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Pan J, Zhou T, Na K, Xu K, Yan C, Song H, Han Y. Identification of hub modules and therapeutic targets associated with CD8 +T-cells in HF and their pan-cancer analysis. Sci Rep 2024; 14:18823. [PMID: 39138291 PMCID: PMC11322555 DOI: 10.1038/s41598-024-68504-6] [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: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024] Open
Abstract
Heart failure (HF) is a terminal condition of multiple cardiovascular disorders. Cancer is a deadly disease worldwide. The relationship between HF and cancer remains poorly understood. The Gene Expression Omnibus database was used to download the RNA sequencing data of 356 patients with hypertrophic cardiomyopathy-induced HF and non-HF. A co-expression network was established through the weighted correlation network analysis (WGCNA) to identify hub genes of HF and cancer. Cox risk analysis was performed to predict the prognostic risks of HF hub genes in pan-cancer. HF was linked to immune response pathway by the analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A positive correlation was observed between the expression levels of 4 hub genes and the infiltration of CD8+T-cells in pan-cancer. 4 hub genes were identified as beneficial prognostic factors in several cancers. Western blotting and real-time polymerase chain reaction validated the high expression of GZMM, NKG7, and ZAP70 in both mice and patients with HF compared to control groups. Our study highlights the shared immune pathogenesis of HF and cancer and provides valuable insights for developing novel therapeutic strategies, offering new opportunities for improving the management and treatment outcomes of both HF and cancer.
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Affiliation(s)
- Jing Pan
- School of Life Science and Biochemistry, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China
| | - Ting Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei Province, China
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China
| | - Kun Na
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China
| | - Kai Xu
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China
| | - Chenghui Yan
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China
| | - Haixu Song
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China.
| | - Yaling Han
- School of Life Science and Biochemistry, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, 110016, Liaoning Province, China.
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Wenhua Road 83, Shenyang, 110016, Liaoning Province, China.
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2
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Na J, Engwerda C. The role of CD4 + T cells in visceral leishmaniasis; new and emerging roles for NKG7 and TGFβ. Front Cell Infect Microbiol 2024; 14:1414493. [PMID: 38881737 PMCID: PMC11176485 DOI: 10.3389/fcimb.2024.1414493] [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: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Visceral leishmaniasis is a potentially devastating neglected tropical disease caused by the protozoan parasites Leishmania donovani and L. infantum (chagasi). These parasites reside in tissue macrophages and survive by deploying a number of mechanisms aimed at subverting the host immune response. CD4+ T cells play an important role in controlling Leishmania parasites by providing help in the form of pro-inflammatory cytokines to activate microbiocidal pathways in infected macrophages. However, because these cytokines can also cause tissue damage if over-produced, regulatory immune responses develop, and the balance between pro-inflammatory and regulatory CD4+ T cells responses determines the outcomes of infection. Past studies have identified important roles for pro-inflammatory cytokines such as IFNγ and TNF, as well as regulatory co-inhibitory receptors and the potent anti-inflammatory cytokine IL-10. More recently, other immunoregulatory molecules have been identified that play important roles in CD4+ T cell responses during VL. In this review, we will discuss recent findings about two of these molecules; the NK cell granule protein Nkg7 and the anti-inflammatory cytokine TGFβ, and describe how they impact CD4+ T cell functions and immune responses during visceral leishmaniasis.
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Affiliation(s)
- Jinrui Na
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
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3
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Wang H, Ji Z. T-cell receptor sequences correlate with and predict gene expression levels in T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568912. [PMID: 38076860 PMCID: PMC10705237 DOI: 10.1101/2023.11.27.568912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
T cells exhibit high heterogeneity in both their gene expression profiles and antigen specificities. We analyzed fifteen single-cell immune profiling datasets to systematically investigate the association between T-cell receptor (TCR) sequences and the gene expression profiles of T cells. Our findings reveal that T cells sharing identical or similar TCR sequences tend to have highly similar gene expression profiles. Additionally, we developed a foundational model that leverages TCR information to predict gene expression levels in T cells.
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Affiliation(s)
- Hao Wang
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
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4
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Wang W, Gao X, Kang N, Wang C, Li C, Yu H, Zhang X. Shared biomarkers and immune cell infiltration signatures in ulcerative colitis and nonalcoholic steatohepatitis. Sci Rep 2023; 13:18497. [PMID: 37898694 PMCID: PMC10613305 DOI: 10.1038/s41598-023-44853-6] [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: 05/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
The coexistence of ulcerative colitis (UC) and nonalcoholic steatohepatitis (NASH) involves a intricate interplay, though the precise pathophysiological mechanisms remain elusive. To shed light on this, our study endeavors to unravel the shared gene signatures and molecular mechanisms by employing quantitative bioinformatics analysis on a publicly available RNA-sequencing database. Gene expression profiles of UC (GSE87466) and NASH (GSE89632) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed using R software. After identifying common DEGs, functional enrichment analysis, protein-protein interaction (PPI) network analysis and module construction were performed to obtain candidate hub genes. GSE47908 for UC and GSE159676 for NASH were selected to validate the obtained candidate genes. A total of 119 common DEGs were found in NASH and UC patients. Functional and pathway analyses emphasized that viral infection, inflammation and immune response were enriched in these two diseases. After module construction and validation, CD2, CD8A, GNLY, IFI44, NKG7 and OAS2 were identified as hub genes. 6 hub genes and their combined prediction scores were found with an impressive accuracy and sensitivity. Functional estimation, gene set enrichment analysis and immune infiltration signature identification showed notable associations of the six hub genes with T cells, natural killer cells and type I interferon levels. In addition, we constructed UC combined with NASH mice model successfully with significantly higher expression of hub genes in both liver and colonic tissues than those in control group. Our study elucidates 6 hub genes of UC and NASH, which may participate in immune, inflammatory and antiviral effects. These findings provide some potential biochemical markers for further exploration of UC coexistence with NASH.
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Affiliation(s)
- Wenxin Wang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Xin Gao
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Ning Kang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chen Wang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chenyang Li
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Huan Yu
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Xiaolan Zhang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
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5
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Zhang W, Yan C, Liu X, Yang P, Wang J, Chen Y, Liu W, Li S, Zhang X, Dong G, He X, Yuan X, Jing H. Global characterization of megakaryocytes in bone marrow, peripheral blood, and cord blood by single-cell RNA sequencing. Cancer Gene Ther 2022; 29:1636-1647. [PMID: 35650393 DOI: 10.1038/s41417-022-00476-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/03/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023]
Abstract
Megakaryocytes (MK) are mainly derived from bone marrow and are mainly involved in platelet production. Studies have shown that MK derived from bone marrow may have immune function, and that MK from peripheral blood are associated with prostate cancer. Single-cell transcriptome sequencing can help us better understand the heterogeneity and potential function of MK cell populations in bone marrow (BM), peripheral Blood (PB), and cord blood (CB) of healthy and diseased people.We integrated more than 1.2 million single-cell transcriptome data from 132 samples of PB, BM, and CB from healthy individuals and patients from different dataset. We examined the MK (including MK and product of MK) by single-cell RNA sequencing data analysis methods and identification of MK-related protein expression by the Human Protein atlas. We investigate the relationship between the MK subtype and Non-Small Cell Lung Cancer (NSCLC) in 77 non-cancer and 402 NSCLC. We found that MK were widely distributed and the amount of MK in peripheral blood was more than that in bone marrow and there were specificity MK subtypes in peripheral blood. We found classical MK1 with typical MK characteristics and non-classical MK2 closely related to immunity which was the most common subtype in bone marrow and cord blood. Classical MK1 was closely related to Non-Small Cell Lung Cancer (NSCLC) and can be used as a diagnostic marker. MK2 may have potential adaptive immune function and play a role in tumor NSCLC and autoimmune diseases Systemic Lupus Erythematosus. MK have 14 subtypes and are widely distributed in PB, CB, and BM. MK subtypes are closely related to immunity and have potential to be a diagnostic indicator of NSCLC.
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Affiliation(s)
- Weilong Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, 100191, Beijing, China
| | - Changjian Yan
- The Second Affiliated Hospital of Fujian Medical University, 362000, Quanzhou, China
| | - Xiaoni Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, 341000, Ganzhou, China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, 100191, Beijing, China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, 100191, Beijing, China
| | - Yingtong Chen
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, 100191, Beijing, China
| | - Weiyou Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, 341000, Ganzhou, China
| | - Shaoxiang Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Xue He
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China.
| | - Xiaoliang Yuan
- Department of Respiratory Medicine, The First Affiliated Hospital of Gannan Medical University, 341000, Ganzhou, China.
| | - Hongmei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, 100191, Beijing, China.
