1
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Manoharan MS, Lee GC, Harper N, Meunier JA, Restrepo MI, Jimenez F, Karekatt S, Branum AP, Gaitan AA, Andampour K, Smith AM, Mader M, Noronha M, Tripathy D, Zhang N, Moreira AG, Pandranki L, Sanchez-Reilly S, Trinh HD, Barnett C, Angel L, Segal LN, Nicholson S, Clark RA, He W, Okulicz JF, Ahuja SK. The 15-Year Survival Advantage: Immune Resilience as a Salutogenic Force in Healthy Aging. Aging Cell 2025:e70063. [PMID: 40264357 DOI: 10.1111/acel.70063] [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: 01/02/2025] [Revised: 03/14/2025] [Accepted: 03/21/2025] [Indexed: 04/24/2025] Open
Abstract
Human aging presents an evolutionary paradox: while aging rates remain constant, healthspan and lifespan vary widely. We address this conundrum via salutogenesis-the active production of health-through immune resilience (IR), the capacity to resist disease despite aging and inflammation. Analyzing ~17,500 individuals across lifespan stages and inflammatory challenges, we identified a core salutogenic mechanism: IR centered on TCF7, a conserved transcription factor maintaining T-cell stemness and regenerative potential. IR integrates innate and adaptive immunity to counter three aging and mortality drivers: chronic inflammation (inflammaging), immune aging, and cellular senescence. By mitigating these aging mechanisms, IR confers survival advantages: At age 40, individuals with poor IR face a 9.7-fold higher mortality rate-a risk equivalent to that of 55.5-year-olds with optimal IR-resulting in a 15.5-year gap in survival. Optimal IR preserves youthful immune profiles at any age, enhances vaccine responses, and reduces burdens of cardiovascular disease, Alzheimer's, and serious infections. Two key salutogenic evolutionary themes emerge: first, female-predominant IR, including TCF7, likely reflects evolutionary pressures favoring reproductive success and caregiving; second, midlife (40-70 years) is a critical window where optimal IR reduces mortality by 69%. After age 70, mortality rates converge between resilient and non-resilient groups, reflecting biological limits on longevity extension. TNFα-blockers restore salutogenesis pathways, indicating IR delays aging-related processes rather than altering aging rates. By reframing aging as a salutogenic-pathogenic balance, we establish TCF7-centered IR as central to healthy longevity. Targeted midlife interventions to enhance IR offer actionable strategies to maximize healthspan before biological constraints limit benefits.
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Affiliation(s)
- Muthu Saravanan Manoharan
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Grace C Lee
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Pharmacotherapy Education and Research Center, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Nathan Harper
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Justin A Meunier
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Marcos I Restrepo
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Fabio Jimenez
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Sreenath Karekatt
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Anne P Branum
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Alvaro A Gaitan
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | - Kian Andampour
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Alisha M Smith
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Michael Mader
- South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Michelle Noronha
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Devjit Tripathy
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Nu Zhang
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Alvaro G Moreira
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Lavanya Pandranki
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Sandra Sanchez-Reilly
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Hanh D Trinh
- South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Clea Barnett
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Luis Angel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Susannah Nicholson
- Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Robert A Clark
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Weijing He
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, Texas, USA
| | | | - Sunil K Ahuja
- Veterans Affairs Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, Texas, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- South Texas Veterans Health Care System, San Antonio, Texas, USA
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2
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Hong Y, Wang Y, Shu W. Immunocyte phenotypes and childhood disease susceptibility: insights from bidirectional Mendelian randomization and implications for immunomodulatory therapies. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04091-1. [PMID: 40178601 DOI: 10.1007/s00210-025-04091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 03/21/2025] [Indexed: 04/05/2025]
Abstract
Immune cells are essential for maintaining immune homeostasis during childhood and influence both growth and disease susceptibility. However, the causal relationships between immunocyte phenotypes and childhood diseases remain unclear. This study employed a two-sample Mendelian Randomization (MR) analysis to assess causal associations between 731 immunocyte phenotypes and four major childhood diseases: childhood obesity, childhood absence epilepsy, childhood asthma, and childhood allergies. Genome-wide association study (GWAS) data were used, and stringent instrumental variable (IV) selection and multiple sensitivity analyses, including MR-Egger, weighted median, and leave-one-out tests, were applied to validate the robustness of the results. Significant associations were identified between specific T cell, monocyte, and B cell phenotypes and childhood diseases. Notably, CD8bright T cells and CD19 + B cells were positively correlated with childhood obesity, while monocyte subtypes were strongly associated with asthma pathophysiology. Reverse MR analysis indicated no significant causal effects of childhood diseases on immune phenotypes, except for negative associations between childhood asthma and TCRgd AC, and childhood allergy and CD28 + CD45RA + CD4 + cells. These findings highlight the critical role of immune dysregulation in childhood disease etiology and suggest potential targets for immunomodulatory therapies. Understanding these immune-disease interactions may inform novel pharmacological interventions, particularly in immune-mediated disorders such as asthma and obesity. Further research into immune-targeted therapies could enhance treatment strategies for pediatric conditions associated with chronic inflammation and immune dysfunction.
