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Lin YT, Hung YC, Chen LH, Lee KT, Han YS. Effects of adding Bacillus subtilis natto NTU-18 in paste feed on growth, intestinal morphology, gastrointestinal microbiota diversity, immunity, and disease resistance of Anguilla japonica glass eels. Fish Shellfish Immunol 2024; 149:109556. [PMID: 38608848 DOI: 10.1016/j.fsi.2024.109556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Japanese eel, Anguilla japonica, holds significant importance in Taiwanese aquaculture. With the intensification of eel farming, the impact of Edwardsiella tarda has become increasingly severe. Consequently, the abusive use of antibiotics has risen. Bacillus subtilis natto NTU-18, a strain of Bacillus with a high survival rate in feed processing, plays a crucial role in promoting intestinal health through competitive rejection, enhancing immune responses against bacterial pathogens, and improving intestinal health by modulating gastrointestinal microbiota to produce beneficial metabolites of mice and grass carp, Ctenopharyngodon idella. This study investigated the effects of different proportions (control, 0.25 %, 0.5 %, 1 %, and 2 %) of B. subtilis natto NTU-18 added to paste feed on the growth performance, intestinal morphology, and microbiota, expression of immune-related genes, and resistance to E. tarda in Japanese glass eel. The results indicated that the growth performance of all groups with B. subtilis natto NTU-18 added was significantly higher than that of the control group and did not impact the villi morphology. The expression of immune-related genes in the kidney, specifically HSP70 and SOD, was significantly higher from 0.5 % and above than the control; however, no significant differences were observed in CAT, POD, and HSP90. In the liver, significant differences were found in HSP70 and IgM above 0.25 % compared to the control group, with no significant differences in SOD, CAT, POD, and HSP90 among all groups. Additionally, intestinal microbiota analysis revealed that the 2 % additional group had significantly lower diversity than other groups, with Cetobacterium as the dominant species. The challenge test observed that the survival rates of the 0.5 % and 1 % groups were significantly higher. This research suggests that adding 0.5 % and 1 % of B. subtilis natto NTU-18 to the diet is beneficial for Japanese glass eel's immunity, growth performance, and disease resistance.
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Affiliation(s)
- Yen-Ting Lin
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chen Hung
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Li-Han Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Kung-Ta Lee
- Department of Biochemical Science & Technology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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Yang L, Long Y, Xiao S. Osteosarcoma-Associated Immune Genes as Potential Immunotherapy and Prognosis Biomarkers. Biochem Genet 2024; 62:798-813. [PMID: 37452172 DOI: 10.1007/s10528-023-10444-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/26/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Immune-modulating therapies exhibit abundant promise compared to traditional treatment for osteosarcoma. We aim to establish an immune-related prognostic signatures in osteosarcoma. We identified the differentially expressed genes in osteosarcoma compared with normal controls using the GEO dataset. The intersection with immune-related genes was considered as differentially expressed immune genes. Potential prognosis-related differentially expressed genes were first analyzed with the multifactor Cox regression and then the step function performed the iteration. The best model was finally chosen as the immunological risk score signature model. And finally, we evaluated the correlation of genes in the prognostic model with immune cells, common immune checkpoints, and immune checkpoint blockade responses. We identified 1527 significantly upregulated and 2407 significantly downregulated genes in osteosarcoma compared to normal samples. In the 258 differentially expressed immune genes, 20 genes with independent prognostic significance were included in the step function. Finally, we constructed a prognostic signature for overall survival based on five immune genes (JAG2, PLXNB1, CMKLR1, NUDT6, and PSMC4) in osteosarcoma. These five genes are closely related to immune infiltration. Osteosarcoma with high JAG2 expression or low CMKLR1 expression may be associated with better immune checkpoint blockade response. JAG2 overexpression or CMKLR1 inhibition induced sensitivity to PD-1 antibody in osteosarcoma cells. We constructed a prognosis prediction signature containing five immune-related genes (JAG2, PLXNB1, CMKLR1, NUDT6, and PSMC4) with a significant prognostic value in osteosarcoma. Significant differences in immune infiltration and immunotherapy responses were identified between groups with different levels of these genes.
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Affiliation(s)
- Li Yang
- Key Laboratory of Geriatric Diseases of Xinyang, Institute of Inspection Technology, Xinyang Vocational and Technical College, Xinyang, 464000, China
| | - Yi Long
- Department of Joint Surgery, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, 412000, China.
| | - Shengshi Xiao
- Department of Joint Surgery, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, 412000, China.
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Xie L, Du B, Yu H, Gui L, Qiu J, Yuan L, Shen Y, Xu X, Li J. MicroRNA-30e-3p regulates the inflammatory response by targeting the gimap8 gene in Ctenopharyngodon idella kidney (CIK) cells. Fish Shellfish Immunol 2024; 149:109524. [PMID: 38527657 DOI: 10.1016/j.fsi.2024.109524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have increasingly linked miRNAs with the modulation of inflammatory responses and immunosuppressive activities. This investigation reveals that mir-30e-3p selectively binds to and modulates gimap8, as demonstrated by luciferase reporter assays and qPCR analyses. Upon LPS stimulation of CIK cells, mir-30e-3p expression was notably elevated, inversely correlating with a decrease in gimap8 mRNA levels. Overexpression of mir-30e-3p attenuated the mRNA levels of pro-inflammatory cytokines beyond the effect of LPS alone, suggesting a regulatory role of mir-30e-3p in inflammation mediated by the gimap8 gene. These insights contribute to our understanding of the complex mechanisms governing inflammatory and immune responses.
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Affiliation(s)
- Lingli Xie
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Biao Du
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Hongyan Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lang Gui
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Li Yuan
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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Zhang L, Wang WQ, Chen JH, Feng J, Liao YZ, Zou Y, Liu R. Tumor-infiltrating immune cells and survival in head and neck squamous cell carcinoma: a retrospective computational study. Sci Rep 2024; 14:6390. [PMID: 38493212 PMCID: PMC10944537 DOI: 10.1038/s41598-024-56738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/08/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
The immune infiltration profiles of the tumor microenvironment have effects on the prognosis of head and neck squamous cell carcinoma (HNSCC). Whereas, HNSCC is a heterogeneous group of tumors, but past work has not taken this into consideration. Herein, we investigate the associations between survival and the function of immune cells in different tumorigenic sites of HNSCC. 1149 samples of HNSCC were collected from publicly accessible databases. Based on gene expression data, CIBERSORTx was applied to determine the proportion of 22 immune cell subpopulations. In the Cox regression model, the associations between overall survival, disease-free survival, and immune cells were examined, modeling gene expression and immune cell proportion as quartiles. Consensus cluster analysis was utilized to uncover immune infiltration profiles. Regardless of tumor sites, CD8+ T cells and activated CD4 memory T cells were associated with favorable survival, while eosinophils were the opposite. The survival of the hypopharynx, oral cavity, and larynx subsites was somewhat affected by immune cells, while the survival of the oropharynx subsite potentially was the most impacted. High expression of TIGIT, CIITA, and CXCR6 was linked to better survival, mainly in the oropharynx subsite. Immune cell clusters with four distinct survival profiles were discovered, of which the cluster with a high CD8+ T cell content had a better prognosis. The immune-infiltration pattern is related to the survival of HNSCC to varying degrees depending on the tumor sites; forthcoming studies into immune-mediated infiltration profiles will lay the groundwork for treating HNSCC with precision therapy.
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Affiliation(s)
- Lei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Wei-Quan Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jun-Hong Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia Feng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ya-Zhou Liao
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
| | - You Zou
- High Performance Computing Center, Central South University, Changsha, 410008, People's Republic of China.
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China.
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Wang J, Chen W, Chen S, Yue G, Hu Y, Xu J. Landscape of infiltrating immune cells and related genes in diabetic kidney disease. Clin Exp Nephrol 2024; 28:181-191. [PMID: 37882850 DOI: 10.1007/s10157-023-02422-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Diabetic kidney disease (DKD) is one of the prominent microvascular complications of diabetes and the leading cause of end-stage renal disease. Inflammation plays a crucial role in the development and progression of DKD. Currently, only a few studies depict the landscape of infiltrating immune cells and their potential regulatory network in DKD. To gain a better understanding of the role of immune cells in the renal microenvironment, we sought to reveal the profile of infiltrating immune cells and their potential regulatory network in DKD. METHODS We obtained the transcriptomes and the corresponding clinical data of 19 DKD and 25 control samples from the Gene Expression Omnibus and Nephroseq databases, respectively. Thereafter, we conducted an analysis on the infiltrating immune cells and identified immune-related differentially expressed genes through bioinformatics. Finally, correlation analyses among immune cells, immune genes, and clinical manifestations were performed, and differentially infiltrating immune cell subsets were verified through multiplex immunofluorescence staining. RESULTS We demonstrated the landscape of infiltrating immune cells in patients with DKD and identified the top five hub immune regulatory genes (C3, IL7R, TYROBP, BMP2, and CXCL6). Three of the core genes (C3, BMP2, and CXCL6) were significantly correlated with the estimated glomerular filtration rate. Through multiplex immunofluorescence staining, we verified that macrophage numbers were remarkably elevated, whereas Treg cells were remarkably reduced in diabetic kidney tissues. Th2 cells were scarce in the kidney tissue. CONCLUSION Collectively, our findings shed light on new, possible therapeutic strategies for DKD, from an immune microenvironment perspective.
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Affiliation(s)
- Jiao Wang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng St., Nanchang, Nanchang, 330006, Jiangxi, People's Republic of China
- Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China
- Jiangxi branch of national clinical research center for metabolic disease, Nanchang, 330006, People's Republic of China
| | - Wen Chen
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng St., Nanchang, Nanchang, 330006, Jiangxi, People's Republic of China
- Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China
- Jiangxi branch of national clinical research center for metabolic disease, Nanchang, 330006, People's Republic of China
| | - Shen Chen
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng St., Nanchang, Nanchang, 330006, Jiangxi, People's Republic of China
- Queen Mary School, Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Guanru Yue
- Department of Medical Genetics and Cell biology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Ying Hu
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng St., Nanchang, Nanchang, 330006, Jiangxi, People's Republic of China
- Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China
- Jiangxi branch of national clinical research center for metabolic disease, Nanchang, 330006, People's Republic of China
| | - Jixiong Xu
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng St., Nanchang, Nanchang, 330006, Jiangxi, People's Republic of China.
- Jiangxi Clinical Research Center for Endocrine and Metabolic Disease, Nanchang, 330006, People's Republic of China.
- Jiangxi branch of national clinical research center for metabolic disease, Nanchang, 330006, People's Republic of China.
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Li S, Zhang N, Yang Y, Liu T. Transcriptionally activates CCL28 expression to inhibit M2 polarization of macrophages and prevent immune escape in colorectal cancer cells. Transl Oncol 2024; 40:101842. [PMID: 38035446 PMCID: PMC10698578 DOI: 10.1016/j.tranon.2023.101842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the potential molecular mechanism of SPDEF in immune evasion of colorectal cancer (CRC) and examine its impact on macrophage M2 polarization using the TCGA and GEO databases. METHODS By combining TCGA and GEO databases, differential gene expression between CRC samples and standard tissue samples was analyzed to screen for immune-related genes (IRGs) associated with the prognosis of CRC patients. A predictive risk model was constructed based on 18 key IRGs, which were then validated using the GEO dataset. The relationship between transcription factors and IRGs was further explored to investigate their regulatory network in CRC. In vivo and in vitro experiments were carried out to validate these regulatory relationships and explore the function of SPDEF and CCL28 in CRC. RESULTS Twelve key IRGs associated with clinical and pathological characteristics of CRC patients were identified. Among them, CCL28 significantly impacted macrophage infiltration in CRC cells and may be a critical factor in immune evasion. In both in vitro and in vivo experiments, overexpression of SPDEF upregulated CCL28 expression, thereby suppressing M2 polarization of macrophages and inhibiting CRC cell proliferation and tumor growth. Notably, interference with CCL28 could reverse the effect of SPDEF overexpression. CONCLUSION SPDEF can suppress immune evasion of CRC cells by activating CCL28, which is achieved through the modulation of M2 polarization of macrophages. This provides a new research direction and potential therapeutic target for immunotherapy in CRC.
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Affiliation(s)
- Shiquan Li
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Nan Zhang
- Department of Burn Surgery, The First Hospital of Jilin University, Changchun 130000, China
| | - Yongping Yang
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Tongjun Liu
- Department of Colorectal and Anal Surgery, The Second Hospital of Jilin University, Changchun 130000, China.
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Miao M, Li S, Yu Y, Liu Y, Li F. Comparative transcriptome analysis of hepatopancreas reveals the potential mechanism of shrimp resistant to Vibrio parahaemolyticus infection. Fish Shellfish Immunol 2024; 144:109282. [PMID: 38081442 DOI: 10.1016/j.fsi.2023.109282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Vibrio parahaemolyticus carrying a pathogenic plasmid (VPAHPND) is one of the main causative agents of acute hepatopancreatic necrosis disease (AHPND) in shrimp aquaculture. Knowledge about the mechanism of shrimp resistant to VPAHPND is very helpful for developing efficient strategy for breeding AHPND resistant shrimp. In order to learn the mechanism of shrimp resistant to AHPND, comparative transcriptome was applied to analyze the different expressions of genes in the hepatopancreas of shrimp from different families with different resistance to VPAHPND. Through comparative analysis on the hepatopancreas of shrimp from VPAHPND resistant family and susceptible family, we found that differentially expressed genes (DEGs) were mainly involved in immune and metabolic processes. Most of the immune-related genes among DEGs were highly expressed in the hepatopancreas of shrimp from resistant family, involved in recognition of pathogen-associated molecular patterns, phagocytosis and elimination of pathogens, maintenance of reactive oxygen species homeostasis and other immune processes etc. However, most metabolic-related genes were highly expressed in the hepatopancreas of shrimp from susceptible family, involved in metabolism of lipid, vitamin, cofactors, glucose, carbohydrate and serine. Interestingly, when we analyzed the expression of above DEGs in the shrimp after VPAHPND infection, we found that the most of identified immune-related genes remained at high expression levels in the hepatopancreas of shrimp from the VPAHPND resistant family, and most of the identified metabolic-related genes were still at high expression levels in the hepatopancreas of shrimp from the VPAHPND susceptible family. The data suggested that the differential expression of these immune-related and metabolic-related genes in hepatopancreas might contribute to the resistance variations of shrimp to VPAHPND. These results provided valuable information for understanding the resistant mechanism of shrimp to VPAHPND.
