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Zhao K, So HC, Lin Z. scParser: sparse representation learning for scalable single-cell RNA sequencing data analysis. Genome Biol 2024; 25:223. [PMID: 39152499 PMCID: PMC11328435 DOI: 10.1186/s13059-024-03345-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 07/23/2024] [Indexed: 08/19/2024] Open
Abstract
The rapid rise in the availability and scale of scRNA-seq data needs scalable methods for integrative analysis. Though many methods for data integration have been developed, few focus on understanding the heterogeneous effects of biological conditions across different cell populations in integrative analysis. Our proposed scalable approach, scParser, models the heterogeneous effects from biological conditions, which unveils the key mechanisms by which gene expression contributes to phenotypes. Notably, the extended scParser pinpoints biological processes in cell subpopulations that contribute to disease pathogenesis. scParser achieves favorable performance in cell clustering compared to state-of-the-art methods and has a broad and diverse applicability.
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Affiliation(s)
- Kai Zhao
- Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China.
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Brain and Mind Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Zhixiang Lin
- Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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2
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Maimaiti A, Ma J, Hao C, Han D, Wang Y, Wang Z, Abudusalamu R. DNA methylation-estimated phenotypes, telomere length and risk of ischemic stroke: epigenetic age acceleration of screening and a Mendelian randomization study. Aging (Albany NY) 2024; 16:206072. [PMID: 39159130 DOI: 10.18632/aging.206072] [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] [Accepted: 07/16/2024] [Indexed: 08/21/2024]
Abstract
BACKGROUND Aging is a complex biological process that may be accelerated in certain pathological conditions. DNA methylation age (DNAmAge) has emerged as a biomarker for biological age, which can differ from chronological age. This research peels back the layers of the relationship between fast-forward aging and ischemic stroke, poking and prodding the potential two-way causal influences between stroke and biological aging indicators. METHODS We analyzed a cohort of ischemic stroke patients, comparing DNAmAge with chronological age to measure age acceleration. We assessed variations in age acceleration among stroke subtypes and between sexes. Using Mendelian randomization, we examined the causal links between stroke, aging biomarkers like telomere length, and age acceleration's effect on stroke risk. RESULTS Our investigation reveals a pronounced association between ischemic stroke and age acceleration, most notably in patients with cardioembolic strokes, who exhibited a striking median difference of 9 years between DNAmAge and chronological age. Furthermore, age acceleration differed significantly across stroke subtypes and was higher in women than in men. In terms of causality, MR analysis indicated a modest negative effect of stroke on telomere length, but no causal effect of age phenotypes on stroke or its subtypes. However, some indication of a potential causal effect of ischemic stroke on PhenoAge acceleration was observed. CONCLUSION The study provides insight into the relationship between DNAmAge and ischemic stroke, particularly cardioembolic stroke, and suggests possible gender differences. These insights carry profound clinical significance and set stage for future investigations into the entwined pathways of stroke and accelerated aging.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Jianhua Ma
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Chenguang Hao
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Dengfeng Han
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Rena Abudusalamu
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
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Goutal S, Tran T, Leroy C, Benhamouda N, Leterrier S, Saba W, Lafont B, Tartour É, Roelens M, Tournier N. Brain Glucose Metabolism as a Readout of the Central Nervous System Impact of Cigarette Smoke Exposure and Withdrawal and the Effects of NFL-101, as an Immune-Based Drug Candidate for Smoking Cessation Therapy. ACS Chem Neurosci 2024; 15:2520-2531. [PMID: 38875216 DOI: 10.1021/acschemneuro.4c00204] [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] [Indexed: 06/16/2024] Open
Abstract
Neuroimaging biomarkers are needed to investigate the impact of smoking withdrawal on brain function. NFL-101 is a denicotinized aqueous extract of tobacco leaves currently investigated as an immune-based smoking cessation therapy in humans. However, the immune response to NFL-101 and its ability to induce significant changes in brain function remain to be demonstrated. Brain glucose metabolism was investigated using [18F]fluoro-deoxy-glucose ([18F]FDG) PET imaging in a mouse model of cigarette smoke exposure (CSE, 4-week whole-body inhalation, twice daily). Compared with control animals, the relative uptake of [18F]FDG in CSE mice was decreased in the thalamus and brain stem (p < 0.001, n = 14 per group) and increased in the hippocampus, cortex, cerebellum, and olfactory bulb (p < 0.001). NFL-101 induced a humoral immune response (specific IgGs) in mice and activated human natural-killer lymphocytes in vitro. In CSE mice, but not in control mice, single-dose NFL-101 significantly increased [18F]FDG uptake in the thalamus (p < 0.01), thus restoring normal brain glucose metabolism after 2-day withdrawal in this nicotinic receptor-rich region. In tobacco research, [18F]FDG PET imaging provides a quantitative method to evaluate changes in the brain function associated with the withdrawal phase. This method also showed the CNS effects of NFL-101, with translational perspectives for future clinical evaluation in smokers.
