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Cho H, Kwon H, Kim SH, Ahn HM, Choi BK, Lee GK, Park SY, Lim HJ, Hwang JA, Lim J, Han JY, Lee Y. Seasonal influences on the efficacy of anti-programmed cell death (ligand) 1 inhibitors in lung cancer. Cancer 2024. [PMID: 38941496 DOI: 10.1002/cncr.35454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/27/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND Seasonal variations in systemic immunity have been reported. This study aimed to evaluate whether seasonality affects the efficacy of anticancer immunotherapy. METHODS A total of 604 patients with lung cancer receiving single anti-programmed cell death (ligand) 1 (anti-PD-[L]1) inhibitors from two prospective observational cohorts were screened. Primary outcomes were progression-free survival (PFS) and overall survival (OS). Patients were classified into two groups according to the season when the treatment started: winter (November-February) and other seasons (March-October). Kaplan-Meier analysis and Cox proportional hazards models were fitted to evaluate the impact of seasonality on survival. For validation, propensity score matching was performed. RESULTS A total of 484 patients with advanced non-small cell lung cancer were included. In an unmatched population, multivariable analysis demonstrated that the winter group (n = 173) had a significantly lower risk of progression or death from immunotherapy than the other group (n = 311) (PFS: hazard ratio [HR], 0.77 [95% confidence interval (CI), 0.62-0.96]; p = .018; OS: HR, 0.77 [95% CI, 0.1-0.98]; p = .032). In a propensity score-matched population, the winter group (n = 162) showed significantly longer median PFS (2.8 months [95% CI, 1.9-4.1 months] vs. 2.0 months [95% CI, 1.4-2.7 months]; p = .009) than the other group (n = 162). The winter group's median OS was also significantly longer than that of the other group (13.4 months [95% CI, 10.2-18.0 months] vs. 8.0 months [95% CI, 3.6-8.7 months]; p = .012). The trend toward longer survival in the winter group continued in subgroup analyses. CONCLUSIONS Starting an anti-PD-(L)1 inhibitor in winter was associated with better treatment outcomes in patients with lung cancer compared to other seasons.
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Affiliation(s)
- Hyunsoon Cho
- Department of Cancer AI and Digital Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
- Integrated Biostatistics Branch, Division of Cancer Data Science, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Hoejun Kwon
- Department of Cancer AI and Digital Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Se Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyung-Min Ahn
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Beom K Choi
- Biomedicine Production Branch, National Cancer Center, Goyang, Republic of Korea
| | - Geon Kook Lee
- Department of Pathology, National Cancer Center, Goyang, Republic of Korea
| | - Seog-Yun Park
- Department of Pathology, National Cancer Center, Goyang, Republic of Korea
| | - Hyun-Ju Lim
- Department of Radiology, National Cancer Center, Goyang, Republic of Korea
| | - Jung-Ah Hwang
- Genomics Core Facility, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jiyeon Lim
- Immuno-Oncology Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
- Division of Hematology and Oncology, Department of Internal Medicine, National Cancer Center, Goyang, Republic of Korea
| | - Youngjoo Lee
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
- Division of Hematology and Oncology, Department of Internal Medicine, National Cancer Center, Goyang, Republic of Korea
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Glehr G, Riquelme P, Kronenberg K, Lohmayer R, López-Madrona VJ, Kapinsky M, Schlitt HJ, Geissler EK, Spang R, Haferkamp S, Hutchinson JA. Restricting datasets to classifiable samples augments discovery of immune disease biomarkers. Nat Commun 2024; 15:5417. [PMID: 38926389 PMCID: PMC11208602 DOI: 10.1038/s41467-024-49094-3] [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: 05/04/2023] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Immunological diseases are typically heterogeneous in clinical presentation, severity and response to therapy. Biomarkers of immune diseases often reflect this variability, especially compared to their regulated behaviour in health. This leads to a common difficulty that frustrates biomarker discovery and interpretation - namely, unequal dispersion of immune disease biomarker expression between patient classes necessarily limits a biomarker's informative range. To solve this problem, we introduce dataset restriction, a procedure that splits datasets into classifiable and unclassifiable samples. Applied to synthetic flow cytometry data, restriction identifies biomarkers that are otherwise disregarded. In advanced melanoma, restriction finds biomarkers of immune-related adverse event risk after immunotherapy and enables us to build multivariate models that accurately predict immunotherapy-related hepatitis. Hence, dataset restriction augments discovery of immune disease biomarkers, increases predictive certainty for classifiable samples and improves multivariate models incorporating biomarkers with a limited informative range. This principle can be directly extended to any classification task.
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Affiliation(s)
- Gunther Glehr
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Paloma Riquelme
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | | | - Robert Lohmayer
- Algorithmic Bioinformatics Research Group, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | | | - Hans J Schlitt
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Edward K Geissler
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, University of Regensburg, Regensburg, Germany
| | - Sebastian Haferkamp
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - James A Hutchinson
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany.
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3
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Balog JÁ, Horti-Oravecz K, Kövesdi D, Bozsik A, Papp J, Butz H, Patócs A, Szebeni GJ, Grolmusz VK. Peripheral immunophenotyping reveals lymphocyte stimulation in healthy women living with hereditary breast and ovarian cancer syndrome. iScience 2024; 27:109882. [PMID: 38799565 PMCID: PMC11126817 DOI: 10.1016/j.isci.2024.109882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 (gpath(BRCA1/2)) represent genetic susceptibility for hereditary breast and ovarian cancer syndrome. Tumor-immune interactions are key contributors to breast cancer pathogenesis. Although earlier studies confirmed pro-tumorigenic immunological alterations in breast cancer patients, data are lacking in healthy carriers of gpath(BRCA1/2). Peripheral blood mononuclear cells of 66 women with or without germline predisposition or breast cancer were studied with a mass cytometry panel that identified 4 immune subpopulations of altered frequencies between healthy controls and healthy gpath(BRCA1) carriers, while no difference was observed in healthy gpath(BRCA2) carriers compared to controls. Moreover, 3 (one IgD-CD27+CD95+ B cell subpopulation and two CD45RA-CCR7+CD38+ CD4+ T cell subpopulations) out of these 4 subpopulations were also elevated in triple-negative breast cancer patients compared to controls. Our results reveal an activated peripheral immune phenotype in healthy carriers of gpath(BRCA1) that needs to be further elucidated to be leveraged in risk-reducing strategies.
