1
|
Chai HC, Mahendran R, Ong KC, Chua KH. Revisiting the gene mutations and protein profile of WT 9-12: An autosomal dominant polycystic kidney disease cell line. Genes Cells 2024. [PMID: 38782708 DOI: 10.1111/gtc.13129] [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: 10/30/2023] [Revised: 03/30/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
WT 9-12 is one of the cell lines commonly used for autosomal dominant polycystic kidney disease (ADPKD) studies. Previous studies had described the PKD gene mutations and polycystin expression in WT 9-12. Nonetheless, the mutations occurring in other ADPKD-associated genes have not been investigated. This study aims to revisit these mutations and protein profile of WT 9-12. Whole genome sequencing verified the presence of truncation mutation at amino acid 2556 (Q2556X) in PKD1 gene of WT 9-12. Besides, those variations with high impacts included single nucleotide polymorphisms (rs8054182, rs117006360, and rs12925771) and insertions and deletions (InDels) (rs145602984 and rs55980345) in PKD1L2; InDel (rs1296698195) in PKD1L3; and copy number variations in GANAB. Protein profiles generated from the total proteins of WT 9-12 and HK-2 cells were compared using isobaric tags for relative and absolute quantitation (iTRAQ) analysis. Polycystin-1 was absent in WT 9-12. The gene ontology enrichment and reactome pathway analyses revealed that the upregulated and downregulated proteins of WT 9-12 relative to HK-2 cell line leaded to signaling pathways related to immune response and amino acid metabolism, respectively. The ADPKD-related mutations and signaling pathways associated with differentially expressed proteins in WT 9-12 may help researchers in cell line selection for their studies.
Collapse
Affiliation(s)
- Hwa Chia Chai
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rhubaniya Mahendran
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kien Chai Ong
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
2
|
Guo N, Han X, Han G, Dai M, Han Z, Li Q. Bioinformation Analysis of Differential Expression Proteins in Different Processes of COVID-19. Viral Immunol 2024; 37:194-201. [PMID: 38717820 DOI: 10.1089/vim.2023.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
COVID-19 is a highly infectious respiratory disease whose progression has been associated with multiple factors. From SARS-CoV-2 infection to death, biomarkers capable of predicting different disease processes are needed to help us further understand the molecular progression of COVID-19 disease. The aim is to find differentially expressed proteins that are associated with the progression of COVID-19 disease or can be potential biomarkers, and to provide a reference for further understanding of the molecular mechanisms of COVID-19 occurrence, progression, and treatment. Data-independent Acquisition (DIA) proteomics to obtain sample protein expression data, using R language screening differentially expressed proteins. Gene Ontology and Kyoto Encyclopedia for Genes and Genomes analysis was performed on differential proteins and protein-protein interaction (PPI) network was constructed to screen key proteins. A total of 47 differentially expressed proteins were obtained from COVID-19 incubation patients and healthy population (L/H), mainly enriched in platelet-related functions, and complement and coagulation cascade reaction pathways, such as platelet degranulation and platelet aggregation. A total of 42 differential proteins were obtained in clinical and latent phase patients (C/L), also mainly enriched in platelet-related functions and in complement and coagulation cascade reactions, platelet activation pathways. A total of 10 differential proteins were screened in recovery and clinical phase patients (R/C), mostly immune-related proteins. The differentially expressed proteins in different stages of COVID-19 are mostly closely associated with coagulation, and key differential proteins, such as FGA, FGB, FGG, ACTB, PFN1, VCL, SERPZNCL, APOC3, LTF, and DEFA1, have the potential to be used as early diagnostic markers.
Collapse
Affiliation(s)
- Nana Guo
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Xu Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Guangyue Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Mingyan Dai
- Hebei Medical University, Shijiazhuang, China
| | - Zhanying Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Qi Li
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| |
Collapse
|
3
|
Sinitsky M, Repkin E, Sinitskaya A, Markova V, Shishkova D, Barbarash O. Proteomic Profiling of Endothelial Cells Exposed to Mitomycin C: Key Proteins and Pathways Underlying Genotoxic Stress-Induced Endothelial Dysfunction. Int J Mol Sci 2024; 25:4044. [PMID: 38612854 PMCID: PMC11011977 DOI: 10.3390/ijms25074044] [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: 03/13/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Mitomycin C (MMC)-induced genotoxic stress can be considered to be a novel trigger of endothelial dysfunction and atherosclerosis-a leading cause of cardiovascular morbidity and mortality worldwide. Given the increasing genotoxic load on the human organism, the decryption of the molecular pathways underlying genotoxic stress-induced endothelial dysfunction could improve our understanding of the role of genotoxic stress in atherogenesis. Here, we performed a proteomic profiling of human coronary artery endothelial cells (HCAECs) and human internal thoracic endothelial cells (HITAECs) in vitro that were exposed to MMC to identify the biochemical pathways and proteins underlying genotoxic stress-induced endothelial dysfunction. We denoted 198 and 71 unique, differentially expressed proteins (DEPs) in the MMC-treated HCAECs and HITAECs, respectively; only 4 DEPs were identified in both the HCAECs and HITAECs. In the MMC-treated HCAECs, 44.5% of the DEPs were upregulated and 55.5% of the DEPs were downregulated, while in HITAECs, these percentages were 72% and 28%, respectively. The denoted DEPs are involved in the processes of nucleotides and RNA metabolism, vesicle-mediated transport, post-translation protein modification, cell cycle control, the transport of small molecules, transcription and signal transduction. The obtained results could improve our understanding of the fundamental basis of atherogenesis and help in the justification of genotoxic stress as a risk factor for atherosclerosis.
Collapse
Affiliation(s)
- Maxim Sinitsky
- Laboratory of Genome Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Egor Repkin
- Centre for Molecular and Cell Technologies, St. Petersburg State University, 7/9 Universitetskaya Embankment, 199034 St. Petersburg, Russia
| | - Anna Sinitskaya
- Laboratory of Genome Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Victoria Markova
- Laboratory for Molecular, Translation and Digital Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Daria Shishkova
- Laboratory for Molecular, Translation and Digital Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Olga Barbarash
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| |
Collapse
|
4
|
Li Y, Yang Y. Label-free quantitative proteomics reveals the mechanisms of Aurora kinase B in renal cell carcinoma. SAGE Open Med 2024; 12:20503121241228474. [PMID: 38516642 PMCID: PMC10956137 DOI: 10.1177/20503121241228474] [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: 10/28/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Background Renal cell carcinoma is the most common form of kidney cancer which is a global threat to human health, needing to explore effective therapeutic targets and treatment methods. Aurora kinase B acts as an important carcinogenic role in various kinds of tumors, while its mechanism in renal cell carcinoma is indistinct. Herein we explore the underlying mechanism of Aurora kinase B in renal cell carcinoma. Methods and results Label-free quantitative proteomics analysis was employed to analyze the differentially expressed proteins in 786-O cells which were treated with si-Aurora kinase B or si-ctrl. In the current study, 169 differentially expressed proteins were identified. The top 10 upregulated proteins were MX2, IFI44L, ISG20, DDX58, F3, IFI44, ECE1, PRIC285, NIT1, and IFIT2. The top 10 downregulated proteins were FKBP9, FSTL1, DDAH1, TGFB2, HMGN3, COIL, FAM65A, PTPN14, ARFGAP2, and EIF2C2. GO enrichment analysis showed that these differentially expressed proteins participated in biological processes, including defense response to virus, response to virus, and type I interferon signaling pathway. These differentially expressed proteins participated in cellular components, including focal adhesion, cell-substrate adherens junction, cell-substrate junction, and endoplasmic reticulum lumen. These differentially expressed proteins participated in molecule functions, including guanyl nucleotide binding, nucleotidase activity, double-stranded RNA binding, 2'-5'-oligoadenylate synthetase activity, and virus receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the significantly changed proteins including OAS3, OAS2, JAK1, TAP1, and RAC1 were involved in Epstein-Barr virus infection. Conclusions Taken together, our results demonstrate the possible mechanisms that Aurora kinase B may participate in renal cell carcinoma. These findings may provide insights into tumorigenesis and a theoretical basis for developing potential therapies of renal cell carcinoma.
Collapse
Affiliation(s)
- Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, China
| |
Collapse
|
5
|
Lan Y, Luo X, Fan X, Wang G, Zheng S, Shi K. Arsenite Mediates Selenite Resistance and Reduction in Enterobacter sp. Z1, Thereby Enhancing Bacterial Survival in Selenium Environments. Environ Sci Technol 2024; 58:4204-4213. [PMID: 38373240 DOI: 10.1021/acs.est.3c08346] [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: 02/21/2024]
Abstract
Arsenic (As) is widely present in the environment, and virtually all bacteria possess a conserved ars operon to resist As toxicity. High selenium (Se) concentrations tend to be cytotoxic. Se has an uneven regional distribution and is added to mitigate As contamination in Se-deficient areas. However, the bacterial response to exogenous Se remains poorly understood. Herein, we found that As(III) presence was crucial for Enterobacter sp. Z1 to develop resistance against Se(IV). Se(IV) reduction served as a detoxification mechanism in bacteria, and our results demonstrated an increase in the production of Se nanoparticles (SeNPs) in the presence of As(III). Tandem mass tag proteomics analysis revealed that the induction of As(III) activated the inositol phosphate, butanoyl-CoA/dodecanoyl-CoA, TCA cycle, and tyrosine metabolism pathways, thereby enhancing bacterial metabolism to resist Se(IV). Additionally, arsHRBC, sdr-mdr, purHD, and grxA were activated to participate in the reduction of Se(IV) into SeNPs. Our findings provide innovative perspectives for exploring As-induced Se biotransformation in prokaryotes.
