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Zhu T, Wang CJ, Lian HY, Ma HH, Wang D, Wang TY, Zhang R, Cui L, Li ZG. The plasma-soluble CSF1R level is a promising prognostic indicator for pediatric Langerhans cell histiocytosis. Pediatr Blood Cancer 2024; 71:e30970. [PMID: 38556751 DOI: 10.1002/pbc.30970] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 04/02/2024]
Abstract
Langerhans cell histiocytosis (LCH) is a rare hematologic neoplasm characterized by the clonal proliferation of Langerhans-like cells. Colony-stimulating factor 1 receptor (CSF1R) is a membrane-bound receptor that is highly expressed in LCH cells and tumor-associated macrophages. In this study, a soluble form of CSF1R protein (sCSF1R) was identified by plasma proteome profiling, and its role in evaluating LCH prognosis was explored. We prospectively measured plasma sCSF1R levels in 104 LCH patients and 10 healthy children using ELISA. Plasma sCSF1R levels were greater in LCH patients than in healthy controls (p < .001) and significantly differed among the three disease extents, with the highest level in MS RO+ LCH patients (p < .001). Accordingly, immunofluorescence showed the highest level of membrane-bound CSF1R in MS RO+ patients. Furthermore, the plasma sCSF1R concentration at diagnosis could efficiently predict the prognosis of LCH patients treated with standard first-line treatment (AUC = 0.782, p < .001). Notably, dynamic monitoring of sCSF1R levels could predict relapse early in patients receiving BRAF inhibitor treatment. In vitro drug sensitivity data showed that sCSF1R increased resistance to Ara-C in THP-1 cells expressing ectopic BRAF-V600E. Overall, the plasma sCSF1R level at diagnosis and during follow-up is of great clinical importance in pediatric LCH patients.
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Affiliation(s)
- Ting Zhu
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chan-Juan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Hong-Yun Lian
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Hong-Hao Ma
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Dong Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Tian-You Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Rui Zhang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Lei Cui
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Zhi-Gang Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Hematology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
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Rady AM, El-Sayed ASA, El-Baz AF, Abdel-Fattah GG, Magdeldin S, Ahmed E, Osama A, Hassanein SE, Saed H, Yassin M. Proteomics and metabolomics analyses of camptothecin-producing Aspergillus terreus reveal the integration of PH domain-containing proteins and peptidylprolyl cis/trans isomerase in restoring the camptothecin biosynthesis. Microbiol Spectr 2023; 11:e0228123. [PMID: 37855596 PMCID: PMC10714794 DOI: 10.1128/spectrum.02281-23] [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: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Decreasing the camptothecin productivity by fungi with storage and subculturing is the challenge that halts their further implementation to be an industrial platform for camptothecin (CPT) production. The highest differentially abundant proteins were Pleckstrin homology (PH) domain-containing proteins and Peptidyl-prolyl cis/trans isomerase that fluctuated with the subculturing of A. terreus with a remarkable relation to CPT biosynthesis and restored with addition of F. elastica microbiome.
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Affiliation(s)
- Amgad M. Rady
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza, Egypt
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ashraf F. El-Baz
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | | | - Sameh Magdeldin
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Aya Osama
- Proteomics and Metabolomics Research Program, Department of Basic Research, Children’s Cancer Hospital, Cairo, Egypt
| | - Sameh E. Hassanein
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center, Cairo, Egypt
| | - Hend Saed
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Marwa Yassin
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
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Xie Y, Li Y, Yao J, Song X, Wang H, Zhang J, Li X. Protein Lactylation Modification and Proteomics Features in Cirrhosis Patients after UC-MSC Treatment. Curr Issues Mol Biol 2023; 45:8444-8460. [PMID: 37886975 PMCID: PMC10605309 DOI: 10.3390/cimb45100532] [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: 09/27/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Umbilical cord mesenchymal stem cell (UC-MSC) therapy improves liver function in liver cirrhosis patients. This study aimed to elucidate the therapeutic mechanism underlying cell therapy by analyzing changes in the modification and expression of proteins 1 month post-treatment with UC-MSCs. This prospective study included 11 cirrhosis patients who received MSC injection. The laboratory indexes before and after treatment were collected to evaluate the clinical treatment effect of UC-MSCs, and the protein expression and lactylation modification in the liver were comprehensively revealed. Meanwhile, weighted gene co-expression network analysis was used to analyze the co-expression protein modules and their relationship with clinical features. The patients with liver cirrhosis showed an improvement trend after receiving UC-MSC treatment; specifically, the liver protein synthesis function was significantly improved and the coagulation function was also significantly improved. Proteomics combined with lactic acid proteomics revealed 160 lysine lactylation (Kla) sites of 119 proteins. Functional analysis showed that the lactylation-modified proteins were enriched in the pathway of glucose and other substances' metabolism, and many key enzymes of glycolysis and gluconeogenesis were lactated. UC-MSC therapy has a certain clinical effect in the treatment of liver cirrhosis and may act by regulating material metabolism, because the lactylation protein points to energy metabolism.
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Affiliation(s)
- Ye Xie
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China
| | - Ying Li
- General Surgery Department, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Jia Yao
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou 730000, China
| | - Xiaojing Song
- General Surgery Department, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Haiping Wang
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou 730000, China
| | - Jianjun Zhang
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou 730000, China
| | - Xun Li
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China
- General Surgery Department, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou 730000, China
- Hepatopancreatobiliary Surgery Institute of Gansu Province, Lanzhou 730000, China
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Shi Y, Wang Y, Zou H, Zhao B, Zhu T, Nakamura Y, Qi H. Detection of Simulated In Vitro Digestion Products of Fucoxanthin and Their Photodamage Alleviation Effect in Retinal Müller Cells Induced by Ultraviolet B Irradiation: A Proteomics Analysis. J Agric Food Chem 2023; 71:14626-14637. [PMID: 37753556 DOI: 10.1021/acs.jafc.3c03853] [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: 09/28/2023]
Abstract
Our previous study reported that the marine dietary bioactive compound fucoxanthin (FX) has the potential to reduce the level of oxidation in retinal Müller cells (RMCs) induced by ultraviolet B (UVB) irradiation. However, the gastrointestinal environment can inhibit the bioavailability and absorption of FX in the cell systems. In the current study, FX was initially digested in a simulated in vitro gastrointestinal fluid. Nine main digestive products were identified, and the photoprotective activities of FX simulated in vitro gastrointestinal digestion products (FX-ID) were assessed in the same RMC model. FX-ID significantly reduced intracellular ROS and alleviated apoptosis. Western blot assays showed that FX-ID inhibited phosphorylated proteins in the MAPK and NF-κB signaling pathways. Our proteomics analysis revealed that the differentially expressed proteins were linked to biological networks associated with antioxidation and metabolic processes. The data may provide insight into the photoprotective mechanisms of FX-ID and promote the development of various functional foods to prevent retinal disorders.
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Affiliation(s)
- Yixin Shi
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Liaoning Provincial Aquatic Products Deep Processing Technology Research Center, Dalian 116034, P. R. China
| | - Yingzhen Wang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Liaoning Provincial Aquatic Products Deep Processing Technology Research Center, Dalian 116034, P. R. China
| | - Haotian Zou
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Liaoning Provincial Aquatic Products Deep Processing Technology Research Center, Dalian 116034, P. R. China
| | - Baomin Zhao
- Jiangsu Palarich Food Co., Ltd., Xuzhou 221116, P. R. China
| | - Taihai Zhu
- Jiangsu Palarich Food Co., Ltd., Xuzhou 221116, P. R. China
| | - Yoshimasa Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Hang Qi
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Liaoning Provincial Aquatic Products Deep Processing Technology Research Center, Dalian 116034, P. R. China
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Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Rep 2023; 42:113087. [PMID: 37665664 DOI: 10.1016/j.celrep.2023.113087] [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: 04/25/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.
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Affiliation(s)
- Thomas Eng
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Menasalvas
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hemant Choudhary
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Edward Baidoo
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuzhong Liu Diercks
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Codik
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Gladden
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970 Horsholm, Denmark; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Christopher J Petzold
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Qin H, Wang W, Hu L, Yu Z, Chen Y, Zhao Y, Liao Y, Yang R. New Insights into the Role of HMGB2 in ST-Segment Elevation Myocardial Infarction. Int J Gen Med 2023; 16:4181-4191. [PMID: 37727529 PMCID: PMC10506601 DOI: 10.2147/ijgm.s429761] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
Background Ischemic heart disease is one of the leading causes of death in the world, of which ST-segment elevation myocardial infarction (STEMI) is an important type. Inappropriate activation and accumulation of platelets typically induced thrombosis, which may result in acute vessel occlusion and STEMI. Multiple cytokines have been shown to regulate platelet activation, but the relationship between HMGB2 and platelet activation has not been elucidated. Methods We collected peripheral blood of STEMI patients and healthy adults, and mass spectrometry analysis of platelet proteins was conducted. The "edgeR" package was used to identify the differentially expressed proteins (DEPs). The Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) were used to identify the significantly changed pathways. Western blot and ELISA were used to detect the expression of a high mobility group box 2 (HMGB2). Flow cytometric analysis and platelet aggregation rate were performed to evaluate the activation of platelets. Results We identified ALOX5, HIST1H1B, S100A11, HMGB2, and RPS15A were the top five up-regulated proteins by differential expression analysis. Western blot verified that the relative protein expression of HMGB2 in platelet was significantly higher in STEMI patients compared with control adults, and the results of ELISA indicated that the serum HMGB2 level increased and significantly correlated with neutrophil count in STEMI patients. Further investigation showed that the platelet aggregation induced by ADP, the activation of integrin αIIbβ3 and CD62P expression on platelet surface were all enhanced by the recombinant HMGB2 (rHMGB2). Conclusion In conclusion, HMGB2 may be the key molecule to regulate platelet activation in patients with STEMI, which may serve as a potential therapeutic target for STEMI.
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Affiliation(s)
- Hao Qin
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Wenjun Wang
- Department of Respiratory Diseases, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Longlong Hu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Zuozhong Yu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Yang Chen
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Yuanbin Zhao
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Yanhui Liao
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Renqiang Yang
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
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Kambey PA, Liu WY, Wu J, Bosco B, Nadeem I, Kanwore K, Gao DS. Single-nuclei RNA sequencing uncovers heterogenous transcriptional signatures in Parkinson's disease associated with nuclear receptor-related factor 1 defect. Neural Regen Res 2023; 18:2037-2046. [PMID: 36926730 DOI: 10.4103/1673-5374.366493] [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] [Indexed: 02/18/2023] Open
Abstract
Previous studies have found that deficiency in nuclear receptor-related factor 1 (Nurr1), which participates in the development, differentiation, survival, and degeneration of dopaminergic neurons, is associated with Parkinson's disease, but the mechanism of action is perplexing. Here, we first ascertained the repercussion of knocking down Nurr1 by performing liquid chromatography coupled with tandem mass spectrometry. We found that 231 genes were highly expressed in dopaminergic neurons with Nurr1 deficiency, 14 of which were linked to the Parkinson's disease pathway based on Kyoto Encyclopedia of Genes and Genomes analysis. To better understand how Nurr1 deficiency autonomously invokes the decline of dopaminergic neurons and elicits Parkinson's disease symptoms, we performed single-nuclei RNA sequencing in a Nurr1 LV-shRNA mouse model. The results revealed cellular heterogeneity in the substantia nigra and a number of activated genes, the preponderance of which encode components of the major histocompatibility II complex. Cd74, H2-Ab1, H2-Aa, H2-Eb1, Lyz2, Mrc1, Slc6a3, Slc47a1, Ms4a4b, and Ptprc2 were the top 10 differentially expressed genes. Immunofluorescence staining showed that, after Nurr1 knockdown, the number of CD74-immunoreactive cells in mouse brain tissue was markedly increased. In addition, Cd74 expression was increased in a mouse model of Parkinson's disease induced by treatment with 6-hydroxydopamine. Taken together, our results suggest that Nurr1 deficiency results in an increase in Cd74 expression, thereby leading to the destruction of dopaminergic neurons. These findings provide a potential therapeutic target for the treatment of Parkinson's disease.