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Affiliation(s)
- József Ágoston Balog
- Institute of Genetics, Laboratory of Functional Genomics, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Core Facility, HUN-REN Biological Research Center, 6726 Szeged, Hungary
| | - Klaudia Horti-Oravecz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- Semmelweis University, Doctoral School, 1085 Budapest, Hungary
| | - Dorottya Kövesdi
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
| | - Janos Papp
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Oncology Biobank, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Gábor János Szebeni
- Institute of Genetics, Laboratory of Functional Genomics, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Core Facility, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Department of Internal Medicine, Hematology Centre, Faculty of Medicine University of Szeged, 6725 Szeged, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
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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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Nakamura N, Kobashi Y, Kim KS, Park H, Tani Y, Shimazu Y, Zhao T, Nishikawa Y, Omata F, Kawashima M, Yoshida M, Abe T, Saito Y, Senoo Y, Nonaka S, Takita M, Yamamoto C, Kawamura T, Sugiyama A, Nakayama A, Kaneko Y, Jeong YD, Tatematsu D, Akao M, Sato Y, Iwanami S, Fujita Y, Wakui M, Aihara K, Kodama T, Shibuya K, Iwami S, Tsubokura M. Modeling and predicting individual variation in COVID-19 vaccine-elicited antibody response in the general population. PLOS DIGITAL HEALTH 2024; 3:e0000497. [PMID: 38701055 PMCID: PMC11068210 DOI: 10.1371/journal.pdig.0000497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/14/2024] [Indexed: 05/05/2024]
Abstract
As we learned during the COVID-19 pandemic, vaccines are one of the most important tools in infectious disease control. To date, an unprecedentedly large volume of high-quality data on COVID-19 vaccinations have been accumulated. For preparedness in future pandemics beyond COVID-19, these valuable datasets should be analyzed to best shape an effective vaccination strategy. We are collecting longitudinal data from a community-based cohort in Fukushima, Japan, that consists of 2,407 individuals who underwent serum sampling two or three times after a two-dose vaccination with either BNT162b2 or mRNA-1273. Using the individually reconstructed time courses of the vaccine-elicited antibody response based on mathematical modeling, we first identified basic demographic and health information that contributed to the main features of the antibody dynamics, i.e., the peak, the duration, and the area under the curve. We showed that these three features of antibody dynamics were partially explained by underlying medical conditions, adverse reactions to vaccinations, and medications, consistent with the findings of previous studies. We then applied to these factors a recently proposed computational method to optimally fit an "antibody score", which resulted in an integer-based score that can be used as a basis for identifying individuals with higher or lower antibody titers from basic demographic and health information. The score can be easily calculated by individuals themselves or by medical practitioners. Although the sensitivity of this score is currently not very high, in the future, as more data become available, it has the potential to identify vulnerable populations and encourage them to get booster vaccinations. Our mathematical model can be extended to any kind of vaccination and therefore can form a basis for policy decisions regarding the distribution of booster vaccines to strengthen immunity in future pandemics.
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Affiliation(s)
- Naotoshi Nakamura
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yurie Kobashi
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima, Japan
| | - Kwang Su Kim
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Science System Simulation, Pukyong National University, Busan, South Korea
- Department of Mathematics, Pusan National University, Busan, South Korea
| | - Hyeongki Park
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuta Tani
- Medical Governance Research Institute, Tokyo, Japan
| | - Yuzo Shimazu
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tianchen Zhao
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoshitaka Nishikawa
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima, Japan
| | - Fumiya Omata
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima, Japan
| | - Moe Kawashima
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Toshiki Abe
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Yuki Senoo
- Medical Governance Research Institute, Tokyo, Japan
| | - Saori Nonaka
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Morihito Takita
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Chika Yamamoto
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Akira Sugiyama
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Aya Nakayama
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yudai Kaneko
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
- Medical & Biological Laboratories Co., Ltd, Tokyo, Japan
| | - Yong Dam Jeong
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Mathematics, Pusan National University, Busan, South Korea
| | - Daiki Tatematsu
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Marwa Akao
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoya Iwanami
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yasuhisa Fujita
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Masatoshi Wakui
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kazuyuki Aihara
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Shibuya
- Soma Medical Center of Vaccination for COVID-19, Fukushima, Japan
- Tokyo Foundation for Policy Research, Tokyo, Japan
| | - Shingo Iwami
- interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Science Groove Inc., Fukuoka, Japan
| | - Masaharu Tsubokura
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
- Department of General Internal Medicine, Hirata Central Hospital, Fukushima, Japan
- Medical Governance Research Institute, Tokyo, Japan
- Minamisoma Municipal General Hospital, Fukushima, Japan
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Kempaiah P, Libertin CR, Chitale RA, Naeyma I, Pleqi V, Sheele JM, Iandiorio MJ, Hoogesteijn AL, Caulfield TR, Rivas AL. Decoding Immuno-Competence: A Novel Analysis of Complete Blood Cell Count Data in COVID-19 Outcomes. Biomedicines 2024; 12:871. [PMID: 38672225 PMCID: PMC11048687 DOI: 10.3390/biomedicines12040871] [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: 02/10/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND While 'immuno-competence' is a well-known term, it lacks an operational definition. To address this omission, this study explored whether the temporal and structured data of the complete blood cell count (CBC) can rapidly estimate immuno-competence. To this end, one or more ratios that included data on all monocytes, lymphocytes and neutrophils were investigated. MATERIALS AND METHODS Longitudinal CBC data collected from 101 COVID-19 patients (291 observations) were analyzed. Dynamics were estimated with several approaches, which included non-structured (the classic CBC format) and structured data. Structured data were assessed as complex ratios that capture multicellular interactions among leukocytes. In comparing survivors with non-survivors, the hypothesis that immuno-competence may exhibit feedback-like (oscillatory or cyclic) responses was tested. RESULTS While non-structured data did not distinguish survivors from non-survivors, structured data revealed immunological and statistical differences between outcomes: while survivors exhibited oscillatory data patterns, non-survivors did not. In survivors, many variables (including IL-6, hemoglobin and several complex indicators) showed values above or below the levels observed on day 1 of the hospitalization period, displaying L-shaped data distributions (positive kurtosis). In contrast, non-survivors did not exhibit kurtosis. Three immunologically defined data subsets included only survivors. Because information was based on visual patterns generated in real time, this method can, potentially, provide information rapidly. DISCUSSION The hypothesis that immuno-competence expresses feedback-like loops when immunological data are structured was not rejected. This function seemed to be impaired in immuno-suppressed individuals. While this method rapidly informs, it is only a guide that, to be confirmed, requires additional tests. Despite this limitation, the fact that three protective (survival-associated) immunological data subsets were observed since day 1 supports many clinical decisions, including the early and personalized prognosis and identification of targets that immunomodulatory therapies could pursue. Because it extracts more information from the same data, structured data may replace the century-old format of the CBC.
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Affiliation(s)
- Prakasha Kempaiah
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (P.K.); (V.P.)
| | | | - Rohit A. Chitale
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Islam Naeyma
- Department of Neuroscience, Division of QHS Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (I.N.); (T.R.C.)
| | - Vasili Pleqi
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (P.K.); (V.P.)
| | | | - Michelle J. Iandiorio
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | | | - Thomas R. Caulfield
- Department of Neuroscience, Division of QHS Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (I.N.); (T.R.C.)
