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Chen Z, Wang C, Huang S, Shi Y, Xi R. Directly selecting cell-type marker genes for single-cell clustering analyses. CELL REPORTS METHODS 2024; 4:100810. [PMID: 38981475 PMCID: PMC11294843 DOI: 10.1016/j.crmeth.2024.100810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
In single-cell RNA sequencing (scRNA-seq) studies, cell types and their marker genes are often identified by clustering and differentially expressed gene (DEG) analysis. A common practice is to select genes using surrogate criteria such as variance and deviance, then cluster them using selected genes and detect markers by DEG analysis assuming known cell types. The surrogate criteria can miss important genes or select unimportant genes, while DEG analysis has the selection-bias problem. We present Festem, a statistical method for the direct selection of cell-type markers for downstream clustering. Festem distinguishes marker genes with heterogeneous distribution across cells that are cluster informative. Simulation and scRNA-seq applications demonstrate that Festem can sensitively select markers with high precision and enables the identification of cell types often missed by other methods. In a large intrahepatic cholangiocarcinoma dataset, we identify diverse CD8+ T cell types and potential prognostic marker genes.
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Affiliation(s)
- Zihao Chen
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Changhu Wang
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Siyuan Huang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yang Shi
- BeiGene (Beijing) Co., Ltd., Beijing 100871, China
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China.
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Lang Y, Huang H, Jiang H, Wu S, Chen Y, Xu B, Liu Y, Zhu D, Zheng X, Chen L, Jiang J. TIGIT Blockade Reshapes the Tumor Microenvironment Based on the Single-cell RNA-Sequencing Analysis. J Immunother 2024; 47:172-181. [PMID: 38545758 DOI: 10.1097/cji.0000000000000511] [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: 07/26/2023] [Accepted: 01/26/2024] [Indexed: 05/09/2024]
Abstract
SUMMARY Immune checkpoint blockade therapy is a pivotal approach in treating malignant tumors. TIGIT has emerged as a focal point of interest among the diverse targets for tumor immunotherapy. Nonetheless, there is still a lack of comprehensive understanding regarding the immune microenvironment alterations following TIGIT blockade treatment. To bridge this knowledge gap, we performed single-cell sequencing on mice both before and after the administration of anti-TIGIT therapy. Our analysis revealed that TIGIT was predominantly expressed on T cells and natural killer (NK) cells. The blockade of TIGIT exhibited inhibitory effects on Treg cells by downregulating the expression of Foxp3 and reducing the secretion of immunosuppressive cytokines. In addition, TIGIT blockade facilitated the activation of NK cells, leading to an increase in cell numbers, and promoted cDC1 maturation through the secretion of XCL1 and Flt3L. This activation, in turn, stimulated the TCR signaling of CD8 + T cells, thereby enhancing their antitumor effect. Consequently, anti-TIGIT therapy demonstrated substantial potential for cancer immunotherapy. Our research provided novel insights into future therapeutic strategies targeting TIGIT for patients with cancer.
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Affiliation(s)
- Yanyan Lang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Hao Huang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Hongwei Jiang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Shaoxian Wu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Yaping Chen
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Bin Xu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Yingting Liu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, People's Republic of China
| | - Dawei Zhu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Xiao Zheng
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Lujun Chen
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, People's Republic of China
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Wang Y, Chen X, Tang N, Guo M, Ai D. Boosting Clear Cell Renal Carcinoma-Specific Drug Discovery Using a Deep Learning Algorithm and Single-Cell Analysis. Int J Mol Sci 2024; 25:4134. [PMID: 38612943 PMCID: PMC11012314 DOI: 10.3390/ijms25074134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Clear cell renal carcinoma (ccRCC), the most common subtype of renal cell carcinoma, has the high heterogeneity of a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have failed to achieve good therapeutic effects. In this article, single-cell transcriptome sequencing (scRNA-seq) data from six patients downloaded from the GEO database were adopted to describe the tumor microenvironment (TME) of ccRCC, including its T cells, tumor-associated macrophages (TAMs), endothelial cells (ECs), and cancer-associated fibroblasts (CAFs). Based on the differential typing of the TME, we identified tumor cell-specific regulatory programs that are mediated by three key transcription factors (TFs), whilst the TF EPAS1/HIF-2α was identified via drug virtual screening through our analysis of ccRCC's protein structure. Then, a combined deep graph neural network and machine learning algorithm were used to select anti-ccRCC compounds from bioactive compound libraries, including the FDA-approved drug library, natural product library, and human endogenous metabolite compound library. Finally, five compounds were obtained, including two FDA-approved drugs (flufenamic acid and fludarabine), one endogenous metabolite, one immunology/inflammation-related compound, and one inhibitor of DNA methyltransferase (N4-methylcytidine, a cytosine nucleoside analogue that, like zebularine, has the mechanism of inhibiting DNA methyltransferase). Based on the tumor microenvironment characteristics of ccRCC, five ccRCC-specific compounds were identified, which would give direction of the clinical treatment for ccRCC patients.