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Affiliation(s)
- Piniel Alphayo Kambey
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China; Organization of African Academic Doctors, Nairobi, Kenya
| | - Wen-Ya Liu
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jiao Wu
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Bakwatanisa Bosco
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Iqra Nadeem
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Kouminin Kanwore
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Dian-Shuai Gao
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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Long S, Su M, Chen X, Hu A, Yu F, Zou Q, Cheng G. Proteomic and Mutant Analysis of Hydrogenase Maturation Protein Gene hypE in Symbiotic Nitrogen Fixation of Mesorhizobium huakuii. Int J Mol Sci 2023; 24:12534. [PMID: 37628715 PMCID: PMC10454058 DOI: 10.3390/ijms241612534] [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: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Hydrogenases catalyze the simple yet important redox reaction between protons and electrons and H2, thus mediating symbiotic interactions. The contribution of hydrogenase to this symbiosis and anti-oxidative damage was investigated using the M. huakuii hypE (encoding hydrogenase maturation protein) mutant. The hypE mutant grew a little faster than its parental 7653R and displayed decreased antioxidative capacity under H2O2-induced oxidative damage. Real-time quantitative PCR showed that hypE gene expression is significantly up-regulated in all the detected stages of nodule development. Although the hypE mutant can form nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 47% reduction in nitrogen fixation capacity. This phenotype was linked to the formation of smaller abnormal nodules containing disintegrating and prematurely senescent bacteroids. Proteomics analysis allowed a total of ninety differentially expressed proteins (fold change > 1.5 or <0.67, p < 0.05) to be identified. Of these proteins, 21 are related to stress response and virulence, 21 are involved in transporter activity, and 18 are involved in energy and nitrogen metabolism. Overall, the HypE protein is essential for symbiotic nitrogen fixation, playing independent roles in supplying energy and electrons, in bacterial detoxification, and in the control of bacteroid differentiation and senescence.
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Affiliation(s)
| | | | | | | | | | | | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
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Hou W, Chen Z, Pan C, Ni M, Ruan H, Song J, Lu S, Bhasin A, Ruan BH. Diselenide Covalent Allosteric Inhibitors of Glutaminase with Strong In Vivo Anticancer Activity. ACS Med Chem Lett 2023; 14:920-928. [PMID: 37465295 PMCID: PMC10351061 DOI: 10.1021/acsmedchemlett.2c00470] [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: 11/03/2022] [Accepted: 04/28/2023] [Indexed: 07/20/2023] Open
Abstract
Allosteric glutaminase inhibitors demonstrate inhibition of glutamine-dependent cancer cells with low general drug toxicity, but have issues with efficacy in vivo. Here, we designed a series of diselenide compounds with 6 atoms in the middle, aiming to target the allosteric site of kidney type glutaminase (KGA) with a covalent linkage to strengthen the interaction. Proteomic analysis demonstrated that the diselenide compounds cross-linked with the Lys320 residue at the KGA allosteric site; this was confirmed by the KGA K320A mutant which showed essentially no binding to the diselenide. Further, structure-activity relationship (SAR) analysis demonstrated that growth inhibition correlated well with KGA inhibition and was enhanced by thioredoxin reductase (TrxR) inhibition. Interestingly, diselenide compounds showed no inhibition of glutamate dehydrogenase (GDH), indicating some enzyme selectivity. Importantly, the designed novel diselenides are glutaminase allosteric inhibitors that showed in vivo efficacy and survival in the xenograft animal model.
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Affiliation(s)
- Wei Hou
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhao Chen
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chuqiao Pan
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Maowei Ni
- Center
for Cancer Research, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Haoqiang Ruan
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Song
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shiying Lu
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Aman Bhasin
- Amity
School of Chemical Sciences, Amity University, Panjab, Sector 82A, Mohali-140306, India
| | - Benfang Helen Ruan
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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10
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Ai L, Binek A, Kreimer S, Ayres M, Stotland A, Van Eyk JE. High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing. J Proteome Res 2023; 22:2124-2130. [PMID: 37040897 PMCID: PMC10243111 DOI: 10.1021/acs.jproteome.3c00027] [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: 01/12/2023] [Indexed: 04/13/2023]
Abstract
Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.
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Affiliation(s)
- Lizhuo Ai
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandra Binek
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Simion Kreimer
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Matthew Ayres
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Aleksandr Stotland
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E. Van Eyk
- Department
of Biomedical Sciences, Cedars-Sinai Medical
Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Smidt Heart institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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11
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Du R, Sun F, Li K, Qi J, Zhong W, Wang W, Sun Q, Deng Q, Wang H, Nie J, Ding C, Hong B. Proteomics Analysis Revealed Smad3 as a Potential Target of the Synergistic Antitumor Activity of Disulfiram and Cisplatin in Ovarian Cancer. Anticancer Agents Med Chem 2023; 23:1754-1764. [PMID: 37194931 DOI: 10.2174/1871520623666230516161200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Among gynecological cancers, ovarian cancer has a high mortality rate. Cisplatin-based chemotherapy is commonly used for the treatment of ovarian cancer. However, the clinical efficacy of cisplatin in ovarian cancer is limited due to the development of chemo-resistance during treatment. OBJECTIVE In the study, we aimed to investigate the synergistic anti-cancer activity and targets of the FDA-approved drug disulfiram combined with cisplatin in ovarian cancer. METHODS The cell viability was determined by Celltier-Glo luminescent assay. The synergistic anti-cancer activity was assessed by combination index. Cell cycle and apoptosis were detected by flow cytometry. The in vivo anti-tumor activity and side effects were evaluated using a xenografted mice model. The synergistic anti-cancer targets were identified by a mass spectrometry-based proteomics analysis. RESULTS In this study, we first found that disulfiram synergistically enhanced the anti-tumor activity of cisplatin in chemo-resistant ovarian cancer cells, which was accompanied by the enhanced induction of cellular apoptosis. Secondly, the in vivo study demonstrated that the combination treatment of disulfiram and cisplatin dramatically inhibited tumor growth and had no apparent side effects in ovarian cancer xenografted mice. Finally, proteomics analysis identified SMAD3 as a potential target of disulfiram-cisplatin combined treatment, and the down-regulation of SMAD3 could increase cisplatin-induced cell death in ovarian cancer. CONCLUSION Combination treatment of disulfiram and cisplatin synergistically inhibited the growth of ovarian cancer through down-regulating SMAD3. As a repurposed drug, disulfiram could be quickly transformed into a clinic to overcome cisplatin resistance for the treatment of ovarian cancer.
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Affiliation(s)
- Ruiping Du
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Feilong Sun
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Qi
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Wen Zhong
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Life Sciences and Medicine, Intelligent Pathology Institute, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Life Sciences and Medicine, Intelligent Pathology Institute, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiuyan Sun
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Qingmei Deng
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bo Hong
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
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12
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Halvorsen TG, Reubsaet L. The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis. Proteomics 2022; 22:e2100395. [PMID: 36217925 DOI: 10.1002/pmic.202100395] [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: 05/20/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022]
Abstract
Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.
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Affiliation(s)
| | - Léon Reubsaet
- Department of Pharmacy, University of Oslo, Oslo, Norway
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13
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Kuo TT, Lin LC, Chang HY, Chiang PJ, Wu HY, Chen TY, Hsia SM, Huang TC. Quantitative Proteome Analysis Reveals Melissa officinalis Extract Targets Mitochondrial Respiration in Colon Cancer Cells. Molecules 2022; 27:4533. [PMID: 35889404 DOI: 10.3390/molecules27144533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022]
Abstract
Melissa officinalis (MO), known as lemon balm, is a popular ingredient blended in herbal tea. In recent decades, the bioactivities of MO have been studied in sub-health and pathological status, highlighting MO possesses multiple pharmacological effects. We previously showed that hot water MO extract exhibited anticancer activity in colorectal cancer (CRC). However, the detailed mechanisms underlying MO-induced cell death remain elusive. To elucidate the anticancer regulation of MO extract in colon cancer, a data-driven analysis by proteomics approaches and bioinformatics analysis was applied. An isobaric tandem mass tags-based quantitative proteome analysis using liquid chromatography–coupled tandem mass spectrometry was performed to acquire proteome-wide expression data. The over-representation analysis and functional class scoring method were implemented to interpret the MO-induced biological regulations. In total, 3465 quantifiable proteoforms were identified from 24,348 peptides, with 67 upregulated and 54 downregulated proteins in the MO-treated group. Mechanistically, MO impeded mitochondrial respiratory electron transport by triggering a reactive oxygen species (ROS)-mediated oxidative stress response. MO hindered the mitochondrial membrane potential by reducing the protein expression in the electron transport chain, specifically the complex I and II, which could be restored by ROS scavenger. The findings comprehensively elucidate how MO hot water extract activates antitumor effects in colorectal cancer (CRC) cells.
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14
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Kobayashi H, Looker HC, Satake E, Saulnier PJ, Md Dom ZI, O'Neil K, Ihara K, Krolewski B, Galecki AT, Niewczas MA, Wilson JM, Doria A, Duffin KL, Nelson RG, Krolewski AS. Results of untargeted analysis using the SOMAscan proteomics platform indicates novel associations of circulating proteins with risk of progression to kidney failure in diabetes. Kidney Int 2022; 102:370-381. [PMID: 35618095 PMCID: PMC9333266 DOI: 10.1016/j.kint.2022.04.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
This study applies a large proteomics panel to search for new circulating biomarkers associated with progression to kidney failure in individuals with diabetic kidney disease. Four independent cohorts encompassing 754 individuals with type 1 and type 2 diabetes and early and late diabetic kidney disease were followed to ascertain progression to kidney failure. During ten years of follow-up, 227 of 754 individuals progressed to kidney failure. Using the SOMAscan proteomics platform, we measured baseline concentration of 1129 circulating proteins. In our previous publications, we analyzed 334 of these proteins that were members of specific candidate pathways involved in diabetic kidney disease and found 35 proteins strongly associated with risk of progression to kidney failure. Here, we examined the remaining 795 proteins using an untargeted approach. Of these remaining proteins, 11 were significantly associated with progression to kidney failure. Biological processes previously reported for these proteins were related to neuron development (DLL1, MATN2, NRX1B, KLK8, RTN4R and ROR1) and were implicated in the development of kidney fibrosis (LAYN, DLL1, MAPK11, MATN2, endostatin, and ROR1) in cellular and animal studies. Specific mechanisms that underlie involvement of these proteins in progression of diabetic kidney disease must be further investigated to assess their value as targets for kidney-protective therapies. Using multivariable LASSO regression analysis, five proteins (LAYN, ESAM, DLL1, MAPK11 and endostatin) were found independently associated with risk of progression to kidney failure. Thus, our study identified proteins that may be considered as new candidate prognostic biomarkers to predict risk of progression to kidney failure in diabetic kidney disease. Furthermore, three of these proteins (DLL1, ESAM, and MAPK11) were selected as candidate biomarkers when all SOMAscan results were evaluated.
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Affiliation(s)
- Hiroki Kobayashi
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Devision of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre Jean Saulnier
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA; CHU Poitiers, University of Poitiers, Inserm, Clinical Investigation Center CIC1402, Poitiers, France
| | - Zaipul I Md Dom
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kristina O'Neil
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
| | - Katsuhito Ihara
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bozena Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrzej T Galecki
- Cognitive Health Services Research Program, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Monika A Niewczas
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jonathan M Wilson
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Alessandro Doria
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kevin L Duffin
- Diabetes and Complication Department, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA.
| | - Andrzej S Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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15
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Chailangkarn T, Tanwattana N, Jaemthaworn T, Sriswasdi S, Wanasen N, Tangphatsornruang S, Leetanasaksakul K, Jantraphakorn Y, Nawae W, Chankeeree P, Lekcharoensuk P, Lumlertdacha B, Kaewborisuth C. Establishment of Human-Induced Pluripotent Stem Cell-Derived Neurons-A Promising In Vitro Model for a Molecular Study of Rabies Virus and Host Interaction. Int J Mol Sci 2021; 22:ijms222111986. [PMID: 34769416 PMCID: PMC8584829 DOI: 10.3390/ijms222111986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/24/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022] Open
Abstract
Rabies is a deadly viral disease caused by the rabies virus (RABV), transmitted through a bite of an infected host, resulting in irreversible neurological symptoms and a 100% fatality rate in humans. Despite many aspects describing rabies neuropathogenesis, numerous hypotheses remain unanswered and concealed. Observations obtained from infected primary neurons or mouse brain samples are more relevant to human clinical rabies than permissive cell lines; however, limitations regarding the ethical issue and sample accessibility become a hurdle for discovering new insights into virus-host interplays. To better understand RABV pathogenesis in humans, we generated human-induced pluripotent stem cell (hiPSC)-derived neurons to offer the opportunity for an inimitable study of RABV infection at a molecular level in a pathologically relevant cell type. This study describes the characteristics and detailed proteomic changes of hiPSC-derived neurons in response to RABV infection using LC-MS/MS quantitative analysis. Gene ontology (GO) enrichment of differentially expressed proteins (DEPs) reveals temporal changes of proteins related to metabolic process, immune response, neurotransmitter transport/synaptic vesicle cycle, cytoskeleton organization, and cell stress response, demonstrating fundamental underlying mechanisms of neuropathogenesis in a time-course dependence. Lastly, we highlighted plausible functions of heat shock cognate protein 70 (HSC70 or HSPA8) that might play a pivotal role in regulating RABV replication and pathogenesis. Our findings acquired from this hiPSC-derived neuron platform help to define novel cellular mechanisms during RABV infection, which could be applicable to further studies to widen views of RABV-host interaction.