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ariel L. Rivas
- Center for Global Health, Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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Quiros-Roldan E, Sottini A, Natali PG, Imberti L. The Impact of Immune System Aging on Infectious Diseases. Microorganisms 2024; 12:775. [PMID: 38674719 PMCID: PMC11051847 DOI: 10.3390/microorganisms12040775] [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: 03/01/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Immune system aging is becoming a field of increasing public health interest because of prolonged life expectancy, which is not paralleled by an increase in health expectancy. As age progresses, innate and adaptive immune systems undergo changes, which are defined, respectively, as inflammaging and immune senescence. A wealth of available data demonstrates that these two conditions are closely linked, leading to a greater vulnerability of elderly subjects to viral, bacterial, and opportunistic infections as well as lower post-vaccination protection. To face this novel scenario, an in-depth assessment of the immune players involved in this changing epidemiology is demanded regarding the individual and concerted involvement of immune cells and mediators within endogenous and exogenous factors and co-morbidities. This review provides an overall updated description of the changes affecting the aging immune system, which may be of help in understanding the underlying mechanisms associated with the main age-associated infectious diseases.
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Affiliation(s)
- Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, ASST- Spedali Civili and DSCS- University of Brescia, 25123 Brescia, Italy;
| | - Alessandra Sottini
- Clinical Chemistry Laboratory, Services Department, ASST Spedali Civili of Brescia, 25123 Brescia, Italy;
| | - Pier Giorgio Natali
- Mediterranean Task Force for Cancer Control (MTCC), Via Pizzo Bernina, 14, 00141 Rome, Italy;
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, P. le Spedali Civili, 1, 25123 Brescia, Italy
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8
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Papotti B, Dessena M, Adorni MP, Paleari D, Rinaldi L, Bernini F. In vitro evaluation of the immunomodulatory activity of the nutraceutical formulation AminoDefence. Int J Food Sci Nutr 2024; 75:173-184. [PMID: 38030612 DOI: 10.1080/09637486.2023.2283688] [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: 09/01/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Immune system (IS) functionality is warranted by inter-dependent processes that balance body defences without exceeding in inflammation. An ideal nutraceutical approach should sustain the protective IS activity while controlling inflammation. The potential immunomodulatory activity of the food supplement (FS) AminoDefence was studied in resting macrophages RAW264.7 and following stimulation of bacterial- and viral-associated inflammation trough LPS and PolyI:C treatments, respectively. In unstimulated macrophages, the formulation exerted a dose-dependent immunostimulant activity by up-regulating NO, IL-6, TNF-α and MCP-1 release, while it dampened the aberrant release of these factors induced by pro-inflammatory stimuli. Exploring the contribution of single components Echinacea purpurea (E. purpurea) extract and quercetin, used at proportional concentrations than in whole formulation, a more pronounced immunostimulant effect was observed for E. purpurea, and an anti-inflammatory activity for quercetin. Hence, AminoDefence exerts an immunomodulatory activity in macrophages by effectively stimulating a protective inflammatory response and limiting it in cases of excessive inflammation.
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Affiliation(s)
- Bianca Papotti
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Mattia Dessena
- Department of Medicine and Surgery, Unit of Neuroscience, University of Parma, Parma, Italy
| | - Maria Pia Adorni
- Department of Medicine and Surgery, Unit of Neuroscience, University of Parma, Parma, Italy
| | | | | | - Franco Bernini
- Department of Food and Drug, University of Parma, Parma, Italy
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Cevirgel A, Shetty SA, Vos M, Nanlohy NM, Beckers L, Bijvank E, Rots N, van Beek J, Buisman A, van Baarle D. Pre-vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination. Aging Cell 2024; 23:e14048. [PMID: 38146131 PMCID: PMC10861208 DOI: 10.1111/acel.14048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/27/2023] Open
Abstract
Effective vaccine-induced immune responses are particularly essential in older adults who face an increased risk of immunosenescence. However, the complexity and variability of the human immune system make predicting vaccine responsiveness challenging. To address this knowledge gap, our study aimed to characterize immune profiles that are predictive of vaccine responsiveness using "immunotypes" as an innovative approach. We analyzed an extensive set of innate and adaptive immune cell subsets in the whole blood of 307 individuals (aged 25-92) pre- and post-influenza vaccination which we associated with day 28 hemagglutination inhibition (HI) antibody titers. Building on our previous work that stratified individuals into nine immunotypes based on immune cell subsets, we identified two pre-vaccination immunotypes associated with weak and one showing robust day 28 antibody response. Notably, the weak responders demonstrated HLA-DR+ T-cell signatures, while the robust responders displayed a high naïve-to-memory T-cell ratio and percentage of nonclassical monocytes. These specific signatures deepen our understanding of the relationship between the baseline of the immune system and its functional potential. This approach could enhance our ability to identify individuals at risk of immunosenescence. Our findings highlight the potential of pre-vaccination immunotypes as an innovative tool for informing personalized vaccination strategies and improving health outcomes, particularly for aging populations.
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Affiliation(s)
- Alper Cevirgel
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Sudarshan A. Shetty
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Martijn Vos
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nening M. Nanlohy
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Lisa Beckers
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Elske Bijvank
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nynke Rots
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Josine van Beek
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Anne‐Marie Buisman
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology research groupUniversity Medical Center GroningenGroningenThe Netherlands
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10
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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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11
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Mettelman RC, Souquette A, Van de Velde LA, Vegesana K, Allen EK, Kackos CM, Trifkovic S, DeBeauchamp J, Wilson TL, St James DG, Menon SS, Wood T, Jelley L, Webby RJ, Huang QS, Thomas PG. Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology. Nat Immunol 2023; 24:1511-1526. [PMID: 37592015 PMCID: PMC10566627 DOI: 10.1038/s41590-023-01590-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/13/2023] [Indexed: 08/19/2023]
Abstract
Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lee-Ann Van de Velde
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina M Kackos
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taylor L Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Deryn G St James
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Smrithi S Menon
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy Wood
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Q Sue Huang
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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12
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Wang R, Xiong K, Wang Z, Wu D, Hu B, Ruan J, Sun C, Ma D, Li L, Liao S. Immunodiagnosis - the promise of personalized immunotherapy. Front Immunol 2023; 14:1216901. [PMID: 37520576 PMCID: PMC10372420 DOI: 10.3389/fimmu.2023.1216901] [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: 05/04/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Immunotherapy showed remarkable efficacy in several cancer types. However, the majority of patients do not benefit from immunotherapy. Evaluating tumor heterogeneity and immune status before treatment is key to identifying patients that are more likely to respond to immunotherapy. Demographic characteristics (such as sex, age, and race), immune status, and specific biomarkers all contribute to response to immunotherapy. A comprehensive immunodiagnostic model integrating all these three dimensions by artificial intelligence would provide valuable information for predicting treatment response. Here, we coined the term "immunodiagnosis" to describe the blueprint of the immunodiagnostic model. We illustrated the features that should be included in immunodiagnostic model and the strategy of constructing the immunodiagnostic model. Lastly, we discussed the incorporation of this immunodiagnosis model in clinical practice in hopes of improving the prognosis of tumor immunotherapy.
