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Gu W, Eke C, Gonzalez Santiago E, Olaloye O, Konnikova L. Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells. Mucosal Immunol 2024; 17:599-617. [PMID: 38555026 DOI: 10.1016/j.mucimm.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Proper development of mucosal immunity is critical for human health. Over the past decade, it has become evident that in humans, this process begins in utero. However, there are limited data on the unique features and functions of fetal mucosal immune cells. To address this gap, we integrated several single-cell ribonucleic acid sequencing datasets of the human small intestine (SI) to create an SI transcriptional atlas throughout the human life span, ranging from the first trimester to adulthood, with a focus on immune cells. Fetal SI displayed a complex immune landscape comprising innate and adaptive immune cells that exhibited distinct transcriptional programs from postnatal samples, especially compared with pediatric and adult samples. We identified shifts in myeloid populations across gestation and progression of memory T-cell states throughout the human lifespan. In particular, there was a marked shift of memory T cells from those with stem-like properties in the fetal samples to fully differentiated cells with a high expression of activation and effector function genes in adult samples, with neonatal samples containing both features. Finally, we demonstrate that the SI developmental atlas can be used to elucidate improper trajectories linked to mucosal diseases by implicating developmental abnormalities underlying necrotizing enterocolitis, a severe intestinal complication of prematurity. Collectively, our data provide valuable resources and important insights into intestinal immunity that will facilitate regenerative medicine and disease understanding.
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Affiliation(s)
- Weihong Gu
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Chino Eke
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale University School of Medicine, New Haven, CT, USA; Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT, USA; Program in Human Translational Immunology, Yale University School of Medicine, New Haven, CT, USA.
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Li C, Xiao M, Geng S, Wang Y, Zeng L, Lai P, Gong Y, Chen X. Comprehensive analysis of human monocyte subsets using full-spectrum flow cytometry and hierarchical marker clustering. Front Immunol 2024; 15:1405249. [PMID: 38742110 PMCID: PMC11089106 DOI: 10.3389/fimmu.2024.1405249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction Exploring monocytes' roles within the tumor microenvironment is crucial for crafting targeted cancer treatments. Methods This study unveils a novel methodology utilizing four 20-color flow cytometry panels for comprehensive peripheral immune system phenotyping, specifically targeting classical, intermediate, and non-classical monocyte subsets. Results By applying advanced dimensionality reduction techniques like t-distributed stochastic neighbor embedding (tSNE) and FlowSom analysis, we performed an extensive profiling of monocytes, assessing 50 unique cell surface markers related to a wide range of immunological functions, including activation, differentiation, and immune checkpoint regulation. Discussion This in-depth approach significantly refines the identification of monocyte subsets, directly supporting the development of personalized immunotherapies and enhancing diagnostic precision. Our pioneering panel for monocyte phenotyping marks a substantial leap in understanding monocyte biology, with profound implications for the accuracy of disease diagnostics and the success of checkpoint-inhibitor therapies. Key findings include revealing distinct marker expression patterns linked to tumor progression and providing new avenues for targeted therapeutic interventions.
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Affiliation(s)
- Chao Li
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Maozhi Xiao
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Suxia Geng
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yulian Wang
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Lingji Zeng
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Peilong Lai
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ying Gong
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaomei Chen
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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López-Navarro B, Simón-Fuentes M, Ríos I, Schiaffino MT, Sanchez A, Torres-Torresano M, Nieto-Valle A, Castrejón I, Puig-Kröger A. Macrophage re-programming by JAK inhibitors relies on MAFB. Cell Mol Life Sci 2024; 81:152. [PMID: 38528207 PMCID: PMC10963568 DOI: 10.1007/s00018-024-05196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/27/2024]
Abstract
Monocyte-derived macrophages play a key pathogenic role in inflammatory diseases. In the case of rheumatoid arthritis (RA), the presence of specific synovial tissue-infiltrating macrophage subsets is associated with either active disease or inflammation resolution. JAK inhibitors (JAKi) are the first targeted synthetic disease-modifying antirheumatic drugs (tsDMARD) approved for treatment of RA with comparable efficacy to biologics. However, the effects of JAKi on macrophage specification and differentiation are currently unknown. We have analyzed the transcriptional and functional effects of JAKi on human peripheral blood monocyte subsets from RA patients and on the differentiation of monocyte-derived macrophages promoted by granulocyte-macrophage colony-stimulating factor (GM-CSF), a factor that drives the development and pathogenesis of RA. We now report that JAKi Upadacitinib restores the balance of peripheral blood monocyte subsets in RA patients and skewed macrophages towards the acquisition of an anti-inflammatory transcriptional and functional profile in a dose-dependent manner. Upadacitinib-treated macrophages showed a strong positive enrichment of the genes that define synovial macrophages associated to homeostasis/inflammation resolution. Specifically, Upadacitinib-treated macrophages exhibited significantly elevated expression of MAFB and MAFB-regulated genes, elevated inhibitory phosphorylation of GSK3β, and higher phagocytic activity and showed an anti-inflammatory cytokine profile upon activation by pathogenic stimuli. These outcomes were also shared by macrophages exposed to other JAKi (baricitinib, tofacitinib), but not in the presence of the TYK2 inhibitor deucravacitinib. As a whole, our results indicate that JAKi promote macrophage re-programming towards the acquisition of a more anti-inflammatory/pro-resolution profile, an effect that correlates with the ability of JAKi to enhance MAFB expression.
