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Li S, Li H, Xu Y, Ning W, Hu S, Wei S, Song H, Sun J, Ziebolz D, Schmalz G, Hu X, Liu M. Implications of Human Antimicrobial Peptide Defensin Beta-1 in Clinical Oral Squamous Cell Carcinoma Patients via an Integrated Bioinformatics Approach. Comput Math Methods Med 2022; 2022:2203615. [PMID: 35222682 PMCID: PMC8881164 DOI: 10.1155/2022/2203615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND The human antimicrobial peptide defensin beta 1 (DEFB1) has been found to play antimicrobial and anti-inflammatory roles in oral diseases; however, its tumor-regulating role in oral squamous cell carcinoma (OSCC) has not yet been researched by using an integrative bioinformatics approach. OBJECTIVE To investigate the regulating mechanisms of the DEFB1 gene in OSCC in terms of its expression patterns, prognostic values, biological functions, and implication for tumor immunity. METHODS The DEFB1 gene expression pattern and regulatory involvement in OSCC were investigated using publically accessible data from TCGA database. R software tools and public web servers were utilized to conduct statistical analysis of data from cancer and noncancerous samples. RESULTS DEFB1 was found to be significantly downregulated in OSCC tumor samples compared with healthy control oral samples. The DEFB1 gene was found associated with the prognostic outcomes of OSCC, and its upregulation represented better survival outcome. Gene set enrichment analysis (GSEA) results showed that DEFB1-significantly correlated genes were mainly enriched in four signaling pathways mediating the antitumor role of DEFB1 in OSCC, including extracellular matrix-related pathway, RTK/PI3K/AKT/mTOR pathway, keratinization, and cytokine-related pathway. The gene-gene interaction network showed that DEFB1 was closely correlated with several genes, for example, CCR6 (C-C motif chemokine receptor 6), CXCL1 (C-X-C motif chemokine ligand 1), MAP4K2 (mitogen-activated protein kinase kinase kinase kinase 2), PTGER3 (prostaglandin E receptor 3), and MMP7 (matrix metallopeptidase 7). Moreover, DEFB1 was found to be involved in the tumor immunity of OSCC by regulating the function of tumor macrophage cells, mast cells, T cells, and NK cells. CONCLUSIONS Given the dysregulation, prognostic value, and tumor progression-related biological pathway alteration, indicating the tumor immune-modulatory role of DEFB1 in OSCC, the DEFB1 gene should be regarded as a potential therapeutic target for treating oral cancer.
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Affiliation(s)
- Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Hu Li
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
| | - Wanchen Ning
- Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Shaonan Hu
- Innovation Center Computer Assisted Surgery (ICCAS), Leipzig University, Semmelweisstraße 14, Leipzig 04103, Germany
| | - Shanzun Wei
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610000, China
| | - Hongning Song
- Department of Stomatology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
| | - Jianghe Sun
- Department of Stomatology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, 04103 Leipzig, Germany
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, 04103 Leipzig, Germany
| | - Xianda Hu
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, 218 Anwaixiaoguanbeili Street, Chaoyang, Beijing 100029, China
| | - Min Liu
- Department of Stomatology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province 271000, China
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Tan W, Peng S, Li Z, Zhang R, Xiao Y, Chen X, Zhu J, Li B, Lv X. Identification of Therapeutic Targets and Prognostic Biomarkers among Genes from the Mediator Complex Family in the Hepatocellular Carcinoma Tumour-Immune Microenvironment. Comput Math Methods Med 2022; 2022:2021613. [PMID: 35069777 PMCID: PMC8776440 DOI: 10.1155/2022/2021613] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is predominant among all types of primary liver cancers characterised by high morbidity and mortality. Genes in the mediator complex (MED) family are engaged in the tumour-immune microenvironment and function as regulatory hubs mediating carcinogenesis and progression across diverse cancer types. Whereas research studies have been conducted to examine the mechanisms in several cancers, studies that systematically focused on the therapeutic and prognostic values of MED in patients with HCC are limited. METHODS The online databases ONCOMINE, GEPIA, UALCAN, GeneMANIA, cBioPortal, OmicStudio, STING, Metascape, and TIMER were used in this study. RESULTS The transcriptional levels of all members of the MED family in HCC presented an aberrant high expression pattern. Significant correlations were found between the MED1, MED6, MED8, MED10, MED12, MED15, MED17, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, and MED27 expression levels and the pathological stage in the patients with HCC. The patients with high expression levels of MED6, MED8, MED10, MED17, MED19, MED20, MED21, MED22, MED24, and MED25 were significantly associated with poor prognosis. Functional enrichment analysis revealed that the members of the MED family were mainly enriched in the nucleobase-containing compound catabolic process, regulation of chromosome organisation, and transcriptional regulation by TP53. Significant correlations were found between the MED6, MED8, MED10, MED17, MED19, MED20, MED21, MED22, MED24, and MED25 expression levels and all types of immune cells (B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells). B cells and MED8 were independent predictors of overall survival. We found significant correlations between the somatic copy number alterations of the MED6, MED8, MED10, MED20, MED21, MED22, MED24, and MED25 molecules and the abundance of immune infiltrates. CONCLUSIONS Our study delineated a thorough landscape to investigate the therapeutic and prognostic potentials of the MED family for HCC cases, which yielded promising results for the development of immunotherapeutic drugs and construction of a prognostic stratification model.
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Affiliation(s)
- Wei Tan
- Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Shuai Peng
- Department of Radiology, The First Affiliated Hospital of Guangxi Medical University, Nanning City, Guangxi Zhuang Autonomous Region 530021, China
| | - Zhuokai Li
- Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Ruiqian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Yangrui Xiao
- Department of Radiology, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Xiao Chen
- Department of Radiology, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Jinde Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Bingrong Li
- Department of Radiology, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
| | - Xinliang Lv
- Department of Hepatobiliary and Pancreatic Surgery, Lishui Central Hospital, Fifth Affiliated Hospital of Wenzhou Medical College, Lishui City, Zhejiang Province 323000, China
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Zandhuis ND, Nicolet BP, Wolkers MC. RNA-Binding Protein Expression Alters Upon Differentiation of Human B Cells and T Cells. Front Immunol 2021; 12:717324. [PMID: 34867946 PMCID: PMC8635512 DOI: 10.3389/fimmu.2021.717324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/27/2021] [Indexed: 12/25/2022] Open
Abstract
B cells and T cells are key players in the defence against infections and malignancies. To exert their function, B cells and T cells differentiate into effector and memory cells. Tight regulation of these differentiation processes is key to prevent their malfunction, which can result in life-threatening disease. Lymphocyte differentiation relies on the appropriate timing and dosage of regulatory molecules, and post-transcriptional gene regulation (PTR) is a key player herein. PTR includes the regulation through RNA-binding proteins (RBPs), which control the fate of RNA and its translation into proteins. To date, a comprehensive overview of the RBP expression throughout lymphocyte differentiation is lacking. Using transcriptome and proteome analyses, we here catalogued the RBP expression for human B cells and T cells. We observed that even though the overall RBP expression is conserved, the relative RBP expression is distinct between B cells and T cells. Differentiation into effector and memory cells alters the RBP expression, resulting into preferential expression of different classes of RBPs. For instance, whereas naive T cells express high levels of translation-regulating RBPs, effector T cells preferentially express RBPs that modulate mRNA stability. Lastly, we found that cytotoxic CD8+ and CD4+ T cells express a common RBP repertoire. Combined, our study reveals a cell type-specific and differentiation-dependent RBP expression landscape in human lymphocytes, which will help unravel the role of RBPs in lymphocyte function.
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Affiliation(s)
- Nordin D. Zandhuis
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Benoit P. Nicolet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Monika C. Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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Wang J, Cheng Y, Ma Y, Wu R, Xu Y, Yang S, Wang Y, Lin Y. Cytokines and chemokines expression pattern in herpes simplex virus type-1 encephalitis. Neurosci Lett 2021; 763:136170. [PMID: 34391869 DOI: 10.1016/j.neulet.2021.136170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 01/20/2023]
Abstract
To explore the differently expressed cytokines and chemokines to understand the pathways that lead to herpes simplex encephalitis (HSE). Mice in the experimental group were inoculated intracranially with HSV-1. A high-throughput cytokine chip assay was employed to assess the expression of cytokines/chemokines in the mice brain. GO, KEGG, and PPIs analyses were used to investigate the biological process (BP), pathways and interaction network of the differently expressed proteins (DEPs) in HSE. 13 DEPs and various proteins-related signal pathways were identified in HSE, including three new factors (IL-1α, MIP-1γ, and sTNF RI). The proteins were mainly implicated in leukocyte activation and chemotaxis. Additionally, the DEPs constituted a pivotal protein interaction network where IL-6 might be a mediator. 13 DEPs and a series of related signal pathways were associated with the pathophysiological mechanisms responsible for HSE. IL-6 might be a key mediator in the inflammatory responses to the disease.
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Affiliation(s)
- Jiaojiao Wang
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yi Cheng
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yueting Ma
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Rihong Wu
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yu Xu
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Shuling Yang
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yongxia Wang
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China.
| | - Yingzi Lin
- School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, China.
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Zhang F, Chen S, Yang T, Ao H, Zhai L, Li Q, Xing K, Liu Y, Liu H, Yu Y, Wang C. Novel DNA methylation markers of PRRSV-specific antibodies and their intergenerational transmission from pregnant sows to piglets. Gene 2021; 801:145831. [PMID: 34274485 DOI: 10.1016/j.gene.2021.145831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 01/11/2023]
Abstract
The main strategy for preventing porcine reproductive and respiratory syndrome (PRRS) is vaccination. However, current commercial porcine reproductive and respiratory syndrome virus (PRRSV) vaccines have limited effectiveness and may even cause infections in pigs. The identification of stable molecular markers associated with immune responses to PRRSV vaccination in pigs provides a new approach for PRRS prevention. DNA methylation, the most stable epigenetic molecular marker related to PRRSV vaccination, has not been investigated. In the current research, we used whole genome bisulfite sequencing (WGBS) to investigate DNA methylation in pregnant sows that received PRRSV vaccination and their piglets with high and low PRRSV-specific antibody levels. By performing methylation data analysis and basing on our previous transcriptomic studies, we identified several differentially methylated genes (DMGs) that are involved in the pathways of inflammatory and immune responses. Among the DMGs, ISG15, MX1, SERPINE1, GNG11 and IFIT3 were common hub genes in the two generations. MX1 and GNG11 were located in quantitative trait loci related with PRRSV antibody titer and PRRSV susceptibility, respectively. These results suggest that PRRSV vaccination in sows induces DNA methylation changes in genes and DNA methylation changes occur through intergenerational transmission. The novel DNA methylation markers and target genes observed in our study provide new insights into the molecular mechanisms of immune responses to PRRSV vaccination across two pig generations.
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Affiliation(s)
- Fengxia Zhang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China; Innovation Team of Pig Health Breeding, Institute of Animal Husbandry and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Siqian Chen
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Ting Yang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hong Ao
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Zhai
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Qianjun Li
- Innovation Team of Pig Health Breeding, Institute of Animal Husbandry and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yibing Liu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Huatao Liu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.