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Affiliation(s)
- Renjie Wang
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kairong Xiong
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhimin Wang
- Division of Endocrinology and Metabolic Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Di Wu
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bai Hu
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinghan Ruan
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Li
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shujie Liao
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Forlin R, James A, Brodin P. Making human immune systems more interpretable through systems immunology. Trends Immunol 2023:S1471-4906(23)00113-8. [PMID: 37402600 DOI: 10.1016/j.it.2023.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023]
Abstract
The human immune system is a distributed system of specialized cell populations with unique functions that collectively give rise to immune responses to infections and during immune-mediated diseases. Cell composition, plasma proteins, and functional responses vary among individuals, making the system difficult to interpret, but this variation is nonrandom. With careful analyses using novel experimental and computational tools, human immune system composition and function carry interpretable information. Here, we propose that systems-level analyses offer an opportunity to make human immune responses more interpretable in the future, and we discuss herein important considerations and lessons learned to this end. Predictable human immunology holds implications for better diagnostic and curative precision in patients with infectious and immune-associated diseases.
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Affiliation(s)
- Rikard Forlin
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden
| | - Anna James
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden
| | - Petter Brodin
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institutet, 17165, Solna, Sweden; Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK; Medical Research Council London Institute of Medical Sciences (LMS), Imperial College Hammersmith Campus, London W12 0NN, UK.
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14
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Souquette A, Allen EK, Oshansky CM, Tang L, Wong SS, Jeevan T, Shi L, Pounds S, Elias G, Kuan G, Balmaseda A, Zapata R, Shaw-Saliba K, Damme PV, Tendeloo VV, Dib JC, Ogunjimi B, Webby R, Schultz-Cherry S, Pekosz A, Rothman R, Gordon A, Thomas PG. Integrated Drivers of Basal and Acute Immunity in Diverse Human Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534227. [PMID: 36993205 PMCID: PMC10055315 DOI: 10.1101/2023.03.25.534227] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Prior studies have identified genetic, infectious, and biological associations with immune competence and disease severity; however, there have been few integrative analyses of these factors and study populations are often limited in demographic diversity. Utilizing samples from 1,705 individuals in 5 countries, we examined putative determinants of immunity, including: single nucleotide polymorphisms, ancestry informative markers, herpesvirus status, age, and sex. In healthy subjects, we found significant differences in cytokine levels, leukocyte phenotypes, and gene expression. Transcriptional responses also varied by cohort, and the most significant determinant was ancestry. In influenza infected subjects, we found two disease severity immunophenotypes, largely driven by age. Additionally, cytokine regression models show each determinant differentially contributes to acute immune variation, with unique and interactive, location-specific herpesvirus effects. These results provide novel insight into the scope of immune heterogeneity across diverse populations, the integrative effects of factors which drive it, and the consequences for illness outcomes.
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15
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Scott RT, Sanders LM, Antonsen EL, Hastings JJA, Park SM, Mackintosh G, Reynolds RJ, Hoarfrost AL, Sawyer A, Greene CS, Glicksberg BS, Theriot CA, Berrios DC, Miller J, Babdor J, Barker R, Baranzini SE, Beheshti A, Chalk S, Delgado-Aparicio GM, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Kalantari J, Khezeli K, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Garcia Martin H, Mason CE, Matar M, Mias GI, Myers JG, Nelson C, Oribello J, Parsons-Wingerter P, Prabhu RK, Qutub AA, Rask J, Saravia-Butler A, Saria S, Singh NK, Snyder M, Soboczenski F, Soman K, Van Valen D, Venkateswaran K, Warren L, Worthey L, Yang JH, Zitnik M, Costes SV. Biomonitoring and precision health in deep space supported by artificial intelligence. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00617-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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16
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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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17
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Lipsa D, Ruiz Moreno A, Desmet C, Bianchi I, Geiss O, Colpo P, Bremer-Hoffmann S. Inter-Individual Variations: A Challenge for the Standardisation of Complement Activation Assays. Int J Nanomedicine 2023; 18:711-720. [PMID: 36816333 PMCID: PMC9930575 DOI: 10.2147/ijn.s384184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 02/13/2023] Open
Abstract
Introduction The role of the human immune system in pathologic responses to chemicals including nanomaterials was identified as a gap in current hazard assessments. However, the complexity of the human immune system as well as interspecies variations make the development of predictive toxicity tests challenging. In the present study, we have analysed to what extent fluctuations of the complement system of different individuals will have an impact on the standardisation of immunological tests. Methods We treated commercially available pooled sera (PS) from healthy males, individual sera from healthy donors and from patients suffering from cancer, immunodeficiency and allergies with small molecules and liposomes. Changes of iC3b protein levels measured in enzyme-linked immunosorbent assays served as biomarker for complement activation. Results The level of complement activation in PS differed significantly from responses of individual donors (p < 0.01). Only seven out of 32 investigated sera from healthy donors responded similarly to the pooled serum. This variability was even more remarkable when investigating the effect of liposomes on the complement activation in sera from donors with pre-existing pathologies. Neither the 26 sera of donors with allergies nor sera of 16 donors with immunodeficiency responded similar to the PS of healthy donors. Allergy sufferers showed an increase in iC3b levels of 4.16-fold changes when compared to PS treated with liposomes. Discussion Our studies demonstrate that the use of pooled serum can lead to an over- or under-estimation of immunological response in particular for individuals with pre-existing pathologies. This is of high relevance when developing medical products based on nanomaterials and asks for a review of the current practice to use PS from healthy donors for the prediction of immunological effects of drugs in patients. A better understanding of individual toxicological responses to xenobiotics should be an essential part in safety assessments.
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Affiliation(s)
- Dorelia Lipsa
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Ana Ruiz Moreno
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Ivana Bianchi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Otmar Geiss
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Pascal Colpo
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Susanne Bremer-Hoffmann
- European Commission, Joint Research Centre (JRC), Ispra, Italy,Correspondence: Susanne Bremer-Hoffmann, Email
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18
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Cevirgel A, Shetty SA, Vos M, Nanlohy NM, Beckers L, Bijvank E, Rots N, van Beek J, Buisman A, van Baarle D. Identification of aging-associated immunotypes and immune stability as indicators of post-vaccination immune activation. Aging Cell 2022; 21:e13703. [PMID: 36081314 PMCID: PMC9577949 DOI: 10.1111/acel.13703] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/20/2022] [Accepted: 08/13/2022] [Indexed: 01/25/2023] Open
Abstract
Immunosenescence describes immune dysfunction observed in older individuals. To identify individuals at-risk for immune dysfunction, it is crucial to understand the diverse immune phenotypes and their intrinsic functional capabilities. We investigated immune cell subsets and variation in the aging population. We observed that inter-individual immune variation was associated with age and cytomegalovirus seropositivity. Based on the similarities of immune subset composition among individuals, we identified nine immunotypes that displayed different aging-associated immune signatures, which explained inter-individual variation better than age. Additionally, we correlated the immune subset composition of individuals over approximately a year as a measure of stability of immune parameters. Immune stability was significantly lower in immunotypes that contained aging-associated immune subsets and correlated with a circulating CD38 + CD4+ T follicular helper cell increase 7 days after influenza vaccination. In conclusion, immune stability is a feature of immunotypes and could be a potential indicator of post-vaccination cellular kinetics.
