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Luthfi M, Pandey RB, Su YC, Sompornpisut P. Deciphering molecular basis of pesticide-induced recurrent pregnancy loss: insights from transcriptomics analysis. Toxicol Mech Methods 2024:1-18. [PMID: 38294000 DOI: 10.1080/15376516.2024.2307975] [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: 10/15/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Recent studies have revealed a notable connection between pesticide exposure and Recurrent Pregnancy Loss (RPL), yet the precise molecular underpinning of this toxicity remains elusive. Through the alignment of Differentially Expressed Genes (DEGs) of healthy and RPL patients with the target genes of 9 pesticide components, we identified a set of 12 genes responsible for RPL etiology. Interestingly, biological process showed that besides RPL, those 12 genes also associated with preeclampsia and cardiovascular disease. Enrichment analysis showed the engagement of these genes associated with essential roles in the molecular transport of small molecules, as well as the aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, mineral absorption, ion homeostasis, and ion transport by P-type ATPases. Notably, the crosstalk targets between pesticide components played crucial roles in influencing RPL results, suggesting a role in attenuating pesticide agents that contribute to RPL. It is important to note that non-significant concentration of the pesticide components observed in both control and RPL samples should not prematurely undermine the potential for pesticides to induce RPL in humans. This study emphasizes the complexity of pesticide induced RPL and highlights avenues for further research and precautionary measures.
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Affiliation(s)
- Muhammad Luthfi
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - R B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pornthep Sompornpisut
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
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2
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Ma Y, Sui J, Wang Y, Sun W, Yi G, Wu J, Qiu S, Wang L, Zhang A, He X. RNA-Seq-Based Transcriptomics and GC-MS Quantitative Analysis Reveal Antifungal Mechanisms of Essential Oil of Clausena lansium (Lour.) Skeels Seeds against Candida albicans. Molecules 2023; 28:8052. [PMID: 38138542 PMCID: PMC10745804 DOI: 10.3390/molecules28248052] [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: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Infections caused by Candida albicans (C. albicans) and increasing resistance to commonly used drugs lead to a variety of mucosal diseases and systemic infectious diseases. We previously confirmed that the essential oil of Clausena lansium (Lour.) Skeels seeds (CSEO) had antifungal activity against C. albicans, but the detailed mechanism between the chemical components and antifungal activity is unclear. In this study, a quantitative analysis of five volatile components of CSEO, including sabinene, α-phellandrene, β-phellandrene, 4-terpineol, and β-caryophyllene, was carried out using the gas chromatography-mass spectrometry (GC-MS) method. Both the broth dilution and kinetic growth methods proved that the antifungal activity of CSEO against fluconazole-resistant C. albicans was better than that of its main components (sabinene and 4-terpineol). To further investigate the inhibitory mechanism, the transcriptional responses of C. albicans to CSEO, sabinene, and 4-terpineol treatment were determined based on RNA-seq. The Venn diagram and clustering analysis pattern of differential expression genes showed the mechanism of CSEO and 4-terpineol's anti-C. albicans activity might be similar from the perspective of the genes. Functional enrichment analysis suggested that CSEO regulated adherence-, hyphae-, and biofilm-formation-related genes, which may be CSEO's active mechanism of inhibiting the growth of fluconazole-resistant C. albicans. Overall, we preliminarily revealed the molecular mechanism between the chemical components and the antifungal activity of CSEO against C. albicans. This study provides new insights to overcome the azole resistance of C. albicans and promote the development and application of C. lansium (Lour.) Skeels seeds.
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Affiliation(s)
- Yinzheng Ma
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
- School of Pharmacy, Hainan Medical University, Haikou 571199, China
| | - Jinlei Sui
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Yan Wang
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Wanying Sun
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Guohui Yi
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Jinyan Wu
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Shi Qiu
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Lili Wang
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Aihua Zhang
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
| | - Xiaowen He
- Public Research Center, Hainan Medical University, Haikou 571199, China; (Y.M.); (J.S.); (Y.W.); (W.S.); (G.Y.); (J.W.); (S.Q.); (L.W.)
- School of Pharmacy, Hainan Medical University, Haikou 571199, China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island, Emergency Medicine of Chinese Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
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3
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Jiang Q, Yuan S, Wang K, Zhu X, Hu Y, Jiang Y, Liu L, Han Y, Xiong F, Xu L, Zhu X, Zhou F. Ginkgo biloba extract ameliorates hyperglycaemia-induced enteric glial cell injury via regulation of the TLR2-related pathway. J Pharm Pharmacol 2023; 75:1430-1441. [PMID: 37738214 DOI: 10.1093/jpp/rgad075] [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: 01/01/2023] [Accepted: 08/11/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND Diabetic gastrointestinal dysfunction (DGD) is a common complication in diabetic patients, and enteric glial cells (EGCs) found in the gastrointestinal tract have been shown to play an essential role in gastrointestinal dysfunction. Thus, targeting EGCs may be helpful for the control of DGD. This study aimed to evaluate the protective effect of Ginkgo biloba extract (GBE) from G. biloba dropping pills against hyperglycaemic stress-induced EGCs injury and its underlying mechanism. METHODS In vitro, the protective effect of GBE on CRL-2690 cells was evaluated by MTT assay and TUNEL assay. The expression of related markers was evaluated by RNA sequencing and validated by using western blotting. In vivo, STZ-induced C57BL/6J WT mice were used as models to evaluate the effects of GBE on blood glucose, body weight, and EGCs' activity and relevant signalling pathways were validated by immunofluorescence. RESULTS The results showed that GBE (25 μg/ml) treatment significantly attenuated hyperglycaemic stress-induced cytotoxicity and cell apoptosis in CRL-2690 cells, which was verified in an STZ-induced (100 mg/kg, 3 days) diabetic mouse model with continuous GBE administration (25/100 mg/kg/day, 6/12 weeks). Further mechanistic study based on transcriptomic data revealed that GBE exerted its beneficial effect by regulating immune-related pathways, and TLR2/BTK/NF-κB/IL-1α/IL-10 comprised the main targets of this drug. CONCLUSIONS This study demonstrates the protective effect of GBE against hyperglycaemic stress-induced EGCs injury using both in vitro and in vivo models and further reveals that the effect was achieved by targeting TLR2 and its downstream molecules BTK/NF-κB/IL-1α/IL-10. This study may be helpful for expanding the clinical application of GBE in treating DGD.
