMs and reveal ten distinct chemokine-expressing IM subsets at steady state and during inflammation. Similar IM subsets that exhibited coordinated chemokine signatures and differentially expressed genes were observed across various tissues and species, indicating conserved specialized functional roles. Other macrophage types shared specific IM chemokine profiles, while also presenting their own unique chemokine signatures. Depletion of CD206hi IMs in Pf4creR26EYFP+DTR and Pf4creR26EYFPCx3cr1DTR mice led to diminished inflammatory cell recruitment, reduced tertiary lymphoid structure formation and fewer germinal center B cells in models of allergen- and infection-driven inflammation. These observations highlight the specialized roles of IMs, defined by their coordinated chemokine production, in regulating immune cell influx and organizing tertiary lymphoid tissue architecture.
Collapse
Affiliation(s)
- Xin Li
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Arlind B Mara
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Shawn C Musial
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | | | - Nikita Gerebtsov
- Lab for Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Claudia V Jakubzick
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA.
| |
Collapse
|
24
|
Qiu X, Nair MG, Jaroszewski L, Godzik A. Deciphering Abnormal Platelet Subpopulations in COVID-19, Sepsis and Systemic Lupus Erythematosus through Machine Learning and Single-Cell Transcriptomics. Int J Mol Sci 2024; 25:5941. [PMID: 38892129 PMCID: PMC11173046 DOI: 10.3390/ijms25115941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
This study focuses on understanding the transcriptional heterogeneity of activated platelets and its impact on diseases such as sepsis, COVID-19, and systemic lupus erythematosus (SLE). Recognizing the limited knowledge in this area, our research aims to dissect the complex transcriptional profiles of activated platelets to aid in developing targeted therapies for abnormal and pathogenic platelet subtypes. We analyzed single-cell transcriptional profiles from 47,977 platelets derived from 413 samples of patients with these diseases, utilizing Deep Neural Network (DNN) and eXtreme Gradient Boosting (XGB) to distinguish transcriptomic signatures predictive of fatal or survival outcomes. Our approach included source data annotations and platelet markers, along with SingleR and Seurat for comprehensive profiling. Additionally, we employed Uniform Manifold Approximation and Projection (UMAP) for effective dimensionality reduction and visualization, aiding in the identification of various platelet subtypes and their relation to disease severity and patient outcomes. Our results highlighted distinct platelet subpopulations that correlate with disease severity, revealing that changes in platelet transcription patterns can intensify endotheliopathy, increasing the risk of coagulation in fatal cases. Moreover, these changes may impact lymphocyte function, indicating a more extensive role for platelets in inflammatory and immune responses. This study identifies crucial biomarkers of platelet heterogeneity in serious health conditions, paving the way for innovative therapeutic approaches targeting platelet activation, which could improve patient outcomes in diseases characterized by altered platelet function.
Collapse
Affiliation(s)
| | | | | | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA 92521, USA; (X.Q.); (M.G.N.); (L.J.)
| |
Collapse
|
25
|
Liu C, Xu S, Zheng Y, Xie Y, Xu K, Chai Y, Luo T, Dai L, Gao GF. Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses. Cell Rep 2024; 43:114235. [PMID: 38748880 DOI: 10.1016/j.celrep.2024.114235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Nanoparticle vaccines displaying mosaic receptor-binding domains (RBDs) or spike (S) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or other sarbecoviruses are used in preparedness against potential zoonotic outbreaks. Here, we describe a self-assembling nanoparticle using lumazine synthase (LuS) as the scaffold to display RBDs from different sarbecoviruses. Mosaic nanoparticles induce sarbecovirus cross-neutralizing antibodies comparable to a nanoparticle cocktail. We find mosaic nanoparticles elicit a B cell receptor repertoire using an immunodominant germline gene pair of IGHV14-3:IGKV14-111. Most of the tested IGHV14-3:IGKV14-111 monoclonal antibodies (mAbs) are broadly cross-reactive to clade 1a, 1b, and 3 sarbecoviruses. Using mAb competition and cryo-electron microscopy, we determine that a representative IGHV14-3:IGKV14-111 mAb, M2-7, binds to a conserved epitope on the RBD, largely overlapping with the pan-sarbecovirus mAb S2H97. This suggests mosaic nanoparticles expand B cell recognition of the common epitopes shared by different clades of sarbecoviruses. These results provide immunological insights into the cross-reactive responses elicited by mosaic nanoparticles against sarbecoviruses.
Collapse
Affiliation(s)
- Chuanyu Liu
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Senyu Xu
- Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxuan Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufeng Xie
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kun Xu
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingrong Luo
- College of Animal Science and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
26
|
Hu WT, Kaluzova M, Dawson A, Sotelo V, Papas J, Lemenze A, Shu C, Jomartin M, Nayyar A, Hussain S. Clinical and CSF single-cell profiling of post-COVID-19 cognitive impairment. Cell Rep Med 2024; 5:101561. [PMID: 38744274 PMCID: PMC11148803 DOI: 10.1016/j.xcrm.2024.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Natural history and mechanisms for persistent cognitive symptoms ("brain fog") following acute and often mild COVID-19 are unknown. In a large prospective cohort of people who underwent testing a median of 9 months after acute COVID-19 in the New York City/New Jersey area, we found that cognitive dysfunction is common; is not influenced by mood, fatigue, or sleepiness; and is correlated with MRI changes in very few people. In a subgroup that underwent cerebrospinal fluid analysis, there are no changes related to Alzheimer's disease or neurodegeneration. Single-cell gene expression analysis in the cerebrospinal fluid shows findings consistent with monocyte recruitment, chemokine signaling, cellular stress, and suppressed interferon response-especially in myeloid cells. Longitudinal analysis shows slow recovery accompanied by key alterations in inflammatory genes and increased protein levels of CXCL8, CCL3L1, and sTREM2. These findings suggest that the prognosis for brain fog following COVID-19 correlates with myeloid-related chemokine and interferon-responsive genes.