Collapse
Affiliation(s)
- Yan Lan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiong Luo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Fan
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, Hubei, China
| | - Gejiao Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shixue Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaixiang Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
6
|
Li J, Jiang W, Cai Y, Ning Z, Zhou Y, Wang C, Chung SK, Huang Y, Sun J, Deng M, Zhou L, Cheng X. Astrocytic endothelin-1 overexpression impairs learning and memory ability in ischemic stroke via altered hippocampal neurogenesis and lipid metabolism. Neural Regen Res 2024; 19:650-656. [PMID: 37721297 PMCID: PMC10581554 DOI: 10.4103/1673-5374.380906] [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: 12/23/2022] [Revised: 04/03/2023] [Accepted: 05/31/2023] [Indexed: 09/19/2023] Open
Abstract
Vascular etiology is the second most prevalent cause of cognitive impairment globally. Endothelin-1, which is produced and secreted by endothelial cells and astrocytes, is implicated in the pathogenesis of stroke. However, the way in which changes in astrocytic endothelin-1 lead to poststroke cognitive deficits following transient middle cerebral artery occlusion is not well understood. Here, using mice in which astrocytic endothelin-1 was overexpressed, we found that the selective overexpression of endothelin-1 by astrocytic cells led to ischemic stroke-related dementia (1 hour of ischemia; 7 days, 28 days, or 3 months of reperfusion). We also revealed that astrocytic endothelin-1 overexpression contributed to the role of neural stem cell proliferation but impaired neurogenesis in the dentate gyrus of the hippocampus after middle cerebral artery occlusion. Comprehensive proteome profiles and western blot analysis confirmed that levels of glial fibrillary acidic protein and peroxiredoxin 6, which were differentially expressed in the brain, were significantly increased in mice with astrocytic endothelin-1 overexpression in comparison with wild-type mice 28 days after ischemic stroke. Moreover, the levels of the enriched differentially expressed proteins were closely related to lipid metabolism, as indicated by Kyoto Encyclopedia of Genes and Genomes pathway analysis. Liquid chromatography-mass spectrometry nontargeted metabolite profiling of brain tissues showed that astrocytic endothelin-1 overexpression altered lipid metabolism products such as glycerol phosphatidylcholine, sphingomyelin, and phosphatidic acid. Overall, this study demonstrates that astrocytic endothelin-1 overexpression can impair hippocampal neurogenesis and that it is correlated with lipid metabolism in poststroke cognitive dysfunction.
Collapse
Affiliation(s)
- Jie Li
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, Guangdong Province, China
| | - Wen Jiang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yuefang Cai
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Zhenqiu Ning
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Yingying Zhou
- Department of Anatomy, Sun Yat-Sen School of Medicine, Sun Yat-Sen University, Shenzhen, Guangdong Province, China
| | - Chengyi Wang
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Sookja Ki Chung
- Faculty of Medicine, Macau University of Science and Technology, Macao Special Administration Region, China
| | - Yan Huang
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, Guangdong Province, China
| | - Jingbo Sun
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, Guangdong Province, China
| | - Minzhen Deng
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Lihua Zhou
- Department of Anatomy, Sun Yat-Sen School of Medicine, Sun Yat-Sen University, Shenzhen, Guangdong Province, China
| | - Xiao Cheng
- Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, Guangdong Province, China
| |
Collapse
|
7
|
Suo L, Liang X, Zhang W, Gao M, Ma T, Hu D, Song Y, Gao Z. Potential prognostic biomarkers of hepatocellular carcinoma based on 4D label-free quantitative proteomics analysis pilot investigation. Int J Biol Markers 2024; 39:59-69. [PMID: 37956648 DOI: 10.1177/03936155231212925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
BACKGROUND Hepatocellular carcinoma carries a poor prognosis and poses a serious threat to global health. Currently, there are few potential prognostic biomarkers available for the prognosis of hepatocellular carcinoma. METHODS This pilot study used 4D label-free quantitative proteomics to compare the proteomes of hepatocellular carcinoma and adjacent non-tumor tissue. A total of 66,075 peptides, 6363 identified proteins, and 772 differentially expressed proteins were identified in specimens from three hepatocellular carcinoma patients. Through functional enrichment analysis of differentially expressed proteins by Gene Ontology, KEGG pathway, and protein domain, we identified proteins with similar functions. RESULTS Twelve differentially expressed proteins (RPL17, RPL27, RPL27A, RPS5, RPS16, RSL1D1, DDX18, RRP12, TARS2, YARS2, MARS2, and NARS1) were selected for identification and validation by parallel reaction monitoring. Subsequent Western blotting confirmed overexpression of RPL27, RPS16, and TARS2 in hepatocellular carcinoma compared to non-tumor tissue in 16 pairs of clinical samples. Analysis of The Cancer Genome Atlas datasets associated the increased expression of these proteins with poor prognosis. Tissue microarray revealed a negative association between high expression of RPL27 and TARS2 and the prognosis of hepatocellular carcinoma patients, although RPS16 was not significant. CONCLUSIONS These data suggest that RPL27 and TARS2 play an important role in hepatocellular carcinoma progression and may be potential prognostic biomarkers of overall survival in hepatocellular carcinoma patients.
Collapse
Affiliation(s)
- Lida Suo
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiangnan Liang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Weibin Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Mingwei Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Taiheng Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Daosheng Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yilin Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhenming Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| |
Collapse
|
8
|
Subramani M, Urrea CA, Tamatamu SR, Sripathi VR, Williams K, Chintapenta LK, Todd A, Ozbay G. Comprehensive Proteomic Analysis of Common Bean ( Phaseolus vulgaris L.) Seeds Reveal Shared and Unique Proteins Involved in Terminal Drought Stress Response in Tolerant and Sensitive Genotypes. Biomolecules 2024; 14:109. [PMID: 38254709 PMCID: PMC10813106 DOI: 10.3390/biom14010109] [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: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This study identified proteomic changes in the seeds of two tolerant (SB-DT3 and SB-DT2) and two sensitive (Merlot and Stampede) common bean genotypes in response to terminal drought stress. Differentially expressed proteins (DEPs) were abundant in the susceptible genotype compared to the tolerant line. DEPs associated with starch biosynthesis, protein-chromophore linkage, and photosynthesis were identified in both genotypes, while a few DEPs and enriched biological pathways exhibited genotype-specific differences. The tolerant genotypes uniquely showed DEPs related to sugar metabolism and plant signaling, while the sensitive genotypes displayed more DEPs involved in plant-pathogen interaction, proteasome function, and carbohydrate metabolism. DEPs linked with chaperone and signal transduction were significantly altered between both genotypes. In summary, our proteomic analysis revealed both conserved and genotype-specific DEPs that could be used as targets in selective breeding and developing drought-tolerant common bean genotypes.
Collapse
Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Carlos A. Urrea
- Panhandle Research Extension and Education Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA;
| | - Sowjanya R. Tamatamu
- Center for Molecular Biology, Alabama A&M University, Normal, AL 35762, USA; (S.R.T.); (V.R.S.)
| | | | - Krystal Williams
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Lathadevi K. Chintapenta
- Biology Department, College of Arts and Sciences (CAS), University of Wisconsin-River Falls, River Falls, WI 54022, USA;
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA; (K.W.); (A.T.)
| | - Gulnihal Ozbay
- Department of Agriculture and Natural Resources, Delaware State University, 1200 North DuPont Highway, Dover, DE 19901, USA
| |
Collapse
|
9
|
Cheng J, Li T, Wei S, Jiang W, Li J, Wang Y, Li Y. Physiological and Proteomic Changes in Camellia semiserrata in Response to Aluminum Stress. Genes (Basel) 2023; 15:55. [PMID: 38254944 PMCID: PMC10815133 DOI: 10.3390/genes15010055] [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: 12/03/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Camellia semiserrata is an important woody edible oil tree species in southern China that is characterized by large fruits and seed kernels with high oil contents. Increasing soil acidification due to increased use of fossil fuels, misuse of acidic fertilizers, and irrational farming practices has led to leaching of aluminum (Al) in the form of free Al3+, Al(OH)2+, and Al(OH)2+, which inhibits the growth and development of C. semiserrata in South China. To investigate the mechanism underlying C. semiserrata responses to Al stress, we determined the changes in photosynthetic parameters, antioxidant enzyme activities, and osmoregulatory substance contents of C. semiserrata leaves under different concentrations of Al stress treatments (0, 1, 2, 3, and 4 mmol/L Alcl3) using a combination of physiological and proteomics approaches. In addition, we identified the differentially expressed proteins (DEPs) under 0 (CK or GNR0), 2 mmol/L (GNR2), and 4 mmol/L (GNR4) Al stress using a 4D-label-free technique. With increasing stress concentration, the photosynthetic indexes of C. semiserrata leaves, peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), soluble protein (SP), and soluble sugar (SS) showed an overall trend of increasing and then decreasing, and proline (Pro) and malondialdehyde (MDA) contents tended to continuously increase overall. Compared with the control group, we identified 124 and 192 DEPs in GNR2 and GNR4, respectively, which were mainly involved in metabolic processes such as photosynthesis, flavonoid metabolism, oxidative stress response, energy and carbohydrate metabolism, and signal transduction. At 2 mmol/L Al stress, carbon metabolism, amino sugar and nucleotide sugar metabolism, and flavonoid metabolism-related proteins were significantly changed, and when the stress was increased to 4 mmol/L Al, the cells accumulated reactive oxygen species (ROS) at a rate exceeding the antioxidant system scavenging capacity. To deal with this change, C. semiserrata leaves enhanced their glutathione metabolism, drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, and other metabolic processes to counteract peroxidative damage to the cytoplasmic membrane caused by stress. In addition, we found that C. semiserrata resisted aluminum toxicity mainly by synthesizing anthocyanidins under 2 mmol/L stress, whereas proanthocyanidins were alleviated by the generation of proanthocyanidins under 4 mmol/L stress, which may be a special mechanism by which C. semiserrata responds to different concentrations of aluminum stress.
Collapse
Affiliation(s)
- Junsen Cheng
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Tong Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Shanglin Wei
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Wei Jiang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Jingxuan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Yi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (J.C.); (T.L.); (S.W.); (W.J.); (J.L.)
| | - Yongquan Li
- Scarce and Quality Economic Forest Engineering Technology Research Center, Guangzhou 510225, China
| |
Collapse
|
10
|
Xin H, Li B, Meng F, Hu B, Wang S, Wang Y, Li J. Quantitative proteomic analysis and verification identify global protein profiling dynamics in pig during the estrous cycle. Front Vet Sci 2023; 10:1247561. [PMID: 37841454 PMCID: PMC10568330 DOI: 10.3389/fvets.2023.1247561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
The current estrus detection method is generally time-consuming and has low accuracy. As such, a deeper understanding of the physiological processes during the estrous cycle accelerates the development of estrus detection efficiency and accuracy. In this study, the label-free acquisition mass spectrometry was used to explore salivary proteome profiles during the estrous cycle (day -3, day 0, day 3, and day 8) in pigs, and the parallel reaction monitoring (PRM) was applied to verify the relative profiles of protein expression. A total of 1,155 proteins were identified in the label-free analysis, of which 115 were identified as differentially expressed proteins (DEPs) among different groups (p ≤ 0.05). Functional annotation revealed that the DEPs were clustered in calcium ion binding, actin cytoskeleton, and lyase activity. PRM verified the relative profiles of protein expression, in which PHB domain-containing protein, growth factor receptor-bound protein 2, elongation factor Tu, carboxypeptidase D, carbonic anhydrase, and trefoil factor 3 were confirmed to be consistent in both label-free and PRM approaches. Comparative proteomic assays on saliva would increase our knowledge of the estrous cycle in sows and provide potential methods for estrus detection.