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Affiliation(s)
- Sébastien Goutal
- CEA, CNRS, Inserm, BioMaps, Université Paris-Saclay, Orsay 91401, France
| | - Thi Tran
- Université Paris Cité, INSERM, PARCC, Paris 75015, France
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Hôpital Necker, Paris 75015,France
| | - Claire Leroy
- CEA, CNRS, Inserm, BioMaps, Université Paris-Saclay, Orsay 91401, France
| | - Nadine Benhamouda
- Université Paris Cité, INSERM, PARCC, Paris 75015, France
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Hôpital Necker, Paris 75015,France
| | - Sarah Leterrier
- CEA, CNRS, Inserm, BioMaps, Université Paris-Saclay, Orsay 91401, France
| | - Wadad Saba
- CEA, CNRS, Inserm, BioMaps, Université Paris-Saclay, Orsay 91401, France
| | | | - Éric Tartour
- Université Paris Cité, INSERM, PARCC, Paris 75015, France
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Hôpital Necker, Paris 75015,France
| | - Marie Roelens
- Université Paris Cité, INSERM, PARCC, Paris 75015, France
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Hôpital Necker, Paris 75015,France
| | - Nicolas Tournier
- CEA, CNRS, Inserm, BioMaps, Université Paris-Saclay, Orsay 91401, France
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Alexandrova Y, Yero A, Olivenstein R, Orlova M, Schurr E, Estaquier J, Costiniuk CT, Jenabian MA. Dynamics of pulmonary mucosal cytotoxic CD8 T-cells in people living with HIV under suppressive antiretroviral therapy. Respir Res 2024; 25:240. [PMID: 38867225 PMCID: PMC11170847 DOI: 10.1186/s12931-024-02859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Despite the success of antiretroviral therapy (ART), people living with HIV (PLWH) suffer from a high burden of pulmonary diseases, even after accounting for their smoking status. Cytotoxic CD8 T-cells are likely implicated in this phenomenon and may act as a double-edged sword. While being essential in viral infection control, their hyperactivation can also contribute to lung mucosal tissue damage. The effects of HIV and smoking on pulmonary mucosal CD8 T-cell dynamics has been a neglected area of research, which we address herein. METHODS Bronchoalveolar lavage (BAL) fluid were obtained from ART-treated PLWH (median duration of supressed viral load: 9 years; smokers: n = 14; non-smokers: n = 21) and HIV-uninfected controls (smokers: n = 11; non-smokers: n = 20) without any respiratory symptoms or active infection. Lymphocytes were isolated and CD8 T-cell subsets and homing markers were characterized by multiparametric flow cytometry. RESULTS Both smoking and HIV infection were independently associated with a significant increase in frequencies of total pulmonary mucosal CD8 T-cell. BAL CD8 T-cells were primarily CD69 + expressing CD103 and/or CD49a, at least one of the two granzymes (GzmA/GzmB), and little Perforin. Higher expression levels of CD103, CD69, and GzmB were observed in smokers versus non-smokers. The ex vivo phenotype of GzmA + and GzmB + cells revealed increased expression of CD103 and CXCR6 in smokers, while PLWH displayed elevated levels of CX3CR1 compared to controls. CONCLUSION Smoking and HIV could promote cytotoxic CD8 T-cell retention in small airways through different mechanisms. Smoking likely increases recruitment and retention of GzmB + CD8 Trm via CXCR6 and CD103. Heightened CX3CR1 expression could be associated with CD8 non-Trm recruitment from the periphery in PLWH.