Collapse
Affiliation(s)
- William T Hu
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Center for Innovation in Health and Aging Research, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, NJ, USA.
| | - Milota Kaluzova
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alice Dawson
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Center for Innovation in Health and Aging Research, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, NJ, USA
| | - Victor Sotelo
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Center for Innovation in Health and Aging Research, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, NJ, USA
| | - Julia Papas
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Center for Innovation in Health and Aging Research, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, NJ, USA
| | - Alexander Lemenze
- Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Carol Shu
- Department of Medicine-Pulmonary and Critical Care, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Mini Jomartin
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Ashima Nayyar
- Department of Neurology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Sabiha Hussain
- Department of Medicine-Pulmonary and Critical Care, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| |
Collapse
|
27
|
Zhang Z, Kean IRL, Dratva LM, Clark JA, Syrimi E, Khan N, Daubney E, White D, O'Neill L, Chisholm C, Payne C, Benkenstein S, Kupiec K, Galassini R, Wright V, Winmill H, Robbins C, Brown K, Ramnarayan P, Scholefield B, Peters M, Klein N, Montgomery H, Meyer KB, Teichmann SA, Bryant C, Taylor G, Pathan N. Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children. Nat Commun 2024; 15:4227. [PMID: 38762592 PMCID: PMC11102542 DOI: 10.1038/s41467-024-48699-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Multisystem inflammatory syndrome in children is a post-infectious presentation SARS-CoV-2 associated with expansion of the T cell receptor Vβ21.3+ T-cell subgroup. Here we apply muti-single cell omics to compare the inflammatory process in children with acute respiratory COVID-19 and those presenting with non SARS-CoV-2 infections in children. Here we show that in Multi-Inflammatory Syndrome in Children (MIS-C), the natural killer cell and monocyte population demonstrate heightened CD95 (Fas) and Interleuking 18 receptor expression. Additionally, TCR Vβ21.3+ CD4+ T-cells exhibit skewed differentiation towards T helper 1, 17 and regulatory T cells, with increased expression of the co-stimulation receptors ICOS, CD28 and interleukin 18 receptor. We observe no functional evidence for NLRP3 inflammasome pathway overactivation, though MIS-C monocytes show elevated active caspase 8. This, coupled with raised IL18 mRNA expression in CD16- NK cells on single cell RNA sequencing analysis, suggests interleukin 18 and CD95 signalling may trigger activation of TCR Vβ21.3+ T-cells in MIS-C, driven by increased IL-18 production from activated monocytes and CD16- Natural Killer cells.
Collapse
MESH Headings
- Humans
- Interleukin-18/metabolism
- Child
- Signal Transduction
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- fas Receptor/metabolism
- fas Receptor/genetics
- Monocytes/immunology
- Monocytes/metabolism
- Systemic Inflammatory Response Syndrome/immunology
- Systemic Inflammatory Response Syndrome/metabolism
- COVID-19/immunology
- COVID-19/virology
- COVID-19/metabolism
- COVID-19/complications
- Inflammasomes/metabolism
- Inflammasomes/immunology
- SARS-CoV-2/immunology
- Adolescent
- Male
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Female
- Child, Preschool
- Single-Cell Analysis
- NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD28 Antigens/metabolism
- Lymphocyte Activation/immunology
- Receptors, Interleukin-18/metabolism
- Receptors, Interleukin-18/genetics
- Receptors, Interleukin-18/immunology
Collapse
Affiliation(s)
- Zhenguang Zhang
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Iain R L Kean
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - John A Clark
- Departments of Paediatrics, University of Cambridge, Cambridge, UK
| | - Eleni Syrimi
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Esther Daubney
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK
| | - Deborah White
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK
| | - Lauran O'Neill
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Catherine Chisholm
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Caroline Payne
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Sarah Benkenstein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | - Klaudia Kupiec
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | | | - Victoria Wright
- Department of Paediatrics, Imperial College London, London, UK
| | - Helen Winmill
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Ceri Robbins
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Katherine Brown
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
| | | | - Barnaby Scholefield
- Paediatric Intensive Care Unit, Birmingham Children's Hospital, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Mark Peters
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
- Departments of Paediatrics, University College London, London, UK
| | - Nigel Klein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital, London, UK
- Departments of Paediatrics, University College London, London, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Theory of Condensed Matter, Cavendish Laboratory, Department of Physics University of Cambridge, Cambridge, UK
| | - Clare Bryant
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Graham Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
| | - Nazima Pathan
- Departments of Paediatrics, University of Cambridge, Cambridge, UK.
- Paediatric Intensive Care Unit, Addenbrookes Hospital, Cambridge, UK.
| |
Collapse
|
28
|
Kotliar D, Curtis M, Agnew R, Weinand K, Nathan A, Baglaenko Y, Zhao Y, Sabeti PC, Rao DA, Raychaudhuri S. Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592310. [PMID: 38746317 PMCID: PMC11092745 DOI: 10.1101/2024.05.03.592310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses - for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.
Collapse
Affiliation(s)
- Dylan Kotliar
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Curtis
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan Agnew
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45219, USA
| | - Yu Zhao
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
29
|
Ng JCF, Montamat Garcia G, Stewart AT, Blair P, Mauri C, Dunn-Walters DK, Fraternali F. sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data. Nat Methods 2024; 21:823-834. [PMID: 37932398 PMCID: PMC11093741 DOI: 10.1038/s41592-023-02060-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023]
Abstract
Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.