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Affiliation(s)
| | | | | | | | - Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.C.); (N.T.); (M.G.)
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Vanhaezebrouck IF, Bakhle KM, Mendez-Valenzuela CR, Lyle LT, Konradt K, Scarpelli ML. Single institution study of the immune landscape for canine oral melanoma based on transcriptome analysis of the primary tumor. Front Vet Sci 2024; 10:1285909. [PMID: 38260202 PMCID: PMC10800815 DOI: 10.3389/fvets.2023.1285909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Understanding a tumor's immune context is paramount in the fight against cancer. Oral melanoma in dogs serves as an excellent translational model for human immunotherapy. However, additional study is necessary to comprehend the immune landscape of dog oral melanomas, including their similarity to human melanomas in this context. Methods This retrospective study utilizes formalin-fixed paraffin-embedded (FFPE) tissue samples to analyze RNA sequences associated with oral melanoma in dogs. Nanostring Technologies was used for conducting RNA sequencing. The focus is on understanding the differences between melanoma tumors restricted to the oral cavity (OL) and the same primary oral tumors with a history of metastasis to the lymph nodes or other organs (OM). Normal buccal mucosa samples are also included as a normal tissue reference. Results In the OM patient group, gene signatures exhibit significant changes relative to the OL patient group, including significantly decreased expression of S100, BRAF, CEACAM1, BCL2, ANXA1, and tumor suppressor genes (TP63). Relative to the OL tumors, the OM tumors had significantly increased expression of hypoxia-related genes (VEGFA expression), cell mobility genes (MCAM), and PTGS2 (COX2). The analysis of the immune landscape in the OM group indicates a shift from a possible "hot" tumor suppressed by immune checkpoints (PDL1) to significantly heightened expression not only of those checkpoints but also the inclusion of other immune blockades such as PD1 and IDO2. In addition, the OM group had significantly reduced expression of Toll-like receptors (TLR4) and IL-18 relative to the OL group, contributing to the tumor's immune escape. Additionally, signs of immune cell exhaustion are evident in both the OM and OL groups through significantly increased expression of TIGIT relative to normal tissue. Both the OM and OL groups had significantly increased expression of the immune cell marker CD4 expression relative to normal tissue. Further, CD4 expression significantly decreased in OM relative to OL; however, this study cannot determine the specific cell types expressing CD4 in OM and OL tumors. Discussion This preliminary study reports significant changes in gene expression for oral melanoma between canine patients with localized disease relative to those with metastatic disease. In the future, a more in-depth investigation involving immunohistochemistry analysis and single-cell RNA expression is necessary to confirm our findings.
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Affiliation(s)
- Isabelle F. Vanhaezebrouck
- Radiation Oncology, Small Animal Medicine, College of Veterinary Medicine Purdue University, West Lafayette, IN, United States
| | - Kimaya M. Bakhle
- College of Veterinary Medicine, Cornell University, New York, NY, United States
| | - Carlos R. Mendez-Valenzuela
- Radiation Oncology, Small Animal Medicine, College of Veterinary Medicine Purdue University, West Lafayette, IN, United States
| | - L. Tiffany Lyle
- Pathology Cook Research Inc., West Lafayette, IN, United States
| | - Kristoph Konradt
- Comparative Pathology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
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Wang J, Gao M, Cheng M, Luo J, Lu M, Xing X, Sun Y, Lu Y, Li X, Shi C, Wang J, Wang N, Yang W, Jiang Y, Huang H, Yang G, Zeng Y, Wang C, Cao X. Single-Cell Transcriptional Analysis of Lamina Propria Lymphocytes in the Jejunum Reveals Innate Lymphoid Cell-like Cells in Pigs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:130-142. [PMID: 37975680 DOI: 10.4049/jimmunol.2300463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Pigs are the most suitable model to study various therapeutic strategies and drugs for human beings, although knowledge about cell type-specific transcriptomes and heterogeneity is poorly available. Through single-cell RNA sequencing and flow cytometry analysis of the types in the jejunum of pigs, we found that innate lymphoid cells (ILCs) existed in the lamina propria lymphocytes (LPLs) of the jejunum. Then, through flow sorting of live/dead-lineage (Lin)-CD45+ cells and single-cell RNA sequencing, we found that ILCs in the porcine jejunum were mainly ILC3s, with a small number of NK cells, ILC1s, and ILC2s. ILCs coexpressed IL-7Rα, ID2, and other genes and differentially expressed RORC, GATA3, and other genes but did not express the CD3 gene. ILC3s can be divided into four subgroups, and genes such as CXCL8, CXCL2, IL-22, IL-17, and NCR2 are differentially expressed. To further detect and identify ILC3s, we verified the classification of ILCs in the porcine jejunum subgroup and the expression of related hallmark genes at the protein level by flow cytometry. For systematically characterizing ILCs in the porcine intestines, we combined our pig ILC dataset with publicly available human and mice ILC data and identified that the human and pig ILCs shared more common features than did those mouse ILCs in gene signatures and cell states. Our results showed in detail for the first time (to our knowledge) the gene expression of porcine jejunal ILCs, the subtype classification of ILCs, and the markers of various ILCs, which provide a basis for an in-depth exploration of porcine intestinal mucosal immunity.