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Affiliation(s)
- Miao Miao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuan Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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Li X, Chen Y, Dong Y, Ma Z, Zheng W, Lin Y. Prediction of immune infiltration and prognosis for patients with gastric cancer based on the immune-related genes signature. Heliyon 2023; 9:e22433. [PMID: 38213590 PMCID: PMC10782158 DOI: 10.1016/j.heliyon.2023.e22433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
Objective The immune microenvironment influenced clinical outcomes and treatment response of gastric cancer (GC) patients. Though thousands of immune-related genes (IRGs) have been identified, their effects on GC are not fully understood. The objective of the study is to analyze the correlations between the expression and effect of IRGs and clinical outcomes. Moreover, we evaluate the efficacy and value of utilizing the immune-related genes signature as a prognosis prediction model for GC patients. Methods We identified the differentially expressed IRGs and systematically analyzed their functions. We constructed a novel GC prognostic signature and a new nomogram, Moreover, we explored the infiltrated immune cell types in the immune microenvironment and discussed the genetic variation in GC IRGs. Results Eight IRGs, including CCL15, MSR1, GNAI1, NR3C1, ITGAV, NMB, AEN, and TGFBR1 were identified. Based on the prognostic signature, GC patients were distinguished into two subtype groups. As verified in multiple datasets, the prognostic signature exhibited good performance in predicting the prognosis (AUC = 0.803, P-value <0.001) and revealed the different clinical features and infiltrated immune cell types in the immune microenvironment. Conclusions In summary, we found that IRGs contributed to GC prognosis prediction and constructed an IRGs-based GC prognostic signature, which could serve as an effective prognostic stratification tool.
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Affiliation(s)
- Xianghui Li
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
- Department of Dermatology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Yuanyuan Chen
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Yuxiang Dong
- Second Clinical College of Nanjing Medical University, Nanjing, 210029, China
| | - Zhongjin Ma
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wenjun Zheng
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Youkun Lin
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
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Meng X, Wang D, Sun X, Yuan J, Han J. Mapping the immunological battlefield in gastric cancer: prognostic implications of an immune gene expression signature. Discov Oncol 2023; 14:212. [PMID: 37999824 PMCID: PMC10673795 DOI: 10.1007/s12672-023-00834-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is a heterogeneous malignancy with variable clinical outcomes. The immune system has been implicated in GC development and progression, highlighting the importance of immune-related gene expression patterns and their prognostic significance. OBJECTIVE This study aimed to identify differentially expressed immune-related genes (DEIRGs) and establish a prognostic index for GC patients using comprehensive bioinformatic analyses. METHODS We integrated RNA sequencing data from multiple databases and identified DEIRGs by overlapping differentially expressed genes with immune-related genes. Functional enrichment analysis was performed to uncover the biological processes and signaling pathways associated with DEIRGs. We conducted a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key gene modules related to with GC. Cox regression analysis was conducted to determine independent prognostic DEIRGs for overall survival prediction. Based on these findings, we developed an immune-related gene prognostic index (IRGPI) based on these findings. The prognostic value of the IRGPI was validated using survival analysis and an independent validation cohort. Functional enrichment analysis, gene mutation analysis, and immune cell profiling were performed to gain insights into the biological functions and immune characteristics associated with the IRGPI-based subgroups. RESULTS We identified 493 DEIRGs significantly enriched in immune-related biological processes and signaling pathways associated with GC. WGCNA analysis revealed a significant module (turquoise module) associated with GC, revealing potential therapeutic targets. Cox regression analysis identified RNASE2, CGB5, CTLA4, and DUSP1 as independent prognostic DEIRGs. The IRGPI, incorporating the expression levels of these genes, demonstrated significant prognostic value in predicting overall survival. The IRGPI-based subgroups exhibited distinct biological functions, genetic alterations, and immune cell compositions. CONCLUSION Our study identified DEIRGs and established a prognostic index (IRGPI) for GC patients. The IRGPI exhibited promising prognostic potential and provided insights into GC tumor biology and immune characteristics. These findings have implications for guiding therapeutic strategies.
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Affiliation(s)
- Xianhong Meng
- The Fourth Affiliated Hospital of Harbin Medical University, Yiyuan Street No. 37, Harbin, Heilongjiang Province, 150001, China
| | - Daxiu Wang
- The Fourth Affiliated Hospital of Harbin Medical University, Yiyuan Street No. 37, Harbin, Heilongjiang Province, 150001, China
| | - Xueying Sun
- The Fourth Affiliated Hospital of Harbin Medical University, Yiyuan Street No. 37, Harbin, Heilongjiang Province, 150001, China
| | - Jiangfeng Yuan
- The Fourth Affiliated Hospital of Harbin Medical University, Yiyuan Street No. 37, Harbin, Heilongjiang Province, 150001, China
| | - Jiwu Han
- The Fourth Affiliated Hospital of Harbin Medical University, Yiyuan Street No. 37, Harbin, Heilongjiang Province, 150001, China.
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Gong X, Li M, Zhang L, Huang S, Wang G. Identification and functional analysis of myeloid differentiation factor 88 (MyD88) in early development of Haliotis diversicolor. Fish Shellfish Immunol 2023; 142:109085. [PMID: 37722440 DOI: 10.1016/j.fsi.2023.109085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/22/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Myeloid differentiation factor 88 (MyD88) is a universal adaptor protein and plays an important role in the signal transduction of Toll like receptors (TLR) family. In this study, the MyD88 gene from the Haliotis diversicolor (hdMyD88) was identified. The full-length cDNA of hdMyD88 has a 1927 base pairs (bp), with an open reading frame of 1314 bp encoding 437 amino acids including a death domain (DD) at the N-terminus and TIR domain at the C-terminus which are typical features of MyD88 family proteins. Three conserved boxes are also found in the hdMyD88, which are similar to MyD88 in vertebrates. The expression levels of hdMyD88 mRNA at different early embryonic developmental stages of abalone were measured by qPCR revealed that their constitutive expression at all developmental stages analyzed with the considerably highest values at 8 cell stage and the lowest level at the trochosphere stage. Additionally, the mRNA expression of hdMyD88 decreased significantly (P < 0.05) after MyD88-dsRNA soak in the stage of trochosphere and veliger than EGFP-dsRNA group and blank control group. Whole embryo in situ hybridization showed that the positive signals of hdMyD88 were in visceral mass of trochophore larvae and veliger larvae. These results indicate hdMyD88 may could respond to pathogenic infection and may play an important role in early innate immunity in the process of abalone larval development.
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Affiliation(s)
- Xiaoting Gong
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Min Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Lili Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Shiyu Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Guodong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China.
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Fei H, Han X, Wang Y, Li S. Novel immune-related gene signature for risk stratification and prognosis prediction in ovarian cancer. J Ovarian Res 2023; 16:205. [PMID: 37858138 PMCID: PMC10585734 DOI: 10.1186/s13048-023-01289-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/27/2021] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND The immune system played a multifaceted role in ovarian cancer (OC) and was a significant mediator of ovarian carcinogenesis. Various immune cells and immune gene products played an integrated role in ovarian cancer (OC) progression, proved the significance of the immune microenvironment in prognosis. Therefore, we aimed to establish and validate an immune gene prognostic signature for OC patients' prognosis prediction. METHODS Differently expressed Immune-related genes (DEIRGs) were identified in 428 OC and 77 normal ovary tissue specimens from 9 independent GEO datasets. The Cancer Genome Atlas (TCGA) cohort was used as a training cohort, Univariate Cox analysis was used to identify prognostic DEIRGs in TCGA cohort. Then, an immune gene-based risk model for prognosis prediction was constructed using the LASSO regression analysis, and validated the accuracy and stability of the model in 374 and 93 OC patients in TCGA training cohort and International Cancer Genome Consortium (ICGC) validation cohort respectively. Finally, the correlation among risk score model, clinicopathological parameters, and immune cell infiltration were analyzed. RESULTS Five DEIRGs were identified to establish the immune gene signature and divided OC patients into the low- and high-risk groups. In TCGA and ICGC datasets, patients in the low-risk group showed a substantially higher survival rate than high-risk group. Receiver operating characteristic (ROC) curves, t-distributed stochastic neighbor embedding (t-SNE) analysis and principal component analysis (PCA) showed the good performance of the risk model. Clinicopathological correlation analysis proved the risk score model could serve as an independent prognostic factor in 2 independent datasets. CONCLUSIONS The prognostic model based on immune-related genes can function as a superior prognostic indicator for OC patients, which could provide evidence for individualized treatment and clinical decision making.
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Affiliation(s)
- Hongjun Fei
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai Jiao Tong University School of Medicine, No.910, Hengshan Road, Shanghai, 200030, China.
| | - Xu Han
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai Jiao Tong University School of Medicine, No.910, Hengshan Road, Shanghai, 200030, China
| | - Yanlin Wang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai Jiao Tong University School of Medicine, No.910, Hengshan Road, Shanghai, 200030, China
| | - Shuyuan Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai Jiao Tong University School of Medicine, No.910, Hengshan Road, Shanghai, 200030, China.
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Hu Y, Zhang X, Li Q, Zhou Q, Fang D, Lu Y. An immune and epigenetics-related scoring model and drug candidate prediction for hepatic carcinogenesis via dynamic network biomarker analysis and connectivity mapping. Comput Struct Biotechnol J 2023; 21:4619-4633. [PMID: 37817777 PMCID: PMC10561057 DOI: 10.1016/j.csbj.2023.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high mortality. This study aimed to build a prognostic signature for HCC patients based on immune-related genes (IRGs) and epigenetics-related genes (EPGs). RNA-seq data from Gene Expression Omnibus were used for dynamic network biomarker (DNB) analysis to identify 56 candidate IRG-EPG-DNBs and their first-neighbor genes. These genes were screened using LASSO-Cox regression analysis to finally obtain five candidate genes-RNF2, YBX1, EZH2, CAD, and PSMD1-which constituted the prognostic signature panel. According to this panel, patients in The Cancer Genome Atlas and International Cancer Genome Consortium were divided into high- and low-risk groups. The prognosis, clinicopathological features, and immune cell infiltration significantly differed between the two risk groups. The prognostic ability of the signature panel and expression profiling were further validated using online databases. We used an independent cohort of patients to validate the expression profiles of the five genes using reverse transcription-PCR. CMap and CellMiner predicted four small molecule drug-protein pairs based on the five prognostic genes. Of them, two market drugs approved by the Food and Drug Administration (AT-13387 and KU-55933) have emerged as candidates for HCC study. This new signature panel may serve as a potential prognostic marker, engendering the possibility of novel personalized therapy with classification of HCC patients.
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Affiliation(s)
- Yuting Hu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xingli Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qingya Li
- Henan University of Chinese Medicine, Henan 450046, China
| | - Qianmei Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dongdong Fang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yiyu Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Wang T, Xu S, Zhang L, Yang T, Fan X, Zhu C, Wang Y, Tong F, Mei Q, Pan A. Identification of immune-related lncRNA in sepsis by construction of ceRNA network and integrating bioinformatic analysis. BMC Genomics 2023; 24:484. [PMID: 37620751 PMCID: PMC10464037 DOI: 10.1186/s12864-023-09535-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/07/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Sepsis is a high mortality disease which seriously threatens human life and health, for which the pathogenetic mechanism still unclear. There is increasing evidence showed that immune and inflammation responses are key players in the development of sepsis pathology. LncRNAs, which act as ceRNAs, have critical roles in various diseases. However, the regulatory roles of ceRNA in the immunopathogenesis of sepsis have not yet been elucidated. RESULTS In this study, we aimed to identify immune biomarkers associated with sepsis. We first generated a global immune-associated ceRNA (IMCE) network based on data describing interactions pairs of gene-miRNA and miRNA-lncRNA. Afterward, we excavated a dysregulated sepsis immune-associated ceRNA (SPIMC) network from the global IMCE network by means of a multi-step computational approach. Functional enrichment indicated that lncRNAs in SPIMC network have pivotal roles in the immune mechanism underlying sepsis. Subsequently, we identified module and hub genes (CD4 and STAT4) via construction of a sepsis immune-related PPI network. Then, we identified hub genes based on the modular structure of PPI network and generated a ceRNA subnetwork to analyze key lncRNAs associated with sepsis. Finally, 6 lncRNAs (LINC00265, LINC00893, NDUFA6-AS1, NOP14-AS1, PRKCQ-AS1 and ZNF674-AS1) that identified as immune biomarkers of sepsis. Moreover, the CIBERSORT algorithm and the infiltration of circulating immune cells types were performed to identify the inflammatory state of sepsis. Correlation analyses between immune cells and sepsis immune biomarkers showed that the LINC00265 was strongly positive correlated with the macrophages M2 (r = 0.77). CONCLUSION Collectively, these results may suggest that these lncRNAs (LINC00265, LINC00893, NDUFA6-AS1, NOP14-AS1, PRKCQ-AS1 and ZNF674-AS1) played important roles in the immune pathogenesis of sepsis and provide potential therapeutic targets for further researches on immune therapy treatment in patients with sepsis.
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Affiliation(s)
- Tianfeng Wang
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Zhang
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Tianjun Yang
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Xiaoqin Fan
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Chunyan Zhu
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Yinzhong Wang
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Fei Tong
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China
| | - Qing Mei
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China.
| | - Aijun Pan
- Department of Critical Care Medicine, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui Province, China.