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Affiliation(s)
- Yulia Alexandrova
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), 141, Avenue President Kennedy, Montreal, QC, H2X 1Y4, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Alexis Yero
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), 141, Avenue President Kennedy, Montreal, QC, H2X 1Y4, Canada
| | - Ronald Olivenstein
- Division of Respirology, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Marianna Orlova
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Departments of Human Genetics and Medicine, McGill University, Montreal, QC, Canada
| | - Jerome Estaquier
- Centre de recherche de CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Cecilia T Costiniuk
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), 141, Avenue President Kennedy, Montreal, QC, H2X 1Y4, Canada.
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Lee EH, Lee KH, Lee KN, Park Y, Do Han K, Han SH. The Relation Between Cigarette Smoking and Development of Sepsis: A 10-Year Follow-Up Study of Four Million Adults from the National Health Screening Program. J Epidemiol Glob Health 2024; 14:444-452. [PMID: 38372892 PMCID: PMC11176127 DOI: 10.1007/s44197-024-00197-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Sepsis remains a growing global health concern with soaring mortality and no direct anti-sepsis drug. Although smoking has distinct deleterious effects on chronic inflammatory illnesses and can impair immune function, a comprehensive analysis of the connection between sepsis and smoking is lacking. METHODS This large-scale longitudinal cohort study retrospectively assessed adults aged ≥ 20 years who underwent national health checkups under the Korean National Health Insurance Service between January and December 2009 (N = 4,234,415) and were followed up for 10 years. Sepsis was identified based on the International Classification of Diseases, 10th Revision codes, and smoking status, including accumulated amount, was collected through a self-administered questionnaire. The Cox proportional hazard regression model was used, adjusting for age, sex, household income, body mass index, drinking, exercise, diabetes, hypertension, dyslipidemia, and chronic renal disease. RESULTS After excluding cases with sepsis occurring before follow-up or after ≤ 1 year of follow-up, 3,881,958 participants, including non-smokers (N = 2,342,841), former smokers (N = 539,850), and active smokers (N = 999,267), were included. Compared to non-smokers, all active smokers (adjust hazard ratio: 1.41, 95% confidence interval 1.38-1.44) and former smokers (1.10, 1.07-1.14) with ≥ 20 pack-years exhibited a significantly higher risk of sepsis (p < 0.001). Smoking of ≥ 30 pack-years in former and active smokers groups significantly increased sepsis incidence (adjust hazard ratio [95% confidence interval] 1.34 [1.31-1.38], p < 0.001). CONCLUSIONS Smoking is closely associated with the incidence of sepsis. Smoking cessation may help in the primary prevention of sepsis.
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Affiliation(s)
- Eun Hwa Lee
- Divison of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Kyoung Hwa Lee
- Divison of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Kyu-Na Lee
- Department of Preventive Medicine and Public Health, College of Medicine, Catholic University of Korea, Seoul, Republic of Korea
| | - Yebin Park
- Department of Statistics and Actuarial Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul, 06978, Republic of Korea
| | - Kyung Do Han
- Department of Statistics and Actuarial Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul, 06978, Republic of Korea.
| | - Sang Hoon Han
- Divison of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul, 06273, Republic of Korea.
- Institute for Innovation in Digital Healthcare, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Türk L, Filippov I, Arnold C, Zaugg J, Tserel L, Kisand K, Peterson P. Cytotoxic CD8 + Temra cells show loss of chromatin accessibility at genes associated with T cell activation. Front Immunol 2024; 15:1285798. [PMID: 38370415 PMCID: PMC10870784 DOI: 10.3389/fimmu.2024.1285798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.
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Affiliation(s)
- Lehte Türk
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Igor Filippov
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Qiagen Aarhus A/S, Aarhus, Denmark
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Judith Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Liina Tserel
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 2024; 15:872. [PMID: 38287014 PMCID: PMC10825117 DOI: 10.1038/s41467-024-45240-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Batch effects in single-cell RNA-seq data pose a significant challenge for comparative analyses across samples, individuals, and conditions. Although batch effect correction methods are routinely applied, data integration often leads to overcorrection and can result in the loss of biological variability. In this work we present STACAS, a batch correction method for scRNA-seq that leverages prior knowledge on cell types to preserve biological variability upon integration. Through an open-source benchmark, we show that semi-supervised STACAS outperforms state-of-the-art unsupervised methods, as well as supervised methods such as scANVI and scGen. STACAS scales well to large datasets and is robust to incomplete and imprecise input cell type labels, which are commonly encountered in real-life integration tasks. We argue that the incorporation of prior cell type information should be a common practice in single-cell data integration, and we provide a flexible framework for semi-supervised batch effect correction.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Paul Gueguen
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ariel J Berenstein
- Laboratorio de Biología Molecular, División Patología, Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Buenos Aires, C1425EFD, Argentina
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland.
