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Rusu EC, Monfort-Lanzas P, Bertran L, Barrientos-Riosalido A, Solé E, Mahmoudian R, Aguilar C, Briansó S, Mohamed F, Garcia S, Camaron J, Auguet T. Towards understanding post-COVID-19 condition: A systematic meta-analysis of transcriptomic alterations with sex-specific insights. Comput Biol Med 2024; 175:108507. [PMID: 38657468 DOI: 10.1016/j.compbiomed.2024.108507] [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: 11/24/2023] [Revised: 03/26/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Post COVID-19 Condition (PCC), characterized by lingering symptoms post-acute COVID-19, poses clinical challenges, highlighting the need to understand its underlying molecular mechanisms. This meta-analysis aims to shed light on the transcriptomic landscapes and sex-specific molecular dynamics intrinsic to PCC. METHODS A systematic review identified three studies suitable for comprehensive meta-analysis, encompassing 135 samples (57 PCC subjects and 78 recovered subjects). We performed meta-analysis on differential gene expression, a gene set enrichment analysis of Reactome pathways, and weighted gene co-expression network analysis (WGCNA). We performed a drug and disease enrichment analysis and also assessed sex-specific differences in expression patterns. KEY FINDINGS A clear difference was observed in the transcriptomic profiles of PCC subjects, with 530 differentially expressed genes (DEGs) identified. Enrichment analysis revealed that the altered pathways were predominantly implicated in cell cycle processes, immune dysregulation and histone modifications. Antioxidant compounds such as hesperitin were predominantly linked to the hub genes of the DEGs. Sex-specific analyses highlighted disparities in DEGs and altered pathways in male and female PCC patients, revealing a difference in the expression of ribosomal proteins. PCC in men was mostly linked to neuro-cardiovascular disorders, while women exhibited more diverse disorders, with a high index of respiratory conditions. CONCLUSION Our study reveals the intricate molecular processes underlying PCC, highlighting that the differences in molecular dynamics between males and females could be key to understanding and effectively managing the varied symptomatology of this condition.
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Affiliation(s)
- Elena Cristina Rusu
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and the Spanish National Research Council (CSIC), 46980, Valencia, Spain.
| | - Pablo Monfort-Lanzas
- Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria; Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Laia Bertran
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Andrea Barrientos-Riosalido
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Emilia Solé
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Razieh Mahmoudian
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Carmen Aguilar
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Silvia Briansó
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Fadel Mohamed
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Susana Garcia
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Javier Camaron
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Teresa Auguet
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain; Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
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2
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Jin G, Wang R, Jin Y, Song Y, Wang T. From intramuscular to nasal: unleashing the potential of nasal spray vaccines against coronavirus disease 2019. Clin Transl Immunology 2024; 13:e1514. [PMID: 38770238 PMCID: PMC11103645 DOI: 10.1002/cti2.1514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected 700 million people worldwide since its outbreak in 2019. The current pandemic strains, including Omicron and its large subvariant series, exhibit strong transmission and stealth. After entering the human body, the virus first infects nasal epithelial cells and invades host cells through the angiotensin-converting enzyme 2 receptor and transmembrane serine protease 2 on the host cell surface. The nasal cavity is an important body part that protects against the virus. Immunisation of the nasal mucosa produces immunoglobulin A antibodies that effectively neutralise viruses. Saline nasal irrigation, a type of physical therapy, can reduce the viral load in the nasal cavity and prevent viral infections to some extent. As a commonly used means to fight SARS-CoV-2, the intramuscular (IM) vaccine can induce the human body to produce a systemic immune response and immunoglobulin G antibody; however, the antibody is difficult to distribute to the nasal mucosa in time and cannot achieve a good preventive effect. Intranasal (IN) vaccines compensate for the shortcomings of IM vaccines, induce mucosal immune responses, and have a better effect in preventing infection. In this review, we discuss the nasal defence barrier, the harm caused by SARS-CoV-2, the mechanism of its invasion into host cells, nasal cleaning, IM vaccines and IN vaccines, and suggest increasing the development of IN vaccines, and use of IN vaccines as a supplement to IM vaccines.
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Affiliation(s)
- Ge Jin
- Faculty of MedicineDalian University of TechnologyDalianLiaoningChina
- Department of RadiotherapyCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoningChina
| | - Runze Wang
- Department of RadiotherapyCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoningChina
| | - Yi Jin
- Department of Breast SurgeryLiaoning Cancer Hospital and InstituteShenyangLiaoningChina
| | - Yingqiu Song
- Department of RadiotherapyCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoningChina
| | - Tianlu Wang
- Faculty of MedicineDalian University of TechnologyDalianLiaoningChina
- Department of RadiotherapyCancer Hospital of China Medical University, Liaoning Cancer Hospital and InstituteShenyangLiaoningChina
- Department of RadiotherapyCancer Hospital of Dalian University of TechnologyDalianLiaoningChina
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3
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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint. Immunity 2024; 57:1160-1176.e7. [PMID: 38697118 DOI: 10.1016/j.immuni.2024.04.009] [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: 03/28/2023] [Revised: 01/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Multimodal single-cell profiling methods can capture immune cell variations unfolding over time at the molecular, cellular, and population levels. Transforming these data into biological insights remains challenging. Here, we introduce a framework to integrate variations at the human population and single-cell levels in vaccination responses. Comparing responses following AS03-adjuvanted versus unadjuvanted influenza vaccines with CITE-seq revealed AS03-specific early (day 1) response phenotypes, including a B cell signature of elevated germinal center competition. A correlated network of cell-type-specific transcriptional states defined the baseline immune status associated with high antibody responders to the unadjuvanted vaccine. Certain innate subsets in the network appeared "naturally adjuvanted," with transcriptional states resembling those induced uniquely by AS03-adjuvanted vaccination. Consistently, CD14+ monocytes from high responders at baseline had elevated phospho-signaling responses to lipopolysaccharide stimulation. Our findings link baseline immune setpoints to early vaccine responses, with positive implications for adjuvant development and immune response engineering.
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Affiliation(s)
- Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; NIH-Oxford-Cambridge Scholars Program, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA.
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4
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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.