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Affiliation(s)
- Yanggang Hong
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang Province, China.
| | - Yi Wang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang Province, China
| | - Wanyi Shu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325035, Zhejiang Province, China
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3
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Jiang RD, Luo YZ, Lin HF, Zheng XS, Zeng WT, Liu MQ, Deng HH, Wang Q, Lai YN, Chen Y, Guo ZS, Zeng Y, Gong QC, Qiu C, Dong M, Wang X, Wang ZY, Ji LN, Hou PP, Li Q, Shen XR, Li B, Gao Y, Zhang AH, Jiang TT, Shi AM, Zhou P, Lin XH, Deng ZQ, Li JM, Shi ZL. Impaired inflammatory resolution with severe SARS-CoV-2 infection in leptin knock out obese hamster. iScience 2025; 28:111837. [PMID: 39981511 PMCID: PMC11841202 DOI: 10.1016/j.isci.2025.111837] [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: 05/12/2024] [Revised: 09/28/2024] [Accepted: 12/13/2024] [Indexed: 02/22/2025] Open
Abstract
Comorbidities, such as obesity, increase the risk of severe COVID-19. However, the mechanisms underlying severe illnesses in individuals with obesity are poorly understood. Here, we used gene-edited leptin knock out (Leptin -/-) obese hamsters to establish a severe infection model. This model exhibits robust viral replication, severe lung lesions, pronounced clinical symptoms, and fatal infection, mirroring severe COVID-19 in patients with obesity. Using single-cell transcriptomics on lung tissues pre- and post-infection, we found that monocyte-derived alveolar macrophages (MD-AM) play a key role in lung hyper-inflammation, including two unique MD-AM cell fate branches specific to Leptin -/- hamsters. Notably, reduced Trem2-dependent efferocytosis pathways in Leptin -/- hamsters indicated weakened inflammation resolution, consistent with the scRNA-seq data from patients with obesity. In summary, our study highlights the obesity-associated mechanisms underlying severe SARS-CoV-2 infections and establishes a reliable preclinical animal model for developing obesity-specific therapeutics for critical COVID-19.
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Affiliation(s)
- Ren-Di Jiang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun-Zhe Luo
- BGI Research, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Feng Lin
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Shuang Zheng
- The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Wen-Tao Zeng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Mei-Qin Liu
- The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Hao-Hao Deng
- BGI Research, Beijing, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Qi Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Na Lai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Ying Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zi-Shuo Guo
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Zeng
- BGI Research, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian-Chun Gong
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Qiu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Mei Dong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Yi Wang
- National Engineering Research Center of Neuromodulation, School of Aerospace Engineering, Tsinghua University, Beijing, China
| | - Li-Na Ji
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, China
| | - Pan-Pan Hou
- Guangzhou National Laboratory, Guangzhou, China
| | - Qian Li
- The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xu-Rui Shen
- Guangzhou National Laboratory, Guangzhou, China
| | - Bei Li
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yun Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Ai-Hua Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Ting-Ting Jiang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ai-Min Shi
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Peng Zhou
- The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Xin-Hua Lin
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Shanghai, China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, China
| | - Zi-Qing Deng
- BGI Research, Beijing, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Jian-Min Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Animal Core facility, Key Laboratory of Model Animal, Department of Cell Biology, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Guangzhou National Laboratory, Guangzhou, China
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4
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Li B, Zhang X, Fang Y, Chen M, Li Q, Zeng Y, Ren C, Wang C, Lv Y, Lu J, Liu H, Liu Y. PD-L1 Promotes Immunological Tolerance and Enhances Visual Protection of hESC-RPE Grafts in Retinal Degeneration. Cell Prolif 2025:e70007. [PMID: 39953740 DOI: 10.1111/cpr.70007] [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: 11/08/2024] [Revised: 01/16/2025] [Accepted: 02/05/2025] [Indexed: 02/17/2025] Open
Abstract