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Affiliation(s)
- Qing Jiang
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Shiqin Yuan
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Ke Wang
- National Health Commission (NHC) Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 210000, China
| | - Xue Zhu
- National Health Commission (NHC) Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 210000, China
| | - Yun Hu
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Yanmin Jiang
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Lin Liu
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Yumeng Han
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Fan Xiong
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Lan Xu
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Xiaowei Zhu
- Department of Endocrinology, Nanjing Medical University, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214043, China
| | - Fanfan Zhou
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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Hasan MS, Wang Y, Feugang JM, Zhou H, Liao SF. RNA sequencing analysis revealed differentially expressed genes and their functional annotation in porcine longissimus dorsi muscle affected by dietary lysine restriction. Front Vet Sci 2023; 10:1233292. [PMID: 38026666 PMCID: PMC10668494 DOI: 10.3389/fvets.2023.1233292] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The objective of this study was to investigate the effects of dietary lysine restriction on the global gene expression profile of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (LDD: a lysine-deficient diet; LAD: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, skeletal muscle was sampled from the longissimus dorsi of individual pigs. The muscle total RNA was isolated and cDNA libraries were prepared for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data obtained was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). A total of 80 genes (padj ≤ 0.05) were differentially expressed in the longissimus dorsi muscle of the pigs fed LDD vs. LAD, of which 46 genes were downregulated and 34 genes were upregulated. Gene Ontology (GO) analysis of the DEGs (padj ≤ 0.05) for functional annotation identified those GO terms that are mostly associated with the molecular functions of structural molecules and metabolic enzymes (e.g., oxidoreductase and endopeptidase), biological process of acute-phase response, and amino acid metabolism including synthesis and degradation in the extracellular matrix region. Collectively, the results of this study have provided some novel insight regarding the molecular mechanisms of muscle growth that are associated with dietary lysine supply.
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Affiliation(s)
- Md. Shamimul Hasan
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Jean M. Feugang
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shengfa F. Liao
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
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Wang F, Xu SJ, Ye F, Zhang B, Sun XB. Integration of Transcriptomics and Lipidomics Profiling to Reveal the Therapeutic Mechanism Underlying Ramulus mori (Sangzhi) Alkaloids for the Treatment of Liver Lipid Metabolic Disturbance in High-Fat-Diet/Streptozotocin-Induced Diabetic Mice. Nutrients 2023; 15:3914. [PMID: 37764698 PMCID: PMC10536214 DOI: 10.3390/nu15183914] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disorder, with a global prevalence of 25%. Currently, there remains no approved therapy. Ramulus mori (Sangzhi) alkaloids (SZ-As), a novel natural medicine, have achieved comprehensive benefits in the treatment of type 2 diabetes; however, few studies have focused on its role in ameliorating hepatic lipid metabolic disturbance. Herein, the therapeutic effect and mechanism of SZ-As on a high-fat diet (HFD) combined with streptozotocin (STZ)-induced NAFLD mice were investigated via incorporating transcriptomics and lipidomics. SZ-As reduced body weight and hepatic lipid levels, restored pathological alternation and converted the blood biochemistry perturbations. SZ-A treatment also remarkedly inhibited lipogenesis and enhanced lipolysis, fatty acid oxidation and thermogenesis. Transcriptomics analysis confirmed that SZ-As mainly altered fatty acid oxidative metabolism and the TNF signaling pathway. SZ-As were further demonstrated to downregulate inflammatory factors and effectively ameliorate hepatic inflammation. Lipidomics analysis also suggested that SZ-As affected differential lipids including triglyceride (TG) and phosphatidylcholine (PC) expression, and the main metabolic pathways included glycerophospholipid, sphingomyelins and choline metabolism. Collectively, combined with transcriptomics and metabolomics data, it is suggested that SZ-As exert their therapeutic effect on NAFLD possibly through regulating lipid metabolism pathways (glycerophospholipid metabolism and choline metabolism) and increasing levels of PC and lysophosphatidylcholine (LPC) metabolites. This study provides the basis for more widespread clinical applications of SZ-As.
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Affiliation(s)
- Fan Wang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (F.W.); (S.-J.X.); (F.Y.)
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing 100193, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glyeolipid Metabolism Disorder Disease, State Administration of Traditional Chinese Medicine, Beijing 100193, China
| | - Sai-Jun Xu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (F.W.); (S.-J.X.); (F.Y.)
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing 100193, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glyeolipid Metabolism Disorder Disease, State Administration of Traditional Chinese Medicine, Beijing 100193, China
| | - Fan Ye
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (F.W.); (S.-J.X.); (F.Y.)
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing 100193, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glyeolipid Metabolism Disorder Disease, State Administration of Traditional Chinese Medicine, Beijing 100193, China
| | - Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (F.W.); (S.-J.X.); (F.Y.)
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing 100193, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glyeolipid Metabolism Disorder Disease, State Administration of Traditional Chinese Medicine, Beijing 100193, China
| | - Xiao-Bo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100193, China; (F.W.); (S.-J.X.); (F.Y.)
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing 100193, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing 100193, China
- Key Laboratory of Efficacy Evaluation of Chinese Medicine against Glyeolipid Metabolism Disorder Disease, State Administration of Traditional Chinese Medicine, Beijing 100193, China
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Mao X, Song F, Jin J, Zou B, Dai P, Sun M, Xu W, Wang L, Kang Y. Prognostic and immunological significance of an M1 macrophage-related gene signature in osteosarcoma. Front Immunol 2023; 14:1202725. [PMID: 37465666 PMCID: PMC10350629 DOI: 10.3389/fimmu.2023.1202725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/18/2023] [Indexed: 07/20/2023] Open
Abstract
As the most abundant infiltrating immune cells in the tumor microenvironment (TME), tumor-associated macrophages (TAMs) are pivotal in tumor development and treatment. The present investigation endeavors to explore the potential of M1 macrophage-related genes (MRGs) as biomarkers for assessing risk in individuals with osteosarcoma. RNA-sequence data and clinical data were derived from TCGA and GEO databases. The CIBERSORT method was utilized to discern subtypes of tumor-infiltrating immune cells. Identification of MRGs was achieved through Pearson correlation analysis. A prognostic risk model for MRGs was developed using Cox and LASSO regression analyses. A tripartite gene signature comprising CD37, GABRD, and ARHGAP25 was an independent prognostic indicator and was employed to develop a risk score model. The internal and external validation cohort confirmed the results. The area under the ROC curve (AUC) was determined for survival periods of 1 year, three years, and five years, yielding values of 0.746, 0.839, and 0.850, respectively. The C-index of the risk score was found to be superior to clinicopathological factors. GO/KEGG enrichment showed that the differences between high- and low-risk groups were predominantly associated with immune response pathways. Immune-related analysis related to proportions of immune cells, immune function, and expression levels of immune checkpoint genes all showed differences between the high- and low-risk groups. The qRT-PCR and Western blotting results indicate that CD37 expression was markedly higher in MG63 and U2OS cell lines when compared to normal osteoblast hFOB1.19. In U2OS cell line, GABRD expression levels were significantly upregulated. ARHGAP25 expression levels were elevated in both 143B and U2OS cell lines. In summary, utilizing a macrophage genes signature demonstrates efficacy in predicting both the prognosis and therapy response of OS. Additionally, immune analysis confirms a correlation between the risk score and the tumor microenvironment. Our findings, therefore, provide a cogent account for the disparate prognoses observed among patients and furnish a justification for further inquiry into biomarkers and anti-tumor treatment strategies.