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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8
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Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
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Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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9
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Alisoltani A, Qiu X, Jaroszewski L, Sedova M, Iyer M, Godzik A. Gender differences in smoking-induced changes in the tumor immune microenvironment. Arch Biochem Biophys 2023; 739:109579. [PMID: 36933758 DOI: 10.1016/j.abb.2023.109579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 03/17/2023]
Abstract
Both gender and smoking are correlated with prevalence and outcomes in many types of cancers. Tobacco smoke is a known carcinogen through its genotoxicity but can also affect cancer progression through its effect on the immune system. In this study, we aim to evaluate the hypothesis that the effects of smoking on the tumor immune microenvironment will be influenced differently by gender using large-scale analysis of publicly available cancer datasets. We used The Cancer Genomic Atlas (TCGA) datasets (n = 2724) to analyze effects of smoking on different cancer immune subtypes and the relative abundance of immune cell types between male and female cancer patients. We further validated our results by analyzing additional datasets, including Expression Project for Oncology (expO) bulk RNA-seq dataset (n = 1118) and single-cell RNA-seq dataset (n = 14). Results of our study indicate that in female patients, two immune subtypes, C1 and C2, are respectively over and under abundant in smokers vs. never smokers. In males, the only significant difference is underabundance of the C6 subtype in smokers. We identified gender-specific differences in the population of immune cell types between smokers and never smokers in all TCGA and expO cancer types. Increased plasma cell population was identified as the most consistent feature distinguishing smokers and never smokers, especially in current female smokers based on both TCGA and expO data. Our analysis of existing single-cell RNA-seq data further revealed that smoking differentially affects the gene expression profile of cancer patients based on the immune cell type and gender. In our analysis, female and male smokers show different smoking-induced patterns of immune cells in tumor microenvironment. Besides, our results suggest cancer tissues directly exposed to tobacco smoke undergo the most significant changes, but all other cancer types are affected as well. Findings of current study also indicate that changes in the populations of plasma cells and their correlations to survival outcomes are stronger in female current smokers, with implications for cancer immunotherapy of women smokers. In conclusion, results of this study can be used to develop personalized treatment plans for cancer patients who smoke, particularly women smokers, taking into account the unique immune cell profile of their tumors.
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Affiliation(s)
- Arghavan Alisoltani
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA; Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Xinru Qiu
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Lukasz Jaroszewski
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Mayya Sedova
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Mallika Iyer
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
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10
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Schreibing F, Hannani MT, Kim H, Nagai JS, Ticconi F, Fewings E, Bleckwehl T, Begemann M, Torow N, Kuppe C, Kurth I, Kranz J, Frank D, Anslinger TM, Ziegler P, Kraus T, Enczmann J, Balz V, Windhofer F, Balfanz P, Kurts C, Marx G, Marx N, Dreher M, Schneider RK, Saez-Rodriguez J, Costa I, Hayat S, Kramann R. Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling. Front Immunol 2022; 13:1066176. [PMID: 36591270 PMCID: PMC9800604 DOI: 10.3389/fimmu.2022.1066176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction SARS-CoV-2 infection results in varying disease severity, ranging from asymptomatic infection to severe illness. A detailed understanding of the immune response to SARS-CoV-2 is critical to unravel the causative factors underlying differences in disease severity and to develop optimal vaccines against new SARS-CoV-2 variants. Methods We combined single-cell RNA and T cell receptor sequencing with CITE-seq antibodies to characterize the CD8+ T cell response to SARS-CoV-2 infection at high resolution and compared responses between mild and severe COVID-19. Results We observed increased CD8+ T cell exhaustion in severe SARS-CoV-2 infection and identified a population of NK-like, terminally differentiated CD8+ effector T cells characterized by expression of FCGR3A (encoding CD16). Further characterization of NK-like CD8+ T cells revealed heterogeneity among CD16+ NK-like CD8+ T cells and profound differences in cytotoxicity, exhaustion, and NK-like differentiation between mild and severe disease conditions. Discussion We propose a model in which differences in the surrounding inflammatory milieu lead to crucial differences in NK-like differentiation of CD8+ effector T cells, ultimately resulting in the appearance of NK-like CD8+ T cell populations of different functionality and pathogenicity. Our in-depth characterization of the CD8+ T cell-mediated response to SARS-CoV-2 infection provides a basis for further investigation of the importance of NK-like CD8+ T cells in COVID-19 severity.