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Zheng D, Wang J, Li G, Sun Y, Deng Q, Li M, Song K, Zhao Z. Preliminary therapeutic and mechanistic evaluation of S-allylmercapto-N-acetylcysteine in the treatment of pulmonary emphysema. Int Immunopharmacol 2021; 98:107913. [PMID: 34218218 DOI: 10.1016/j.intimp.2021.107913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/10/2021] [Accepted: 06/20/2021] [Indexed: 12/24/2022]
Abstract
The objective of this work was to study the effects and mechanisms of S-allylmercapto-N-acetylcysteine (ASSNAC) in the treatment of pulmonary emphysema based on network pharmacology analysis and other techniques. Firstly, the potential targets associated with ASSNAC and COPD were integrated using public databases. Then, a protein-protein interaction network was constructed using String database and Cytoscape software. The Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed on DAVID platform. The molecular docking of ASSNAC with some key disease targets was implemented on the SwissDock platform. To verify the results of the network pharmacology, a pulmonary emphysema mice model was established and treated with ASSNAC. Besides, the expressions of the predicted targets were detected by immunohistochemistry, Western blot analysis or enzyme-linked immunosorbent assay. Results showed that 33 overlapping targets are achieved, including CXCL8, ICAM1, MAP2K1, PTGS2, ACE and so on. The critical pathways of ASSNAC against COPD involved arachidonic acid metabolism, chemokine pathway, MAPK pathway, renin-angiotensin system, and others. Pharmacodynamic experiments demonstrated that ASSNAC decreased the pulmonary emphysema and inflammation in the pulmonary emphysema mice. Therefore, these results confirm the perspective of network pharmacology in the target verification, and indicate the treatment potential of ASSNAC against COPD.
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Affiliation(s)
- Dandan Zheng
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Jinglong Wang
- College of Food Sciences and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, PR China
| | - Genju Li
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Yueyue Sun
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Qi Deng
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Muhan Li
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Kaili Song
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Zhongxi Zhao
- Department of Pharmaceutics, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China; Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, PR China; Pediatric Pharmaceutical Engineering Laboratory of Shandong Province, Shandong Dyne Marine Biopharmaceutical Company Limited, Rongcheng, Shandong 264300, PR China; Chemical Immunopharmaceutical Engineering Laboratory of Shandong Province, Shandong Xili Pharmaceutical Company Limited, Heze, Shandong 274300, PR China.
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Yu L, Cao S, Li J, Han B, Zhong H, Zhong R. Prognostic value and immune infiltration of a novel stromal/immune score-related P2RY12 in lung adenocarcinoma microenvironment. Int Immunopharmacol 2021; 98:107734. [PMID: 34175738 DOI: 10.1016/j.intimp.2021.107734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Increasing evidence highlights the clinical implications of P2RY12 that belongs to the family of G-protein coupled receptors in carcinogenesis. Here, this study was designed to explore the associations between P2RY12 and tumor immune microenvironment of lung adenocarcinoma (LUAD). METHODS Based on 352 LUAD samples from The Cancer Genome Atlas (TCGA), stromal and immune scores of each sample were estimated by ESTIMATE algorithm. Differential expression analysis was presented between stromal/immune high- and low-score groups. Protein-protein interaction (PPI) was then constructed by STRING database. Univariate and multivariate Cox regression analysis was utilized to screen prognosis-related factors. Co-expressed genes of P2RY12 were analyzed, followed by functional enrichment analysis. Furthermore, the correlation between P2RY12 and immune cell infiltrations was estimated using the TIMER database. P2RY12 expression was validated between 37 pairs of LUAD and normal tissues using RT-qPCR and immunohistochemistry. After overexpressing P2RY12, the proliferation and migration of A549 cells was detected by CCK-8 and scratch test. RESULTS 145 up- and 102 down-regulated stromal- and immune-related mRNAs were identified for LUAD. Based on 145 up-regulated mRNAs, a PPI network was conducted, consisting of 95 nodes and 210 relationship pairs. Ten hub genes were then identified. Among them, CCR8, CNR2, CXCR5, GPR18, GPR31 and P2RY12 were in association with overall survival of patients with LUAD. After adjusting other variables, P2RY12 expression was an independent prognostic factor for LUAD. 288 co-expressed genes of P2RY12 were determined and these co-expressed genes were primarily involved in immune-related biological processes or pathways. Moreover, P2RY12 was significantly correlated with M2 macrophage and dendritic cell infiltration. After validation, P2RY12 expression was significantly decreased in LUAD than normal tissues. Its overexpression distinctly suppressed proliferation and migration of A549 cells. CONCLUSION Our findings suggest that P2RY12 is an immune infiltration-related prognostic marker for LUAD.
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Affiliation(s)
- Lian Yu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Shuhui Cao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Jingwen Li
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Hua Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.
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Zhao N, Jia L, He X, Zhang B. Proteomics of mucosal exosomes of Cynoglossus semilaevis altered when infected by Vibrio harveyi. Dev Comp Immunol 2021; 119:104045. [PMID: 33582105 DOI: 10.1016/j.dci.2021.104045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The cargo of exosomes contains proteins with various functions, which might be promising biomarkers for disease diagnosis and prognosis. To explore the impact of the Vibrio harveyi pathogen on Cynoglossus semilaevis from a different perspective and develop promising biomarkers for infection, the exosomes from epidermal mucus of healthy controls(EC)and sick fish(ES)were extracted and identified, coupled with proteomic screening through iTRAQ followed with LC-MS/MS. 1531 credible proteins were obtained relating to structural, metabolic and immunological functions. 359 different expressed proteins (DEPs) (FC > 2 or FC < 0.5) were found, with 161 up-regulated and 198 down-regulated in ES. Based on the database of C. semilaevis on Uniprot, 71 proteins were characterized as concrete names, including 19 up-regulated proteins and 52 down-regulated proteins, and were selected as subjects for further studies. Ferritin, Toll-like receptor 5S protein and Calcium-transporting ATPase were upregulated, while Histone H2B and Eukaryotic translation initiation factor 5A were downregulated, consistent with the expression levels of related mRNAs in skin tissue verified by qRT-PCR. The integrated analysis between miRomics and proteomics also provided possible regulatory relationships mediated by mucous exosomes during infection. The signature proteins in mucosal exosomes could make sense in the explanation of the infection defending mechanism and the development of biomarkers which can differentiate diseased and healthy C. semilaevis individuals.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin, China.
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Yingjuan W, Li Z, Wei C, Xiaoyuan W. Identification of prognostic genes and construction of a novel gene signature in the skin melanoma based on the tumor microenvironment. Medicine (Baltimore) 2021; 100:e26017. [PMID: 34032721 PMCID: PMC8154473 DOI: 10.1097/md.0000000000026017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
Skin melanoma remains a highly prevalent and yet deadly form of cancer, with the exact degree of melanoma-associated mortality being strongly dependent upon the local tumor microenvironment. The exact composition of stromal and immune cells within this microenvironmental region has the potential to profoundly impact melanoma progression and prognosis. As such, the present study was designed with the goal of clarifying the predictive relevance of stromal and immune cell-related genes in melanoma patients through comprehensive bioinformatics analyses. We therefore analyzed melanoma sample gene expression within The Cancer Genome Atlas database and employed the ESTIMATE algorithm as a means of calculating both stromal and immune scores that were in turn used for identifying differentially expressed genes (DEGs). Subsequently, univariate analyses were used to detect DEGs associated with melanoma patient survival, and through additional functional enrichment analyses, we determined that these survival-related DEGs are largely related to inflammatory and immune responses. A prognostic signature comprised of 10 genes (IL15, CCL8, CLIC2, SAMD9L, TLR2, HLA.DQB1, IGHV1-18, RARRES3, GBP4, APOBEC3G) was generated. This 10-gene signature effectively separated melanoma patients into low- and high-risk groups based upon their survival. These low- and high-risk groups also exhibited distinct immune statuses and differing degrees of immune cell infiltration. In conclusion, our results offer novel insights into a number of microenvironment-associated genes that impact survival outcomes in melanoma patients, potentially highlighting these genes as viable therapeutic targets.
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Luo L, Zhou H, Su H. Identification of 4-genes model in papillary renal cell tumor microenvironment based on comprehensive analysis. BMC Cancer 2021; 21:553. [PMID: 33993869 PMCID: PMC8127234 DOI: 10.1186/s12885-021-08319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/04/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The tumor microenvironment acts a pivotal part in the occurrence and development of tumor. However, there are few studies on the microenvironment of papillary renal cell carcinoma (PRCC). Our study aims to explore prognostic genes related to tumor microenvironment in PRCC. METHODS PRCC expression profiles and clinical data were extracted from The Cancer Gene Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Immune/stromal scores were performed utilizing the ESTIMATE algorithm. Three hundred fifty-seven samples were split into two groups on the basis of median immune/stromal score, and comparison of gene expression was conducted. Intersect genes were obtained by Venn diagrams. Hub genes were selected through protein-protein interaction (PPI) network construction, and relevant functional analysis was conducted by DAVID. We used Kaplan-Meier analysis to identify the correlations between genes and overall survival (OS) and progression-free survival (PFS). Univariate and multivariate cox regression analysis were employed to construct survival model. Cibersort was used to predict the immune cell composition of high and low risk group. Combined nomograms were built to predict PRCC prognosis. Immune properties of PRCC were validated by The Cancer Immunome Atlas (TCIA). RESULTS We found immune/stromal score was correlated with T pathological stages and PRCC subtypes. Nine hundred eighty-nine differentially expressed genes (DEGs) and 1169 DEGs were identified respectively on the basis of immune and stromal score. Venn diagrams indicated that 763 co-upregulated genes and 4 co-downregulated genes were identified. Kaplan-Meier analysis revealed that 120 genes were involved in tumor prognosis. Then PPI network analysis identified 22 hub genes, and four of which were significantly related to OS in patients with PRCC confirmed by cox regression analysis. Finally, we constructed a prognostic nomogram which combined with influence factors. CONCLUSIONS Four tumor microenvironment-related genes (CD79A, CXCL13, IL6 and CCL19) were identified as biomarkers for PRCC prognosis.