Immune rejection is a major barrier to the successful human embryonic stem cell-derived retinal pigment epithelial (hESC-RPE) transplantation for age-related macular degeneration (AMD). Traditional strategies to mitigate immune rejection involve ablating major histocompatibility complex (MHC) molecules on hESC-RPE. An alternative approach is immune checkpoint overexpression, avoiding natural killer (NK) cell-mediated destruction due to MHC-I deficiency. Our study highlights the benefits of PD-L1 overexpression without requiring MHC gene deletion, which preserved the immunosuppressive functions of hESC-RPE on NK cells. In Vivo experiments in retinal degeneration models showed that PD-L1-expressing hESC-RPE grafts exhibited significantly higher survival, reduced apoptosis and enhanced visual protection. Single-cell transcriptomics revealed reduced immune activation and oxidative stress in PD-L1-overexpressing grafts. PD-L1's protective role was further evidenced by improved light transduction in host photoreceptors. These findings support PD-L1 overexpression as a promising strategy to improve the efficiency of hESC-RPE-based therapy for AMD.
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Affiliation(s)
- Bowen Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Xue Zhang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yajie Fang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Min Chen
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Qiyou Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yuxiao Zeng
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Chunge Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Chengang Wang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yingxue Lv
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Jia Lu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Hongling Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yong Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
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5
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Kuang S, Yang J, Shen Z, Xia J, Lin Z. Single-Cell and Spatial Multi-Omics Analysis Reveal That Targeting JAG1 in Epithelial Cells Reduces Periodontal Inflammation and Alveolar Bone Loss. Int J Mol Sci 2024; 25:13255. [PMID: 39769019 PMCID: PMC11675447 DOI: 10.3390/ijms252413255] [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: 11/07/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025] Open
Abstract
Mucosal immunity plays a critical role in the pathogenesis of inflammatory immune diseases. This study leverages single-cell RNA sequencing, spatial transcriptomics, and spatial proteomics to compare the cellular mechanisms involved in periodontitis between humans and mice, aiming to develop precise strategies to protect the gingival mucosal barrier. We identified key conserved and divergent features in cellular landscapes and transcriptional profiles across the two species, underscoring the complexity of inflammatory responses and immune dynamics in periodontitis. Additionally, we revealed a novel regulatory mechanism by which epithelial cells modulate macrophage behavior and inflammation through the JAG1-Notch pathway. Validation through animal experiments revealed that JAG1 inhibition reduces inflammation in epithelial cells, mitigating periodontitis. Our findings advance the understanding of periodontal disease pathogenesis and highlight the importance of integrating human and animal model data to develop treatments aligned with human physiology, offering potential therapeutic targets for controlling inflammation and enhancing tissue regeneration.
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Affiliation(s)
| | | | | | - Juan Xia
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510000, China; (S.K.); (J.Y.); (Z.S.)
| | - Zhengmei Lin
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510000, China; (S.K.); (J.Y.); (Z.S.)
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6
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Zhang S, Fang X, Chang M, Zheng M, Guo L, Xu Y, Shu J, Nie Q, Li Z. Cross-species single-cell analysis reveals divergence and conservation of peripheral blood mononuclear cells. BMC Genomics 2024; 25:1169. [PMID: 39623297 PMCID: PMC11613757 DOI: 10.1186/s12864-024-11030-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 11/11/2024] [Indexed: 12/06/2024] Open
Abstract
BACKGROUND Single-cell transcriptome sequencing (scRNA-seq) has revolutionized the study of immune cells by overcoming the limitations of traditional antibody-based identification and isolation methods. This advancement allows us to obtain comprehensive gene expression profiles from a diverse array of vertebrate species, facilitating the identification of various cell types. Comparative immunology across vertebrates presents a promising approach to understanding the evolution of immune cell types. In this study, we conducted a comparative transcriptome analysis of peripheral blood mononuclear cells (PBMCs) at the single-cell level across 12 species. RESULTS Our findings shed light on the cellular compositional features of PBMCs, spanning from fish to mammals. Notably, we identified genes that exhibit vertebrate universality in characterizing immune cells. Moreover, our investigation revealed that monocytes have maintained a conserved transcriptional regulatory program throughout evolution, emphasizing their pivotal role in orchestrating immune cells to execute immune programs. CONCLUSIONS This comprehensive analysis provides valuable insights into the evolution of immune cells across vertebrates.