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Affiliation(s)
- Thanathom Chailangkarn
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (N.W.); (Y.J.)
- Correspondence: (T.C.); (C.K.)
| | - Nathiphat Tanwattana
- Interdisciplinary Program in Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok 10900, Thailand;
| | - Thanakorn Jaemthaworn
- Computational Molecular Biology Group, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand; (T.J.); (S.S.)
| | - Sira Sriswasdi
- Computational Molecular Biology Group, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand; (T.J.); (S.S.)
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand
| | - Nanchaya Wanasen
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (N.W.); (Y.J.)
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (S.T.); (W.N.)
| | - Kantinan Leetanasaksakul
- Functional Proteomics Technology, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Yuparat Jantraphakorn
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (N.W.); (Y.J.)
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (S.T.); (W.N.)
| | - Penpicha Chankeeree
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (P.C.); (P.L.)
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (P.C.); (P.L.)
- Center for Advance Studies in Agriculture and Food, KU Institute Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Boonlert Lumlertdacha
- Queen Saovabha Memorial Institute, Thai Red Cross Society, WHO Collaborating Center for Research and Training Prophylaxis on Rabies, 1871 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand;
| | - Challika Kaewborisuth
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (N.W.); (Y.J.)
- Correspondence: (T.C.); (C.K.)
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16
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Chida K, Sakurai Y, Ohtani A, Masuda T, Ohtsuki S, Tanaka H, Akita H. Proteomics Analysis of Lymphatic Metastasis-Related Proteins Using Highly Metastatic Human Melanoma Cells Originated by Sequential in Vivo Implantation. Biol Pharm Bull 2021; 44:1551-1556. [PMID: 34602565 DOI: 10.1248/bpb.b21-00463] [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] [Indexed: 11/22/2022]
Abstract
Metastasis of cancer cells to lymph nodes (LN) is a common modality of metastasis in clinical settings, but the mechanisms involved in lymphatic metastasis remain unclear compared to hematogenous metastasis to bones and the brain. To elucidate the molecular mechanisms responsible for melanoma LN metastasis, we first generated LN metastasis-prone melanoma cells (C8161F2) by the sequential in vivo transplantation of parental melanoma cells (C8161F0). Although the in vitro/in vivo proliferative potential of these melanoma cells were similar, the metastatic potential of the C8161F2 for LNs was significantly enhanced. We then conducted a proteomics analysis to identify the proteins and pathways that contribute to LN metastasis. We identified six proteins (three: up-regulated and three: down-regulated) whose expressions were statistically significantly different by more than 2-fold in the two cell groups. Some of these genes are responsible for the activation of the transforming growth factor-β (TGF-β)-related pathway, a well-known inducer of epithelial-mesenchymal transition (EMT). In addition, a gene ontology analysis revealed that the enhanced cell-cell adhesion appears to be involved in lymphatic metastasis. In conclusion, we established highly lymphatic metastatic melanoma cells, which would be valuable for studies of the molecular mechanisms responsible for lymphatic metastasis.
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Affiliation(s)
- Katsuyuki Chida
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Yu Sakurai
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Asa Ohtani
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Hiroki Tanaka
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Hidetaka Akita
- Graduate School of Pharmaceutical Sciences, Chiba University
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17
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Abstract
PURPOSE The proteome during lipopolysaccharide (LPS)-induced acute lung injury (ALI) in mice is unclear. MATERIALS AND METHODS In this study, eight-week-old male C57BL/6 mice were intraperitoneally injected with LPS and sacrificed 18 hours after LPS administration to identify protein expression levels in lung tissue using tandem mass tag (TMT) analysis for relative quantification. Hematoxylin-eosin (HE) staining was used to evaluate lung injury in mice. Immunohistochemical staining was used to calculate the production of myeloperoxidase (MPO) and TUNEL staining was performed to detect apoptosis. GO functional clustering and KEGG pathway enrichment analyses were performed to determine functions of differentially expressed proteins (DEPs) and transduction pathways. Domain annotation and subcellular localization analysis of the DEPs were also performed. Furthermore, parallel reaction monitoring (PRM) analysis was used to verify the top 30 DEPs. RESULTS A total of 5188 proteins were found to be expressed in lung tissues from LPS- and saline-treated mice. Among these proteins, 293 were differentially expressed between the two groups; 255 proteins were upregulated in the LPS-treated ALI mice, while 38 were downregulated. GO analysis showed that the DEPs are mainly extracellular, and KEGG analysis suggested that the DEPs are mainly enriched in the NOD-like receptor signaling pathway, complement and coagulation cascades and natural killer cell-mediated cytotoxicity. Enrichment of the DEPs is mainly peptidase S1A, serine proteases, peptidase S1, and the serpin domain. 26.6% of the DEPs are in the nucleus, 24.6% are in the cytosol, 19.1% are in the extracellular space, and 18.8% are in the plasma membrane. PRM validation showed that the trend of 30 DEPs was same with TMT analysis. Among these, Cytochrome b-245 heavy chain (Cybb), Monocyte differentiation antigen CD14 (Cd14) and Neutrophil gelatinase-associated lipocalin (NGAL) were the most obvious change. CONCLUSIONS Our results may help to identify markers and therapeutic targets for LPS-induced ALI.
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Affiliation(s)
- Shengsong Chen
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
| | - Qingyuan Zhan
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
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Yin YP, Shi WH, Deng K, Liu XL, Li H, Lv XT, Lui VWY, Ding C, Hong B, Lin WC. Combinations of proteasome inhibitors with obatoclax are effective for small cell lung cancer. Acta Pharmacol Sin 2021; 42:1298-1310. [PMID: 33139838 PMCID: PMC8285499 DOI: 10.1038/s41401-020-00544-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
Proteasome inhibitors, bortezomib (BTZ), and carfilzomib (CFZ) are approved drugs for hematological malignancies, but lack anticancer activities against most solid tumors. Small cell lung cancer (SCLC) is a very aggressive neuroendocrine carcinoma of the lungs demanding effective therapy. In this study we investigated whether BTZ or CFZ combined with obatoclax (OBX), an antagonist for MCL-1 and a pan-BCL family inhibitor, could cause synergistic growth inhibition of SCLC cells. We showed that combined application of BTZ or CFZ with OBX caused synergistic growth inhibition of human SCLC cell lines (H82, H526, DMS79, H196, H1963, and H69) than single agent alone. Both BTZ-OBX and CFZ-OBX combinations displayed marked synergism on inducing apoptosis (~50% increase vs BTZ or CFZ alone). A comprehensive proteomics analysis revealed that BTZ preferentially induced the expression of MCL-1, an antiapoptotic protein, in SCLC cells. Thus, proteasome inhibitor-OBX combinations could specifically induce massive growth inhibition and apoptosis in SCLC cells. Subsequent proteome-wide profiling analysis of activated transcription factors suggested that BTZ- or CFZ-induced MCL-1 upregulation was transcriptionally driven by FOXM1. In nude mice bearing in SCLC H82 xenografts, both BTZ-OBX, and CFZ-OBX combinations exhibited remarkable antitumor activities against SCLC tumors evidenced by significant reduction of tumor size and the proliferation marker Ki-67 signals in tumor tissues as compared with single agent alone. Thus, proteasome inhibitor-OBX combinations are worth immediate assessments for SCLC in clinical settings.
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Affiliation(s)
- Yan-Ping Yin
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230036, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wen-Hao Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Ke Deng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230036, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Xiao-Li Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230036, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Hong Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Xiao-Tong Lv
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230036, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Vivian Wai Yan Lui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, 453007, China.
- Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China.
| | - Bo Hong
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China.
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
| | - Wen-Chu Lin
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China.
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
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Ohashi K, Hataya S, Nakata A, Matsumoto K, Kato N, Sato W, Carlos-Shanley C, Beebe ET, Currie CR, Fox BG, Takasuka TE. Mannose- and Mannobiose-Specific Responses of the Insect-Associated Cellulolytic Bacterium Streptomyces sp. Strain SirexAA-E. Appl Environ Microbiol 2021; 87:e0271920. [PMID: 33990299 DOI: 10.1128/AEM.02719-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The cellulolytic insect symbiont bacterium Streptomyces sp. strain SirexAA-E secretes a suite of carbohydrate-active enzymes (CAZymes), which are involved in the degradation of various polysaccharides in the plant cell wall, in response to the available carbon sources. Here, we examined a poorly understood response of this bacterium to mannan, one of the major plant cell wall components. SirexAA-E grew well on mannose, carboxymethyl cellulose (CMC), and locust bean gum (LBG) as sole carbon sources in the culture medium. The secreted proteins from each culture supernatant were tested for their polysaccharide-degrading ability, and the composition of secreted CAZymes in each sample was determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results indicated that mannose, LBG, and CMC induced the secretion of mannan and cellulose-degrading enzymes. Interestingly, two α-1,2-mannosidases were abundantly secreted during growth on mannose and LBG. Using genomic analysis, we found a unique 12-bp palindromic sequence motif at 4 locations in the SirexAA-E genome, two of which were found upstream of the above-mentioned α-1,2-mannosidase genes, along with a newly identified mannose and mannobiose-responsive transcriptional regulator, SsManR. Furthermore, the previously reported cellobiose-responsive repressor, SsCebR, was determined to also use mannobiose as an effector ligand. To test whether mannobiose induces the sets of genes under the control of the two regulators, SirexAA-E was grown on mannobiose, and the secretome composition was analyzed. As hypothesized, the composition of the mannobiose secretome combined sets of CAZymes found in both LBG and CMC secretomes, and thus they are likely under the regulation of both SsManR and SsCebR. IMPORTANCE Streptomyces sp. SirexAA-E, a microbial symbiont of biomass-harvesting insects, secretes a suite of polysaccharide-degrading enzymes dependent on the available carbon sources. However, the response of this bacterium to mannan has not been documented. In this study, we investigated the response of this bacterium to mannose, mannobiose, and galactomannan (LBG). By combining biochemical, proteomic, and genomic approaches, we discovered a novel mannose and mannobiose responsive transcriptional regulator, SsManR, which selectively regulates three α-1,2-mannosidase-coding genes. We also demonstrated that the previously described cellobiose responsive regulator, SsCebR, could use mannobiose as an effector ligand. Overall, our findings suggest that the Streptomyces sp. SirexAA-E responds to mannose and mannooligosaccharides through two different transcriptional repressors that regulate the secretion of the plant cell wall-degrading enzymes to extract carbon sources in the host environment.
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Li KT, Yang Y, Cheng X. Revealing the promoting effect of betaine on vitamin B12 biosynthetic pathway of Pseudomonas denitrificans by using a proteomics analysis. Curr Pharm Biotechnol 2021; 23:466-475. [PMID: 34061014 DOI: 10.2174/1389201022666210531120935] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/12/2020] [Accepted: 03/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Our previous comparative metabolomics research revealed that betaine (N,N,N-trimethylglycine, a typically essential methyl-group donor for vitamin B12 biosynthesis) had a powerful promoting effect on the generation of vitamin B12 precursors and intermediates in vitamin B12-producing Pseudomonas denitrificans. However, the integral effect of betaine on the vitamin B12 biosynthetic pathway is still unclear. OBJECTIVE Considering the vitamin B12 biosynthetic pathway of P. denitrificans as a whole, this work aimed to reveal the biological function of betaine on the vitamin B12 biosynthetic pathway in P. denitrificans, which would sharpen and expand the understanding of betaine as the methyl-group donor for vitamin B12 biosynthesis. MATERIALS AND METHODS By using a proteomics method based on the iTRAQ technique, the present study compared and analyzed the differential expression of proteins involved in vitamin B12 biosynthetic pathway under 10 g/L betaine addition to P. denitrificans fermentation medium. RESULTS The results showed that betaine could significantly up-regulate the expression of proteins related to the vitamin B12 biosynthetic pathway, which was mainly reflected in the following three aspects: 1) the δ-aminolevulinic acid (ALA) synthase and porphobilinogen synthase that were responsible for the formation of the committed precursors for tetrapyrrole-derived macrocycle in vitamin B12 molecule; 2) the C-methylation-related enzymes (such as precorrin-4 C(11)-methyltransferase, Precorrin-2 C(20)-methyltransferase, Precorrin-8X methylmutase, and Precorrin-6Y C5,15-methyltransferase) and methionine synthase that were crucial to the C-methylation reactions for vitamin B12 biosynthesis; 3) the late-stage key enzymes (Cobaltochelatase, and Cob(I)yrinic acid a,c-diamide adenosyltransferase) that were related to cobalt chelation of vitamin B12 molecule. CONCLUSIONS The present study clearly demonstrated that betaine could significantly promote the expression of the integral enzymes involved in the vitamin B12 biosynthetic pathway of P. denitrificans, thus promoting vitamin B12 biosynthesis.