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Affiliation(s)
- Liang Luo
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Tianhe Road 600, Guangzhou, 510630, China.
| | - Haiyi Zhou
- Department of Gynecology of Traditional Chinese Medicine, Shanxi Academy of Traditional Chinese Medicine, Taiyuan, 030000, China
| | - Hao Su
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Tianhe Road 600, Guangzhou, 510630, China
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11
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Dong Q, Chen K, Xie J, Han H, Feng Y, Lu J, Wang W. Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis. Medicine (Baltimore) 2021; 100:e25433. [PMID: 33879674 PMCID: PMC8078291 DOI: 10.1097/md.0000000000025433] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 02/11/2021] [Accepted: 03/13/2021] [Indexed: 01/04/2023] Open
Abstract
ABSTRACT Discoid lupus erythematosus (DLE) is the most common skin manifestation of lupus; however, the molecular mechanisms underlying DLE remain unknown. Therefore, we aimed to identify key differentially expressed genes (DEGs) in discoid lupus skin and investigate their potential pathways.To identify candidate genes involved in the occurrence and development of the disease, we downloaded the microarray datasets GSE52471 and GSE72535 from the Gene Expression Database (GEO). DEGs between discoid lupus skin and normal controls were selected using the GEO2R tool and Venn diagram software (http://bioinformatics.psb.ugent.be/webtools/Venn/). The Database for Annotation, Visualization, and Integrated Discovery (DAVID), Enrichr, and Cytoscape ClueGo were used to analyze the Kyoto Encyclopedia of Gene and Genome pathways and gene ontology. Protein-protein interactions (PPIs) of these DEGs were further assessed using the Search Tool for the Retrieval Interacting Genes version 10.0.Seventy three DEGs were co-expressed in both datasets. DEGs were predominantly upregulated in receptor signaling pathways of the immune response. In the PPI network, 69 upregulated genes were selected. Furthermore, 4 genes (CXCL10, ISG15, IFIH1, and IRF7) were found to be significantly upregulated in the RIG-I-like receptor signaling pathway, from analysis of Enrichr and Cytoscape ClueGo.The results of this study may provide new insights into the potential molecular mechanisms of DLE. However, further experimentation is required to confirm these findings.
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Chen F, Yao C, Feng Y, Yu Y, Guo H, Yan J, Chen J. The identification of neutrophils-mediated mechanisms and potential therapeutic targets for the management of sepsis-induced acute immunosuppression using bioinformatics. Medicine (Baltimore) 2021; 100:e24669. [PMID: 33761636 PMCID: PMC9282053 DOI: 10.1097/md.0000000000024669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/18/2021] [Indexed: 01/05/2023] Open
Abstract
Neutrophils have crucial roles in defensing against infection and adaptive immune responses. This study aimed to investigate the genetic mechanism in neutrophils in response to sepsis-induced immunosuppression.The GSE64457 dataset was downloaded from the Gene Expression Omnibus database and the neutrophil samples (D3-4 and D6-8 post sepsis shock) were assigned into two groups. The differentially expressed genes (DEGs) were identified. The Short Time-series Expression Miner (STEM) clustering analysis was conducted to select the consistently changed DEGs post sepsis shock. The overlapping genes between the DEGs and the deposited genes associated with immune, sepsis, and immunosuppression in the AmiGO2 and Comparative Toxicogenomics Database were screened out and used for the construction of the protein-protein interaction (PPI) network. The expression of several hub genes in sepsis patients was validated using the PCR analysis. The drugs targeting the hub genes and the therapy strategies for sepsis or immunosuppression were reviewed and used to construct the drug-gene-therapy-cell network to illustrate the potential therapeutic roles of the hub genes.A total of 357 overlapping DEGs between the two groups were identified and were used for the STEM clustering analysis, which generated four significant profiles with 195 upregulated (including annexin A1, ANXA1; matrix metallopeptidase 9, MMP9; and interleukin 15, IL-15) and 151 downregulated DEGs (including, AKT1, IFN-related genes, and HLA antigen genes). Then, a total of 34 of the 151 downregulated DEGs and 39 of the 195 upregulated DEGs were shared between the databases and above DEGs, respectively. The PPI network analysis identified a downregulated module including IFN-related genes. The deregulation of DEGs including AKT1 (down), IFN-inducible protein 6 (IFI6, down), IL-15 (up), and ANXA1 (up) was verified in the neutrophils from patients with sepsis-induced immunosuppression as compared with controls. Literature review focusing on the therapy showed that the upregulation of IL-15, IFN, and HLA antigens are the management targets. Besides, the AKT1 gene was targeted by gemcitabine.These findings provided additional clues for understanding the mechanisms of sepsis-induced immunosuppression. The drugs targeting AKT1 might provide now clues for the management strategy of immunosuppression with the intention to prevent neutrophil infiltration.
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Affiliation(s)
- Fang Chen
- Nursing Department, Zhejiang Hospital
| | - Chunyan Yao
- Institute of Health Food, Zhejiang Academy of Medical Sciences
| | - Yue Feng
- Radiology Department, Zhejiang Hospital
| | - Ying Yu
- Institute of Health Food, Zhejiang Academy of Medical Sciences
| | - Honggang Guo
- Zhejiang Experimental Animal Center, Zhejiang Academy of Medical Sciences
| | - Jing Yan
- Intensive Care Unit, Zhejiang Hospital
| | - Jin Chen
- General Practice Department, Zhejiang Hospital, Hangzhou, Zhejiang, China
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13
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Silva-Junior AL, Garcia NP, Cardoso EC, Dias S, Tarragô AM, Fraiji NA, Gomes MS, Amaral LR, Teixeira-Carvalho A, Martins-Filho OA, De Paula EV, Costa AG, Malheiro A. Immunological Hallmarks of Inflammatory Status in Vaso-Occlusive Crisis of Sickle Cell Anemia Patients. Front Immunol 2021; 12:559925. [PMID: 33776989 PMCID: PMC7990896 DOI: 10.3389/fimmu.2021.559925] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Sickle Cell Anemia (SCA) is the most common genetic disorder around the world. The mutation in the β-globin gene is responsible for a higher hemolysis rate, with further involvement of immunological molecules, especially cytokines, chemokines, growth factors, and anaphylatoxins. These molecules are responsible for inducing and attracting immune cells into circulation, thus contributing to increases in leukocytes and other pro-inflammatory mediators, and can culminate in a vaso-occlusive crisis (VOC). This study aimed to characterize the levels of these molecules in SCA patients in different clinical conditions in order to identify potential hallmarks of inflammation in these patients. An analytical prospective study was conducted using the serum of SCA patients in steady-state (StSt; n = 27) and VOC (n = 22), along with 53 healthy donors (HD). Samples from the VOC group were obtained on admission and on discharge, in the convalescent phase (CV). Levels of chemokines (CXCL8, CXCL10, CL2, CLL3, CCL4, CL5, and CCL11), cytokines (IL-1β, IL-1ra, IL-2, IL-4, IL-5, IL-6, IL-7, IL-10, IL-12p70, IL-13, IL-17A, TNF-α, and IFN-γ) and growth factors (VEGF, FGFb, PDGF-BB, GM-CSF, and G-CSF) were measured using a Luminex assay, and anaphylatoxins (C3a, C4a, and C5a) were measured using Cytometric Bead Array. SCA patients in StSt showed a pro-inflammatory profile, and were indicated as being higher producers of CCL2, IL-1β, IL-12p70, IFN-γ, IL-17A, and GM-CSF, while VOC is highlighted by molecules IL-4 and IL-5, but also IL-2, IL-7, PDGF-BB, and G-CSF. PDGF-BB and IL-1ra seemed to be two important hallmarks for the acute-to-chronic stage, due to their significant decrease after crisis inflammation and statistical difference in VOC and CV groups. These molecules show higher levels and a strong correlation with other molecules in VOC. Furthermore, they remain at higher levels even after crisis recovery, which suggest their importance in the role of inflammation during crisis and participation in immune cell adhesion and activation. These results support a relevant role of cytokines, neutrophil and monocytes, since these may act as markers of VOC inflammation in SCA patients.
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Affiliation(s)
- Alexander Leonardo Silva-Junior
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Nadja Pinto Garcia
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Evilázio Cunha Cardoso
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Stephanny Dias
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Andrea Monteiro Tarragô
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
| | - Nelson Abrahim Fraiji
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Matheus Souza Gomes
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Universidade Federal de Uberlândia, Patos de Minas, Brazil
| | - Laurence Rodrigues Amaral
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Universidade Federal de Uberlândia, Patos de Minas, Brazil
| | - Andréa Teixeira-Carvalho
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Grupo Integrado de Pesquisas em Biomarcadores de Diagnóstico e Monitoração, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Olindo Assis Martins-Filho
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Grupo Integrado de Pesquisas em Biomarcadores de Diagnóstico e Monitoração, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Erich Vinicius De Paula
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Escola de Ciências Médicas, Universidade de Campinas, Campinas, Brazil
| | - Allyson Guimarães Costa
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
- Escola de Enfermagem de Manaus, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
| | - Adriana Malheiro
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
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Xu J, Yang Y, Yang Y, Xiong C. Identification of Potential Risk Genes and the Immune Landscape of Idiopathic Pulmonary Arterial Hypertension via Microarray Gene Expression Dataset Reanalysis. Genes (Basel) 2021; 12:genes12010125. [PMID: 33478117 PMCID: PMC7835985 DOI: 10.3390/genes12010125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Gene dysfunction and immune cell infiltration play an essential role in the pathogenesis of idiopathic pulmonary arterial hypertension (IPAH). We aimed to investigate the immune landscape and novel differentially expressed genes (DEGs) of IPAH. In addition, potential druggable molecular targets for IPAH were also explored. In this study, the GSE117261 dataset was reanalyzed to explore the immune landscape and hub DEGs of IPAH. Lasso Cox regression analysis and receiver operating characteristic curve analysis were performed to detect the predictive value of IPAH. Additionally, the underlying drug targets for IPAH treatment were determined by drug-gene analysis. IPAH was significantly associated with the transforming growth factor-β (TGF-β) signaling pathway and Wnt signaling pathway as well as energetic metabolism dysfunction. We identified 31 upregulated and 39 downregulated DEGs in IPAH patients. Six hub genes, namely, SAA1, CCL5, CXCR1, CXCR2, CCR1, and ADORA3, were related to IPAH pathogenesis regardless of sex differences. Prediction model analysis showed that the area under the curve values of the hub DEGs except CXCR2 were all above 0.9 for distinguishing IPAH patients. In addition, the relative proportions of 5 subtypes of immune cells, namely, CD8
+ T cells, CD4
+ memory resting T cells, γ delta T cells, M1 macrophages, and resting mast cells, were significantly upregulated in the IPAH samples, while 6 subtypes of immune cells, namely, CD4
+ naive T cells, resting NK cells, monocytes, M0 macrophages, activated mast cells, and neutrophils, were downregulated. Additionally, a total of 17 intersecting drugs targeting 5 genes, CCL5, CXCR1, CXCR2, CCR1, and ADORA3, were generated as potential druggable molecular targets for IPAH. Our study revealed the underlying correlations between genes and immune cells in IPAH and demonstrated for the first time that SAA1, CCL5, CXCR1, CCR1, and ADORA3 may be novel genetic targets for IPAH.
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Affiliation(s)
- Jing Xu
- Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China;
| | - Yicheng Yang
- Pulmonary Vascular Disease Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China;
| | - Yuejin Yang
- Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China;
- Correspondence: (Y.Y.); (C.X.)
| | - Changming Xiong
- Pulmonary Vascular Disease Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China;
- Correspondence: (Y.Y.); (C.X.)