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Affiliation(s)
- Alper Cevirgel
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands,Department of Medical Microbiology and Infection preventionVirology and Immunology Research GroupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Sudarshan A. Shetty
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands,Department of Medical Microbiology and Infection preventionVirology and Immunology Research GroupUniversity Medical Center GroningenGroningenThe Netherlands
| | - Martijn Vos
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nening M. Nanlohy
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Lisa Beckers
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Elske Bijvank
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Nynke Rots
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Josine van Beek
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Anne‐Marie Buisman
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease ControlNational Institute for Public Health and the EnvironmentBilthovenThe Netherlands,Department of Medical Microbiology and Infection preventionVirology and Immunology Research GroupUniversity Medical Center GroningenGroningenThe Netherlands
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19
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Thétis-Soulié M, Hosotte M, Grozelier I, Baillez C, Scurati S, Mercier V. The MaDo real-life study of dose adjustment of allergen immunotherapy liquid formulations in an indication of respiratory allergic disease: Reasons, practices, and outcomes. FRONTIERS IN ALLERGY 2022; 3:971155. [PMID: 36017469 PMCID: PMC9395981 DOI: 10.3389/falgy.2022.971155] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
Sublingual allergen immunotherapy (SLIT) is a safe, effective, disease-modifying treatment for moderate-to-severe respiratory allergies. The function and responsiveness of the immune system components underlying the effects of allergen immunotherapy may vary from one patient to another. Furthermore, the severity of the symptoms of allergic disease can fluctuate over time, due to changes in environmental allergen exposure, effector cell responsiveness, and cell signaling. Hence, the allergen dose provided through SLIT can be fine-tuned to establish an optimal balance between effectiveness and tolerability. The objective of the MaDo study was to describe and understand dose adjustments of SLIT liquid formulations in France. We performed a retrospective, observational, cross-sectional, real-life study of allergists and other specialist physicians. Physicians described their patients via an anonymous case report form (CRF). The main patient inclusion criteria were age 5 years or over, at least one physician-confirmed IgE-driven respiratory allergy, and treatment for at least 2 years with one or more SLIT liquid preparations. A nationally representative sample of 33 specialist physicians participated in the study. The physicians' main stated reasons for dose adjustment were adverse events (according to 90.9% of the physicians), treatment effectiveness (60.6%), sensitivity to the allergen (42.4%) and other characteristics (30.3%: mainly symptom severity, type of allergen, and asthma). 392 CRFs (mean ± standard deviation patient age: 27.8 ± 17.5; under-18s: 42.1%; polyallergy: 30.9%) were analyzed. Respectively 53.6%, 25.8%, 15.3%, and 8.7% of the patients received house dust mite, grass pollen, birch pollen and cypress pollen SLIT. Dose adjustments were noted in 258 (65.8%) patients (at the start of the maintenance phase for 101 patients (39.2%) and later for 247 (95.7%)). Dose adjustment was not linked to sex, age, or the number of allergens administered. All measures of disease severity (including symptom severity noted on a 0-to-10 visual analogue scale by the physician) decreased significantly during SLIT. Notably, the mean AR symptom severity score decreased to a clinically relevant extent from 7.6 at SLIT initiation to 2.4 at last follow-up, and the mean asthma symptom severity score decreased from 5.0 to 1.3. The few differences in effectiveness between patients with vs. without dose adjustment were not major. For about one patient in five, a specialist physician decided to reduce or increase the SLIT liquid dose at the start of maintenance treatment and/or during maintenance treatment. This decision was influenced by a broad range of patient and treatment factors, mainly to improve tolerability to treatment and/or enhance effectiveness. In France, dose adjustment of SLIT liquid preparations as a function of the patient profile and/or treatment response is anchored in clinical practice. Precision dosing might optimize the overall benefit-risk profile of AIT for individual patients throughout their entire treatment course, enabling them to achieve both short- and long-term treatment goals, whilst maximizing the safety and tolerability.
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Affiliation(s)
| | | | | | | | - Silvia Scurati
- Global Medical Affairs Department, Stallergenes Greer, Antony, France
| | - Valérie Mercier
- Private Office, Toulouse, France
- Correspondence: Valérie Mercier
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20
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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21
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Mauracher AA, Henrickson SE. Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:910243. [PMID: 37670772 PMCID: PMC10477056 DOI: 10.3389/fsysb.2022.910243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Inborn errors of immunity (IEI) are monogenic disorders that can cause diverse symptoms, including recurrent infections, autoimmunity and malignancy. While many factors have contributed, the increased availability of next-generation sequencing has been central in the remarkable increase in identification of novel monogenic IEI over the past years. Throughout this phase of disease discovery, it has also become evident that a given gene variant does not always yield a consistent phenotype, while variants in seemingly disparate genes can lead to similar clinical presentations. Thus, it is increasingly clear that the clinical phenotype of an IEI patient is not defined by genetics alone, but is also impacted by a myriad of factors. Accordingly, we need methods to amplify our current diagnostic algorithms to better understand mechanisms underlying the variability in our patients and to optimize treatment. In this review, we will explore how systems immunology can contribute to optimizing both diagnosis and treatment of IEI patients by focusing on identifying and quantifying key dysregulated pathways. To improve mechanistic understanding in IEI we must deeply evaluate our rare IEI patients using multimodal strategies, allowing both the quantification of altered immune cell subsets and their functional evaluation. By studying representative controls and patients, we can identify causative pathways underlying immune cell dysfunction and move towards functional diagnosis. Attaining this deeper understanding of IEI will require a stepwise strategy. First, we need to broadly apply these methods to IEI patients to identify patterns of dysfunction. Next, using multimodal data analysis, we can identify key dysregulated pathways. Then, we must develop a core group of simple, effective functional tests that target those pathways to increase efficiency of initial diagnostic investigations, provide evidence for therapeutic selection and contribute to the mechanistic evaluation of genetic results. This core group of simple, effective functional tests, targeting key pathways, can then be equitably provided to our rare patients. Systems biology is thus poised to reframe IEI diagnosis and therapy, fostering research today that will provide streamlined diagnosis and treatment choices for our rare and complex patients in the future, as well as providing a better understanding of basic immunology.