Collapse
Affiliation(s)
- Joseph C F Ng
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Guillem Montamat Garcia
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Paul Blair
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Claudia Mauri
- Division of Infection and Immunity and Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, UK
| | | | - Franca Fraternali
- Department of Structural and Molecular Biology, Division of Biosciences and Institute of Structural and Molecular Biology, University College London, London, UK.
| |
Collapse
|
30
|
Xu J, Huang D, Zhang X. scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307835. [PMID: 38483032 PMCID: PMC11109621 DOI: 10.1002/advs.202307835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/24/2024] [Indexed: 05/23/2024]
Abstract
Transformer-based models have revolutionized single cell RNA-seq (scRNA-seq) data analysis. However, their applicability is challenged by the complexity and scale of single-cell multi-omics data. Here a novel single-cell multi-modal/multi-task transformer (scmFormer) is proposed to fill up the existing blank of integrating single-cell proteomics with other omics data. Through systematic benchmarking, it is demonstrated that scmFormer excels in integrating large-scale single-cell multimodal data and heterogeneous multi-batch paired multi-omics data, while preserving shared information across batchs and distinct biological information. scmFormer achieves 54.5% higher average F1 score compared to the second method in transferring cell-type labels from single-cell transcriptomics to proteomics data. Using COVID-19 datasets, it is presented that scmFormer successfully integrates over 1.48 million cells on a personal computer. Moreover, it is also proved that scmFormer performs better than existing methods on generating the unmeasured modality and is well-suited for spatial multi-omic data. Thus, scmFormer is a powerful and comprehensive tool for analyzing single-cell multi-omics data.
Collapse
Affiliation(s)
- Jing Xu
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhan430074China
- University of Chinese Academy of SciencesBeijing100049China
| | - De‐Shuang Huang
- Eastern Institute for Advanced StudyEastern Institute of TechnologyNingbo315200China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhan430074China
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhan430074China
| |
Collapse
|
31
|
Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
Collapse
Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
32
|
Suzuki T, Sato Y, Okuno Y, Torii Y, Fukuda Y, Haruta K, Yamaguchi M, Kawamura Y, Hama A, Narita A, Muramatsu H, Yoshikawa T, Takahashi Y, Kimura H, Ito Y, Kawada JI. Single-Cell Transcriptomic Analysis of Epstein-Barr Virus-Associated Hemophagocytic Lymphohistiocytosis. J Clin Immunol 2024; 44:103. [PMID: 38642164 DOI: 10.1007/s10875-024-01701-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
Epstein-Barr virus (EBV) infection can lead to infectious mononucleosis (EBV-IM) and, more rarely, EBV-associated hemophagocytic lymphohistiocytosis (EBV-HLH), which is characterized by a life-threatening hyperinflammatory cytokine storm with immune dysregulation. Interferon-gamma (IFNγ) has been identified as a critical mediator for primary HLH; however, the detailed role of IFNγ and other cytokines in EBV-HLH is not fully understood. In this study, we used single-cell RNA sequencing to characterize the immune landscape of EBV-HLH and compared it with EBV-IM. Three pediatric patients with EBV-HLH with different backgrounds, one with X-linked lymphoproliferative syndrome type 1 (XLP1), two with chronic active EBV disease (CAEBV), and two patients with EBV-IM were enrolled. The TUBA1B + STMN1 + CD8 + T cell cluster, a responsive proliferating cluster with rich mRNA detection, was explicitly observed in EBV-IM, and the upregulation of SH2D1A-the gene responsible for XLP1-was localized in this cluster. This proliferative cluster was scarcely observed in EBV-HLH cases. In EBV-HLH cases with CAEBV, upregulation of LAG3 was observed in EBV-infected cells, which may be associated with an impaired response by CD8 + T cells. Additionally, genes involved in type I interferon (IFN) signaling were commonly upregulated in each cell fraction of EBV-HLH, and activation of type II IFN signaling was observed in CD4 + T cells, natural killer cells, and monocytes but not in CD8 + T cells in EBV-HLH. In conclusion, impaired responsive proliferation of CD8 + T cells and upregulation of type I IFN signaling were commonly observed in EBV-HLH cases, regardless of the patients' background, indicating the key features of EBV-HLH.
Collapse
Affiliation(s)
- Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Departments of Pediatrics, Aichi Medical University, Nagakute, Aichi, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| |
Collapse
|
33
|
Croce G, Bobisse S, Moreno DL, Schmidt J, Guillame P, Harari A, Gfeller D. Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells. Nat Commun 2024; 15:3211. [PMID: 38615042 PMCID: PMC11016097 DOI: 10.1038/s41467-024-47461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/03/2024] [Indexed: 04/15/2024] Open
Abstract
T cells have the ability to eliminate infected and cancer cells and play an essential role in cancer immunotherapy. T cell activation is elicited by the binding of the T cell receptor (TCR) to epitopes displayed on MHC molecules, and the TCR specificity is determined by the sequence of its α and β chains. Here, we collect and curate a dataset of 17,715 αβTCRs interacting with dozens of class I and class II epitopes. We use this curated data to develop MixTCRpred, an epitope-specific TCR-epitope interaction predictor. MixTCRpred accurately predicts TCRs recognizing several viral and cancer epitopes. MixTCRpred further provides a useful quality control tool for multiplexed single-cell TCR sequencing assays of epitope-specific T cells and pinpoints a substantial fraction of putative contaminants in public databases. Analysis of epitope-specific dual α T cells demonstrates that MixTCRpred can identify α chains mediating epitope recognition. Applying MixTCRpred to TCR repertoires from COVID-19 patients reveals enrichment of clonotypes predicted to bind an immunodominant SARS-CoV-2 epitope. Overall, MixTCRpred provides a robust tool to predict TCRs interacting with specific epitopes and interpret TCR-sequencing data from both bulk and epitope-specific T cells.
Collapse
Affiliation(s)
- Giancarlo Croce
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Sara Bobisse
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Dana Léa Moreno
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Schmidt
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillame
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
- Agora Cancer Research Centre, Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
| |
Collapse
|
34
|
O'Leary K, Zheng D. Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs. NPJ Syst Biol Appl 2024; 10:36. [PMID: 38580667 PMCID: PMC10997786 DOI: 10.1038/s41540-024-00364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as "replicates" for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.