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Affiliation(s)
- Junhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ming Gao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mingyang Cheng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jiawei Luo
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mei Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xinyuan Xing
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Sun
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yiyuan Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunwei Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nan Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wentao Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yanlong Jiang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Haibin Huang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guilian Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunfeng Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China; Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China; Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China; and Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
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Ng CYJ, Bun HH, Zhao Y, Zhong LLD. TCM "medicine and food homology" in the management of post-COVID disorders. Front Immunol 2023; 14:1234307. [PMID: 37720220 PMCID: PMC10500073 DOI: 10.3389/fimmu.2023.1234307] [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: 06/04/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Background The World Health Organization declared that COVID-19 is no longer a public health emergency of global concern on May 5, 2023. Post-COVID disorders are, however, becoming more common. Hence, there lies a growing need to develop safe and effective treatment measures to manage post-COVID disorders. Investigating the use of TCM medicinal foods in the long-term therapy of post-COVID illnesses may be beneficial given contemporary research's emphasis on the development of medicinal foods. Scope and approach The use of medicinal foods for the long-term treatment of post-COVID disorders is highlighted in this review. Following a discussion of the history of the TCM "Medicine and Food Homology" theory, the pathophysiological effects of post-COVID disorders will be briefly reviewed. An analysis of TCM medicinal foods and their functions in treating post-COVID disorders will then be provided before offering some insight into potential directions for future research and application. Key findings and discussion TCM medicinal foods can manage different aspects of post-COVID disorders. The use of medicinal foods in the long-term management of post-COVID illnesses may be a safe and efficient therapy choice because they are typically milder in nature than chronic drug use. These findings may also be applied in the long-term post-disease treatment of similar respiratory disorders.
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Affiliation(s)
- Chester Yan Jie Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hung Hung Bun
- The University of Hong Kong (HKU) School of Professional and Continuing Education, Hong Kong, Hong Kong SAR, China
| | - Yan Zhao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Linda L. D. Zhong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Hong Kong, Hong Kong SAR, China
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Pan T, Cao G, Tang E, Zhao Y, Penaloza-MacMaster P, Fang Y, Huang J. A single-cell atlas reveals shared and distinct immune responses and metabolic profiles in SARS-CoV-2 and HIV-1 infections. Front Genet 2023; 14:1105673. [PMID: 36992700 PMCID: PMC10040851 DOI: 10.3389/fgene.2023.1105673] [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: 11/22/2022] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
Introduction: Within the inflammatory immune response to viral infection, the distribution and cell type-specific profiles of immune cell populations and the immune-mediated viral clearance pathways vary according to the specific virus. Uncovering the immunological similarities and differences between viral infections is critical to understanding disease progression and developing effective vaccines and therapies. Insight into COVID-19 disease progression has been bolstered by the integration of single-cell (sc)RNA-seq data from COVID-19 patients with data from related viruses to compare immune responses. Expanding this concept, we propose that a high-resolution, systematic comparison between immune cells from SARS-CoV-2 infection and an inflammatory infectious disease with a different pathophysiology will provide a more comprehensive picture of the viral clearance pathways that underscore immunological and clinical differences between infections. Methods: Using a novel consensus single-cell annotation method, we integrate previously published scRNA-seq data from 111,566 single PBMCs from 7 COVID-19, 10 HIV-1+, and 3 healthy patients into a unified cellular atlas. We compare in detail the phenotypic features and regulatory pathways in the major immune cell clusters. Results: While immune cells in both COVID-19 and HIV-1+ cohorts show shared inflammation and disrupted mitochondrial function, COVID-19 patients exhibit stronger humoral immunity, broader IFN-I signaling, elevated Rho GTPase and mTOR pathway activity, and downregulated mitophagy. Discussion: Our results indicate that differential IFN-I signaling regulates the distinct immune responses in the two diseases, revealing insight into fundamental disease biology and potential therapeutic candidates.