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Affiliation(s)
- Andrea A. Mauracher
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah E. Henrickson
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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22
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Fiocchi C, Iliopoulos D. Inflammatory Bowel Disease Therapy: Beyond the Immunome. Front Immunol 2022; 13:864762. [PMID: 35615360 PMCID: PMC9124778 DOI: 10.3389/fimmu.2022.864762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/11/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute Cleveland, Cleveland, OH, United States
- Department of Gastroenterology, Hepatology & Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH, United States
- *Correspondence: Claudio Fiocchi,
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23
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Bernicke B, Engelbogen N, Klein K, Franzenburg J, Borzikowsky C, Peters C, Janssen O, Junker R, Serrano R, Kabelitz D. Analysis of the Seasonal Fluctuation of γδ T Cells and Its Potential Relation with Vitamin D3. Cells 2022; 11:cells11091460. [PMID: 35563767 PMCID: PMC9099506 DOI: 10.3390/cells11091460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/07/2023] Open
Abstract
In addition to its role in bone metabolism, vitamin D3 exerts immunomodulatory effects and has been proposed to contribute to seasonal variation of immune cells. This might be linked to higher vitamin D3 levels in summer than in winter due to differential sun exposure. γδ T cells comprise a numerically small subset of T cells in the blood, which contribute to anti-infective and antitumor immunity. We studied the seasonal fluctuation of γδ T cells, the possible influence of vitamin D3, and the effect of the active metabolite 1α,25(OH)2D3 on the in vitro activation of human γδ T cells. In a retrospective analysis with 2625 samples of random blood donors, we observed higher proportions of γδ T cells in winter when compared with summer. In a prospective study over one year with a small cohort of healthy adults who did or did not take oral vitamin D3 supplementation, higher proportions of γδ T cells were present in donors without oral vitamin D3 uptake, particularly in spring. However, γδ T cell frequency in blood did not directly correlate with serum levels of 25(OH)D3. The active metabolite 1α,25(OH)2D3 inhibited the in vitro activation of γδ T cells at the level of proliferation, cytotoxicity, and interferon-γ production. Our study reveals novel insights into the seasonal fluctuation of γδ T cells and the immunomodulatory effects of vitamin D3.
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Affiliation(s)
- Birthe Bernicke
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
| | - Nils Engelbogen
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (N.E.); (J.F.); (R.J.)
| | - Katharina Klein
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
| | - Jeanette Franzenburg
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (N.E.); (J.F.); (R.J.)
| | - Christoph Borzikowsky
- Institute of Bioinformatics and Statistics, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany;
| | - Christian Peters
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
| | - Ottmar Janssen
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
| | - Ralf Junker
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (N.E.); (J.F.); (R.J.)
| | - Ruben Serrano
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
- Correspondence: (R.S.); (D.K.)
| | - Dieter Kabelitz
- Institute of Immunology, University Hospital Schleswig-Holstein (UKSH) Campus Kiel, 24105 Kiel, Germany; (B.B.); (K.K.); (C.P.); (O.J.)
- Correspondence: (R.S.); (D.K.)
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24
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Jones RP, Ponomarenko A. System Complexity in Influenza Infection and Vaccination: Effects upon Excess Winter Mortality. Infect Dis Rep 2022; 14:287-309. [PMID: 35645214 PMCID: PMC9149983 DOI: 10.3390/idr14030035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Unexpected outcomes are usually associated with interventions in complex systems. Excess winter mortality (EWM) is a measure of the net effect of all competing forces operating each winter, including influenza(s) and non-influenza pathogens. In this study over 2400 data points from 97 countries are used to look at the net effect of influenza vaccination rates in the elderly aged 65+ against excess winter mortality (EWM) each year from the winter of 1980/81 through to 2019/20. The observed international net effect of influenza vaccination ranges from a 7.8% reduction in EWM estimated at 100% elderly vaccination for the winter of 1989/90 down to a 9.3% increase in EWM for the winter of 2018/19. The average was only a 0.3% reduction in EWM for a 100% vaccinated elderly population. Such outcomes do not contradict the known protective effect of influenza vaccination against influenza mortality per se—they merely indicate that multiple complex interactions lie behind the observed net effect against all-causes (including all pathogen causes) of winter mortality. This range from net benefit to net disbenefit is proposed to arise from system complexity which includes environmental conditions (weather, solar cycles), the antigenic distance between constantly emerging circulating influenza clades and the influenza vaccine makeup, vaccination timing, pathogen interference, and human immune diversity (including individual history of host-virus, host-antigen interactions and immunosenescence) all interacting to give the observed outcomes each year. We propose that a narrow focus on influenza vaccine effectiveness misses the far wider complexity of winter mortality. Influenza vaccines may need to be formulated in different ways, and perhaps administered over a shorter timeframe to avoid the unanticipated adverse net outcomes seen in around 40% of years.
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Affiliation(s)
- Rodney P. Jones
- Healthcare Analysis & Forecasting, Wantage OX12 0NE, UK
- Correspondence:
| | - Andriy Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine;
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25
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Engler-Chiurazzi EB, Chastain WH, Citron KK, Lambert LE, Kikkeri DN, Shrestha SS. Estrogen, the Peripheral Immune System and Major Depression – A Reproductive Lifespan Perspective. Front Behav Neurosci 2022; 16:850623. [PMID: 35493954 PMCID: PMC9051447 DOI: 10.3389/fnbeh.2022.850623] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/17/2022] [Indexed: 12/01/2022] Open
Abstract
Major depression is a significant medical issue impacting millions of individuals worldwide. Identifying factors contributing to its manifestation has been a subject of intense investigation for decades and several targets have emerged including sex hormones and the immune system. Indeed, an extensive body of literature has demonstrated that sex hormones play a critical role in modulating brain function and impacting mental health, especially among female organisms. Emerging findings also indicate an inflammatory etiology of major depression, revealing new opportunities to supplement, or even supersede, currently available pharmacological interventions in some patient populations. Given the established sex differences in immunity and the profound impact of fluctuations of sex hormone levels on the immune system within the female, interrogating how the endocrine, nervous, and immune systems converge to impact women’s mental health is warranted. Here, we review the impacts of endogenous estrogens as well as exogenously administered estrogen-containing therapies on affect and immunity and discuss these observations in the context of distinct reproductive milestones across the female lifespan. A theoretical framework and important considerations for additional study in regards to mental health and major depression are provided.
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Affiliation(s)
- Elizabeth B. Engler-Chiurazzi
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Neurology, Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Elizabeth B. Engler-Chiurazzi,
| | - Wesley H. Chastain
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
| | - Kailen K. Citron
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
| | - Lillian E. Lambert
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
| | - Divya N. Kikkeri
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
| | - Sharhana S. Shrestha
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
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26
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Kashima Y, Kaneko K, Reteng P, Yoshitake N, Runtuwene LR, Nagasawa S, Onishi M, Seki M, Suzuki A, Sugano S, Sakata-Yanagimoto M, Imai Y, Nakayama-Hosoya K, Kawana-Tachikawa A, Mizutani T, Suzuki Y. Intensive single-cell analysis reveals immune-cell diversity among healthy individuals. Life Sci Alliance 2022; 5:5/7/e202201398. [PMID: 35383111 PMCID: PMC8983398 DOI: 10.26508/lsa.202201398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/25/2022] Open
Abstract
Immune responses are different between individuals and personal health histories and unique environmental conditions should collectively determine the present state of immune cells. However, the molecular systems underlying such heterogeneity remain elusive. Here, we conducted a systematic time-lapse single-cell analysis, using 171 single-cell libraries and 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune-cell profiles between different individuals. These patterns showed daily fluctuations even within the same individual. Similar diversities were also observed for the T-cell and B-cell receptor repertoires. Detailed immune-cell profiles at healthy statuses should give essential background information to understand their immune responses, when the individual is exposed to various environmental conditions. To demonstrate this idea, we conducted the similar analysis for the same individuals on the vaccination of influenza and SARS-CoV-2. In fact, we detected distinct responses to vaccines between individuals, although key responses are common. Single-cell immune-cell profile data should make fundamental data resource to understand variable immune responses, which are unique to each individual.