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Affiliation(s)
- Felix Schreibing
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Renal and Hypertensive Disorders, Rheumatological and Immunological Diseases (Medical Clinic II), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Monica T. Hannani
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Hyojin Kim
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - James S. Nagai
- Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, Aachen, Germany,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Fabio Ticconi
- Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, Aachen, Germany,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Eleanor Fewings
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Tore Bleckwehl
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Natalia Torow
- Institute of Medical Microbiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Renal and Hypertensive Disorders, Rheumatological and Immunological Diseases (Medical Clinic II), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jennifer Kranz
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Urology and Pediatric Urology, RWTH Aachen University, Aachen, Germany,Department of Urology and Kidney Transplantation, Martin Luther University (Saale), Halle, Germany
| | - Dario Frank
- Department of Medicine, St Antonius Hospital, Eschweiler, Germany
| | - Teresa M. Anslinger
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Renal and Hypertensive Disorders, Rheumatological and Immunological Diseases (Medical Clinic II), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Patrick Ziegler
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Kraus
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jürgen Enczmann
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Vera Balz
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Frank Windhofer
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Paul Balfanz
- Department of Cardiology, Angiology and Intensive Care Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christian Kurts
- Institute of Molecular Medicine and Experimental Immunology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Gernot Marx
- Department of Intensive and Intermediate Care, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Nikolaus Marx
- Department of Cardiology, Angiology and Intensive Care Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Dreher
- Department of Pneumology and Intensive Care Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rebekka K. Schneider
- Institute of Cell and Tumor Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Ivan Costa
- Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, Aachen, Germany,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Renal and Hypertensive Disorders, Rheumatological and Immunological Diseases (Medical Clinic II), Medical Faculty, RWTH Aachen University, Aachen, Germany,Department of Internal Medicine, Erasmus Medical Center (MC), Rotterdam, Netherlands,*Correspondence: Rafael Kramann,
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11
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Leffler J, Trend S, Hart PH, French MA. Epstein-Barr virus infection, B-cell dysfunction and other risk factors converge in gut-associated lymphoid tissue to drive the immunopathogenesis of multiple sclerosis: a hypothesis. Clin Transl Immunology 2022; 11:e1418. [PMID: 36325491 PMCID: PMC9621333 DOI: 10.1002/cti2.1418] [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: 07/14/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Multiple sclerosis is associated with Epstein-Barr virus (EBV) infection, B-cell dysfunction, gut dysbiosis, and environmental and genetic risk factors, including female sex. A disease model incorporating all these factors remains elusive. Here, we hypothesise that EBV-infected memory B cells (MBCs) migrate to gut-associated lymphoid tissue (GALT) through EBV-induced expression of LPAM-1, where they are subsequently activated by gut microbes and/or their products resulting in EBV reactivation and compartmentalised anti-EBV immune responses. These responses involve marginal zone (MZ) B cells that activate CD4+ T-cell responses, via HLA-DRB1, which promote downstream B-cell differentiation towards CD11c+/T-bet+ MBCs, as well as conventional MBCs. Intrinsic expression of low-affinity B-cell receptors (BCRs) by MZ B cells and CD11c+/T-bet+ MBCs promotes polyreactive BCR/antibody responses against EBV proteins (e.g. EBNA-1) that cross-react with central nervous system (CNS) autoantigens (e.g. GlialCAM). EBV protein/autoantigen-specific CD11c+/T-bet+ MBCs migrate to the meningeal immune system and CNS, facilitated by their expression of CXCR3, and induce cytotoxic CD8+ T-cell responses against CNS autoantigens amplified by BAFF, released from EBV-infected MBCs. An increased abundance of circulating IgA+ MBCs, observed in MS patients, might also reflect GALT-derived immune responses, including disease-enhancing IgA antibody responses against EBV and gut microbiota-specific regulatory IgA+ plasma cells. Female sex increases MZ B-cell and CD11c+/T-bet+ MBC activity while environmental risk factors affect gut dysbiosis. Thus, EBV infection, B-cell dysfunction and other risk factors converge in GALT to generate aberrant B-cell responses that drive pathogenic T-cell responses in the CNS.