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Affiliation(s)
- Tony Pan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Guoshuai Cao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Erting Tang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Yu Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | | | - Yun Fang
- Biological Sciences Division, University of Chicago, Chicago, IL, United States
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
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Cheng Y, Wang H, Shang J, Wang J, Yin J, Zhang J, Guo X, Wang S, Duan YG, Lee CL, Chiu PCN, Zhang J, Yeung WSB, Cao D, Yao Y. Transcriptomic analysis of mid-secretory endometrium reveals essential immune factors associated with pregnancy after single euploid blastocyst transfer. Am J Reprod Immunol 2023; 89:e13672. [PMID: 36542433 DOI: 10.1111/aji.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Implantation is a limiting factor for treatment success in assisted reproduction. Both embryonic and endometrial factors contribute to implantation. Embryonic factors have often been ignored in previous studies about the role of endometrium in implantation. In this study, we sought to identify the endometrial genes associated with negative pregnancy outcomes following the transfer of a single euploid blastocyst. METHODS Computational analyses of the transcriptomes of mid-secretory endometria from nine pregnant and seven non-pregnant patients in a cycle preceding the transfer of a single euploid blastocyst in a vitrified-warmed cycle were performed. RESULTS Principal component analysis of two reported endometrial receptivity gene sets showed close clustering of the pregnant and non-pregnant samples. Differential gene expression analysis and co-expression module analysis identified 131 genes associated with the pregnancy status. The endometrial signatures identified highlight the importance of immune and metabolic regulation in pregnancy outcome. Network analysis identified 20 hub genes that could predict pregnancy outcomes with 88.9% sensitivity and 85.7% specificity. Single-cell gene expression analysis highlighted the regulation of endometrial natural killer (NK) cells, T cells, and macrophages during embryo implantation. Immune cell abundance analysis supported the dysregulation of cytotoxic immune cells in the endometria of non-pregnant women. CONCLUSIONS We reported the first endometrial gene signature associated with pregnancy after elimination of embryo aneuploidy and highlighted the importance of the endometrial immune microenvironment and metabolic status in pregnancy outcomes.
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Affiliation(s)
- Yanfei Cheng
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wang
- Department of Obstetrics and Gynecology, the First Medical Center of PLA General Hospital, Beijing, China
| | - Jin Shang
- Medical School of Chinese PLA, Beijing, China
| | - Jue Wang
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Jingwen Yin
- Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, China
| | | | - Xinmeng Guo
- College of Medicine, Nankai University, Tianjin, China
| | - Sidong Wang
- Medical School of Chinese PLA, Beijing, China
| | - Yong-Gang Duan
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Cheuk-Lun Lee
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong S.A.R., China
| | - Philip C N Chiu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong S.A.R., China
| | - Jian Zhang
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Laboratory of Metabolic Health, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - William S B Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong S.A.R., China
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yuanqing Yao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynecology, the First Medical Center of PLA General Hospital, Beijing, China
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9
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Vu R, Jin S, Sun P, Haensel D, Nguyen QH, Dragan M, Kessenbrock K, Nie Q, Dai X. Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication. Cell Rep 2022; 40:111155. [PMID: 35926463 PMCID: PMC9901190 DOI: 10.1016/j.celrep.2022.111155] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/13/2022] [Accepted: 07/12/2022] [Indexed: 02/08/2023] Open
Abstract
Delayed and often impaired wound healing in the elderly presents major medical and socioeconomic challenges. A comprehensive understanding of the cellular/molecular changes that shape complex cell-cell communications in aged skin wounds is lacking. Here, we use single-cell RNA sequencing to define the epithelial, fibroblast, immune cell types, and encompassing heterogeneities in young and aged skin during homeostasis and identify major changes in cell compositions, kinetics, and molecular profiles during wound healing. Our comparative study uncovers a more pronounced inflammatory phenotype in aged skin wounds, featuring neutrophil persistence and higher abundance of an inflammatory/glycolytic Arg1Hi macrophage subset that is more likely to signal to fibroblasts via interleukin (IL)-1 than in young counterparts. We predict systems-level differences in the number, strength, route, and signaling mediators of putative cell-cell communications in young and aged skin wounds. Our study exposes numerous cellular/molecular targets for functional interrogation and provides a hypothesis-generating resource for future wound healing studies.