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Affiliation(s)
- Kun-Tai Li
- College of Food Science and Technology, Guangdong Provincial Key Labotatory of Aquatic Product Processing and Safety, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yong Yang
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai 200093, China
| | - Xin Cheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
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21
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Wang L, Luo X, Pan Y, Zheng Z, Yin R, Tian X, Zhang L. Mechanism of Laccase Induction via Emodin in Trametes versicolor. Front Bioeng Biotechnol 2021; 9:653800. [PMID: 34095096 PMCID: PMC8171328 DOI: 10.3389/fbioe.2021.653800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Secondary metabolites of traditional Chinese herbs can prominently stimulate the production of laccase from white rot fungi during submerged fermentation. However, the molecular mechanism through which these natural products induce the production of laccase remains unknown. In this study, the Chinese herbal medicine Polygonum cuspidatum was used to induce laccase production in Trametes versicolor, and the best inducer was identified in emodin, even under conditions of 1000-L, large-scale fermentation. Proteomics analysis identified a selection of proteins that were differentially expressed in the presence of emodin, indicating that emodin may affect the expression of laccase genes through three mechanisms: reducing bioenergy productivity, the aryl hydrocarbon receptor (AHR)/xenobiotic response element (XRE) pathway, and the nuclear erythroid 2-related factor 2 (Nrf2)/antioxidant response element (ARE) pathway. Combined with protoplast flow cytometry and fluorescence, it is revealed that emodin might reduce the synthesis of ATP by lowering the mitochondrial membrane potential, leading to the subsequent responses.
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Affiliation(s)
- Lin Wang
- School of Life Sciences, Anhui University, Hefei, China
- Hefei Tingxiandu Biological Technology Co., Ltd., Hefei, China
| | - Xuecai Luo
- Hefei Tingxiandu Biological Technology Co., Ltd., Hefei, China
| | - Yu Pan
- School of Life Sciences, Anhui University, Hefei, China
| | - Zai Zheng
- School of Life Sciences, Anhui University, Hefei, China
| | - Ruochun Yin
- School of Life Sciences, Anhui University, Hefei, China
| | - Xiaohe Tian
- School of Life Sciences, Anhui University, Hefei, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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22
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Abstract
Background Antiphospholipid syndrome (APS) is a systemic autoimmune disease that can lead to thrombosis and/or pregnancy complications. Exosomes, membrane-encapsulated vesicles that are released into the extracellular environment by many types of cells, can carry signals to recipient cells to affect angiogenesis, apoptosis, and inflammation. There is increasing evidence suggesting that exosomes play critical roles in pregnancy. However, the contribution of exosomes to APS is still unknown. Methods Peripheral plasma was collected from healthy early pregnancy patients (NC-exos) and early pregnancy patients with APS (APS-exos) for exosome extraction and characterization. The effect of exosomes from different sources on pregnancy outcomes was determined by establishing a mouse pregnancy model. Following the coincubation of exosomes and human umbilical vein endothelial cells (HUVECs), functional tests examined the features of APS-exos. The APS-exos and NC-exos were analyzed by quantitative proteomics of whole protein tandem mass tag (TMT) markers to explore the different compositions and identify key proteins. After incubation with HUVECs, functional tests investigated the characteristics of key exosomal proteins. Western blot analysis was used to identify the key pathways. Results In the mouse model, APS-exos caused an APS-like birth outcome. In vitro experiments showed that APS-exos inhibited the migration and tube formation of HUVECs. Quantitative proteomics analysis identified 27 upregulated proteins and 9 downregulated proteins in APS-exos versus NC-exos. We hypothesized that apolipoprotein H (APOH) may be a core protein, and the analysis of clinical samples was consistent with finding from the proteomic TMT analysis. APOH-exos led to APS-like birth outcomes. APOH-exos directly enter HUVECs and may play a role through the phospho-extracellular signal-regulated kinase pathway. Conclusions Our study suggests that both APS-exos and APOH-exos impair vascular development and lead to pregnancy complications. APOH-exos may be key actors in the pathogenesis of APS. This study provides new insights into the pathogenesis of APS and potential new targets for therapeutic intervention.
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Affiliation(s)
- Yuan Tan
- Department of Integrated Traditional Chinese Medicine (TCM) & Western Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yiding Bian
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yunfeng Song
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qinhua Zhang
- Department of Integrated Traditional Chinese Medicine (TCM) & Western Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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Cheng X, Zhao W, Zhu M, Wang B, Wang X, Yang X, Huang Y, Tan M, Li J. Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0218. [PMID: 33893730 PMCID: PMC8762999 DOI: 10.20892/j.issn.2095-3941.2020.0218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/26/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Drug repurposing, the application of existing therapeutics to new indications, holds promise in achieving rapid clinical effects at a much lower cost than that of de novo drug development. The aim of our study was to perform a more comprehensive drug repurposing prediction of diseases, particularly cancers. METHODS Here, by targeting 4,096 human diseases, including 384 cancers, we propose a greedy computational model based on a heterogeneous multilayer network for the repurposing of 1,419 existing drugs in DrugBank. We performed additional experimental validation for the dominant repurposed drugs in cancer. RESULTS The overall performance of the model was well supported by cross-validation and literature mining. Focusing on the top-ranked repurposed drugs in cancers, we verified the anticancer effects of 5 repurposed drugs widely used clinically in drug sensitivity experiments. Because of the distinctive antitumor effects of nifedipine (an antihypertensive agent) and nortriptyline (an antidepressant drug) in prostate cancer, we further explored their underlying mechanisms by using quantitative proteomics. Our analysis revealed that both nifedipine and nortriptyline affected the cancer-related pathways of DNA replication, the cell cycle, and RNA transport. Moreover, in vivo experiments demonstrated that nifedipine and nortriptyline significantly inhibited the growth of prostate tumors in a xenograft model. CONCLUSIONS Our predicted results, which have been released in a public database named The Predictive Database for Drug Repurposing (PAD), provide an informative resource for discovering and ranking drugs that may potentially be repurposed for cancer treatment and determining new therapeutic effects of existing drugs.
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Affiliation(s)
- Xi Cheng
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wensi Zhao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengdi Zhu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuege Wang
- Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai 200031, China
| | - Xiaoyun Yang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqi Huang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Zou Q, Zhou Y, Cheng G, Peng Y, Luo S, Wu H, Yan C, Li X, He D. Antioxidant ability of glutaredoxins and their role in symbiotic nitrogen fixation in Rhizobium leguminosarum bv. viciae 3841. Appl Environ Microbiol 2021; 87:AEM. [PMID: 33277272 DOI: 10.1128/AEM.01956-20] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Glutaredoxins (Grx) are redoxin family proteins that reduce disulfides and mixed disulfides between glutathione and proteins. Rhizobium leguminosarum bv. Viciae 3841 contains three genes coding for glutaredoxins: RL4289 (grxA) codes for a dithiolic glutaredoxin, RL2615 (grxB) codes for a monothiol glutaredoxin, while RL4261 (grxC) codes for a glutaredoxin-like NrdH protein. We generated mutants interrupted in one, two, or three glutaredoxin genes. These mutants had no obvious differences in growth phenotypes from the wild type RL3841. However, while a mutant of grxC did not affect the antioxidant or symbiotic capacities of R. leguminosarum, grxA-derived or grxB mutants decreased antioxidant and nitrogen fixation capacities. Furthermore, grxA mutants were severely impaired in rhizosphere colonization, and formed smaller nodules with defects of bacteroid differentiation, whereas nodules induced by grxB mutants contained abnormally thick cortices and prematurely senescent bacteroids. The grx triple mutant had the greatest defect in antioxidant and symbiotic capacities of R. leguminosarum and quantitative proteomics revealed it had 56 up-regulated and 81 down-regulated proteins relative to wildtype. Of these proteins, twenty-eight are involved in transporter activity, twenty are related to stress response and virulence, and sixteen are involved in amino acid metabolism. Overall, R. leguminosarum glutaredoxins behave as antioxidant proteins mediating root nodule symbiosis.IMPORTANCE Glutaredoxin catalyzes glutathionylation/deglutathionylation reactions, protects SH-groups from oxidation and restores functionally active thiols. Three glutaredoxins exist in R. leguminosarum and their properties were investigated in free-living bacteria and during nitrogen-fixing symbiosis. All the glutaredoxins were necessary for oxidative stress defense. Dithiol GrxA affects nodulation and nitrogen fixation of bacteroids by altering deglutathionylation reactions, monothiol GrxB is involved in symbiotic nitrogen fixation by regulating Fe-S cluster biogenesis, and GrxC may participate in symbiosis by an unknown mechanism. Proteome analysis provides clues to explain the differences between the grx triple mutant and wild-type nodules.
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Rasouli F, Kiani-Pouya A, Shabala L, Li L, Tahir A, Yu M, Hedrich R, Chen Z, Wilson R, Zhang H, Shabala S. Salinity Effects on Guard Cell Proteome in Chenopodium quinoa. Int J Mol Sci 2021; 22:E428. [PMID: 33406687 DOI: 10.3390/ijms22010428] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 11/23/2022] Open
Abstract
Epidermal fragments enriched in guard cells (GCs) were isolated from the halophyte quinoa (Chenopodium quinoa Wild.) species, and the response at the proteome level was studied after salinity treatment of 300 mM NaCl for 3 weeks. In total, 2147 proteins were identified, of which 36% were differentially expressed in response to salinity stress in GCs. Up and downregulated proteins included signaling molecules, enzyme modulators, transcription factors and oxidoreductases. The most abundant proteins induced by salt treatment were desiccation-responsive protein 29B (50-fold), osmotin-like protein OSML13 (13-fold), polycystin-1, lipoxygenase, alpha-toxin, and triacylglycerol lipase (PLAT) domain-containing protein 3-like (eight-fold), and dehydrin early responsive to dehydration (ERD14) (eight-fold). Ten proteins related to the gene ontology term “response to ABA” were upregulated in quinoa GC; this included aspartic protease, phospholipase D and plastid-lipid-associated protein. Additionally, seven proteins in the sucrose–starch pathway were upregulated in the GC in response to salinity stress, and accumulation of tryptophan synthase and L-methionine synthase (enzymes involved in the amino acid biosynthesis) was observed. Exogenous application of sucrose and tryptophan, L-methionine resulted in reduction in stomatal aperture and conductance, which could be advantageous for plants under salt stress. Eight aspartic proteinase proteins were highly upregulated in GCs of quinoa, and exogenous application of pepstatin A (an inhibitor of aspartic proteinase) was accompanied by higher oxidative stress and extremely low stomatal aperture and conductance, suggesting a possible role of aspartic proteinase in mitigating oxidative stress induced by saline conditions.
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Ju Y, Kelly HG, Dagley LF, Reynaldi A, Schlub TE, Spall SK, Bell CA, Cui J, Mitchell AJ, Lin Z, Wheatley AK, Thurecht KJ, Davenport MP, Webb AI, Caruso F, Kent SJ. Person-Specific Biomolecular Coronas Modulate Nanoparticle Interactions with Immune Cells in Human Blood. ACS Nano 2020; 14:15723-15737. [PMID: 33112593 DOI: 10.1021/acsnano.0c06679] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
When nanoparticles interact with human blood, a multitude of plasma components adsorb onto the surface of the nanoparticles, forming a biomolecular corona. Corona composition is known to be influenced by the chemical composition of nanoparticles. In contrast, the possible effects of variations in the human blood proteome between healthy individuals on the formation of the corona and its subsequent interactions with immune cells in blood are unknown. Herein, we prepared and examined a matrix of 11 particles (including organic and inorganic particles of three sizes and five surface chemistries) and plasma samples from 23 healthy donors to form donor-specific biomolecular coronas (personalized coronas) and investigated the impact of the personalized coronas on particle interactions with immune cells in human blood. Among the particles examined, poly(ethylene glycol) (PEG)-coated mesoporous silica (MS) particles, irrespective of particle size (800, 450, or 100 nm in diameter), displayed the widest range (up to 60-fold difference) of donor-dependent variance in immune cell association. In contrast, PEG particles (after MS core removal) of 860, 518, or 133 nm in diameter displayed consistent stealth behavior (negligible cell association), irrespective of plasma donor. For comparison, clinically relevant PEGylated doxorubicin-encapsulated liposomes (Doxil) (74 nm in diameter) showed significant variance in association with monocytes and B cells across all plasma donors studied. An in-depth proteomic analysis of each biomolecular corona studied was performed, and the results were compared against the nanoparticle-blood cell association results, with individual variance in the proteome driving differential association with specific immune cell types. We identified key immunoglobulin and complement proteins that explicitly enriched or depleted within the corona and which strongly correlated with the cell association pattern observed across the 23 donors. This study demonstrates how plasma variance in healthy individuals significantly influences the blood immune cell interactions of nanoparticles.