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Affiliation(s)
- Jonatan Leffler
- Telethon Kids InstituteUniversity of Western AustraliaPerthWAAustralia
| | - Stephanie Trend
- Telethon Kids InstituteUniversity of Western AustraliaPerthWAAustralia,Perron Institute for Neurological and Translational ScienceUniversity of Western AustraliaPerthWAAustralia
| | - Prue H Hart
- Telethon Kids InstituteUniversity of Western AustraliaPerthWAAustralia
| | - Martyn A French
- School of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia,Immunology DivisionPathWest Laboratory MedicinePerthWAAustralia
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12
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Li X, Li S, Wu B, Xu Q, Teng D, Yang T, Sun Y, Zhao Y, Li T, Liu D, Yang S, Gong W, Cai J. Landscape of Immune Cells Heterogeneity in Liver Transplantation by Single-Cell RNA Sequencing Analysis. Front Immunol 2022; 13:890019. [PMID: 35619708 PMCID: PMC9127089 DOI: 10.3389/fimmu.2022.890019] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022] Open
Abstract
Rejection is still a critical barrier to the long-term survival of graft after liver transplantation, requiring clinicians to unveil the underlying mechanism of liver transplant rejection. The cellular diversity and the interplay between immune cells in the liver graft microenvironment remain unclear. Herein, we performed single-cell RNA sequencing analysis to delineate the landscape of immune cells heterogeneity in liver transplantation. T cells, NK cells, B cells, and myeloid cell subsets in human liver and blood were enriched to characterize their tissue distribution, gene expression, and functional modules. The proportion of CCR6+CD4+ T cells increased within an allograft, suggesting that there are more memory CD4+ T cells after transplantation, in parallel with exhausted CTLA4+CD8+ T and actively proliferating MKI67+CD8+ T cells increased significantly, where they manifested heterogeneity, distinct function, and homeostatic proliferation. Remarkably, the changes of CD1c+ DC, CADM+ DC, MDSC, and FOLR3+ Kupffer cells increase significantly, but the proportion of CD163+ Kupffer, APOE+ Kupffer, and GZMA+ Kupffer decreased. Furthermore, we identified LDLR as a novel marker of activated MDSC to prevent liver transplant rejection. Intriguingly, a subset of CD4+CD8+FOXP3+ T cells included in CTLA4+CD8+ T cells was first detected in human liver transplantation. Furthermore, intercellular communication and gene regulatory analysis implicated the LDLR+ MDSC and CTLA4+CD8+ T cells interact through TIGIT-NECTIN2 signaling pathway. Taken together, these findings have gained novel mechanistic insights for understanding the immune landscape in liver transplantation, and it outlines the characteristics of immune cells and provides potential therapeutic targets in liver transplant rejection.