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Shen T, Wang H, Hu R, Lv Y. Developing neural network diagnostic models and potential drugs based on novel identified immune-related biomarkers for celiac disease. Hum Genomics 2023; 17:76. [PMID: 37587523 PMCID: PMC10433645 DOI: 10.1186/s40246-023-00526-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/02/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND As one of the most common intestinal inflammatory diseases, celiac disease (CD) is typically characterized by an autoimmune disorder resulting from ingesting gluten proteins. Although the incidence and prevalence of CD have increased over time, the diagnostic methods and treatment options are still limited. Therefore, it is urgent to investigate the potential biomarkers and targeted drugs for CD. METHODS Gene expression data was downloaded from GEO datasets. Differential gene expression analysis was performed to identify the dysregulated immune-related genes. Multiple machine algorithms, including randomForest, SVM-RFE, and LASSO, were used to select the hub immune-related genes (HIGs). The immune-related genes score (IG score) and artificial neural network (ANN) were constructed based on HIGs. Potential drugs targeting HIGs were identified by using the Enrichr platform and molecular docking method. RESULTS We identified the dysregulated immune-related genes at a genome-wide level and demonstrated their roles in CD-related immune pathways. The hub genes (MR1, CCL25, and TNFSF13B) were further screened by integrating several machine algorithms. Meanwhile, the CD patients were divided into distinct subtypes with either high- or low-immunoactivity using single-sample gene set enrichment analysis (ssGSEA) and consensus clustering. By constructing IG score based on HIGs, we found that patients with high IG score were mainly attributed to high-immunoactivity subgroups, which suggested a strong link between HIGs and immunoactivity of CD patients. In addition, the novel constructed ANN model showed the sound diagnostic ability of HIGs. Mechanistically, we validated that the HIGs play pivotal roles in regulating CD's immune and inflammatory state. Through targeting the HIGs, we also found potential drugs for anti-CD treatment by using the Enrichr platform and molecular docking method. CONCLUSIONS This study unveils the HIGs and elucidates the networks regulated by these genes in the context of CD. It underscores the pivotal significance of HIGs in accurately predicting the presence or absence of CD in patients. Consequently, this research offers promising prospects for the development of diagnostic biomarkers and therapeutic targets for CD.
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Affiliation(s)
- Tao Shen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China.
| | - Haiyang Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Rongkang Hu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yanni Lv
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases, Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, China
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Feng J, Huang Y, Huang M, Luo J, Que L, Yang S, Jian J. A novel perlucin-like protein (PLP) protects Litopenaeus vannamei against Vibrio harveyi infection. Fish Shellfish Immunol 2023; 139:108932. [PMID: 37414305 DOI: 10.1016/j.fsi.2023.108932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/02/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
C-type lectins (CTLs), as pattern recognition receptors (PRRs), play an important role in the innate immunity of Litopenaeus vannamei. In this study, a novel CTL, named perlucin-like protein (PLP), was identified from L. vannamei, which shared homology sequences of PLP from Penaeus monodon. PLP from L. vannamei was expressed in the hepatopancreas, eyestalk, muscle and brain and could be activated in the tissues (hepatopancreas, muscle, gill and intestine) after infection with the pathogen Vibrio harveyi. Bacteria (Vibrio alginolyticus, V. parahaemolyticus, V. harveyi, Streptococcus agalactiae and Bacillus subtilis) could be bound and agglutinated by the PLP recombinant protein in a Ca2+-dependent manner. Moreover, PLP could stabilise the expression of the immune-related genes (ALF, SOD, HSP70, Toll4 and IMD) and apoptosis gene (Caspase2). The RNAi of PLP could remarkably affect the expression of antioxidant gene, antimicrobial peptide genes, other CTLs, apoptosis genes, Toll signaling pathways, and IMD signaling pathways. Moreover, PLP reduced the bacterial load in the hepatopancreas. These results suggested that PLP was involved in the innate immune response against V. harveyi infection by recognising bacterial pathogens and activating the expression of immune-related and apoptosis genes.
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Affiliation(s)
- Jiamin Feng
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Yongxiong Huang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Meiling Huang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Junliang Luo
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Liwen Que
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Shiping Yang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
| | - Jichang Jian
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
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Xie JY, Wang WJ, Wang N, Dong Q, Han H, Feng YP, Yuan Y, Feng J, Chen K. A novel immune-related gene signature correlated with serum IL33 expression in acute myeloid leukemia prognosis. Am J Transl Res 2023; 15:4332-4344. [PMID: 37434810 PMCID: PMC10331686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/15/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE To identify and validate the immune-related gene signature in patients with acute myeloid leukemia (AML). METHODS Differentially expressed genes (DEGs) profiles and survival data were obtained from The Cancer Genome Atlas (TCGA), following screened immune-associated genes from the InnateDB database. Subsequently, the weighted gene co-expression network analysis (WGCNA) was used to detect functional modules, and survival analysis was performed. The least absolute shrinkage and selection operator (LASSO) regression model combined with a partial likelihood-based Cox proportional hazard regression model was applied to select prognostic genes, and the ESTIMATE algorithm was used to construct an immune score-based risk assessment model. Finally, two independent datasets from the Gene Expression Omnibus (GEO) and our clinical data were used for external validation. Moreover, a subpopulation of the immune microenvironment cells was analyzed by the CIBERSORT algorithm, and its related serum indicator was identified by the enzyme-linked immunosorbent assay (ELISA) in clinical samples. RESULTS Finally, CTSD, GNB2, CDK6, and WAS were identified as the immune-related gene signature, and the risk stratification model was validated in both the GSE12417 database and our clinical cohort. Furthermore, the fraction of activated mast cells was identified. CIBERSORT algorithm showed that these cells have a positive association with prognosis. In addition, mast cell stimulator IL-33 was markedly decreased in AML patients with poor prognoses. CONCLUSION A novel immune-related gene signature (CTSD, GNB2, CDK6 and WAS) and its associated plasma indicator (mast cells activator, IL-33) were found to have prognostic value in AML patients.
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Affiliation(s)
- Jin-Ye Xie
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Wei-Jia Wang
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
- Department of Medical Research, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Nan Wang
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Qian Dong
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Hui Han
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Yan-Pin Feng
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Yong Yuan
- Department of Cardiovascular Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
- Department of Medical Research, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Juan Feng
- School of Medicine, Foshan UniversityFoshan 528225, Guangdong, China
| | - Kang Chen
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
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Yao J, Liang Z, Duan L, G Y, Liu J, An G. Construction of a novel immune response prediction signature to predict the efficacy of immune checkpoint inhibitors in clear cell renal cell carcinoma patients. Heliyon 2023; 9:e15925. [PMID: 37484396 PMCID: PMC10360603 DOI: 10.1016/j.heliyon.2023.e15925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 07/25/2023] Open
Abstract
Background Immune checkpoint inhibitor (ICI) treatment has enhanced survival outcomes in clear cell renal cell carcinoma (ccRCC) patients. Nevertheless, the effectiveness of immunotherapy in ccRCC patients is restricted and we intended to develop and characterize an immune response prediction signature (IRPS) to forecast the efficacy of immunotherapy. Methods RNA-seq expression profile and clinicopathologic characteristics of 539 kidney cancer and 72 patients with normal specimens, were downloaded from the Cancer Genome Atlas (TCGA) database, while the Gene Expression Omnibus (GEO) database was used as the validation set, which included 24 ccRCC samples. Utilization of the TCGA data and immune genes databases (ImmPort and the InnateDB), we explored through Weighted Gene Co-expression Network Analysis (WGCNA), along with Least Absolute Shrinkage and Selection Operator method (LASSO), and constructed an IRPS for kidney cancer patients. GSEA and CIBERSORT were performed to declare the molecular and immunologic mechanism underlying the predictive value of IRPS. The Human Protein Atlas (HPA) was deployed to verify the protein expressions of IRPS genes. Tumor immune dysfunction and exclusion (TIDE) score and immunophenoscore (IPS) were computed to determine the risk of immune escape and value the discrimination of IRPS. A ccRCC cohort with anti-PD-1 therapy was obtained as an external validation data set to verify the predictive value of IRPS. Results We constructed a 10 gene signature related to the prognosis and immune response of ccRCC patients. Considering the IRPS risk score, patients were split into high and low risk groups. Patients with high risk in the TCGA cohort tended towards advanced tumor stage and grade with poor prognosis (p < 0.001), which was validated in GEO database (p = 0.004). High-risk group tumors were related with lower PD-L1 expression, higher TMB, higher MSIsensor score, lower IPS, higher TIDE score, and enriched Treg cells, which might be the potential mechanism of immune dysfunction and exclusion. Patients in the IRPS low risk group had better PFS (HR:0.73; 95% CI: 0.54-1.0; P = 0.047). Conclusion A novel biomarker of IRPS was constructed to predict the benefit of immunotherapy, which might lead to more individualized prognoses and tailored therapy for kidney cancer patients.
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Affiliation(s)
- Jiannan Yao
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ziwei Liang
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ling Duan
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yang G
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jian Liu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Guangyu An
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
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Chen ZD, Luo JY, Ye YP, Dang YW. Identification of immune-related genes and patient selection for hepatocellular carcinoma immunotherapy. Transl Cancer Res 2023; 12:1210-1231. [PMID: 37304539 PMCID: PMC10248567 DOI: 10.21037/tcr-22-2304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/07/2023] [Indexed: 06/13/2023]
Abstract
Background Hepatocellular carcinoma (HCC) is a malignant disease with a poor prognosis. Among the treatment strategies for HCC, tumor immunotherapy (TIT) is a promising research hotspot, in which identifying novel immune-related biomarkers and selecting suitable patient population are urgent issues to be solved. Methods In this study, an abnormal expression map of HCC cell genes was constructed using public high-throughput data from 7,384 samples (3,941 HCC vs. 3,443 non-HCC tissues). Through single-cell RNA sequencing (scRNA-seq) cell trajectory analysis, the genes defined as potential drivers of HCC cell differentiation and development were selected. By screening for both immune-related genes and those associated with high differentiation potential in HCC cell development, a series of target genes were identified. Coexpression analysis was performed using Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) to find the specific candidate genes involved in similar biological processes. Subsequently, nonnegative matrix factorization (NMF) was conducted to select patients suitable for HCC immunotherapy based on the coexpression network of candidate genes. Results HSP90AA1, CDK4, HSPA8, HSPH1, and HSPA5 were identified as promising biomarkers for prognosis prediction and immunotherapy of HCC. Through the use of our molecular classification system, which was based on a function module containing 5 candidate genes, patients with specific characteristics were found to be suitable candidates for TIT. Conclusions These findings provide new insights into the selection of candidate biomarkers and patient populations for future HCC immunotherapy.
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Affiliation(s)
- Zhen-Dong Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jia-Yuan Luo
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu-Ping Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Song J, Ma Z, Zhang H, Liang T, Zhang J. Identification of novel biomarkers linking depressive disorder and Alzheimer's disease based on an integrative bioinformatics analysis. BMC Genom Data 2023; 24:22. [PMID: 37061663 PMCID: PMC10105463 DOI: 10.1186/s12863-023-01120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 03/16/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Previous reports revealed that a history of major depressive disorder (MDD) increased the risk of Alzheimer's disease (AD). The immune disorder is associated with MDD and AD pathophysiology. We aimed to identify differentially expressed immune-related genes (DEIRGs) that are involved in the pathogenesis of MDD and AD. METHODS We downloaded mRNA expression profiles (GSE76826 and GSE5281) from the Gene Expression Omnibus (GEO) database. The R software was used to identify DEIRGs for the two diseases separately. Functional enrichment analysis and PPI network of DEIRGs were performed. Finally, the relationship between shared DEIRGs and immune infiltrates of AD and MDD were analyzed, respectively. RESULTS A total of 121 DEIRGs linking AD and MDD were identified. These genes were significantly enriched in immune-related pathways, such as the JAK-STAT signaling pathway, regulation of chemotaxis, chemotaxis, cytokine-cytokine receptor interaction, and primary immunodeficiency. Furthermore, three shared DEIRGs (IL1R1, CHGB, and NRG1) were identified. Correlation analysis between DEIRGs and immune cells revealed that IL1R1 and NRG1 had a negative or positive correlation with some immune cells both in AD and MDD. CONCLUSION Both DEIRGs and immune cell infiltrations play a vital role in the pathogenesis of AD and MDD. Our findings indicated that there are common genes and biological processes between MDD and AD, which provides a theoretical basis for the study of the comorbidity of MDD and AD.
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Affiliation(s)
- Jin Song
- Out-Patient Department, Wuhan Mental Health Center, Wuhan, 430012, Hubei Province, China
- Out-Patient Department, Wuhan Hospital for Psychotherapy, Wuhan, 430012, Hubei Province, China
| | - Zilong Ma
- Ward of Sleep Disorders, Wuhan Mental Health Center, Wuhan, 430012, Hubei Province, China
- Ward of Sleep Disorders, Wuhan Hospital for Psychotherapy, Wuhan, 430012, Hubei Province, China
| | - Huishi Zhang
- Out-Patient Department, Wuhan Mental Health Center, Wuhan, 430012, Hubei Province, China.
- Out-Patient Department, Wuhan Hospital for Psychotherapy, Wuhan, 430012, Hubei Province, China.
- Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei Province, 430012, China.
| | - Ting Liang
- National Medical Institution Conducting Clinical Trials Office, Wuhan Mental Health Center, Wuhan, 430012, Hubei Province, China
- National Medical Institution Conducting Clinical Trials Office, Wuhan Hospital for Psychotherapy, Wuhan, 430012, Hubei Province, China
| | - Jun Zhang
- Ward of Traditional Chinese Medicine, Wuhan Mental Health Center, Wuhan, 430012, Hubei Province, China
- Ward of Traditional Chinese Medicine, Wuhan Hospital for Psychotherapy, Wuhan, 430012, Hubei Province, China
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20
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Farhadi A, Tang S, Huang M, Yu Q, Xu C, Li E. Identification of key immune and stress related genes and pathways by comparative analysis of the gene expression profile under multiple environmental stressors in pacific white shrimp (Litopenaeus vannamei). Fish Shellfish Immunol 2023; 135:108695. [PMID: 36935045 DOI: 10.1016/j.fsi.2023.108695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 11/27/2022] [Revised: 03/01/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Water salinity, pH, and nitrite concentration are considered environmental factors affecting the growth rate, survival, health, and physiological conditions of aquatic animals. The identification of key genes that are involved in the response to environmental stressors is essential for controlling stress in aquatic animals and sustainable aquaculture. In this study, RNA sequencing was performed to identify the differentially expressed genes (DEGs) and biological pathways that are involved in the response of the hepatopancreas to environmental stressors, including low salinity stress, nitrite stress, low pH stress, and high pH stress. The DEGs were enriched in biological pathways related to immune response, energy metabolism, oxidative stress response, hemostasis, and enzymatic activity of the hepatopancreas. In addition to the identification of DEGs related to each stressor, some DEGs were found to be expressed among all groups. The most important overlapping DEGs under multiple stressors were juvenile hormone esterase-like protein 2 (JHE-like), myosin light chain, C-type lectin 2, myosin-9-like, anti-lipopolysaccharide factor 1 (ALF-1), peroxisomal acyl-coenzyme An oxidase 1-like (ACX1), hepatic lectin-like, venom phosphodiesterase 2-like, hemolymph clottable protein-like (CP), cathepsin L, and Ras-like protein 2. The results of the present study provide additional information regarding the transcriptional response of the hepatopancreas to low salinity, nitrite, low pH, and high pH stress. Moreover, the discovery of several overlapping DEGs among different stressors provided a better understanding of the molecular function of the hepatopancreas.