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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
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5
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Ni CQ, Xie WQ. Quantifying sodium hypochlorite content in hypochlorite-based disinfectants via phase-conversion headspace technique. J Chromatogr A 2024; 1721:464812. [PMID: 38569297 DOI: 10.1016/j.chroma.2024.464812] [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: 10/29/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024]
Abstract
In this work, a novel and efficient approach for sodium hypochlorite analysis is proposed via phase-conversion headspace technique, which is based on the gas chromatography (GC) detection of generated carbon dioxide (CO2) from the redox reaction of sodium hypochlorite with sodium oxalate. The data obtained by the proposed method suggest the high detecting precision and accuracy. In addition, the method has low detection limits (limit of quantification (LOQ) = 0.24 μg/mL), and the recoveries of added standard ranged from 98.33 to 101.27 %. The proposed phase-conversion headspace technique is efficient and automated, thereby offering an efficient strategy for highly efficient analysis of sodium hypochlorite and related products.
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Affiliation(s)
- Chen-Quan Ni
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Wei-Qi Xie
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.
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6
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Montini F, Nozzolillo A, Tedone N, Mistri D, Rancoita PM, Zanetta C, Mandelli A, Furlan R, Moiola L, Martinelli V, Rocca MA, Filippi M. COVID-19 has no impact on disease activity, progression and cognitive performance in people with multiple sclerosis: a 2-year study. J Neurol Neurosurg Psychiatry 2024; 95:342-347. [PMID: 37857497 DOI: 10.1136/jnnp-2023-332073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Sequelae of COVID-19 in people with multiple sclerosis (PwMS) have not been characterised. We explored whether COVID-19 is associated with an increased risk of disease activity, disability worsening, neuropsychological distress and cognitive dysfunction during the 18-24 months following SARS-COV-2 infection. METHODS We enrolled 174 PwMS with history of COVID-19 (MS-COVID) between March 2020 and March 2021 and compared them to an age, sex, disease duration, Expanded Disability Status Scale (EDSS), and a line of treatment-matched group of 348 PwMS with no history of COVID-19 in the same period (MS-NCOVID). We collected clinical, MRI data and SARS-CoV2 immune response in the 18-24 months following COVID-19 or baseline evaluation. At follow-up, PwMS also underwent a complete neuropsychological assessment with brief repeatable battery of neuropsychological tests and optimised scales for fatigue, anxiety, depression and post-traumatic stress symptoms. RESULTS 136 MS-COVID and 186 MS-NCOVID accepted the complete longitudinal evaluation. The two groups had similar rate of EDSS worsening (15% vs 11%, p=1.00), number of relapses (6% vs 5%, p=1.00), disease-modifying therapy change (7% vs 4%, p=0.81), patients with new T2-lesions (9% vs 11%, p=1.00) and gadolinium-enhancing lesions (7% vs 4%, p=1.00) on brain MRI. 22% of MS-COVID and 23% MS-NCOVID were cognitively impaired at 18-24 months evaluation, with similar prevalence of cognitive impairment (p=1.00). The z-scores of global and domain-specific cognitive functions and the prevalence of neuropsychiatric manifestations were also similar. No difference was detected in terms of SARS-CoV2 cellular immune response. CONCLUSIONS In PwMS, COVID-19 has no impact on disease activity, course and cognitive performance 18-24 months after infection.
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Affiliation(s)
| | | | - Nicolò Tedone
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Damiano Mistri
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Paola Mv Rancoita
- University Centre for Statistics in the Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milano, Italy
| | - Chiara Zanetta
- Neurology Unit, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Alessandra Mandelli
- Clinical Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Roberto Furlan
- Clinical Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Lucia Moiola
- Neurology Unit, IRCCS Ospedale San Raffaele, Milano, Italy
| | | | - Maria A Rocca
- Neurology Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Massimo Filippi
- Neurology Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
- Neurorehabilitation Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Neurophysiology Service, IRCCS Ospedale San Raffaele, Milano, Italy
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7
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Sugrue JA, Duffy D. Systems vaccinology studies - achievements and future potential. Microbes Infect 2024:105318. [PMID: 38460935 DOI: 10.1016/j.micinf.2024.105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Human immune responses to vaccination are variable both within and between populations. Systems vaccinology, which is the application of multi-omics technologies to vaccine studies, seeks to understand such variation and predict responses to optimise vaccine strategies. Here, we outline new approaches to systems vaccinology, focusing on the incorporation of additional cohorts, endpoints and technologies.
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Affiliation(s)
- Jamie A Sugrue
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université de Paris Cité, F75015, Paris, France.
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8
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Peluso MJ, Abdel-Mohsen M, Henrich TJ, Roan NR. Systems analysis of innate and adaptive immunity in Long COVID. Semin Immunol 2024; 72:101873. [PMID: 38460395 DOI: 10.1016/j.smim.2024.101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/11/2024]
Abstract
Since the onset of the COVID-19 pandemic, significant progress has been made in developing effective preventive and therapeutic strategies against severe acute SARS-CoV-2 infection. However, the management of Long COVID (LC), an infection-associated chronic condition that has been estimated to affect 5-20% of individuals following SARS-CoV-2 infection, remains challenging due to our limited understanding of its mechanisms. Although LC is a heterogeneous disease that is likely to have several subtypes, immune system disturbances appear common across many cases. The extent to which these immune perturbations contribute to LC symptoms, however, is not entirely clear. Recent advancements in multi-omics technologies, capable of detailed, cell-level analysis, have provided valuable insights into the immune perturbations associated with LC. Although these studies are largely descriptive in nature, they are the crucial first step towards a deeper understanding of the condition and the immune system's role in its development, progression, and resolution. In this review, we summarize the current understanding of immune perturbations in LC, covering both innate and adaptive immune responses, and the cytokines and analytes involved. We explore whether these findings support or challenge the primary hypotheses about LC's underlying mechanisms. We also discuss the crosstalk between various immune system components and how it can be disrupted in LC. Finally, we emphasize the need for more tissue- and subtype-focused analyses of LC, and for enhanced collaborative efforts to analyze common specimens from large cohorts, including those undergoing therapeutic interventions. These collective efforts are vital to unravel the fundaments of this new disease, and could also shed light on the prevention and treatment of the larger family of chronic illnesses linked to other microbial infections.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | | | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA; Department of Urology, University of California, San Francisco, USA.