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6
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Chen S, Zhan Y, Chen J, Wu J, Gu Y, Huang Q, Deng Z, Wu X, Lv Y, Xie J. Identification and validation of genetic signature associated with aging in chronic obstructive pulmonary disease. Aging (Albany NY) 2022; 14:8568-8580. [DOI: 10.18632/aging.204358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/12/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Shanshan Chen
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Yuan Zhan
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jinkun Chen
- Department of Science, Western University, London, Ontario N6A 3K7, Canada
| | - Jixing Wu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Yiya Gu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Qian Huang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhesong Deng
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiaojie Wu
- Department of Respiratory and Critical Care Medicine, Wuhan No.1 Hospital, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan 430022, China
| | - Yongman Lv
- Health Management Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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7
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Li H, Wang D, Zhou X, Ding S, Guo W, Zhang S, Li Z, Huang T, Cai YD. Characterization of spleen and lymph node cell types via CITE-seq and machine learning methods. Front Mol Neurosci 2022; 15:1033159. [PMID: 36311013 PMCID: PMC9608858 DOI: 10.3389/fnmol.2022.1033159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The spleen and lymph nodes are important functional organs for human immune system. The identification of cell types for spleen and lymph nodes is helpful for understanding the mechanism of immune system. However, the cell types of spleen and lymph are highly diverse in the human body. Therefore, in this study, we employed a series of machine learning algorithms to computationally analyze the cell types of spleen and lymph based on single-cell CITE-seq sequencing data. A total of 28,211 cell data (training vs. test = 14,435 vs. 13,776) involving 24 cell types were collected for this study. For the training dataset, it was analyzed by Boruta and minimum redundancy maximum relevance (mRMR) one by one, resulting in an mRMR feature list. This list was fed into the incremental feature selection (IFS) method, incorporating four classification algorithms (deep forest, random forest, K-nearest neighbor, and decision tree). Some essential features were discovered and the deep forest with its optimal features achieved the best performance. A group of related proteins (CD4, TCRb, CD103, CD43, and CD23) and genes (Nkg7 and Thy1) contributing to the classification of spleen and lymph nodes cell types were analyzed. Furthermore, the classification rules yielded by decision tree were also provided and analyzed. Above findings may provide helpful information for deepening our understanding on the diversity of cell types.
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Affiliation(s)
- Hao Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- State Key Laboratory of Oncology in South China, Department of Radiology, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xianchao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences (SIBS), Shanghai Jiao Tong University School of Medicine (SJTUSM), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Shiqi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
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8
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Aarsund M, Nyman TA, Stensland ME, Wu Y, Inngjerdingen M. Isolation of a cytolytic subpopulation of extracellular vesicles derived from NK cells containing NKG7 and cytolytic proteins. Front Immunol 2022; 13:977353. [PMID: 36189227 PMCID: PMC9520454 DOI: 10.3389/fimmu.2022.977353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
NK cells can broadly target and kill malignant cells via release of cytolytic proteins. NK cells also release extracellular vesicles (EVs) that contain cytolytic proteins, previously shown to induce apoptosis of a variety of cancer cells in vitro and in vivo. The EVs released by NK cells are likely very heterogeneous, as vesicles can be released from the plasma membrane or from different intracellular compartments. In this study, we undertook a fractionation scheme to enrich for cytolytic NK-EVs. NK-EVs were harvested from culture medium from the human NK-92 cell line or primary human NK cells grown in serum-free conditions. By combining ultracentrifugation with downstream density-gradient ultracentrifugation or size-exclusion chromatography, distinct EV populations were identified. Density-gradient ultracentrifugation led to separation of three subpopulations of EVs. The different EV isolates were characterized by label-free quantitative mass spectrometry and western blotting, and we found that one subpopulation was primarily enriched for plasma membrane proteins and tetraspanins CD37, CD82, and CD151, and likely represents microvesicles. The other major subpopulation was enriched in intracellularly derived markers with high expression of the endosomal tetraspanin CD63 and markers for intracellular organelles. The intracellularly derived EVs were highly enriched in cytolytic proteins, and possessed high apoptotic activity against HCT-116 colon cancer spheroids. To further enrich for cytolytic EVs, immunoaffinity pulldowns led to the isolation of a subset of EVs containing the cytolytic granule marker NKG7 and the majority of vesicular granzyme B content. We therefore propose that EVs containing cytolytic proteins may primarily be released via cytolytic granules.
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9
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Weymar GHJ, Bar-On Y, Oliveira TY, Gaebler C, Ramos V, Hartweger H, Breton G, Caskey M, Cohn LB, Jankovic M, Nussenzweig MC. Distinct gene expression by expanded clones of quiescent memory CD4 + T cells harboring intact latent HIV-1 proviruses. Cell Rep 2022; 40:111311. [PMID: 36070690 PMCID: PMC9471989 DOI: 10.1016/j.celrep.2022.111311] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023] Open
Abstract
Antiretroviral therapy controls, but does not cure, HIV-1 infection due to a reservoir of rare CD4+ T cells harboring latent proviruses. Little is known about the transcriptional program of latent cells. Here, we report a strategy to enrich clones of latent cells carrying intact, replication-competent HIV-1 proviruses from blood based on their expression of unique T cell receptors. Latent cell enrichment enabled single-cell transcriptomic analysis of 1,050 CD4+ T cells belonging to expanded clones harboring intact HIV-1 proviruses from 6 different individuals. The analysis reveals that most of these cells are T effector memory cells that are enriched for expression of HLA-DR, HLA-DP, CD74, CCL5, granzymes A and K, cystatin F, LYAR, and DUSP2. We conclude that expanded clones of latent cells carrying intact HIV-1 proviruses persist preferentially in a distinct CD4+ T cell population, opening possibilities for eradication.
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Affiliation(s)
- Georg H J Weymar
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yotam Bar-On
- Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Lillian B Cohn
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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10
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Lelliott EJ, Ramsbottom KM, Dowling MR, Shembrey C, Noori T, Kearney CJ, Michie J, Parish IA, Jordan MA, Baxter AG, Young ND, Brennan AJ, Oliaro J. NKG7 Enhances CD8+ T Cell Synapse Efficiency to Limit Inflammation. Front Immunol 2022; 13:931630. [PMID: 35874669 PMCID: PMC9299089 DOI: 10.3389/fimmu.2022.931630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
Cytotoxic lymphocytes are essential for anti-tumor immunity, and for effective responses to cancer immunotherapy. Natural killer cell granule protein 7 (NKG7) is expressed at high levels in cytotoxic lymphocytes infiltrating tumors from patients treated with immunotherapy, but until recently, the role of this protein in cytotoxic lymphocyte function was largely unknown. Unexpectedly, we found that highly CD8+ T cell-immunogenic murine colon carcinoma (MC38-OVA) tumors grew at an equal rate in Nkg7+/+ and Nkg7-/- littermate mice, suggesting NKG7 may not be necessary for effective CD8+ T cell anti-tumor activity. Mechanistically, we found that deletion of NKG7 reduces the ability of CD8+ T cells to degranulate and kill target cells in vitro. However, as a result of inefficient cytotoxic activity, NKG7 deficient T cells form a prolonged immune synapse with tumor cells, resulting in increased secretion of inflammatory cytokines, including tumor necrosis factor alpha (TNF). By deleting the TNF receptor, TNFR1, from MC38-OVA tumors, we demonstrate that this hyper-secretion of TNF compensates for reduced synapse-mediated cytotoxic activity against MC38-OVA tumors in vivo, via increased TNF-mediated tumor cell death. Taken together, our results demonstrate that NKG7 enhances CD8+ T cell immune synapse efficiency, which may serve as a mechanism to accelerate direct cytotoxicity and limit potentially harmful inflammatory responses.
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Affiliation(s)
- Emily J Lelliott
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kelly M Ramsbottom
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mark R Dowling
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Carolyn Shembrey
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Tahereh Noori
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Conor J Kearney
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jessica Michie
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ian A Parish
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Margaret A Jordan
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Alan G Baxter
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia.,Central Clinical School, Monash University, Prahran, VIC, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amelia J Brennan
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jane Oliaro
- Centre for Cancer Immunotherapy, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Density and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
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11
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Zhai H, Huang L, Gong Y, Liu Y, Wang Y, Liu B, Li X, Peng C, Li T. Human Plasma Transcriptome Implicates Dysregulated S100A12 Expression: A Strong, Early-Stage Prognostic Factor in ST-Segment Elevated Myocardial Infarction: Bioinformatics Analysis and Experimental Verification. Front Cardiovasc Med 2022; 9:874436. [PMID: 35722095 PMCID: PMC9200219 DOI: 10.3389/fcvm.2022.874436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The ability of blood transcriptome analysis to identify dysregulated pathways and outcome-related genes following myocardial infarction remains unknown. Two gene expression datasets (GSE60993 and GSE61144) were downloaded from Gene Expression Omnibus (GEO) Datasets to identify altered plasma transcriptomes in patients with ST-segment elevated myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention. GEO2R, Gene Ontology/Kyoto Encyclopedia of Genes and Genomes annotations, protein–protein interaction analysis, etc., were adopted to determine functional roles and regulatory networks of differentially expressed genes (DEGs). Dysregulated expressomes were verified at transcriptional and translational levels by analyzing the GSE49925 dataset and our own samples, respectively. A total of 91 DEGs were identified in the discovery phase, consisting of 15 downregulated genes and 76 upregulated genes. Two hub modules consisting of 12 hub genes were identified. In the verification phase, six of the 12 hub genes exhibited the same variation patterns at the transcriptional level in the GSE49925 dataset. Among them, S100A12 was shown to have the best discriminative performance for predicting in-hospital mortality and to be the only independent predictor of death during follow-up. Validation of 223 samples from our center showed that S100A12 protein level in plasma was significantly lower among patients who survived to discharge, but it was not an independent predictor of survival to discharge or recurrent major adverse cardiovascular events after discharge. In conclusion, the dysregulated expression of plasma S100A12 at the transcriptional level is a robust early prognostic factor in patients with STEMI, while the discrimination power of the protein level in plasma needs to be further verified by large-scale, prospective, international, multicenter studies.