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Affiliation(s)
- Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hannah G Kelly
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sukhdeep K Spall
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Craig A Bell
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Andrew J Mitchell
- Department of Chemical Engineering, Materials Characterisation and Fabrication Platform, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhixing Lin
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adam K Wheatley
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kristofer J Thurecht
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen J Kent
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
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Santha S, Ling X, Aljahdali IAM, Rasam SS, Wang X, Liao J, Wang J, Fountzilas C, Li Q, Qu J, Li F. Mutant Kras as a Biomarker Plays a Favorable Role in FL118-Induced Apoptosis, Reactive Oxygen Species (ROS) Production and Modulation of Survivin, Mcl-1 and XIAP in Human Bladder Cancer. Cancers (Basel) 2020; 12:E3413. [PMID: 33217967 DOI: 10.3390/cancers12113413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary FL118 is a novel orally available small molecule anticancer drug. We found that bladder cancer cells with a mutant Kras is highly sensitive to FL118-induced cell growth inhibition and cell death induction through inhibiting the anti-cancer cell death and drug resistance factors (survivin, Mcl-1, XIAP). In the Kras-mutation bladder cancer cells, FL118 can stimulate the reactive oxygen species (ROS) over-production for killing bladder cancer cells and inhibiting bladder cancer cell-established tumor growth. Elimination of mutant Kras by Kras-specific shRNA technology in mutant Kras-containing bladder cancer cell-established tumor decreased FL118 effectiveness to inhibit bladder cancer tumor growth. In this regard, mutant Kras is a potential favorable biomarker for FL118. This finding is significant because mutant Kras is known to be a formidable challenge treatment resistant factor in various types of cancer. Thus, FL118 could use mutant Kras as favorable biomarker for patient selection to carry out precision medicine. Abstract Tumor heterogeneity in key gene mutations in bladder cancer (BC) is a major hurdle for the development of effective treatments. Using molecular, cellular, proteomics and animal models, we demonstrated that FL118, an innovative small molecule, is highly effective at killing T24 and UMUC3 high-grade BC cells, which have Hras and Kras mutations, respectively. In contrast, HT1376 BC cells with wild-type Ras are insensitive to FL118. This concept was further demonstrated in additional BC and colorectal cancer cells with mutant Kras versus those with wild-type Kras. FL118 strongly induced PARP cleavage (apoptosis hallmark) and inhibited survivin, XIAP and/or Mcl-1 in both T24 and UMUC3 cells, but not in the HT1376 cells. Silencing mutant Kras reduced both FL118-induced PARP cleavage and downregulation of survivin, XIAP and Mcl-1 in UMUC3 cells, suggesting mutant Kras is required for FL118 to exhibit higher anticancer efficacy. FL118 increased reactive oxygen species (ROS) production in T24 and UMUC3 cells, but not in HT1376 cells. Silencing mutant Kras in UMUC3 cells reduced FL118-mediated ROS generation. Proteomics analysis revealed that a profound and opposing Kras-relevant signaling protein is changed in UMUC3 cells and not in HT1376 cells. Consistently, in vivo studies indicated that UMUC3 tumors are highly sensitive to FL118 treatment, while HT1376 tumors are highly resistant to this agent. Silencing mutant Kras in UMUC3 cell-derived tumors decreases UMUC3 tumor sensitivity to FL118 treatment. Together, our studies revealed that mutant Kras is a favorable biomarker for FL118 targeted treatment.
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Zheng Z, Ao X, Li P, Lian Z, Jiang T, Zhang Z, Wang L. CRLF1 Is a Key Regulator in the Ligamentum Flavum Hypertrophy. Front Cell Dev Biol 2020; 8:858. [PMID: 33072735 PMCID: PMC7533558 DOI: 10.3389/fcell.2020.00858] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 04/14/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Hypertrophy of the ligamentum flavum (HLF) is one of the common causes of lumbar spinal stenosis (LSS). The key molecules and mechanisms responsible for HLF remain unclear. Here, we used an integrated transcriptome and proteomics analysis of human ligamentum flavum (LF), and subsequent immunohistochemistry and real-time PCR assays, to show upregulation of CRLF1 to be the dominant response to HLF. TGF-β1 significantly increased mRNA expression of CRLF1 through SMAD3 pathway. CRLF1 enhanced LF fibrosis via ERK signaling pathway at the post-transcriptional level and was required for the pro-fibrotic effect of TGF-β1. Knockdown of CRLF1 was shown here to reduce fibrosis caused by inflammatory cytokines and mechanical stress. Furthermore, we found that bipedal standing posture can cause HLF and upregulation of CRLF1 expression in mice LF. Overexpression of CRLF1 was indicated to cause HLF in vivo, whereas CRLF1 knockdown impeded the formation of HLF in bipedal standing mice. These results revealed a crucial role of CRLF1 in LF hypertrophy. We propose that inhibition of CRLF1 is a potential therapeutic strategy to treat HLF.
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Affiliation(s)
- Zhenyu Zheng
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
| | - Xiang Ao
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
| | - Peng Li
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
| | - Zhengnan Lian
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
| | - Tao Jiang
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
| | - Zhongmin Zhang
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China.,Division of Spine Surgery, Department of Orthopadics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liang Wang
- Department of Orthopedics, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China.,Academy of Orthopedics, Guangzhou, China
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29
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Weiss ACG, Herold HM, Lentz S, Faria M, Besford QA, Ang CS, Caruso F, Scheibel T. Surface Modification of Spider Silk Particles to Direct Biomolecular Corona Formation. ACS Appl Mater Interfaces 2020; 12:24635-24643. [PMID: 32369330 DOI: 10.1021/acsami.0c06344] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/11/2023]
Abstract
In recent years, spider silk-based materials have attracted attention because of their biocompatibility, processability, and biodegradability. For their potential use in biomaterial applications, i.e., as drug delivery systems and implant coatings for tissue regeneration, it is vital to understand the interactions between the silk biomaterial surface and the biological environment. Like most polymeric carrier systems, spider silk material surfaces can adsorb proteins when in contact with blood, resulting in the formation of a biomolecular corona. Here, we assessed the effect of surface net charge of materials made of recombinant spider silk on the biomolecular corona composition. In-depth proteomic analysis of the biomolecular corona revealed that positively charged spider silk materials surfaces interacted predominantly with fibrinogen-based proteins. This fibrinogen enrichment correlated with blood clotting observed for both positively charged spider silk films and particles. In contrast, negative surface charges prevented blood clotting. Genetic engineering allows the fine-tuning of surface properties of the spider silk particles providing a whole set of recombinant spider silk proteins with different charges or peptide tags to be used for, for example, drug delivery or cell docking, and several of these were analyzed concerning the composition of their biomolecular corona. Taken together this study demonstrates how the surface net charge of recombinant spider silk surfaces affects the composition of the biomolecular corona, which in turn affects macroscopic effects such as fibrin formation and blood clotting.
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Affiliation(s)
- Alessia C G Weiss
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and the Department of Chemical Engineering, The University of Melbourne, Victoria 3010, Australia
| | - Heike M Herold
- Lehrstuhl für Biomaterialien, Universität Bayreuth, Prof. Rüdiger-Bormann-Strasse 1, Bayreuth 95447, Germany
| | - Sarah Lentz
- Lehrstuhl für Biomaterialien, Universität Bayreuth, Prof. Rüdiger-Bormann-Strasse 1, Bayreuth 95447, Germany
| | - Matthew Faria
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Parkville, Victoria 3052, Australia
- Systems Biology Laboratory, School of Mathematics and Statistics, and the Department of Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Quinn A Besford
- Leibniz-Institute für Polymerforschung, Hohe Straβe 6, Dresden 01069 , Germany
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and the Department of Chemical Engineering, The University of Melbourne, Victoria 3010, Australia
| | - Thomas Scheibel
- Lehrstuhl für Biomaterialien, Universität Bayreuth, Prof. Rüdiger-Bormann-Strasse 1, Bayreuth 95447, Germany
- Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG), Universität Bayreuth, Bayreuth 95440, Germany
- Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB), Universität Bayreuth, Bayreuth 95440, Germany
- Bayreuther Materialzentrum (BayMAT), Universität Bayreuth, Bayreuth 95440, Germany
- Bayerisches Polymerinstitut (BPI), Universität Bayreuth, Bayreuth 95440, Germany
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30
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Chen C, Geng L, Xu X, Kong W, Hou Y, Yao G, Feng X, Zhang H, Liang J. Comparative proteomics analysis of plasma protein in patients with neuropsychiatric systemic lupus erythematosus. Ann Transl Med 2020; 8:579. [PMID: 32566606 PMCID: PMC7290550 DOI: 10.21037/atm.2020.04.58] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background The aim of this study was to evaluate serum biomarkers of systemic lupus erythematous (SLE) patients, with and without neuropsychiatric (NP) manifestation by high-resolution proteomic analysis. Methods SLE patients with NP (NPSLE, n=9), SLE patients without NP (non-NPSLE, n=9) and healthy controls (HC, n=9) were prospectively enrolled in this study, and their plasma samples were collected and pooled into 3 NPSLE, 3 non-NPSLE and 3 HC samples for discovery profile. The TMT-LC-MS/MS-based proteomics approach was used to identify the differential proteome among the three matched groups, and the data were analyzed by bioinformatics tools, including Gene Ontology (GO) categories, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, to explore canonical pathways and networks involved in the pathogenesis of NPSLE. To validation of differentially expressed proteomics results, four proteins were measured by ELISA. Results There were altogether 223 differentially expressed proteins in NPSLE groups compared with healthy controls (HC), of which 96 proteins increased while 127 proteins decreased. Compared with non-NPSLE, there were only 49 differentially expressed proteins in NPSLE groups, of which 37 proteins increased while 12 proteins decreased. The significantly changed pathway that those proteins are involved in was complement and coagulation cascades in NPSLE group compared with health controls. However, we didn't find significantly changed pathway between NPSLE group and non-NPSLE group. Five proteins were found significantly changed in all group-comparisons with consistent tendencies using Venn analysis, including Vitamin D binding protein (VDBP), C-reactive protein (CRP), KRT16, IGHV4-4 and CTRP3. Four proteins including CTRP3, VDBP, PAPPA and TRYP2 were selected to estimate the validity of the proteomics approach by ELISA. The expression levels of CTRP3 and TRYP2 were significantly changed in NPSLE patients compared with either HC or non-NPSLE patients. Conclusions Our research has successfully established serum protein profiles of NPSLE and non-NPSLE patients through TMT technology and screened out five proteins significantly changed in group-comparisons with consistent tendencies. The pathway of complement and coagulation cascades may participate in pathogenesis of NPSLE and non-NPSLE.
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Affiliation(s)
- Chen Chen
- Department of Clinical Nutrition, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Linyu Geng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Xue Xu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Wei Kong
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yayi Hou
- Institute of Brain Sciences, Medical School, Nanjing University, Nanjing 210093, China
| | - Genhong Yao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Xuebing Feng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Huayong Zhang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jun Liang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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31
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Li Q, Zeng H, Zhao Y, Gong Y, Ma X. Proteomic Analysis of Cerebrospinal Fluid From Patients With Extranodal NK-/T-Cell Lymphoma of Nasal-Type With Ethmoidal Sinus Metastasis. Front Oncol 2020; 9:1489. [PMID: 31998645 PMCID: PMC6966716 DOI: 10.3389/fonc.2019.01489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/02/2019] [Accepted: 12/11/2019] [Indexed: 02/05/2023] Open
Abstract
Objective: Extranodal natural killer /T-cell lymphoma (ENKTL) is an aggressive and unusual subtype of non-Hodgkin lymphoma (NHL) that it is related with the Epstein-Barr virus (EBV). CSF is considered as an ideal source of high-concenrtation disease-related proteins. We aimed at identifying the proteomic markers changes of CSF in ENKTL patients and used such changes to diagnose ENKTL. Materials and methods: In this study, CSF samples were acquired from hospitalization patients from the Cancer Center of West China Hospital, Chengdu, China. Comparative proteomic profiling are commonly used to do label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). And in this study the same method was used to characterize the variety of proteins in ENKTL patients and none-ENKTL people. Results: In the aggregate, 421 non-excrescent and functional proteins were identified among the samples. Of these proteins, 45 proteins quantified match the involved criteria. HRG, TIMP-1, SERPINA3, FGA, FGG, TF, FGB, APP, and AGT were significantly up-regulated. Discussion: We discovered that some proteins were significantly up-regulated. Also, these proteins themselves or with others proteins may be potential markers to diagnose ENKTL. The changes of proteomics may be a potential method to precisely identify the pathogenesis of the ENKTL.