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Affiliation(s)
- Xiaoyu Mao
- Department of Orthopedics, Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Fanglong Song
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ju Jin
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Naval Medical University, Shanghai, China
| | - Bin Zou
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Naval Medical University, Shanghai, China
- Department of Traditional Chinese Medicine, Dujiangyan Air Force Special Service Sanatorium, Chengdu, Sichuan, China
| | - Peijun Dai
- Department of Orthopedics, Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Naval Medical University, Shanghai, China
| | - Weicheng Xu
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical, Naval Medical University, Shanghai, China
| | - Yifan Kang
- Department of Orthopedics, Third Affiliated Hospital of Naval Medical University, Shanghai, China
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7
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Luna-Flores CH, Wang A, Cui Z, von Hellens J, Speight RE. An enhanced electron transport chain improved astaxanthin production in Phaffia rhodozyma. Biotechnol Bioeng 2023; 120:1382-1398. [PMID: 36639843 DOI: 10.1002/bit.28332] [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: 06/02/2022] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Astaxanthin (AX) is a carotenoid pigment with antioxidant properties widely used as a feed supplement. Wild-type strains of Phaffia rhodozyma naturally produce low AX yields, but we increased AX yields 50-fold in previous research using random mutagenesis of P. rhodozyma CBS6938 and fermentation optimization. On that study, genome changes were linked with phenotype, but relevant metabolic changes were not resolved. In this study, the wild-type and the superior P. rhodozyma mutant strains were grown in chemically defined media and instrumented fermenters. Differential kinetic, metabolomics, and transcriptomics data were collected. Our results suggest that carotenoid production was mainly associated with cell growth and had a positive regulation of central carbon metabolism metabolites, amino acids, and fatty acids. In the stationary phase, amino acids associated with the TCA cycle increased, but most of the fatty acids and central carbon metabolism metabolites decreased. TCA cycle metabolites were in abundance and media supplementation of citrate, malate, α-ketoglutarate, succinate, or fumarate increased AX production in the mutant strain. Transcriptomic data correlated with the metabolic and genomic data and found a positive regulation of genes associated with the electron transport chain suggesting this to be the main driver for improved AX production in the mutant strain.
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Affiliation(s)
- Carlos H Luna-Flores
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Australia
| | | | - Zhenling Cui
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | | | - Robert E Speight
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
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8
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Shi Y, Guo S, Zhao X, Xu M, Xu J, Xing G, Zhang Y, Ahammed GJ. Comparative physiological and transcriptomics analysis revealed crucial mechanisms of silicon-mediated tolerance to iron deficiency in tomato. Front Plant Sci 2022; 13:1094451. [PMID: 36618612 PMCID: PMC9811145 DOI: 10.3389/fpls.2022.1094451] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/02/2022] [Indexed: 06/07/2023]
Abstract
Iron (Fe) deficiency is a common abiotic stress in plants grown in alkaline soil that causes leaf chlorosis and affects root development due to low plant-available Fe concentration. Silicon (Si) is a beneficial element for plant growth and can also improve plant tolerance to abiotic stress. However, the effect of Si and regulatory mechanisms on tomato plant growth under Fe deficiency remain largely unclear. Here, we examined the effect of Si application on the photosynthetic capacity, antioxidant defense, sugar metabolism, and organic acid contents under Fe deficiency in tomato plants. The results showed that Si application promoted plant growth by increasing photosynthetic capacity, strengthening antioxidant defense, and reprogramming sugar metabolism. Transcriptomics analysis (RNA-seq) showed that Si application under Fe deficiency up-regulated the expression of genes related to antioxidant defense, carbohydrate metabolism and organic acid synthesis. In addition, Si application under Fe deficiency increased Fe distribution to leaves and roots. Combined with physiological assessment and molecular analysis, these findings suggest that Si application can effectively increase plant tolerance to low Fe stress and thus can be implicated in agronomic management of Fe deficiency for sustainable crop production. Moreover, these findings provide important information for further exploring the genes and underlying regulatory mechanisms of Si-mediated low Fe stress tolerance in crop plants.
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Affiliation(s)
- Yu Shi
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shuxun Guo
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xin Zhao
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Mengzhu Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yi Zhang
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, Henan, China
- Henan International Joint Laboratory of Stress Resistance Regulation and Safe Production of Protected Vegetables, Luoyang, Henan, China
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9
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Pittari D, Dalla Torre M, Borini E, Hummel B, Sawarkar R, Semino C, van Anken E, Panina-Bordignon P, Sitia R, Anelli T. CREB3L1 and CREB3L2 control Golgi remodelling during decidualization of endometrial stromal cells. Front Cell Dev Biol 2022; 10:986997. [PMID: 36313580 PMCID: PMC9608648 DOI: 10.3389/fcell.2022.986997] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Upon progesterone stimulation, Endometrial Stromal Cells (EnSCs) undergo a differentiation program into secretory cells (decidualization) to release in abundance factors crucial for embryo implantation. We previously demonstrated that decidualization requires massive reshaping of the secretory pathway and, in particular, of the Golgi complex. To decipher the underlying mechanisms, we performed a time-course transcriptomic analysis of in vitro decidualizing EnSC. Pathway analysis shows that Gene Ontology terms associated with vesicular trafficking and early secretory pathway compartments are the most represented among those enriched for upregulated genes. Among these, we identified a cluster of co-regulated genes that share CREB3L1 and CREB3L2 binding elements in their promoter regions. Indeed, both CREB3L1 and CREB3L2 transcription factors are up-regulated during decidualization. Simultaneous downregulation of CREB3L1 and CREB3L2 impairs Golgi enlargement, and causes dramatic changes in decidualizing EnSC, including Golgi fragmentation, collagen accumulation in dilated Endoplasmic Reticulum cisternae, and overall decreased protein secretion. Thus, both CREB3L1 and CREB3L2 are required for Golgi reshaping and efficient protein secretion, and, as such, for successful decidualization.