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Affiliation(s)
- Hu Zhai
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
- *Correspondence: Hu Zhai,
| | - Lei Huang
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Yijie Gong
- The Third Central Clinical College, Tianjin Medical University, Tianjin, China
| | - Yingwu Liu
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Yu Wang
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Bojiang Liu
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Xiandong Li
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chunyan Peng
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
- Chunyan Peng,
| | - Tong Li
- Department of Heart Center, The Tianjin Third Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Tianjin Institute of Hepatobiliary Disease, Tianjin, China
- Tong Li,
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12
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Zhang H, Ma Y, Zhang Q, Liu R, Luo H, Wang X. A pancancer analysis of the carcinogenic role of receptor-interacting serine/threonine protein kinase-2 (RIPK2) in human tumours. BMC Med Genomics 2022; 15:97. [PMID: 35473583 PMCID: PMC9040268 DOI: 10.1186/s12920-022-01239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/13/2022] [Indexed: 11/15/2022] Open
Abstract
Background To explore the expression and carcinogenic mechanism of RIPK2 in human tumours, and to provide the theoretical basis for the further study of RIPK2. Methods We used the TCGA, CPTAC, HPA databases to analyse the expression, mutation, and prognosis of RIPK2 in human tumours. Through the Cbioportal, Ualcan, TIMER2.0, and STRING websites, We understand the genetic variation, immune infiltration and enrichment analysis of RIPK2 related genes. Results RIPK2 was highly expressed in most tumours (such as BRCA, COAD and LUSC, etc.), and the high expression of RIPK2 was correlated with tumour stage and prognosis. In addition, Amplification was the main type of RIPK2 in tumour mutation state, and the amplification rate was about 8.5%. In addition, RIPK2 was positively associated with tumour-infiltrating immune cells (such as CD8+ T, Tregs, and cancer-associated fibroblasts). According to the KEGG analysis, RIPK2 may play a role in tumour mainly through NOD-like signaling pathway and NF-kappaB signaling pathway. GO enrichment analysis showed that the RIPK2 is mainly related to I-kappaB kinase/NF-kappaB signaling, Ribonucleoprotein granule and Ubiquitin-like protein ligase binding. Conclusion RIPK2 plays an important role in the occurrence, development and prognosis of malignant tumours. Our pancancer study provided a relatively comprehensive description of the carcinogenic effects of RIPK2 in different tumours, and provided useful information for further study of RIPK2. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01239-3.
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Affiliation(s)
- Hanqun Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, People's Republic of China.,Department of Oncology, Guizhou Provincial People's Hospital, Guizhou, 550002, People's Republic of China
| | - Yan Ma
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Qiuning Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Lanzhou Heavy Ion Hospital, Lanzhou, 730000, People's Republic of China
| | - Ruifeng Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Lanzhou Heavy Ion Hospital, Lanzhou, 730000, People's Republic of China
| | - Hongtao Luo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Lanzhou Heavy Ion Hospital, Lanzhou, 730000, People's Republic of China
| | - Xiaohu Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, People's Republic of China. .,Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China. .,Lanzhou Heavy Ion Hospital, Lanzhou, 730000, People's Republic of China.
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13
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Wen T, Barham W, Li Y, Zhang H, Gicobi JK, Hirdler JB, Liu X, Ham H, Peterson Martinez KE, Lucien F, Lavoie RR, Li H, Correia C, Monie DD, An Z, Harrington SM, Wu X, Guo R, Dronca RS, Mansfield AS, Yan Y, Markovic SN, Park SS, Sun J, Qin H, Liu MC, Vasmatzis G, Billadeau DD, Dong H. NKG7 Is a T-cell-Intrinsic Therapeutic Target for Improving Antitumor Cytotoxicity and Cancer Immunotherapy. Cancer Immunol Res 2022; 10:162-181. [PMID: 34911739 PMCID: PMC8816890 DOI: 10.1158/2326-6066.cir-21-0539] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/19/2021] [Accepted: 12/09/2021] [Indexed: 01/22/2023]
Abstract
Cytotoxic CD8+ T cells (CTL) are a crucial component of the immune system notable for their ability to eliminate rapidly proliferating malignant cells. However, the T-cell intrinsic factors required for human CTLs to accomplish highly efficient antitumor cytotoxicity are not well defined. By evaluating human CD8+ T cells from responders versus nonresponders to treatment with immune checkpoint inhibitors, we sought to identify key factors associated with effective CTL function. Single-cell RNA-sequencing analysis of peripheral CD8+ T cells from patients treated with anti-PD-1 therapy showed that cells from nonresponders exhibited decreased expression of the cytolytic granule-associated molecule natural killer cell granule protein-7 (NKG7). Functional assays revealed that reduced NKG7 expression altered cytolytic granule number, trafficking, and calcium release, resulting in decreased CD8+ T-cell-mediated killing of tumor cells. Transfection of T cells with NKG7 mRNA was sufficient to improve the tumor-cell killing ability of human T cells isolated from nonresponders and increase their response to anti-PD-1 or anti-PD-L1 therapy in vitro. NKG7 mRNA therapy also improved the antitumor activity of murine tumor antigen-specific CD8+ T cells in an in vivo model of adoptive cell therapy. Finally, we showed that the transcription factor ETS1 played a role in regulating NKG7 expression. Together, our results identify NKG7 as a necessary component for the cytotoxic function of CD8+ T cells and establish NKG7 as a T-cell-intrinsic therapeutic target for enhancing cancer immunotherapy.See related article by Li et al., p. 154.
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Affiliation(s)
- Ti Wen
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Whitney Barham
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Ying Li
- Division of Computational Biology, Mayo Clinic, Rochester, MN
| | - Henan Zhang
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Joanina K. Gicobi
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | | | - Xin Liu
- Department of Urology, Mayo Clinic, Rochester, MN
| | - Hyoungjun Ham
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | | | | | | | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Cristina Correia
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Dileep D. Monie
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Zesheng An
- Department of Urology, Mayo Clinic, Rochester, MN
| | | | - Xiaosheng Wu
- Division of Hematology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Yiyi Yan
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Sean S. Park
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Jie Sun
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN.,Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Hong Qin
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Minetta C. Liu
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Daniel D. Billadeau
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN
| | - Haidong Dong
- Department of Urology, Mayo Clinic, Rochester, MN.,Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN.,Corresponding Author: Haidong Dong, M.D., Ph.D., 200 First Street SW, Rochester, MN 55905; Phone: 507-284-5482;
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14
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Li XY, Corvino D, Nowlan B, Aguilera AR, Ng SS, Braun M, Cillo AR, Bald T, Smyth MJ, Engwerda CR. NKG7 Is Required for Optimal Antitumor T-cell Immunity. Cancer Immunol Res 2022; 10:154-161. [PMID: 35013002 DOI: 10.1158/2326-6066.cir-20-0649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/12/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Tumor antigen-specific CD8+ T cells play a critical role in antitumor immunity. Clinical trials reinvigorating the immune system via immune checkpoint blockade (ICB) have shown remarkable clinical promise. Numerous studies have identified an association between NKG7 expression and patient outcome across different malignancies. However, aside from these correlative observations, very little is known about NKG7 and its role in antitumor immunity. Herein, we utilized single-cell RNA sequencing (scRNA-seq) datasets, NKG7-deficient mice, NKG7-reporter mice, and mouse tumor models to investigate the role of NKG7 in neoantigen-mediated tumor rejection and ICB immunotherapy. scRNA-seq of tumors from patients with metastatic melanoma or head and neck squamous cell carcinoma revealed that NKG7 expression is highly associated with cytotoxicity and specifically expressed by CD8+ T cells and natural killer (NK) cells. Furthermore, we identified a key role for NKG7 in controlling intratumor T-cell accumulation and activation. NKG7 was upregulated on intratumor antigen-specific CD8+ T cells and NK cells and required for the accumulation of T cells in the tumor microenvironment. Accordingly, neoantigen-expressing mouse tumors grew faster in Nkg7-deficient mice. Strikingly, efficacy of single or combination ICB was significantly reduced in Nkg7-deficient mice.