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15
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Li XP, Zhang J. A live attenuated Edwardsiella tarda vaccine induces immunological expression pattern in Japanese flounder (Paralichthys olivaceus) in the early phase of immunization. Comp Biochem Physiol C Toxicol Pharmacol 2021; 239:108872. [PMID: 32814144 DOI: 10.1016/j.cbpc.2020.108872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/03/2020] [Accepted: 08/09/2020] [Indexed: 12/29/2022]
Abstract
A previous study showed that an attenuated Edwardsiella tarda strain, TXhfq, as a live vaccine could elicit protective immune effects in fish against E. tarda infection. In the current study, in order to clarify the molecular mechanism of fish immune response at the early stage after TXhfq vaccination, RNA-Seq technology was used to compare the transcriptomes of skin, intestine, and spleen between bath-vaccinated and unvaccinated Japanese flounder (Paralichthys olivaceus). An average of 46.6 million clean reads per library was obtained, ~88.04% of which were successfully mapped to the reference genome, and approximately 24,600 genes were detected in each sample. A total of 565, 878, and 1258 differential expression genes (DEGs) were found in skin, intestine, and spleen, respectively, including 1263 up-regulated genes and 1438 down-regulated genes. The DEGs exhibited different characteristics in each tissue. One hundred and sixteen DEGs belonging to six immune related categories were scrutinized, i.e., inflammatory factors, cytokines, complement and coagulation system, mucins, phagocytosis, and antigen processing and presentation. A protein-protein interaction network was constructed to get the interaction network between immune genes during the early stage of immunization. The top six hub genes highly regulated by TXhfq formed complicated interaction relationship with each other, which were involved in immune processes, notably inflammation and phagocytosis. Our results provide valuable information for the understanding of the immune mechanism underlying the protection of live attenuated vaccines in fish.
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Affiliation(s)
- Xue-Peng Li
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; School of Ocean, Yantai University, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; School of Ocean, Yantai University, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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16
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020; 11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex formation, which in turn constitutes the basis for protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes. In this study, we extend co-fractionation and mass spectrometric data analysis to perform quantitative, network-based studies of proteome organization, via the size-exclusion chromatography algorithmic toolkit (SECAT). This framework explicitly accounts for the dynamic nature and rewiring of protein complexes across multiple cell states and samples, thus, elucidating molecular mechanisms that are differentially implemented across different experimental settings. Systematic analysis of multiple datasets shows that SECAT represents a highly scalable and effective methodology to assess condition/state-specific protein-network state. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York NY, USA; Department of Biomedical Informatics, Columbia University, New York NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA.
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Kim KI, Lee UH, Cho M, Jung SH, Min EY, Park JW. Transcriptome analysis based on RNA-seq of common innate immune responses of flounder cells to IHNV, VHSV, and HIRRV. PLoS One 2020; 15:e0239925. [PMID: 32986779 PMCID: PMC7521715 DOI: 10.1371/journal.pone.0239925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Viral hemorrhagic septicemia virus (VHSV) and hirame rhabdovirus (HIRRV) belong to the genus Novirhabdovirus and are the causative agents of a serious disease in cultured flounder. However, infectious hematopoietic necrosis virus (IHNV), a prototype of the genus Novirhabdovirus, does not cause disease in flounder. To determine whether IHNV growth is restricted in flounder cells, we compared the growth of IHNV with that of VHSV and HIRRV in hirame natural embryo (HINAE) cells infected with novirhabdoviruses at 1 multiplicity of infection. Unexpectedly, we found that IHNV grew as well as VHSV and HIRRV. For successful growth in host cells, viruses modulate innate immune responses exerted by virus-infected cells. Our results suggest that IHNV, like VHSV and HIRRV, has evolved the ability to overcome the innate immune response of flounder cells. To determine the innate immune response genes of virus-infected HINAE cells which are commonly modulated by the three novirhabdoviruses, we infected HINAE cells with novirhabdoviruses at multiplicity of infection (MOI) 1 and performed an RNA sequencing-based transcriptome analysis at 24 h post-infection. We discovered ~12,500 unigenes altered by novirhabdovirus infection and found that many of these were involved in multiple cellular pathways. After novirhabdovirus infection, 170 genes involved in the innate immune response were differentially expressed compared to uninfected cells. Among them, 9 genes changed expression by more than 2-fold and were commonly modulated by all three novirhabdoviruses. Interferon regulatory factor 8 (IRF8), C-X-C motif chemokine receptor 1 (CXCR1), Toll/interleukin-1 receptor domain-containing adapter protein (TIRAP), cholesterol 25-hydroxylase (CH25H), C-X-C motif chemokine ligand 11, duplicate 5 (CXCL11.5), and Toll-like receptor 2 (TLR2) were up-regulated, whereas C-C motif chemokine receptor 6a (CCR6a), interleukin-12a (IL12a), and Toll-like receptor 1 (TLR1) were down-regulated. These genes have been reported to be involved in antiviral responses and, thus, their modulation may be critical for the growth of novirhabdovirus in flounder cells. This is the first report to identify innate immune response genes in flounder that are commonly modulated by IHNV, VHSV, and HIRRV. These data will provide new insights into how novirhabdoviruses survive the innate immune response of flounder cells.
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Affiliation(s)
- Kwang Il Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Unn Hwa Lee
- Department of Biological Sciences, University of Ulsan, Ulsan, Korea
| | - Miyoung Cho
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Sung-Hee Jung
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Eun Young Min
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jeong Woo Park
- Department of Biological Sciences, University of Ulsan, Ulsan, Korea
- * E-mail:
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Xuan X, Sun Z, Yu C, Chen J, Chen M, Wang Q, Li L. Network pharmacology-based study of the protective mechanism of conciliatory anti-allergic decoction on asthma. Allergol Immunopathol (Madr) 2020; 48:441-449. [PMID: 32359824 DOI: 10.1016/j.aller.2019.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/09/2019] [Accepted: 12/23/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND This study aimed to explore the underlying anti-asthma pharmacological mechanisms of conciliatory anti-allergic decoction (CAD) with a network pharmacology approach. METHODS Traditional Chinese medicine related databases were utilized to screen the active ingredients of CAD. Targets of CAD for asthma treatment were also identified based on related databases. The protein-protein interaction network, biological function and KEGG pathway enrichment analysis, and molecular docking of the targets were performed. Furthermore, an asthma mouse model experiment involving HE staining, AB-PAS staining, and ELISA was also performed to assess the anti-asthma effect of CAD. RESULTS There were 77 active ingredients in CAD, including quercetin, kaempferol, stigmasterol, luteolin, cryptotanshinone, beta-sitosterol, acacetin, naringenin, baicalin, and 48 related targets for asthma treatment, mainly including TNF, IL4, IL5, IL10, IL13 and IFN-γ, were identified with ideal molecular docking binding scores by network pharmacology analysis. KEGG pathway analysis revealed that these targets were directly involved in the asthma pathway, Th1 and Th2 cell differentiation, and signaling pathways correlated with asthma (NF-κB, IL17, T cell receptor, TNF, JAK-STAT signaling pathways, etc.). Animal experiments also confirmed that CAD could attenuate inflammatory cell invasion, goblet cell hyperplasia and mucus secretion. The levels of the major targets TNF-α, IL4, IL5, and IL13 can also be regulated by CAD in an asthma mouse model. CONCLUSION The anti-asthma mechanism of CAD possibly stemmed from the active ingredients targeting asthma-related targets, which are involved in the asthma pathway and signaling pathways to exhibit therapeutic effects.
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Affiliation(s)
- Xiaobo Xuan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Ziyan Sun
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Chenhuan Yu
- Experimental Animal centre, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310013, China
| | - Jian Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Mei Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Qili Wang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Lan Li
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China.
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19
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Maucourant C, Filipovic I, Ponzetta A, Aleman S, Cornillet M, Hertwig L, Strunz B, Lentini A, Reinius B, Brownlie D, Cuapio A, Ask EH, Hull RM, Haroun-Izquierdo A, Schaffer M, Klingström J, Folkesson E, Buggert M, Sandberg JK, Eriksson LI, Rooyackers O, Ljunggren HG, Malmberg KJ, Michaëlsson J, Marquardt N, Hammer Q, Strålin K, Björkström NK. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol 2020; 5:eabd6832. [PMID: 32826343 PMCID: PMC7665314 DOI: 10.1126/sciimmunol.abd6832] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023]
Abstract
Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease.
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Affiliation(s)
- Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Hertwig
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Angelica Cuapio
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eivind Heggernes Ask
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Ryan M Hull
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Schaffer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Folkesson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars I Eriksson
- Department of Physiology and Pharmacology, Section for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Rooyackers
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
- Department Clinical Interventions and Technology CLINTEC, Division for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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20
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Maucourant C, Filipovic I, Ponzetta A, Aleman S, Cornillet M, Hertwig L, Strunz B, Lentini A, Reinius B, Brownlie D, Cuapio A, Ask EH, Hull RM, Haroun-Izquierdo A, Schaffer M, Klingström J, Folkesson E, Buggert M, Sandberg JK, Eriksson LI, Rooyackers O, Ljunggren HG, Malmberg KJ, Michaëlsson J, Marquardt N, Hammer Q, Strålin K, Björkström NK. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol 2020. [PMID: 32826343 DOI: 10.1126/sciimmunol.abd68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease.
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Affiliation(s)
- Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Hertwig
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Angelica Cuapio
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eivind Heggernes Ask
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Ryan M Hull
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Schaffer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Folkesson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars I Eriksson
- Department of Physiology and Pharmacology, Section for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Rooyackers
- Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
- Department Clinical Interventions and Technology CLINTEC, Division for Anesthesiology and Intensive Care, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of .Oslo, Oslo, Norway
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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21
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Wang J, Li Q, Yin Y, Zhang Y, Cao Y, Lin X, Huang L, Hoffmann D, Lu M, Qiu Y. Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19. Front Immunol 2020; 11:2063. [PMID: 33013872 PMCID: PMC7461898 DOI: 10.3389/fimmu.2020.02063] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Cases of excessive neutrophil counts in the blood in severe coronavirus disease (COVID-19) patients have drawn significant attention. Neutrophil infiltration was also noted on the pathological findings from autopsies. It is urgent to clarify the pathogenesis of neutrophils leading to severe pneumonia in COVID-19. Methods: A retrospective analysis was performed on 55 COVID-19 patients classified as mild (n = 22), moderate (n = 25), and severe (n = 8) according to the Guidelines released by the National Health Commission of China. Trends relating leukocyte counts and lungs examined by chest CT scan were quantified by Bayesian inference. Transcriptional signatures of host immune cells of four COVID19 patients were analyzed by RNA sequencing of lung specimens and BALF. Results: Neutrophilia occurred in 6 of 8 severe patients at 7-19 days after symptom onset, coinciding with lesion progression. Increasing neutrophil counts paralleled lesion CT values (slope: 0.8 and 0.3-1.2), reflecting neutrophilia-induced lung injury in severe patients. Transcriptome analysis revealed that neutrophil activation was correlated with 17 neutrophil extracellular trap (NET)-associated genes in COVID-19 patients, which was related to innate immunity and interacted with T/NK/B cells, as supported by a protein-protein interaction network analysis. Conclusion: Excessive neutrophils and associated NETs could explain the pathogenesis of lung injury in COVID-19 pneumonia.