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Affiliation(s)
- Daniele Pittari
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Marco Dalla Torre
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Elena Borini
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Medical Research Council (MRC), University of Cambridge, Cambridge, United Kingdom
| | - Claudia Semino
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Eelco van Anken
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Panina-Bordignon
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Roberto Sitia
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tiziana Anelli
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
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10
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Ye MS, Chen HL, Liu CX, Ren AJ, Yang HW, Wang SS. Caspofungin at Sub-inhibitory Concentration Promotes the Formation of Candida Albicans Persister Cells. J Appl Microbiol 2022; 133:2466-2473. [PMID: 35858676 DOI: 10.1111/jam.15718] [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: 03/30/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022]
Abstract
AIMS Low caspofungin exposure is frequently encountered in patients with invasive candidiasis caused by Candida albicans (C. albicans). This study aimed to investigate the effects of caspofungin on C. albicans at sub-inhibitory concentrations. METHODS AND RESULTS First, a comparative transcriptomics analysis was performed on C. albicans receiving caspofungin at sub-minimum inhibitory concentrations (sub-MIC). The results showed that caspofungin significantly changed the mRNA expression profile in DAY185, with DE-mRNAs enriched in the functions of cell wall biosynthesis, metabolism, etc. Subsequently, cellular fitness, cell aggregation, energy metabolism activity, and the proportion of persister cells of C. albicans were quantitatively and/or qualitatively assessed after sub-MIC caspofungin exposure. No significant changes in cell fitness and aggregation formation were observed during treatment of C. albicans with sub-MIC caspofungin. In C. albicans aggregation treated with sub-MIC caspofungin, we observed a decrease in respiratory metabolism and an increase in persister cells; this effect was more pronounced in als1ΔΔ than in DAY185. CONCLUSIONS Pre-exposure to sub-MIC caspofungin suppresses C. albicans respiratory metabolism and promotes persister cell development. SIGNIFICANCE AND IMPACT OF STUDY Caspofungin should be used with caution in patients with C. albicans infections, as anti-infection therapy may fail due to persister cells.
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Affiliation(s)
| | - Hua-le Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Cai-Xia Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Ai-Juan Ren
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Hai-Wei Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Shi-Shi Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
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11
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Xu Y, Wang Y, Wang L, Liang W, Yang Q. Sodium Valproate Is Effective Against Botrytis cinerea Infection of Tomato by Enhancing Histone H3 Acetylation-Directed Gene Transcription and Triggering Tomato Fruit Immune Response. Phytopathology 2022; 112:1264-1272. [PMID: 34982575 DOI: 10.1094/phyto-11-21-0483-r] [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] [Indexed: 06/14/2023]
Abstract
Botrytis cinerea causes gray mold resulting in enormous financial loss. Fungicide resistance of B. cinerea has become a serious issue in food safety and agricultural environmental protection. Sodium valproate (SV) has been used in clinical trials; thus, it is an excellent candidate for fungicide development, considering its safety. However, the antifungal activity remains unclear. SV was effective against B. cinerea by enhancing acetylation of histone H3, including H3K9ac, H3K14ac, and H3K56ac. A transcriptomics analysis revealed that the expression of 1,557 genes changed significantly in response to SV. A pathway enrichment analysis identified 16 significant GO terms, in which molecular functions were mainly involved. In addition, the expression levels of 13 genes involved in B. cinerea virulence and five genes involved in tomato immune response were altered by the SV treatment. These results indicate that SV inhibits B. cinerea by enhancing acetylation of histone H3 and modifying gene transcription. Thus, SV is an effective, safe, potential antifungal agent for control of both pre- and postharvest losses caused by B. cinerea.
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Affiliation(s)
- Yang Xu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yameng Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Lulu Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Qianqian Yang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
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12
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Wang J, Su H, Han H, Wang W, Li M, Zhou Y, Li Y, Li M. Transcriptomics Reveals Host-Dependent Differences of Polysaccharides Biosynthesis in Cynomorium songaricum. Molecules 2021; 27:44. [PMID: 35011276 DOI: 10.3390/molecules27010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/31/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Cynomorium songaricum is a root holoparasitic herb that is mainly hosted in the roots of Nitraria roborowskii and Nitraria sibirica distributed in the arid desert and saline-alkaline regions. The stem of C. songaricum is widely used as a traditional Chinese medicine and applied in anti-viral, anti-obesity and anti-diabetes, which largely rely on the bioactive components including: polysaccharides, flavonoids and triterpenes. Although the differences in growth characteristics of C. songaricum between N. roborowskii and N. sibirica have been reported, the difference of the two hosts on growth and polysaccharides biosynthesis in C. songaricum as well as regulation mechanism are not limited. Here, the physiological characteristics and transcriptome of C. songaricum host in N. roborowskii (CR) and N. sibirica (CS) were conducted. The results showed that the fresh weight, soluble sugar content and antioxidant capacity on a per stem basis exhibited a 3.3-, 3.0- and 2.1-fold increase in CR compared to CS. A total of 16,921 differentially expressed genes (DEGs) were observed in CR versus CS, with 2573 characterized genes, 1725 up-regulated and 848 down-regulated. Based on biological functions, 50 DEGs were associated with polysaccharides and starch metabolism as well as their transport. The expression levels of the selected 37 genes were validated by qRT-PCR and almost consistent with their Reads Per kb per Million values. These findings would provide useful references for improving the yield and quality of C. songaricum.
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13
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Wang X, Liao Q, Chen H, Gong G, Siu SWI, Chen Q, Kam H, Ung COL, Cheung KK, Rádis-Baptista G, Wong CTT, Lee SMY. Toxic Peptide From Palythoa caribaeorum Acting on the TRPV1 Channel Prevents Pentylenetetrazol-Induced Epilepsy in Zebrafish Larvae. Front Pharmacol 2021; 12:763089. [PMID: 34925021 PMCID: PMC8672801 DOI: 10.3389/fphar.2021.763089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
PcActx peptide, identified from the transcriptome of zoantharian Palythoa caribaeorum, was clustered into the phylogeny of analgesic polypeptides from sea anemone Heteractis crispa (known as APHC peptides). APHC peptides were considered as inhibitors of transient receptor potential cation channel subfamily V member 1 (TRPV1). TRPV1 is a calcium-permeable channel expressed in epileptic brain areas, serving as a potential target for preventing epileptic seizures. Through in silico and in vitro analysis, PcActx peptide was shown to be a potential TRPV1 channel blocker. In vivo studies showed that the linear and oxidized PcActx peptides caused concentration-dependent increases in mortality of zebrafish larvae. However, monotreatment with PcActx peptides below the maximum tolerated doses (MTD) did not affect locomotor behavior. Moreover, PcActx peptides (both linear and oxidized forms) could effectively reverse pentylenetetrazol (PTZ)-induced seizure-related behavior in zebrafish larvae and prevent overexpression of c-fos and npas4a at the mRNA level. The excessive production of ROS induced by PTZ was markedly attenuated by both linear and oxidized PcActx peptides. It was also verified that the oxidized PcActx peptide was more effective than the linear one. In particular, oxidized PcActx peptide notably modulated the mRNA expression of genes involved in calcium signaling and γ-aminobutyric acid (GABA)ergic-glutamatergic signaling, including calb1, calb2, gabra1, grm1, gria1b, grin2b, gat1, slc1a2b, gad1b, and glsa. Taken together, PcActx peptide, as a novel neuroactive peptide, exhibits prominent anti-epileptic activity, probably through modulating calcium signaling and GABAergic-glutamatergic signaling, and is a promising candidate for epilepsy management.