Collapse
Affiliation(s)
- Haiyun Xin
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Baohong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Fanming Meng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Bin Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Sutian Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Ying Wang
- Guangzhou Customs Technical Center, Guangzhou, China
| | - Jianhao Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| |
Collapse
|
11
|
Liu P, Li L, He F, Meng F, Liu X, Su Y, Su X, Luo B, Peng G. Identification of Candidate Biomarkers of Alzheimer's Disease via Multiplex Cerebrospinal Fluid and Serum Proteomics. Int J Mol Sci 2023; 24:14225. [PMID: 37762527 PMCID: PMC10532410 DOI: 10.3390/ijms241814225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia among elderly people worldwide. Cerebrospinal fluid (CSF) is the optimal fluid source for AD biomarkers, while serum biomarkers are much more achievable. To search for novel diagnostic AD biomarkers, we performed a quantitative proteomic analysis of CSF and serum samples from AD and normal cognitive controls (NC). CSF and serum proteomes were analyzed via data-independent acquisition quantitative mass spectrometry. Our bioinformatic analysis was based on Gene Ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. In comparison to the controls, 8 proteins were more abundant in AD CSF, and 60 were less abundant in AD CSF, whereas 55 proteins were more and 10 were less abundant in the serum samples. ATPase-associated activity for CSF and mitochondrial functions for CSF and serum were the most enriched GO terms of the DEPs. KEGG enrichment analysis showed that the most significant pathways for the differentially expressed proteins were the N-glycan biosynthesis pathways. The area under the curve (AUC) values for CSF sodium-/potassium-transporting ATPase subunit beta-1 (AT1B1), serglycin (SRGN), and thioredoxin-dependent peroxide reductase, mitochondrial (PRDX3) were 0.867 (p = 0.004), 0.833 (p = 0.008), and 0.783 (p = 0.025), respectively. A panel of the above three CSF proteins accurately differentiated AD (AUC = 0.933, p = 0.001) from NC. The AUC values for serum probable phospholipid-transporting ATPase IM (AT8B4) and SRGN were moderate. The AUC of the CSF SRGN + serum SRGN was 0.842 (p = 0.007). These novel AD biomarker candidates are mainly associated with inflammation, ATPase activity, oxidative stress, and mitochondrial dysfunction. Further studies are needed to investigate the molecular mechanisms by which these potential biomarkers are involved in AD.
Collapse
Affiliation(s)
- Ping Liu
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Lingxiao Li
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Fangping He
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Fanxia Meng
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Xiaoyan Liu
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Yujie Su
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Xinhui Su
- Department of Neuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China;
| | - Benyan Luo
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| | - Guoping Peng
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; (P.L.); (L.L.); (F.H.); (F.M.); (X.L.); (Y.S.); (B.L.)
| |
Collapse
|
12
|
Chen J, Huang W, Zhang H, Peng X, Yang J, Yang Y, Su J, Wang S, Zhou W. Corrigendum: Quantitative proteomics on the cerebrospinal fluid of hydrocephalus in neonatal bacterial meningitis. Front Pediatr 2023; 11:1273209. [PMID: 37711596 PMCID: PMC10499512 DOI: 10.3389/fped.2023.1273209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fped.2022.972032.].
Collapse
Affiliation(s)
- Juncao Chen
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Weiben Huang
- Department of Neonatology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hong Zhang
- Department of Neonatology, Dali Autonomous Prefecture Children’s Hospital, Dali, China
| | - Xiangwen Peng
- Department of Key Laboratory, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Jun Yang
- Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Yong Yang
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Jinzhen Su
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Siyao Wang
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Wei Zhou
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
13
|
Gao Y, Zhang Z, Qi D, Liu S. Ischemic Stroke Shifts the Protein and Metabolite Profiles of Colon in Mice. Neuroscience 2023; 526:237-245. [PMID: 37419408 DOI: 10.1016/j.neuroscience.2023.07.006] [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: 04/13/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Over half of all stroke patients present gastrointestinal complications. It has been speculated that there is an intriguing brain-gut connection. However, molecular mechanisms of the connection remain poorly illuminated. Thus, this study is aimed to investigate molecular alternations regarding proteins and metabolites in the colon upon ischemic stroke using multi-omics analyses. Here, stroke mouse model was induced by means of transient middle cerebral artery occlusion. After the confirmation of successful model evaluated as evidenced by neurological deficit and cerebral blood flow decrease, the proteins and metabolites of colon and brain were respectively measured using multiple omics. Functional analysis of differentially expressed proteins (DEPs) and differential metabolites was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. There were 434 common DEPs in the colon and brain after stroke. The DEPs in the two tissues displayed common enrichment in several pathways upon GO/KEGG analyses. The common KEGG pathways of DEPs were mainly linked to the inflammation and immune network. Although there was no common differential metabolite and its corresponding pathway in the two tissues, several metabolism pathways in the colon were also changed after stroke. In conclusion, we have demonstrated that the proteins and metabolites in the colon are significantly changed after ischemic stroke, which provides molecular-level evidence regarding the brain-gut connection. In this light, several common enriched pathways of DEPs may become potential therapeutic targets for stroke upon the brain-gut axis. Notably, we have discovered a promising colon-derived metabolite enterolactone possibly beneficial for tackling stroke.
Collapse
Affiliation(s)
- Ying Gao
- Department of Neurology of Traditional Chinese Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China; Institute for Brain Disorders, Beijing University of Chinese Medicine, Beijing, China
| | - Zhaoxu Zhang
- Department of Neurology, Peking University People's Hospital, Beijing, China
| | - Dahe Qi
- Department of Neurology of Traditional Chinese Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shen Liu
- Department of Neurology of Traditional Chinese Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China; Department of Rehabilitation Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China.
| |
Collapse
|
14
|
Wu S, Huang K, Chang C, Chu X, Zhang K, Li B, Yang T. Serum Proteomic Profiling in Patients with Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:1623-1635. [PMID: 37533772 PMCID: PMC10392904 DOI: 10.2147/copd.s413924] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with high morbidity and mortality rates. This study used proteomic profiling of serum to identify the differentially expressed proteins in COPD patients compared with healthy controls, to expand the knowledge of COPD pathogenesis and to ascertain potential new targets for diagnosis and treatment of COPD. Methods Serum samples were collected from 56 participants (COPD group n = 28; Healthy Control group n = 28). A data-independent acquisition quantitative proteomics approach was used to identify differentially expressed proteins (DEPs) between the two groups. Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichment, and protein-protein interaction analyses of DEPs were conducted to identify their relevant biological processes, cellular components, and related pathways. We used a parallel reaction monitoring (PRM)-based targeted quantitative proteomics approach to validate those findings. Results Of 8484 peptides identified by searching the UniProtKB/Swiss-Prot knowledgebase, 867 proteins were quantifiable, of which 20 were upregulated and 35 were downregulated in the COPD group. GO functional annotation indicated that the subcellular localization of most DEPs was extracellular. The top three molecular functions of the DEPs were signaling receptor binding, antigen binding, and immunoglobulin receptor binding. The most relevant biological process was immune response. The transforming growth factor-β signaling pathway, Staphylococcus aureus infection, and hematopoietic cell lineage were the top three pathways identified in the KEGG pathway functional enrichment. Our PRM analyses confirmed the identification of 11 DEPs identified in our data-independent acquisition analyses, 8 DEPs were upregulated and 3 DEPs were downregulated. Conclusion This study using data-independent acquisition analyses with PRM confirmation of findings identified 11 DEPs in the serum of patients with COPD. These DEPs are potential diagnostic or prognostic biomarkers or may be future targets for the treatment of COPD.
Collapse
Affiliation(s)
- Sinan Wu
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Ke Huang
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Chenli Chang
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Xu Chu
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Kun Zhang
- Biotree-Shanghai, Focus Dream Park, Shanghai, People’s Republic of China
| | - Baicun Li
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Ting Yang
- National Center for Respiratory Medicine, Beijing, People’s Republic of China
- National Clinical Research Center for Respiratory Diseases, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| |
Collapse
|
15
|
Li S, Zhang K, Wen J, Zeng Y, Deng Y, Hu Q, Weng Q. Molecular Mechanism of Male Sterility Induced by 60Co γ-Rays on Plutella xylostella (Linnaeus). Molecules 2023; 28:5727. [PMID: 37570697 PMCID: PMC10420029 DOI: 10.3390/molecules28155727] [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: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plutella xylostella (Linnaeus) is one of the notorious pests causing substantial loses to numerous cruciferous vegetables across many nations. The sterile insect technique (SIT) is a safe and effective pest control method, which does not pollute the environment and does not produce drug resistance. We used proteomics technology and bioinformatics analysis to investigate the molecular mechanisms responsible for the effects of different doses of radiation treatment on the reproductive ability of male P. xylostella. A total of 606 differentially expressed proteins (DEPs) were identified in the 200 Gy/CK group, 1843 DEPs were identified in the 400 Gy/CK group, and 2057 DEPs were identified in the 400 Gy/200 Gy group. The results showed that after 200 Gy irradiation, the testes resisted radiation damage by increasing energy supply, amino acid metabolism and transport, and protein synthesis, while transcription-related pathways were inhibited. After 400 Gy irradiation, the mitochondria and DNA in the testis tissue of P. xylostella were damaged, which caused cell autophagy and apoptosis, affected the normal life activities of sperm cells, and greatly weakened sperm motility and insemination ability. Meanwhile, Western blotting showed that irradiation affects tyrosine phosphorylation levels, which gradually decrease with increasing irradiation dose.