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Affiliation(s)
- Remy Vu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA,The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA,These authors contributed equally
| | - Suoqin Jin
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China,Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA,These authors contributed equally
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA,The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA,These authors contributed equally
| | - Daniel Haensel
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA,The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA,Present address: Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Quy Hoa Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Morgan Dragan
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA,The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA,Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA,Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA,Correspondence: (Q.N.), (X.D.)
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA,The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92627, USA,Lead contact,Correspondence: (Q.N.), (X.D.)
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10
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Stevens J, Steinmeyer S, Bonfield M, Peterson L, Wang T, Gray J, Lewkowich I, Xu Y, Du Y, Guo M, Wynn JL, Zacharias W, Salomonis N, Miller L, Chougnet C, O’Connor DH, Deshmukh H. The balance between protective and pathogenic immune responses to pneumonia in the neonatal lung is enforced by gut microbiota. Sci Transl Med 2022; 14:eabl3981. [PMID: 35704600 PMCID: PMC10032669 DOI: 10.1126/scitranslmed.abl3981] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although modern clinical practices such as cesarean sections and perinatal antibiotics have improved infant survival, treatment with broad-spectrum antibiotics alters intestinal microbiota and causes dysbiosis. Infants exposed to perinatal antibiotics have an increased likelihood of life-threatening infections, including pneumonia. Here, we investigated how the gut microbiota sculpt pulmonary immune responses, promoting recovery and resolution of infection in newborn rhesus macaques. Early-life antibiotic exposure interrupted the maturation of intestinal commensal bacteria and disrupted the developmental trajectory of the pulmonary immune system, as assessed by single-cell proteomic and transcriptomic analyses. Early-life antibiotic exposure rendered newborn macaques more susceptible to bacterial pneumonia, concurrent with increases in neutrophil senescence and hyperinflammation, broad inflammatory cytokine signaling, and macrophage dysfunction. This pathogenic reprogramming of pulmonary immunity was further reflected by a hyperinflammatory signature in all pulmonary immune cell subsets coupled with a global loss of tissue-protective, homeostatic pathways in the lungs of dysbiotic newborns. Fecal microbiota transfer was associated with partial correction of the broad immune maladaptations and protection against severe pneumonia. These data demonstrate the importance of intestinal microbiota in programming pulmonary immunity and support the idea that gut microbiota promote the balance between pathways driving tissue repair and inflammatory responses associated with clinical recovery from infection in infants. Our results highlight a potential role for microbial transfer for immune support in these at-risk infants.
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Affiliation(s)
- Joseph Stevens
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shelby Steinmeyer
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Madeline Bonfield
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Laura Peterson
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Timothy Wang
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Jerilyn Gray
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ian Lewkowich
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yan Xu
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Bioinformatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yina Du
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Minzhe Guo
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - James L. Wynn
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - William Zacharias
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Bioinformatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lisa Miller
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
- California National Primate Research Center, Davis, CA 95616, USA
| | - Claire Chougnet
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Dennis Hartigan O’Connor
- California National Primate Research Center, Davis, CA 95616, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Hitesh Deshmukh
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Corresponding author.
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11
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Traxinger B, Vick SC, Woodward-Davis A, Voillet V, Erickson JR, Czartoski J, Teague C, Prlic M, Lund JM. Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues. Mucosal Immunol 2022; 15:1012-1027. [PMID: 35821289 PMCID: PMC9391309 DOI: 10.1038/s41385-022-00542-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023]
Abstract
Regulatory T cells (Tregs) mediate immune homeostasis, yet also facilitate nuanced immune responses during infection, balancing pathogen control while limiting host inflammation. Recent studies have identified Treg populations in non-lymphoid tissues that are phenotypically distinct from Tregs in lymphoid tissues (LT), including performance of location-dependent roles. Mucosal tissues serve as critical barriers to microbes while performing unique physiologic functions, so we sought to identify distinct phenotypical and functional aspects of mucosal Tregs in the female reproductive tract. In healthy human and mouse vaginal mucosa, we found that Tregs are highly activated compared to blood or LT Tregs. To determine if this phenotype reflects acute activation or a general signature of vaginal tract (VT)-residency, we infected mice with HSV-2 to discover that VT Tregs express granzyme-B (GzmB) and acquire a VT Treg signature distinct from baseline. To determine the mechanisms that drive GzmB expression, we performed ex vivo assays to reveal that a combination of type-I interferons and interleukin-2 is sufficient for GzmB expression. Together, we highlight that VT Tregs are activated at steady state and become further activated in response to infection; thus, they may exert robust control of local immune responses, which could have implications for mucosal vaccine design.