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Affiliation(s)
- Ardavan Farhadi
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Shangshang Tang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Maoxian Huang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Qiuran Yu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Erchao Li
- School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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21
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Yu J, Lai M, Zhou Z, Zhou J, Hu Q, Li J, Li H, Chen L, Wen L, Zhou M, Cai L. The PTEN-associated immune prognostic signature reveals the landscape of the tumor microenvironment in glioblastoma. J Neuroimmunol 2023; 376:578034. [PMID: 36791582 DOI: 10.1016/j.jneuroim.2023.578034] [Citation(s) in RCA: 1] [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: 11/23/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Glioblastoma (GBM) is a common brain tumor with a complex and diverse tumor microenvironment (TME). As PTEN mutation is the most common mutation in GBM, we aimed to investigate how PTEN mutation regulates the immune response in GBM TME and thus affects the prognosis of GBM patients. In this study, we conducted a comprehensive analysis of multiple levels of data, including whole-exome sequencing (WES), transcriptome RNA sequencing, patient survival and immune signatures, to study the relationship between PTEN mutation and TME in GBM. We developed an immune-related prognostic signature (IPS) based on the PTEN-associated immune-related genes (IRGs), and the IPS exhibited a powerful prognosis prediction capacity in different GBM cohorts. A scoring nomogram based on the IPS was also established for clinical application. In addition, the correlations of the IPS with tumor immune cell infiltration and immune checkpoints were systematically analyzed. This study illustrates the influence of PTEN mutation on the immune microenvironment of GBM. Our IPS, which is sensitive to PTEN mutation status, can enhance the prognosis prediction ability for GBM patients and provides potential targets for immunotherapy.
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Affiliation(s)
- Jiayin Yu
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Mingyao Lai
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Zhaoming Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China; Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China.
| | - Jiangfen Zhou
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Qingjun Hu
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Juan Li
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Hainan Li
- Department of Pathology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Longhua Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Lei Wen
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Linbo Cai
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou 510510, China.
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Bidkhori HR, Farshchian M, Kazemi Noughabi M, Hassanzadeh H, Rafatpanah H. Alteration of immunoregulatory genes expression in mesenchymal stromal cells upon priming with B18R as an interferon binding protein. Iran J Basic Med Sci 2023; 26:241-247. [PMID: 36742146 PMCID: PMC9869884 DOI: 10.22038/ijbms.2022.67353.14771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/06/2022] [Indexed: 02/07/2023]
Abstract
Objectives The B18R protein encoded by the Vaccinia virus decoys Type 1 interferons and inhibits the activity of several type I IFN members. In vitro transcription protocols benefit from this molecule's involvement in enhancing cell viability by inhibiting interferon signal transduction. As a result of their immunomodulatory properties and potential to regenerate, mesenchymal stromal cells (MSCs) are increasingly considered an alternative treatment for a wide range of immune disorders. In this study, we investigated the modification of expression of several genes involved in immune-related pathways after preconditioning MSCs with two immune stimuli, including poly(I:C) and LPS. Materials and Methods ASCs were isolated and primed with B18R, and after exposure to poly(I:C) and LPS, the expression of the same sets of genes as in the previous experiment was evaluated. Following total RNA isolation from primed cells and cDNA preparation, real-time quantitative PCR was performed for several immunomodulatory and immune-related genes, including IDO1, TDO2, COX-2, TGF- β 1, TNF- α, IL-1 β , IL-6, TLR3, TLR4, and MCP-1. Results Pretreatment of MSCs with poly(I:C) and LPS significantly increased the expression of all mentioned genes, while upon the B18R challenge followed by poly(I:C) and LPS treatment, they were down-regulated. Finally, it was observed that the relative expression level of IFN -β has significantly decreased in MSCs+B18R+poly(I:C) and LPS in comparison with these groups without B18R. Conclusion The data indicated that the presence of B18R prevents the overexpression of several immune-related genes, which are overexpressed in the in vitro inflammatory environment.
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Affiliation(s)
- Hamid Reza Bidkhori
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Moein Farshchian
- Stem Cells and Regenerative Medicine Department, Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran
| | | | - Halimeh Hassanzadeh
- Stem Cells and Regenerative Medicine Department, Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran
| | - Houshang Rafatpanah
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran,Corresponding author: Houshang Rafatpanah. Immunology Research Center, Inflammation and Inflammatory Diseases Division, Faculty of Medicine, Mashhad University of Medical Sciences, Azadi-Square, Medical Campus, Mashhad, Iran. Tel: +98-51-3 800 2376;
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Sourani Z, Shirian S, Shafiei S, Mosayebi N, Nematollahi A. Modulation of Immune-Related Gene Expressions in Zebrafish (Danio rerio) by Dietary Purslane (Portulaca oleracea) Extract. Mar Biotechnol (NY) 2023; 25:214-221. [PMID: 36609893 DOI: 10.1007/s10126-022-10195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/08/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
To promote fish's immunity against pathogens in the aquaculture industry, fish dietary fortification with additives or compounds has increasingly attracted attention. In the present study, zebrafish (Danio rerio) was used as an animal model to investigate the effects of purslane, Portulaca oleracea, extract (PE) on the relative expression level of some immune-related genes. A total of 300 zebrafish were randomly divided into four treatment groups and fed for 8 weeks with the basal diets supplemented with 0.5, 1, 1.5, and 2% of PE. The control group was fed with a basal diet without PE. At the end of 8 weeks, the mRNA expression levels of interleukin 1-beta (IL-1β), interleukin 10 (IL-10), transforming growth factor-beta (TGF-β), tumor necrosis factor-alpha (TNF-α), superoxide dismutase (SOD), and lysozyme (LYZ) in the fish were evaluated. The results showed that the mRNA expression level of IL-1β was significantly upregulated in the fish fed with 1 and 2% PE compared to the control group (p < 0.05). Moreover, the evaluation of the mRNA expression level of TGF-β was significantly increased in a dose-dependent manner in the 1.5 and 2% fed groups compared to the control group (p < 0.05). However, the IL-10 was significantly downregulated in all treated groups compared to the control group (p < 0.05). The expression of the TNF-α gene was not affected amongst all groups by the inclusion of PE in the zebrafish diet (p > 0.05). Based on the results, the diet supplemented with 1.5 and 2% PE significantly upregulated the mRNA expression levels of LYZ and SOD, respectively, compared to the control group (p < 0.05). In conclusion, dietary inclusion of PE may result in beneficial effects on some immune responses via upregulation of some immune genes in zebrafish.
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Affiliation(s)
- Zahra Sourani
- Department of Pathology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Sadegh Shirian
- Department of Pathology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Shafigh Shafiei
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.
| | - Nadia Mosayebi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Amin Nematollahi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
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Chen ZH, Zhang WY, Ye H, Guo YQ, Zhang K, Fang XM. A signature of immune-related genes correlating with clinical prognosis and immune microenvironment in sepsis. BMC Bioinformatics 2023; 24:20. [PMID: 36650470 PMCID: PMC9843880 DOI: 10.1186/s12859-023-05134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Immune-related genes (IRGs) remain poorly understood in their function in the onset and progression of sepsis. METHODS GSE65682 was obtained from the Gene Expression Omnibus database. The IRGs associated with survival were screened for subsequent modeling using univariate Cox regression analysis and least absolute shrinkage and selection operator in the training cohort. Then, we assessed the reliability of the 7 IRGs signature's independent predictive value in the training and validation cohorts following the creation of a signature applying multivariable Cox regression analysis. After that, we utilized the E-MTAB-4451 external dataset in order to do an independent validation of the prognostic signature. Finally, the CIBERSORT algorithm and single-sample gene set enrichment analysis was utilized to investigate and characterize the properties of the immune microenvironment. RESULTS Based on 7 IRGs signature, patients could be separated into low-risk and high-risk groups. Patients in the low-risk group had a remarkably increased 28-day survival compared to those in the high-risk group (P < 0.001). In multivariable Cox regression analyses, the risk score calculated by this signature was an independent predictor of 28-day survival (P < 0.001). The signature's predictive ability was confirmed by receiver operating characteristic curve analysis with the area under the curve reaching 0.876 (95% confidence interval 0.793-0.946). Moreover, both the validation set and the external dataset demonstrated that the signature had strong clinical prediction performance. In addition, patients in the high-risk group were characterized by a decreased neutrophil count and by reduced inflammation-promoting function. CONCLUSION We developed a 7 IRGs signature as a novel prognostic marker for predicting sepsis patients' 28-day survival, indicating possibilities for individualized reasonable resource distribution of intensive care unit.
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Affiliation(s)
- Zhong-Hua Chen
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China ,grid.415644.60000 0004 1798 6662Department of Anesthesiology, Shaoxing People’s Hospital, Shaoxing, China
| | - Wen-Yuan Zhang
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China
| | - Hui Ye
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China
| | - Yu-Qian Guo
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China
| | - Kai Zhang
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China
| | - Xiang-Ming Fang
- grid.13402.340000 0004 1759 700XDepartment of Anesthesiology and Intensive Care, The First Affiliated Hospital, School of Medicine, Zhejiang University, QingChun Road 79, Hangzhou, 310003 China
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Zhou L, Chu L, Du J, Nie Z, Cao L, Gao J, Xu G. Oxidative stress and immune response of hepatopancreas in Chinese mitten crab Eriocheir sinensis under lipopolysaccharide challenge. Comp Biochem Physiol C Toxicol Pharmacol 2023; 263:109495. [PMID: 36280105 DOI: 10.1016/j.cbpc.2022.109495] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022]
Abstract
Chinese mitten crab (Eriocheir sinensis; H. Milne Edwards, 1853) is one of the important farmed crustaceans in China. Lipopolysaccharide (LPS), as a harmful factor, is prone to occur during the farming process of crabs. Aiming to test the hypothesis that damage degrees of the hepatopancreas in E. sinensis is correlated to LPS concentrations, in this study, E. sinensis were injected with LPS (50 μg/kg, and 500 μg/kg) and analyzed for the activity of antioxidant and immune-related enzymes, immune-related gene expression, and histopathological of hepatopancreas. As result, the hepatopancreas of E. sinensis immune-related genes, i.e., Dorsal, HSP90, Toll2, TLRs, Tube, and proPO, were significantly affected by LPS challenge. Among immune-related genes, Dorsal and proPO might play key roles in combating the LPS challenge. The activity of CAT gradually decreased with the increase of time, and the total antioxidant capacity was decreased after LPS challenge, indicating the inhibition of LPS on the antioxidant system. Interestingly, the decreasing trend of AKP and ACP activity suggested the immune system of crabs was affected by LPS challenge. The hepatopancreas section showed that the damage degree of hepatopancreas was different under the challenge of LPS with different concentrations, and the damage degree was proportional to the concentration. Our findings provide useful information for understanding the mechanism of hepatopancreas injury of E. sinensis induced by LPS infection.
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Affiliation(s)
- Lin Zhou
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Lanlu Chu
- Wuxi Biologics, 108 Meiliang Road, Mashan, Wuxi 214092, China
| | - Jinliang Du
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zhijuan Nie
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Liping Cao
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jiancao Gao
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Gangchun Xu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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Liu X, Liang C, Zhou M, Chang Z, Li L. Exposure of Cyprinus carpio var. larvae to PVC microplastics reveals significant immunological alterations and irreversible histological organ damage. Ecotoxicol Environ Saf 2023; 249:114377. [PMID: 36508842 DOI: 10.1016/j.ecoenv.2022.114377] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/19/2022] [Revised: 11/15/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Microplastics have become pervasive in ambient aquatic ecosystems over the last decade and are currently a serious global scale concern. To evaluate the potential toxic effects of PVC (polyvinyl chloride) microplastics on the immune functions of freshwater fish, this study undertook a conducted chronic 60-day dietary exposure experiment with Cyprinus carpio var. larvae. We exposed the fish to four microplastic treatments of different concentrations (food rationed diets): no-plastic (control), 10%, 20% and 30%. At the end of the experimental period the impacts of microplastics on the histology, biochemistry, ROS (reactive oxygen species) levels and gene transcription of immune organs were investigated. The results revealed that PVC microplastics induced cytoplasmic vacuolation in the liver, damaged villi in the intestine, inflammatory cell infiltration, hemosiderosis and vacuolar degeneration in the spleen, glomeruli tuft shrinkage and aggregation of melanin macrophage cells in the kidney. Moreover, following PVC microplastics exposure, ROS levels in the liver and protein levels of pro-inflammatory cytokines including IL-6, IL-8, and TNFα in the liver and serum were increased. Furthermore, modifications in the activities of non-specific immunoenzyme ACP (Acid phosphatase), AKP (alkaline phosphatase), LZM (lysozyme), and expression levels of a range of immune-related genes were observed. Using various techniques at the histological, biochemical and molecular levels, our findings demonstrated the effects of PVC microplastics on changes and imbalances in the immune status of carp. The results of this study provide basic toxicological data toward elucidating and quantifying the impacts of microplastics immunotoxicity on aquatic organisms.
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Affiliation(s)
- Xinya Liu
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang 453007, Henan, China
| | - Chaonan Liang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang 453007, Henan, China
| | - Miao Zhou
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang 453007, Henan, China
| | - Zhongjie Chang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang 453007, Henan, China
| | - Li Li
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang 453007, Henan, China.