Collapse
Affiliation(s)
- Shifan Li
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Ke Zhang
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Jiaqi Wen
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Yuhao Zeng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Yukun Deng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Qiongbo Hu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Qunfang Weng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
16
|
Fan Y, Feng Z, Fan K, Yin W, Sun N, Sun P, Sun Y, Li H. [Procine recombinant NK-lysin inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 and inhibiting oxidative phosphorylation and glycolysis: a proteomic analysis]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:1116-1126. [PMID: 37488794 PMCID: PMC10366521 DOI: 10.12122/j.issn.1673-4254.2023.07.08] [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] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
OBJECTIVE To investigate the potential mechanisms that mediate the inhibitory effect of porcine recombinant NKlysin (prNK-lysin) against liver cancer cell metastasis. METHODS HPLC-tandem mass spectrometry was used to identify the differentially expressed proteins in prNK-lysin-treated hepatocellular carcinoma SMMOL/LC-7721 cells in comparison with the control and PBS-treated cells. GO functional annotation and KEGG pathway analysis of the differentially expressed proteins were performed using GO and KEGG databases. RT-qPCR was used to determine the mRNA expression levels of polypeptide-N-acetylgalactosaminotransferase 13 (GALNT13), transmembrane protein 51 (TMEM51) and FKBP prolyl isomerase 3 (FKBP3) in the cells, and the protein expression of FKBP3 was verified using Western blotting. RESULTS Proteomic analysis identified 1989 differentially expressed proteins in prNK-lysin-treated cells compared with the control cells, and 2753 compared with PBS-treated cells. Fifteen proteins were differentially expressed between PBS-treated and the control cells, and 1909 were differentially expressed in prNK- lysin group compared with both PBS and control groups. These differentially expressed proteins were involved mainly in the viral process, translational initiation and RNA binding and were enriched mainly in ribosome, protein process in endoplasmic reticulum, and RNA transport pathways. RT-qPCR showed that compared with the control group, prNK-lysin treatment significantly increased the mRNA expressions of GALNT13 (P < 0.05) and TMEM51 (P < 0.01) and lowered FKBP3 mRNA expression (P < 0.05). Western blotting also showed a significantly decreased expression of FKBP3 protein in prNK-lysin-treated cells (P < 0.001). CONCLUSION Treatment with prNK-lysin causes significant changes in protein expression profile of SMMOL/LC-7721 cells and inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 protein and affecting the cellular oxidative phosphorylation and glycolysis pathways.
Collapse
Affiliation(s)
- Y Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - Z Feng
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - K Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - W Yin
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - N Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - P Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - Y Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
- Shanxi Key Laboratory for Modernization of TCVM, Taigu 030801, China
| | - H Li
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| |
Collapse
|
17
|
Guo J, Chen N, Tan F, Zhou J, Xiang H, Luo Y, Zhou Z. iTRAQ-based proteomic analysis of imiquimod in the treatment of ulcerative colitis. Am J Transl Res 2023; 15:4454-4466. [PMID: 37560232 PMCID: PMC10408506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/07/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVE In this study, we explored the potential mechanisms and the signaling pathways involved in the treatment of Ulcerative Colitis (UC) with imiquimod (IMQ). METHODS The UC mouse model was established by treating C57BL/6J mice with 3% Dextran Sulfate Sodium (DSS). Then, the UC-related symptoms were examined. Disease Activity Index (DAI) was estimated based on weight loss, stool consistency, and occult bleeding or hematochezia. Histological changes were evaluated by Hematoxylin and Eosin (H&E) staining. Furthermore, we used multiplexed Isobaric Tagging for Relative and Absolute Protein Quantification (iTRAQ) technique coupled with high-throughput liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine the differentially expressed proteins (DEPs). RESULTS Administration of 3% DSS for 7 days induced acute colitis associated with diarrhea, hematochezia, weight loss, and colon shortening. However, after IMQ administration, almost all the above symptoms were improved by different degrees. Specifically, the DAI, histological disorder, and colon shortening were attenuated. In iTRAQ analysis, a total of 4170 proteins were identified with a high confidence (≥ 95% confidence). The numbers of DEPs between the normal and UC model mice, between the normal and the IMQ-treated therapy mice, as well as between the model and the therapy mice were 317, 253, and 209, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the DEPs involved in the complement and coagulation cascades were downregulated in IMQ-treated therapy group. CONCLUSIONS IMQ might ameliorate colitis by suppressing the complement and coagulation cascades pathway, which might serve as new therapeutic strategies for the treatment of patients with UC.
Collapse
Affiliation(s)
- Jinkun Guo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Na Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Feifei Tan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Julan Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Hongyu Xiang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Yu Luo
- Jingmen Hospital of Traditional Chinese MedicineJingmen 448001, Hubei, China
| | - Zhongyin Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| |
Collapse
|
18
|
Sun J, Li X, Qu Z, Wang H, Cheng Y, Dong S, Zhao H. Comparative proteomic analysis reveals novel insights into the continuous cropping induced response in Scrophularia ningpoensis. J Sci Food Agric 2023; 103:1832-1845. [PMID: 36271763 DOI: 10.1002/jsfa.12284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/23/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Scrophularia ningpoensis is a well-known medicinal crop. Continuous cropping seriously affects the yield and quality, but little is known about the influence of continuous cropping on metabolic pathways. In this study, the difference in protein abundance between continuous cropping and non-continuous cropping of S. ningpoensis roots was studied by proteomics, and the molecular mechanism that protects S. ningpoensis against continuous cropping was explored. RESULTS The results suggested that continuous cropping in S, ningpoensis altered the expression of proteins related to starch and sucrose metabolism, glycolysis/gluconeogenesis, pentose phosphate pathway, citric acid cycle, phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, monoterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and steroid biosynthesis. Among these processes, the most affected were phenylpropanoid biosynthesis and starch and sucrose metabolism, which may be important for continuous cropping resistance. CONCLUSION The effect of continuous cropping on S. ningpoensis was demonstrated at the proteome level in this work, and identified candidate proteins that may cause continuous cropping reactions. The paper provides the theoretical foundation and scientific reference for enhancing the continuous cropping resistance of S. ningpoensis. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jiachen Sun
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Xuejiao Li
- Endocrine and Metabolic Disease Center, Medical Key Laboratory of Hereditary Rare Diseases of Henan, Luoyang Sub-Center of National Clinical Research Center for Metabolic Diseases, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Zhuo Qu
- School of Pharmacy, Ningxia Medical University, Yinchuan, China
| | - Huairui Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Yao Cheng
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Shengjie Dong
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Faculty of Education and Sports, Guangdong Baiyun University, Guangzhou, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, State Experimental and Training Centre of Food and Drug, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| |
Collapse
|
19
|
Li H, He X, Gao Y, Liu W, Song J, Zhang J. Integrative Analysis of Transcriptome, Proteome, and Phosphoproteome Reveals Potential Roles of Photosynthesis Antenna Proteins in Response to Brassinosteroids Signaling in Maize. Plants (Basel) 2023; 12:1290. [PMID: 36986978 PMCID: PMC10058427 DOI: 10.3390/plants12061290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Brassinosteroids are a recently discovered group of substances that promote plant growth and productivity. Photosynthesis, which is vital for plant growth and high productivity, is strongly influenced by brassinosteroid signaling. However, the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize remains obscure. Here, we performed integrated transcriptome, proteome, and phosphoproteomic analyses to identify the key photosynthesis pathway that responds to brassinosteroid signaling. Transcriptome analysis suggested that photosynthesis antenna proteins and carotenoid biosynthesis, plant hormone signal transduction, and MAPK signaling in CK VS EBR and CK VS Brz were significantly enriched in the list of differentially expressed genes upon brassinosteroids treatment. Consistently, proteome and phosphoproteomic analyses indicated that photosynthesis antenna and photosynthesis proteins were significantly enriched in the list of differentially expressed proteins. Thus, transcriptome, proteome, and phosphoproteome analyses showed that major genes and proteins related to photosynthesis antenna proteins were upregulated by brassinosteroids treatment in a dose-dependent manner. Meanwhile, 42 and 186 transcription factor (TF) responses to brassinosteroid signals in maize leaves were identified in the CK VS EBR and CK VS Brz groups, respectively. Our study provides valuable information for a better understanding of the molecular mechanism underlying the photosynthetic response to brassinosteroid signaling in maize.
Collapse
Affiliation(s)
- Hui Li
- Institute of Quality Standard and Testing Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 611130, China
| | - Xuewu He
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Yuanfen Gao
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Wenjuan Liu
- Institute of Quality Standard and Testing Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 611130, China
| | - Jun Song
- Institute of Quality Standard and Testing Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| |
Collapse
|
20
|
Canderan J, Stamboulian M, Ye Y. MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. J Proteome Res 2023; 22:442-453. [PMID: 36688801 PMCID: PMC9903327 DOI: 10.1021/acs.jproteome.2c00614] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 01/24/2023]
Abstract
The microbiome has been shown to be important for human health because of its influence on disease and the immune response. Mass spectrometry is an important tool for evaluating protein expression and species composition in the microbiome but is technically challenging and time-consuming. Multiplexing has emerged as a way to make spectrometry workflows faster while improving results. Here, we present MetaProD (MetaProteomics in Django) as a highly configurable metaproteomic data analysis pipeline supporting label-free and multiplexed mass spectrometry. The pipeline is open-source, uses fully open-source tools, and is integrated with Django to offer a web-based interface for configuration and data access. Benchmarking of MetaProD using multiple metaproteomics data sets showed that MetaProD achieved fast and efficient identification of peptides and proteins. Application of MetaProD to a multiplexed cancer data set resulted in identification of more differentially expressed human proteins in cancer tissues versus healthy tissues as compared to previous studies; in addition, MetaProD identified bacterial proteins in those samples, some of which are differentially abundant.