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Affiliation(s)
- Qingfang Li
- State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Zeng
- State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yunuo Zhao
- State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanqiu Gong
- State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelei Ma
- State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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Bonuccelli G, Sotgia F, Lisanti MP. Matcha green tea (MGT) inhibits the propagation of cancer stem cells (CSCs), by targeting mitochondrial metabolism, glycolysis and multiple cell signalling pathways. Aging (Albany NY) 2019; 10:1867-1883. [PMID: 30153655 PMCID: PMC6128439 DOI: 10.18632/aging.101483] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022]
Abstract
Matcha green tea (MGT) is a natural product that is currently used as a dietary supplement and may have significant anti-cancer properties. However, the molecular mechanism(s) underpinning its potential health benefits remain largely unknown. Here, we used MCF7 cells (an ER(+) human breast cancer cell line) as a model system, to systematically dissect the effects of MGT at the cellular level, via i) metabolic phenotyping and ii) unbiased proteomics analysis. Our results indicate that MGT is indeed sufficient to inhibit the propagation of breast cancer stem cells (CSCs), with an IC-50 of ~0.2 mg/ml, in tissue culture. Interestingly, metabolic phenotyping revealed that treatment with MGT is sufficient to suppress both oxidative mitochondrial metabolism (OXPHOS) and glycolytic flux, shifting cancer cells towards a more quiescent metabolic state. Unbiased label-free proteomics analysis identified the specific mitochondrial proteins and glycolytic enzymes that were down-regulated by MGT treatment. Moreover, to discover the underlying signalling pathways involved in this metabolic shift, we subjected our proteomics data sets to bio-informatics interrogation via Ingenuity Pathway Analysis (IPA) software. Our results indicate that MGT strongly affected mTOR signalling, specifically down-regulating many components of the 40S ribosome. This raises the intriguing possibility that MGT can be used as inhibitor of mTOR, instead of chemical compounds, such as rapamycin. In addition, other key pathways were affected, including the anti-oxidant response, cell cycle regulation, as well as interleukin signalling. Our results are consistent with the idea that MGT may have significant therapeutic potential, by mediating the metabolic reprogramming of cancer cells.
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Affiliation(s)
- Gloria Bonuccelli
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre, University of Salford, Greater Manchester, United Kingdom
| | - Federica Sotgia
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre, University of Salford, Greater Manchester, United Kingdom
| | - Michael P Lisanti
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre, University of Salford, Greater Manchester, United Kingdom
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33
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Daubon T, Guyon J, Raymond AA, Dartigues B, Rudewicz J, Ezzoukhry Z, Dupuy JW, Herbert JMJ, Saltel F, Bjerkvig R, Nikolski M, Bikfalvi A. The invasive proteome of glioblastoma revealed by laser-capture microdissection. Neurooncol Adv 2019; 1:vdz029. [PMID: 32642662 PMCID: PMC7212852 DOI: 10.1093/noajnl/vdz029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Indexed: 01/31/2023] Open
Abstract
Background Glioblastomas are heterogeneous tumors composed of a necrotic and tumor core and an invasive periphery. Methods Here, we performed a proteomics analysis of laser-capture micro-dissected glioblastoma core and invasive areas of patient-derived xenografts. Results Bioinformatics analysis identified enriched proteins in central and invasive tumor areas. Novel markers of invasion were identified, the genes proteolipid protein 1 (PLP1) and Dynamin-1 (DNM1), which were subsequently validated in tumors and by functional assays. Conclusions In summary, our results identify new networks and molecules that may play an important role in glioblastoma development and may constitute potential novel therapeutic targets.
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Affiliation(s)
- Thomas Daubon
- INSERM U1029, Pessac, France.,LAMC, University of Bordeaux, Bordeaux, France.,KG Jebsen Brain Tumour Research Center, University of Bergen, Bergen, Norway
| | - Joris Guyon
- INSERM U1029, Pessac, France.,LAMC, University of Bordeaux, Bordeaux, France
| | | | | | - Justine Rudewicz
- INSERM U1029, Pessac, France.,LAMC, University of Bordeaux, Bordeaux, France.,Bordeaux Bioinformatics Center, CBiB University of Bordeaux, France
| | | | | | | | - Frédéric Saltel
- University Bordeaux, INSERM UMR1053, BaRITOn Bordeaux Research in Translational Oncology, Bordeaux, France.,Oncoprot, TBM Core US005 University of Bordeaux, France
| | - Rolf Bjerkvig
- KG Jebsen Brain Tumour Research Center, University of Bergen, Bergen, Norway.,NorLux Neuro-Oncology, Department of Biomedicine University of Bergen, Norway.,Oncology Department, Luxembourg Institute of Health 84, Val Fleuri, Luxembourg
| | - Macha Nikolski
- Bordeaux Bioinformatics Center, CBiB University of Bordeaux, France.,LaBRI, UMR5800 University of Bordeaux, Talence, France
| | - Andreas Bikfalvi
- INSERM U1029, Pessac, France.,LAMC, University of Bordeaux, Bordeaux, France
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34
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Dong XZ, Wang DX, Zhang TY, Liu X, Liu P, Hu Y. Identification of protein targets for the antidepressant effects of Kai-Xin-San in Chinese medicine using isobaric tags for relative and absolute quantitation. Neural Regen Res 2019; 15:302-310. [PMID: 31552903 PMCID: PMC6905330 DOI: 10.4103/1673-5374.265555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Kai-Xin-San consists of Ginseng Radix, Polygalae Radix, Acori Tatarinowii Rhizoma, and Poria at a ratio of 3:3:2:2. Kai-Xin-San has been widely used for the treatment of emotional disorders in China. However, no studies have identified the key proteins implicated in response to Kai-Xin-San treatment. In this study, rat models of chronic mild stress were established using different stress methods over 28 days. After 14 days of stress stimulation, rats received daily intragastric administrations of 600 mg/kg Kai-Xin-San. The sucrose preference test was used to determine depression-like behavior in rats, while isobaric tags were used for relative and absolute quantitation-based proteomics to identify altered proteins following Kai-Xin-San treatment. Kai-Xin-San treatment for 2 weeks noticeably improved depression-like behaviors in rats with chronic mild stress. We identified 33 differentially expressed proteins: 7 were upregulated and 26 were downregulated. Functional analysis showed that these differentially expressed proteins participate in synaptic plasticity, neurodevelopment, and neurogenesis. Our results indicate that Kai-Xin-San has an important role in regulating the key node proteins in the synaptic signaling network, and are helpful to better understand the mechanism of the antidepressive effects of Kai-Xin-San and to provide objective theoretical support for its clinical application. The study was approved by the Ethics Committee for Animal Research from the Chinese PLA General Hospital (approval No. X5-2016-07) on March 5, 2016.
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Affiliation(s)
- Xian-Zhe Dong
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital; Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Dong-Xiao Wang
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital, Beijing, China
| | - Tian-Yi Zhang
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital, Beijing, China
| | - Xu Liu
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital, Beijing, China
| | - Ping Liu
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital, Beijing, China
| | - Yuan Hu
- Department of Clinical Pharmacology and Pharmacy, Center of Pharmacy, Chinese PLA General Hospital, Beijing, China
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Madani A, Ridenour JN, Martin BP, Paudel RR, Abdul Basir A, Le Moigne V, Herrmann JL, Audebert S, Camoin L, Kremer L, Spilling CD, Canaan S, Cavalier JF. Cyclipostins and Cyclophostin Analogues as Multitarget Inhibitors That Impair Growth of Mycobacterium abscessus. ACS Infect Dis 2019; 5:1597-1608. [PMID: 31299146 DOI: 10.1021/acsinfecdis.9b00172] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Twelve new Cyclophostin and Cyclipostins analogues (CyC19-30) were synthesized, thus extending our series to 38 CyCs. Their antibacterial activities were evaluated against four pathogenic mycobacteria (Mycobacterium abscessus, Mycobacterium marinum, Mycobacterium bovis BCG, and Mycobacterium tuberculosis) and two Gram negative bacteria. The CyCs displayed very low toxicity toward host cells and were only active against mycobacteria. Importantly, several CyCs were active against extracellular M. abscessus (CyC17/CyC18β/CyC25/CyC26) or intramacrophage residing mycobacteria (CyC7(α,β)/CyC8(α,β)) with minimal inhibitory concentrations (MIC50) values comparable to or better than those of amikacin or imipenem, respectively. An activity-based protein profiling combined with mass spectrometry allowed identification of the potential target enzymes of CyC17/CyC26, mostly being involved in lipid metabolism and/or in cell wall biosynthesis. Overall, these results strengthen the selective activity of the CyCs against mycobacteria, including the most drug-resistant M. abscessus, through the cumulative inhibition of a large number of Ser- and Cys-enzymes participating in key physiological processes.
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Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jeremy N. Ridenour
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin P. Martin
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Rishi R. Paudel
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Anosha Abdul Basir
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Vincent Le Moigne
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
- 2I, UVSQ, INSERM UMR 1173, Université Paris-Saclay, 78035 Versailles, France
| | - Stéphane Audebert
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Luc Camoin
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293 Montpellier, France
- IRIM, INSERM, 34293 Montpellier, France
| | - Christopher D. Spilling
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jean-François Cavalier
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
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36
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Chen S, Sun X, Shi Y, Wei Y, Han X, Li H, Chen L, Sun B, Sun H, Shi Y. Cucurbit Chlorotic Yellows Virus p22 Protein Interacts with Cucumber SKP1LB1 and Its F-Box-Like Motif Is Crucial for Silencing Suppressor Activity. Viruses 2019; 11:E818. [PMID: 31487883 DOI: 10.3390/v11090818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/11/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 11/17/2022] Open
Abstract
Plants use RNA silencing as a defense against viruses. In response, viruses encode various RNA silencing suppressors to counteract the antiviral silencing. Here, we identified p22 as a silencing suppressor of cucurbit chlorotic yellows crinivirus and showed that p22 interacts with CsSKP1LB1, a Cucumis sativus ortholog of S-phase kinase-associated protein 1 (SKP1). The F-box-like motif of p22 was identified through sequence analysis and found to be necessary for the interaction using a yeast two-hybrid assay. The involvement of the F-box-like motif in p22 silencing suppressor activity was determined. Proteomics analysis of Nicotiana benthamiana leaves expressing p22, and its F-box-like motif deletion mutant showed 228 differentially expressed proteins and five enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ABC transporters, sesquiterpenoid and triterpenoid biosynthesis, ubiquitin-mediated proteolysis, riboflavin metabolism, and cysteine and methionine metabolism. Collectively, our results demonstrate the interaction between p22 and CsSKP1LB1 and show that the deletion of F-box-like motif inhibits p22 silencing suppressor activity. The possible pathways regulated by the p22 through the F-box-like motif were identified using proteomics analysis.
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37
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Mir DA, Balamurugan K. Global Proteomic Response of Caenorhabditis elegans Against PemK Sa Toxin. Front Cell Infect Microbiol 2019; 9:172. [PMID: 31214513 PMCID: PMC6555269 DOI: 10.3389/fcimb.2019.00172] [Citation(s) in RCA: 9] [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: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Bacterial exotoxins are major causative agents that infect by promoting cell and tissue damages through disabling the invading host immune system. However, the mode of action by which toxins modulate host immune system and lead cell death is still not completely understood. The nematode, Caenorhabditis elegans has been used as an attractive model host for toxicological studies. In this regard, the present study was undertaken to assess the impact of Staphylococcus aureus toxin (PemK) on the host C. elegans through global proteomics approach. Our proteomic data obtained through LC-MS/MS, subsequent bioinformatics and biochemical analyses revealed that in response to PemKSa a total of 601 proteins of C. elegans were differentially regulated in response to PemKSa. The identified proteins were found to mainly participate in ATP generation, protein synthesis, lipid synthesis, cytoskeleton, heat shock proteins, innate immune defense, stress response, neuron degeneration, and muscle assembly. Current findings suggested that involvement of several regulatory proteins that appear to play a role in various molecular functions in combating PemKSa toxin-mediated microbial pathogenicity and/or host C. elegans immunity modulation. The results provided a preliminary view of the physiological and molecular response of a host toward a toxin and provided insight into highly complex host-toxin interactions.