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Affiliation(s)
- Siyu Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiang Fang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, 999077, China
| | - Mengyang Chang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, Liaoning, 266071, China
| | - Ming Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Lijin Guo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yibin Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China.
| | - Qinghua Nie
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
| | - Zhenhui Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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7
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Wong KH, Rodriguez NA, Traylor-Knowles N. Exploring the Unknown: How Can We Improve Single-cell RNAseq Cell Type Annotations in Non-model Organisms? Integr Comp Biol 2024; 64:1291-1299. [PMID: 39013613 DOI: 10.1093/icb/icae112] [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: 03/16/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell RNA sequencing (scRNAseq) is a powerful tool to describe cell types in multicellular organisms across the animal kingdom. In standard scRNAseq analysis pipelines, clusters of cells with similar transcriptional signatures are given cell type labels based on marker genes that infer specialized known characteristics. Since these analyses are designed for model organisms, such as humans and mice, problems arise when attempting to label cell types of distantly related, non-model species that have unique or divergent cell types. Consequently, this leads to limited discovery of novel species-specific cell types and potential mis-annotation of cell types in non-model species while using scRNAseq. To address this problem, we discuss recently published approaches that help annotate scRNAseq clusters for any non-model organism. We first suggest that annotating with an evolutionary context of cell lineages will aid in the discovery of novel cell types and provide a marker-free approach to compare cell types across distantly related species. Secondly, machine learning has greatly improved bioinformatic analyses, so we highlight some open-source programs that use reference-free approaches to annotate cell clusters. Lastly, we propose the use of unannotated genes as potential cell markers for non-model organisms, as many do not have fully annotated genomes and these data are often disregarded. Improving single-cell annotations will aid the discovery of novel cell types and enhance our understanding of non-model organisms at a cellular level. By unifying approaches to annotate cell types in non-model organisms, we can increase the confidence of cell annotation label transfer and the flexibility to discover novel cell types.
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Affiliation(s)
- Kevin H Wong
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA, 33149
| | - Natalia Andrade Rodriguez
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA, 33149
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA, 33149
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8
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Ramarapu R, Wulcan JM, Chang H, Moore PF, Vernau W, Keller SM. Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes. Front Immunol 2024; 15:1438004. [PMID: 39620216 PMCID: PMC11604454 DOI: 10.3389/fimmu.2024.1438004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/23/2024] [Indexed: 12/11/2024] Open
Abstract
Introduction The domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. Methods Peripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, αβ T cell receptor transcripts and γδ T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Results Unsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and γδ T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis identified a subset of CD8+ cytotoxic T cells with skewed TRA and TRB gene usage, conserved TRA and TRB junctional motifs, restricted TRA/TRB pairing and reduced diversity in TRG junctional length. We also identified a public γδ T cell subset with invariant TRD and TRG chains and a CD4+ TEM-like phenotype. Among monocytic cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. Discussion Our study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.