Collapse
Affiliation(s)
- Jamie Canderan
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Moses Stamboulian
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Yuzhen Ye
- Computer
Science Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| |
Collapse
|
21
|
Tan X, He Y, He Y, Yan Z, Chen J, Zhao R, Sui X, Zhang L, Du X, Irwin DM, Zhang S, Li B. Comparative Proteomic Analysis of Glycolytic and Oxidative Muscle in Pigs. Genes (Basel) 2023; 14:genes14020361. [PMID: 36833290 PMCID: PMC9957308 DOI: 10.3390/genes14020361] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The quality of meat is highly correlated with muscle fiber type. However, the mechanisms via which proteins regulate muscle fiber types in pigs are not entirely understood. In the current study, we have performed proteomic profiling of fast/glycolytic biceps femoris (BF) and slow/oxidative soleus (SOL) muscles and identified several candidate differential proteins among these. We performed proteomic analyses based on tandem mass tags (TMTs) and identified a total of 26,228 peptides corresponding to 2667 proteins among the BF and SOL muscle samples. Among these, we found 204 differentially expressed proteins (DEPs) between BF and SOL muscle, with 56 up-regulated and 148 down-regulated DEPs in SOL muscle samples. KEGG and GO enrichment analyses of the DEPs revealed that the DEPs are involved in some GO terms (e.g., actin cytoskeleton, myosin complex, and cytoskeletal parts) and signaling pathways (PI3K-Akt and NF-kappa B signaling pathways) that influence muscle fiber type. A regulatory network of protein-protein interaction (PPI) between these DEPs that regulates muscle fiber types was constructed, which demonstrates how three down-regulated DEPs, including PFKM, GAPDH, and PKM, interact with other proteins to potentially control the glycolytic process. This study offers a new understanding of the molecular mechanisms in glycolytic and oxidative muscles as well as a novel approach for enhancing meat quality by transforming the type of muscle fibers in pigs.
Collapse
Affiliation(s)
- Xiaofan Tan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yu He
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuqiao He
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhiwei Yan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Ruixue Zhao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin Sui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Lei Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Xuehai Du
- Liaoning Provincial Animal Husbandry Development Center, Liaoning Province Agricultural Development Service Center, Shenyang 110032, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence:
| |
Collapse
|
22
|
Gong R, Luo H, Long G, Xu J, Huang C, Zhou X, Shang Y, Zhang D. Integrative proteomic profiling of lung tissues and blood in acute respiratory distress syndrome. Front Immunol 2023; 14:1158951. [PMID: 37197655 PMCID: PMC10184823 DOI: 10.3389/fimmu.2023.1158951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Introduction Acute respiratory distress syndrome and acute lung injury (ARDS/ALI) still lack a recognized diagnostic test and pharmacologic treatments that target the underlying pathology. Methods To explore the sensitive non-invasive biomarkers associated with pathological changes in the lung of direct ARDS/ALI, we performed an integrative proteomic analysis of lung and blood samples from lipopolysaccharide (LPS)-induced ARDS mice and COVID-19-related ARDS patients. The common differentially expressed proteins (DEPs) were identified based on combined proteomic analysis of serum and lung samples in direct ARDS mice model. The clinical value of the common DEPs was validated in lung and plasma proteomics in cases of COVID-19-related ARDS. Results We identified 368 DEPs in serum and 504 in lung samples from LPS-induced ARDS mice. Gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEPs in lung tissues were primarily enriched in pathways, including IL-17 and B cell receptor signaling pathways, and the response to stimuli. In contrast, DEPs in the serum were mostly involved in metabolic pathways and cellular processes. Through network analysis of protein-protein interactions (PPI), we identified diverse clusters of DEPs in the lung and serum samples. We further identified 50 commonly upregulated and 10 commonly downregulated DEPs in the lung and serum samples. Internal validation with a parallel-reacted monitor (PRM) and external validation in the Gene Expression Omnibus (GEO) datasets further showed these confirmed DEPs. We then validated these proteins in the proteomics of patients with ARDS and identified six proteins (HP, LTA4H, S100A9, SAA1, SAA2, and SERPINA3) with good clinical diagnostic and prognostic value. Discussion These proteins can be viewed as sensitive and non-invasive biomarkers associated with lung pathological changes in the blood and could potentially serve as targets for the early detection and treatment of direct ARDS especially in hyperinflammatory subphenotype.
Collapse
Affiliation(s)
- Rui Gong
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Hong Luo
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Gangyu Long
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Jiqian Xu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Chaolin Huang
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
| | - Xin Zhou
- SpecAlly Life Technology Co., Ltd, Wuhan, Hubei, China
| | - You Shang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- *Correspondence: Dingyu Zhang, ; You Shang,
| | - Dingyu Zhang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Center for Translational Medicine, Wuhan Jinyintan Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- *Correspondence: Dingyu Zhang, ; You Shang,
| |
Collapse
|
23
|
Chhikara N, Tomar AK, Datta SK, Yadav S. Proteomic changes in human spermatozoa during in vitro capacitation and acrosome reaction in normozoospermia and asthenozoospermia. Andrology 2023; 11:73-85. [PMID: 36057948 DOI: 10.1111/andr.13289] [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: 04/04/2022] [Revised: 07/31/2022] [Accepted: 08/28/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND The cellular and molecular mechanisms of the events that help spermatozoa acquire their fertilizing capability during capacitation and acrosome reaction are not completely understood. OBJECTIVE This study was performed with a postulation that the identification of sperm proteins and their changes during in vitro capacitation and acrosome reaction will unravel unknown molecular aspects of fertilization that impact male fertility. MATERIALS AND METHODS Spermatozoa collected from sequential conditions, that is, separation of ejaculated spermatozoa by Percoll gradient centrifugation, in vitro capacitation, and acrosome reaction were processed for tandem mass spectrometric analysis, followed by protein identification, label-free quantitation, and statistical analysis. RESULTS AND DISCUSSION Collectively, a total of 1088 sperm proteins were identified. In comparison to ejaculated spermatozoa, 44 and 141 proteins were differentially expressed in capacitated and acrosome reacted spermatozoa, respectively. A large number of proteins were found downregulated, including clusterin, pyruvate dehydrogenase E1 component, semenogelin-1 and 2, heat shock protein 90, beta-microseminoprotein, and keratin. It was expected as sperm-membrane-associated proteins are removed during capacitation. There were significant proteomic alterations in asthenozoospermia compared to normozoospermia; however, variation was more noticeable among proteins of acrosome reacted spermatozoa and those released during the acrosome reaction. The processes enriched among downregulated proteins in asthenozoospermia included acrosome assembly, binding of spermatozoa to zona pellucida, nucleosome assembly, flagellated sperm motility, protein folding, oxidative phosphorylation, tricarboxylic acid cycle, chromatin silencing, gluconeogenesis, glycolytic process, and glycolysis. CONCLUSION The dynamic information generated about proteomic alterations in spermatozoa during capacitation and acrosome reaction and their variability in asthenozoospermia will contribute not only to enhancing our understanding of processes that prepare spermatozoa to acquire fertilization capability but also help in deciphering novel factors of male infertility.
Collapse
Affiliation(s)
- Nirmal Chhikara
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sudip Kumar Datta
- Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
24
|
Lou Y, Lv Y, Li Z, Kang Y, Hou M, Fu Z, Lu L, Liu L, Cai Z, Qi Z, Jian H, Shen W, Li X, Zhou H, Feng S. Identification of Differentially Expressed Proteins in Rats with Early Subacute Spinal Cord Injury using an iTRAQ-based Quantitative Analysis. Comb Chem High Throughput Screen 2023; 26:1960-1973. [PMID: 36642874 DOI: 10.2174/1386207326666230113152622] [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: 04/23/2022] [Revised: 10/02/2022] [Accepted: 11/17/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Injuries to the central nervous system (CNS), such as spinal cord injury (SCI), may devastate families and society. Subacute SCI may majorly impact secondary damage during the transitional period between the acute and subacute phases. A range of CNS illnesses has been linked to changes in the level of protein expression. However, the importance of proteins during the early subacute stage of SCI remains unknown. The role of proteins in the early subacute phase of SCI has not been established yet. METHODS SCI-induced damage in rats was studied using isobaric tagging for relative and absolute protein quantification (iTRAQ) to identify proteins that differed in expression 3 days after the injury, as well as proteins that did not alter in expression. Differentially expressed proteins (DEPs) were analyzed employing Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to discover the biological processes, cell components, and molecular functions of the proteins. We also performed Gene Set Enrichment Analysis (GSEA) software BP pathway and KEGG analysis on all proteins to further identify their functions. In addition, the first 15 key nodes of a protein-protein interaction (PPI) system were found. RESULTS During the early subacute stage of SCI, we identified 176 DEPs in total between the control and damage groups, with 114 (64.77%) being up-regulated and 62 (35.23%) being downregulated. As a result of this study, we discovered the most important cellular components and molecular activities, as well as biological processes and pathways, in the early subacute phase of SCI. The top 15 high-degree core nodes were Alb, Plg, F2, Serpina1, Fgg, Apoa1, Vim, Hpx, Apoe, Agt, Ambp, Pcna, Gc, F12, and Gfap. CONCLUSION Our study could provide new views on regulating the pathogenesis of proteins in the early subacute phase after SCI, which provides a theoretical basis for exploring more effective therapeutic targets for SCI in the future.
Collapse
Affiliation(s)
- Yongfu Lou
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yigang Lv
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhen Li
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yi Kang
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Mengfan Hou
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zheng Fu
- Key Laboratory of Immuno Microenvironment and Disease of the Educational Ministry of China, Department of Immunology, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin 300070, China
| | - Lu Lu
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Lu Liu
- Department of Traumatic Orthopedics, Honghui Hospital, Xi'an Jiaotong University, 555 West Youyi Road, Xi'an, 710061, Shaanxi, China
| | - Zhiwei Cai
- Department of Burn and Plastic Surgery, Burns Institute, Burn & Plastic Hospital of PLA General Hospital, Fourth Medical Center of PLA General Hospital, Beijing, 100048, China
| | - Zhangyang Qi
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Huan Jian
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Wenyuan Shen
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xueying Li
- Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Hengxing Zhou
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
- Department of Orthopaedics, Shandong University Centre for Orthopaedics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shiqing Feng
- Department of Orthopaedics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China
- Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Medical University General Hospital, Tianjin 300052, China
- Department of Orthopaedics, Shandong University Centre for Orthopaedics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| |
Collapse
|
25
|
Jing F, Liu G, Zhang R, Xue W, Lin J, Zhu H, Zhu Y, Wu C, Luo Y, Chen T, Li S, Bao M. PYY modulates the tumorigenesis and progression of colorectal cancer unveiled by proteomics. Am J Cancer Res 2022; 12:5500-5515. [PMID: 36628274 PMCID: PMC9827100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/20/2022] [Indexed: 01/12/2023] Open
Abstract
Despite decrease in mortality caused by colorectal cancer (CRC), there remains no effective therapeutic method for patients with CRC. We attempted to screen biomarkers with therapeutic values in CRC. Proteomic analysis was performed on tumor, tumor-adjacent, and normal tissues derived from five patients with colon adenocarcinoma (COAD) via label-free proteome profiling. Differentially expressed proteins (DEPs) were identified, and functional annotation was performed based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The effect of marker proteins on CRC was determined via cell function experiments and using tumor organoid models. The localization of the marker proteins was determined via immunofluorescence. A total of 126 DEPs were identified in COAD tissues compared with normal tissues, of which Peptide YY (PYY) overlapped among the tumor, adjacent, and normal groups. DEPs in the cancer group vs. normal group were enriched in the regulation of cell cycle checkpoint, developmental process, focal adhesion, and apoptosis-related pathways. The low expression of PYY in CRC tissues was verified via qRT-PCR, western blotting, and immunohistochemistry. Overexpression of PYY promoted apoptosis and inhibited the proliferation, migration, and invasion of HCT116 and HT29 cells. Furthermore, PYY was secreted by neurons and its supplementation suppressed tumor organoid growth in a dose-dependent manner. In conclusion, PYY exerted inhibitory action on CRC and could be a therapeutic target for CRC.