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Affiliation(s)
- Xinqiang Li
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shipeng Li
- Department of General Surgery, Jiaozuo Women's and Children's Hospital, Jiaozuo, China.,The Second Clinical Medical College, Capital Medical University, Beijing, China
| | - Bin Wu
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Qingguo Xu
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Dahong Teng
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Tongwang Yang
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Yandong Sun
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Yang Zhao
- Department of Urology Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Tianxiang Li
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Dan Liu
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
| | - Shuang Yang
- Department of Molecular Biology, Medical College, Nankai University, Tianjin, China
| | - Weihua Gong
- Department of Surgery, Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinzhen Cai
- Organ Transplantation Center, Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Organ Donation and Transplantation, Medical College of Qingdao University, Qingdao, China
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13
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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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14
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Zhang H, Weyand CM, Goronzy JJ. Hallmarks of the aging T-cell system. FEBS J 2021; 288:7123-7142. [PMID: 33590946 PMCID: PMC8364928 DOI: 10.1111/febs.15770] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
The adaptive immune system has the enormous challenge to protect the host through the generation and differentiation of pathogen-specific short-lived effector T cells while in parallel developing long-lived memory cells to control future encounters with the same pathogen. A complex regulatory network is needed to preserve a population of naïve cells over lifetime that exhibit sufficient diversity of antigen receptors to respond to new antigens, while also sustaining immune memory. In parallel, cells need to maintain their proliferative potential and the plasticity to differentiate into different functional lineages. Initial signs of waning immune competence emerge after 50 years of age, with increasing clinical relevance in the 7th-10th decade of life. Morbidity and mortality from infections increase, as drastically exemplified by the current COVID-19 pandemic. Many vaccines, such as for the influenza virus, are poorly effective to generate protective immunity in older individuals. Age-associated changes occur at the level of the T-cell population as well as the functionality of its cellular constituents. The system highly relies on the self-renewal of naïve and memory T cells, which is robust but eventually fails. Genetic and epigenetic modifications contribute to functional differences in responsiveness and differentiation potential. To some extent, these changes arise from defective maintenance; to some, they represent successful, but not universally beneficial adaptations to the aging host. Interventions that can compensate for the age-related defects and improve immune responses in older adults are increasingly within reach.
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Affiliation(s)
- Huimin Zhang
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
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15
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Mukund K, Nayak P, Ashokkumar C, Rao S, Almeda J, Betancourt-Garcia MM, Sindhi R, Subramaniam S. Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. Front Immunol 2021; 12:738073. [PMID: 34721400 PMCID: PMC8548832 DOI: 10.3389/fimmu.2021.738073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 12/18/2022] Open
Abstract
The mechanisms underlying the immune remodeling and severity response in coronavirus disease 2019 (COVID-19) are yet to be fully elucidated. Our comprehensive integrative analyses of single-cell RNA sequencing (scRNAseq) data from four published studies, in patients with mild/moderate and severe infections, indicate a robust expansion and mobilization of the innate immune response and highlight mechanisms by which low-density neutrophils and megakaryocytes play a crucial role in the cross talk between lymphoid and myeloid lineages. We also document a marked reduction of several lymphoid cell types, particularly natural killer cells, mucosal-associated invariant T (MAIT) cells, and gamma-delta T (γδT) cells, and a robust expansion and extensive heterogeneity within plasmablasts, especially in severe COVID-19 patients. We confirm the changes in cellular abundances for certain immune cell types within a new patient cohort. While the cellular heterogeneity in COVID-19 extends across cells in both lineages, we consistently observe certain subsets respond more potently to interferon type I (IFN-I) and display increased cellular abundances across the spectrum of severity, as compared with healthy subjects. However, we identify these expanded subsets to have a more muted response to IFN-I within severe disease compared to non-severe disease. Our analyses further highlight an increased aggregation potential of the myeloid subsets, particularly monocytes, in COVID-19. Finally, we provide detailed mechanistic insights into the interaction between lymphoid and myeloid lineages, which contributes to the multisystemic phenotype of COVID-19, distinguishing severe from non-severe responses.