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Affiliation(s)
- Jun Wang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
- Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Qian Li
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Yongmei Yin
- Radiology Department, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Yingying Zhang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Yingying Cao
- Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany
| | - Xiaoming Lin
- Radiology Department, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Lihua Huang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
- Department of Infectious Diseases, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany
| | - Mengji Lu
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Yuanwang Qiu
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
- Radiology Department, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
- Department of Infectious Diseases, The Fifth People's Hospital of Wuxi, Jiangnan University, Wuxi, China
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22
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Zhou H, Zhang H, Shi M, Wang J, Huang Z, Shi J. A robust signature associated with patient prognosis and tumor immune microenvironment based on immune-related genes in lung squamous cell carcinoma. Int Immunopharmacol 2020; 88:106856. [PMID: 32777677 DOI: 10.1016/j.intimp.2020.106856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is one common type of lung cancer. Immune-related genes (IRGs) are closely associated with cancer prognosis. This study aims to screen the key genes associated with LUSC and establish an immune-related prognostic model. METHODS Based on the Cancer Genome Atlas (TCGA) database, we screened the differentially expressed genes (DEGs) between LUSC and normal samples. Intersecting the DEGs with the immune-related genes (IRGs), we obtained the differentially expressed IRGs (DEIRGs). Univariate as well as multivariate Cox regression analyses were performed to identify the survival-associated IRGs and establish an immune-related prognostic model. The relationship between the prognostic model and tumor-infiltrating immune cells was analyzed by TIMER and CIBERSORT. RESULTS A total of 229 DEIRGs were screened, and 14 IRGs associated with survival were identified using univariate Cox analysis. Among the 14 IRGs, six genes were selected out using Lasso and multivariate Cox analyses, and they were used to build the prognostic model. Further analysis indicated that overall survival (OS) of high-risk groups was lower than that of low-risk groups. High risk score was independently related to worse OS. Moreover, the risk score was positively correlated with several immune infiltration cells. Finally, the efficacy of the prognostic model was validated by another independent cohort GSE73403. CONCLUSION The DEIRGs described in the study may have the potential to be the prognostic molecular markers for LUSC. In addition, the risk score model could predict the OS and provides more information for the immunotherapy of patients with LUSC.
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MESH Headings
- Biomarkers, Tumor/immunology
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/immunology
- Correlation of Data
- Databases, Genetic
- Gene Expression Regulation, Neoplastic/immunology
- Humans
- Lung Neoplasms/diagnosis
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- MicroRNAs/immunology
- MicroRNAs/metabolism
- Prognosis
- Protein Interaction Maps/immunology
- RNA, Long Noncoding/immunology
- RNA, Long Noncoding/metabolism
- Risk Factors
- Survival Analysis
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Hao Zhou
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Muqi Shi
- Medical College of Nantong University, Nantong 226001, Jiangsu, China
| | - Jinjie Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Zhanghao Huang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China.
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23
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Brant EJ, Rietman EA, Klement GL, Cavaglia M, Tuszynski JA. Personalized therapy design for systemic lupus erythematosus based on the analysis of protein-protein interaction networks. PLoS One 2020; 15:e0226883. [PMID: 32191711 PMCID: PMC7081981 DOI: 10.1371/journal.pone.0226883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 12/08/2019] [Indexed: 12/26/2022] Open
Abstract
We analyzed protein expression data for Lupus patients, which have been obtained from publicly available databases. A combination of systems biology and statistical thermodynamics approaches was used to extract topological properties of the associated protein-protein interaction networks for each of the 291 patients whose samples were used to provide the molecular data. We have concluded that among the many proteins that appear to play critical roles in this pathology, most of them are either ribosomal proteins, ubiquitination pathway proteins or heat shock proteins. We propose some of the proteins identified in this study to be considered for drug targeting.
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Affiliation(s)
- Elizabeth J. Brant
- Nephrology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, United States of America
| | - Edward A. Rietman
- BINDS lab, College of Information and Computer Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
- Department of Mechanical and Industrial Engineering, University of Mass, Amherst, Massachusetts, United States of America
| | | | | | - Jack A. Tuszynski
- DIMEAS, Politecnico di Torino, Torino, Italy
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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24
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Song X, Zhang Y, Dai E, Wang L, Du H. Prediction of triptolide targets in rheumatoid arthritis using network pharmacology and molecular docking. Int Immunopharmacol 2020; 80:106179. [PMID: 31972422 DOI: 10.1016/j.intimp.2019.106179] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/09/2019] [Accepted: 12/30/2019] [Indexed: 12/14/2022]
Abstract
Network pharmacology is a novel approach that uses bioinformatics to predict and identify multiple drug targets and interactions in disease. Here, we used network pharmacology to investigate the mechanism by which triptolide acts in rheumatoid arthritis (RA). We first searched public databases for genes and proteins known to be associated with RA, as well as those predicted to be targets of triptolide, and then used Ingenuity Pathway Analysis (IPA) to identify enriched gene pathways and networks. Networks and pathways that overlapped between RA-associated proteins and triptolide target proteins were then used to predict candidate protein targets of triptolide in RA. The following proteins were found to occur in both RA-associated networks and triptolide target networks: CD274, RELA, MCL1, MAPK8, CXCL8, STAT1, STAT3, c-JUN, JNK, c-Fos, NF-κB, and TNF-α. Docking studies suggested that triptolide can fit in the binding pocket of the six top candidate triptolide target proteins (CD274, RELA, MCL1, MAPK8, CXCL8 and STAT1). The overlapping pathways were activation of Th1 and Th2 cells, macrophages, fibroblasts and endothelial cells in RA, while the overlapping networks were involved in cellular movement, hematological system development and function, immune cell trafficking, cell-to-cell signaling and interaction, inflammatory response, cellular function and maintenance, and cell death and survival. These results show that network pharmacology can be used to generate hypotheses about how triptolide exerts therapeutic effects in RA. Network pharmacology may be a useful method for characterizing multi-target drugs in complex diseases.
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Affiliation(s)
- Xinqiang Song
- Department of Biological Sciences, Xinyang Normal University, Xinyang 464000, China; Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang 464000, China.
| | - Yu Zhang
- Department of Biological Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Erqin Dai
- Department of Biological Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Lei Wang
- Department of Biological Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Hongtao Du
- Department of Biological Sciences, Xinyang Normal University, Xinyang 464000, China.
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Aguilar D, Lemonnier N, Koppelman GH, Melén E, Oliva B, Pinart M, Guerra S, Bousquet J, Anto JM. Understanding allergic multimorbidity within the non-eosinophilic interactome. PLoS One 2019; 14:e0224448. [PMID: 31693680 PMCID: PMC6834334 DOI: 10.1371/journal.pone.0224448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The mechanisms explaining multimorbidity between asthma, dermatitis and rhinitis (allergic multimorbidity) are not well known. We investigated these mechanisms and their specificity in distinct cell types by means of an interactome-based analysis of expression data. METHODS Genes associated to the diseases were identified using data mining approaches, and their multimorbidity mechanisms in distinct cell types were characterized by means of an in silico analysis of the topology of the human interactome. RESULTS We characterized specific pathomechanisms for multimorbidities between asthma, dermatitis and rhinitis for distinct emergent non-eosinophilic cell types. We observed differential roles for cytokine signaling, TLR-mediated signaling and metabolic pathways for multimorbidities across distinct cell types. Furthermore, we also identified individual genes potentially associated to multimorbidity mechanisms. CONCLUSIONS Our results support the existence of differentiated multimorbidity mechanisms between asthma, dermatitis and rhinitis at cell type level, as well as mechanisms common to distinct cell types. These results will help understanding the biology underlying allergic multimorbidity, assisting in the design of new clinical studies.
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MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/immunology
- Blood Cells/immunology
- Blood Cells/metabolism
- Cytokines/immunology
- Cytokines/metabolism
- Datasets as Topic
- Dermatitis, Allergic Contact/epidemiology
- Dermatitis, Allergic Contact/genetics
- Dermatitis, Allergic Contact/immunology
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Gene Expression Profiling
- Humans
- Immunity, Cellular/genetics
- Multimorbidity
- Protein Interaction Maps/genetics
- Protein Interaction Maps/immunology
- Rhinitis, Allergic/epidemiology
- Rhinitis, Allergic/genetics
- Rhinitis, Allergic/immunology
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Affiliation(s)
- Daniel Aguilar
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Barcelona, Spain
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- 6AM Data Mining, Barcelona, Spain
| | - Nathanael Lemonnier
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Gerard H. Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, GRIAC Research Institute
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mariona Pinart
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Stefano Guerra
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Jean Bousquet
- Hopital Arnaud de Villeneuve University Hospital, Montpellier, France
- Charité, Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany
| | - Josep M. Anto
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
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Fatehi R. Assessment of the genes and molecular mechanisms of B cells activation through systems biology approaches. Hum Antibodies 2019; 28:83-87. [PMID: 31524152 DOI: 10.3233/hab-190393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Two classes of T helper lymphocytes, Th1 and Th2, have different roles in B cell activation based on specific cytokines. To understand the difference of molecular mechanisms of B cell activation, the microarray dataset of B cells co-cultured with type 1 and 2 T helper, Be1 and Be2, were investigated. After quality assessment, using the GEO2R tool, the GSE84948 dataset was re-analyzed. Genes with adjusted p-value ⩽ 0.05 were assumed as differentially expressed (DE). The protein-protein interaction (PPI) networks were constructed using CluePedia plugin of Cytoscape, and analyzed by NetworkAnalyzer tool and MCODE plugin. Using ClueGO plugin of Cytoscape software, gene ontology (GO) analysis was performed. The comparison of Be1 and Be2 cells with naive B cells revealed 8742 and 8748 DE genes, respectively. The topology analysis of PPI networks predicted central genes. Among these, Jak3, Actrt3, and Pik3cb genes were determined as crucial genes in Be1 network. Prkx, Smarca4, and Jak2 genes were defined as critical genes in Be2 PPI network. GO analysis with PPI networks genes resulted in the promotion of immune system activation. In conclusion, we explored holistic methods for molecular assay of the difference between B cell activation mechanisms with Th1 and Th2.
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Huang XB, He YG, Zheng L, Feng H, Li YM, Li HY, Yang FX, Li J. Identification of hepatitis B virus and liver cancer bridge molecules based on functional module network. World J Gastroenterol 2019; 25:4921-4932. [PMID: 31543683 PMCID: PMC6737318 DOI: 10.3748/wjg.v25.i33.4921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/29/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The potential role of chronic inflammation in the development of cancer has been widely recognized. However, there has been little research fully and thoroughly exploring the molecular link between hepatitis B virus (HBV) and hepatocellular carcinoma (HCC). AIM To elucidate the molecular links between HBV and HCC through analyzing the molecular processes of HBV-HCC using a multidimensional approach. METHODS First, maladjusted genes shared between HBV and HCC were identified by disease-related differentially expressed genes. Second, the protein-protein interaction network based on dysfunctional genes identified a series of dysfunctional modules and significant crosstalk between modules based on the hypergeometric test. In addition, key regulators were detected by pivot analysis. Finally, targeted drugs that have regulatory effects on diseases were predicted by modular methods and drug target information. RESULTS The study found that 67 genes continued to increase in the HBV-HCC process. Moreover, 366 overlapping genes in the module network participated in multiple functional blocks. It could be presumed that these genes and their interactions play an important role in the relationship between inflammation and cancer. Correspondingly, significant crosstalk constructed a module level bridge for HBV-HCC molecular processes. On the other hand, a series of non-coding RNAs and transcription factors that have potential pivot regulatory effects on HBV and HCC were identified. Among them, some of the regulators also had persistent disorders in the process of HBV-HCC including microRNA-192, microRNA-215, and microRNA-874, and early growth response 2, FOS, and Kruppel-like factor 4. Therefore, the study concluded that these pivots are the key bridge molecules outside the module. Last but not least, a variety of drugs that may have some potential pharmacological or toxic side effects on HBV-induced HCC were predicted, but their mechanisms still need to be further explored. CONCLUSION The results suggest that the persistent inflammatory environment of HBV can be utilized as an important risk factor to induce the occurrence of HCC, which is supported by molecular evidence.