Collapse
Affiliation(s)
- Fangyan Jing
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Guanglong Liu
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Renyi Zhang
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Weisong Xue
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Jiabao Lin
- Department of Health Management, Nanfang Hospital, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Huacong Zhu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Yu Zhu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Chaosong Wu
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Yang Luo
- Department of Urology, The Fifth Affiliated Hospital of Southern Medical UniversityGuangzhou 510900, Guangdong, China
| | - Tao Chen
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Shenglong Li
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| | - Ming Bao
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, China
| |
Collapse
|
26
|
Wu X, Dong N, Yu L, Liu M, Jiang J, Tang T, Zhao H, Fang Q. Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis. Front Immunol 2022; 13:1017423. [PMID: 36483550 PMCID: PMC9724784 DOI: 10.3389/fimmu.2022.1017423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
Background We aimed to investigate the biological mechanism and feature genes of Duchenne muscular dystrophy (DMD) by multi-omics and experimental verification strategy. Methods We integrated the transcriptomic and proteomic methods to find the differentially expressed mRNAs (DEMs) and proteins (DEPs) between DMD and Control groups. Weighted gene co-expression network analysis (WGCNA) was then used to identify modules of highly correlated genes and hub genes. In the following steps, the immune and stromal cells infiltrations were accomplished by xCELL algorithm. Furthermore, TF and miRNA prediction were performed with Networkanalyst. ELISA, western blot and external datasets were performed to verify the key proteins/mRNAs in DMD patient and mouse. Finally, a nomogram model was established based on the potential biomarkers. Results 4515 DEMs and 56 DEPs were obtained from the transcriptomic and proteomic study respectively. 14 common genes were identified, which is enriched in muscle contraction and inflammation-related pathways. Meanwhile, we observed 33 significant differences in the infiltration of cells in DMD. Afterwards, a total of 22 miRNAs and 23 TF genes interacted with the common genes, including TFAP2C, MAX, MYC, NFKB1, RELA, hsa-miR-1255a, hsa-miR-130a, hsa-miR-130b, hsa-miR-152, and hsa-miR-17. In addition, three genes (ATP6AP2, CTSS, and VIM) showed excellent diagnostic performance on discriminating DMD in GSE1004, GSE3307, GSE6011 and GSE38417 datasets (all AUC > 0.8), which is validated in patients (10 DMD vs. 10 controls), DMD with exon 55 mutations, mdx mouse, and nomogram model. Conclusion Taken together, ATP6AP2, CTSS, and VIM play important roles in the inflammatory response in DMD, which may serve as diagnostic biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Xuan Wu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China,Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Nan Dong
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Liqiang Yu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Meirong Liu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianhua Jiang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tieyu Tang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Hongru Zhao
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Hongru Zhao, ; Qi Fang,
| | - Qi Fang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Hongru Zhao, ; Qi Fang,
| |
Collapse
|
27
|
Li R, Zhao X, Liu P, Wang D, Chen C, Wang Y, Zhang N, Shen B, Zhao D. Differential Expression of Serum Proteins in Chronic Obstructive Pulmonary Disease Assessed Using Label-Free Proteomics and Bioinformatics Analyses. Int J Chron Obstruct Pulmon Dis 2022; 17:2871-2891. [PMID: 36411774 PMCID: PMC9675428 DOI: 10.2147/copd.s383976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2023] Open
Abstract
PURPOSE As a common respiratory disease, chronic obstructive pulmonary disease (COPD) has a high morbidity and mortality. Current clinical therapies are not ideal and do not improve lung function or long-term life quality. It is very important to find new potential pathogenic mechanisms, biomarkers, and targets with therapeutic value in COPD. METHODS Serum samples collected from acute exacerbation and stable COPD and healthy participants were analyzed using label-free liquid chromatography tandem mass spectrometry to identify the differentially expressed proteins (DEPs) between two groups. Bioinformatics analyses were performed to determine the biological processes associated with those DEPs. Key proteins were validated by enzyme linked immunosorbent assay (ELISA). RESULTS In total, 661 proteins were detected in serum from patients with COPD and healthy participants. Compared with healthy participants, patients with acute exacerbation of COPD had 45 DEPs, 13 were upregulated and 32 were downregulated; and patients with stable COPD had 79 DEPs, 18 were upregulated and 61 were downregulated. Gene Ontology functional annotation results indicated that the DEPs identified in patients with COPD were associated with the terms cellular anatomical entity, binding, and cellular process. Kyoto Encyclopedia of Genes and Genomes functional annotation analysis and the Clusters of Orthologous Genes database analysis indicated that the functions of these DEPs were primarily in signal transduction mechanisms and amino acid transport and metabolism. The ELISA results for three key proteins of IGFBP2, LRG1 and TAGLN were consistent with the LC-MS/MS results and the area under the receiver operating characteristic of the combined index was 0.893 (95% CI: 0.813, 0.974). CONCLUSION Our findings suggested pathogenic mechanisms underlying COPD stages and indicated three key proteins that may warrant further study as potential biomarkers for early diagnosis or prognosis of COPD or as therapeutic targets.
Collapse
Affiliation(s)
- Renming Li
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Xiaomin Zhao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Pengcheng Liu
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Dandan Wang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Chen Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Ningning Zhang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, People’s Republic of China
| | - Dahai Zhao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| |
Collapse
|
28
|
Chen J, Huang W, Zhang H, Peng X, Yang J, Yang Y, Su J, Wang S, Zhou W. Quantitative proteomics on the cerebrospinal fluid of hydrocephalus in neonatal bacterial meningitis. Front Pediatr 2022; 10:972032. [PMID: 36052359 PMCID: PMC9424622 DOI: 10.3389/fped.2022.972032] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Hydrocephalus in bacterial meningitis (BM) is a devastating infectious neurological disease and the proteins and pathways involved in its pathophysiology are not fully understood. Materials and methods Label-free quantitative (LFQ) proteomics analyses was used to identify differentially expressed proteins (DEPs) in cerebrospinal fluid (CSF) samples from infants with hydrocephalus and bacterial meningitis (HBM group, N = 8), infants with bacterial meningitis (BM group, N = 9); and healthy infants (N group, N = 11). Bioinformatics analysis was subsequently performed to investigate Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched signaling pathways of these DEPs. Six proteins (AZU1, COX4I1, EDF1, KRT31, MMP12, and PRG2) were selected for further validation via enzyme-linked immunosorbent assay (ELISA). Results Compared with BM group and N group, HBM group had a higher whole CSF protein level (5.6 ± 2.7 vs. 1.7 ± 1.0 vs. 1.2 ± 0.5 g/l) and lower whole CSF glucose level (0.8 ± 0.6 vs. 1.8 ± 0.7 vs. 3.3 ± 0.8 mmol/l) (both P < 0.05). Over 300 DEPs were differentially expressed in HBM group compared with BM group and BM compared with N group, of which 78% were common to both. Cluster analysis indicated that the levels of 226 proteins were increased in BM group compared with N group and were decreased in HBM group compared with BM group. Bioinformatics analysis indicated the involvement of the cell adhesion, immune response and extracellular exosome signaling were significantly enriched in HBM compared with BM group and BM compared with N group. 267 DEPs were identified between HBM group with N group, KEGG analysis indicated that DEPs mainly involved in filament cytoskeleton and immune response. The ELISA results further verified that the expression levels of AZU1 were significantly different from among three groups (both P < 0.05). Conclusion This is the first reported characterization of quantitative proteomics from the CSF of infants with HBM. Our study also demonstrated that AZU1 could be a potential biomarker for the diagnosis of hydrocephalus in bacterial meningitis.
Collapse
Affiliation(s)
- Juncao Chen
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Weiben Huang
- Department of Neonatology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hong Zhang
- Department of Neonatology, Dali Autonomous Prefecture Children’s Hospital, Dali, China
| | - Xiangwen Peng
- Department of Key Laboratory, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Jun Yang
- Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Yong Yang
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Jinzhen Su
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Siyao Wang
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Wei Zhou
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
29
|
Prathaphan P, Reamtong O, Ngaokrajang U, Janvilisri T, Swainson NM, Kiatwuthinon P. Comparative Proteomic Profiling of Cisplatin-resistant Nasopharyngeal Carcinoma Cell Lines: Novel Biomarkers for Improving Chemotherapy of NPC. Anticancer Res 2022; 42:3507-3522. [PMID: 35790268 DOI: 10.21873/anticanres.15837] [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: 05/10/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Nasopharyngeal carcinoma (NPC) originates in the hidden nasopharynx, causing NPC patients to be diagnosed at a late stage and develop drug resistance. Therefore, the identification of drug-resistance biomarkers is indispensable to improve NPC detection and treatment. Hence, this study aimed to identify novel cisplatinresistance biomarkers using comparative proteomic profiles of cisplatin-resistant (CDDP/NPC) cell lines. MATERIALS AND METHODS Two cisplatin-resistant NPC cell lines (CDDP/5-8F and CDDP/6-10B) were established by a continuous cisplatin treatment. Then, morphology, proliferation, and migration of all NPC cells were evaluated, followed by the examination of protein profiles using 1D in-gel digestion coupled with mass spectrometry. The potential drugresistance biomarkers were transcriptionally and translationally validated by qPCR and western blotting, respectively. RESULTS CDDP/5-8F and CDDP/6-10B cells were successfully developed with a resistance index of 8.42 and 2.46, respectively. Furthermore, both CDDP/NPC cells demonstrated relatively altered morphology, retarded growth, and decreased migration. Additionally, the comparative proteomic analysis of CDDP/NPC revealed 92 differentially expressed proteins (DEPs). Specifically, up-regulated DEPs were notably enriched in cellular metabolic processes, while down-regulated DEPs were predominantly enriched in actin filament-based movement, methylation, and programmed cell death. Six up-regulated, namely ALPI, CKB, HMGB1, KHSRP, PDIA4, and STMN1, and three down-regulated proteins, FUBP1, YWHAZ, and PLEC, were validated at the transcriptional level. CKB and FUBP1 were further validated at the translational level and demonstrated corresponding expression levels at both protein and gene levels. CONCLUSION Our findings suggest novel biomarkers to indicate cisplatin resistance in NPC, expanding the drug resistance knowledge and paving the way for in-depth mechanism studies in NPC.