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Affiliation(s)
- Baltasar López-Navarro
- Unidad de Inmunometabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Israel Ríos
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, Madrid, Spain
| | - María Teresa Schiaffino
- Unidad de Inmunometabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alicia Sanchez
- Unidad de Inmunometabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Mónica Torres-Torresano
- Unidad de Inmunometabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alicia Nieto-Valle
- Unidad de Microscopía Confocal, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Isabel Castrejón
- Servicio de Reumatología, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Departamento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Amaya Puig-Kröger
- Unidad de Inmunometabolismo e Inflamación, Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
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Koren O, Konnikova L, Brodin P, Mysorekar IU, Collado MC. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat Rev Gastroenterol Hepatol 2024; 21:35-45. [PMID: 38097774 DOI: 10.1038/s41575-023-00864-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiome has important roles in host metabolism and immunity, and microbial dysbiosis affects human physiology and health. Maternal immunity and microbial metabolites during pregnancy, microbial transfer during birth, and transfer of immune factors, microorganisms and metabolites via breastfeeding provide critical sources of early-life microbial and immune training, with important consequences for human health. Only a few studies have directly examined the interactions between the gut microbiome and the immune system during pregnancy, and the subsequent effect on offspring development. In this Review, we aim to describe how the maternal microbiome shapes overall pregnancy-associated maternal, fetal and early neonatal immune systems, focusing on the existing evidence and highlighting current gaps to promote further research.
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Affiliation(s)
- Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Liza Konnikova
- Department of Paediatrics and Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Petter Brodin
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Indira U Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.
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Qiao S, Zhang SC, Li HY, Wang ZH, Jin Y, Wang AH, Liu XW. Cytokines/chemokines and immune checkpoint molecules in anti-leucine-rich glioma-inactivated 1 encephalitis. Neurol Sci 2023; 44:1017-1029. [PMID: 36445543 DOI: 10.1007/s10072-022-06526-6] [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: 08/21/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
OBJECTIVE We aimed to investigate levels of cytokines/chemokines and immune checkpoint molecules in patients with anti-leucine-rich glioma-inactivated 1 (LGI1) encephalitis. METHODS The study recruited 12 patients with anti-LGI1 encephalitis and six non-inflammatory controls from the Qilu Hospital of Shandong University treated between January 2019 and December 2020. Serum levels of 30 cytokines/chemokines and 10 checkpoint molecules were measured in participants of both the groups. RESULTS In contrast to those in the control group, 24 cytokines/chemokines and 5 immune checkpoint molecules were differentially expressed in patients with anti-LGI1 encephalitis, with 14 cytokines being upregulated and 10 being downregulated. There were 1033 enriched biological processes and 61 enriched Kyoto Encyclopedia of Genes and Genomes signaling pathways. CONCLUSION A wide range of cytokines/chemokines and immune checkpoint molecules are implicated in immune regulation in anti-LGI1 encephalitis, indicating that they may serve as important targets in the development and treatment of the disease.
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Affiliation(s)
- Shan Qiao
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China.,Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shan-Chao Zhang
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Hai-Yun Li
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhi-Hao Wang
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
| | - Yang Jin
- Institute of Epilepsy, Shandong University, Jinan, China
| | - Ai-Hua Wang
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Xue-Wu Liu
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China. .,Institute of Epilepsy, Shandong University, Jinan, China.