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27
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Feng B, Zhou T, Guo Z, Jin J, Zhang S, Qiu J, Cao J, Li J, Peng X, Wang J, Xing Y, Ji R, Qiao L, Liang Y. Comprehensive analysis of immune-related genes for classification and immune microenvironment of asthma. Am J Transl Res 2023; 15:1052-1062. [PMID: 36915798 PMCID: PMC10006808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVES To determine the effects of immune-related genes (IRGs) and immune landscape of induced sputum, and develop novel, non-invasive diagnostic molecular therapeutic targets for asthma. METHODS GSE76262 datasets were used to identify differentially expressed IRGs in asthma. Key IRGs were detected using a protein-protein interaction network. Receiver operating characteristic (ROC) curves were analyzed to investigate the diagnostic value of key IRGs. Gene set enrichment analysis (GSEA) was performed with WebGestalt. Single-sample gene set enrichment analysis and CIBERSORT were used to investigate the immune landscape of induced sputum. RESULTS A total of 75 potential IRGs were associated with asthma, most of which were involved in the NF-kappa B signaling pathway. ROC analysis showed AUC values for the hub pathway ranging from 0.676-0.767, with moderate diagnostic value for asthma. We also identified IRGs-related cytokines (TNF-α, IL-1β, IL-8 and IL-6) in 76 asthma and 91 control serum samples to further explore diagnostic efficacy, showing a cumulative AUC of 0.998 for these four related cytokines. Analysis of immune cell infiltration levels showed that follicular helper T cells, activated dendritic cells, activated mast cells and eosinophils were significantly higher and macrophages M0 and macrophages M2 were significantly reduced in sputum from patients with asthma. CONCLUSIONS IRGs-related cytokines and immune infiltration may contribute to the diagnosis and immune classification of asthma.
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Affiliation(s)
- Bin Feng
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
| | - Tong Zhou
- Medical College of Soochow University Suzhou 215006, Jiangsu, China
| | - Zhiyi Guo
- Medical College of Soochow University Suzhou 215006, Jiangsu, China
| | - Jieyu Jin
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
| | - Sheng Zhang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
| | - Jun Qiu
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
| | - Jun Cao
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
| | - Jia Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine Shanghai 201209, China
| | - Xia Peng
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine Shanghai 201209, China
| | - Juan Wang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine Shanghai 201209, China
| | - Yanru Xing
- Basecare Medical Device Co., Ltd. Suzhou 215006, China
| | - Renxin Ji
- The School of International Medical Technology of Shanghai Sanda University Shanghai 201209, China
| | - Longwei Qiao
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University Suzhou 215006, Jiangsu, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University Suzhou 215006, Jiangsu, China
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Huang H, Zhou S, Zhao X, Wang S, Yu H, Lan L, Li L. Construction of a metabolism-related gene prognostic model to predict survival of pancreatic cancer patients. Heliyon 2022; 9:e12378. [PMID: 36820187 PMCID: PMC9938416 DOI: 10.1016/j.heliyon.2022.e12378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/15/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Pancreatic cancer (PC) is one of the most fatal malignant tumors, and is commonly diagnosed at an advanced stage with no effective therapy. Metabolism-related genes (MRGs) and immune-related genes (IRGs) play considerable roles in the tumor microenvironment. Therefore, an effective prediction model based on MRGs and IRGs could aid in the prognosis of PC. In this study, differential expression analysis was performed to gain 25 intersectional genes from 857 differentially expressed MRGs (DEMRGs), and 1353 differentially expressed IRGs, from The Cancer Genome Atlas database of PC. Cox and Lasso regression were applied and a five-DEMRGs prognostic model constructed. Survival analysis, ROC values, risk curve and validation analysis showed that the model could independently predict PC prognosis. In addition, the correlation analysis suggested that the five-DEMRGs prognostic model could reflect the status of the immune microenvironment, including Tregs, M1 macrophages and Mast cell resting. Therefore, our study provides new underlying predictive biomarkers and associated immunotherapy targets.
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Affiliation(s)
- Huimin Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, University Town, Chashan District, Wenzhou, Zhejiang Province, 325000, PR China,Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China
| | - Shipeng Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China
| | - Xingling Zhao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China
| | - Shitong Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China
| | - Huajun Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China,Corresponding author.
| | - Linhua Lan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Fanhai West Road, Wenzhou, Zhejiang Province, 325000, PR China,Corresponding author.
| | - Liyi Li
- The general surgery department of second affiliated hospital of Wenzhou medical university, No. 109, College West Road, Wenzhou, Zhejiang Province, 325002, Zhejiang, PR China,Corresponding author.
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Zhang Y, Zhu M, Xie L, Zhang H, Deng T. Identification and validation of key immune-related genes with promising diagnostic and predictive value in systemic sclerosis. Life Sci 2022; 312:121238. [PMID: 36460097 DOI: 10.1016/j.lfs.2022.121238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
AIMS To screen and confirm key immune-related genes (IRGs) with diagnostic and predictive value in systemic sclerosis (SSc) and provide potential therapeutic targets for patients with SSc. MATERIALS AND METHODS In Gene Expression Omnibus database (GEO), four datasets of gene expression profiling related to SSc were downloaded and used for the analysis in this study. After differential analysis of SSc cases and controls in GSE130955, the differentially expressed genes (DEGs) were overlapped with IRGs to obtain the immune-related differentially expressed genes (IR-DEGs) in SSc. In addition, functional annotation and pathway enrichment of IR-DEGs were conducted. The protein-protein interaction network (PPI) was constructed to identify key IR-DEGs. Using GSE58095, GSE181549 and GSE130953, the diagnostic and predictive abilities for the key IR-DEGs in SSc were validated. Finally, the screened key genes were confirmed in skin derived bleomycin (BLM)-induced SSc mice by Real-time PCR. KEY FINDINGS NGFR, TNFSF13B, FCER1G, GIMAP5, TYROBP and CSF1R may have important or very high diagnostic value for SSc. TYROBP and TNFSF13B had moderate and mild predictive value respectively in SSc patients after treatment. Real-time PCR assay further confirmed that the expressions of Ngfr, Tyrobp, Csf1r, Fcer1g and Gimap5 were significantly higher in skin of BLM-induced SSc mice than that in controls. SIGNIFICANCE The key IR-DEGs, including NGFR, TNFSF13B, TYROBP, CSF1R, FCER1G and GIMAP5, may become auxiliary diagnostic indicators and potential biomarkers for SSc. Moreover, TNFSF13B and TYROBP could have good prospects as predictive indicators in SSc patients that accepted cyclophosphamide or transplantation therapy.
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Affiliation(s)
- Yajie Zhang
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China; Key Laboratory of Diabetes Immunology, Ministry of Education, Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - Mingxin Zhu
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China; Key Laboratory of Diabetes Immunology, Ministry of Education, Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - Limin Xie
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China; Key Laboratory of Diabetes Immunology, Ministry of Education, Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - Haowei Zhang
- The First Affiliated Hospital, Department of Orthopedics, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China; Key Laboratory of Diabetes Immunology, Ministry of Education, Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, China; Clinical Immunology Center, The Second Xiangya Hospital of Central South University, Changsha, China.
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Zhou R, Gao Z, Ju Y. Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes. BMC Bioinformatics 2022; 23:418. [PMID: 36221049 PMCID: PMC9552517 DOI: 10.1186/s12859-022-04909-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal tumors worldwide, and immunotherapy is one of the most promising treatments for it. Identifying immune genes involved in the development and maintenance of cancer is key to the use of tumor immunotherapy. This study aimed to determine the prognostic value of immune genes in patients with COAD and to establish an immune-related gene signature. Differentially expressed genes, immune-related genes (DEIGs), and transcription factors (DETFs) were screened using the following databases: Cistrome, The Cancer Genome Atlas (TCGA), the Immunology Database and Analysis Portal, and InnateDB. We constructed a network showing the regulation of DEIGs by DETFs. Using weighted gene co-expression network analysis, we prepared 5 co-expressed gene modules; 6 hub genes (CD1A, CD1B, FGF9, GRP, SERPINE1, and F2RL2) obtained using univariate and multivariate regression analysis were used to construct a risk model. Patients from TCGA database were divided into high- and low-risk groups based on whether their risk score was greater or less than the mean; the public dataset GSE40967, which contains gene expression profiles of 566 colon cancer patients, was used for validation. Results Survival analysis, somatic gene mutations, and tumor-infiltrating immune cells differed significantly between the high- and low-risk groups. Conclusions This immune-related gene signature could play an important role in guiding treatment, making prognoses, and potentially developing future clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04909-2.
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Affiliation(s)
- Rui Zhou
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China
| | - Zhuowei Gao
- Medical Department of Traditional Chinese Medicine, Shunde Hospital of Guangzhou University of Traditional Chinese Medicine, No. 12, Jinsha Avenue, Shunde District, Foshan, 510006, Guangdong, China
| | - Yongle Ju
- Surgical Department of Gastrointestinal Surgery, Shunde Hospital of Southern Medical University, No. 1 Jiazi Road, Shunde District, Foshan, 528399, Guangdong, China.
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Dhandapani H, Bose M, Kesavan S. The Immune-related ceRNA Network in Prognosis of Cervical Cancer. Asian Pac J Cancer Prev 2022; 23:3347-3354. [PMID: 36308358 PMCID: PMC9924325 DOI: 10.31557/apjcp.2022.23.10.3347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Immunotherapy is gaining attention and it is being included as one of the treatment strategies for cancer patients. However, the molecular mechanisms of immune-related genes and their affinity for cervical cancer progression remain unclear. In this study, we have developed an immune-related competing endogenous RNA [ceRNA] network and assessed the tumour infiltrating immune cells towards the prognosis of cervical cancer. METHODS Differential RNA expression pattern between stages I and II-IV of cervical cancer patients from The Cancer Genome Atlas [TCGA] was analyzed. Immune-related ceRNA network based on the immune gene signatures were retrieved and their targets were predicted using miRwalk 3.0. CIBERSORT was employed to identify the immune cell types based on their respective transcripts. The prognostic significance of RNAs in the ceRNA network and immune cell subsets was analyzed. RESULTS Significant differences in 22 long non-coding RNAs [lncRNAs], 15 microRNAs [miRNAs], and 252 messenger RNAs [mRNAs] between stages I and II-IV of cervical cancer were observed. Further, we shortlisted the 49 immune-related mRNAs based on immune gene signature and predicted their target miRNAs and lncRNAs. A potential ceRNA network of 4 lncRNAs, 10 miRNAs, and 11 mRNAs had a strong correlation for prognosis. Out of 11 protein-coding immune mRNAs, IRF4 and AZGP1 had high degrees of interaction. In addition, the evaluation of immune cell subsets showed increased infiltration of M1 macrophages had better survival outcome. CONCLUSIONS We have identified an immune-related ceRNA network based on differentially expressed transcripts between stages I and II-IV which may help predict the prognosis of cervical cancer.
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Huang C, Hu D, Li K. Identification of Biomarkers in Intracranial Aneurysm and Their Immune Infiltration Characteristics. World Neurosurg 2022; 166:e199-e214. [PMID: 35798291 DOI: 10.1016/j.wneu.2022.06.138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Intracranial aneurysm (IA), known as the intracranial "unscheduled bomb," is one of the most dangerous cerebrovascular diseases, with unclear pathogenesis. This study aimed to show the mechanisms and identify the new biological targets by applying bioinformatics analysis. METHODS Expression profiling for control superficial temporal artery and IA walls in GSE26969 and GSE75436 datasets were downloaded. By executing the LIMMA package in R software, the differentially expressed genes (DEGs) were filtered, and the functional enrichments were consequently performed. Further cross-linking with the 2483 immune-related genes (IRGs) from the ImmPort database, the differentially expressed IRGs were identified. Based on them, the least absolute shrinkage and selection operator logistic regression and support vector machine-recursive feature elimination algorithms were used to screen the biomarkers, which were validated in the GSE54083 datasets. The CIBERSORT algorithm was applied to evaluate the infiltration of immune cells in tissues. RESULTS A total of 668 DEGs were obtained, and the functional enrichment suggested that they were closely related to the immune process. After intersecting them with the IRGs, 90 differentially expressed IRGs emerged, and ADIPOQ and ESM1 were identified as the biomarkers. Besides, we found that the infiltrated immune cells, such as the mast cells resting, might be associated with them. CONCLUSIONS We explored the contributing factors involving IA, which may generate a better understanding of the complex interactions among them and inspire a promising strategy for clinical works.
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Affiliation(s)
- Cheng Huang
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China; Clinical Neuroscience Institute of Jinan University, Guangzhou, China
| | - Di Hu
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China; Clinical Neuroscience Institute of Jinan University, Guangzhou, China
| | - Keshen Li
- Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China; Clinical Neuroscience Institute of Jinan University, Guangzhou, China.
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Feng X, Zhang Y, Du M, Li S, Ding J, Wang J, Wang Y, Liu P. Identification of diagnostic biomarkers and therapeutic targets in peripheral immune landscape from coronary artery disease. J Transl Med 2022; 20:399. [PMID: 36064568 PMCID: PMC9444127 DOI: 10.1186/s12967-022-03614-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Peripheral biomarkers are increasingly vital non-invasive methods for monitoring coronary artery disease (CAD) progression. Their superiority in early detection, prognosis evaluation and classified diagnosis is becoming irreplaceable. Nevertheless, they are still less explored. This study aimed to determine and validate the diagnostic and therapeutic values of differentially expressed immune-related genes (DE-IRGs) in CAD. Methods We downloaded clinical information and RNA sequence data from the GEO database. We used R software, GO, KEGG and Cytoscape to analyze and visualize the data. A LASSO method was conducted to identify key genes for diagnostic model construction. The ssGSEA analysis was used to investigate the differential immune cell infiltration. Besides, we constructed CAD mouse model (low-density lipoprotein receptor deficient mice with high fat diet) to discover the correlation between the screened genes and severe CAD progress. We further uncovered the role of IL13RA1 might play in atherosclerosis. Results A total of 762 differential genes were identified between the peripheral blood of 218 controls and 199 CAD patients, which were significantly associated with infection, immune response and neural activity. 58 DE-IRGs were obtained by overlapping the differentially expressed genes(DEGs) and immune-related genes downloaded from ImmpDb database. Through LASSO regression, CCR9, CER1, CSF2, IL13RA1, INSL5, MBL2, MMP9, MSR1, NTS, TNFRSF19, CXCL2, HTR3C, IL1A, and NR4A2 were distinguished as peripheral biomarkers of CAD with eligible diagnostic capabilities in the training set (AUC = 0.968) and test set (AUC = 0.859). The ssGSEA analysis showed that the peripheral immune cells had characteristic distribution in CAD and also close relationship with specific DE-IRGs. RT-qPCR test showed that CCR9, CSF2, IL13RA1, and NTS had a significant correlation with LDLR−/− mice. IL13RA1 knocked down in RAW264.7 cell lines decreased SCARB1 and ox-LDL-stimulated CD36 mRNA expression, TGF-β, VEGF-C and α-SMA protein levels and increased the production of IL-6, with downregulation of JAK1/STAT3 signal pathway. Conclusions We constructed a diagnostic model of advanced-stage CAD based on the screened 14 DE-IRGs. We verified 4 genes of them to have a strong correlation with CAD, and IL13RA1 might participate in the inflammation, fibrosis, and cholesterol efflux process of atherosclerosis by regulating JAK1/STAT3 pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03614-1.