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9
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Sampson OL, Jay C, Adland E, Csala A, Lim N, Ebbrecht SM, Gilligan LC, Taylor AE, George SS, Longet S, Jones LC, Barnes E, Frater J, Klenerman P, Dunachie S, Carrol M, Hawley J, Arlt W, Groll A, Goulder P. Gonadal androgens are associated with decreased type I interferon production by plasmacytoid dendritic cells and increased IgG titres to BNT162b2 following co-vaccination with live attenuated influenza vaccine in adolescents. Front Immunol 2024; 15:1329805. [PMID: 38481993 PMCID: PMC10933029 DOI: 10.3389/fimmu.2024.1329805] [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: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 04/09/2024] Open
Abstract
mRNA vaccine technologies introduced following the SARS-CoV-2 pandemic have highlighted the need to better understand the interaction of adjuvants and the early innate immune response. Type I interferon (IFN-I) is an integral part of this early innate response that primes several components of the adaptive immune response. Women are widely reported to respond better than men to tri- and quadrivalent influenza vaccines. Plasmacytoid dendritic cells (pDCs) are the primary cell type responsible for IFN-I production, and female pDCs produce more IFN-I than male pDCs since the upstream pattern recognition receptor Toll-like receptor 7 (TLR7) is encoded by X chromosome and is biallelically expressed by up to 30% of female immune cells. Additionally, the TLR7 promoter contains several putative androgen response elements, and androgens have been reported to suppress pDC IFN-I in vitro. Unexpectedly, therefore, we recently observed that male adolescents mount stronger antibody responses to the Pfizer BNT162b2 mRNA vaccine than female adolescents after controlling for natural SARS-CoV-2 infection. We here examined pDC behaviour in this same cohort to determine the impact of IFN-I on anti-spike and anti-receptor-binding domain IgG titres to BNT162b2. Through flow cytometry and least absolute shrinkage and selection operator (LASSO) modelling, we determined that serum-free testosterone was associated with reduced pDC IFN-I, but contrary to the well-described immunosuppressive role for androgens, the most bioactive androgen dihydrotestosterone was associated with increased IgG titres to BNT162b2. Also unexpectedly, we observed that co-vaccination with live attenuated influenza vaccine boosted the magnitude of IgG responses to BNT162b2. Together, these data support a model where systemic IFN-I increases vaccine-mediated immune responses, yet for vaccines with intracellular stages, modulation of the local IFN-I response may alter antigen longevity and consequently improve vaccine-driven immunity.
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Affiliation(s)
- Oliver L. Sampson
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Cecilia Jay
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Anna Csala
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Stella M. Ebbrecht
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Lorna C. Gilligan
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Angela E. Taylor
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Sherley Sherafin George
- Biochemistry Department, Clinical Science Building, Wythenshawe Hospital, Manchester, United Kingdom
| | - Stephanie Longet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucy C. Jones
- Department of Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Ellie Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - John Frater
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Susie Dunachie
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Miles Carrol
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Hawley
- Biochemistry Department, Clinical Science Building, Wythenshawe Hospital, Manchester, United Kingdom
| | - Wiebke Arlt
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- Medical Research Council London Institute of Medical Sciences (MRC LMS), Imperial College London, London, United Kingdom
| | - Andreas Groll
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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10
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Ye X, Yang S, Tu J, Xu L, Wang Y, Chen H, Yu R, Huang P. Leveraging baseline transcriptional features and information from single-cell data to power the prediction of influenza vaccine response. Front Cell Infect Microbiol 2024; 14:1243586. [PMID: 38384303 PMCID: PMC10879619 DOI: 10.3389/fcimb.2024.1243586] [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: 06/21/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Vaccination is still the primary means for preventing influenza virus infection, but the protective effects vary greatly among individuals. Identifying individuals at risk of low response to influenza vaccination is important. This study aimed to explore improved strategies for constructing predictive models of influenza vaccine response using gene expression data. Methods We first used gene expression and immune response data from the Immune Signatures Data Resource (IS2) to define influenza vaccine response-related transcriptional expression and alteration features at different time points across vaccination via differential expression analysis. Then, we mapped these features to single-cell resolution using additional published single-cell data to investigate the possible mechanism. Finally, we explored the potential of these identified transcriptional features in predicting influenza vaccine response. We used several modeling strategies and also attempted to leverage the information from single-cell RNA sequencing (scRNA-seq) data to optimize the predictive models. Results The results showed that models based on genes showing differential expression (DEGs) or fold change (DFGs) at day 7 post-vaccination performed the best in internal validation, while models based on DFGs had a better performance in external validation than those based on DEGs. In addition, incorporating baseline predictors could improve the performance of models based on days 1-3, while the model based on the expression profile of plasma cells deconvoluted from the model that used DEGs at day 7 as predictors showed an improved performance in external validation. Conclusion Our study emphasizes the value of using combination modeling strategy and leveraging information from single-cell levels in constructing influenza vaccine response predictive models.
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Affiliation(s)
- Xiangyu Ye
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- Department of Biostatistics, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junlan Tu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifan Wang
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Hongbo Chen
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Rongbin Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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11
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Ren J, Zhou X, Huang K, Chen L, Guo W, Feng K, Huang T, Cai YD. Identification of key genes associated with persistent immune changes and secondary immune activation responses induced by influenza vaccination after COVID-19 recovery by machine learning methods. Comput Biol Med 2024; 169:107883. [PMID: 38157776 DOI: 10.1016/j.compbiomed.2023.107883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
COVID-19 is hypothesized to exert enduring effects on the immune systems of patients, leading to alterations in immune-related gene expression. This study aimed to scrutinize the persistent implications of SARS-CoV-2 infection on gene expression and its influence on subsequent immune activation responses. We designed a machine learning-based approach to analyze transcriptomic data from both healthy individuals and patients who had recovered from COVID-19. Patients were categorized based on their influenza vaccination status and then compared with healthy controls. The initial sample set encompassed 86 blood samples from healthy controls and 72 blood samples from recuperated COVID-19 patients prior to influenza vaccination. The second sample set included 123 blood samples from healthy controls and 106 blood samples from recovered COVID-19 patients who had been vaccinated against influenza. For each sample, the dataset captured expression levels of 17,060 genes. Above two sample sets were first analyzed by seven feature ranking algorithms, yielding seven feature lists for each dataset. Then, each list was fed into the incremental feature selection method, incorporating three classic classification algorithms, to extract essential genes, classification rules and build efficient classifiers. The genes and rules were analyzed in this study. The main findings included that NEXN and ZNF354A were highly expressed in recovered COVID-19 patients, whereas MKI67 and GZMB were highly expressed in patients with secondary immune activation post-COVID-19 recovery. These pivotal genes could provide valuable insights for future health monitoring of COVID-19 patients and guide the creation of continued treatment regimens.