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Affiliation(s)
- Yukie Kashima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Keiya Kaneko
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Patrick Reteng
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nina Yoshitake
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | | | - Satoi Nagasawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masaya Onishi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Sumio Sugano
- Institute of Kashiwa-no-ha Omics Gate, Kashiwa, Japan.,Future Medicine Education and Research Organization at Chiba University, Chiba-city, Japan
| | | | - Yumiko Imai
- Laboratory of Regulation for Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | | | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Disease, Tokyo, Japan
| | - Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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27
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Human immune diversity: from evolution to modernity. Nat Immunol 2021; 22:1479-1489. [PMID: 34795445 DOI: 10.1038/s41590-021-01058-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023]
Abstract
The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.
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28
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Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health. Cell Syst 2021; 13:241-255.e7. [PMID: 34856119 DOI: 10.1016/j.cels.2021.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 09/15/2021] [Accepted: 11/09/2021] [Indexed: 01/04/2023]
Abstract
We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activity and sleep. We generated a resource of >20,000 biological samples from this study and a compendium of >53 million primary data points for 558,032 distinct features. Multiomics factor analysis revealed distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet, and hormonal effects. For example, ethinyl estradiol, a common oral contraceptive, produced characteristic molecular and physiological effects, including increased levels of inflammation and impact on thyroid, cortisol levels, and pulse, that were distinct from other sources of variability observed in our study. In total, this work illustrates the value of combining deep molecular and digital monitoring of human health. A record of this paper's transparent peer review process is included in the supplemental information.
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29
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Syrimi E, Fennell E, Richter A, Vrljicak P, Stark R, Ott S, Murray PG, Al-Abadi E, Chikermane A, Dawson P, Hackett S, Jyothish D, Kanthimathinathan HK, Monaghan S, Nagakumar P, Scholefield BR, Welch S, Khan N, Faustini S, Davies K, Zelek WM, Kearns P, Taylor GS. The immune landscape of SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Children (MIS-C) from acute disease to recovery. iScience 2021; 24:103215. [PMID: 34632327 PMCID: PMC8487319 DOI: 10.1016/j.isci.2021.103215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/10/2021] [Accepted: 09/26/2021] [Indexed: 01/08/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening disease occurring several weeks after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Deep immune profiling showed acute MIS-C patients had highly activated neutrophils, classical monocytes and memory CD8+ T-cells, with increased frequencies of B-cell plasmablasts and double-negative B-cells. Post treatment samples from the same patients, taken during symptom resolution, identified recovery-associated immune features including increased monocyte CD163 levels, emergence of a new population of immature neutrophils and, in some patients, transiently increased plasma arginase. Plasma profiling identified multiple features shared by MIS-C, Kawasaki Disease and COVID-19 and that therapeutic inhibition of IL-6 may be preferable to IL-1 or TNF-α. We identified several potential mechanisms of action for IVIG, the most commonly used drug to treat MIS-C. Finally, we showed systemic complement activation with high plasma C5b-9 levels is common in MIS-C suggesting complement inhibitors could be used to treat the disease.
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Affiliation(s)
- Eleni Syrimi
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Eanna Fennell
- Health Research Institute and the Bernal Institute, University of Limerick, Limerick, Ireland
| | - Alex Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Pavle Vrljicak
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Richard Stark
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, UK
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Paul G. Murray
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
- Health Research Institute and the Bernal Institute, University of Limerick, Limerick, Ireland
| | - Eslam Al-Abadi
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ashish Chikermane
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Pamela Dawson
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Scott Hackett
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Deepthi Jyothish
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Sean Monaghan
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Prasad Nagakumar
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Barnaby R. Scholefield
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Steven Welch
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Naeem Khan
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Sian Faustini
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Kate Davies
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Wioleta M. Zelek
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Pamela Kearns
- NIHR Birmingham Biomedical Research Centre and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Graham S. Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
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30
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Barone SM, Paul AGA, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. eLife 2021; 10:e64653. [PMID: 34350827 PMCID: PMC8370768 DOI: 10.7554/elife.64653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 08/02/2021] [Indexed: 12/31/2022] Open
Abstract
For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease-specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders EXpanding (T-REX) was created to identify changes in both rare and common cells across human immune monitoring settings. T-REX identified cells with highly similar phenotypes that localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized MHCII tetramer reagents that mark rhinovirus-specific CD4+ cells were left out during analysis and then used to test whether T-REX identified biologically significant cells. T-REX identified rhinovirus-specific CD4+ T cells based on phenotypically homogeneous cells expanding by ≥95% following infection. T-REX successfully identified hotspots of virus-specific T cells by comparing infection (day 7) to either pre-infection (day 0) or post-infection (day 28) samples. Plotting the direction and degree of change for each individual donor provided a useful summary view and revealed patterns of immune system behavior across immune monitoring settings. For example, the magnitude and direction of change in some COVID-19 patients was comparable to blast crisis acute myeloid leukemia patients undergoing a complete response to chemotherapy. Other COVID-19 patients instead displayed an immune trajectory like that seen in rhinovirus infection or checkpoint inhibitor therapy for melanoma. The T-REX algorithm thus rapidly identifies and characterizes mechanistically significant cells and places emerging diseases into a systems immunology context for comparison to well-studied immune changes.
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Affiliation(s)
- Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashvilleUnited States
| | - Alberta GA Paul
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Lyndsey M Muehling
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Joanne A Lannigan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - William W Kwok
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Ronald B Turner
- Department of Pediatrics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Judith A Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashvilleUnited States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
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31
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Zhong W, Edfors F, Gummesson A, Bergström G, Fagerberg L, Uhlén M. Next generation plasma proteome profiling to monitor health and disease. Nat Commun 2021; 12:2493. [PMID: 33941778 PMCID: PMC8093230 DOI: 10.1038/s41467-021-22767-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
The need for precision medicine approaches to monitor health and disease makes it important to develop sensitive and accurate assays for proteome profiles in blood. Here, we describe an approach for plasma profiling based on proximity extension assay combined with next generation sequencing. First, we analyze the variability of plasma profiles between and within healthy individuals in a longitudinal wellness study, including the influence of genetic variations on plasma levels. Second, we follow patients newly diagnosed with type 2 diabetes before and during therapeutic intervention using plasma proteome profiling. The studies show that healthy individuals have a unique and stable proteome profile and indicate that a panel of proteins could potentially be used for early diagnosis of diabetes, including stratification of patients with regards to response to metformin treatment. Although validation in larger cohorts is needed, the analysis demonstrates the usefulness of comprehensive plasma profiling for precision medicine efforts.