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Affiliation(s)
- Xiaoteng Feng
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifan Zhang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Min Du
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sijin Li
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Ding
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiarou Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiru Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ping Liu
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Wang C, Lu T, Xu R, Chang X, Luo S, Peng B, Wang J, Yao L, Wang K, Shen Z, Zhao J, Zhang L. A bioinformatics-based immune-related prognostic index for lung adenocarcinoma that predicts patient response to immunotherapy and common treatments. J Thorac Dis 2022; 14:2131-2146. [PMID: 35813746 PMCID: PMC9264088 DOI: 10.21037/jtd-22-494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/27/2022] [Indexed: 12/25/2022]
Abstract
Background There is increasing evidence of the effectiveness of immune checkpoint blockade (ICB) therapy for the treatment of lung adenocarcinoma (LUAD). However, the benefits of ICB therapy vary among LUAD patients. Due to the research dimension, existing biomarkers, such as programmed death-ligand 1 (PD-L1) expression and tumor mutation burden (TMB), could not reflect the complex tumor environment, and had low prediction accuracy of ICB. Therefore, we aimed to uncover a prognostic biomarker that could also predict whether a patient would benefit from ICB therapy and other common treatments from multiple dimensions, so as to improve the prediction accuracy of pre-treatment patients. Methods Based on the LUAD dataset retrieved from The Cancer Genome Atlas (TCGA) database, 50 immune-related hub genes were identified using weighted gene co-expression network analysis and univariate Cox regression analyses. An immune-related gene prognostic index (IRGPI) was constructed using a Cox proportional-hazards model based on 15 genes and validated using GSE72094 dataset. We tested its prognostic accuracy by Kaplan-Meier (K-M) survival curves of the two datasets and assessed its predictive power by comparing area under curve (AUC) of IRGPI with existing biomarkers. Subsequently, we analyzed the molecular and immune characteristics, and evaluated the benefits of ICB by PD-L1 expression and Tumor Immune Dysfunction and Exclusion (TIDE) analysis, predicted the inhibitory concentration 50 of common treatments drugs for two IRGPI score-related subgroups. Results Patients in the IRGPI-high subgroup had lower overall survival (OS) than patients in the IRGPI-low subgroup in K-M survival curve in two cohorts. And IRGPI has AUC values of 0.715, 0.724, and 0.743 in 1, 2, and 3 years, respectively. A higher tumor mutation burden and PD-L1 expression and the tumor microenvironment (TME) landscape demonstrated that IRGPI-high subgroup patients may respond better to ICB therapy. Genomics of Drug Sensitivity in Cancer (GDSC) analysis indicated that the IRGPI-high subgroup showed greater sensitivity to chemotherapy. Conclusions IRGPI is a prospective biomarker for evaluating whether a patient will benefit from ICB therapy and other treatments, and distinguishing patients with different molecular and immune characteristics.
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Affiliation(s)
- Chenghao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoyan Chang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shan Luo
- Second Clinical College of Medicine, Harbin Medical University, Harbin, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lingqi Yao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kaiyu Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhiping Shen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaying Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Lyu F, Li Y, Yan Z, He Q, Cheng L, Zhang P, Liu B, Liu C, Song Y, Xing Y. Identification of ISG15 and ZFP36 as novel hypoxia- and immune-related gene signatures contributing to a new perspective for the treatment of prostate cancer by bioinformatics and experimental verification. J Transl Med 2022; 20:202. [PMID: 35538543 PMCID: PMC9092714 DOI: 10.1186/s12967-022-03398-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
Background Prostatic cancer (PCa) is one of the most common malignant tumors in men worldwide. Emerging evidence indicates significance of hypoxia and immunity in PCa invasion and metastasis. This study aimed to develop a hypoxia- and immune-related gene risk signature and explore the molecular mechanisms to formulate a better prognostic tool for PCa patients. Methods The hypoxia and immune scores of all PCa patients in The Cancer Genome Atlas (TCGA) dataset were calculated via the maximally selected rank statistics method and the ESTIMATE algorithm. From common genes identified overlapping hypoxia- and immune-related differentially expressed genes (DE-HRGs and DE-IRGs), a hypoxia- and immune-related gene risk signature was developed utilizing univariate and multivariate Cox regression analyses, and validated in the Memorial Sloan Kettering Cancer Centre (MSKCC) database. The immune cell infiltration level of PCa samples were evaluated with ssGSEA algorithm. Differential expression of prognostic genes was evidenced by immunohistochemistry and western blot (WB) in paired PCa samples. Expression levels of these genes and their variations under regular and hypoxic conditions were examined in cell lines. The functional effects of the prognostic gene on PCa cells were examined by wound healing and transwell assays. Results A hypoxia- and immune-related gene risk signature constructed by ISG15 and ZFP36 displays significant predictive potency, with higher risk score representing worse survival. A nomogram based on independent prognostic factors including the risk score and Gleason score exhibited excellent clinical value in the survival prediction of PCa. Infiltration levels of eosinophils, neutrophils, Tcm, Tem, TFH, Th1 cells, and Th17 cells were significantly lower in the high-risk group. Conversely, aDC, pDC, T helper cells, and Tregs were significantly higher. Additionally, the two prognostic genes were closely correlated with the tumor-infiltrating immune cell subset in PCa progression. RT-qPCR and WB presented higher and lower expression of ISG15 and ZFP36 in PCa cells, respectively. They were correspondingly increased and decreased in PCa cells under hypoxic conditions. Wound healing and transwell assays showed that over-expression of ISG15 promoted the migration and invasion of PCa cells. Conclusion Our study identified a novel hypoxia- and immune-related gene signature, contributing a new perspective to the treatment of PCa Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03398-4.
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Affiliation(s)
- Fang Lyu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yunxue Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhecheng Yan
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qingliu He
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lulin Cheng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Pu Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bing Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chunyu Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yarong Song
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yifei Xing
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Balasundaram A, Udhaya Kumar S, George Priya Doss C. A computational model revealing the immune-related hub genes and key pathways involved in rheumatoid arthritis (RA). Adv Protein Chem Struct Biol 2022; 129:247-273. [PMID: 35305721 DOI: 10.1016/bs.apcsb.2021.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rheumatoid arthritis (RA) has one of the highest disability rates among inflammatory joint disorders. However, the reason and possible molecular events are still unclear. There are various treatment options available, but no complete cure. To obtain early diagnosis and successful medication in RA, it is necessary to explore gene susceptibility and pathogenic factors. The main intend of our work is to explore the immune-related hub genes with similar functions that are differentially expressed in RA patients. Three datasets such as GSE21959, GSE55457, and GSE77298, were taken to analyze the differently expressed genes (DEGs) among 55 RA and 33 control samples. We obtained 331 upregulated and 275 downregulated DEGs from three Gene Expression Omnibus (GEO) datasets using the R package. Furthermore, a protein-protein interaction network was built for upregulated and downregulated DEGs using Cytoscape. Subsequently, MCODE analysis was performed and obtained the top two modules in each DEG's upregulated and downregulated protein-protein interactions (PPIs) network. CytoNCA and cytoHubba were performed and identified overlapping DEGs. In addition, we narrowed down DEGs by filtering with immune-related genes and identified DE-IRGs. Gene ontology (GO) and KEGG pathway analysis in upregulated and downregulated DEGs were executed with the DAVID platform. Our study obtained the nine most significant DE-IRGs in RA such as CXCR4, CDK1, BUB1, BIRC5, AGTR1, EGFR, EDNRB, KALRN, and GHSR. Among them, CXCR4, CDK1, BUB1, and BIRC5 are overexpressed in RA and may contribute to the pathophysiology of the disease. Similarly, AGTR1, EGFR, EDNRB, KALRN, and GHSR are all low expressed in RA and may have a contribution to pathogenesis. GO, KEGG functional enrichment, and GeneMANIA showed that the dysregulated process of DE-IRGs causes RA development and progression. These findings may be helpful in future studies in RA diagnosis and therapy.
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Affiliation(s)
- Ambritha Balasundaram
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, TN, India
| | - S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, TN, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, TN, India.
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Zhan Y, Zha S, Peng Z, Lin Z, Bao Y. Hypoxia-mediated immunotoxicity in the blood clam Tegillarca granosa. Mar Environ Res 2022; 177:105632. [PMID: 35439659 DOI: 10.1016/j.marenvres.2022.105632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/08/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In marine ecosystems, dissolved oxygen (DO) is essential for maintaining intracellular energy balance during aerobic metabolism. Bivalve mollusks are frequently exposed to hypoxia environments due to tides, temperature changes, and anthropogenic activities. The blood clam, Tegillarca granosa, mainly inhabits intertidal mudflats and is more susceptible to low oxygen events. In this study, we investigated the effect of hypoxia on immune responses in clams, and showed that hypoxia exposure reduced total hemocyte counts (THC), hemoglobin concentrations, and intracellular reactive oxygen species (ROS) levels. Also, phagocytic and cell activities of hemocyte were significantly inhibited. Furthermore, immune-related gene expression was also down-regulated. In conclusion, hypoxia greatly affected immune functions in blood clams, and our research provided the foundation for further mechanistic studies on hypoxia tolerance in clams.
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Affiliation(s)
- Yu Zhan
- School of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Shanjie Zha
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Zhilan Peng
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Zhihua Lin
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.
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Ren L, Li P, Li Z, Chen Q. AQP9 and ZAP70 as immune-related prognostic biomarkers suppress proliferation, migration and invasion of laryngeal cancer cells. BMC Cancer 2022; 22:465. [PMID: 35477402 DOI: 10.1186/s12885-022-09458-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Laryngeal cancer represents a common malignancy that originates from the larynx, with unfavorable prognosis. Herein, this study systematically analyzed the immune signatures of laryngeal cancer and to evaluate their roles on tumor progression. METHODS Differentially expressed immune-related genes (IRGs) were screened between laryngeal cancer and normal tissues from TCGA dataset. Then, two prognosis-related IRGs AQP9 and ZAP70 were analyzed by a series of survival analysis. Based on them, molecular subtypes were constructed by unsupervised cluster analysis. Differences in survival outcomes, HLA expression and immune cell infiltrations were assessed between subtypes. Expression of AQP9 and ZAP70 was validated in laryngeal cancer tissues and cells by RT-qPCR and immunohistochemistry. After silencing and overexpressing AQP9 and ZAP70, CCK-8, EdU, wound healing and transwell assays were performed in TU212 and LCC cells. RESULTS Totally, 315 IRGs were abnormally expressed in laryngeal cancer. Among them, AQP9 and ZAP70 were distinctly correlated to patients' prognosis. Two subtypes were developed with distinct survival outcomes, HLA expression and immune microenvironment. Low expression of AQP9 and ZAP70 was confirmed in laryngeal cancer. AQP9 and ZAP70 up-regulation distinctly suppressed proliferation, migration, and invasion of laryngeal cancer cells. The opposite results were investigated when their knockdown. CONCLUSIONS Our findings revealed the roles of AQP9 and ZAP70 in progression of laryngeal cancer, and suggested that AQP9 and ZAP70 could potentially act as candidate immunotherapeutic targets for laryngeal cancer.
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Zhuang Y, Huang H, Liu XL, Wang NA, Zhong GF. Effect of bovine lactoferricin on the growth performance, digestive capacity, immune responses and disease resistance in Pacific white shrimp, Penaeus vannamei. Fish Shellfish Immunol 2022; 123:282-289. [PMID: 35306176 DOI: 10.1016/j.fsi.2022.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/08/2021] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The present study evaluated the growth performance, digestive enzyme activity, non-specific immunity, immunity and growth genes in Penaeus vannamei fed diets supplemented with Bovine lactoferricin (the basal diet without Bovine lactoferricin, the control; 1.0‰ Bovine lactoferricin,LCB1; 1.5‰ Bovine lactoferricin,LCB1.5; 2.0‰ Bovine lactoferricin, LCB2; 2.5‰ Bovine lactoferricin, LCB2.5) for 56 days. The feeding trial showed that the final weight, weight gain rate, and specific growth rate of the shrimp were improved significantly, while the feed conversion ratio was reduced significantly in the LCB1.5 group compared to the control (P < 0.05). The challenge test of Vibrio parahaemolyticus showed that the cumulative mortalities of shrimp in the LCB1.5, LCB2 and LCB2.5 groups were significantly lower than that in the control (P < 0.05). Compared with the control, Lipase and Trypsin activities in the hepatopancreas of LCB1.5 and LCB2 groups were significantly enhanced (P < 0.05). Compared with the control, alkaline phosphatase, acid phosphatase activities in the hepatopancreas and the relative expression levels of Relish, Toll, JAK, STAT, TOR, Raptor, 4E-BP, eIF4E1α, eIF4E2 genes in the hepatopancreas of LCB1.5, LCB2 and LCB2.5 groups were all significantly enhanced (P < 0.05). These results suggested that dietary Bovine lactoferricin could improve the growth performance, digestive capacity and immune responses of shrimp. When resistance against Vibrio parahaemolyticus in shrimp is considered, high dosage of Bovine lactoferricin showed a better effect than low dosage of Bovine lactoferricin. However, high dosage of Bovine lactoferricin can have a negative impact on the growth performance of shrimp. Considering collectively the above, Bovine lactoferricin could improve the growth performance, digestive enzymes activities, immune responses and disease resistance of P. vannamei.
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Affiliation(s)
- Yi Zhuang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - He Huang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xue-Liang Liu
- Zhejiang Hangzhou Tiao Wang Biological Technology Co., Ltd., Hangzhou, 310015, China
| | - Nu-An Wang
- South China Agricultural University, Guangzhou, 510640, China
| | - Guo-Fang Zhong
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China.