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Affiliation(s)
- Xiao-Bing Huang
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Yong-Gang He
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Lu Zheng
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Huan Feng
- Division of Nursing, Second Hospital Affiliated to Third Military Medical University, Xinqiao Hospital, Chongqing 400037, China
| | - Yu-Ming Li
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Hong-Yan Li
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Feng-Xia Yang
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
| | - Jing Li
- Department of Hepatobiliary Surgery, Second Hospital Affiliated to Third Military Medical University of Xinqiao Hospital, Chongqing 400037, China
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Cabral-Marques O, Marques A, Giil LM, De Vito R, Rademacher J, Günther J, Lange T, Humrich JY, Klapa S, Schinke S, Schimke LF, Marschner G, Pitann S, Adler S, Dechend R, Müller DN, Braicu I, Sehouli J, Schulze-Forster K, Trippel T, Scheibenbogen C, Staff A, Mertens PR, Löbel M, Mastroianni J, Plattfaut C, Gieseler F, Dragun D, Engelhardt BE, Fernandez-Cabezudo MJ, Ochs HD, Al-Ramadi BK, Lamprecht P, Mueller A, Heidecke H, Riemekasten G. GPCR-specific autoantibody signatures are associated with physiological and pathological immune homeostasis. Nat Commun 2018; 9:5224. [PMID: 30523250 PMCID: PMC6283882 DOI: 10.1038/s41467-018-07598-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/07/2018] [Indexed: 12/27/2022] Open
Abstract
Autoantibodies have been associated with autoimmune diseases. However, studies have identified autoantibodies in healthy donors (HD) who do not develop autoimmune disorders. Here we provide evidence of a network of immunoglobulin G (IgG) autoantibodies targeting G protein-coupled receptors (GPCR) in HD compared to patients with systemic sclerosis, Alzheimer's disease, and ovarian cancer. Sex, age and pathological conditions affect autoantibody correlation and hierarchical clustering signatures, yet many of the correlations are shared across all groups, indicating alterations to homeostasis. Furthermore, we identify relationships between autoantibodies targeting structurally and functionally related molecules, such as vascular, neuronal or chemokine receptors. Finally, autoantibodies targeting the endothelin receptor type A (EDNRA) exhibit chemotactic activity, as demonstrated by neutrophil migration toward HD-IgG in an EDNRA-dependent manner and in the direction of IgG from EDNRA-immunized mice. Our data characterizing the in vivo signatures of anti-GPCR autoantibodies thus suggest that they are a physiological part of the immune system.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany.
- Department of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
| | - Alexandre Marques
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
- Department of Statistic, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | | | - Roberta De Vito
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA
| | - Judith Rademacher
- Department of Gastroenterology, Infectiology and Rheumatology, Charité University Hospital, Berlin, 12203, Germany
- Berlin Institute of Health (BIH), Berlin, 10178, Germany
| | - Jeannine Günther
- Dept. of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, 10117, Germany
- Cell Autoimmunity Group, German Rheumatism Research Center (DRFZ), Berlin, 10117, Germany
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Jens Y Humrich
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Sebastian Klapa
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Susanne Schinke
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Lena F Schimke
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Gabriele Marschner
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Silke Pitann
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Sabine Adler
- University Hospital and University of Bern, Bern, 3012, Switzerland
| | - Ralf Dechend
- Experimental and Clinical Research Center, a collaboration of Max Delbruck Center for Molecular Medicine and Charité Universitätsmedizin, Berlin, 13125, Germany
- Department of Cardiology and Nephrology, HELIOS-Klinikum Berlin, Berlin, 13125, Germany
| | - Dominik N Müller
- Experimental and Clinical Research Center, a collaboration of Max Delbruck Center for Molecular Medicine and Charité Universitätsmedizin, Berlin, 13125, Germany
- Berlin Institute of Health (BIH), Berlin, 10178, Germany
| | - Ioana Braicu
- Department of Nephrology and Cardiovascular Research, Campus Virchow, Charité University Hospital, Berlin, 13353, Germany
| | - Jalid Sehouli
- Department of Gynecology, Charité University Hospital, Berlin and Tumor Bank Ovarian Cancer Network (TOC), Berlin, 13353, Germany
| | - Kai Schulze-Forster
- Department of Urology, Charité University Hospital, Berlin, 10117, Germany
- CellTrend GmbH, Luckenwalde, 14943, Germany
| | - Tobias Trippel
- Dept. of Internal Medicine & Cardiology, Charité University Hospital, Berlin, 13353, Germany
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité University Hospital Berlin, Campus Virchow, Berlin, 10117, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité University Hospital Berlin, Berlin, 13353, Germany
| | - Annetine Staff
- University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Peter R Mertens
- University Clinic for Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University Magdeburg, Magdeburg, 39106, Germany
| | - Madlen Löbel
- Institute for Medical Immunology, Charité University Hospital Berlin, Campus Virchow, Berlin, 10117, Germany
| | - Justin Mastroianni
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Albert Ludwigs University (ALU) of Freiburg, Freiburg, 79106, Germany
- Faculty of Biology, Albert-Ludwigs-University (ALU), Freiburg, 79104, Germany
| | - Corinna Plattfaut
- Section Experimental Oncology, University Hospital and Medical School (UKSH), University of Lübeck, Lübeck, 23538, Germany
| | - Frank Gieseler
- Section Experimental Oncology, University Hospital and Medical School (UKSH), University of Lübeck, Lübeck, 23538, Germany
| | - Duska Dragun
- Department of Nephrology and Cardiovascular Research, Campus Virchow, Charité University Hospital, Berlin, 13353, Germany
| | | | - Maria J Fernandez-Cabezudo
- Department of Biochemistry College of Medicine and Health Sciences, UAE University, Al Ain, 17666, United Arab Emirates
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, Seattle Children's Research Institute, Seattle, WA, 98191, USA
| | - Basel K Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, 17666, United Arab Emirates
| | - Peter Lamprecht
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Antje Mueller
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany
| | - Harald Heidecke
- Department of Urology, Charité University Hospital, Berlin, 10117, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 23538, Germany.
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Huang W, Li H, Cheng C, Ren C, Chen T, Jiang X, Cheng K, Luo P, Hu C. Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress. PLoS One 2018; 13:e0207771. [PMID: 30517152 PMCID: PMC6281221 DOI: 10.1371/journal.pone.0207771] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9.3 ± 0.1) was conducted. After analyzing, the cyclic nucleotide gated channel-Ca2+ (CNGC-Ca2+) and patched 1 (Ptc1) were detected as the majority annotated components in the cAMP signaling pathway (KO04024), indicating that the CNGC-Ca2+ and Ptc1 might be the candidate components for transducing and maintaining the high-pH stress signals, respectively. The immunoglobulin superfamily (IgSF), heat shock protein (HSP), glutathione s-transferase (GST), prophenoloxidase/phenoloxidase (proPO/PO), superoxide dismutase (SOD), anti-lipopolysaccharide factor (ALF) and lipoprotein were discovered as the major transcribed immune factors in response to high-pH stress. To further detect hub regulation-genes, protein-protein interaction (PPI) networks were constructed; the genes/proteins "Polymerase (RNA) II (DNA directed) polypeptide A" (POLR2A), "Histone acetyltransferase p300" (EP300) and "Heat shock 70kDa protein 8" (HSPA8) were suggested as the top three hub regulation-genes in response to acute high-pH stress; the genes/proteins "Heat shock 70kDa protein 4" (HSPA4), "FBJ murine osteosarcoma viral oncogene homolog" (FOS) and "Nucleoporin 54kDa" (NUP54) were proposed as the top three hub regulation-genes involved in adapting endurance high-pH stress; the protein-interactions of "EP300-HSPA8" and "HSPA4-NUP54" were detected as the most important biological interactions in response to the high-pH stress; and the HSP70 family genes might play essential roles in the adaptation of the high-pH stress environment in L. vannamei. These findings provide the first insight into the molecular and immune basis of L. vannamei in terms of high-pH environments, and the construction of a PPI network might improve our understanding in revealing the hub regulation-genes in response to abiotic stress in shrimp species and might be beneficial for further studies.
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Affiliation(s)
- Wen Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Hongmei Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuhang Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | | | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (CH); (PL)
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (CH); (PL)
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Lapek JD, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ. Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Syst 2018; 6:579-592.e4. [PMID: 29778837 PMCID: PMC7868092 DOI: 10.1016/j.cels.2018.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022]
Abstract
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.
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Affiliation(s)
- John D Lapek
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ronnie H Fang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xiaoli Wei
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kirsten van de Groep
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands; Department of Intensive Care Medicine, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Araceli Perez-Lopez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, G04.614, 3584 CX Utrecht, the Netherlands
| | - Manuela Raffatellu
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Hong CC, Sucheston-Campbell LE, Liu S, Hu Q, Yao S, Lunetta KL, Haddad SA, Ruiz-Narváez EA, Bensen JT, Cheng TYD, Bandera EV, Rosenberg LA, Haiman CA, Lee K, Evans SS, Abrams SI, Repasky EA, Olshan AF, Palmer JR, Ambrosone CB. Genetic Variants in Immune-Related Pathways and Breast Cancer Risk in African American Women in the AMBER Consortium. Cancer Epidemiol Biomarkers Prev 2018; 27:321-330. [PMID: 29339359 PMCID: PMC5835191 DOI: 10.1158/1055-9965.epi-17-0434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/23/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Constitutional immunity shaped by exposure to endemic infectious diseases and parasitic worms in Sub-Saharan Africa may play a role in the etiology of breast cancer among African American (AA) women.Methods: A total of 149,514 gene variants in 433 genes across 45 immune pathways were analyzed in the AMBER consortium among 3,663 breast cancer cases and 4,687 controls. Gene-based pathway analyses were conducted using the adaptive rank truncated product statistic for overall breast cancer risk, and risk by estrogen receptor (ER) status. Unconditional logistic regression analysis was used to estimate ORs and 95% confidence intervals (CIs) for single variants.Results: The top pathways were Interleukin binding (P = 0.01), Biocarta TNFR2 (P = 0.005), and positive regulation of cytokine production (P = 0.024) for overall, ER+, and ER- cancers, respectively. The most significant gene was IL2RB (P = 0.001) for overall cancer, with rs228952 being the top variant identified (OR = 0.85; 95% CI, 0.79-0.92). Only BCL3 contained a significant variant for ER+ breast cancer. Variants in IL2RB, TLR6, IL8, PRKDC, and MAP3K1 were associated with ER- disease. The only genes showing heterogeneity between ER- and ER+ cancers were TRAF1, MAP3K1, and MAPK3 (P ≤ 0.02). We also noted genes associated with autoimmune and atopic disorders.Conclusions: Findings from this study suggest that genetic variants in immune pathways are relevant to breast cancer susceptibility among AA women, both for ER+ and ER- breast cancers.Impact: Results from this study extend our understanding of how inherited genetic variation in immune pathways is relevant to breast cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 27(3); 321-30. ©2018 AACR.