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Affiliation(s)
- Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden. .,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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32
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Barone SM, Paul AG, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.31.190454. [PMID: 32766581 PMCID: PMC7402038 DOI: 10.1101/2020.07.31.190454] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders Expanding (T-REX) was created to identify changes in both very rare and common cells in diverse human immune monitoring settings. T-REX identified cells that were highly similar in phenotype and localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized reagents used to detect the rhinovirus-specific CD4+ cells, MHCII tetramers, were not used during unsupervised analysis and instead 'left out' to serve as a test of whether T-REX identified biologically significant cells. In the rhinovirus challenge study, T-REX identified virus-specific CD4+ T cells based on these cells being a distinct phenotype that expanded by ≥95% following infection. T-REX successfully identified hotspots containing virus-specific T cells using pairs of samples comparing Day 7 of infection to samples taken either prior to infection (Day 0) or after clearing the infection (Day 28). Mapping pairwise comparisons in samples according to both the direction and degree of change provided a framework to compare systems level immune changes during infectious disease or therapy response. This revealed that the magnitude and direction of systemic immune change in some COVID-19 patients was comparable to that of blast crisis acute myeloid leukemia patients undergoing induction chemotherapy and characterized the identity of the immune cells that changed the most. Other COVID-19 patients instead matched an immune trajectory like that of individuals with rhinovirus infection or melanoma patients receiving checkpoint inhibitor therapy. T-REX analysis of paired blood samples provides an approach to rapidly identify and characterize mechanistically significant cells and to place emerging diseases into a systems immunology context.
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Affiliation(s)
- Sierra M. Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alberta G.A. Paul
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Lyndsey M. Muehling
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Joanne A. Lannigan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Ronald B. Turner
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Judith A. Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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33
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Tebani A, Gummesson A, Zhong W, Koistinen IS, Lakshmikanth T, Olsson LM, Boulund F, Neiman M, Stenlund H, Hellström C, Karlsson MJ, Arif M, Dodig-Crnković T, Mardinoglu A, Lee S, Zhang C, Chen Y, Olin A, Mikes J, Danielsson H, von Feilitzen K, Jansson PA, Angerås O, Huss M, Kjellqvist S, Odeberg J, Edfors F, Tremaroli V, Forsström B, Schwenk JM, Nilsson P, Moritz T, Bäckhed F, Engstrand L, Brodin P, Bergström G, Uhlen M, Fagerberg L. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 2020; 11:4487. [PMID: 32900998 PMCID: PMC7479148 DOI: 10.1038/s41467-020-18148-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022] Open
Abstract
An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine. An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, the authors sample a longitudinal wellness cohort and analyse blood molecular profiles as well as gut microbiota composition.
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Affiliation(s)
- Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ina Schuppe Koistinen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Lisa M Olsson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Boulund
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maja Neiman
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Cecilia Hellström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Max J Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjae Lee
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Axel Olin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Danielsson
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Internal Medicine, Gothenburg, Sweden
| | - Oskar Angerås
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Cardiology, Gothenburg, Sweden
| | - Mikael Huss
- Codon Consulting, 118 26, Stockholm, Sweden.,Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Sanela Kjellqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Björn Forsström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thomas Moritz
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 907 36, Umeå, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Engstrand
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Göran Bergström
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Biosustainability, Danish Technical University, Copenhagen, Denmark
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
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34
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Rodriguez L, Brodin P. Unraveling the Immune Response in Severe COVID-19. J Clin Immunol 2020; 40:958-959. [PMID: 32827284 PMCID: PMC7442888 DOI: 10.1007/s10875-020-00849-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Lucie Rodriguez
- Science for life Laboratory, Department of Women's and Children Health, Karolinska Institutet, Stockholm, Sweden
| | - Petter Brodin
- Science for life Laboratory, Department of Women's and Children Health, Karolinska Institutet, Stockholm, Sweden. .,Pediatric Rheumatology, Karolinska University Hospital, Stockholm, Sweden.
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35
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Rodriguez L, Pekkarinen PT, Lakshmikanth T, Tan Z, Consiglio CR, Pou C, Chen Y, Mugabo CH, Nguyen NA, Nowlan K, Strandin T, Levanov L, Mikes J, Wang J, Kantele A, Hepojoki J, Vapalahti O, Heinonen S, Kekäläinen E, Brodin P. Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19. CELL REPORTS MEDICINE 2020; 1:100078. [PMID: 32838342 PMCID: PMC7405891 DOI: 10.1016/j.xcrm.2020.100078] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022]
Abstract
Severe disease of SARS-CoV-2 is characterized by vigorous inflammatory responses in the lung, often with a sudden onset after 5–7 days of stable disease. Efforts to modulate this hyperinflammation and the associated acute respiratory distress syndrome rely on the unraveling of the immune cell interactions and cytokines that drive such responses. Given that every patient is captured at different stages of infection, longitudinal monitoring of the immune response is critical and systems-level analyses are required to capture cellular interactions. Here, we report on a systems-level blood immunomonitoring study of 37 adult patients diagnosed with COVID-19 and followed with up to 14 blood samples from acute to recovery phases of the disease. We describe an IFNγ-eosinophil axis activated before lung hyperinflammation and changes in cell-cell co-regulation during different stages of the disease. We also map an immune trajectory during recovery that is shared among patients with severe COVID-19. Immunomonitoring from acute to recovery phase COVID-19 An IFNγ-eosinophil axis precedes lung hyperinflammation Basophils modulate SARS-CoV-2 IgG responses A shared trajectory of immunological recovery in COVID-19
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Affiliation(s)
- Lucie Rodriguez
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Pirkka T Pekkarinen
- Division of Intensive Care Medicine, Department of Anesthesiology, Intensive Care and Pain Medicine, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Ziyang Tan
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Camila Rosat Consiglio
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Christian Pou
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Constantin Habimana Mugabo
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Ngoc Anh Nguyen
- Translational Immunology Research Program, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Kirsten Nowlan
- Translational Immunology Research Program, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Tomas Strandin
- Department of Virology, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Lev Levanov
- Department of Virology, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Jun Wang
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden
| | - Anu Kantele
- Inflammation Center, Division of Infectious Diseases, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Santtu Heinonen
- New Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Eliisa Kekäläinen
- Translational Immunology Research Program, University of Helsinki, and Helsinki University Hospital, Helsinki 00100, Finland
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna 171 77, Sweden.,Department of Pediatric Rheumatology, Karolinska University Hospital, Solna 171 76, Sweden
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