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Yan D, Cai S, Bai L, Du Z, Li H, Sun P, Cao J, Yi N, Liu SB, Tang Z. Integration of immune and hypoxia gene signatures improves the prediction of radiosensitivity in breast cancer. Am J Cancer Res 2022; 12:1222-1240. [PMID: 35411250 PMCID: PMC8984882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023] Open
Abstract
Immunity and hypoxia are two important factors that affect the response of cancer patients to radiotherapy. At the same time, considering the limited predictive value of a single predictive model and the uncertainty of grouping patients near the cutoff value, we developed and validated a combined model based on immune- and hypoxia-related gene expression profiles to predict the radiosensitivity of breast cancer patients. This study was based on breast cancer data from The Cancer Genome Atlas (TCGA). Spike-and-slab Lasso regression analysis was performed to select three immune-related genes and develop a radiosensitivity model. Lasso Cox regression modeling selected 11 hypoxia-related genes for development of radiosensitivity model. Three independent datasets (Molecular Taxonomy of Breast Cancer International Consortium [METABRIC], E-TABM-158, GSE103746) were used to validate the predictive value of radiosensitivity signatures. In the TCGA dataset, the 10-year survival probabilities of the immune radioresistant (IRR) and hypoxia radioresistant (HRR) groups were 0.189 (0.037, 0.973) and 0.477 (0.293, 0.776), respectively. The 10-year survival probabilities of the immune radiosensitive (IRS) and hypoxia radiosensitive (HRS) groups were 0.778 (0.676, 0.895) and 0.824 (0.723, 0.939), respectively. Based on these two gene signatures, we further constructed a combined model and divided all patients into three groups (IRS/HRS, mixed, IRR/HRR). We identified the IRS/HRS patients most likely to benefit from radiotherapy; the 10-year survival probability was 0.886 (0.806, 0.976). The 10-year survival probability of the IRR/HRR group was 0. In conclusion, a combined model integrating immune- and hypoxia-related gene signatures could effectively predict the radiosensitivity of breast cancer and more accurately identify radiosensitive and radioresistant patients than a single model.
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Affiliation(s)
- Derui Yan
- Department of Biostatistics, School of Public Health, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health CollegeSuzhou 215009, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
| | - Shang Cai
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu, China
| | - Lu Bai
- Department of Biostatistics, School of Public Health, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health CollegeSuzhou 215009, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
| | - Zixuan Du
- Department of Biostatistics, School of Public Health, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
| | - Huijun Li
- Department of Biostatistics, School of Public Health, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
| | - Peng Sun
- Department of Otolaryngology, The First Affiliated Hospital of Soochow UniversitySuzhou 215006, Jiangsu, China
| | - Jianping Cao
- School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow UniversitySuzhou 215031, Jiangsu, China
| | - Nengjun Yi
- Department of Biostatistics, University of Alabama at BirminghamBirmingham, AL 35294, USA
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health CollegeSuzhou 215009, Jiangsu, China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow UniversitySuzhou 215123, Jiangsu, China
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Lu J, Chen R, Ou Y, Jiang Q, Wang L, Liu G, Liu Y, Yang B, Zhou Z, Zuo L, Chen Z. Characterization of immune-related genes andimmune infiltration features for early diagnosis, prognosis and recognition of immunosuppression in sepsis. Int Immunopharmacol 2022; 107:108650. [PMID: 35272172 DOI: 10.1016/j.intimp.2022.108650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/23/2022] [Accepted: 02/20/2022] [Indexed: 12/29/2022]
Abstract
Among the body systems, the immune system plays a fundamental role in the pathophysiology of sepsis. The effects of immunogenomic and immune cell infiltration in sepsis were still not been systematically understood. Based on modified Lasso penalized regression and RF, 8 DEIRGs (ADM, CX3CR1, DEFA4, HLA-DPA1, MAPK14, ORM1, RETN, and SLPI) were combined to construct an IRG classifier. In the discovery cohort, IRG classifier exhibited superior diagnostic efficacy and performed better in predicting mortality than clinical characteristics or MARS/SRS endotypes. Encouragingly, similar results were observed in the ArrayExpress databases. The use of hydrocortisone in IRG high-risk subgroup was associated with increased risk of mortality. In IRG low-risk phenotypes, NK cells, T helper cells, and infiltrating lymphocyte (IL) are significantly richer, while T cells regulatory (Tregs) and myeloid-derived suppressor cells (MDSC) are more abundant in IRG high-risk phenotypes. IRG score were significantly negatively correlated with Cytokine cytokine receptor interaction (CCR) and human leukocyte antigen (HLA). Between the IRG subgroups, the expression levels of several cytokines (IL-10, IFNG, TNF) were significantly different, and IRG score was significantly positively correlated with ratio of IL-10/TNF. Results of qRT-PCR validated that higher expression level of ADM, DEFA4, MAPK14, ORM1, RETN, and SLPI as well as lower expression level of CX3CR1 and HLA-DPA1 in sepsis samples compared to control sample. A diagnostic and prognostic model, namely IRG classifier, was established based on 8 IRGs that is closely correlated with responses to hydrocortisone and immunosuppression status and might facilitate personalized counseling for specific therapy.
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Affiliation(s)
- Jianhai Lu
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Rui Chen
- Department of Medical Intensive Care Unit, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, Guangdong Province, PR China
| | - Yangpeng Ou
- Department of Oncology, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, 516000, Guangdong Province, PR China
| | - Qianhua Jiang
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Liping Wang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, PR China
| | - Genglong Liu
- Department of Pathology, The Third Affiliated Hospital of Guangdong Medical University (Longjiang Hospital of Shunde District), Foshan 528318, Guangdong Province, PR China
| | - Yayun Liu
- Department of Endocrinology, GuiYang Huaxi District People's Hospital. Guiyang 550025, Guizhou Province, PR China
| | - Ben Yang
- Department of Burn Surgery, Huizhou Municipal Central Hospital, Huizhou 516000, Guangdong Province, PR China
| | - Zhujiang Zhou
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China
| | - Liuer Zuo
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China.
| | - Zhen Chen
- Department of Intensive Care Unit, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, Guangdong Province, PR China.
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Xie W, Zhou QJ, Xu YX, Zhang M, Zhong SP, Lu LL, Qiu HT. Transcriptome analysis reveals potential key immune genes of Hong Kong oyster (Crassostrea hongkongensis) against Vibrio parahaemolyticus infection. Fish Shellfish Immunol 2022; 122:316-324. [PMID: 35122949 DOI: 10.1016/j.fsi.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/18/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Hong Kong oyster (Crassostrea hongkongensis) is one of the main species of economic shellfish cultivated in the coastal areas of southern China. The cultivation of this shellfish may be adversely impacted by Vibrio parahaemolyticus, a harmful pathogenic bacterium for many mariculture species, as it usually exists on the surface of Hong Kong oysters. Although previous studies have discovered that oysters rely on non-specific immune system to fight pathogen invasion, the genes corresponding to the complex immune system against Vibrio is still not fully elucidated. Therefore, we conducted a transcriptome analysis on the gill from Hong Kong oysters at two time points (i.e., 12 h and 24 h after V. parahaemolyticus or PBS challenge) to identify potential immune genes against V. parahaemolyticus infection. A total of 61779 unigenes with the average length of 1221 bp were obtained, and the annotation information of 39917 unigenes were obtained from Nr, SwissProt, KEGG and COG/KOG. After a pairwise comparison between V. parahaemolyticus or PBS challenge at the two time points, three groups of differentially expressed genes induced by V. parahaemolyticus were captured and analyzed. GO and KEGG analyses showed that multiple immune-related genes played an important role in pathogen infection, including HSP70, PCDP3 and TLR4. Furthermore, genes annotation indicated that LITAF, TNFSF10, Duox2 and big defensin family are also involved in immune regulation. Our study provides a reference for further exploration the molecular mechanism that defenses the pathogen infection regarding the identified immune-related genes in Hong Kong oysters.
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Affiliation(s)
- Wei Xie
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Qi-Jia Zhou
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Nanning Normal University), Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation (Nanning Normal University), Nanning, 530001, China.
| | - Yi-Xiao Xu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Nanning Normal University), Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation (Nanning Normal University), Nanning, 530001, China
| | - Man Zhang
- School of Marine Sciences, Guangxi University, Nanning, 530001, China
| | - Sheng-Ping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Li-Li Lu
- Guangxi Zhuang Autonomous Region Institute of Product Quality Inspection, Nanning, 530001, China
| | - Heng-Tong Qiu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Nanning Normal University), Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation (Nanning Normal University), Nanning, 530001, China
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Salehi M, Bagheri D, Sotoudeh E, Ghasemi A, Mozanzadeh MT. The Combined Effects of Propionic Acid and a Mixture of Bacillus spp. Probiotic in a Plant Protein-Rich Diet on Growth, Digestive Enzyme Activities, Antioxidant Capacity, and Immune-Related Genes mRNA Transcript Abundance in Lates calcarifer Fry. Probiotics Antimicrob Proteins 2022. [PMID: 35000111 DOI: 10.1007/s12602-021-09902-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2021] [Indexed: 01/13/2023]
Abstract
A 7-week feeding trial was conducted to evaluate the combined effects of propionic acid (PA, 5 or 10 g/kg) and a multi-strain Bacillus spp. (Bacillus subtilis IS02 (accession no. JN856456) and B. licheniformis IBRC-M 11,319) (1.7 × 107 CFU/g) probiotic in a plant protein source (PP)-rich diet (∼70% of dietary protein derived from PP sources) on performance of Asian sea bass (Lates calcarifer) fry (initial body weight 2.97 ± 0.11 g). In this regard, six isoproteic (∼48%) diets were formulated as follows: a control (without supplementation of the additives); probiotic (only contained Bacillus spp. mixture); 5 g PA/kg diet; 10 g PA/kg diet; probiotic + 5 g PA/kg diet, and probiotic + 10 g PA/kg diet. Specific growth rate in fish fed with 10 g PA/kg (2.84 ± 0.1%) and diets contained blends of probiotic and PA (2.76 ± 0.19% in probiotic + 5 g PA, and 2.79 ± 0.04% in probiotic + 10 g PA) was better than in the control (2.45 ± 0.1%) (P < 0.05). Feed conversion ratio in fish fed with 10 g PA/kg (0.92 ± 0.12) and diets contained blends of probiotic and PA (0.94 ± 0.06 in probiotic + 5 g PA and 0.91 ± 0.02 in probiotic + 10 g PA) was better than in the control (1.24 ± 0.08) (P < 0.05). Digestive enzymes including α-amylase, total alkaline proteases, and bile salt dependent lipase activities improved in fish fed diets contained additives. The activity of glutathione-S-transferase and glutathione reductase enhanced in the liver of fish fed diets contained additives. The relative abundance of lysozyme, interleukin 1β, and insulin-like growth factor-1 genes mRNA transcript showed multifold increase in the liver of fish fed with the 10 g PA/kg and diets contained blends of probiotic and PA (P < 0.05). By considering the above mentioned results, supplementing a PP-rich diet with 10 g PA/kg diet or combination of PA and a mixture of Bacillus spp. probiotic recommended for L. calcarifer.
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Yan Z, Lijuan Y, Yinhang W, Yin J, Jiamin X, Wei W, Yuefen P, Shuwen H. Screening and analysis of RNAs associated with activated memory CD4 and CD8 T cells in liver cancer. World J Surg Oncol 2022; 20:2. [PMID: 34980144 PMCID: PMC8725365 DOI: 10.1186/s12957-021-02461-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Background Liver cancer is one of the most common malignant tumors in the world. T cell-mediated antitumor immune response is the basis of liver cancer immunotherapy. Objective To screen and analyze the RNAs associated with activated memory CD4 T cells and CD8 T cells in liver cancer. Methods
ESTIMATE was used to calculate the stromal and immune scores of tumor samples, which were downloaded from The Cancer Genome Atlas (TCGA). The differentially expressed genes (DEGs) in high and low stromal and immune scores were screened, followed by functional enrichment of overlapped DEGs. We then conducted a survival analysis to identify immune-related prognostic indicators and constructed protein-protein interaction (PPI) networks and ceRNA networks. Finally, chemical small-molecule–target interaction pairs associated with liver cancer were screened. Results A total of 55,955 stromal-related DEGs and 1811 immune-related DEGs were obtained. The 1238 overlapped DEGs were enriched in 1457 biological process terms and 74 KEGG pathways. In addition, a total of 120 activated memory CD4 T cell-related genes and 309 CD8 T cell-related genes were identified. The survival analysis revealed that upregulated expression of T cell-related genes including EOMES, CST7, and CD5L indicated the favorable prognosis of liver cancer. EOMES was regulated by has-miR-23b-3p and has-miR-23b-3p was regulated by lncRNA AC104820.2 in the ceRNA network of activated memory CD4 T cell-related genes. In addition, EOMES was regulated by has-miR-23a-3p and has-miR-23a-3p was regulated by lncRNA AC000476.1 in the ceRNA network of CD8 T cells. Conclusion T cell-related RNAs EOMES, CST7, CD5L, has-miR-23b-3p, and has-miR-23a-3p may be associated with the prognosis of liver cancer. And the molecular characteristics of these T cell-related genes were plotted. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02461-6. A total of 309 CD8 T cell-related genes and 120 activated memory CD4 T cell-related genes were screened in liver cancer tumor samples. Forty-four chemical small-molecule–target interaction pairs associated with activated memory CD4 T cells and 276 pairs associated with CD8 T cells were screened. Upregulated expression of T cell-related genes including EOMES, CST7, and CD5L indicated the favorable prognosis of liver cancer.
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Affiliation(s)
- Zhang Yan
- Department of Infectious Disease, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
| | - Yin Lijuan
- Department of Rheumatology, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
| | - Wu Yinhang
- Graduate School of Second Clinical Medicine Faculty, Zhejiang Chinese Medical University, No. 548 Binwen Road, Binjiang District, Hangzhou, 310053, Zhejiang Province, China
| | - Jin Yin
- Department of Laboratory Medicine, Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
| | - Xu Jiamin
- Department of Nursing, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, No. 568 North Zhongxing Road, Yuecheng District, Shaoxing, 312000, Zhejiang Province, China
| | - Wu Wei
- Department of Gastroenterology, Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
| | - Pan Yuefen
- Department of Oncology, Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China.
| | - Han Shuwen
- Department of Oncology, Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, No.1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China.