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Affiliation(s)
- Brianna Traxinger
- Department of Global Health, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | - Sarah C Vick
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | | | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | - Jami R Erickson
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | - Candice Teague
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | - Martin Prlic
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Jennifer M Lund
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA.
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12
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Characterizing cell interactions at scale with made-to-order droplet ensembles (MODEs). Proc Natl Acad Sci U S A 2022; 119:2110867119. [PMID: 35074872 PMCID: PMC8812558 DOI: 10.1073/pnas.2110867119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/22/2023] Open
Abstract
The study of specific cell–cell interactions at scale would be a significant advancement in single-cell biology with clear utility in immuno-oncology. Our development of Droplet Assembly provides a tool for such studies by extending the benefits of single-cell droplet microfluidics to high-order cell analyses. This technology allows for the construction, sorting, and downstream processing of cell–cell interactions and is compatible with single-cell genomic readouts. Cell–cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multicell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically relevant scales. Here, we describe a paradigm in cell interaction profiling that allows accurate grouping of cells and characterization of their interactions for tens to hundreds of thousands of combinations. Our approach leverages high-throughput droplet microfluidics to construct multicellular combinations in a deterministic process that allows inclusion of programmed reagent mixtures and beads. The combination droplets are compatible with common manipulation and measurement techniques, including imaging, barcode-based genomics, and sorting. We demonstrate the approach by using it to enrich for chimeric antigen receptor (CAR)-T cells that activate upon incubation with target cells, a bottleneck in the therapeutic T cell engineering pipeline. The speed and control of our approach should enable valuable cell interaction studies.
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13
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Single-Cell RNA-Seq Reveals a Crosstalk between Hyaluronan Receptor LYVE-1-Expressing Macrophages and Vascular Smooth Muscle Cells. Cells 2022; 11:cells11030411. [PMID: 35159221 PMCID: PMC8834524 DOI: 10.3390/cells11030411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Background: Atherosclerosis is a chronic inflammatory disease where macrophages participate in the progression of the disease. However, the role of resident-like macrophages (res-like) in the atherosclerotic aorta is not completely understood. Methods: A single-cell RNA sequencing analysis of CD45+ leukocytes in the atherosclerotic aorta of apolipoprotein E–deficient (Apoe−/−) mice on a normal cholesterol diet (NCD) or a high cholesterol diet (HCD), respecting the side-to-specific predisposition to atherosclerosis, was performed. A population of res-like macrophages expressing hyaluronan receptor LYVE-1 was investigated via flow cytometry, co-culture experiments, and immunofluorescence in human atherosclerotic plaques from carotid artery disease patients (CAD). Results: We identified 12 principal leukocyte clusters with distinct atherosclerosis disease-relevant gene expression signatures. LYVE-1+ res-like macrophages, expressing a high level of CC motif chemokine ligand 24 (CCL24, eotaxin-2), expanded under hypercholesteremia in Apoe−/− mice and promoted VSMC phenotypic modulation to osteoblast/chondrocyte-like cells, ex vivo, in a CCL24-dependent manner. Moreover, the abundance of LYVE-1+CCL24+ macrophages and elevated systemic levels of CCL24 were associated with vascular calcification and CAD events. Conclusions: LYVE-1 res-like macrophages, via the secretion of CCL24, promote the transdifferentiation of VSMC to osteogenic-like cells with a possible role in vascular calcification and likely a detrimental role in atherosclerotic plaque destabilization.
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14
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Pan T, Cao G, Tang E, Zhao Y, Penaloza-MacMaster P, Fang Y, Huang J. A single-cell atlas reveals shared and distinct immune responses and metabolism during SARS-CoV-2 and HIV-1 infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.10.475725. [PMID: 35043114 PMCID: PMC8764725 DOI: 10.1101/2022.01.10.475725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
UNLABELLED SARS-CoV-2 and HIV-1 are RNA viruses that have killed millions of people worldwide. Understanding the similarities and differences between these two infections is critical for understanding disease progression and for developing effective vaccines and therapies, particularly for 38 million HIV-1 + individuals who are vulnerable to SARS-CoV-2 co-infection. Here, we utilized single-cell transcriptomics to perform a systematic comparison of 94,442 PBMCs from 7 COVID-19 and 9 HIV-1 + patients in an integrated immune atlas, in which 27 different cell types were identified using an accurate consensus single-cell annotation method. While immune cells in both cohorts show shared inflammation and disrupted mitochondrial function, COVID-19 patients exhibit stronger humoral immunity, broader IFN-I signaling, elevated Rho GTPase and mTOR pathway activities, and downregulated mitophagy. Our results elucidate transcriptional signatures associated with COVID-19 and HIV-1 that may reveal insights into fundamental disease biology and potential therapeutic targets to treat these viral infections. HIGHLIGHTS COVID-19 and HIV-1 + patients show disease-specific inflammatory immune signatures COVID-19 patients show more productive humoral responses than HIV-1 + patients SARS-CoV-2 elicits more enriched IFN-I signaling relative to HIV-IDivergent, impaired metabolic programs distinguish SARS-CoV-2 and HIV-1 infections.