Collapse
Affiliation(s)
- Kevin O'Leary
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
| |
Collapse
|
35
|
Li Z, Brittan M, Mills NL. A Multimodal Omics Framework to Empower Target Discovery for Cardiovascular Regeneration. Cardiovasc Drugs Ther 2024; 38:223-236. [PMID: 37421484 PMCID: PMC10959818 DOI: 10.1007/s10557-023-07484-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2023] [Indexed: 07/10/2023]
Abstract
Ischaemic heart disease is a global healthcare challenge with high morbidity and mortality. Early revascularisation in acute myocardial infarction has improved survival; however, limited regenerative capacity and microvascular dysfunction often lead to impaired function and the development of heart failure. New mechanistic insights are required to identify robust targets for the development of novel strategies to promote regeneration. Single-cell RNA sequencing (scRNA-seq) has enabled profiling and analysis of the transcriptomes of individual cells at high resolution. Applications of scRNA-seq have generated single-cell atlases for multiple species, revealed distinct cellular compositions for different regions of the heart, and defined multiple mechanisms involved in myocardial injury-induced regeneration. In this review, we summarise findings from studies of healthy and injured hearts in multiple species and spanning different developmental stages. Based on this transformative technology, we propose a multi-species, multi-omics, meta-analysis framework to drive the discovery of new targets to promote cardiovascular regeneration.
Collapse
Affiliation(s)
- Ziwen Li
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| | - Mairi Brittan
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas L Mills
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
36
|
Hetland G, Fagerhol MK, Mirlashari MR, Nissen-Meyer LSH, Croci S, Lonati PA, Bonacini M, Salvarani C, Marvisi C, Bodio C, Muratore F, Borghi MO, Meroni PL. Elevated NET, Calprotectin, and Neopterin Levels Discriminate between Disease Activity in COVID-19, as Evidenced by Need for Hospitalization among Patients in Northern Italy. Biomedicines 2024; 12:766. [PMID: 38672123 PMCID: PMC11048478 DOI: 10.3390/biomedicines12040766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) displays clinical heterogeneity, but little information is available for patients with mild or very early disease. We aimed to characterize biomarkers that are useful for discriminating the hospitalization risk in a COVID-19 cohort from Northern Italy during the first pandemic wave. We enrolled and followed for four weeks 76 symptomatic SARS-CoV-2 positive patients and age/sex-matched healthy controls. Patients with mild disease were discharged (n.42), and the remaining patients were hospitalized (n.34). Blood was collected before any anti-inflammatory/immunosuppressive therapy and assessed for soluble C5b-9/C5a, H3-neutrophil extracellular traps (NETs), calprotectin, and DNase plasma levels via ELISA and a panel of proinflammatory cytokines via ELLA. Calprotectin and NET levels discriminate between hospitalized and non-hospitalized patients, while DNase negatively correlates with NET levels; there are positive correlations between calprotectin and both NET and neopterin levels. Neopterin levels increase in patients at the beginning of the disease and do so more in hospitalized than non-hospitalized patients. C5a and sC5b-9, and other acute phase proteins, correlate with neopterin, calprotectin, and DNase. Both NET and neopterin levels negatively correlate with platelet count. We show that calprotectin, NETs, and neopterin are important proinflammatory parameters potentially useful for discriminating between COVID-19 patients at risk of hospitalization.
Collapse
Affiliation(s)
- Geir Hetland
- Department of Immunology and Transfusion Medicine, Oslo University Hospital Ullevål, 0450 Oslo, Norway; (G.H.); (M.K.F.); (M.R.M.); (L.S.H.N.-M.)
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0451 Oslo, Norway
| | - Magne Kristoffer Fagerhol
- Department of Immunology and Transfusion Medicine, Oslo University Hospital Ullevål, 0450 Oslo, Norway; (G.H.); (M.K.F.); (M.R.M.); (L.S.H.N.-M.)
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0451 Oslo, Norway
| | - Mohammad Reza Mirlashari
- Department of Immunology and Transfusion Medicine, Oslo University Hospital Ullevål, 0450 Oslo, Norway; (G.H.); (M.K.F.); (M.R.M.); (L.S.H.N.-M.)
| | - Lise Sofie Haug Nissen-Meyer
- Department of Immunology and Transfusion Medicine, Oslo University Hospital Ullevål, 0450 Oslo, Norway; (G.H.); (M.K.F.); (M.R.M.); (L.S.H.N.-M.)
| | - Stefania Croci
- Clinical Immunology, Allergy and Advanced Biotechnologies Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (S.C.); (M.B.)
| | - Paola Adele Lonati
- Research Laboratory of Immunorheumatology, IRCCS Istituto Auxologico Italiano, 20095 Cusano Milanino, Italy; (P.A.L.); (C.B.); or (M.O.B.)
| | - Martina Bonacini
- Clinical Immunology, Allergy and Advanced Biotechnologies Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (S.C.); (M.B.)
| | - Carlo Salvarani
- Azienda USL-IRCCS di Reggio Emilia e Università di Modena e Reggio Emilia, 42123 Reggio Emilia, Italy; (C.S.); (C.M.); (F.M.)
| | - Chiara Marvisi
- Azienda USL-IRCCS di Reggio Emilia e Università di Modena e Reggio Emilia, 42123 Reggio Emilia, Italy; (C.S.); (C.M.); (F.M.)
| | - Caterina Bodio
- Research Laboratory of Immunorheumatology, IRCCS Istituto Auxologico Italiano, 20095 Cusano Milanino, Italy; (P.A.L.); (C.B.); or (M.O.B.)
| | - Francesco Muratore
- Azienda USL-IRCCS di Reggio Emilia e Università di Modena e Reggio Emilia, 42123 Reggio Emilia, Italy; (C.S.); (C.M.); (F.M.)
| | - Maria Orietta Borghi
- Research Laboratory of Immunorheumatology, IRCCS Istituto Auxologico Italiano, 20095 Cusano Milanino, Italy; (P.A.L.); (C.B.); or (M.O.B.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Pier Luigi Meroni
- Research Laboratory of Immunorheumatology, IRCCS Istituto Auxologico Italiano, 20095 Cusano Milanino, Italy; (P.A.L.); (C.B.); or (M.O.B.)
| |
Collapse
|
37
|
Xie Y, Chen H, Chellamuthu VR, Lajam ABM, Albani S, Low AHL, Petretto E, Behmoaras J. Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing. Int J Mol Sci 2024; 25:3828. [PMID: 38612639 PMCID: PMC11011421 DOI: 10.3390/ijms25073828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10x Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10x data where samples were not multiplexed. Despite relatively lower cell capture affecting library preparation, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, a comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.