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Affiliation(s)
- Xian-Yang Li
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Zhuhai Precision Medical Center, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong, P.R. China
| | - Dillon Corvino
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Bianca Nowlan
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amelia Roman Aguilera
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Susanna S Ng
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
- Immunology and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Griffith University, School of Environment and Science, Nathan, Queensland, Australia
| | - Matthias Braun
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Tobias Bald
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Christian R Engwerda
- Immunology and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
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15
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Dong X, Dong S, Pan S, Zhan X. RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms. BMC Bioinformatics 2022; 23:26. [PMID: 34991454 PMCID: PMC8740077 DOI: 10.1186/s12859-021-04549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 12/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results. Results We present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub: https://github.com/dongxuemin666/RNA-combine. Conclusion Our results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.
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Affiliation(s)
- Xuemin Dong
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shanshan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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16
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Jiang Y, Deng S, Hu X, Luo L, Zhang Y, Zhang D, Li X, Feng J. Identification of potential biomarkers and immune infiltration characteristics in severe asthma. Int J Immunopathol Pharmacol 2022; 36:3946320221114194. [PMID: 35817495 PMCID: PMC9280849 DOI: 10.1177/03946320221114194] [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] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES We hope to identify key molecules that can be used as markers of asthma severity and investigate their correlation with immune cell infiltration in severe asthma. METHODS An asthma dataset was downloaded from the Gene Expression Omnibus database and then processed by R software to obtain differentially expressed genes (DEGs). First, multiple enrichment platforms were applied to analyze crucial biological processes and pathways and protein-protein interaction networks related to the DEGs. We next combined least absolute shrinkage and selection operator logistic regression and the support vector machine-recursive feature elimination algorithms to screen diagnostic markers of severe asthma. Then, a local cohort consisting of 40 asthmatic subjects (24 with moderate asthma and 16 with severe asthma) was used for biomarker validation. Finally, infiltration of immune cells in asthma bronchoalveolar lavage fluid and their correlation with the screened markers was evaluated by CIBERSORT. RESULTS A total of 97 DEGs were identified in this study. Most of these genes are enriched in T cell activation and immune response in the asthma biological process. CC-chemokine receptor 7 (CCR7) and natural killer cell protein 7(NKG7) were identified as markers of severe asthma. The highest area under the ROC curve (AUC) was from a new indicator combining CCR7 and NKG7 (AUC = 0.851, adj. p < 0.05). Resting and activated memory CD4 T cells, activated NK cells, and CD8 T cells were found to be significantly higher in the severe asthma group (adj. p < 0.01). CCR7 and NKG7 were significantly correlated with these infiltrated cells that showed differences between the two groups. In addition, CCR7 was found to be significantly positively correlated with eosinophils (r = 0.38, adj. p < 0.05) infiltrated in bronchoalveolar lavage fluid. CONCLUSION CCR7 and NKG7 might be used as potential markers for asthma severity, and their expression may be associated with differences in immune cell infiltration in the moderate and severe asthma groups.
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Affiliation(s)
- Yuanyuan Jiang
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Shuanglinzi Deng
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Xinyue Hu
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Lisha Luo
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Yingyu Zhang
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Daimo Zhang
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Xiaozhao Li
- Department of Nephrology, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
| | - Juntao Feng
- Center of Respiratory Medicine, Xiangya Hospital, 12570Central South University, Changsha, Hunan, China
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17
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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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18
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Natural Killer Cells and Type 1 Innate Lymphoid Cells in Hepatocellular Carcinoma: Current Knowledge and Future Perspectives. Int J Mol Sci 2021; 22:ijms22169044. [PMID: 34445750 PMCID: PMC8396475 DOI: 10.3390/ijms22169044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1) are specific innate lymphoid cell subsets that are key for the detection and elimination of pathogens and cancer cells. In liver, while they share a number of characteristics, they differ in many features. These include their developmental pathways, tissue distribution, phenotype and functions. NK cells and ILC1 contribute to organ homeostasis through the production of key cytokines and chemokines and the elimination of potential harmful bacteria and viruses. In addition, they are equipped with a wide range of receptors, allowing them to detect “stressed cells’ such as cancer cells. Our understanding of the role of innate lymphoid cells in hepatocellular carcinoma (HCC) is growing owing to the development of mouse models, the progress in immunotherapeutic treatment and the recent use of scRNA sequencing analyses. In this review, we summarize the current understanding of NK cells and ILC1 in hepatocellular carcinoma and discuss future strategies to take advantage of these innate immune cells in anti-tumor immunity. Immunotherapies hold great promise in HCC, and a better understanding of the role and function of NK cells and ILC1 in liver cancer could pave the way for new NK cell and/or ILC1-targeted treatment.
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19
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Agonistic CD40 Antibodies in Cancer Treatment. Cancers (Basel) 2021; 13:cancers13061302. [PMID: 33804039 PMCID: PMC8000216 DOI: 10.3390/cancers13061302] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/16/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary CD40 is a costimulatory molecule that is key for the activation of antigen-presenting cells and other innate immune cells. It plays an important role in anti-tumor immunity, and agonists of CD40 have been shown to eliminate tumors in both pre-clinical and clinical settings, alone and in combination with other treatment modalities. Here we assess the expression of CD40 and associations with other mediators of immunity in a variety of tumor types and review the potential of CD40 agonists for cancer treatment, given the promise of enhancing the interplay between innate and adaptive immunity. Abstract CD40 is expressed on a variety of antigen-presenting cells. Stimulation of CD40 results in inflammation by upregulation of other costimulatory molecules, increased antigen presentation, maturation (licensing) of dendritic cells, and activation of CD8+ T cells. Here we analyzed gene expression data from The Cancer Genome Atlas in melanoma, renal cell carcinoma, and pancreatic adenocarcinoma and found correlations between CD40 and several genes involved in antigen presentation and T cell function, supporting further exploration of CD40 agonists to treat cancer. Agonist CD40 antibodies have induced anti-tumor effects in several tumor models and the effect has been more pronounced when used in combination with other treatments (immune checkpoint inhibition, chemotherapy, and colony-stimulating factor 1 receptor inhibition). The reduction in tumor growth and ability to reprogram the tumor microenvironment in preclinical models lays the foundation for clinical development of agonistic CD40 antibodies (APX005M, ChiLob7/4, ADC-1013, SEA-CD40, selicrelumab, and CDX-1140) that are currently being evaluated in early phase clinical trials. In this article, we focus on CD40 expression and immunity in cancer, agonistic human CD40 antibodies, and their pre-clinical and clinical development. With the broad pro-inflammatory effects of CD40 and its ligand on dendritic cells and macrophages, and downstream B and T cell activation, agonists of this pathway may enhance the anti-tumor activity of other systemic therapies.
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20
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Gaurav R, Mikuls TR, Thiele GM, Nelson AJ, Niu M, Guda C, Eudy JD, Barry AE, Wyatt TA, Romberger DJ, Duryee MJ, England BR, Poole JA. High-throughput analysis of lung immune cells in a combined murine model of agriculture dust-triggered airway inflammation with rheumatoid arthritis. PLoS One 2021; 16:e0240707. [PMID: 33577605 PMCID: PMC7880471 DOI: 10.1371/journal.pone.0240707] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/18/2020] [Indexed: 01/10/2023] Open
Abstract
Rheumatoid arthritis (RA)-associated lung disease is a leading cause of mortality in RA, yet the mechanisms linking lung disease and RA remain unknown. Using an established murine model of RA-associated lung disease combining collagen-induced arthritis (CIA) with organic dust extract (ODE)-induced airway inflammation, differences among lung immune cell populations were analyzed by single cell RNA-sequencing. Additionally, four lung myeloid-derived immune cell populations including macrophages, monocytes/macrophages, monocytes, and neutrophils were isolated by fluorescence cell sorting and gene expression was determined by NanoString analysis. Unsupervised clustering revealed 14 discrete clusters among Sham, CIA, ODE, and CIA+ODE treatment groups: 3 neutrophils (inflammatory, resident/transitional, autoreactive/suppressor), 5 macrophages (airspace, differentiating/recruited, recruited, resident/interstitial, and proliferative airspace), 2 T-cells (differentiating and effector), and a single cluster each of inflammatory monocytes, dendritic cells, B-cells and natural killer cells. Inflammatory monocytes, autoreactive/suppressor neutrophils, and recruited/differentiating macrophages were predominant with arthritis induction (CIA and CIA+ODE). By specific lung cell isolation, several interferon-related and autoimmune genes were disproportionately expressed among CIA and CIA+ODE (e.g. Oasl1, Oas2, Ifit3, Gbp2, Ifi44, and Zbp1), corresponding to RA and RA-associated lung disease. Monocytic myeloid-derived suppressor cells were reduced, while complement genes (e.g. C1s1 and Cfb) were uniquely increased in CIA+ODE mice across cell populations. Recruited and inflammatory macrophages/monocytes and neutrophils expressing interferon-, autoimmune-, and complement-related genes might contribute towards pro-fibrotic inflammatory lung responses following airborne biohazard exposures in setting of autoimmune arthritis and could be predictive and/or targeted to reduce disease burden.