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Affiliation(s)
- Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York.
| | | | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ting-Yuan David Cheng
- Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainsville, Florida
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Lynn A Rosenberg
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California
| | - Kelvin Lee
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | - Sharon S Evans
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | - Scott I Abrams
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York
| | | | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
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Chandran U, Patwardhan B. Network ethnopharmacological evaluation of the immunomodulatory activity of Withania somnifera. J Ethnopharmacol 2017; 197:250-256. [PMID: 27487266 DOI: 10.1016/j.jep.2016.07.080] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 07/23/2016] [Accepted: 07/30/2016] [Indexed: 05/27/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Withania somnifera (L.) Dunal (Ashwagandha, WS) is one of the extensively explored Ayurvedic botanicals. Several properties including immunomodulation, anti-cancer and neuro-protection of the botanical have been reported. Even though, in indigenous medicine, WS is well known for its immunomodulatory activity, the molecular mechanism of immunomodulation has not been elucidated. AIM OF THE STUDY This study aimed the evaluation of the immunomodulatory effect of WS using network ethnopharmacology technique to elucidate the in silico molecular mechanism. MATERIALS AND METHODS Databases- DPED, UNPD, PubChem, Binding DB, ChEMBL, KEGG and STRING were used to gather information to develop the networks. The networks were constructed using Cytoscape 3.2.1. Data analysis was performed with the help of Excel pivot table and Cytoscape network analyzer tool. RESULTS Investigation for WS immune modulation mechanism identified five bioactives that are capable of regulating 15 immune system pathways through 16 target proteins by bioactive-target and protein-protein interactions. The study also unveils the potential of withanolide-phytosterol combination to achieve effective immunomodulation and seven novel bioactive-immune target combinations. CONCLUSION The study elucidated an in silico molecular mechanism of immunomodulation of WS. It unveils the potential of withanolide-phytosterol combination to achieve a better immunomodulation. Experimental validation of the network findings would aid in understanding the rationale behind WS immunomodulation as well as aid in bioactive formulation based drug discovery.
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Affiliation(s)
- Uma Chandran
- Bioprospecting Laboratory, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune 411 007, India
| | - Bhushan Patwardhan
- Bioprospecting Laboratory, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune 411 007, India.
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Kumar A, Gaur GK, Gandham RK, Panigrahi M, Ghosh S, Saravanan BC, Bhushan B, Tiwari AK, Sulabh S, Priya B, V N MA, Gupta JP, Wani SA, Sahu AR, Sahoo AP. Global gene expression profile of peripheral blood mononuclear cells challenged with Theileria annulata in crossbred and indigenous cattle. Infect Genet Evol 2016; 47:9-18. [PMID: 27840256 DOI: 10.1016/j.meegid.2016.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022]
Abstract
Bovine tropical theileriosis is an important haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints of the livestock development programmes in India and Southeast Asia. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance to tropical theileriosis in indigenous cattle is not well documented. Recent studies incited an idea that differentially expressed genes in exotic and indigenous cattle play significant role in breed specific resistance to tropical theileriosis. The present study was designed to determine the global gene expression profile in peripheral blood mononuclear cells derived from indigenous (Tharparkar) and cross-bred cattle following in vitro infection of T. annulata (Parbhani strain). Two separate microarray experiments were carried out each for cross-bred and Tharparkar cattle. The cross-bred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were down-regulated and 485 were up-regulated. Their fold change varied from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes including 451 down-regulated and 424 up-regulated. The fold change varied from 94.93 to -19.20. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level. Functional annotation study of DEGs confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. It is therefore, hypothesized that the different susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against T. annulata infection.
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Affiliation(s)
- Amod Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Gyanendra Kumar Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shrikant Ghosh
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B C Saravanan
- Division of Parasitology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ashok Kumar Tiwari
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sourabh Sulabh
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bhuvana Priya
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Muhasin Asaf V N
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Jay Prakash Gupta
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Aditya Prasad Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Zhang C, Li Y, Tang W, Zhou Z, Sun P, Ma Z. The Relationship between B-cell Epitope and Mimotope Sequences. Protein Pept Lett 2016; 23:132-41. [PMID: 26715528 PMCID: PMC5427807 DOI: 10.2174/0929866523666151230124538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/30/2015] [Accepted: 11/23/2015] [Indexed: 11/22/2022]
Abstract
B-cell epitope is a group of residues which is on the surface of an antigen. It invokes humoral responses. Locating B-cell epitope is important for effective vaccine design, and the development of diagnostic reagents. Mimotope-based B-cell epitope prediction method is a kind of conformational B-cell epitope prediction, and the core idea of the method is mapping the mimotope sequences which are obtained from a random phage display library. However, current mimotope-based B-cell epitope prediction methods cannot maintain a high degree of satisfaction in the circumstances of employing only mimotope sequences. In this study, we did a multi-perspective analysis on parameters for conformational B-cell epitopes and characteristics between epitope and mimotope on a benchmark datasets which contains 67 mimotope sets, corresponding to 40 unique complex structures. In these 67 cases, there are 25 antigen-antibody complexes and 42 protein-protein interactions. We analyzed the two parts separately. The results showed the mimotope sequences do have some epitope features, but there are also some epitope properties that mimotope sequences do not contain. In addition, the numbers of epitope segments with different lengths were obviously different between the antigen-antibody complexes and the protein-protein interactions. This study reflects how similar do mimotope sequence and genuine epitopes have; and evaluates existing mimotope-based B-cell epitope prediction methods from a novel viewpoint.
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Affiliation(s)
- Chunhua Zhang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Yunyun Li
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Ganjingzi District Dalian City Hengyuan Primary School, Dalian 116000, China
| | - Weina Tang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Zhiguo Zhou
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
| | - Pingping Sun
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
| | - Zhiqiang Ma
- School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Intelligent Information
Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
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Zábrady M, Hrdinová V, Müller B, Conrad U, Hejátko J, Janda L. Targeted in vivo inhibition of specific protein-protein interactions using recombinant antibodies. PLoS One 2014; 9:e109875. [PMID: 25299686 PMCID: PMC4192540 DOI: 10.1371/journal.pone.0109875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022] Open
Abstract
With the growing availability of genomic sequence information, there is an increasing need for gene function analysis. Antibody-mediated "silencing" represents an intriguing alternative for the precise inhibition of a particular function of biomolecules. Here, we describe a method for selecting recombinant antibodies with a specific purpose in mind, which is to inhibit intrinsic protein-protein interactions in the cytosol of plant cells. Experimental procedures were designed for conveniently evaluating desired properties of recombinant antibodies in consecutive steps. Our selection method was successfully used to develop a recombinant antibody inhibiting the interaction of ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 3 with such of its upstream interaction partners as the receiver domain of CYTOKININ INDEPENDENT HISTIDINE KINASE 1. The specific down-regulation of the cytokinin signaling pathway in vivo demonstrates the validity of our approach. This selection method can serve as a prototype for developing unique recombinant antibodies able to interfere with virtually any biomolecule in the living cell.
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Affiliation(s)
- Matej Zábrady
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vendula Hrdinová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Bruno Müller
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Udo Conrad
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jan Hejátko
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lubomír Janda
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail:
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Yadav S, Gupta S, Selvaraj C, Doharey PK, Verma A, Singh SK, Saxena JK. In silico and in vitro studies on the protein-protein interactions between Brugia malayi immunomodulatory protein calreticulin and human C1q. PLoS One 2014; 9:e106413. [PMID: 25184227 PMCID: PMC4153637 DOI: 10.1371/journal.pone.0106413] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022] Open
Abstract
Filarial parasites modulate effective immune response of their host by releasing a variety of immunomodulatory molecules, which help in the long persistence of the parasite within the host. The present study was aimed to characterize an immunomodulatory protein of Brugia malayi and its interaction with the host immune component at the structural and functional level. Our findings showed that Brugia malayi Calreticulin (BmCRT) is responsible for the prevention of classical complement pathway activation via its interaction with the first component C1q of the human host. This was confirmed by inhibition of C1q dependent lysis of immunoglobulin-sensitized Red Blood Cells (S-RBCs). This is possibly the first report which predicts CRT-C1q interaction on the structural content of proteins to explain how BmCRT inhibits this pathway. The molecular docking of BmCRT-C1q complex indicated that C1qB chain (IgG/M and CRP binding sites on C1q) played a major role in the interaction with conserved and non-conserved regions of N and P domain of BmCRT. Out of 37 amino acids of BmCRT involved in the interaction, nine amino acids (Pro(126), Glu(132), His(147), Arg(151), His(153), Met(154), Lys(156), Ala(196) and Lys(212)) are absent in human CRT. Both ELISA and in silico analysis showed the significant role of Ca(+2) in BmCRT-HuC1q complex formation and deactivation of C1r2-C1s2. Molecular dynamics studies of BmCRT-HuC1q complex showed a deviation from ∼ 0.4 nm to ∼ 1.0 nm. CD analyses indicated that BmCRT is composed of 49.6% α helix, 9.6% β sheet and 43.6% random coil. These findings provided valuable information on the architecture and chemistry of BmCRT-C1q interaction and supported the hypothesis that BmCRT binds with huC1q at their targets (IgG/M, CRP) binding sites. This interaction enables the parasite to interfere with the initial stage of host complement activation, which might be helpful in parasites establishment. These results might be utilized for help in blocking the C1q/CRT interaction and preventing parasite infection.