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Affiliation(s)
- Xiufen Wang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Qiwen Liao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Hanbin Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Guiyi Gong
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Shirley Weng In Siu
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Macau, China
| | - Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Hiotong Kam
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Carolina Oi Lam Ung
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Kwok-Kuen Cheung
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, China
| | - Gandhi Rádis-Baptista
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará, Fortaleza, Brazil
| | - Clarence Tsun Ting Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
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14
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Lin X, Li H, Yang T, Liu X, Fan F, Zhou X, Luo Y. Transcriptomics Analysis of Lens from Patients with Posterior Subcapsular Congenital Cataract. Genes (Basel) 2021; 12:1904. [PMID: 34946854 PMCID: PMC8702110 DOI: 10.3390/genes12121904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 01/30/2023] Open
Abstract
To gain insight into the aetiology of posterior subcapsular congenital cataract from the perspective of transcriptional changes, we conducted an mRNA sequencing analysis of the lenses in posterior subcapsular congenital cataract patients and in normal children. There were 1533 differentially expressed genes from 19,072 genes in the lens epithelial cells of the posterior subcapsular congenital cataract patients compared to in the normal controls at a cut-off criteria of |log2 fold change| of >1 and a p-value of <0.05, including 847 downregulated genes and 686 upregulated genes. To further narrow down the DEGs, we utilised the stricter criteria of |log2 fold change| of >1 and an FDR value of <0.05, and we identified 551 DEGs, including 97 upregulated genes and 454 downregulated genes. This study also identified 1263 differentially expressed genes of the 18,755 genes in lens cortex and nuclear fibres, including 646 downregulated genes and 617 upregulated genes. The downregulated genes in epithelial cells were significantly enriched in the structural constituent of lenses, lens development and lens fibre cell differentiation. After filtering the DEGs using the databases iSyTE and Cat-Map, several high-priority candidate genes related to posterior subcapsular congenital cataract such as GRIFIN, HTRA1 and DAPL1 were identified. The findings of our study may provide a deeper understanding of the mechanisms of posterior subcapsular congenital cataract and help in the prevention and treatment of this disease.
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Affiliation(s)
| | | | | | | | | | | | - Yi Luo
- Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China; (X.L.); (H.L.); (T.Y.); (X.L.); (F.F.); (X.Z.)
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15
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Yu X, Wang Z, Chen Y, Yin G, Liu J, Chen W, Zhu L, Xu W, Li X. The Predictive Role of Immune Related Subgroup Classification in Immune Checkpoint Blockade Therapy for Lung Adenocarcinoma. Front Genet 2021; 12:771830. [PMID: 34721552 PMCID: PMC8554034 DOI: 10.3389/fgene.2021.771830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/30/2021] [Indexed: 01/17/2023] Open
Abstract
Background: In lung adenocarcinoma (LUAD), the predictive role of immune-related subgroup classification in immune checkpoint blockade (ICB) therapy remains largely incomplete. Methods: Transcriptomics analysis was performed to evaluate the association between immune landscape and ICB therapy in lung adenocarcinoma and the associated underlying mechanism. First, the least absolute shrinkage and selection operator (LASSO) algorithm and K-means algorithm were used to identify immune related subgroups for LUAD cohort from the Cancer Genome Atlas (TCGA) database (n = 572). Second, the immune associated signatures of the identified subgroups were characterized by evaluating the status of immune checkpoint associated genes and the immune cell infiltration. Then, potential responses to ICB therapy based on the aforementioned immune related subgroup classification were evaluated via tumor immune dysfunction and exclusion (TIDE) algorithm analysis, and survival analysis and further Cox proportional hazards regression analysis were also performed for LUAD. In the end, gene set enrichment analysis (GSEA) was performed to explore the metabolic mechanism potentially responsible for immune related subgroup clustering. Additionally, two LUAD cohorts from the Gene Expression Omnibus (GEO) database were used as validation cohort. Results: A total of three immune related subgroups with different immune-associated signatures were identified for LUAD. Among them, subgroup 1 with higher infiltration scores for effector immune cells and immune checkpoint associated genes exhibited a potential response to IBC therapy and a better survival, whereas subgroup 3 with lower scores for immune checkpoint associated genes but higher infiltration scores for suppressive immune cells tended to be insensitive to ICB therapy and have an unfavorable prognosis. GSEA revealed that the status of glucometabolic reprogramming in LUAD was potentially responsible for the immune-related subgroup classification. Conclusion: In summary, immune related subgroup clustering based on distinct immune associated signatures will enable us to screen potentially responsive LUAD patients for ICB therapy before treatment, and the discovery of metabolism associated mechanism is beneficial to comprehensive therapeutic strategies making involving ICB therapy in combination with metabolism intervention for LUAD.
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Affiliation(s)
- Xiaozhou Yu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ziyang Wang
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Molecular Imaging and Nuclear Medicine, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
| | - Yiwen Chen
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Guotao Yin
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jianjing Liu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wei Chen
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiaofeng Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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16
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Wang Y, Liu S, Yin X, Yu D, Xie X, Huang B. Functional Analysis of Keto-Acid Reductoisomerase ILVC in the Entomopathogenic Fungus Metarhizium robertsii. J Fungi (Basel) 2021; 7:737. [PMID: 34575775 DOI: 10.3390/jof7090737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/04/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 11/28/2022] Open
Abstract
Ketol-acid reductoisomerase (ILVC) is the second enzyme in the branched-chain amino acid (BCAA) biosynthesis, which regulates many physiological activities in a variety of organisms from bacteria to fungi and plants. In this work, function mechanisms of ILVC in Metarhizium robertsii Metchnikoff (Hypocreales: Clavicipitaceae) were explored with site-directed mutagenesis, reductase activity assays and transcriptomics analysis. The reductase activity assays showed that ILVC from phytopathogenic fungi exhibited significantly higher activities than those from entomopathogenic fungi but lower than those from yeast. Site-directed mutagenesis and enzymatic activities of MrILVC with different active-site mutants (Arg-113, Ser-118, Asp-152, Asp-260, and Glu-264) confirmed that active sites of MrILVC are conserved with plant and bacterial ILVCs. Deleting MrilvC causes the complete failures of vegetative growth and conidial germination, feeding with branched-chain amino acids (BCAAs) recovers the fungal growth but not conidial germination, while both characteristics are restored when supplemented with yeast extract. Compared to ΔMrilvC cultured in czapek agar (CZA), plenty of genes involved in the biosynthesis of antibiotics and amino acids were up- or down-regulated in the wild type or ΔMrilvC feeding with either BCAAs or yeast extract. Further analysis showed some genes, such as catalase A, participate in mycelial growth and conidial germination was down-regulated in ΔMrilvC from CZA, revealing that MrILVC might control the fungal development by gene regulation and BCAAs or yeast extract could play partial roles of MrILVC. This study will advance our understanding of ILVC function mechanisms in fungi.