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Affiliation(s)
- Rohit Gaurav
- Division of Allergy and Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
- * E-mail:
| | - Ted R. Mikuls
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Rheumatology & Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Geoffrey M. Thiele
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Rheumatology & Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Amy J. Nelson
- Division of Allergy and Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Meng Niu
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - James D. Eudy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Austin E. Barry
- Division of Allergy and Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Todd A. Wyatt
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Pulmonary, Critical Care & Sleep, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
- Department of Environmental, Agricultural & Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Debra J. Romberger
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Pulmonary, Critical Care & Sleep, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Michael J. Duryee
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Rheumatology & Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Bryant R. England
- Veterans Affairs Nebraska-Western Iowa Health Care System, Research Service, Omaha, NE, United States of America
- Division of Rheumatology & Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Jill A. Poole
- Division of Allergy and Immunology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
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21
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Affiliation(s)
- Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Versiti, Milwaukee, WI, USA. .,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA. .,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA. .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
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22
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Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease. Proc Natl Acad Sci U S A 2020; 117:25712-25721. [PMID: 32989127 DOI: 10.1073/pnas.2002476117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a systemic autoimmune disorder affecting multiple organs, including eyes, skin, and central nervous system. It is known that monocytes significantly contribute to the development of autoimmune disease. However, the subset heterogeneity with unique functions and signatures in human circulating monocytes and the identity of disease-specific monocytic populations remain largely unknown. Here, we employed an advanced single-cell RNA sequencing technology to systematically analyze 11,259 human circulating monocytes and genetically defined their subpopulations. We constructed a precise atlas of human blood monocytes, identified six subpopulations-including S100A12, HLA, CD16, proinflammatory, megakaryocyte-like, and NK-like monocyte subsets-and uncovered two previously unidentified subsets: HLA and megakaryocyte-like monocyte subsets. Relative to healthy individuals, cellular composition, gene expression signatures, and activation states were markedly alternated in VKH patients utilizing cell type-specific programs, especially the CD16 and proinflammatory monocyte subpopulations. Notably, we discovered a disease-relevant subgroup, proinflammatory monocytes, which showed a discriminative gene expression signature indicative of inflammation, antiviral activity, and pathologic activation, and converted into a pathologic activation state implicating the active inflammation during VKH disease. Additionally, we found the cell type-specific transcriptional signature of proinflammatory monocytes, ISG15, whose production might reflect the treatment response. Taken together, in this study, we present discoveries on accurate classification, molecular markers, and signaling pathways for VKH disease-associated monocytes. Therapeutically targeting this proinflammatory monocyte subpopulation would provide an attractive approach for treating VKH, as well as other autoimmune diseases.
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23
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Sage AP, Ng KW, Marshall EA, Stewart GL, Minatel BC, Enfield KSS, Martin SD, Brown CJ, Abraham N, Lam WL. Assessment of long non-coding RNA expression reveals novel mediators of the lung tumour immune response. Sci Rep 2020; 10:16945. [PMID: 33037279 PMCID: PMC7547676 DOI: 10.1038/s41598-020-73787-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022] Open
Abstract
The tumour immune microenvironment is a crucial mediator of lung tumourigenesis, and characterizing the immune landscape of patient tumours may guide immunotherapy treatment regimens and uncover novel intervention points. We sought to identify the landscape of tumour-infiltrating immune cells in the context of long non-coding RNA (lncRNAs), known regulators of gene expression. We examined the lncRNA profiles of lung adenocarcinoma (LUAD) tumours by interrogating RNA sequencing data from microdissected and non-microdissected samples (BCCRC and TCGA). Subsequently, analysis of single-cell RNA sequencing data from lung tumours and flow-sorted healthy peripheral blood mononuclear cells identified lncRNAs in immune cells, highlighting their biological and prognostic relevance. We discovered lncRNA expression patterns indicative of regulatory relationships with immune-related protein-coding genes, including the relationship between AC008750.1 and NKG7 in NK cells. Activation of NK cells in vitro was sufficient to induce AC008750.1 expression. Finally, siRNA-mediated knockdown of AC008750.1 significantly impaired both the expression of NKG7 and the anti-tumour capacity of NK cells. We present an atlas of cancer-cell extrinsic immune cell-expressed lncRNAs, in vitro evidence for a functional role of lncRNAs in anti-tumour immune activity, which upon further exploration may reveal novel clinical utility as markers of immune infiltration.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Spencer D Martin
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ninan Abraham
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
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24
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Schuster IS, Andoniou CE. NKG7 - regulating endosomal pathways? Immunol Cell Biol 2020; 98:802-804. [PMID: 33016375 DOI: 10.1111/imcb.12403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 11/26/2022]
Abstract
Ng et al. have identified NKG7 as a regulator of inflammation in response to diverse immunological challenges. While NKG7 was required for the degranulation of cytotoxic cells, additional defects including reduced expansion and trafficking of CD8 T cells, and altered antigen presentation, were noted in NKG7-deficient mice. The precise mechanism by which NKG7 mediates its effects has not been resolved but may involve regulation of endosomal vesicle trafficking.
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Affiliation(s)
- Iona S Schuster
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
| | - Christopher E Andoniou
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA, Australia
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25
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Ng SS, De Labastida Rivera F, Yan J, Corvino D, Das I, Zhang P, Kuns R, Chauhan SB, Hou J, Li XY, Frame TCM, McEnroe BA, Moore E, Na J, Engel JA, Soon MSF, Singh B, Kueh AJ, Herold MJ, Montes de Oca M, Singh SS, Bunn PT, Aguilera AR, Casey M, Braun M, Ghazanfari N, Wani S, Wang Y, Amante FH, Edwards CL, Haque A, Dougall WC, Singh OP, Baxter AG, Teng MWL, Loukas A, Daly NL, Cloonan N, Degli-Esposti MA, Uzonna J, Heath WR, Bald T, Tey SK, Nakamura K, Hill GR, Kumar R, Sundar S, Smyth MJ, Engwerda CR. The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation. Nat Immunol 2020; 21:1205-1218. [PMID: 32839608 PMCID: PMC7965849 DOI: 10.1038/s41590-020-0758-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
Abstract
Immune-modulating therapies have revolutionized the treatment of chronic diseases, particularly cancer. However, their success is restricted and there is a need to identify new therapeutic targets. Here, we show that natural killer cell granule protein 7 (NKG7) is a regulator of lymphocyte granule exocytosis and downstream inflammation in a broad range of diseases. NKG7 expressed by CD4+ and CD8+ T cells played key roles in promoting inflammation during visceral leishmaniasis and malaria-two important parasitic diseases. Additionally, NKG7 expressed by natural killer cells was critical for controlling cancer initiation, growth and metastasis. NKG7 function in natural killer and CD8+ T cells was linked with their ability to regulate the translocation of CD107a to the cell surface and kill cellular targets, while NKG7 also had a major impact on CD4+ T cell activation following infection. Thus, we report a novel therapeutic target expressed on a range of immune cells with functions in different immune responses.