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Affiliation(s)
- Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ke Huang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China.
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China.
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200030, China.
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, 510507, China.
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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12
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Souquette A, Thomas PG. Variation in the basal immune state and implications for disease. eLife 2024; 13:e90091. [PMID: 38275224 PMCID: PMC10817719 DOI: 10.7554/elife.90091] [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: 06/13/2023] [Accepted: 01/21/2024] [Indexed: 01/27/2024] Open
Abstract
Analysis of pre-existing immunity and its effects on acute infection often focus on memory responses associated with a prior infectious exposure. However, memory responses occur in the context of the overall immune state and leukocytes must interact with their microenvironment and other immune cells. Thus, it is important to also consider non-antigen-specific factors which shape the composite basal state and functional capacity of the immune system, termed here as I0 ('I naught'). In this review, we discuss the determinants of I0. Utilizing influenza virus as a model, we then consider the effect of I0 on susceptibility to infection and disease severity. Lastly, we outline a mathematical framework and demonstrate how researchers can build and tailor models to specific needs. Understanding how diverse factors uniquely and collectively impact immune competence will provide valuable insights into mechanisms of immune variation, aid in screening for high-risk populations, and promote the development of broadly applicable prophylactic and therapeutic treatments.
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Affiliation(s)
- Aisha Souquette
- Department of Immunology, St. Jude Children's Research HospitalMemphisUnited States
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research HospitalMemphisUnited States
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13
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Chen L, Wan Y, Yang T, Zhang Q, Zeng Y, Zheng S, Ling Z, Xiao Y, Wan Q, Liu R, Yang C, Huang G, Zeng Q. Bibliometric and visual analysis of single-cell sequencing from 2010 to 2022. Front Genet 2024; 14:1285599. [PMID: 38274109 PMCID: PMC10808606 DOI: 10.3389/fgene.2023.1285599] [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: 09/04/2023] [Accepted: 12/31/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Single-cell sequencing (SCS) is a technique used to analyze the genome, transcriptome, epigenome, and other genetic data at the level of a single cell. The procedure is commonly utilized in multiple fields, including neurobiology, immunology, and microbiology, and has emerged as a key focus of life science research. However, a thorough and impartial analysis of the existing state and trends of SCS-related research is lacking. The current study aimed to map the development trends of studies on SCS during the years 2010-2022 through bibliometric software. Methods: Pertinent papers on SCS from 2010 to 2022 were obtained using the Web of Science Core Collection. Research categories, nations/institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords were analyzed using VOSviewer, the R package "bibliometric", and CiteSpace. Results: The bibliometric analysis included 9,929 papers published between 2010 and 2022, and showed a consistent increase in the quantity of papers each year. The United States was the source of the highest quantity of articles and citations in this field. The majority of articles were published in the periodical Nature Communications. Butler A was the most frequently quoted author on this topic, and his article "Integrating single-cell transcriptome data across diverse conditions, technologies, and species" has received numerous citations to date. The literature and keyword analysis showed that studies involving single-cell RNA sequencing (scRNA-seq) were prominent in this discipline during the study period. Conclusion: This study utilized bibliometric techniques to visualize research in SCS-related domains, which facilitated the identification of emerging patterns and future directions in the field. Current hot topics in SCS research include COVID-19, tumor microenvironment, scRNA-seq, and neuroscience. Our results are significant for scholars seeking to identify key issues and generate new research ideas.
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Affiliation(s)
- Ling Chen
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of BasicMedical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Yang
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qi Zhang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yuting Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuqi Zheng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Zhishan Ling
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yupeng Xiao
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qingyi Wan
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Ruili Liu
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Chun Yang
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, Guangdong Medical University, Dongguan, China
| | - Guozhi Huang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qing Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
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14
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Do WL, Wang L, Forgues M, Liu J, Rabibhadana S, Pupacdi B, Zhao Y, Gholian H, Bhudhisawasdi V, Pairojkul C, Sukeepaisarnjaroen W, Pugkhem A, Luvira V, Lertprasertsuke N, Chotirosniramit A, Auewarakul CU, Ungtrakul T, Sricharunrat T, Sangrajrang S, Phornphutkul K, Budhu A, Harris CC, Mahidol C, Ruchirawat M, Wang XW. Pan-viral serology uncovers distinct virome patterns as risk predictors of hepatocellular carcinoma and intrahepatic cholangiocarcinoma. Cell Rep Med 2023; 4:101328. [PMID: 38118412 PMCID: PMC10772458 DOI: 10.1016/j.xcrm.2023.101328] [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: 03/13/2023] [Revised: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
This study evaluates the pan-serological profiles of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) compared to several diseased and non-diseased control populations to identify risk factors and biomarkers of liver cancer. We used phage immunoprecipitation sequencing, an anti-viral antibody screening method using a synthetic-phage-displayed human virome epitope library, to screen patient serum samples for exposure to over 1,280 strains of pathogenic and non-pathogenic viruses. Using machine learning methods to develop an HCC or iCCA viral score, we discovered that both viral scores were positively associated with several liver function markers in two separate at-risk populations independent of viral hepatitis status. The HCC score predicted all-cause mortality over 8 years in patients with chronic liver disease at risk of HCC, while the viral hepatitis status was not predictive of survival. These results suggest that non-hepatitis viral infections may contribute to HCC and iCCA development and could be biomarkers in at-risk populations.