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17
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Delavari A, Zinati Z, Sazegari S, Tahmasebi A. Integrating expression data and genomic sequences to investigate transcriptional regulation in barley in response to abiotic stress. BioTechnologia (Pozn) 2021; 102:21-32. [PMID: 36605711 DOI: 10.5114/bta.2021.103759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/18/2020] [Revised: 10/01/2020] [Accepted: 11/13/2020] [Indexed: 01/07/2023] Open
Abstract
Abiotic stress responses are regulated critically at the transcriptional level. Clarifying the intricate mechanisms that regulate gene expression in response to abiotic stress is crucial and challenging. For this purpose, the factors that regulate gene expression and their binding sites in DNA should be determined. By using bioinformatics tools, the differentially expressed probe sets were studied. A meta-analysis of transcriptomic responses to several abiotic stresses in barley was performed. Motif enrichments revealed that AP2/ERF (APETALA2/Ethylene-Responsive Factor) has the most frequent binding sites. We found that the bHLH transcription factor family has the highest number of transcription factor members. Moreover, network construction revealed that AP2 has the highest number of connections with other genes, which indicates its critical role in abiotic stress responses. The present research further predicted 49 miRNAs belonging to 23 miRNA families. This study identified the probable conserved and enriched motifs, which might have a role in the regulation of differentially expressed genes under abiotic stresses. In addition to shedding light on gene expression regulation, a toolbox of available promoters for genetic engineering of crop plants under such abiotic stresses was developed.
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Abstract
Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied, the gene expression changes in the facial nerve trunk after injury are still unknown. In this study, we established an adult rat model of facial nerve crush injury by compressing the right lateral extracranial nerve trunk. Transcriptome sequencing, differential gene expression analysis, and cluster analysis of the injured facial nerve trunk were performed, and 39 intersecting genes with significant variance in expression were identified. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the 39 intersecting genes revealed that these genes are mostly involved in leukocyte cell-cell adhesion and phagocytosis and have essential roles in regulating nerve repair. Quantitative real-time polymerase chain reaction assays were used to validate the expression of pivotal genes. Finally, nine pivotal genes that contribute to facial nerve recovery were identified, including Arhgap30, Akr1b8, C5ar1, Csf2ra, Dock2, Hcls1, Inpp5d, Sla, and Spi1. Primary Schwann cells were isolated from the sciatic nerve of neonatal rats. After knocking down Akr1b8 in Schwann cells with an Akr1b8-specific small interfering RNA plasmid, expression levels of monocyte chemoattractant protein-1 and interleukin-6 were decreased, while cell proliferation and migration were not obviously altered. These findings suggest that Akr1b8 likely regulates the interaction between Schwann cells and macrophages through regulation of cytokine expression to promote facial nerve regeneration. This study is the first to reveal a transcriptome change in the facial nerve trunk after facial nerve injury, thereby revealing the potential mechanism underlying repair of facial nerve injury. This study was approved by the Animal Ethics Committee of Nantong University, China in 2018 (approval No. S20180923-007).
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Affiliation(s)
- Qian-Qian Cao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Shuo Li
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yan Lu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Di Wu
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Wei Feng
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Yong Shi
- Department of Otolaryngology, Head and Neck Surgery, Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Lu-Ping Zhang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
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Southan J, McHugh E, Walker H, Ismail HM. Metabolic Signature of Articular Cartilage Following Mechanical Injury: An Integrated Transcriptomics and Metabolomics Analysis. Front Mol Biosci 2020; 7:592905. [PMID: 33392255 PMCID: PMC7773849 DOI: 10.3389/fmolb.2020.592905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/10/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Mechanical injury to the articular cartilage is a key risk factor in joint damage and predisposition to osteoarthritis. Integrative multi-omics approaches provide a valuable tool to understand tissue behavior in response to mechanical injury insult and help to identify key pathways linking injury to tissue damage. Global or untargeted metabolomics provides a comprehensive characterization of the metabolite content of biological samples. In this study, we aimed to identify the metabolic signature of cartilage tissue post injury. We employed an integrative analysis of transcriptomics and global metabolomics of murine epiphyseal hip cartilage before and after injury. Transcriptomics analysis showed a significant enrichment of gene sets involved in regulation of metabolic processes including carbon metabolism, biosynthesis of amino acids, and steroid biosynthesis. Integrative analysis of enriched genes with putatively identified metabolite features post injury showed a significant enrichment for carbohydrate metabolism (glycolysis, galactose, and glycosylate metabolism and pentose phosphate pathway) and amino acid metabolism (arginine biosynthesis and tyrosine, glycine, serine, threonine, and arginine and proline metabolism). We then performed a cross analysis of global metabolomics profiles of murine and porcine ex vivo cartilage injury models. The top commonly modulated metabolic pathways post injury included arginine and proline metabolism, arginine biosynthesis, glycolysis/gluconeogenesis, and vitamin B6 metabolic pathways. These results highlight the significant modulation of metabolic responses following mechanical injury to articular cartilage. Further investigation of these pathways would provide new insights into the role of the early metabolic state of articular cartilage post injury in promoting tissue damage and its link to disease progression of osteoarthritis.
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Affiliation(s)
- Jennifer Southan
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Emily McHugh
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Heather Walker
- biOMICS Mass Spectrometry Facility, Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom
| | - Heba M Ismail
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, United Kingdom
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20
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Dissanayake TK, Schäuble S, Mirhakkak MH, Wu WL, Ng ACK, Yip CCY, López AG, Wolf T, Yeung ML, Chan KH, Yuen KY, Panagiotou G, To KKW. Corrigendum: Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection. Front Microbiol 2020; 11:602854. [PMID: 33193285 PMCID: PMC7658905 DOI: 10.3389/fmicb.2020.602854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/21/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Sascha Schäuble
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Mohammad Hassan Mirhakkak
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Wai-Lan Wu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anthony Chin-Ki Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Albert García López
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Man-Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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21
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Lozoya OA, McClelland KS, Papas BN, Li JL, Yao HHC. Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA. Front Genet 2020; 11:511286. [PMID: 33193599 PMCID: PMC7586319 DOI: 10.3389/fgene.2020.511286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have precipitated the development of bioinformatic tools to reconstruct cell lineage specification and differentiation processes with single-cell precision. However, current start-up costs and recommended data volumes for statistical analysis remain prohibitively expensive, preventing scRNA-seq technologies from becoming mainstream. Here, we introduce single-cell amalgamation by latent semantic analysis (SALSA), a versatile workflow that combines measurement reliability metrics with latent variable extraction to infer robust expression profiles from ultra-sparse sc-RNAseq data. SALSA uses a matrix focusing approach that starts by identifying facultative genes with expression levels greater than experimental measurement precision and ends with cell clustering based on a minimal set of Profiler genes, each one a putative biomarker of cluster-specific expression profiles. To benchmark how SALSA performs in experimental settings, we used the publicly available 10X Genomics PBMC 3K dataset, a pre-curated silver standard from human frozen peripheral blood comprising 2,700 single-cell barcodes, and identified 7 major cell groups matching transcriptional profiles of peripheral blood cell types and driven agnostically by < 500 Profiler genes. Finally, we demonstrate successful implementation of SALSA in a replicative scRNA-seq scenario by using previously published DropSeq data from a multi-batch mouse retina experimental design, thereby identifying 10 transcriptionally distinct cell types from > 64,000 single cells across 7 independent biological replicates based on < 630 Profiler genes. With these results, SALSA demonstrates that robust pattern detection from scRNA-seq expression matrices only requires a fraction of the accrued data, suggesting that single-cell sequencing technologies can become affordable and widespread if meant as hypothesis-generation tools to extract large-scale differential expression effects.