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Affiliation(s)
- Susanna S Ng
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Juming Yan
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Dillon Corvino
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Indrajit Das
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ping Zhang
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rachel Kuns
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Shashi Bhushan Chauhan
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jiajie Hou
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Xian-Yang Li
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Teija C M Frame
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin A McEnroe
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Eilish Moore
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Jinrui Na
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Jessica A Engel
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Bhawana Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Andrew J Kueh
- Division of Blood Cells and Blood Cancer, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marco J Herold
- Division of Blood Cells and Blood Cancer, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Siddharth Sankar Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Patrick T Bunn
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Institute of Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Amy Roman Aguilera
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mika Casey
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthias Braun
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nazanin Ghazanfari
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Shivangi Wani
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Institute of Molecular Biology, University of Queensland, Brisbane, Queensland, Australia
| | - Yulin Wang
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
| | - Fiona H Amante
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chelsea L Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Ashraful Haque
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - William C Dougall
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Om Prakash Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Alan G Baxter
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Michele W L Teng
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Nicole Cloonan
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- The Centre for Experimental Immunology, Lions Eye Institute, Perth, Western Australia, Australia
| | - Jude Uzonna
- Department of Immunology, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - William R Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Tobias Bald
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Siok-Keen Tey
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kyohei Nakamura
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Geoffrey R Hill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rajiv Kumar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Mark J Smyth
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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26
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Cheng L, Yu H, Wrobel JA, Li G, Liu P, Hu Z, Xu XN, Su L. Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-Seq. JCI Insight 2020; 5:135344. [PMID: 32406872 DOI: 10.1172/jci.insight.135344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
Depletion of CD4+ T cells during HIV-1 infection is mostly mediated by inflammatory cells via indirect but not clearly defined mechanisms. In this report, we used single-cell RNA-Seq (scRNA-Seq) technology to study HIV-induced transcriptomic change in innate immune cells in lymphoid organs. We performed scRNA-Seq on hCD45+hCD3-hCD19- human leukocytes isolated from spleens of humanized NOD/Rag2-/-γc-/- (NRG) mice transplanted with human CD34+ hematopoietic stem progenitor cells (NRG-hu HSC mice). We identified major populations of innate immune cells, including plasmacytoid dendritic cells (pDCs), myeloid dendritic cells (mDCs), macrophages, NK cells, and innate lymphoid cells (ILCs). HIV-1 infection significantly upregulated genes involved in type I IFN inflammatory pathways in each of the innate immune subsets. Interestingly, we found that TRAIL was upregulated in the innate immune populations, including pDCs, mDCs, macrophages, NK cells, and ILCs. We further demonstrated that blockade of the TRAIL signaling pathway in NRG-hu HSC mice prevented HIV-1-induced CD4+ T cell depletion in vivo. In summary, we characterized HIV-induced transcriptomic changes of innate immune cells in the spleen at single-cell levels, identified the TRAIL+ innate immune cells, and defined an important role of the TRAIL signaling pathway in HIV-1-induced CD4+ T cell depletion in vivo.
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Affiliation(s)
- Liang Cheng
- Lineberger Comprehensive Cancer Center and.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haisheng Yu
- Lineberger Comprehensive Cancer Center and.,Key Laboratory of Human Disease Comparative Medicine of Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | | | - Peng Liu
- Lineberger Comprehensive Cancer Center and
| | - Zhiyuan Hu
- Lineberger Comprehensive Cancer Center and
| | - Xiao-Ning Xu
- Department of Medicine, Chelsea and Westminster Hospital, Imperial College London, London, United Kingdom
| | - Lishan Su
- Lineberger Comprehensive Cancer Center and.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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27
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Alessandrì L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino S, Licheri N, De Libero G, Pace L, Calogero RA. rCASC: reproducible classification analysis of single-cell sequencing data. Gigascience 2020; 8:5565135. [PMID: 31494672 PMCID: PMC6732171 DOI: 10.1093/gigascience/giz105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/12/2019] [Accepted: 08/08/2019] [Indexed: 01/05/2023] Open
Abstract
Background Single-cell RNA sequencing is essential for investigating cellular heterogeneity and highlighting cell subpopulation-specific signatures. Single-cell sequencing applications have spread from conventional RNA sequencing to epigenomics, e.g., ATAC-seq. Many related algorithms and tools have been developed, but few computational workflows provide analysis flexibility while also achieving functional (i.e., information about the data and the tools used are saved as metadata) and computational reproducibility (i.e., a real image of the computational environment used to generate the data is stored) through a user-friendly environment. Findings rCASC is a modular workflow providing an integrated analysis environment (from count generation to cell subpopulation identification) exploiting Docker containerization to achieve both functional and computational reproducibility in data analysis. Hence, rCASC provides preprocessing tools to remove low-quality cells and/or specific bias, e.g., cell cycle. Subpopulation discovery can instead be achieved using different clustering techniques based on different distance metrics. Cluster quality is then estimated through the new metric "cell stability score" (CSS), which describes the stability of a cell in a cluster as a consequence of a perturbation induced by removing a random set of cells from the cell population. CSS provides better cluster robustness information than the silhouette metric. Moreover, rCASC's tools can identify cluster-specific gene signatures. Conclusions rCASC is a modular workflow with new features that could help researchers define cell subpopulations and detect subpopulation-specific markers. It uses Docker for ease of installation and to achieve a computation-reproducible analysis. A Java GUI is provided to welcome users without computational skills in R.
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Affiliation(s)
- Luca Alessandrì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10125 Torino, Italy
| | - Francesca Cordero
- Department of Computer Science, University of Torino, Corso Svizzera 185, 10149 Torino, Italy
| | - Marco Beccuti
- Department of Computer Science, University of Torino, Corso Svizzera 185, 10149 Torino, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10125 Torino, Italy
| | - Martina Olivero
- Department of Oncology, University of Torino, SP142, 95, 10060 Candiolo (TO), Italy
| | - Greta Romano
- Department of Computer Science, University of Torino, Corso Svizzera 185, 10149 Torino, Italy
| | - Sergio Rabellino
- Department of Computer Science, University of Torino, Corso Svizzera 185, 10149 Torino, Italy
| | - Nicola Licheri
- Department of Computer Science, University of Torino, Corso Svizzera 185, 10149 Torino, Italy
| | - Gennaro De Libero
- Department Biomedizin, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Luigia Pace
- Italian Istitute for Genomic Medicine, IIGM, c/o IRCCS 10060 Candiolo (TO), Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10125 Torino, Italy
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28
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Sinha D, Kumar A, Kumar H, Bandyopadhyay S, Sengupta D. dropClust: efficient clustering of ultra-large scRNA-seq data. Nucleic Acids Res 2019; 46:e36. [PMID: 29361178 PMCID: PMC5888655 DOI: 10.1093/nar/gky007] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/07/2018] [Indexed: 11/18/2022] Open
Abstract
Droplet based single cell transcriptomics has recently enabled parallel screening of tens of thousands of single cells. Clustering methods that scale for such high dimensional data without compromising accuracy are scarce. We exploit Locality Sensitive Hashing, an approximate nearest neighbour search technique to develop a de novo clustering algorithm for large-scale single cell data. On a number of real datasets, dropClust outperformed the existing best practice methods in terms of execution time, clustering accuracy and detectability of minor cell sub-types.
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Affiliation(s)
- Debajyoti Sinha
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.,Department of Computer Science and Engineering, University of Calcutta, Kolkata 700098, West Bengal, India
| | - Akhilesh Kumar
- Laboratory of Immunology and Infectious Disease Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, Madhya Pradesh, India
| | - Himanshu Kumar
- Laboratory of Immunology and Infectious Disease Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, Madhya Pradesh, India
| | | | - Debarka Sengupta
- Center for Computational Biology and Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi 110020, India
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29
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Irigoyen A, Jimenez-Luna C, Benavides M, Caba O, Gallego J, Ortuño FM, Guillen-Ponce C, Rojas I, Aranda E, Torres C, Prados J. Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers. PLoS One 2018; 13:e0194844. [PMID: 29617451 PMCID: PMC5884535 DOI: 10.1371/journal.pone.0194844] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/09/2018] [Indexed: 01/16/2023] Open
Abstract
Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses (‘gained’ genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.
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Affiliation(s)
- Antonio Irigoyen
- Department of Medical Oncology, Virgen de la Salud Hospital, Toledo, Spain
| | - Cristina Jimenez-Luna
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Manuel Benavides
- Department of Medical Oncology, Virgen de la Victoria Hospital, Malaga, Spain
| | - Octavio Caba
- Department of Health Sciences, University of Jaen, Jaen, Spain
- * E-mail:
| | - Javier Gallego
- Department of Medical Oncology, University General Hospital of Elche, Alicante, Spain
| | - Francisco Manuel Ortuño
- Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada, Spain
| | | | - Ignacio Rojas
- Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada, Spain
| | - Enrique Aranda
- Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Carolina Torres
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
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30
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Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH. Massively parallel digital transcriptional profiling of single cells. Nat Commun 2017; 8:14049. [PMID: 28091601 PMCID: PMC5241818 DOI: 10.1038/ncomms14049] [Citation(s) in RCA: 3580] [Impact Index Per Article: 511.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023] Open
Abstract
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
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Affiliation(s)
| | | | | | - Paul Ryvkin
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Ryan Wilson
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Junjie Zhu
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Joe Shuga
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Jason G Underwood
- 10x Genomics Inc., Pleasanton, California, 94566, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | - Paul W Wyatt
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Kevin D Ness
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Lan W Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Christopher McFarland
- Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory, Seattle, Washington 98109, USA
| | - Keith R Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emily A Stevens
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | | | | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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31
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Distinctive gene expression profile in women with history of postpartum depression. Genomics 2016; 109:1-8. [PMID: 27816578 DOI: 10.1016/j.ygeno.2016.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/12/2016] [Accepted: 10/20/2016] [Indexed: 11/20/2022]
Abstract
Postpartum depression (PPD) is a disease which incorporates a variety of depressive states differing in nature and severity. To assist in the understanding of the pathogenesis of the disease, we aimed to ascertain a molecular mechanism underlying PPD development. We applied microarray technology to characterize gene expression of euthymic women with a history of PPD and compared the results with healthy controls. Our study demonstrated that women who considered euthymic on a clinical level, in fact, had an altered molecular profile when compared to participants with no PPD history. We identified nine genes significantly distinguished expression in post- depressive women; they may serve as a diagnostic tool for the detection of a predisposition to PPD. Our findings contribute significantly to the understanding of PPD etiology and its pathogenesis, offer a plausible explanation for the risk of the PPD recurrence, and may also contribute to clinical treatment.