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Qin H, Wang C, He Y, Lu A, Li T, Zhang B, Shen J. Silencing miR-146a-5p Protects against Injury-Induced Osteoarthritis in Mice. Biomolecules 2023; 13:123. [PMID: 36671508 PMCID: PMC9856058 DOI: 10.3390/biom13010123] [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: 12/18/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Osteoarthritis (OA), the most prevalent joint disease and the leading cause of disability, remains an incurable disease largely because the etiology and pathogenesis underlying this degenerative process are poorly understood. Low-grade inflammation within joints is a well-established factor that disturbs joint homeostasis and leads to an imbalance between anabolic and catabolic processes in articular cartilage; however, the complexity of the network between inflammatory factors that often involves positive and negative feedback loops makes current anti-cytokine therapy ineffective. MicroRNAs (miRNAs) have emerged as key regulators to control inflammation, and aberrant miRNAs expression has recently been linked to OA pathophysiology. In the present study, we characterized transcriptomic profiles of miRNAs in primary murine articular chondrocytes in response to a proinflammatory cytokine, IL-1β, and identified miR-146a-5p as the most responsive miRNA to IL-1β. miR-146a-5p was also found to be upregulated in human OA cartilage. We further demonstrated that knockdown of miR-146a-5p antagonized IL-1β-mediated inflammatory responses and IL-1β-induced catabolism in vitro, and silencing of miR-146a in chondrocytes ameliorated articular cartilage destruction and reduced OA-evoked pain in an injury-induced murine OA model. Moreover, parallel RNA sequencing revealed that differentially expressed genes in response to IL-1β were enriched in pathways related to inflammatory processes, cartilage matrix homeostasis, and cell metabolism. Bioinformatic analyses of putative miR-146a-5p gene targets and following prediction of protein-protein interactions suggest a functional role of miR-146a-5p in mediating inflammatory processes and regulation of cartilage homeostasis. Our genetic and transcriptomic data define a crucial role of miR-146a-5p in OA pathogenesis and implicate modulation of miR-146a-5p in articular chondrocytes as a potential therapeutic strategy to alleviate OA.
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Affiliation(s)
- Haocheng Qin
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO 63110, USA
- The 2nd Xiangya Hospital, Central South University, Changsha 410021, China
| | - Cuicui Wang
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Yonghua He
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Aiwu Lu
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tiandao Li
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University, St. Louis, MO 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University, St. Louis, MO 63110, USA
| | - Jie Shen
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO 63110, USA
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Cramer M, Pineda Molina C, Hussey G, Turnquist HR, Badylak SF. Transcriptomic Regulation of Macrophages by Matrix-Bound Nanovesicle-Associated Interleukin-33. Tissue Eng Part A 2022; 28:867-878. [PMID: 35770892 PMCID: PMC9634988 DOI: 10.1089/ten.tea.2022.0006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022] Open
Abstract
The innate immune response, particularly the phenotype of responding macrophages, has significant clinical implications in the remodeling outcome following implantation of biomaterials and engineered tissues. In general, facilitation of an anti-inflammatory (M2-like) phenotype is associated with tissue repair and favorable outcomes, whereas pro-inflammatory (M1-like) activation can contribute to chronic inflammation and a classic foreign body response. Biologic scaffolds composed of extracellular matrix (ECM) and, more recently, matrix-bound nanovesicles (MBV) embedded within the ECM are known to direct macrophages toward an anti-inflammatory phenotype and stimulate a constructive remodeling outcome. The mechanisms of MBV-mediated macrophage activation are not fully understood, but interleukin-33 (IL-33) within the MBV appears critical for M2-like activation. Previous work has shown that IL-33 is encapsulated within the lumen of MBV and stimulates phenotypical changes in macrophages independent of its canonical surface receptor stimulation-2 (ST2). In the present study, we used next-generation RNA sequencing to determine the gene signature of macrophages following exposure to MBV with and without intraluminal IL-33. MBV-associated IL-33 instructed an anti-inflammatory phenotype in both wild-type and st2-/- macrophages by upregulating M2-like and downregulating M1-like genes. The repertoire of genes regulated by ST2-independent IL-33 signaling were broadly related to the inflammatory response and crosstalk between cells of both the innate and adaptive immune systems. These results signify the importance of the MBV intraluminal protein IL-33 in stimulating a pro-remodeling M2-like phenotype in macrophages and provides guidance for the designing of next-generation biomaterials and tissue engineering strategies. Impact statement The phenotype of responding macrophages is predictive of the downstream remodeling response to an implanted biomaterial. The clinical impact of macrophage phenotype has motivated studies to investigate the factors that regulate macrophage activation. Matrix-bound nanovesicles (MBV) embedded within the extracellular matrix direct macrophages toward an anti-inflammatory (M2)-like phenotype that is indicative of a favorable remodeling response. Although the mechanisms of MBV-mediated macrophage activation are not fully understood, the intraluminal protein interleukin-33 (IL-33) is clearly a contributing signaling molecule. The present study identifies those genes regulated by MBV-associated IL-33 that promote a pro-remodeling M2-like macrophage activation state and can guide future therapies in regenerative medicine.
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Affiliation(s)
- Madeline Cramer
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Catalina Pineda Molina
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - George Hussey
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Surgery and School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Heth R. Turnquist
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Surgery and School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen F. Badylak
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Surgery and School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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