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MESH Headings
- Animals
- Cats
- Single-Cell Analysis
- Transcriptome
- Species Specificity
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Dogs
- Sequence Analysis, RNA
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- RNA-Seq
- V(D)J Recombination/genetics
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Affiliation(s)
- Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Judit M. Wulcan
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
| | - Peter F. Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Stefan M. Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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9
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Secombes CJ. Cytokines - Early vertebrate genes and evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 160:105239. [PMID: 39117166 DOI: 10.1016/j.dci.2024.105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/12/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
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10
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Yan Y, Zhu S, Jia M, Chen X, Qi W, Gu F, Valencak TG, Liu JX, Sun HZ. Advances in single-cell transcriptomics in animal research. J Anim Sci Biotechnol 2024; 15:102. [PMID: 39090689 PMCID: PMC11295521 DOI: 10.1186/s40104-024-01063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024] Open
Abstract
Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand for high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of animal research, offering an effective method to study the gene expression of high-throughput single cells of different tissues/organs in animals. In an unprecedented manner, researchers have identified cell types/subtypes and their marker genes, inferred cellular fate trajectories, and revealed cell‒cell interactions in animals using single-cell transcriptomics. In this paper, we introduce the development of single-cell technology and review the processes, advancements, and applications of single-cell transcriptomics in animal research. We summarize recent efforts using single-cell transcriptomics to obtain a more profound understanding of animal nutrition and health, reproductive performance, genetics, and disease models in different livestock species. Moreover, the practical experience accumulated based on a large number of cases is highlighted to provide a reference for determining key factors (e.g., sample size, cell clustering, and cell type annotation) in single-cell transcriptomics analysis. We also discuss the limitations and outlook of single-cell transcriptomics in the current stage. This paper describes the comprehensive progress of single-cell transcriptomics in animal research, offering novel insights and sustainable advancements in agricultural productivity and animal health.
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Affiliation(s)
- Yunan Yan
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Senlin Zhu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minghui Jia
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi Chen
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenlingli Qi
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fengfei Gu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Teresa G Valencak
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Agency for Health and Food Safety Austria, 1220, Vienna, Austria
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
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Dubovik T, Lukačišin M, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G'Sell M, Shen-Orr SS. Interactions between immune cell types facilitate the evolution of immune traits. Nature 2024; 632:350-356. [PMID: 38866051 PMCID: PMC11306095 DOI: 10.1038/s41586-024-07661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.
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Affiliation(s)
- Tania Dubovik
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Martin Lukačišin
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Elina Starosvetsky
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Benjamin LeRoy
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Nike, Beaverton, OR, USA
| | - Rachelly Normand
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Massachusetts General Hospital, Boston, MA, USA
| | - Yasmin Admon
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Yishai Ofran
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Haematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
- Haematology and Bone Marrow Transplantation Department and the Eisenberg R&D Authority, Shaare Zedek Medical Centre, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Max G'Sell
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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12
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Kan H, Chen Y. Revealing endogenous conditions for Peto's paradox via an ordinary differential equation model. J Math Biol 2024; 89:27. [PMID: 38970664 PMCID: PMC11227477 DOI: 10.1007/s00285-024-02123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Cancer, a disease intimately linked to cellular mutations, is commonly believed to exhibit a positive association with the cell count and lifespan of a species. Despite this assumption, the observed uniformity in cancer rates across species, referred to as the Peto's paradox, presents a conundrum. Recognizing that tumour progression is not solely dependent on cancer cells but involves intricate interactions among various cell types, this study employed a Lotka-Volterra (LV) ordinary differential equation model to analyze the evolution of cancerous cells and the cancer incidence in an immune environment. As a result, this study uncovered the sufficient conditions underlying the absence of correlation in Peto's paradox and provide insights into the reasons for the equitable distribution of cancer incidence across diverse species by applying nondimensionalization and drawing an analogy between the characteristic time interval for the variation of cell populations in the ODE model and that of cell cycles of a species.
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Affiliation(s)
- Haichun Kan
- SCS Laboratory, Department of Human and Engineered Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yu Chen
- SCS Laboratory, Department of Human and Engineered Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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13
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Lyons A, Brown J, Davenport KM. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Curr Issues Mol Biol 2024; 46:5291-5306. [PMID: 38920988 PMCID: PMC11202421 DOI: 10.3390/cimb46060316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/27/2024] Open
Abstract
Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.