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Affiliation(s)
- Kavitha Mukund
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Priya Nayak
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Chethan Ashokkumar
- Plexision Inc., Pittsburgh, PA, United States
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sohail Rao
- DHR Health and DHR Health Institute for Research and Development, Edinburg, TX, United States
| | - Jose Almeda
- DHR Health and DHR Health Institute for Research and Development, Edinburg, TX, United States
| | | | - Rakesh Sindhi
- Plexision Inc., Pittsburgh, PA, United States
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, Pittsburgh, PA, United States
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
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16
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Wang CI, Chang YF, Sie ZL, Ho AS, Chang JS, Peng CL, Cheng CC. Irradiation Suppresses IFNγ-Mediated PD-L1 and MCL1 Expression in EGFR-Positive Lung Cancer to Augment CD8 + T Cells Cytotoxicity. Cells 2021; 10:cells10102515. [PMID: 34685495 PMCID: PMC8533912 DOI: 10.3390/cells10102515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022] Open
Abstract
Tumor cells express immune checkpoints to exhaust CD8+ T cells. Irradiation damages tumor cells and augments tumor immunotherapy in clinical applications. However, the radiotherapy-mediated molecular mechanism affecting CD8+ T cell activity remains elusive. We aimed to uncover the mechanism of radiotherapy augmenting cytotoxic CD8+ T cells in non-small-cell lung cancer (NSCLC). EGFR-positive NSCLC cell lines were co-cultured with CD8+ T cells from healthy volunteers. Tumor cell viability and apoptosis were consequently measured. IFNγ was identified secreted by CD8+ T cells and PBMCs. Therefore, RNAseq was used to screen the IFNγ-mediated gene expression in A549 cells. The irradiation effect to IFNγ-mediated gene expression was investigated using qPCR and western blots. We found that the co-culture of tumor cells stimulated the increase of granzyme B and IFNγ in CD8+ T, but A549 exhibited resistance against CD8+ T cytotoxicity compared to HCC827. Irradiation inhibited A549 proliferation and enhanced apoptosis, augmenting PBMCs-mediated cytotoxicity against A549. We found that IFNγ simultaneously increased phosphorylation on STAT1 and STAT3 in EGFR-positive lung cancer, resulting in overexpression of PD-L1 (p < 0.05). In RNAseq analysis, MCL1 was identified and increased by the IFNγ-STAT3 axis (p < 0.05). We demonstrated that irradiation specifically inhibited phosphorylation on STAT1 and STAT3 in IFNγ-treated A549, resulting in reductions of PD-L1 and MCL1 (both p < 0.05). Moreover, knockdowns of STAT3 and MCL1 increased the PBMCs-mediated anti-A549 effect. This study demonstrated that A549 expressed MCL1 to resist CD8+ T cell-mediated tumor apoptosis. In addition, we found that irradiation suppressed IFNγ-mediated STAT3 phosphorylation and PD-L1 and MCL1 expression, revealing a potential mechanism of radiotherapy augmenting immune surveillance.
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Affiliation(s)
- Chun-I. Wang
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou 333, Taiwan; (C.-I.W.); (Z.-L.S.)
| | - Yi-Fang Chang
- Division of Hematology and Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 104, Taiwan;
- Laboratory of Good Clinical Research Center, Department of Medical Research, Mackay Memorial Hospital, Tamsui District, New Taipei City 251, Taiwan
- Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan
| | - Zong-Lin Sie
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou 333, Taiwan; (C.-I.W.); (Z.-L.S.)
| | - Ai-Sheng Ho
- Division of Gastroenterology, Cheng Hsin General Hospital, Taipei 112, Taiwan;
| | - Jung-Shan Chang
- Graduate Institute of Medical Sciences, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Cheng-Liang Peng
- Institute of Nuclear Energy Research, Atomic Energy Council, Taoyuan 325, Taiwan;
| | - Chun-Chia Cheng
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou 333, Taiwan; (C.-I.W.); (Z.-L.S.)
- Correspondence:
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17
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Venosa A. Senescence in Pulmonary Fibrosis: Between Aging and Exposure. Front Med (Lausanne) 2020; 7:606462. [PMID: 33282895 PMCID: PMC7689159 DOI: 10.3389/fmed.2020.606462] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022] Open
Abstract
To date, chronic pulmonary pathologies represent the third leading cause of death in the elderly population. Evidence-based projections suggest that >65 (years old) individuals will account for approximately a quarter of the world population before the turn of the century. Genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication, are described as the nine “hallmarks” that govern cellular fitness. Any deviation from the normal pattern initiates a complex cascade of events culminating to a disease state. This blueprint, originally employed to describe aberrant changes in cancer cells, can be also used to describe aging and fibrosis. Pulmonary fibrosis (PF) is the result of a progressive decline in injury resolution processes stemming from endogenous (physiological decline or somatic mutations) or exogenous stress. Environmental, dietary or occupational exposure accelerates the pathogenesis of a senescent phenotype based on (1) window of exposure; (2) dose, duration, recurrence; and (3) cells type being targeted. As the lung ages, the threshold to generate an irreversibly senescent phenotype is lowered. However, we do not have sufficient knowledge to make accurate predictions. In this review, we provide an assessment of the literature that interrogates lung epithelial, mesenchymal, and immune senescence at the intersection of aging, environmental exposure and pulmonary fibrosis.
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Affiliation(s)
- Alessandro Venosa
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, UT, United States
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