Collapse
Affiliation(s)
- Yi Xie
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
| | - Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
| | - Vasuki Ranjani Chellamuthu
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Ahmad bin Mohamed Lajam
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, Academia, Singapore 169856, Singapore; (V.R.C.)
| | - Andrea Hsiu Ling Low
- Department of Rheumatology and Immunology, Singapore General Hospital, Academia, Singapore 169856, Singapore;
- SingHealth Duke-NUS Medicine Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Jacques Behmoaras
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; (Y.X.)
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
| |
Collapse
|
38
|
He X, Cui X, Zhao Z, Wu R, Zhang Q, Xue L, Zhang H, Ge Q, Leng Y. A generalizable and easy-to-use COVID-19 stratification model for the next pandemic via immune-phenotyping and machine learning. Front Immunol 2024; 15:1372539. [PMID: 38601145 PMCID: PMC11004273 DOI: 10.3389/fimmu.2024.1372539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic has affected billions of people worldwide, and the lessons learned need to be concluded to get better prepared for the next pandemic. Early identification of high-risk patients is important for appropriate treatment and distribution of medical resources. A generalizable and easy-to-use COVID-19 severity stratification model is vital and may provide references for clinicians. Methods Three COVID-19 cohorts (one discovery cohort and two validation cohorts) were included. Longitudinal peripheral blood mononuclear cells were collected from the discovery cohort (n = 39, mild = 15, critical = 24). The immune characteristics of COVID-19 and critical COVID-19 were analyzed by comparison with those of healthy volunteers (n = 16) and patients with mild COVID-19 using mass cytometry by time of flight (CyTOF). Subsequently, machine learning models were developed based on immune signatures and the most valuable laboratory parameters that performed well in distinguishing mild from critical cases. Finally, single-cell RNA sequencing data from a published study (n = 43) and electronic health records from a prospective cohort study (n = 840) were used to verify the role of crucial clinical laboratory and immune signature parameters in the stratification of COVID-19 severity. Results Patients with COVID-19 were determined with disturbed glucose and tryptophan metabolism in two major innate immune clusters. Critical patients were further characterized by significant depletion of classical dendritic cells (cDCs), regulatory T cells (Tregs), and CD4+ central memory T cells (Tcm), along with increased systemic interleukin-6 (IL-6), interleukin-12 (IL-12), and lactate dehydrogenase (LDH). The machine learning models based on the level of cDCs and LDH showed great potential for predicting critical cases. The model performances in severity stratification were validated in two cohorts (AUC = 0.77 and 0.88, respectively) infected with different strains in different periods. The reference limits of cDCs and LDH as biomarkers for predicting critical COVID-19 were 1.2% and 270.5 U/L, respectively. Conclusion Overall, we developed and validated a generalizable and easy-to-use COVID-19 severity stratification model using machine learning algorithms. The level of cDCs and LDH will assist clinicians in making quick decisions during future pandemics.
Collapse
Affiliation(s)
- Xinlei He
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Xiao Cui
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Zhiling Zhao
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Rui Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Qiang Zhang
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Lei Xue
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Hua Zhang
- Department of Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, China
| | - Qinggang Ge
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Yuxin Leng
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| |
Collapse
|
39
|
Yang Q, Song W, Reheman H, Wang D, Qu J, Li Y. PANoptosis, an indicator of COVID-19 severity and outcomes. Brief Bioinform 2024; 25:bbae124. [PMID: 38555477 PMCID: PMC10981763 DOI: 10.1093/bib/bbae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/02/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been wreaking havoc for 3 years. PANoptosis, a distinct and physiologically relevant inflammatory programmed cell death, perpetuates cytokine storm and multi-organ injuries in COVID-19. Although PANoptosis performs indispensable roles in host defense, further investigation is needed to elucidate the exact processes through which PANoptosis modulates immunological responses and prognosis in COVID-19. This study conducted a bioinformatics analysis of online single-cell RNA sequence (scRNA-seq) and bulk RNA-seq datasets to explore the potential of PANoptosis as an indicator of COVID-19 severity. The degree of PANoptosis in bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) indicated the severity of COVID-19. Single-cell transcriptomics identified pro-inflammatory monocytes as one of the primary sites of PANoptosis in COVID-19. The study subsequently demonstrated the immune and metabolic characteristics of this group of pro-inflammatory monocytes. In addition, the analysis illustrated that dexamethasone was likely to alleviate inflammation in COVID-19 by mitigating PANoptosis. Finally, the study showed that the PANoptosis-related genes could predict the intensive care unit admission (ICU) and outcomes of COVID-19 patients who are hospitalized.