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Affiliation(s)
- Whitney L Do
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Limin Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jinping Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Yongmei Zhao
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Heelah Gholian
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Vor Luvira
- Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | | | | | | | | | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Mathuros Ruchirawat
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, Thailand.
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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15
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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16
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Wang B, Chen Z, Huang Y, Ding J, Lin Y, Wang M, Li X. Mitochondrial mass of circulating NK cells as a novel biomarker in severe SARS-CoV-2 infection. Int Immunopharmacol 2023; 124:110839. [PMID: 37639852 DOI: 10.1016/j.intimp.2023.110839] [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: 05/22/2023] [Revised: 08/05/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Severe SARS-CoV-2 infection results in lymphopenia and impaired function of T, B, and NK (TBNK-dominant) lymphocytes. Mitochondria are essential targets of SARS-CoV-2 and the efficacy of lymphocyte mitochondrial function for immunosurveillance in COVID-19 patients has not been evaluated. METHODS Multi-parametric flow cytometry was used to characterize mitochondrial function, including mitochondrial mass (MM) and low mitochondrial membrane potential (MMPlow), in TBNK-dominant lymphocytes from severe (n = 93) and moderate (n = 77) hospitalized COVID-19 patients. We compared the role of novel lymphocyte mitochondrial indicators and routine infection biomarkers as early predictors of severity and death in COVID-19 patients. We then developed a mortality decision tree prediction model based on immunosurveillance indicators through machine learning. RESULTS At admission, the MM of circulating NK cells (NK-MM) was the best discriminator of severe/moderate disease (AUC = 0.8067) compared with the routine infection biomarkers. The NK cell count and NK-MM displayed superior diagnostic effects to distinguish patients with non-fatal or fatal outcomes. Interestingly, NK-MM was significantly polarized in non-survivors, with some patients showing a decrease and others showing an abnormal increase. Kaplan-Meier analysis showed that NK-MM had the optimal predictive efficacy (hazard ratio = 11.66). The decision tree model has the highest proportion of importance for NK-MM, which is superior to the single diagnostic effect of the above indicators (AUC = 0.8900). CONCLUSION NK-MM was not only associated with disease severity, its abnormal increases or decreases also predicted mortality risk. The resulting decision tree prediction model is the first to focus on immune monitoring indicators to provide decision-making clues for COVID-19 clinical management.
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Affiliation(s)
- Bingqi Wang
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhenni Chen
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yiran Huang
- School of Clinical Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Jiayi Ding
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yingrui Lin
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Min Wang
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Xianping Li
- Department of Laboratory Medicine, the Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
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17
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Jay C, Adland E, Csala A, Lim N, Longet S, Ogbe A, Ratcliff J, Sampson O, Thompson CP, Turtle L, Barnes E, Dunachie S, Klenerman P, Carroll M, Goulder P. Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents. Front Immunol 2023; 14:1248630. [PMID: 37942333 PMCID: PMC10627794 DOI: 10.3389/fimmu.2023.1248630] [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: 06/27/2023] [Accepted: 09/15/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction The key to understanding the COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Young people are at a lower risk of COVID-19 mortality, females are at a lower risk than males, and females often generate stronger immune responses to vaccination. Methods We studied immune responses to two doses of BNT162b2 Pfizer COVID-19 vaccine in an adolescent cohort (n = 34, ages 12-16), an age group previously shown to elicit significantly greater immune responses to the same vaccine than young adults. Adolescents were studied with the aim of comparing their response to BNT162b2 to that of adults; and to assess the impacts of other factors such as sex, ongoing SARS-CoV-2 infection in schools, and prior exposure to endemic coronaviruses that circulate at high levels in young people. At the same time, we were able to evaluate immune responses to the co-administered live attenuated influenza vaccine. Blood samples from 34 adolescents taken before and after vaccination with COVID-19 and influenza vaccines were assayed for SARS-CoV-2-specific IgG and neutralising antibodies and cellular immunity specific for SARS-CoV-2 and endemic betacoronaviruses. The IgG targeting influenza lineages contained in the influenza vaccine were also assessed. Results Robust neutralising responses were identified in previously infected adolescents after one dose, and two doses were required in infection-naïve adolescents. As previously demonstrated, total IgG responses to SARS-CoV-2 Spike were significantly higher among vaccinated adolescents than among adults (aged 32-52) who received the BNT162b2 vaccine (comparing infection-naïve, 49,696 vs. 33,339; p = 0.03; comparing SARS-CoV-2 previously infected, 743,691 vs. 269,985; p <0.0001) by the MSD v-plex assay. There was no evidence of a stronger vaccine-induced immunity in females compared than in males. Discussion These findings may result from the introduction of novel mRNA vaccination platforms, generating patterns of immunity divergent from established trends and providing new insights into what might be protective following COVID-19 vaccination.
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Affiliation(s)
- Cecilia Jay
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anna Csala
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver Sampson
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Craig P. Thompson
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Warwick, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Susanna Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
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18
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Altmann DM, Whettlock EM, Liu S, Arachchillage DJ, Boyton RJ. The immunology of long COVID. Nat Rev Immunol 2023; 23:618-634. [PMID: 37433988 DOI: 10.1038/s41577-023-00904-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 07/13/2023]
Abstract
Long COVID is the patient-coined term for the disease entity whereby persistent symptoms ensue in a significant proportion of those who have had COVID-19, whether asymptomatic, mild or severe. Estimated numbers vary but the assumption is that, of all those who had COVID-19 globally, at least 10% have long COVID. The disease burden spans from mild symptoms to profound disability, the scale making this a huge, new health-care challenge. Long COVID will likely be stratified into several more or less discrete entities with potentially distinct pathogenic pathways. The evolving symptom list is extensive, multi-organ, multisystem and relapsing-remitting, including fatigue, breathlessness, neurocognitive effects and dysautonomia. A range of radiological abnormalities in the olfactory bulb, brain, heart, lung and other sites have been observed in individuals with long COVID. Some body sites indicate the presence of microclots; these and other blood markers of hypercoagulation implicate a likely role of endothelial activation and clotting abnormalities. Diverse auto-antibody (AAB) specificities have been found, as yet without a clear consensus or correlation with symptom clusters. There is support for a role of persistent SARS-CoV-2 reservoirs and/or an effect of Epstein-Barr virus reactivation, and evidence from immune subset changes for broad immune perturbation. Thus, the current picture is one of convergence towards a map of an immunopathogenic aetiology of long COVID, though as yet with insufficient data for a mechanistic synthesis or to fully inform therapeutic pathways.