Collapse
Affiliation(s)
- Parisa Prathaphan
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Utapin Ngaokrajang
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pichamon Kiatwuthinon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand;
| |
Collapse
|
30
|
Chen X, Xu Z, Zhao B, Yang Y, Mi J, Zhao Z, Liu J. Physiological and Proteomic Analysis Responsive Mechanisms for Salt Stress in Oat. Front Plant Sci 2022; 13:891674. [PMID: 35783977 PMCID: PMC9240473 DOI: 10.3389/fpls.2022.891674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Oat is considered as a moderately salt-tolerant crop that can be used to improve saline and alkaline soils. Previous studies have focused on short-term salt stress exposure, and the molecular mechanisms of salt tolerance in oat have not yet been elucidated. In this study, the salt-tolerant oat cultivar Vao-9 and the salt-sensitive oat cultivar Bai5 were treated with 6 days of 0 and 150 mmol L-1 salt stress (nNaCl:nNa2SO4 = 1:1). Label-Free technology was then used to analyze the differentially expressed proteins in leaves under 0 and 150 mmol L-1 salt stress. The obtained results indicated that total of 2,631 proteins were identified by mass spectrometry in the four samples. The salt-tolerant cultivar Vao-9 mainly enhances its carbohydrate and energy metabolism through the pentose and glucuronate interconversions, and carbon fixation pathways in prokaryotes, thereby reducing the damage caused by salt stress. In addition, the down-regulation of ribosomes expression and the up-regulated expression of HSPs and CRT are all through the regulation of protein synthesis in response to salt stress. However, GABA metabolism presents a different synthesis pattern in Bai5 and Vao-9. The main KEGG function of differential expressed protein (DEP) in Bai5 is classified into protein processing in the endoplasmic reticulum, estrogen signaling pathway, antigen processing and presentation, longevity regulating pathway-multiple species, arginine and proline metabolism, beta-alanine metabolism, vitamin B6 metabolism, salmonella infection, chloroalkane and chloroalkene degradation, and limonene and pinene degradation. Moreover, the main KEGG functions of DEP in Vao-9 are classified as ribosome and carbon fixation pathways in prokaryotes, pentose and glucuronate interconversions, GABA ergic synapse, and taurine and hypotaurine metabolism. The results obtained in this study provide an important basis for further research on the underlying mechanisms of salt response and tolerance in oat and other plant species.
Collapse
Affiliation(s)
- Xiaojing Chen
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhongshan Xu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Baoping Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Yanming Yang
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Junzhen Mi
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhou Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Jinghui Liu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| |
Collapse
|
31
|
Wang Q, Yan S, Zhang J, Du R, Xue L, Li J, Yu C. The differentially expressed proteins related to clinical viral encephalitis revealed by proteomics. Ibrain 2022; 8:148-164. [PMID: 37786892 PMCID: PMC10528792 DOI: 10.1002/ibra.12036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 02/05/2023]
Abstract
To screen out the prospective biomarkers of viral encephalitis (VE), analyze the biological process and signaling pathways involved by differentially expressed proteins (DEPs). A total of 11 cerebrospinal fluid (CSF) samples with VE and 5 with non-nervous system infection were used to perform label-free proteomic techniques. Then, the bioinformatic analysis of DEPs was applied by Interproscan software. Moreover, 73 CSF samples in the VE group and 53 in the control group were used to verify the changes of some DEPs by enzyme-linked immunosorbent assay (ELISA). Thirty-nine DEPs were identified, including 18 upregulated DEPs and 21 downregulated DEPs. DEPs were mainly enriched in cell adhesion molecules by Kyoto Encyclopedia of Genes and Genomes analysis pathway analysis. The DEPs related to axon tissue were obviously downregulated and the most significant downregulated proteins were neurexin 3, neurofascin, and neuroligin 2 (NLGN2). Moreover, the protein expression of NLGN2 in the VE group was significantly higher than that in the control group by ELISA. The correlation analysis of NLGN2 in the VE group revealed that there was a weak positive correlation with CSF protein and a weak negative correlation with CSF chloride. The clinical VE may be closely related to NLGN2 and the cell adhesion molecule pathway.
Collapse
Affiliation(s)
- Qian Wang
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | | | | | - Ruo‐Lan Du
- Institute of Neurological Disease and Department of Anesthesiology, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Lu‐Lu Xue
- Kunming Medical UniversityKunmingYunnanChina
| | - Juan Li
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Chang‐Yin Yu
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| |
Collapse
|
32
|
Abstract
Retinal pigment epithelium (RPE) is an important component of the outer blood-retinal barrier and plays a critical role in maintaining retinal homeostasis. Alterations in RPE can be detected during the early stages of diabetic retinopathy (DR). However, the molecular mechanisms underlying these early changes remain unclear. We investigated the molecular changes induced in the RPE by high glucose concentrations by constructing a high glucose-induced ARPE-19 cell injury model simulating the DR environment in vitro. Proteomic analysis was conducted to measure differences in protein expression between cells treated with normal (5 mM) and high (25 mM) glucose concentrations, and bioinformatics techniques were used to analyze the mechanism of action. The results of the proteomic analyses were validated using western blotting. High glucose levels inhibited the proliferation of ARPE-19 cells. We identified 88 upregulated proteins and 114 downregulated proteins. Six of these proteins were selected for further validation. Changes in the proteome mainly affected the lysosome and cell cycle pathways. Proteomic differences between ARPE-19 cells treated with normal and high glucose concentrations indicate that damage to the RPE in DR may be caused by specific mechanisms. Our study verified protein changes in ARPE-19 cells in a high-glucose environment and may provide new strategies for understanding the molecular mechanisms underlying DR.
Collapse
Affiliation(s)
- Huanran Zhou
- Department of Endocrinology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui Province, China.,Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qian Xu
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hongxue Li
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuxin Hu
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hongyu Kuang
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| |
Collapse
|
33
|
Feng J, Feng J, Li C, Xu S, Wang X, Chen K. Proteomics Reveal the Effect of Exogenous Electrons on Electroactive Escherichia coli. Front Microbiol 2022; 13:815366. [PMID: 35464959 PMCID: PMC9019752 DOI: 10.3389/fmicb.2022.815366] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial cells utilizing electricity to produce high-value fuels and chemicals are the foundation of the biocathodic bioelectrochemical system. However, molecular mechanisms of electron transfer and utilization have not been elucidated. In this work, Escherichia coli engineered by introducing the Mtr pathway from Shewanella oneidensis exhibited stronger electrochemical activity than control and could utilize exogenous electrons to stimulate metabolite profiles and boost succinate production in the bioelectrochemical system. Proteomic analysis and real-time PCR were performed to investigate the effect of exogenous electrons on electroactive E. coli. Bioinformatics analysis suggested that the proteins of molecular function associated with oxidoreductase activity, 4 iron, 4 sulfur([4Fe-4S]) cluster binding, iron-sulfur cluster binding, and metal cluster binding were positively affected by exogenous electrons. Moreover, mapping to the Kyoto Encyclopedia of Genes and Genomes pathway database showed that the up-regulated proteins were mainly involved in metabolic pathways of tricarboxylic acid cycle, pyruvate metabolism, and nitrogen metabolism pathway, providing support for the metabolic balance of microbial cells shifting toward reduced end-products due to electron utilization. Using a biochemical method, the ompF-overexpressed strain was employed to investigate the function of the channel protein. These findings provided a theoretical basis for further improving electron transfer and utilization efficiency, and contributed to the potential applications of the bioelectrochemical system.
Collapse
|
34
|
Li R, Pu J, Cai Y, Zheng K, Qin X, Zhang Z, Xu X. Proteomic characteristics of PM 2.5-induced differentially expressed proteins in k-ras-silenced HBE cells. Toxicol Mech Methods 2022; 32:431-438. [PMID: 35014587 DOI: 10.1080/15376516.2022.2028328] [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: 10/19/2022]
Abstract
The human bronchial epithelial cells (HBE) and K-ras-silenced HBE cells were treated with fine particulate matter (PM2.5) samples from Taiyuan for 24 h. To screen the proteomic characteristics of PM2.5-induced differentially expressed proteins (DEPs), the Q Exactive mass spectrometer was used. Gene ontology (GO) analysis, Kyoto encyclopedia of genes and genomes (KEGG) analysis, functional prediction, protein-protein interaction (PPI) network analysis, and visualization of differential protein interactions were performed. 251 DEPs in K-ras silenced cells and 535 DEPs in normal HBE cells were identified, respectively. KEGG analysis showed that the differentially expressed proteins of PM2.5-treated cells were related to the biosynthesis of ribosomes, antibiotics, and amino acids. On the other hand, K-ras silenced cells were related to metabolic pathways, RNA transport, and DNA replication. Through the construction of a PPI network, the top 10 hub proteins were screened from the two cell groups, among which MRPL13, RPS20, and EIF1AX were of great significance. Our results indicated that the K-ras gene plays an important role in PM2.5-induced DEPs, and the findings provide a scientific basis for the further study of PM2.5 toxic mechanisms and biomarkers.