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38
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Li M, Müller C, Fröhlich K, Gorka O, Zhang L, Groß O, Schilling O, Einsle O, Jessen-Trefzer C. Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol. Cell Chem Biol 2019; 26:852-862.e6. [PMID: 31006617 DOI: 10.1016/j.chembiol.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 09/04/2018] [Revised: 11/23/2018] [Accepted: 03/01/2019] [Indexed: 02/06/2023]
Abstract
Nutrient uptake is essential for survival of organisms, and carbohydrates serve as a crucial carbon and energy source for most microorganisms. Given the importance of mycobacteria as human pathogens a detailed knowledge of carbohydrate uptake transporters is highly desirable, but currently available information is severely limited and mainly based on in silico analyses. Moreover, there is only very little data available on the in vitro characterization of carbohydrate transporters from mycobacterial species. To overcome these significant limitations there is a strong demand for innovative approaches to experimentally match substrates to ATP-binding cassette (ABC) transporters in a straightforward manner. Our study focuses on the model organism Mycobacterium smegmatis and identifies a mycobacterial ABC transport system based on a rapid label-free mass spectrometry lipoproteomics assay with broad applicability. Further validation and X-ray structure analyses reveal a highly selective mycobacterial L-arabinose uptake system.
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Affiliation(s)
- Miaomiao Li
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
| | - Christoph Müller
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Klemens Fröhlich
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Albertstraße 19A, 79104 Freiburg, Germany
| | - Oliver Gorka
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Lin Zhang
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Olaf Groß
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany.
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39
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Jung RH, Kim M, Bhatt B, Choi JM, Roh JH. Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis. Int J Environ Res Public Health 2019; 16:E912. [PMID: 30875719 DOI: 10.3390/ijerph16060912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]
Abstract
Hazardous organisms may thrive on surfaces that are often exposed to human contact, including children’s library books. In this study, swab samples were taken from 42 children’s books collected from four public libraries in Texas and California. Samples were then cultivated in brain–heart infusion (BHI) medium and then in Luria broth (LB) medium containing either ampicillin or kanamycin. All 42 samples (100%) were positive for bacterial growth in normal BHI medium. Furthermore, 35 samples (83.3%) and 20 samples (47.6%) in total were positive in LB medium containing ampicillin or kanamycin, respectively. Bacterial populations were then identified in samples using an Orbitrap Fusion™ Tribrid ™ mass spectrometer, a state-of-the-art proteomic analysis tool. Identified bacterial species grown in ampicillin included Bacillus, Acinetobacter, Pseudomonas, Staphylococcus, Enterobacter, Klebsiella, Serratia, Streptococcus, Escherichia, Salmonella, and Enterococcus. In contrast, identified bacteria grown in kanamycin included Staphylococcus, Streptococcus, Enterococcus, and Bacillus. The presences of pathogenic bacteria species were also confirmed. The results of this study warrant follow up studies to assess the potential health risks of identified pathogens. This study demonstrates the utility of proteomics in identifying environmental pathogenic bacteria for specific public health risk evaluations.
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40
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Campos A, Salomon C, Bustos R, Díaz J, Martínez S, Silva V, Reyes C, Díaz-Valdivia N, Varas-Godoy M, Lobos-González L, Quest AF. Caveolin-1-containing extracellular vesicles transport adhesion proteins and promote malignancy in breast cancer cell lines. Nanomedicine (Lond) 2018; 13:2597-2609. [PMID: 30338706 DOI: 10.2217/nnm-2018-0094] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is one of the most frequently diagnosed cancers and the leading cause of cancer-related deaths in women worldwide, whereby mortality is largely attributable to the development of distant metastasis. Caveolin-1 (CAV1) is a multifunctional membrane protein that is typically upregulated in the final stages of cancer and promotes migration and invasion of tumor cells. Elevated levels of CAV1 have been detected in extracellular vesicles (EVs) from advanced cancer patients. EVs are lipid enclosed vesicular structures that contain bioactive proteins, DNA and RNAs, which can be transferred to other cells and promote metastasis. Therefore, we hypothesized that CAV1 containing EVs released from breast cancer cells may enhance migration and invasion of recipient cells. EVs were purified from conditioned media of MDA-MB-231 wild-type (WT), MDA-MB-231 (shCAV1; possessing the plasmid pLKO.1 encoding a 'small hairpin' directed against CAV1) and MDA-MB-231 (shC) short hairpin control cells. Nanoparticle tracking analysis revealed an average particle size of 40-350 nm for all preparations. As anticipated, CAV1 was detected in MDA-MB-231 WT and shC EVs, but not in MDA-MB-231 (shCAV1) EVs. Mass spectrometry analysis revealed the presence of specific cell adhesion-related proteins, such as Cyr61, tenascin (TNC) and S100A9 only in WT and shC, but not in shCAV1 EVs. Importantly, EVs containing CAV1 promoted migration and invasion of cells lacking CAV1. We conclude that the presence of CAV1 in EVs from metastatic breast cancer cells is associated with enhanced migration and invasiveness of recipient cells in vitro, suggesting that intercellular communication promoted by EVs containing CAV1 will likely favor metastasis in vivo.
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Affiliation(s)
- America Campos
- Laboratory of Cellular Communication, Center for Studies of Exercise, Metabolism & Cancer (CEMC), Program of Cell & Molecular Biology, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Fundación Ciencia & Vida, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile
| | - Carlos Salomon
- Centro de Investigación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile.,Exosome Biology Laboratory, UQ Centre for Clinical Research, Brisbane, Australia
| | | | - Jorge Díaz
- Laboratory of Cellular Communication, Center for Studies of Exercise, Metabolism & Cancer (CEMC), Program of Cell & Molecular Biology, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile
| | - Samuel Martínez
- Laboratory of Cellular Communication, Center for Studies of Exercise, Metabolism & Cancer (CEMC), Program of Cell & Molecular Biology, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile
| | | | | | - Natalia Díaz-Valdivia
- Laboratory of Cellular Communication, Center for Studies of Exercise, Metabolism & Cancer (CEMC), Program of Cell & Molecular Biology, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile
| | - Manuel Varas-Godoy
- Department of Clinical Biochemistry & Immunology, Faculty of Pharmacy, University of Concepción, Bío Bío Region, Chile
| | - Lorena Lobos-González
- Fundación Ciencia & Vida, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile.,Centro de Medicina Regenerativa, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, La Barnechea, Santiago, Chile
| | - Andrew Fg Quest
- Laboratory of Cellular Communication, Center for Studies of Exercise, Metabolism & Cancer (CEMC), Program of Cell & Molecular Biology, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Independencia, Santiago, Chile
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41
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Li J, Zhang X, Li L, Liu J, Zhang Y, Pan H. Proteomics Analysis of SsNsd1-Mediated Compound Appressoria Formation in Sclerotinia sclerotiorum. Int J Mol Sci 2018; 19:E2946. [PMID: 30262736 PMCID: PMC6213358 DOI: 10.3390/ijms19102946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/25/2022] Open
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary is a devastating necrotrophic fungal pathogen attacking a broad range of agricultural crops. In this study, although the transcript accumulation of SsNsd1, a GATA-type IVb transcription factor, was much lower during the vegetative hyphae stage, its mutants completely abolished the development of compound appressoria. To further elucidate how SsNsd1 influenced the appressorium formation, we conducted proteomics-based analysis of the wild-type and ΔSsNsd1 mutant by two-dimensional electrophoresis (2-DE). A total number of 43 differentially expressed proteins (≥3-fold change) were observed. Of them, 77% were downregulated, whereas 14% were upregulated. Four protein spots fully disappeared in the mutants. Further, we evaluated these protein sequences by mass spectrometry analysis of the peptide mass and obtained functionally annotated 40 proteins, among which only 17 proteins (38%) were identified to have known functions including energy production, metabolism, protein fate, stress response, cellular organization, and cell growth and division. However, the remaining 23 proteins (56%) were characterized as hypothetical proteins among which four proteins (17%) were predicted to contain the signal peptides. In conclusion, the differentially expressed proteins identified in this study shed light on the ΔSsNsd1 mutant-mediated appressorium deficiency and can be used in future investigations to better understand the signaling mechanisms of SsNsd1 in S. sclerotiorum.
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Affiliation(s)
- Jingtao Li
- College of Plant Science, Jilin University, Changchun 130062, China.
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xianghui Zhang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Le Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Jinliang Liu
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yanhua Zhang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Hongyu Pan
- College of Plant Science, Jilin University, Changchun 130062, China.
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42
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Zhang XY, Zhu MK, Yuan C, Zou XT. Proteomic analysis of hypothalamus and liver proteins affected by dietary l-arginine supplementation in laying hens. J Anim Physiol Anim Nutr (Berl) 2018; 102:1553-1563. [PMID: 30091229 DOI: 10.1111/jpn.12916] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/31/2018] [Indexed: 12/11/2022]
Abstract
The goal of this study was to investigate the influence of l-arginine (l-Arg) supplementation on diet-induced changes in hypothalamus and liver proteome of laying hens. Layers were fed either an isonitrogenous control diet or a l-Arg diet. The test included a 2-week acclimation period and a 12-week experimental period. Eight layers per group were sacrificed at terminal of the experiment underwent 12 fasting. Blood and tissue samples of hypothalamus and liver were collected for further analysis. The levels of serum nitric oxide and hypothalamus neuropeptide Y of layers in l-Arg group were increased in comparison with those in control group. Quantitative proteomic analyses showed that a total of 3,715 hypothalamus proteins (235 differentially expressed) and 3797 liver proteins (373 differentially expressed) were detected between control and l-Arg-fed groups. A further enriched Gene Ontology term analysis of proteins found that 17 hypothalamus proteins (11 upregulated and six downregulated) and 29 liver proteins (14 upregulated and 15 downregulated) were altered differentially between the two groups. Our findings revealed the changes in metabolic and hormonal signals in central nervous system and peripheral tissues by responding to l-Arg feeding, which provides a possible way to gain a better understanding of l-Arg function in laying hens.
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Affiliation(s)
- X Y Zhang
- Key laboratory for Molecular Animal Nutrition of Ministry of Education, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou, China
| | - M K Zhu
- Key laboratory for Molecular Animal Nutrition of Ministry of Education, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou, China
| | - C Yuan
- Key laboratory for Molecular Animal Nutrition of Ministry of Education, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou, China
| | - X T Zou
- Key laboratory for Molecular Animal Nutrition of Ministry of Education, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou, China
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43
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Fletcher SJ, Hapon MB, Callegari EA, Crosbie ML, Santiso N, Ursino A, Amato AR, Gutiérrez A, Sacca PA, Dreszman R, Pérez A, Carón RW, Calvo JC, Pistone-Creydt V. Comparative proteomics of soluble factors secreted by human breast adipose tissue from tumor and normal breast. Oncotarget 2018; 9:31007-31017. [PMID: 30123423 PMCID: PMC6089553 DOI: 10.18632/oncotarget.25749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 12/30/2017] [Accepted: 06/24/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor progression depends on the tumor-stroma interaction. In the breast, adipose tissue is the predominant stromal type. We have previously demonstrated that conditioned media (CMs) from explants of human adipose tissue of tumor breasts (hATT) increase proliferation and migration of breast cancer epithelial cells when compared to human adipose tissue from normal breasts (hATN). In this work, we aim to identify specific proteins and molecular/biological pathways associated with the secretion profile of hATT and hATN explants. hATT-CMs and hATN-CMs were separated by SDS-PAGE and analyzed by means of two-dimensional nano-liquid chromatography-mass spectrometry. The data was analyzed using ProteoIQ and FunRich software. In addition, 42 cytokines from hATT-CMs and hATN-CMs were assayed by a protein antibody assay. Compared to hATN-CMs, hATT-CMs showed greater protein diversity. We found that hATT-CMs presented a greater amount of proteins related to complement system activity, metabolism and immune system, as well as proteins involved in a variety of biological processes such as signal transduction and cell communication. Specifically, apolipoprotein AI and AII, complement component 3, and vimentin and desmin were significantly increased in hATT-CMs versus hATN-CMs. Moreover, a multivariate discriminant analysis of the cytokines detected by the array showed that IL-6, MCP-2 and GRO cytokines were sufficient and necessary to differentiate hATT-CMs from hATN-CMs. This analysis also showed that the levels of these three cytokines, taken together, correlated with stage and histological grade of the tumor in the hATT-CMs group, and with body mass index in the hATN-CMs group.