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Affiliation(s)
- Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, Hammersmith Hospital, London, UK.
| | - Emily M Whettlock
- Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Siyi Liu
- Department of Immunology and Inflammation, Imperial College London, Hammersmith Hospital, London, UK
- Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Deepa J Arachchillage
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, Hammersmith Hospital, London, UK
- Department of Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
- Lung Division, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
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19
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Limoges MA, Quenum AJI, Chowdhury MMH, Rexhepi F, Namvarpour M, Akbari SA, Rioux-Perreault C, Nandi M, Lucier JF, Lemaire-Paquette S, Premkumar L, Durocher Y, Cantin A, Lévesque S, Dionne IJ, Menendez A, Ilangumaran S, Allard-Chamard H, Piché A, Ramanathan S. SARS-CoV-2 spike antigen-specific B cell and antibody responses in pre-vaccination period COVID-19 convalescent males and females with or without post-covid condition. Front Immunol 2023; 14:1223936. [PMID: 37809081 PMCID: PMC10551145 DOI: 10.3389/fimmu.2023.1223936] [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: 05/16/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Background Following SARS-CoV-2 infection a significant proportion of convalescent individuals develop the post-COVID condition (PCC) that is characterized by wide spectrum of symptoms encompassing various organs. Even though the underlying pathophysiology of PCC is not known, detection of viral transcripts and antigens in tissues other than lungs raise the possibility that PCC may be a consequence of aberrant immune response to the viral antigens. To test this hypothesis, we evaluated B cell and antibody responses to the SARS-CoV-2 antigens in PCC patients who experienced mild COVID-19 disease during the pre-vaccination period of COVID-19 pandemic. Methods The study subjects included unvaccinated male and female subjects who developed PCC or not (No-PCC) after clearing RT-PCR confirmed mild COVID-19 infection. SARS-CoV-2 D614G and omicron RBD specific B cell subsets in peripheral circulation were assessed by flow cytometry. IgG, IgG3 and IgA antibody titers toward RBD, spike and nucleocapsid antigens in the plasma were evaluated by ELISA. Results The frequency of the B cells specific to D614G-RBD were comparable in convalescent groups with and without PCC in both males and females. Notably, in females with PCC, the anti-D614G RBD specific double negative (IgD-CD27-) B cells showed significant correlation with the number of symptoms at acute of infection. Anti-spike antibody responses were also higher at 3 months post-infection in females who developed PCC, but not in the male PCC group. On the other hand, the male PCC group also showed consistently high anti-RBD IgG responses compared to all other groups. Conclusions The antibody responses to the spike protein, but not the anti-RBD B cell responses diverge between convalescent males and females who develop PCC. Our findings also suggest that sex-related factors may also be involved in the development of PCC via modulating antibody responses to the SARS-CoV-2 antigens.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | | | | | - Fjolla Rexhepi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Mozhdeh Namvarpour
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Sara Ali Akbari
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Christine Rioux-Perreault
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Madhuparna Nandi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Jean-François Lucier
- Department of Biology, Faculty of Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Samuel Lemaire-Paquette
- Unité de Recherche Clinique et épidémiologique, Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yves Durocher
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - André Cantin
- Departments of Medicine, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
- Laboratoire de Microbiologie, CIUSSS de l’Estrie – CHUS, Sherbrooke, QC, Canada
| | - Isabelle J. Dionne
- Faculty of Physical Activity Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
- Research Centre on Aging, Affiliated with CIUSSS de l’Estrie-CHUS, Sherbrooke, QC, Canada
| | - Alfredo Menendez
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Hugues Allard-Chamard
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alain Piché
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Sherbrooke, QC, Canada
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20
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Zhang JY, Whalley JP, Knight JC, Wicker LS, Todd JA, Ferreira RC. SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile. Genome Med 2023; 15:69. [PMID: 37700317 PMCID: PMC10498514 DOI: 10.1186/s13073-023-01227-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/04/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND The immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in COVID-19 patients has been extensively investigated. However, much less is known about the long-term effects of infection in patients and how it could affect the immune system and its capacity to respond to future perturbations. METHODS Using a targeted single-cell multiomics approach, we have recently identified a prolonged anti-inflammatory gene expression signature in T and NK cells in type 1 diabetes patients treated with low-dose IL-2. Here, we investigated the dynamics of this signature in three independent cohorts of COVID-19 patients: (i) the Oxford COVID-19 Multi-omics Blood Atlas (COMBAT) dataset, a cross-sectional cohort including 77 COVID-19 patients and ten healthy donors; (ii) the INCOV dataset, consisting of 525 samples taken from 209 COVID-19 patients during and after infection; and (iii) a longitudinal dataset consisting of 269 whole-blood samples taken from 139 COVID-19 patients followed for a period of up to 7 months after the onset of symptoms using a bulk transcriptomic approach. RESULTS We discovered that SARS-CoV-2 infection leads to a prolonged alteration of the gene expression profile of circulating T, B and NK cells and monocytes. Some of the genes affected were the same as those present in the IL-2-induced anti-inflammatory gene expression signature but were regulated in the opposite direction, implying a pro-inflammatory status. The altered transcriptional profile was detected in COVID-19 patients for at least 2 months after the onset of the disease symptoms but was not observed in response to influenza infection or sepsis. Gene network analysis suggested a central role for the transcriptional factor NF-κB in the regulation of the observed transcriptional alterations. CONCLUSIONS SARS-CoV-2 infection causes a prolonged increase in the pro-inflammatory transcriptional status that could predispose post-acute patients to the development of long-term health consequences, including autoimmune disease, reactivation of other viruses and disruption of the host immune system-microbiome ecosystem.