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14
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Ramarapu R, Wulcan JM, Chang H, Moore PF, Vernau W, Keller SM. Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595010. [PMID: 38826195 PMCID: PMC11142102 DOI: 10.1101/2024.05.21.595010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Introduction The domestic cat (Felis catus) is a valued companion animal and a model for virally induced cancers and immunodeficiencies. However, species-specific limitations such as a scarcity of immune cell markers constrain our ability to resolve immune cell subsets at sufficient detail. The goal of this study was to characterize circulating feline T cells and other leukocytes based on their transcriptomic landscape and T-cell receptor repertoire using single cell RNA-sequencing. Methods Peripheral blood from 4 healthy cats was enriched for T cells by flow cytometry cell sorting using a mouse anti-feline CD5 monoclonal antibody. Libraries for whole transcriptome, alpha/beta T cell receptor transcripts and gamma/delta T cell receptor transcripts were constructed using the 10x Genomics Chromium Next GEM Single Cell 5' reagent kit and the Chromium Single Cell V(D)J Enrichment Kit with custom reverse primers for the feline orthologs. Results Unsupervised clustering of whole transcriptome data revealed 7 major cell populations - T cells, neutrophils, monocytic cells, B cells, plasmacytoid dendritic cells, mast cells and platelets. Sub cluster analysis of T cells resolved naive (CD4+ and CD8+), CD4+ effector T cells, CD8+ cytotoxic T cells and gamma/delta T cells. Cross species analysis revealed a high conservation of T cell subsets along an effector gradient with equitable representation of veterinary species (horse, dog, pig) and humans with the cat. Our V(D)J repertoire analysis demonstrated a skewed T-cell receptor alpha gene usage and a restricted T-cell receptor gamma junctional length in CD8+ cytotoxic T cells compared to other alpha/beta T cell subsets. Among myeloid cells, we resolved three clusters of classical monocytes with polarization into pro- and anti-inflammatory phenotypes in addition to a cluster of conventional dendritic cells. Lastly, our neutrophil sub clustering revealed a larger mature neutrophil cluster and a smaller exhausted/activated cluster. Discussion Our study is the first to characterize subsets of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species analysis. In addition, we characterize the transcriptome of several myeloid cell subsets and demonstrate immune cell relatedness across different species.
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Affiliation(s)
- Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Judit M Wulcan
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Haiyang Chang
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Stefan M Keller
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, United States
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15
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Guito JC, Kirejczyk SGM, Schuh AJ, Amman BR, Sealy TK, Graziano J, Spengler JR, Harmon JR, Wozniak DM, Prescott JB, Towner JS. Coordinated inflammatory responses dictate Marburg virus control by reservoir bats. Nat Commun 2024; 15:1826. [PMID: 38418477 PMCID: PMC10902335 DOI: 10.1038/s41467-024-46226-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Bats are increasingly recognized as reservoirs of emerging zoonotic pathogens. Egyptian rousette bats (ERBs) are the known reservoir of Marburg virus (MARV), a filovirus that causes deadly Marburg virus disease (MVD) in humans. However, ERBs harbor MARV asymptomatically, likely due to a coadapted and specific host immunity-pathogen relationship. Recently, we measured transcriptional responses in MARV-infected ERB whole tissues, showing that these bats possess a disease tolerant strategy that limits pro-inflammatory gene induction, presumably averting MVD-linked immunopathology. However, the host resistant strategy by which ERBs actively limit MARV burden remains elusive, which we hypothesize requires localized inflammatory responses unresolvable at bulk-tissue scale. Here, we use dexamethasone to attenuate ERB pro-inflammatory responses and assess MARV replication, shedding and disease. We show that MARV-infected ERBs naturally mount coordinated pro-inflammatory responses at liver foci of infection, comprised of recruited mononuclear phagocytes and T cells, the latter of which proliferate with likely MARV-specificity. When pro-inflammatory responses are diminished, ERBs display heightened MARV replication, oral/rectal shedding and severe MVD-like liver pathology, demonstrating that ERBs balance immunoprotective tolerance with discreet MARV-resistant pro-inflammatory responses. These data further suggest that natural ERB immunomodulatory stressors like food scarcity and habitat disruption may potentiate viral shedding, transmission and therefore outbreak risk.
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Affiliation(s)
- Jonathan C Guito
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Shannon G M Kirejczyk
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- StageBio, Mount Jackson, VA, 22842, USA
| | - Amy J Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Brian R Amman
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Tara K Sealy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - James Graziano
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jessica R Harmon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - David M Wozniak
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany
- Virology Department, Bernhard-Nocht-Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Joseph B Prescott
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany.