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32
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Uterine activin receptor-like kinase 5 is crucial for blastocyst implantation and placental development. Proc Natl Acad Sci U S A 2015; 112:E5098-107. [PMID: 26305969 DOI: 10.1073/pnas.1514498112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Members of the transforming growth factor β (TGF-β) superfamily are key regulators in most developmental and physiological processes. However, the in vivo roles of TGF-β signaling in female reproduction remain uncertain. Activin receptor-like kinase 5 (ALK5) is the major type 1 receptor for the TGF-β subfamily. Absence of ALK5 leads to early embryonic lethality because of severe defects in vascular development. In this study, we conditionally ablated uterine ALK5 using progesterone receptor-cre mice to define the physiological roles of ALK5 in female reproduction. Despite normal ovarian functions and artificial decidualization in conditional knockout (cKO) mice, absence of uterine ALK5 resulted in substantially reduced female reproduction due to abnormalities observed at different stages of pregnancy, including implantation defects, disorganization of trophoblast cells, fewer uterine natural killer (uNK) cells, and impairment of spiral artery remodeling. In our microarray analysis, genes encoding proteins involved in cytokine-cytokine receptor interactions and NK cell-mediated cytotoxicity were down-regulated in cKO decidua compared with control decidua. Flow cytometry confirmed a 10-fold decrease in uNK cells in cKO versus control decidua. According to these data, we hypothesize that TGF-β acts on decidual cells via ALK5 to induce expression of other growth factors and cytokines, which are key regulators in luminal epithelium proliferation, trophoblast development, and uNK maturation during pregnancy. Our findings not only generate a mouse model to study TGF-β signaling in female reproduction but also shed light on the pathogenesis of many pregnancy complications in human, such as recurrent spontaneous abortion, preeclampsia, and intrauterine growth restriction.
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33
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Fu J, Wang D, Yu Y, Heinrichs J, Wu Y, Schutt S, Kaosaard K, Liu C, Haarberg K, Bastian D, McDonald DG, Anasetti C, Yu XZ. T-bet is critical for the development of acute graft-versus-host disease through controlling T cell differentiation and function. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:388-97. [PMID: 25404360 PMCID: PMC4314960 DOI: 10.4049/jimmunol.1401618] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
T-bet is a master regulator for IFN-γ production and Th1 differentiation. We evaluated the roles of T-bet and IFN-γ in T cell responses in acute graft-versus-host disease (GVHD) and found that T-bet(-/-) T cells induced significantly less GVHD compared with wild-type or IFN-γ(-/-) counterparts in both MHC-mismatched and MHC-matched but minor histocompatibility Ag-mismatched models driven by CD4 T cells. T-bet(-/-), but not IFN-γ(-/-), CD4 T cells had a markedly reduced ability to cause tissue damage in liver and gut. This distinct outcome is reflected by the differential gene expression on donor CD4 T cells deficient for T-bet or IFN-γ. At mRNA and protein levels, we defined several T-bet-dependent molecules that may account for the impaired ability of T-bet(-/-) T cells to migrate into target organs and to produce Th1-related cytokines. Moreover, these molecules were independent of either endogenous IFN-γ, such as CXCR3 and programmed death-1, or systematic IFN-γ, such as NKG2D, I-A(b), and granzyme B. Although both T-bet(-/-) and IFN-γ(-/-) CD4 T cells are prone to differentiate into Th17 cells, polarized Th17 cells deficient for T-bet but not for IFN-γ had a significantly reduced ability to cause GVHD. Finally, T-bet(-/-) T cells had a compromised graft-versus-leukemia effect, which could be essentially reversed by neutralization of IL-17 in the recipients. We conclude that T-bet is required for Th1 differentiation and migration, as well as for optimal function of Th17 cells. Thus, targeting T-bet or regulating its downstream effectors independent of IFN-γ may be a promising strategy to control GVHD in the clinic.
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Affiliation(s)
- Jianing Fu
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33612; Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612; Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425
| | - Dapeng Wang
- Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Yu Yu
- Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Jessica Heinrichs
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425; Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612
| | - Yongxia Wu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425
| | - Steven Schutt
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425
| | - Kane Kaosaard
- Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611
| | - Kelley Haarberg
- Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - David Bastian
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425
| | - Daniel G McDonald
- Department of Radiation Oncology, Medical University of South Carolina, Charleston, SC 29425; and
| | - Claudio Anasetti
- Immunology, Blood and Marrow Transplantation, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Xue-Zhong Yu
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425; Department of Medicine, Medical University of South Carolina, Charleston, SC 29425
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34
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Effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. PLoS One 2013; 8:e72302. [PMID: 23991086 PMCID: PMC3749122 DOI: 10.1371/journal.pone.0072302] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing. Remarkably, a subtle difference in methionine supplementation in maternal diet was sufficient to cause significant changes in the transcriptome of the embryos. A total of 276 genes out of 10,662 showed differential expression between treatments (FDR <0.10). Interestingly, several of the most significant genes are related to embryonic development (e.g., VIM, IFI6, BCL2A1, and TBX15) and immune response (e.g., NKG7, TYROBP, SLAMF7, LCP1, and BLA-DQB). Likewise, gene set enrichment analysis revealed that several Gene Ontology terms, InterPro entries, and KEGG pathways were enriched (FDR <0.05) with differentially expressed genes involved in embryo development and immune system. The expression of most genes was decreased by maternal methionine supplementation, consistent with reduced transcription of genes with increased methylation of specific genes by increased methionine. Overall, our findings provide evidence that supplementing methionine to dams prior to conception and during the preimplantation period can modulate gene expression in bovine blastocysts. The ramifications of the observed gene expression changes for subsequent development of the pregnancy and physiology of the offspring warrant further investigation in future studies.
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35
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Morscio J, Dierickx D, Ferreiro JF, Herreman A, Van Loo P, Bittoun E, Verhoef G, Matthys P, Cools J, Wlodarska I, De Wolf-Peeters C, Sagaert X, Tousseyn T. Gene expression profiling reveals clear differences between EBV-positive and EBV-negative posttransplant lymphoproliferative disorders. Am J Transplant 2013; 13:1305-16. [PMID: 23489474 DOI: 10.1111/ajt.12196] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/03/2013] [Accepted: 01/22/2013] [Indexed: 01/25/2023]
Abstract
Posttransplant patients are at risk of developing a potentially life-threatening posttransplantation lymphoproliferative disorder (PTLD), most often of diffuse large B cell lymphoma (DLBCL) morphology and associated with Epstein-Barr Virus (EBV) infection. The aim of this study was to characterize the clinicopathological and molecular-genetic characteristics of posttransplant DLBCL and to elucidate whether EBV(+) and EBV(-) posttransplant DLBCL are biologically different. We performed gene expression profiling studies on 48 DLBCL of which 33 arose posttransplantation (PT-DLBCL; 72% EBV+) and 15 in immunocompetent hosts (IC-DLBCL; none EBV+). Unsupervised hierarchical analysis showed clustering of samples related to EBV-status rather than immune status. Except for decreased T cell signaling these cases were inseparable from EBV(-) IC-DLBCL. In contrast, a viral response signature clearly segregated EBV(+) PT-DLBCL from EBV(-) PT-DLBCL and IC-DLBCL cases that were intermixed. The broad EBV latency profile (LMP1+/EBNA2+) was expressed in 59% of EBV(+) PT-DLBCL and associated with a more elaborate inflammatory response compared to intermediate latency (LMP1+/EBNA2-). Inference analysis revealed a role for innate and tolerogenic immune responses (including VSIG4 and IDO1) in EBV(+) PT-DLBCL. In conclusion we can state that the EBV signature is the most determining factor in the pathogenesis of EBV(+) PT-DLBCL.