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Affiliation(s)
- Jia-Yuan Zhang
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Justin P Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Linda S Wicker
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ricardo C Ferreira
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
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21
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Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young K, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527892. [PMID: 36798286 PMCID: PMC9934605 DOI: 10.1101/2023.02.09.527892] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.
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Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Kyrlia Young
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
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22
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Kervevan J, Staropoli I, Slama D, Jeger-Madiot R, Donnadieu F, Planas D, Pietri MP, Loghmari-Bouchneb W, Alaba Tanah M, Robinot R, Boufassa F, White M, Salmon-Ceron D, Chakrabarti LA. Divergent adaptive immune responses define two types of long COVID. Front Immunol 2023; 14:1221961. [PMID: 37559726 PMCID: PMC10408302 DOI: 10.3389/fimmu.2023.1221961] [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: 05/13/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Background The role of adaptive immune responses in long COVID remains poorly understood, with contrasting hypotheses suggesting either an insufficient antiviral response or an excessive immune response associated with inflammatory damage. To address this issue, we set to characterize humoral and CD4+ T cell responses in long COVID patients prior to SARS-CoV-2 vaccination. Methods Long COVID patients who were seropositive (LC+, n=28) or seronegative (LC-, n=23) by spike ELISA assay were recruited based on (i) an initial SARS-CoV-2 infection documented by PCR or the conjunction of three major signs of COVID-19 and (ii) the persistence or resurgence of at least 3 symptoms for over 3 months. They were compared to COVID patients with resolved symptoms (RE, n=29) and uninfected control individuals (HD, n=29). Results The spectrum of persistent symptoms proved similar in both long COVID groups, with a trend for a higher number of symptoms in the seronegative group (median=6 vs 4.5; P=0.01). The use a highly sensitive S-flow assay enabled the detection of low levels of SARS-CoV-2 spike-specific IgG in 22.7% of ELISA-seronegative long COVID (LC-) patients. In contrast, spike-specific IgG levels were uniformly high in the LC+ and RE groups. Multiplexed antibody analyses to 30 different viral antigens showed that LC- patients had defective antibody responses to all SARS-CoV-2 proteins tested but had in most cases preserved responses to other viruses. A sensitive primary T cell line assay revealed low but detectable SARS-CoV-2-specific CD4 responses in 39.1% of LC- patients, while response frequencies were high in the LC+ and RE groups. Correlation analyses showed overall strong associations between humoral and cellular responses, with exceptions in the LC- group. Conclusions These findings provide evidence for two major types of antiviral immune responses in long COVID. Seropositive patients showed coordinated cellular and humoral responses at least as high as those of recovered patients. In contrast, ELISA-seronegative long COVID patients showed overall low antiviral responses, with detectable specific CD4+ T cells and/or antibodies in close to half of patients (52.2%). These divergent findings in patients sharing a comparable spectrum of persistent symptoms raise the possibility of multiple etiologies in long COVID.
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Affiliation(s)
- Jérôme Kervevan
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Dorsaf Slama
- Department of Infectious Diseases and Immunology, Hôtel Dieu Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité, Paris, France
| | - Raphaël Jeger-Madiot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Françoise Donnadieu
- Infectious Disease Analytics and Epidemiology G5 Unit, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Marie-Pierre Pietri
- Department of Infectious Diseases and Immunology, Hôtel Dieu Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité, Paris, France
| | - Wiem Loghmari-Bouchneb
- Department of Infectious Diseases and Immunology, Hôtel Dieu Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité, Paris, France
| | - Motolete Alaba Tanah
- Department of Infectious Diseases and Immunology, Hôtel Dieu Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité, Paris, France
| | - Rémy Robinot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Center for Research in Epidemiology and Population Health (CESP), Le Kremlin-Bicêtre, France
| | - Michael White
- Infectious Disease Analytics and Epidemiology G5 Unit, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Dominique Salmon-Ceron
- Department of Infectious Diseases and Immunology, Hôtel Dieu Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris Cité, Paris, France
| | - Lisa A. Chakrabarti
- Virus and Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR3569, Paris, France
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23
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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24
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Strobl J, Haniffa M. Functional heterogeneity of human skin-resident memory T cells in health and disease. Immunol Rev 2023; 316:104-119. [PMID: 37144705 PMCID: PMC10952320 DOI: 10.1111/imr.13213] [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: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The human skin is populated by a diverse pool of memory T cells, which can act rapidly in response to pathogens and cancer antigens. Tissue-resident memory T cells (TRM ) have been implicated in range of allergic, autoimmune and inflammatory skin diseases. Clonal expansion of cells with TRM properties is also known to contribute to cutaneous T-cell lymphoma. Here, we review the heterogeneous phenotypes, transcriptional programs, and effector functions of skin TRM . We summarize recent studies on TRM formation, longevity, plasticity, and retrograde migration and contextualize the findings to skin TRM and their role in maintaining skin homeostasis and altered functions in skin disease.