Collapse
Affiliation(s)
- Qingyuan Yang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Wanmei Song
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Hanizaier Reheman
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Dan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Yanan Li
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| |
Collapse
|
40
|
Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
Collapse
Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
41
|
Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
| |
Collapse
|
42
|
Garcia G, Labrouche-Colomer S, Duvignaud A, Clequin E, Dussiau C, Trégouët DA, Malvy D, Prevel R, Zouine A, Pellegrin I, Goret J, Mamani-Matsuda M, Dewitte A, James C. Impaired balance between neutrophil extracellular trap formation and degradation by DNases in COVID-19 disease. J Transl Med 2024; 22:246. [PMID: 38454482 PMCID: PMC10919029 DOI: 10.1186/s12967-024-05044-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Thrombo-inflammation and neutrophil extracellular traps (NETs) are exacerbated in severe cases of COVID-19, potentially contributing to disease exacerbation. However, the mechanisms underpinning this dysregulation remain elusive. We hypothesised that lower DNase activity may be associated with higher NETosis and clinical worsening in patients with COVID-19. METHODS Biological samples were obtained from hospitalized patients (15 severe, 37 critical at sampling) and 93 non-severe ambulatory cases. Our aims were to compare NET biomarkers, functional DNase levels, and explore mechanisms driving any imbalance concerning disease severity. RESULTS Functional DNase levels were diminished in the most severe patients, paralleling an imbalance between NET markers and DNase activity. DNase1 antigen levels were higher in ambulatory cases but lower in severe patients. DNase1L3 antigen levels remained consistent across subgroups, not rising alongside NET markers. DNASE1 polymorphisms correlated with reduced DNase1 antigen levels. Moreover, a quantitative deficiency in plasmacytoid dendritic cells (pDCs), which primarily express DNase1L3, was observed in critical patients. Analysis of public single-cell RNAseq data revealed reduced DNase1L3 expression in pDCs from severe COVID-19 patient. CONCLUSION Severe and critical COVID-19 cases exhibited an imbalance between NET and DNase functional activity and quantity. Early identification of NETosis imbalance could guide targeted therapies against thrombo-inflammation in COVID-19-related sepsis, such as DNase administration, to avert clinical deterioration. TRIAL REGISTRATION COVERAGE trial (NCT04356495) and COLCOV19-BX study (NCT04332016).
Collapse
Affiliation(s)
- Geoffrey Garcia
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
| | - Sylvie Labrouche-Colomer
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - Alexandre Duvignaud
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Etienne Clequin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Charles Dussiau
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - David-Alexandre Trégouët
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Denis Malvy
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Renaud Prevel
- Medical Intensive Care Unit, Bordeaux University Hospital, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM, UMR 1045, Bordeaux University, 33000, Bordeaux, France
| | - Atika Zouine
- CNRS, INSERM, TBM-Core, US5, UAR 3427, Flow Cytometry Facility, Bordeaux University, 33000, Bordeaux, France
| | - Isabelle Pellegrin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Centre de Ressources Biologiques, Bordeaux University Hospital, 33000, Bordeaux, France
| | - Julien Goret
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - Maria Mamani-Matsuda
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
| | - Antoine Dewitte
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Chloe James
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France.
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France.
| |
Collapse
|
43
|
Ma R, Sun ED, Donoho D, Zou J. Principled and interpretable alignability testing and integration of single-cell data. Proc Natl Acad Sci U S A 2024; 121:e2313719121. [PMID: 38416677 DOI: 10.1073/pnas.2313719121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 03/01/2024] Open
Abstract
Single-cell data integration can provide a comprehensive molecular view of cells, and many algorithms have been developed to remove unwanted technical or biological variations and integrate heterogeneous single-cell datasets. Despite their wide usage, existing methods suffer from several fundamental limitations. In particular, we lack a rigorous statistical test for whether two high-dimensional single-cell datasets are alignable (and therefore should even be aligned). Moreover, popular methods can substantially distort the data during alignment, making the aligned data and downstream analysis difficult to interpret. To overcome these limitations, we present a spectral manifold alignment and inference (SMAI) framework, which enables principled and interpretable alignability testing and structure-preserving integration of single-cell data with the same type of features. SMAI provides a statistical test to robustly assess the alignability between datasets to avoid misleading inference and is justified by high-dimensional statistical theory. On a diverse range of real and simulated benchmark datasets, it outperforms commonly used alignment methods. Moreover, we show that SMAI improves various downstream analyses such as identification of differentially expressed genes and imputation of single-cell spatial transcriptomics, providing further biological insights. SMAI's interpretability also enables quantification and a deeper understanding of the sources of technical confounders in single-cell data.