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Affiliation(s)
- Oswaldo A. Lozoya
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Kathryn S. McClelland
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Brian N. Papas
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
| | - Humphrey H.-C. Yao
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States
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22
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Dissanayake TK, Schäuble S, Mirhakkak MH, Wu WL, Ng ACK, Yip CCY, López AG, Wolf T, Yeung ML, Chan KH, Yuen KY, Panagiotou G, To KKW. Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection. Front Microbiol 2020; 11:1580. [PMID: 32849329 PMCID: PMC7396524 DOI: 10.3389/fmicb.2020.01580] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 02/28/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Rhinovirus (RV) and influenza virus are the most frequently detected respiratory viruses among adult patients with community acquired pneumonia. Previous clinical studies have identified major differences in the clinical presentations and inflammatory or immune response during these infections. A systematic transcriptomic analysis directly comparing influenza and RV is lacking. Here, we sought to compare the transcriptomic response to these viral infections. Human airway epithelial Calu-3 cells were infected with contemporary clinical isolates of RV, influenza A virus (IAV), or influenza B virus (IBV). Host gene expression was determined using RNA-seq. Differentially expressed genes (DEGs) with respect to mock-infected cells were identified using the overlapping gene-set of four different statistical models. Transcriptomic analysis showed that RV-infected cells have a more blunted host response with fewer DEGs than IAV or IBV-infected cells. IFNL1 and CXCL10 were among the most upregulated DEGs during RV, IAV, and IBV infection. Other DEGs that were highly expressed for all 3 viruses were mainly genes related to type I or type III interferons (RSAD2, IDO1) and chemokines (CXCL11). Notably, ICAM5, a known receptor for enterovirus D68, was highly expressed during RV infection only. Gene Set Enrichment Analysis (GSEA) confirmed that pathways associated with interferon response, innate immunity, or regulation of inflammatory response, were most perturbed for all three viruses. Network analysis showed that steroid-related pathways were enriched. Taken together, our data using contemporary virus strains suggests that genes related to interferon and chemokine predominated the host response associated with RV, IAV, and IBV infection. Several highly expressed genes, especially ICAM5 which is preferentially-induced during RV infection, deserve further investigation.
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Affiliation(s)
| | - Sascha Schäuble
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Mohammad Hassan Mirhakkak
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Wai-Lan Wu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anthony Chin-Ki Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Albert García López
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Man-Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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23
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Auray G, Talker SC, Keller I, Python S, Gerber M, Liniger M, Ganges L, Bruggmann R, Ruggli N, Summerfield A. High-Resolution Profiling of Innate Immune Responses by Porcine Dendritic Cell Subsets in vitro and in vivo. Front Immunol 2020; 11:1429. [PMID: 32733474 PMCID: PMC7358342 DOI: 10.3389/fimmu.2020.01429] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 04/03/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
The present study investigated the transcriptomic response of porcine dendritic cells (DC) to innate stimulation in vitro and in vivo. The aim was to identify DC subset-specialization, suitable Toll-like receptor (TLR) ligands targeting plasmacytoid DC (pDC), and the DC activation profile during highly and low virulent classical swine fever virus (CSFV, strain Eystrup and Pinar del Rio, respectively) infection, chosen as model for a virus causing a severe immunopathology. After identification of porcine conventional DC (cDC) 1, cDC2, pDC and a monocyte-derived subset in lymphoid tissues, we characterized DC activation using transcriptomics, and focused on chemokines, interferons, cytokines, as well as on co-stimulatory and inhibitory molecules. We demonstrate that porcine pDC provide important signals for Th1 and interferon responses, with CpG triggering the strongest responses in pDC. DC isolated early after infection of pigs with either of the two CSFV strains showed prominent upregulation of CCL5, CXCL9, CXCL10, CXCL11, and XCL1, as well as of the cytokines TNFSF13B, IL6, IL7, IL12B, IL15, IL27. Transcription of IL12B and many interferon genes were mostly restricted to pDC. Interestingly, the infection was associated with a prominent induction of inhibitory and cell death receptors. When comparing low and highly virulent CSFV strains, the latter induced a stronger inflammatory and antiviral response but a weaker cell cycle response, and reduced antigen presentation functions of DC. Taken together, we provide high-resolution information on DC activation in pigs, as well as information on how DC modulation could be linked to CSFV immunopathology.
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Affiliation(s)
- Gaël Auray
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Stephanie C Talker
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department for Biomedical Research and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Sylvie Python
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Markus Gerber
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Matthias Liniger
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Llilianne Ganges
- OIE Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Nicolas Ruggli
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
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24
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Sigdel T, Nguyen M, Liberto J, Dobi D, Junger H, Vincenti F, Laszik Z, Sarwal MM. Assessment of 19 Genes and Validation of CRM Gene Panel for Quantitative Transcriptional Analysis of Molecular Rejection and Inflammation in Archival Kidney Transplant Biopsies. Front Med (Lausanne) 2019; 6:213. [PMID: 31632976 PMCID: PMC6781675 DOI: 10.3389/fmed.2019.00213] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 05/31/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background: There is an urgent need to develop and implement low cost, high-throughput standardized methods for routine molecular assessment of transplant biopsies. Given the vast archive of formalin-fixed and paraffin-embedded (FFPE) tissue blocks in transplant centers, a reliable protocol for utilizing this tissue bank for clinical validation of target molecules as predictors of graft outcome over time, would be of great value. Methods: We designed and optimized assays to quantify 19 target genes, including previously reported set of tissue common rejection module (tCRM) genes. We interrogated their performance for their clinical utility for detection of graft rejection and inflammation by analyzing gene expression microarrays analysis of 163 renal allograft biopsies, and subsequently validated in 40 independent FFPE archived kidney transplant biopsies at a single center. Results: A QPCR (Fluidigm) and a barcoded oligo-based (NanoString) gene expression platform were compared for evaluation of amplification of gene expression signal for 19 genes from degraded RNA extracted from FFPE biopsy sections by a set protocol. Increased expression of the selected 19 genes, that reflect a combination of specific cellular infiltrates (8/19 genes) and a graft inflammation score (11/19 genes which computes the tCRM score allowed for segregation of kidney transplant biopsies with stable allograft function and normal histology from those with histologically confirmed acute rejection (AR; p = 0.0022, QPCR; p = 0.0036, barcoded assay) and many cases of histological borderline inflammation (BL). Serial biopsy shaves used for gene expression were also processed for in-situ hybridization (ISH) for a subset of genes. ISH confirmed a high degree of correlation of signal amplification and tissue localization. Conclusions: Target gene expression amplification across a custom set of genes can identify AR independent of histology, and quantify inflammation from archival kidney transplant biopsy tissue, providing a new tool for clinical correlation and outcome analysis of kidney allografts, without the need for prospective kidney biopsy biobanking efforts.