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Affiliation(s)
- J Morscio
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
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36
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Ashokkumar C, Ningappa M, Ranganathan S, Higgs BW, Sun Q, Schmitt L, Snyder S, Dobberstein J, Branca M, Jaffe R, Zeevi A, Squires R, Alissa F, Shneider B, Soltys K, Bond G, Abu-Elmagd K, Humar A, Mazariegos G, Hakonarson H, Sindhi R. Increased expression of peripheral blood leukocyte genes implicate CD14+ tissue macrophages in cellular intestine allograft rejection. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:1929-38. [PMID: 21854741 DOI: 10.1016/j.ajpath.2011.06.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 06/14/2011] [Accepted: 06/28/2011] [Indexed: 12/27/2022]
Abstract
Recurrent rejection shortens graft survival after intestinal transplantation (ITx) in children, most of whom also experience early acute cellular rejection (rejectors). To elucidate mechanisms common to early and recurrent rejection, we used a test cohort of 20 recipients to test the hypothesis that candidate peripheral blood leukocyte genes that trigger rejection episodes would be evident late after ITx during quiescent periods in genome-wide gene expression analysis and would achieve quantitative real-time PCR replication pre-ITx (another quiescent period) and in the early post-ITx period during first rejection episodes. Eight genes were significantly up-regulated among rejectors in the late post-ITx and pre-ITx periods, compared with nonrejectors: TBX21, CCL5, GNLY, SLAMF7, TGFBR3, NKG7, SYNE1, and GK5. Only CCL5 was also up-regulated in the early post-ITx period. Among resting peripheral blood leukocyte subsets in randomly sampled nonrejectors, CD14(+) monocytes expressed the CCL5 protein maximally. Compared with nonrejectors, rejectors demonstrated higher counts of both circulating CCL5(+)CD14(+) monocytes and intragraft CD14(+) monocyte-derived macrophages in immunohistochemistry of postperfusion and early post-ITx biopsies from the test and an independent replication cohort. Donor-specific alloreactivity measured with CD154(+) T-cytotoxic memory cells correlated with the CCL5 gene and intragraft CD14(+) monocyte-derived macrophages at graft reperfusion and early post-ITx. CCL5 gene up-regulation and CD14(+) macrophages likely prime cellular ITx rejection. Infiltration of reperfused intestine allografts with CD14(+) macrophages may predict rejection events.
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Affiliation(s)
- Chethan Ashokkumar
- Hillman Center for Pediatric Transplantation, Children's Hospital of Pittsburgh of University of Pennsylvania Medical Center, Pittsburgh, Pennsylvania, USA
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37
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Sugimoto N, Oida T, Hirota K, Nakamura K, Nomura T, Uchiyama T, Sakaguchi S. Foxp3-dependent and -independent molecules specific for CD25+CD4+ natural regulatory T cells revealed by DNA microarray analysis. Int Immunol 2006; 18:1197-209. [PMID: 16772372 DOI: 10.1093/intimm/dxl060] [Citation(s) in RCA: 274] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Naturally occurring CD25(+)CD4(+) regulatory T cells (Tregs) actively engage in the maintenance of immunologic self-tolerance and immunoregulation. They specifically express the transcription factor Forkhead box P3 (Foxp3) as a master control molecule for their development and function. Although several cell-surface molecules have been reported as Treg-specific markers, such as CD25, glucocorticoid-induced TNFR family-related gene/protein and CTL-associated molecule-4, they are also expressed on activated T cells derived from CD25(-)CD4(+) naive T cells. To identify Treg-specific molecules controlled by Foxp3, we performed DNA microarray analysis by comparing the following pairs of cell populations: fresh CD25(+)CD4(+) T cells versus fresh CD25(-)CD4(+) T cells, activated CD25(+)CD4(+) T cells versus activated CD25(-)CD4(+) T cells and retrovirally Foxp3-transduced CD25(-)CD4(+) T cells versus mock-transduced CD25(-)CD4(+) T cells. We found that the Gpr83, Ecm1, Cmtm7, Nkg7, Socs2 and glutaredoxin genes are predominantly transcribed in fresh and activated natural Treg as well as in Foxp3-transduced cells, while insulin-like 7, galectin-1, granzyme B and helios genes are natural Treg specific but Foxp3 independent. G protein-coupled receptor 83 (Gpr83) expression on the cell surface of natural Treg was confirmed by staining with Gpr83-specific antibody. Retroviral transduction of either group of genes in CD25(-)CD4(+) T cells failed to confer in vitro suppressive activity. Thus, there are several genes that are expressed in a highly Treg-specific fashion. Some of these genes are controlled by Foxp3, and others are not. These genes, in particular, Gpr83, Ecm1 and Helios, could potentially be used as specific markers for natural Treg.
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Affiliation(s)
- Naoshi Sugimoto
- Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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38
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Shin HJ, Park KK, Lee BH, Moon CK, Lee MO. Identification of genes that are induced after cadmium exposure by suppression subtractive hybridization. Toxicology 2003; 191:121-31. [PMID: 12965115 DOI: 10.1016/s0300-483x(03)00210-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The heavy metal cadmium is a xenobiotic toxicant of environmental and occupational concern and it has been classified as a human carcinogen. Inhalation of cadmium has been implicated in the development of emphysema and pulmonary fibrosis, but, the detailed mechanism by which cadmium induces adverse biological effects is not yet known. Therefore, we undertook the investigation of genes that are induced after cadmium exposure to illustrate the mechanism of cadmium toxicity. For this purpose, we employed the polymerase chain reaction (PCR)-based suppression subtractive hybridization (SSH) technique. We identified 29 different cadmium-inducible genes in human peripheral blood mononuclear cells (PBMCs), such as macrophage migration inhibitory factor (MIF), lysophosphatidic acid acyltransferase-alpha, enolase-1alpha, VEGF, Bax, and neuron-derived orphan receptor-1 (Nor-1), which are known to be associated with inflammation, cell survival, and apoptosis. Induction of these genes by cadmium treatment was further confirmed by semi-quantitative reverse-transcription PCR. Further, we found that these genes were also induced after cadmium exposure in normal human lung fibroblast cell line, WI-38, suggesting potential use of this induction profile to monitor cadmium toxicity in the lung.
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Affiliation(s)
- Hye-Jin Shin
- Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-dong, Kwangjin-gu, 140-747, Seoul, South Korea.
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39
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Diaz LS, Stone MR, Mackewicz CE, Levy JA. Differential gene expression in CD8+ cells exhibiting noncytotoxic anti-HIV activity. Virology 2003; 311:400-9. [PMID: 12842629 DOI: 10.1016/s0042-6822(03)00177-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Suppressive subtractive hybridization with polymerase chain reaction was used to identify the gene(s) associated with the CD8+ cell noncytotoxic anti-HIV response. The differences in gene expression profiles of CD8+ cells from a pair of discordant HIV-positive identical twins were studied. Forty-nine genes were identified as expressed at higher levels in the CD8+ cells from the infected twin that inhibited viral replication. The differential expression of these genes was then evaluated using Q-PCR to determine if this gene expression pattern is evident in CD8+ cells from other HIV-positive subjects showing this antiviral activity. Three genes, including one unknown, were found to have significantly increased expression in antiviral CD8+ cells.
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Affiliation(s)
- Leyla S Diaz
- Department of Medicine, Division of Hematology/Oncology, University of California, San Francisco, CA 94143-1270, USA
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40
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Medley QG, Kedersha N, O'Brien S, Tian Q, Schlossman SF, Streuli M, Anderson P. Characterization of GMP-17, a granule membrane protein that moves to the plasma membrane of natural killer cells following target cell recognition. Proc Natl Acad Sci U S A 1996; 93:685-9. [PMID: 8570616 PMCID: PMC40113 DOI: 10.1073/pnas.93.2.685] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cytotoxic lymphocytes are characterized by their inclusion of cytoplasmic granules that fuse with the plasma membrane following target cell recognition. We previously identified a cytotoxic granule membrane protein designated p15-TIA-1 that is immunochemically related to an RNA-recognition motif (RRM)-type RNA-binding protein designated p40-TIA-1. Although it was suggested that p15-TIA-1 might be derived from p40-T1A-1 by proteolysis, N-terminal amino acid sequencing of p15-TIA-1 immunoaffinity purified from a natural killer (NK) cell line by using monoclonal antibody (mAb) 2G9 revealed that p15-T1A-1 is identical to the deduced amino acid sequence of NKG7 and GIG-1, cDNAs isolated from NK cells and granulocyte-colony-stimulating factor-treated mononuclear cells, respectively. Epitope mapping revealed that mAb 2G9 recognizes the C terminus of p15-T1A-1 and p40-T1A-1. The deduced amino acid sequence of p15-T1A-1/NKG7/GIG-1 predicts that the protein possesses four transmembrane domains, and immuno-electron microscopy localizes the endogenous protein to the membranes of cytotoxic granules in NK cells. Given its subcellular localization, we propose to rename-this protein GMP-17, for granule membrane protein of 17 kDa. Immunofluorescence microscopy of freshly isolated NK cells confirms this granular localization. Target cell-induced NK cell degranulation results in translocation of GMP-17 from granules to the plasma membrane, suggesting a possible role for GMP-17 in regulating the effector function of lymphocytes and neutrophils.
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Affiliation(s)
- Q G Medley
- Division of Tumor Immunology Dana Farber Cancer Institute, Boston, MA 02115, USA
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