Collapse
Affiliation(s)
- Rong Ma
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Eric D Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| | - David Donoho
- Department of Statistics, Stanford University, Stanford, CA 94305
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
| |
Collapse
|
44
|
Long MB, Abo-Leyah H, Giam YH, Vadiveloo T, Hull RC, Keir HR, Pembridge T, Alferes De Lima D, Delgado L, Inglis SK, Hughes C, Gilmour A, Gierlinski M, New BJ, MacLennan G, Dinkova-Kostova AT, Chalmers JD. SFX-01 in hospitalised patients with community-acquired pneumonia during the COVID-19 pandemic: a double-blind, randomised, placebo-controlled trial. ERJ Open Res 2024; 10:00917-2023. [PMID: 38469377 PMCID: PMC10926007 DOI: 10.1183/23120541.00917-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Sulforaphane can induce the transcription factor, Nrf2, promoting antioxidant and anti-inflammatory responses. In this study, hospitalised patients with community-acquired pneumonia (CAP) were treated with stabilised synthetic sulforaphane (SFX-01) to evaluate impact on clinical status and inflammation. Methods Double-blind, randomised, placebo-controlled trial of SFX-01 (300 mg oral capsule, once daily for 14 days) conducted in Dundee, UK, between November 2020 and May 2021. Patients had radiologically confirmed CAP and CURB-65 (confusion, urea >7 mmol·L-1, respiratory rate ≥30 breaths·min-1, blood pressure <90 mmHg (systolic) or ≤60 mmHg (diastolic), age ≥65 years) score ≥1. The primary outcome was the seven-point World Health Organization clinical status scale at day 15. Secondary outcomes included time to clinical improvement, length of stay and mortality. Effects on Nrf2 activity and inflammation were evaluated on days 1, 8 and 15 by measurement of 45 serum cytokines and mRNA sequencing of peripheral blood leukocytes. Results The trial was terminated prematurely due to futility with 133 patients enrolled. 65 patients were randomised to SFX-01 treatment and 68 patients to placebo. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was the cause of CAP in 103 (77%) cases. SFX-01 treatment did not improve clinical status at day 15 (adjusted OR 0.87, 95% CI 0.41-1.83; p=0.71), time to clinical improvement (adjusted hazard ratio (aHR) 1.02, 95% CI 0.70-1.49), length of stay (aHR 0.84, 95% CI 0.56-1.26) or 28-day mortality (aHR 1.45, 95% CI 0.67-3.16). The expression of Nrf2 targets and pro-inflammatory genes, including interleukin (IL)-6, IL-1β and tumour necrosis factor-α, was not significantly changed by SFX-01 treatment. At days 8 and 15, respectively, 310 and 42 significant differentially expressed genes were identified between groups (false discovery rate adjusted p<0.05, log2FC >1). Conclusion SFX-01 treatment did not improve clinical status or modulate key Nrf2 targets in patients with CAP primarily due to SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Merete B. Long
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- These authors contributed equally
| | - Hani Abo-Leyah
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- These authors contributed equally
| | - Yan Hui Giam
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Thenmalar Vadiveloo
- Centre for Healthcare Randomised Trials, University of Aberdeen, Aberdeen, UK
| | - Rebecca C. Hull
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Holly R. Keir
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Thomas Pembridge
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Daniela Alferes De Lima
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lilia Delgado
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Sarah K. Inglis
- Tayside Clinical Trials Unit, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Chloe Hughes
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Amy Gilmour
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Marek Gierlinski
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Graeme MacLennan
- Centre for Healthcare Randomised Trials, University of Aberdeen, Aberdeen, UK
| | - Albena T. Dinkova-Kostova
- Division of Cellular and Systems Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| |
Collapse
|
45
|
Hanson AL, Mulè MP, Ruffieux H, Mescia F, Bergamaschi L, Pelly VS, Turner L, Kotagiri P, Göttgens B, Hess C, Gleadall N, Bradley JR, Nathan JA, Lyons PA, Drakesmith H, Smith KGC. Iron dysregulation and inflammatory stress erythropoiesis associates with long-term outcome of COVID-19. Nat Immunol 2024; 25:471-482. [PMID: 38429458 PMCID: PMC10907301 DOI: 10.1038/s41590-024-01754-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Persistent symptoms following SARS-CoV-2 infection are increasingly reported, although the drivers of post-acute sequelae (PASC) of COVID-19 are unclear. Here we assessed 214 individuals infected with SARS-CoV-2, with varying disease severity, for one year from COVID-19 symptom onset to determine the early correlates of PASC. A multivariate signature detected beyond two weeks of disease, encompassing unresolving inflammation, anemia, low serum iron, altered iron-homeostasis gene expression and emerging stress erythropoiesis; differentiated those who reported PASC months later, irrespective of COVID-19 severity. A whole-blood heme-metabolism signature, enriched in hospitalized patients at month 1-3 post onset, coincided with pronounced iron-deficient reticulocytosis. Lymphopenia and low numbers of dendritic cells persisted in those with PASC, and single-cell analysis reported iron maldistribution, suggesting monocyte iron loading and increased iron demand in proliferating lymphocytes. Thus, defects in iron homeostasis, dysregulated erythropoiesis and immune dysfunction due to COVID-19 possibly contribute to inefficient oxygen transport, inflammatory disequilibrium and persisting symptomatology, and may be therapeutically tractable.
Collapse
Affiliation(s)
- Aimee L Hanson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew P Mulè
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- NIH-Oxford-Cambridge Scholars Program, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hélène Ruffieux
- MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Victoria S Pelly
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Berthold Göttgens
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicholas Gleadall
- Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
- Botnar Research Centre for Child Health (BRCCH), University of Basel and ETH Zurich, Basel, Switzerland
| | - John R Bradley
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Hal Drakesmith
- MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- University of Melbourne, Melbourne, Victoria, Australia.
| |
Collapse
|
46
|
Inokuchi S, Shimamoto K. Persistent Risk of Developing Autoimmune Diseases Associated With COVID-19: An Observational Study Using an Electronic Medical Record Database in Japan. J Clin Rheumatol 2024; 30:65-72. [PMID: 38190730 DOI: 10.1097/rhu.0000000000002054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
OBJECTIVE This study aimed to investigate the risk of developing autoimmune diseases associated with coronavirus disease 2019 (COVID-19) in Japan, including long-term risks and risks specific to different variants of concern. METHODS This observational study used an electronic medical record database in Japan. The COVID-19 group is composed of patients diagnosed with COVID-19, whereas the non-COVID-19 group had data sampled from the database. The outcomes of interest encompassed several autoimmune diseases, including rheumatoid arthritis, systemic sclerosis, and immunoglobulin G4-related disease, as well as a composite of these diseases (any autoimmune disease). We examined the relative risk of autoimmune diseases using standardized mortality ratio weighting and the Cox proportional hazards model. Subgroup analyses based on epidemic variants were performed. In addition, short- and long-term risks were investigated using piecewise constant hazard models. RESULTS A total of 90,855 COVID-19 and 459,827 non-COVID-19 patients were included between January 16, 2020, and December 31, 2022. The relative risk of any autoimmune disease was 2.32 (95% confidence interval, 2.08-2.60). All the investigated outcomes showed a significant risk associated with COVID-19. Several autoimmune diseases exhibit a risk associated with COVID-19 in the short to long term, and the long-term risk is substantial for systemic sclerosis and immunoglobulin G4-related disease. The variant-specific risk varied across outcomes. CONCLUSIONS COVID-19 is associated with an increased risk of developing autoimmune diseases in the Japanese population, and this effect persists for a long time. This study provides insights into the association between viral infections and autoimmunity.