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Affiliation(s)
- Tara Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Mark Nguyen
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Dejan Dobi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Henrik Junger
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Flavio Vincenti
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
| | - Zoltan Laszik
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Nephrology, University of California, San Francisco, San Francisco, CA, United States
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25
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Hartnell F, Brown A, Capone S, Kopycinski J, Bliss C, Makvandi-Nejad S, Swadling L, Ghaffari E, Cicconi P, Del Sorbo M, Sbrocchi R, Esposito I, Vassilev V, Marriott P, Gardiner CM, Bannan C, Bergin C, Hoffmann M, Turner B, Nicosia A, Folgori A, Hanke T, Barnes E, Dorrell L. A Novel Vaccine Strategy Employing Serologically Different Chimpanzee Adenoviral Vectors for the Prevention of HIV-1 and HCV Coinfection. Front Immunol 2019; 9:3175. [PMID: 30713538 PMCID: PMC6346592 DOI: 10.3389/fimmu.2018.03175] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 07/25/2018] [Accepted: 12/24/2018] [Indexed: 12/21/2022] Open
Abstract
Background: Nearly 3 million people worldwide are coinfected with HIV and HCV. Affordable strategies for prevention are needed. We developed a novel vaccination regimen involving replication-defective and serologically distinct chimpanzee adenovirus (ChAd3, ChAd63) vector priming followed by modified vaccinia Ankara (MVA) boosts, for simultaneous delivery of HCV non-structural (NSmut) and HIV-1 conserved (HIVconsv) region immunogens. Methods: We conducted a phase I trial in which 33 healthy volunteers were sequentially enrolled and vaccinated via the intramuscular route as follows: 9 received ChAd3-NSmut [2.5 × 1010 vp] and MVA-NSmut [2 × 108 pfu] at weeks 0 and 8, respectively; 8 received ChAdV63.HIVconsv [5 × 1010 vp] and MVA.HIVconsv [2 × 108 pfu] at the same interval; 16 were co-primed with ChAd3-NSmut [2.5 × 1010 vp] and ChAdV63.HIVconsv [5 × 1010 vp] followed at week 8 by MVA-NSmut and MVA.HIVconsv [both 1 × 108 pfu]. Immunogenicity was assessed using peptide pools in ex vivo ELISpot and intracellular cytokine assays. Vaccine-induced whole blood transcriptome changes were assessed by microarray analysis. Results: All vaccines were well tolerated and no vaccine-related serious adverse events occurred. Co-administration of the prime-boost vaccine regimens induced high magnitude and broad T cell responses that were similar to those observed following immunization with either regimen alone. Median (interquartile range, IQR) peak responses to NSmut were 3,480 (2,728–4,464) and 3,405 (2,307–7,804) spot-forming cells (SFC)/106 PBMC for single and combined HCV vaccinations, respectively (p = 0.8). Median (IQR) peak responses to HIVconsv were 1,305 (1,095–4,967) and 1,005 (169–2,482) SFC/106 PBMC for single and combined HIV-1 vaccinations, respectively (p = 0.5). Responses were maintained above baseline to 34 weeks post-vaccination. Intracellular cytokine analysis indicated that the responding populations comprised polyfunctional CD4+ and CD8+ T cells. Canonical pathway analysis showed that in the single and combined vaccination groups, pathways associated with antiviral and innate immune responses were enriched for upregulated interferon-stimulated genes 24 h after priming and boosting vaccinations. Conclusions: Serologically distinct adenoviral vectors encoding HCV and HIV-1 immunogens can be safely co-administered without reducing the immunogenicity of either vaccine. This provides a novel strategy for targeting these viruses simultaneously and for other pathogens that affect the same populations. Clinical trial registration:https://clinicaltrials.gov, identifier: NCT02362217
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Affiliation(s)
- Felicity Hartnell
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony Brown
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jakub Kopycinski
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Carly Bliss
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Leo Swadling
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emma Ghaffari
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paola Cicconi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Ilaria Esposito
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Paula Marriott
- Centre for Clinical Vaccinology and Tropical Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Clair M Gardiner
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | | | | | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Bethany Turner
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alfredo Nicosia
- Keires AG, Basel, Switzerland.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | | | - Tomáš Hanke
- Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Headington, United Kingdom
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Headington, United Kingdom
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26
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Zhang H, Jin B, Bu J, Guo J, Chen T, Ma Y, Tang J, Cui G, Huang L. Transcriptomic Insight into Terpenoid Biosynthesis and Functional Characterization of Three Diterpene Synthases in Scutellaria barbata. Molecules 2018; 23:molecules23112952. [PMID: 30424547 PMCID: PMC6278268 DOI: 10.3390/molecules23112952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022] Open
Abstract
Scutellaria barbata (Lamiaceae) is an important medicinal herb widely used in China, Korea, India, and other Asian countries. Neo-clerodane diterpenoids are the largest known group of Scutellaria diterpenoids and show promising cytotoxic activity against several cancer cell lines. Here, Illumina-based deep transcriptome analysis of flowers, the aerial parts (leaf and stem), and roots of S. barbata was used to explore terpenoid-related genes. In total, 121,958,564 clean RNA-sequence reads were assembled into 88,980 transcripts, with an average length of 1370 nt and N50 length of 2144 nt, indicating high assembly quality. We identified nearly all known terpenoid-related genes (33 genes) involved in biosynthesis of the terpenoid backbone and 14 terpene synthase genes which generate skeletons for different terpenoids. Three full length diterpene synthase genes were functionally identified using an in vitro assay. SbTPS8 and SbTPS9 were identified as normal-CPP and ent-CPP synthase, respectively. SbTPS12 reacts with SbTPS8 to produce miltiradiene. Furthermore, SbTPS12 was proven to be a less promiscuous class I diterpene synthase. These results give a comprehensive understanding of the terpenoid biosynthesis in S. barbata and provide useful information for enhancing the production of bioactive neo-clerodane diterpenoids through genetic engineering.
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Affiliation(s)
- Huabei Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Junling Bu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
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