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15
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Chu TH, Khairallah C, Shieh J, Cho R, Qiu Z, Zhang Y, Eskiocak O, Thanassi DG, Kaplan MH, Beyaz S, Yang VW, Bliska JB, Sheridan BS. γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathog 2021; 17:e1010103. [PMID: 34871329 PMCID: PMC8648121 DOI: 10.1371/journal.ppat.1010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
Yersinia pseudotuberculosis is a foodborne pathogen that subverts immune function by translocation of Yersinia outer protein (Yop) effectors into host cells. As adaptive γδ T cells protect the intestinal mucosa from pathogen invasion, we assessed whether Y. pseudotuberculosis subverts these cells in mice and humans. Tracking Yop translocation revealed that the preferential delivery of Yop effectors directly into murine Vγ4 and human Vδ2+ T cells inhibited anti-microbial IFNγ production. Subversion was mediated by the adhesin YadA, injectisome component YopB, and translocated YopJ effector. A broad anti-pathogen gene signature and STAT4 phosphorylation levels were inhibited by translocated YopJ. Thus, Y. pseudotuberculosis attachment and translocation of YopJ directly into adaptive γδ T cells is a major mechanism of immune subversion in mice and humans. This study uncovered a conserved Y. pseudotuberculosis pathway that subverts adaptive γδ T cell function to promote pathogenicity. Unconventional γδ T cells are a dynamic immune population important for mucosal protection of the intestine against invading pathogens. We determined that the foodborne pathogen Y. pseudotuberculosis preferentially targets an adaptive subset of these cells to subvert immune function. We found that direct injection of Yersinia outer proteins (Yop) into adaptive γδ T cells inhibited their anti-pathogen functions. We screened all Yop effectors and identified YopJ as the sole effector to inhibit adaptive γδ T cell production of IFNγ. We determined that adaptive γδ T cell subversion occurred by limiting activation of the transcription factor STAT4. When we infected mice with Y. pseudotuberculosis expressing an inactive YopJ, this enhanced the adaptive γδ T cell response and led to greater cytokine production from this subset of cells to aid mouse recovery. This mechanism of immune evasion appears conserved in humans as direct injection of Y. pseudotuberculosis YopJ into human γδ T cells inhibited cytokine production. This suggested to us that Y. pseudotuberculosis actively inhibits the adaptive γδ T cell response through YopJ as a mechanism to evade immune surveillance at the site of pathogen invasion.
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Affiliation(s)
- Timothy H. Chu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Camille Khairallah
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Jason Shieh
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Rhea Cho
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Zhijuan Qiu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Yue Zhang
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - David G. Thanassi
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Vincent W. Yang
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - James B. Bliska
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Dartmouth, New Hampshire, United States of America
| | - Brian S. Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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16
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Identification of Biomarkers Related to Immune Cell Infiltration with Gene Coexpression Network in Myocardial Infarction. DISEASE MARKERS 2021; 2021:2227067. [PMID: 34777632 PMCID: PMC8589498 DOI: 10.1155/2021/2227067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Background There is evidence that the immune system plays a key critical role in the pathogenesis of myocardial infarction (MI). However, the exact mechanisms associated with immunity have not been systematically uncovered. Methods This study used the weighted gene coexpression network analysis (WGCNA) and the CIBERSORT algorithm to analyze the MI expression data from the Gene Expression Omnibus database and then identify the module associated with immune cell infiltration. In addition, we built the coexpression network and protein-protein interactions network analysis to identify the hub genes. Furthermore, the relationship between hub genes and NK cell resting was validated by using another dataset GSE123342. Finally, receiver operating characteristic (ROC) curve analyses were used to assess the diagnostic value of verified hub genes. Results Monocytes and neutrophils were markedly increased, and T cell CD8, T cell CD4 naive, T cell CD4 memory resting, and NK cell resting were significantly decreased in MI groups compared with stable coronary artery disease (CAD) groups. The WGCNA results showed that the pink model had the highest correlation with the NK cell resting infiltration level. We identified 11 hub genes whose expression correlated to the NK cell resting infiltration level, among which, 7 hub genes (NKG7, TBX21, PRF1, CD247, KLRD1, FASLG, and EOMES) were successfully validated in GSE123342. And these 7 genes had diagnostic value to distinguish MI and stable CAD. Conclusions NKG7, TBX21, PRF1, CD247, KLRD1, FASLG, and EOMES may be a diagnostic biomarker and therapeutic target associated with NK cell resting infiltration in MI.