Collapse
Affiliation(s)
- Shoichiro Inokuchi
- From the Research and Analytics Department, Real World Data Co, Ltd, Kyoto, Japan
| | | |
Collapse
|
47
|
Chattopadhyay P, Mehta P, Soni J, Tardalkar K, Joshi M, Pandey R. Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genom Bioinform 2024; 6:lqae023. [PMID: 38426128 PMCID: PMC10903533 DOI: 10.1093/nargab/lqae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
A plethora of studies have demonstrated the roles of lncRNAs in modulating disease severity and outcomes during infection. However, the spatio-temporal expression of these lncRNAs is poorly understood. In this study, we used single-cell RNA-seq to understand the spatio-temporal expression dynamics of lncRNAs across healthy, SARS-CoV-2-infected, and recovered individuals and their functional role in modulating the disease and recovery. We identified 203 differentially expressed lncRNAs, including cell type-specific ones like MALAT1, NEAT1, ZFAS1, SNHG7, SNHG8, and SNHG25 modulating immune function in classical monocyte, NK T, proliferating NK, plasmablast, naive, and activated B/T cells. Interestingly, we found invariant lncRNAs (no significant change in expression across conditions) regulating essential housekeeping functions (for example, HOTAIR, NRAV, SNHG27, SNHG28, and UCA1) in infected and recovered individuals. Despite similar repeat element abundance, variant lncRNAs displayed higher Alu content, suggesting increased interactions with proximal and distal genes, crucial for immune response modulation. The comparable repeat abundance but distinct expression levels of variant and invariant lncRNAs highlight the significance of investigating the regulatory mechanisms of invariant lncRNAs. Overall, this study offers new insights into the spatio-temporal expression patterns and functional roles of lncRNAs in SARS-CoV-2-infected and recovered individuals while highlighting the importance of invariant lncRNAs in the disease context.
Collapse
Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| |
Collapse
|
48
|
Long MB, Howden AJM, Keir HR, Rollings CM, Giam YH, Pembridge T, Delgado L, Abo-Leyah H, Lloyd AF, Sollberger G, Hull R, Gilmour A, Hughes C, New BJM, Cassidy D, Shoemark A, Richardson H, Lamond AI, Cantrell DA, Chalmers JD, Brenes AJ. Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection. Eur Respir J 2024; 63:2300787. [PMID: 38097207 PMCID: PMC10918319 DOI: 10.1183/13993003.00787-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/23/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Neutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery. METHODS Prospective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale. RESULTS Neutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified, with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature, but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism, immunosuppression and pattern recognition, while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins, chemokine and leukotriene receptors, integrins and inhibitory receptors. CONCLUSIONS SARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.
Collapse
Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Andrew J M Howden
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Holly R Keir
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Christina M Rollings
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Yan Hui Giam
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Thomas Pembridge
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Lilia Delgado
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hani Abo-Leyah
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amy F Lloyd
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gabriel Sollberger
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Rebecca Hull
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Amy Gilmour
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Chloe Hughes
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Benjamin J M New
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Diane Cassidy
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Angus I Lamond
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Doreen A Cantrell
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates joint senior authorship
| | - Alejandro J Brenes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates joint senior authorship
| |
Collapse
|
49
|
Liu T, Li K, Wang Y, Li H, Zhao H. Evaluating the Utilities of Foundation Models in Single-cell Data Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.08.555192. [PMID: 38464157 PMCID: PMC10925156 DOI: 10.1101/2023.09.08.555192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Foundation Models (FMs) have made significant strides in both industrial and scientific domains. In this paper, we evaluate the performance of FMs in single-cell sequencing data analysis through comprehensive experiments across eight downstream tasks pertinent to single-cell data. By comparing ten different single-cell FMs with task-specific methods, we found that single-cell FMs may not consistently excel in all tasks than task-specific methods. However, the emergent abilities and the successful applications of cross-species/cross-modality transfer learning of FMs are promising. In addition, we present a systematic evaluation of the effects of hyper-parameters, initial settings, and stability for training single-cell FMs based on a proposed scEval framework, and provide guidelines for pre-training and fine-tuning. Our work summarizes the current state of single-cell FMs and points to their constraints and avenues for future development.
Collapse
|
50
|
Pullin JM, McCarthy DJ. A comparison of marker gene selection methods for single-cell RNA sequencing data. Genome Biol 2024; 25:56. [PMID: 38409056 PMCID: PMC10895860 DOI: 10.1186/s13059-024-03183-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalog and probe the transcriptional heterogeneity of individual cells in unprecedented detail. A common step in the analysis of scRNA-seq data is the selection of so-called marker genes, most commonly to enable annotation of the biological cell types present in the sample. In this paper, we benchmark 59 computational methods for selecting marker genes in scRNA-seq data. RESULTS We compare the performance of the methods using 14 real scRNA-seq datasets and over 170 additional simulated datasets. Methods are compared on their ability to recover simulated and expert-annotated marker genes, the predictive performance and characteristics of the gene sets they select, their memory usage and speed, and their implementation quality. In addition, various case studies are used to scrutinize the most commonly used methods, highlighting issues and inconsistencies. CONCLUSIONS Overall, we present a comprehensive evaluation of methods for selecting marker genes in scRNA-seq data. Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Student's t-test, and logistic regression.
Collapse
Affiliation(s)
- Jeffrey M Pullin
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, 3065, VIC, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, 3010, VIC, Australia
- Melbourne Integrative Genomics, University of Melbourne, Parkville, 3010, VIC, Australia
| | - Davis J McCarthy
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, 3065, VIC, Australia.
- School of Mathematics and Statistics, University of Melbourne, Parkville, 3010, VIC, Australia.
- Melbourne Integrative Genomics, University of Melbourne, Parkville, 3010, VIC, Australia.
| |
Collapse
|