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
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16
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Islam M, Behura SK. Single-Cell Transcriptional Response of the Placenta to the Ablation of Caveolin-1: Insights into the Adaptive Regulation of Brain-Placental Axis in Mice. Cells 2024; 13:215. [PMID: 38334607 PMCID: PMC10854826 DOI: 10.3390/cells13030215] [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: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Caveolin-1 (Cav1) is a major plasma membrane protein that plays important functions in cellular metabolism, proliferation, and senescence. Mice lacking Cav1 show abnormal gene expression in the fetal brain. Though evidence for placental influence on brain development is emerging, whether the ablation of Cav1 affects the regulation of the brain-placental axis remains unexamined. The current study tests the hypothesis that gene expression changes in specific cells of the placenta and the fetal brain are linked to the deregulation of the brain-placental axis in Cav1-null mice. By performing single-nuclei RNA sequencing (snRNA-seq) analyses, we show that the abundance of the extravillious trophoblast (EVT) and stromal cells, but not the cytotrophoblast (CTB) or syncytiotrophoblast (STB), are significantly impacted due to Cav1 ablation in mice. Interestingly, specific genes related to brain development and neurogenesis were significantly differentially expressed in trophoblast cells due to Cav1 deletion. Comparison of single-cell gene expression between the placenta and the fetal brain further showed that specific genes such as plexin A1 (Plxna1), phosphatase and actin regulator 1 (Phactr1) and amyloid precursor-like protein 2 (Aplp2) were differentially expressed between the EVT and STB cells of the placenta, and also, between the radial glia and ependymal cells of the fetal brain. Bulk RNA-seq analysis of the whole placenta and the fetal brain further identified genes differentially expressed in a similar manner between the placenta and the fetal brain due to the absence of Cav1. The deconvolution of reference cell types from the bulk RNA-seq data further showed that the loss of Cav1 impacted the abundance of EVT cells relative to the stromal cells in the placenta, and that of the glia cells relative to the neuronal cells in the fetal brain. Together, the results of this study suggest that the ablation of Cav1 causes deregulated gene expression in specific cell types of the placenta and the fetal brain in mice.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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17
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Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. BIOLOGY 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
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Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
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18
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Quan F, Liang X, Cheng M, Yang H, Liu K, He S, Sun S, Deng M, He Y, Liu W, Wang S, Zhao S, Deng L, Hou X, Zhang X, Xiao Y. Annotation of cell types (ACT): a convenient web server for cell type annotation. Genome Med 2023; 15:91. [PMID: 37924118 PMCID: PMC10623726 DOI: 10.1186/s13073-023-01249-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge. METHODS To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods. RESULTS By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT ( http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/ ), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified. CONCLUSIONS We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.
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Affiliation(s)
- Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Mingjiang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Huan Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Kun Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shengyuan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shangqin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Menglan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Yanzhen He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuai Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Shuxiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Lantian Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xiaobo Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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19
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Yaparla A, Stern DB, Hossainey MRH, Crandall KA, Grayfer L. Amphibian myelopoiesis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 146:104701. [PMID: 37196852 DOI: 10.1016/j.dci.2023.104701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Macrophage-lineage cells are indispensable to immunity and physiology of all vertebrates. Amongst these, amphibians represent a key stage in vertebrate evolution and are facing decimating population declines and extinctions, in large part due to emerging infectious agents. While recent studies indicate that macrophages and related innate immune cells are critically involved during these infections, much remains unknown regarding the ontogeny and functional differentiation of these cell types in amphibians. Accordingly, in this review we coalesce what has been established to date about amphibian blood cell development (hematopoiesis), the development of key amphibian innate immune cells (myelopoiesis) and the differentiation of amphibian macrophage subsets (monopoiesis). We explore the current understanding of designated sites of larval and adult hematopoiesis across distinct amphibian species and consider what mechanisms may lend to these species-specific adaptations. We discern the identified molecular mechanisms governing the functional differentiation of disparate amphibian (chiefly Xenopus laevis) macrophage subsets and describe what is known about the roles of these subsets during amphibian infections with intracellular pathogens. Macrophage lineage cells are at the heart of so many vertebrate physiological processes. Thus, garnering greater understanding of the mechanisms responsible for the ontogeny and functionality of these cells in amphibians will lend to a more comprehensive view of vertebrate evolution.
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Affiliation(s)
- Amulya Yaparla
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
| | - David B Stern
- Milken Institute School of Public Health, Computational Biology Institute, George Washington University, Washington, DC, 20052, USA
| | | | - Keith A Crandall
- Milken Institute School of Public Health, Computational Biology Institute, George Washington University, Washington, DC, 20052, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA.
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