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17
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Yan K, Lu Y, Yan Z, Wang Y. 9-Gene Signature Correlated With CD8 + T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma. Front Immunol 2021; 12:622563. [PMID: 34220795 PMCID: PMC8248551 DOI: 10.3389/fimmu.2021.622563] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose To identify CD8+ T cell-related factors and the co-expression network in melanoma and illustrate the interactions among CD8+ T cell-related genes in the melanoma tumor microenvironment. Method We obtained melanoma and paracancerous tissue mRNA matrices from TCGA-SKCM and GSE65904. The CIBERSORT algorithm was used to assess CD8+ T cell proportions, and the “estimate” package was used to assess melanoma tumor microenvironment purity. Weighted gene co-expression network analysis was used to identify the most related co-expression modules in TCGA-SKCM and GSE65904. Subsequently, a co-expression network was built based on the joint results in the two cohorts. Subsequently, we identified the core genes of the two most relevant modules of CD8+T lymphocytes according to the module correlation, and constructed the signature using ssGSEA. Later, we compared the signature with the existing classical pathways and gene sets, and confirmed the important prognostic significance of the signature in this paper. Results Nine co-expressed genes were identified as CD8+ T cell-related genes enriched in the cellular response to interferon−gamma process and antigen processing and presentation of peptide antigen. In the low expression level group, inflammation and immune responses were weaker. Single-cell sequencing and immunohistochemistry indicated that these nine genes were highly expressed in CD8+ T cells group. Conclusion We identified nine-gene signature, and the signature is considered as the biomarker for T lymphocyte response and clinical response to immune checkpoint inhibitors for melanoma
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Affiliation(s)
- Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Yuxiu Lu
- Department of Pharmacy, Fuzhou No. 1 Hospital Affiliated With Fujian Medical University, Fuzhou, China
| | - Zhangyong Yan
- Department of Stomatology, Fuzhou No. 1 Hospital Affiliated with Fujian Medical University, Fuzhou, China
| | - Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
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18
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Motamedi M, Xiao MZX, Iyer A, Gniadecki R. Patterns of Gene Expression in Cutaneous T-Cell Lymphoma: Systematic Review of Transcriptomic Studies in Mycosis Fungoides. Cells 2021; 10:cells10061409. [PMID: 34204115 PMCID: PMC8229125 DOI: 10.3390/cells10061409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Mycosis fungoides (MF) is the most prevalent type of skin lymphoma. In its early stages, it has a favorable prognosis. However, in its late stages, it is associated with an increased risk of mortality. This systematic review aimed to identify the transcriptomic changes involved in MF pathogenesis and progression. A literature search was conducted using the database PubMed, followed by the extraction of 2245 genes which were further filtered to 150 recurrent genes that appeared in two or more publications. Categorization of these genes identified activated pathways involved in pathways such as cell cycle and proliferation, chromosomal instability, and DNA repair. We identified 15 genes implicated in MF progression, which were involved in cell proliferation, immune checkpoints, resistance to apoptosis, and immune response. In highlighting the discrepancies in the way MF transcriptomic data is obtained, further research can focus on not only unifying their approach but also focus on the 150 pertinent genes identified in this review.
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Affiliation(s)
- Melika Motamedi
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada; (M.M.); (M.Z.X.X.); (A.I.)
| | - Maggie Z. X. Xiao
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada; (M.M.); (M.Z.X.X.); (A.I.)
| | - Aishwarya Iyer
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada; (M.M.); (M.Z.X.X.); (A.I.)
| | - Robert Gniadecki
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada; (M.M.); (M.Z.X.X.); (A.I.)
- 8-112 Clinical Sciences Building, University of Alberta, Edmonton, AB T6G 2G3, Canada
- Correspondence: ; Tel.: +1-(780)-407-1555
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