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Affiliation(s)
- Sunita Yadav
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram extension, Lucknow, Uttar Pradesh, India
| | - Smita Gupta
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram extension, Lucknow, Uttar Pradesh, India
| | - Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India
| | - Pawan Kumar Doharey
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram extension, Lucknow, Uttar Pradesh, India
| | - Anita Verma
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram extension, Lucknow, Uttar Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India
| | - Jitendra Kumar Saxena
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram extension, Lucknow, Uttar Pradesh, India
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He W, Kuang Y, Xing X, Simpson RJ, Huang H, Yang T, Chen J, Yang L, Liu E, He W, Gu J. Proteomic comparison of 3D and 2D glioma models reveals increased HLA-E expression in 3D models is associated with resistance to NK cell-mediated cytotoxicity. J Proteome Res 2014; 13:2272-81. [PMID: 24742303 DOI: 10.1021/pr500064m] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Three-dimensional cell culture techniques can better reflect the in vivo characteristics of tumor cells compared with traditional monolayer cultures. Compared with their 2D counterparts, 3D-cultured tumor cells showed enhanced resistance to the cytotoxic T cell-mediated immune response. However, it remains unclear whether 3D-cultured tumor cells have an enhanced resistance to NK cell cytotoxicity. In this study, a total of 363 differentially expressed proteins were identified between the 2D- and 3D-cultured U251 cells by comparative proteomics, and an immune-associated protein-protein interaction (PPI) network based on these differential proteins was constructed by bioinformatics. Within the network, HLA-E, as a molecule for inhibiting NK cell activation, was significantly up-regulated in the 3D-cultured tumor cells. Then, we found that the 3D-cultured U251 cells exhibited potent resistance to NK cell cytotoxicity in vitro and were prone to tumor formation in vivo. The resistance of the 3D-cultured tumor cells to NK cell lysis was mediated by the HLA-E/NKG2A interaction because the administration of antibodies that block either HLA-E or NKG2A completely eliminated this resistance and significantly decreased tumor formation. Taken together, our findings indicate that HLA-E up-regulation in 3D-cultured cells may result in enhanced tumor resistance to NK cell-mediated immune response.
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MESH Headings
- Animals
- Antibodies, Blocking/immunology
- Antibodies, Blocking/pharmacology
- Blotting, Western
- Cell Culture Techniques/methods
- Cell Line, Tumor
- Chromatography, Liquid
- Cytotoxicity, Immunologic/drug effects
- Cytotoxicity, Immunologic/immunology
- Gene Expression/immunology
- Glioma/immunology
- Glioma/metabolism
- Glioma/pathology
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Humans
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Mice, Inbred BALB C
- Mice, Nude
- Models, Biological
- NK Cell Lectin-Like Receptor Subfamily C/immunology
- NK Cell Lectin-Like Receptor Subfamily C/metabolism
- Protein Binding/drug effects
- Protein Binding/immunology
- Protein Interaction Maps/immunology
- Proteomics/methods
- Reverse Transcriptase Polymerase Chain Reaction
- Tandem Mass Spectrometry
- Xenograft Model Antitumor Assays/methods
- HLA-E Antigens
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Affiliation(s)
- Weiqi He
- Department of Neurosurgery, General Hospital of People's Liberation Army Chengdu Military Region, Chengdu 610083, China
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Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O. The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. PLoS Comput Biol 2014; 10:e1003470. [PMID: 24550720 PMCID: PMC3923659 DOI: 10.1371/journal.pcbi.1003470] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/25/2013] [Indexed: 01/21/2023] Open
Abstract
Interleukin-1 (IL-1) is a large cytokine family closely related to innate immunity and inflammation. IL-1 proteins are key players in signaling pathways such as apoptosis, TLR, MAPK, NLR and NF-κB. The IL-1 pathway is also associated with cancer, and chronic inflammation increases the risk of tumor development via oncogenic mutations. Here we illustrate that the structures of interfaces between proteins in this pathway bearing the mutations may reveal how. Proteins are frequently regulated via their interactions, which can turn them ON or OFF. We show that oncogenic mutations are significantly at or adjoining interface regions, and can abolish (or enhance) the protein-protein interaction, making the protein constitutively active (or inactive, if it is a repressor). We combine known structures of protein-protein complexes and those that we have predicted for the IL-1 pathway, and integrate them with literature information. In the reconstructed pathway there are 104 interactions between proteins whose three dimensional structures are experimentally identified; only 15 have experimentally-determined structures of the interacting complexes. By predicting the protein-protein complexes throughout the pathway via the PRISM algorithm, the structural coverage increases from 15% to 71%. In silico mutagenesis and comparison of the predicted binding energies reveal the mechanisms of how oncogenic and single nucleotide polymorphism (SNP) mutations can abrogate the interactions or increase the binding affinity of the mutant to the native partner. Computational mapping of mutations on the interface of the predicted complexes may constitute a powerful strategy to explain the mechanisms of activation/inhibition. It can also help explain how an oncogenic mutation or SNP works. Structural pathways are important because they provide insight into signaling mechanisms; help understand the mechanism of disease-related mutations; and help in drug discovery. While extremely useful, common pathway diagrams lacking structural data are unable to provide mechanistic insight to explain oncogenic mutations or SNPs. Here we focus on the construction of the IL-1 structural pathway and map oncogenic mutations and SNPs to complexes in this pathway. Our results indicate that computational modeling of protein-protein interactions on a large scale can provide accurate, structural atom-level detail of signaling pathways in the human cell and help delineate the mechanism through which a mutation leads to disease. We show that the mutations either thwart the interactions, activating the proteins even in their absence or stabilize them, leading to the same uncontrolled outcome. Computational mapping of mutations on the interface of the predicted complexes may constitute an effective strategy to explain the mechanisms of mutations- constitutive activation or deactivation.
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Affiliation(s)
- Saliha Ece Acuner Ozbabacan
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Sariyer Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Sariyer Istanbul, Turkey
- * E-mail: (AG); (OK)
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick National Laboratory, Frederick, Maryland, United States of America
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Sariyer Istanbul, Turkey
- * E-mail: (AG); (OK)
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Patil A, Kumagai Y, Liang KC, Suzuki Y, Nakai K. Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PLoS Comput Biol 2013; 9:e1003323. [PMID: 24244133 PMCID: PMC3820512 DOI: 10.1371/journal.pcbi.1003323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 09/21/2013] [Indexed: 01/09/2023] Open
Abstract
The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub-networks in other biological systems.
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Affiliation(s)
- Ashwini Patil
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaro Kumagai
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Kuo-ching Liang
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Tai HY, Zhou JK, Chou H, Tam MF, Chen YS, Sheu SY, Shen HD. Epitope mapping and in silico characterization of interactions between Der p 7 allergen and MoAb WH9. PLoS One 2013; 8:e71269. [PMID: 23940735 PMCID: PMC3734125 DOI: 10.1371/journal.pone.0071269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/28/2013] [Indexed: 12/23/2022] Open
Abstract
Der p 7 is an important house dust mite allergen. However, antigenic determinants of Der p 7 are largely unknown. The purpose of this study is to analyze the determinants of Der p 7 and determine the structural basis of interactions between Der p 7 and WH9, an IgE-binding inhibition mouse monoclonal antibody (MoAb). IgE and WH9-reactive determinant(s) was identified by immunoblot using allergen mutants. A 3-D binary complex structure of Der p 7 and WH9 was simulated with homology modeling and docking methods. Our results obtained showed that among the five Der p 7 mutants (S156A, I157A, L158A, D159A, P160A), serum no. 1045 with IgE-binding against Der p 7 exhibited a reduced IgE immunoblot reactivity against Der p 7 L158A and D159A mutants. WH9 showed reduced immunoblot reactivity against S156A, L158A, D159A and P160A and the observation was confirmed by immunoblot inhibition. The WH9-binding determinant on Der p 7 containing S156, L158, D159 and P160 assumes a loop-like structure. The structural model of the Der p 7-WH9 complex suggests residues S156, I157, L158, D159 and P160 of Der p 7 contribute to WH9 binding via potential hydrogen bonds, electrostatic and hydrophobic interactions. In conclusion, MoAb WH9 interacts with critical residues L158 and D159 of Der p 7 and inhibits IgE-binding to Der p 7. Results obtained advance our understanding on molecular and structural bases of the antigenicity of Der p 7, its interactions with MoAb WH9 and facilitate the design of safer immunotherapy of human atopic disorders.
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Affiliation(s)
- Hsiao-Yun Tai
- Department of Medical Research and Education, Taipei Veterans General Hospital, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Hong Chou
- Department of Medical Research and Education, Taipei Veterans General Hospital, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Ming F. Tam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Yu-Sen Chen
- Department of Medical Research and Education, Taipei Veterans General Hospital, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China
| | - Horng-Der Shen
- Department of Medical Research and Education, Taipei Veterans General Hospital, National Yang-Ming University, Taipei, Taiwan, Republic of China
- * E-mail:
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Wang XL, Chai Q, Charlesworth MC, Figueroa JJ, Low P, Shen WK, Lee HC. Autoimmunoreactive IgGs from patients with postural orthostatic tachycardia syndrome. Proteomics Clin Appl 2012; 6:615-25. [PMID: 23002038 PMCID: PMC3786406 DOI: 10.1002/prca.201200049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 08/10/2012] [Accepted: 08/14/2012] [Indexed: 11/11/2022]
Abstract
PURPOSE Autoantibodies are implicated in the pathogenesis of cardiovascular diseases and cardiac arrhythmias. In this pilot study, we tested the hypothesis that autoantibodies are present in patients with postural orthostatic tachycardia syndrome (POTS). EXPERIMENTAL DESIGN Seven control subjects (6 F:1 M, average age 36.1 years) and ten patients with the diagnosis of POTS (7 F: 3 M, average age 35.1 years) provided informed consent and 30 mL of venous blood. Human heart membrane proteins were resolved by 2DE and immunoblotted against purified IgGs from controls and patients. RESULTS Eighteen protein spots immunoreactive specifically against patient IgGs were detected and they were excised from gels, trypsin-digested, and analyzed by nanoLC-electrospray MS/MS. Forty unique proteins were identified and these include proteins that are associated with cardiac hypertrophy (mimecan, myozenin), cardiac remodeling (periostin), cardiomyopathy (desmin, desmoplakin), cell survival (laminin), structural integrity (filamin), chaperone proteins (crystalline, HSP70), mitochondrial enzymes, and channel proteins. Ingenuity Pathway Analysis showed multiple pathways were involved including those that regulate energy metabolism, redox, fibrosis, cardiac hypertrophy, and degeneration. CONCLUSIONS AND CLINICAL RELEVANCE Autoantibodies are present in patients with POTS. These autoantibodies cross-react with a wide range of cardiac proteins and may induce alterations in cardiac function. Autoimmune pathogenetic mechanisms should be further explored in these patients.
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Affiliation(s)
- Xiao-Li Wang
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Gassmann W, Bhattacharjee S. Effector-triggered immunity signaling: from gene-for-gene pathways to protein-protein interaction networks. Mol Plant Microbe Interact 2012; 25:862-8. [PMID: 22414439 DOI: 10.1094/mpmi-01-12-0024-ia] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In its simplicity and testability, Flor's gene-for-gene hypothesis has been a powerful driver in plant immunity research for decades. Once the molecular underpinnings of gene-for-gene resistance had come into sharper focus, there was a reassessment of Flor's hypothesis and a name change to effector-triggered immunity. As implied by the name change and exemplified by pioneering studies, plant immunity is increasingly described in terms of protein rather than genetic interactions. This progress leads to a reinterpretation of old concepts of pathogen recognition and resistance signaling and, of course, opens up new questions. Here, we provide a brief historical overview of resistance gene function and how a new focus on protein interactions can lead to a deeper understanding of the logic of plant innate immunity signaling.
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Affiliation(s)
- Walter Gassmann
- Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
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