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Affiliation(s)
- Sabrina Johanna Fletcher
- Laboratorio de Química de Proteoglicanos y Matriz Extracelular, Instituto de Biología y Medicina Experimental (IBYME), Buenos Aires, Argentina
| | - María Belén Hapon
- Laboratorio de Reproducción y Lactancia, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Centro Científico y Tecnológico Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina
| | - Eduardo A Callegari
- University of South Dakota, Sanford School of Medicine, Vermillion, South Dakota, USA
| | - María Luján Crosbie
- Sección de Patología Mamaria, Servicio de Ginecología, Complejo Médico Policial "Churruca-Visca", Buenos Aires, Argentina
| | - Natalia Santiso
- Sección de Patología Mamaria, Servicio de Ginecología, Complejo Médico Policial "Churruca-Visca", Buenos Aires, Argentina
| | - Anabela Ursino
- Sección de Patología Mamaria, Servicio de Ginecología, Complejo Médico Policial "Churruca-Visca", Buenos Aires, Argentina
| | - Alicia Rita Amato
- Sección de Patología Mamaria, Servicio de Ginecología, Complejo Médico Policial "Churruca-Visca", Buenos Aires, Argentina
| | - Alberto Gutiérrez
- Sección de Patología Mamaria, Servicio de Ginecología, Complejo Médico Policial "Churruca-Visca", Buenos Aires, Argentina
| | - Paula Alejandra Sacca
- Laboratorio de Química de Proteoglicanos y Matriz Extracelular, Instituto de Biología y Medicina Experimental (IBYME), Buenos Aires, Argentina
| | | | - Adriana Pérez
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rubén Walter Carón
- Laboratorio de Hormonas y Biología del Cáncer, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Centro Científico y Tecnológico Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina
| | - Juan Carlos Calvo
- Laboratorio de Química de Proteoglicanos y Matriz Extracelular, Instituto de Biología y Medicina Experimental (IBYME), Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Virginia Pistone-Creydt
- Laboratorio de Química de Proteoglicanos y Matriz Extracelular, Instituto de Biología y Medicina Experimental (IBYME), Buenos Aires, Argentina.,Laboratorio de Hormonas y Biología del Cáncer, Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Centro Científico y Tecnológico Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mendoza, Argentina.,Departamento de Fisiología, Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Mendoza, Argentina
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44
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Li H, Hu J, Liu Y, Wang X, Tang S, Chen X, Niu M, Waili N, Bai Y, Wei Y. Effects of prenatal hypoxia on fetal sheep heart development and proteomics analysis. Int J Clin Exp Pathol 2018; 11:1909-1922. [PMID: 31938297 PMCID: PMC6958198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/14/2018] [Indexed: 06/10/2023]
Abstract
The present study aimed to investigate abnormal fetal cardiac pathological injury with exposure to a hypoxic environment during pregnancy. Pregnant hypoxia sheep models were prepared using artificial cabins. Sixteen pregnant sheep were randomly divided into three groups: normal group (NG), mild hypoxia group (MHG), and severe hypoxia group (SHG). The degree of SpO2, SaO2, breathing and heart rate, CO, and MDA were determined. HE staining, SEM, and TEM were used to evaluate the pathological changes of fetal myocardium. iTRAQ-based quantitative proteomics was employed to identify differentially expressed proteins. At day 30 and 90, the levels of SpO2 and SaO2 in SHG and MHG sheep met the diagnostic criteria. Ninety days after modeling, a dramatic reduction of breathing rate and increase of heart rate was observed in MHG and SHG comparing with that in NG (P < 0.05). At day 120, CO and MDA increased significantly in SHG and MHG than those in NG (P < 0.05), also in SHG compared with that in MHG (P < 0.05). HE staining and electron microscopy scanning showed that the myocardium in SHG and MHG had different levels of tissue edema and abnormal distribution of mitochondrion compared to NG. Eighty differentially expressed proteins were identified in fetal cardiac tissues. In conclusion, different degrees of pregnant hypoxia sheep models were successfully established. Prenatal hypoxia can cause serious damage to heart development of fetal sheep, as well as lead to the significant changes of hypoxia-associated proteins expression, which may be used to the further investigation for clinical applications.
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45
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Csősz É, Márkus B, Darula Z, Medzihradszky KF, Nemes J, Szabó E, Tőzsér J, Kiss C, Márton I. Salivary proteome profiling of oral squamous cell carcinoma in a Hungarian population. FEBS Open Bio 2018; 8:556-569. [PMID: 29632809 PMCID: PMC5881539 DOI: 10.1002/2211-5463.12391] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 10/17/2017] [Revised: 12/23/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the seventh most common malignancy and the ninth most frequent cause of cancer death in Europe. Within Europe, Hungary has one of the highest rates of OSCC incidence and mortality. Thus, there is an urgent need to improve early detection. Saliva, as a readily available body fluid, became an increasingly important substance for the detection of biomarkers for many diseases. Different research groups have identified salivary biomarkers specific for OSCC for different countries. In this study, saliva samples of Hungarian patients with OSCC were studied to discover disease‐specific and perhaps region‐specific biomarkers. LC‐mass spectrometry (MS)/MS analysis on a linear ion trap‐Orbitrap mass spectrometer was used for qualitative and quantitative salivary protein profiling. More than 500 proteins were identified from saliva by shotgun proteomics. The up‐ and downregulated proteins in the saliva of patients with OSCC highlighted the importance of protein–protein interaction networks involving the immune system and proteolysis in disease development. Two potential biomarkers from our shotgun analysis and a third candidate reported earlier by a Taiwanese group were further examined by ELISA on a larger reference set of samples. Resistin, a biomarker reported in Taiwan but not validated in our study, highlights the necessity of application of standardized analysis methods in different ethnic or geographical populations to identify biomarkers with sufficient specificity and sensitivity.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Bernadett Márkus
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research Biological Research Centre of the Hungarian Academy of Sciences Szeged Hungary
| | - Katalin F Medzihradszky
- Laboratory of Proteomics Research Biological Research Centre of the Hungarian Academy of Sciences Szeged Hungary
| | - Judit Nemes
- Department of Pedodontics Faculty of Dentistry University of Debrecen Hungary
| | - Emese Szabó
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - József Tőzsér
- Proteomics Core Facility Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary.,Biomarker Research Group Department of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Hungary
| | - Csongor Kiss
- Department of Pediatrics Faculty of Medicine University of Debrecen Hungary
| | - Ildikó Márton
- Department of Restorative Dentistry Faculty of Dentistry University of Debrecen Hungary
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Abstract
The ascomycete fungus Fusarium oxysporum f.sp. cubense race 4 (Foc TR4) causes vascular wilt diseases in banana (Musa spp.). In the present study, the role of SGE1 in regulating growth, conidiation, and pathogenicity of Foc TR4 was investigated. Deletion of SGE1 did not influence vegetative growth but impaired the conidiation of Foc TR4. Besides, the SGE1 deletion mutant basically lost pathogenicity on banana plantlets. Observation under the microscope indicated that the penetration and colonization processes were severely impaired in the SGE1 deletion mutant. Proteomics analysis suggested that SGE1 regulated the production of a series of proteins of Foc TR4. Taken together, our results suggest that SGE1 plays an important role in regulating conidiation and pathogenicity in fungal pathogen Foc TR4.
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Affiliation(s)
- Xingrong Hou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
| | - Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
| | - Yunfeng Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, People's Republic of China
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47
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Tenzer S, Leidinger P, Backes C, Huwer H, Hildebrandt A, Lenhof HP, Wesse T, Franke A, Meese E, Keller A. Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase. Oncotarget 2018; 7:14857-70. [PMID: 26930711 PMCID: PMC4924757 DOI: 10.18632/oncotarget.7562] [Citation(s) in RCA: 11] [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: 07/07/2015] [Accepted: 01/01/2016] [Indexed: 01/02/2023] Open
Abstract
Proteomics analysis of paired cancer and control tissue can be applied to investigate pathological processes in tumors. Advancements in data-independent acquisition mass spectrometry allow for highly reproducible quantitative analysis of complex proteomic patterns. Optimized sample preparation workflows enable integrative multi-omics studies from the same tissue specimens.We performed ion mobility enhanced, data-independent acquisition MS to characterize the proteome of 21 lung tumor tissues including adenocarcinoma and squamous cell carcinoma (SCC) as compared to control lung tissues of the same patient each. Transcriptomic data were generated for the same specimens. The quantitative proteomic patterns and mRNA abundances were subsequently analyzed using systems biology approaches.We report a significantly (p = 0.0001) larger repertoire of proteins in cancer tissues. 12 proteins were higher in all tumor tissues as compared to matching control tissues. Three proteins, CAV1, CAV2, and RAGE, were vice versa higher in all controls. We also identified characteristic SCC and adenocarcinoma protein patterns. Principal Component Analysis provided evidence that not only cancer from control tissue but also tissue from adenocarcinoma and SCC can be differentiated. Transcriptomic levels of key proteins measured from the same matched tissue samples correlated with the observed protein patterns.The applied study set-up with paired lung tissue specimens of which different omics are measured, is generally suited for an integrated multi-omics analysis.
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Affiliation(s)
- Stefan Tenzer
- Institute for Immunology, University Medical Center of The Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Christina Backes
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Andreas Hildebrandt
- Software Engineering and Bioinformatics, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | | | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
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48
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Yazaki M, Yoshinaga T, Sekijima Y, Kametani F, Okumura N. Hereditary Fibrinogen Aα-Chain Amyloidosis in Asia: Clinical and Molecular Characteristics. Int J Mol Sci 2018; 19:E320. [PMID: 29361747 DOI: 10.3390/ijms19010320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/26/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023] Open
Abstract
Hereditary fibrinogen Aα-chain amyloidosis (Aα-chain amyloidosis) is a type of autosomal dominant systemic amyloidosis caused by mutations in fibrinogen Aα-chain gene (FGA). Patients with Aα-chain amyloidosis have been mainly reported in Western countries but have been rarely reported in Asia, with only five patients with Aα-chain amyloidosis being reported in Korea, China, and Japan. Clinically, the most prominent manifestation in Asian patients with Aα-chain amyloidosis is progressive nephropathy caused by excessive amyloid deposition in the glomeruli, which is similar to that observed in patients with Aα-chain amyloidosis in Western countries. In molecular features in Asian Aα-chain amyloidosis, the most common variant, E526V, was found in only one Chinese kindred, and other four kindred each had a different variant, which have not been identified in other countries. These variants are located in the C-terminal region (amino acid residues 517–555) of mature Aα-chain, which was similar to that observed in patients with Aα-chain amyloidosis in other countries. The precise number of Asian patients with Aα-chain amyloidosis is unclear. However, patients with Aα-chain amyloidosis do exist in Asian countries, and the majority of these patients may be diagnosed with other types of systemic amyloidosis.
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49
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Wang Q, An B, Hou X, Guo Y, Luo H, He C. Dicer-like Proteins Regulate the Growth, Conidiation, and Pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis. Front Microbiol 2018; 8:2621. [PMID: 29403443 PMCID: PMC5777394 DOI: 10.3389/fmicb.2017.02621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 06/06/2017] [Accepted: 12/15/2017] [Indexed: 11/17/2022] Open
Abstract
Colletotrichum gloeosporioides from Hevea brasiliensis is the hemibiotrophic fungi which could cause anthracnose in rubber trees. Dicer like proteins (DCL) were the core enzymes for generation of small RNAs. In the present study, the knocking-out mutants of two dicer like proteins encoding genes of C. gloeosporioides were constructed; and functions of two proteins were investigated. The results showed that DCL play important roles in regulating the growth, conidiation and pathogenicity of C. gloeosporioides; and there is a functional redundancy between DCL1 and DCL2. Microscopy analysis and DAB staining revealed that loss of penetration ability into the host cells, instead of the decreased growth rate, was the main cause for the impaired pathogenicity of the ΔDcl1ΔDcl2 double mutant. Proteomics analysis suggested that DCL proteins affected the expression of functional proteins to regulating multiple biological processes of C. gloeosporioides. These data lead to a better understanding of the functions of DCL proteins in regulating the development and pathogenesis of C. gloeosporioides.
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Affiliation(s)
- Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xingrong Hou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yunfeng Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
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50
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Xiong L, Liao D, Lu X, Yan H, Shi L, Mo Z. Proteomic analysis reveals that a global response is induced by subinhibitory concentrations of ampicillin. Bioengineered 2017; 8:732-741. [PMID: 28881168 DOI: 10.1080/21655979.2017.1373532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In this study, a recipient-donor co-culture system was used to research the effect of subinhibitory concentrations of antibiotics on horizontal transmission in bacteria and the influence of antibiotics on protein expression. We employed two-dimensional gel electrophoresis combined with mass spectrometry to compare the protein expression profiles in systems with or without 0.5 × the minimum inhibitory concentration of ampicillin. RT-PCR was used to assess the transcriptional levels of the differentially expressed genes. Fifty-seven different proteins were induced or suppressed. The upregulated proteins were involved in transcription and translation, cell wall synthesis, bacterial SOS response, and detoxifying functions, and the downregulated proteins were involved in metabolism. These results indicated that a global response was induced in the recipient-donor co-culture system by the subinhibitory concentration of ampicillin. Further analysis revealed that a global regulatory network based on key pathways was induced in the system in response to the antibiotic pressure. These findings provide a new, more comprehensive view for research on antibiotic-resistance mechanisms in recipient-donor co-culture.
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Affiliation(s)
- Lina Xiong
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China.,b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Dongjiang Liao
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - Xinpeng Lu
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - He Yan
- c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Lei Shi
- b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Ziyao Mo
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
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