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Affiliation(s)
- Johanna Strobl
- Department of DermatologyMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular MedicineViennaAustria
| | - Muzlifah Haniffa
- Wellcome Sanger InstituteCambridgeUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUK
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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25
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Barmada A, Klein J, Ramaswamy A, Brodsky NN, Jaycox JR, Sheikha H, Jones KM, Habet V, Campbell M, Sumida TS, Kontorovich A, Bogunovic D, Oliveira CR, Steele J, Hall EK, Pena-Hernandez M, Monteiro V, Lucas C, Ring AM, Omer SB, Iwasaki A, Yildirim I, Lucas CL. Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine-associated myocarditis. Sci Immunol 2023; 8:eadh3455. [PMID: 37146127 PMCID: PMC10468758 DOI: 10.1126/sciimmunol.adh3455] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/19/2023] [Indexed: 05/07/2023]
Abstract
Rare immune-mediated cardiac tissue inflammation can occur after vaccination, including after SARS-CoV-2 mRNA vaccines. However, the underlying immune cellular and molecular mechanisms driving this pathology remain poorly understood. Here, we investigated a cohort of patients who developed myocarditis and/or pericarditis with elevated troponin, B-type natriuretic peptide, and C-reactive protein levels as well as cardiac imaging abnormalities shortly after SARS-CoV-2 mRNA vaccination. Contrary to early hypotheses, patients did not demonstrate features of hypersensitivity myocarditis, nor did they have exaggerated SARS-CoV-2-specific or neutralizing antibody responses consistent with a hyperimmune humoral mechanism. We additionally found no evidence of cardiac-targeted autoantibodies. Instead, unbiased systematic immune serum profiling revealed elevations in circulating interleukins (IL-1β, IL-1RA, and IL-15), chemokines (CCL4, CXCL1, and CXCL10), and matrix metalloproteases (MMP1, MMP8, MMP9, and TIMP1). Subsequent deep immune profiling using single-cell RNA and repertoire sequencing of peripheral blood mononuclear cells during acute disease revealed expansion of activated CXCR3+ cytotoxic T cells and NK cells, both phenotypically resembling cytokine-driven killer cells. In addition, patients displayed signatures of inflammatory and profibrotic CCR2+ CD163+ monocytes, coupled with elevated serum-soluble CD163, that may be linked to the late gadolinium enhancement on cardiac MRI, which can persist for months after vaccination. Together, our results demonstrate up-regulation in inflammatory cytokines and corresponding lymphocytes with tissue-damaging capabilities, suggesting a cytokine-dependent pathology, which may further be accompanied by myeloid cell-associated cardiac fibrosis. These findings likely rule out some previously proposed mechanisms of mRNA vaccine--associated myopericarditis and point to new ones with relevance to vaccine development and clinical care.
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Affiliation(s)
- Anis Barmada
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anjali Ramaswamy
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nina N. Brodsky
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Jillian R. Jaycox
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Hassan Sheikha
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Kate M. Jones
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Victoria Habet
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Melissa Campbell
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Tomokazu S. Sumida
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Amy Kontorovich
- The Zena and Michael A. Wiener Cardiovascular Institute; Mindich Child Health and Development Institute; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- The Zena and Michael A. Wiener Cardiovascular Institute; Mindich Child Health and Development Institute; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Inborn Errors of Immunity; Precision Immunology Institute; Mindich Child Health and Development Institute; Department of Pediatrics; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos R. Oliveira
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Jeremy Steele
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - E. Kevin Hall
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Mario Pena-Hernandez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Valter Monteiro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Infection and Immunity, Yale University, New Haven, CT, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Saad B. Omer
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Yale Center for Infection and Immunity, Yale University, New Haven, CT, USA
| | - Inci Yildirim
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Yale Center for Infection and Immunity, Yale University, New Haven, CT, USA
| | - Carrie L. Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers B, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287474. [PMID: 37090674 PMCID: PMC10120791 DOI: 10.1101/2023.03.20.23287474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Advances in multimodal single cell analysis can empower high-resolution dissection of human vaccination responses. The resulting data capture multiple layers of biological variations, including molecular and cellular states, vaccine formulations, inter- and intra-subject differences, and responses unfolding over time. Transforming such data into biological insight remains a major challenge. Here we present a systematic framework applied to multimodal single cell data obtained before and after influenza vaccination without adjuvants or pandemic H5N1 vaccination with the AS03 adjuvant. Our approach pinpoints responses shared across or unique to specific cell types and identifies adjuvant specific signatures, including pro-survival transcriptional states in B lymphocytes that emerged one day after vaccination. We also reveal that high antibody responders to the unadjuvanted vaccine have a distinct baseline involving a rewired network of cell type specific transcriptional states. Remarkably, the status of certain innate immune cells in this network in high responders of the unadjuvanted vaccine appear "naturally adjuvanted": they resemble phenotypes induced early in the same cells only by vaccination with AS03. Furthermore, these cell subsets have elevated frequency in the blood at baseline and increased cell-intrinsic phospho-signaling responses after LPS stimulation ex vivo in high compared to low responders. Our findings identify how variation in the status of multiple immune cell types at baseline may drive robust differences in innate and adaptive responses to vaccination and thus open new avenues for vaccine development and immune response engineering in humans.
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Affiliation(s)
- Matthew P. Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Brian Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Juan A. Quiel
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Arjun Jain
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Pamela L. Schwartzberg
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cell Signaling and Immunity Section, NIAID, NIH, Bethesda, MD, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
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Tang W, Xie H, Ye Z, Eick-Cost AA, Scheckelhoff M, Gustin CE, Bream JH, Plant EP. Post-vaccination serum cytokines levels correlate with breakthrough influenza infections. Sci Rep 2023; 13:1174. [PMID: 36670200 PMCID: PMC9857916 DOI: 10.1038/s41598-023-28295-8] [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: 10/03/2022] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Post-vaccination cytokine levels from 256 young adults who subsequently suffered breakthrough influenza infections were compared with matched controls. Modulation within the immune system is important for eliciting a protective response, and the optimal response differs according to vaccine formulation and delivery. For both inactivated influenza vaccine (IIV) and live attenuated influenza vaccines (LAIV) lower levels of IL-8 were observed in post-vaccination sera. Post-vaccination antibody levels were higher and IFN-γ levels were lower in IIV sera compared to LAIV sera. Subjects who suffered breakthrough infections after IIV vaccination had higher levels of sCD25 compared to the control group. There were differences in LAIV post-vaccination interleukin levels for subjects who subsequently suffered breakthrough infections, but these differences were masked in subjects who received concomitant vaccines. Wide variances, sex-based differences and confounders such as concomitant vaccines thwart the establishment of specific cytokine responses as a correlate of protection, but our results provide real world evidence that the status of the immune system following vaccination is important for successful vaccination and subsequent protection against disease.
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Affiliation(s)
- Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Angelia A Eick-Cost
- Armed Forces Health Surveillance Division, Defense Health Agency, Silver Spring, MD, USA
| | - Mark Scheckelhoff
- Armed Forces Health Surveillance Division, Defense Health Agency, Silver Spring, MD, USA
| | - Courtney E Gustin
- Armed Forces Health Surveillance Division, Defense Health Agency, Silver Spring, MD, USA
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ewan P Plant
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA.
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