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Huang Y, Zhang L, Huang S, Wang G. Full-length transcriptome sequencing of Heliocidaris crassispina using PacBio single-molecule real-time sequencing. Fish Shellfish Immunol 2022; 120:507-514. [PMID: 34920131 DOI: 10.1016/j.fsi.2021.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/12/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The lack of high-throughput sequencing data makes the research progress of Heliocidaris crassispina slow. Therefore, we used PacBio single-molecule real-time sequencing to generate the first full-length transcriptome. Here, 31,181 isoforms were obtained, with an average length of 2383.20 and a N50 length of 2732 bp. Meanwhile, 764 alternative splicing (AS) events, 5098 long-noncoding RNAs (LncRNAs), 6978 simple sequence repeats (SSRs), and 950 hypothetical transcript factors (TFs) were identified. Moreover, five key innate immune pattern recognition receptors (PRRs), including toll-like receptor (TLR), NACHT domain and leucine-rich repeat (NLR), scavenger receptor cysteine-rich (SRCR), peptidoglycan recognition proteins (PGRP), and gram-negative binding proteins (GNBP), were searched in the transcriptome. In addition, 37 isoforms enriched in KEGG and GO immune systems were also detected. The study provid abundant data support for the current research on H. crassispina.
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Affiliation(s)
- Yongyu Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Lili Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Shiyu Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Guodong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China.
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Zhao K, Wu H, Hou R, Wu J, Wang Y, Huang S, Cheng D, Xu H, Zhang Z. Effects of sublethal azadirachtin on the immune response and midgut microbiome of Apis cerana cerana (Hymenoptera: Apidae). Ecotoxicol Environ Saf 2022; 229:113089. [PMID: 34929506 DOI: 10.1016/j.ecoenv.2021.113089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/30/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
As a wildly used plant-derived insecticide, azadirachtin (AZA) is commonly reported as harmless to a range of beneficial insects. However, with the research on the effect of AZA against pollinators in recent years, various negative physiological effects on other Apidae species have been demonstrated. Thus to explore the safety of azadirachtin to Apis cerana cerana, the different physiological effects of sublethal concentration of azadirachtin on worker bees A.c.cerana has been studied. With the exposure of 5 mg·L-1 and 10 mg·L-1 azadirachtin for 5 d, the relative expression of Apidaecin, Abaecin and Lysosome genes in workers has decreased significantly at 1, 2,3 and 5 d, and the mRNA levels of Defensin 2 and Hymenoptaecin were also significantly inhibited by 10 mg·L-1 azadirachtin at each check point. Besides, the activity of midgut antioxidant enzymes Superoxide Dismutase (SOD) and Catalase (CAT) which are the first line of defence in antioxidant systems was not affected by AZA, the activity of Peroxidase (POD) showed a fluctuating pattern at 24 h and 48 h, while the activity of polyphenol oxidase (PPO) has significantly inhibited by AZA. However, through 16sRNA analysis it was observed that 5 mg·L-1 AZA did not affect the midgut microbiome colony composition and relative abundance, as well as its main function. Therefore, to a certain extent, azadirachtin is safe for workers, but we should pay more attention to the sublethal effect of AZA that also detrimental to the healthy development of the honeybee colony.
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Affiliation(s)
- Kunyu Zhao
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
| | - Hao Wu
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
| | - Ruiquan Hou
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
| | - Jiyingzi Wu
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Wang
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China
| | - Suqing Huang
- Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dongmei Cheng
- Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Hanhong Xu
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China.
| | - Zhixiang Zhang
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou 510642, China.
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47
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Salehpour R, Amrollahi Biuki N, Mohammadi M, Dashtiannasab A, Ebrahimnejad P. The dietary effect of fucoidan extracted from brown seaweed, Cystoseira trinodis (C. Agardh) on growth and disease resistance to WSSV in shrimp Litopenaeus vannamei. Fish Shellfish Immunol 2021; 119:84-95. [PMID: 34560287 DOI: 10.1016/j.fsi.2021.09.005] [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] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The polysaccharide-fucoidan plays a fundamental role in shrimp aquaculture by being used as a natural immunostimulant and dietary supplementation. In this study, Cystoseira trinodis fucoidan (FCT) was extracted, its structure was determined using FT-IR analysis, and its effect of fucoidan on growth performance and WSSV resistance in Litopenaeus vannamei was evaluated. Four experimental diets, including the control (without FCT), 0.1, 0.2, and 0.4% FCT, were formulated and fed to shrimps for 60 days. Next, they were exposed to WSSV, and their mortality rate was noted daily up to 20 days. The results of the growth experiment demonstrated a significant increase in the final weight, WG, and SGR, and a lower FCR in treatments than in control. During the challenge trial, 100% mortality was recorded in control within ten days. However, FCT-treated shrimps indicated a mortality increase from 43.33 to 75.00% during 20 days of infection. The immunological and biochemical parameters and the expression of immune-related genes in individuals fed the FCT-incorporated diet considerably (p < 0.01) improved over control before the challenge (0 days) and after the challenge on days 5, 10, 15, and 20. It was concluded that L. vannamei fed on diets supplemented with all concentrations of FCT (especially 0.4%) had improved the growth, immunological and biochemical parameters, and the expression of immune-related genes, as well as enhancing the resistance against WSSV.
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Affiliation(s)
- Razieh Salehpour
- Faculty of Marine Science and Technology, Department of Marine Biology, University of Hormozgan, Bandar Abbas, Iran.
| | - Narges Amrollahi Biuki
- Faculty of Marine Science and Technology, Department of Marine Biology, University of Hormozgan, Bandar Abbas, Iran.
| | - Mehdi Mohammadi
- Faculty of Persian Gulf Research Institute, Department of Biotechnology, University of Persian Gulf, Bushehr, Iran.
| | - Aghil Dashtiannasab
- Iran Shrimp Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research Education and Extension Organization (AREEO), Bushehr, Iran.
| | - Pedram Ebrahimnejad
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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Azodi M, Bahabadi MN, Ghasemi A, Morshedi V, Mozanzadeh MT, Shahraki R, Khademzadeh O, Hamedi S, Avizhgan S. Effects of salinity on gills' chloride cells, stress indices, and gene expression of Asian seabass (Lates calcarifer, Bloch, 1790). Fish Physiol Biochem 2021; 47:2027-2039. [PMID: 34716532 DOI: 10.1007/s10695-021-01024-6] [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] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
A 2-week research was carried out to assess water salinity (WS) effects including 0, 15, 35, and 50‰ on osmoregulatory mechanisms and stress indices in Asian sea bass (34.4 g) juveniles. Except for fish reared at 50‰, in the other treatments, it gradually decreased to the prescribed WS during a 10-day period (- 5‰ a day). After a 10-day acclimation period, fish were reared at the prescribed WS for 2 weeks. Fish reared at 15 and 35‰ had higher chloride cell (CC) counts in the interlamellar region. The number of CC in the interlamellar region elevated with increment of WS up to 35‰, but they were pronouncedly reduced in 50‰ group. The diameter of CC in the interlamellar region was not affected by WS. The smallest nucleus diameter of CC in the interlamellar region was observed in fish reared at 15‰ (P < 0.05). The largest and the smallest amounts of serum aspartate aminotransferase were observed in fish reared at freshwater and 15‰, respectively. Fish reared at 35‰ had the highest serum sodium and potassium contents. Serum chloride content and total osmolality increased with increment of WS (P < 0.05). Serum cortisol and glucose contents gradually increased with elevation of WS up to 35‰; then, their contents remarkably decreased. The relative expression of insulin like growth factor-1 in the liver of fish reared at 35‰ was strikingly higher than that in the other groups. The relative expression of HSP70 gene in fresh water group was pronouncedly elevated compared to other treatments. The relative expression of interleukin-1β in 15 and 35‰ groups was higher than that in the other groups; however, the relative expression of lysozyme gene in the liver of fish reared at fresh water was pronouncedly lower than that in the other treatments. The results of this study suggested rearing L. calcarifer at 15‰ closer to the isosmotic point and better provide its welfare.
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Affiliation(s)
- Maryam Azodi
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran
| | - Mahmoud Nafisi Bahabadi
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran
- Department of Fisheries and Biology, Persian Gulf Research Institute, Persian Gulf University, 7516913798, Bushehr, Iran
| | - Ahmad Ghasemi
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran
| | - Vahid Morshedi
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran.
| | - Mansour Torfi Mozanzadeh
- Agricultural Research Education and Extension Organization (AREEO), South Iran Aquaculture Research Centre, Iranian Fisheries Science Institute (IFSRI), Ahwaz, Iran.
| | - Raheleh Shahraki
- Department of Basic Sciences, Division of Histology, Faculty of Veterinary Medicine, Shahid Chamran University, Ahwaz, Iran
| | - Omid Khademzadeh
- Department of Fisheries, Faculty of Marine Natural Resources, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - Shirin Hamedi
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran
| | - Sakineh Avizhgan
- Persian Gulf Research Institute, University of Persian Gulf, 7516913798, Bushehr, Iran
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Zhang Y, Lu L, Li C, Shao G, Chen X. Transcriptome analysis revealed multiple immune processes and energy metabolism pathways involved in the defense response of the large yellow croaker Larimichthys crocea against Pseudomonas plecoglossicida. Comp Biochem Physiol Part D Genomics Proteomics 2021; 40:100886. [PMID: 34418783 DOI: 10.1016/j.cbd.2021.100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 01/08/2023]
Abstract
The large yellow croaker (Larimichthys crocea) aquaculture industry is suffering substantial financial losses caused by visceral white nodules disease resulting from Pseudomonas plecoglossicida infection. However, how L. crocea responds to P. plecoglossicida infection remains largely unknown. Here, we characterized the changes in the mRNA profile in the spleen of L. crocea upon P. plecoglossicida infection and explored the related defensive strategies. Sample clustering analysis and qRT-PCR indicated that P. plecoglossicida induced profound and reproducible transcriptome remodeling in the L. crocea spleen. Many innate immune-related genes, such as IL-17 signaling molecules, chemokines and chemokine receptors, complement components, TLR5 signaling molecules, and antimicrobial peptide hepcidins (Hamps), were upregulated by P. plecoglossicida and may play important roles in the L. crocea defense against P. plecoglossicida. The antibacterial activity of Hamp2-5 against P. plecoglossicida was further confirmed by using synthetic mature peptide of Hamp2-5. Additionally, significant enrichment of "Glycolysis/Gluconeogenesis", "Citrate cycle" and "Oxidative phosphorylation" pathways and a significant upregulation of all 6 rate-limiting enzyme genes (HK1, PFK, PKM, CS, IDH2, DLST) in the Glycolysis and Citrate cycle pathways in P. plecoglossicida-infected fish suggested that ATP synthesis may be accelerated to ensure energy supply in response to pathogenic infection. Altogether, our results not only identified the key immune-related genes and immune pathways that participated in the defense response of L. crocea against P. plecoglossicida, but also revealed a novel defensive strategy involving ATP synthesis in this species.
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Lin R, Fogarty CE, Ma B, Li H, Ni G, Liu X, Yuan J, Wang T. Identification of ferroptosis genes in immune infiltration and prognosis in thyroid papillary carcinoma using network analysis. BMC Genomics 2021; 22:576. [PMID: 34315405 PMCID: PMC8314640 DOI: 10.1186/s12864-021-07895-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. While many patients survive, a portion of PTC cases display high aggressiveness and even develop into refractory differentiated thyroid carcinoma. This may be alleviated by developing a novel model to predict the risk of recurrence. Ferroptosis is an iron-dependent form of regulated cell death (RCD) driven by lethal accumulation of lipid peroxides, is regulated by a set of genes and shows a variety of metabolic changes. To elucidate whether ferroptosis occurs in PTC, we analyse the gene expression profiles of the disease and established a new model for the correlation. METHODS The thyroid carcinoma (THCA) datasets were downloaded from The Cancer Genome Atlas (TCGA), UCSC Xena and MisgDB, and included 502 tumour samples and 56 normal samples. A total of 60 ferroptosis related genes were summarised from MisgDB database. Gene set enrichment analysis (GSEA) and Gene set variation analysis (GSVA) were used to analyse pathways potentially involving PTC subtypes. Single sample GSEA (ssGSEA) algorithm was used to analyse the proportion of 28 types of immune cells in the tumour immune infiltration microenvironment in THCA and the hclust algorithm was used to conduct immune typing according to the proportion of immune cells. Spearman correlation analysis was performed on the ferroptosis gene expression and the correlation between immune infiltrating cells proportion. We established the WGCNA to identify genes modules that are highly correlated with the microenvironment of immune invasion. DEseq2 algorithm was further used for differential analysis of sequencing data to analyse the functions and pathways potentially involving hub genes. GO and KEGG enrichment analysis was performed using Clusterprofiler to explore the clinical efficacy of hub genes. Univariate Cox analysis was performed for hub genes combined with clinical prognostic data, and the results was included for lasso regression and constructed the risk regression model. ROC curve and survival curve were used for evaluating the model. Univariate Cox analysis and multivariate Cox analysis were performed in combination with the clinical data of THCA and the risk score value, the clinical efficacy of the model was further evaluated. RESULTS We identify two subtypes in PTC based on the expression of ferroptosis related genes, with the proportion of cluster 1 significantly higher than cluster 2 in ferroptosis signature genes that are positively associated. The mutations of Braf and Nras are detected as the major mutations of cluster 1 and 2, respectively. Subsequent analyses of TME immune cells infiltration indicated cluster 1 is remarkably richer than cluster 2. The risk score of THCA is in good performance evaluated by ROC curve and survival curve, in conjunction with univariate Cox analysis and multivariate Cox analysis results based on the clinical data shows that the risk score of the proposed model could be used as an independent prognostic indicator to predict the prognosis of patients with papillary thyroid cancer. CONCLUSIONS Our study finds seven crucial genes, including Ac008063.2, Apoe, Bcl3, Acap3, Alox5ap, Atxn2l and B2m, and regulation of apoptosis by parathyroid hormone-related proteins significantly associated with ferroptosis and immune cells in PTC, and we construct the risk score model which can be used as an independent prognostic index to predict the prognosis of patients with PTC.
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Affiliation(s)
- Ruoting Lin
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Conor E Fogarty
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Bowei Ma
- Department of TCM Resident Training, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Hejie Li
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Guoying Ni
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Xiaosong Liu
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Jianwei Yuan
- Department of Nuclear Medicine, The First Affiliated Hospital/Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China.
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
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