Collapse
Affiliation(s)
- Runbing Li
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Jiening Pu
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Ying Cai
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Kai Zheng
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Xiaoyun Qin
- Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Zhaohui Zhang
- School of Public Health, University of South China, Hengyang, China
| | - Xinyun Xu
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| |
Collapse
|
35
|
Wu Y, Huang Z, Zhang C, Shi C, Lyu L, Li W, Wu W. Comparative Analysis of the Morphological, Physiological, Proteomic, and Metabolic Mechanisms of the "Biloxi" Blueberry Response to Shade Stress. Front Plant Sci 2022; 13:877789. [PMID: 35592566 PMCID: PMC9111170 DOI: 10.3389/fpls.2022.877789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
Blueberry is an important small berry crop in economic forests. In hot summers, the top tip of blueberry often burns and withers due to water loss. Therefore, this study subjected blueberry to shading treatment in the summer to study the effects of different shading treatments on the growth, morphology, physiology and protein levels of the plant. The results showed that the 50% shading (T1) treatment yielded the highest average increases in plant height, crown width, and ground diameter of blueberry. Under the 80% shading (T2) treatment, the cells of the leaves dissolved, the morphology was incomplete, the vascular bundles disappeared, and no supporting skeleton was detected. As demonstrated by physiological and biochemical data and the proteome expression levels, the T1 shading treatment was beneficial to the growth of blueberry and significantly enriched the photosynthetic pathway and flavonoid biosynthesis. An analysis of the interaction network of differentially expressed proteins indicated that trans-cinnamate 4-monooxygenase (C4H, CYP73A), naringenin 3-dioxygenase (F3H) and bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) exhibited high connectivity and mutual regulation. In short, 50% shading can improve the growth index of blueberry and lead to an enrichment of flavonoid biosynthesis. This study provides a scientific basis for the breeding and summer protection of blueberry seedlings.
Collapse
Affiliation(s)
- Yaqiong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Zhengjin Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chunhong Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chong Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lianfei Lyu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Weilin Li,
| | - Wenlong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Wenlong Wu,
| |
Collapse
|
36
|
Wu Q, Chen H, Zhang Z, Chen C, Yu F, Guy RD. Effects of Fruit Shading on Gene and Protein Expression During Starch and Oil Accumulation in Developing Styrax tonkinensis Kernels. Front Plant Sci 2022; 13:905633. [PMID: 35720550 PMCID: PMC9201641 DOI: 10.3389/fpls.2022.905633] [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] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/06/2022] [Indexed: 05/03/2023]
Abstract
Styrax tonkinensis has great potential as a biofuel feedstock source having industrial oilseeds with excellent fatty acids (FAs) composition and good fuel properties. Photosynthesis in the developing pericarp could affect the carbon distribution in kernel. During kernel development, more carbon sources are allocated to starch rather than lipid, when the pericarp photosynthesis is reduced by fruit shading treatment. After shading the fruits at 50 days after flowering (DAF), samples of shaded fruit (FSK) and controls (CK) were collected at 80 DAF and analyzed using the proteomic method. We identified 3,181 proteins, of which 277 were differentially expressed proteins, all downregulated in the FSK group. There were 56 proteins found involved in carbohydrate metabolism and lipid biosynthesis leading to oil accumulation with their iTRAQ ratios of FSK/CK ranging from 0.7123 to 1.1075. According to the qRT-PCR analyses, the key genes related to FA and triacylglycerol (TAG) biosynthesis were significantly downregulated between 60 and 90 DAF especially at 80 DAF, while the key genes involved in starch biosynthesis and FA desaturase had no significant difference between the two groups at 80 DAF. Fruit shading is a negative treatment for lipid accumulation but not starch accumulation by restraining enzymic protein expression involved in FA and TAG biosynthesis during S. tonkinensis kernel development.
Collapse
Affiliation(s)
- Qikui Wu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Hong Chen
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
| | - Zihan Zhang
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Tree Genetics and Breeding and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Chen Chen
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
| | - Fangyuan Yu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
- *Correspondence: Fangyuan Yu,
| | - Robert D. Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Robert D. Guy,
| |
Collapse
|
37
|
Athar HUR, Zulfiqar F, Moosa A, Ashraf M, Zafar ZU, Zhang L, Ahmed N, Kalaji HM, Nafees M, Hossain MA, Islam MS, El Sabagh A, Siddique KHM. Salt stress proteins in plants: An overview. Front Plant Sci 2022; 13:999058. [PMID: 36589054 PMCID: PMC9800898 DOI: 10.3389/fpls.2022.999058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.
Collapse
Affiliation(s)
- Habib-ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| | - Anam Moosa
- Department of Plant Pathology, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Zafar Ullah Zafar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Lixin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nadeem Ahmed
- College of Life Sciences, Northwest A&F University, Yangling, China
- Department of Botany, Mohy-ud-Din Islamic University, Nerian Sharif, Pakistan
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, Warsaw, Poland
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Sohidul Islam
- Department of Agronomy, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Ayman El Sabagh
- Faculty of Agriculture, Department of Field Crops, Siirt University, Siirt, Türkiye
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Petrth WA, Australia
- *Correspondence: Faisal Zulfiqar, ; Kadambot H. M. Siddique,
| |
Collapse
|
38
|
Qian W, Yu H, Zhang C, Zhang H, Fu S, Xia C. Plasma Proteomics Characteristics of Subclinical Vitamin E Deficiency of Dairy Cows During Early Lactation. Front Vet Sci 2021; 8:723898. [PMID: 34957273 PMCID: PMC8703030 DOI: 10.3389/fvets.2021.723898] [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: 06/11/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
Vitamin E (VE) is an essential fat-soluble nutrient for dairy cows. Vitamin E deficiency leads to immune suppression and oxidative stress and increases the susceptibility of cows to reproductive disorders in the early post-partum period. However, studies on plasma proteomics of VE deficiency have not been reported so far. Therefore, the purpose of this study was to understand the changes of blood protein profile in cows with subclinical VE deficiency in the early post-partum period. In this study, plasma protein levels of 14 healthy cows (>4 μg/ml α-tocopherol) and 13 subclinical VE-deficient cows (2–3 μg/ml α-tocopherol) were analyzed by tandem mass tag (TMT). The results showed that there were 26 differentially expressed proteins (DEPs) in the plasma of cows with subclinical VE deficiency compared with healthy controls. Twenty-one kinds of proteins were downregulated, and five kinds were upregulated, among which eight proteins in protein–protein interactions (PPI) network had direct interaction. These proteins are mainly involved in the MAPK signaling pathway, pantothenic acid and coenzyme A (CoA) biosynthesis, PPAR signaling pathway, and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The top four DEPs in PPI (APOC3, APOC4, SAA4, PHLD) and one important protein (VNN1) by literature review were further verified by ELISA and Western blot. The expression levels of APOC3, VNN1, and SAA4 were significantly lower than those of healthy controls by ELISA. VNN1 was significantly lower than those of healthy controls by Western blot. VNN1 is closely related to dairy cow subclinical VE deficiency and can be a potential biomarker. It lays a foundation for further research on the lack of pathological mechanism and antioxidative stress of VE.
Collapse
Affiliation(s)
- Weidong Qian
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hongyi Yu
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Cuiyu Zhang
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hongyou Zhang
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shixin Fu
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Cheng Xia
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| |
Collapse
|
39
|
Sokołowska P, Siatkowska M, Białkowska K, Rosowski M, Komorowski P, Walkowiak B. Osteosarcoma cells in early and late stages as cancer in vitro progression model for assessing the responsiveness of cells to silver nanoparticles. J Biomed Mater Res B Appl Biomater 2021; 110:1319-1334. [PMID: 34953019 DOI: 10.1002/jbm.b.35002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/09/2021] [Accepted: 12/13/2021] [Indexed: 11/07/2022]
Abstract
Understanding of biology of osteosarcoma malignant progression is indispensable for enhancement of conventional chemotherapy by the use of silver nanoparticles (AgNPs). We presented an in vitro model of cancer progression closely resembling processes occurring in vivo in terms of protein profile. A comparison of cytotoxic and genotoxic potential of AgNPs in Saos-2 cells in early stages of cancerous progression (early passages) with the cells in advanced stages (late passages) demonstrated significantly reduced responsiveness of the late passage cells to nanoparticles toxicity. It was also confirmed by proteome analysis as we identified considerably higher number of differentially expressed proteins in Saos-2 cells in early passages compared to the late passage cells. Our studies showed that the ability of AgNPs as potential drug carriers to deliver a medication and/or to evoke toxic effects might be significantly diminished in advanced stages of cancer progression.
Collapse
Affiliation(s)
- Paulina Sokołowska
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland.,Department of Pharmacology and Toxicology, Medical University of Lodz, Lodz, Poland
| | | | - Kamila Białkowska
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland.,Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Marcin Rosowski
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland.,Department of Chemical Textiles Technologies, Lukasiewicz Research Network, Textile Research Institute, Lodz, Poland
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland.,Division of Biophysics, Institute of Materials Science, Lodz University of Technology, Lodz, Poland
| | - Bogdan Walkowiak
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Lodz, Poland.,Division of Biophysics, Institute of Materials Science, Lodz University of Technology, Lodz, Poland
| |
Collapse
|
40
|
Zheng K, Cai Y, Lei Y, Liu Y, Sun Z, Wang Y, Xu X, Zhang Z. Proteomic characteristics of beryllium sulfate-induced differentially expressed proteins in rats. Toxicol Res (Camb) 2021; 10:962-974. [PMID: 34733481 DOI: 10.1093/toxres/tfab051] [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: 02/18/2021] [Revised: 04/06/2021] [Accepted: 05/10/2021] [Indexed: 11/12/2022] Open
Abstract
Sprague Dawley rats were exposed to beryllium sulfate (BeSO4), and proteomic and bioinformatic techniques were applied to screen for differentially expressed proteins in their lung tissue and serum. A total of 12 coexpression modules were constructed for 18 samples with 2333 proteins. Four modules were found to have significant differences in the regulation of protein coexpression modules in the serum following exposure to BeSO4. A further three modules had significant differences in the regulation of protein coexpression modules in the lung tissues. Five modules with good correlation were obtained by calculating the gene significance and module membership values, whereas these module Hub proteins included: Hspbp1, Rps15a, Srsf2, Hadhb, Elmo3, Armt1, Rpl18, Afap1L1, Eif3d, Eif3c, and Rps3. The five proteins correlating highest with the Hub proteins in the lung tissue and serum samples were obtained using string analysis. KEGG and GO enrichment analyses showed that these proteins are mainly involved in ribosome formation, apoptosis, cell cycle regulation, and tumor necrosis factor regulation. By analyzing the biological functions of these proteins, proteins that can be used as biomarkers, such as Akt1, Prpf19, Cct2, and Rpl18, are finally obtained.
Collapse
Affiliation(s)
- Kai Zheng
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Ying Cai
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Yuandi Lei
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Yanping Liu
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Zhanbing Sun
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Ye Wang
- School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Xinyun Xu
- Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Zhaohui Zhang
- School of public health, University of South China, Hengyang, Hunan 421001, China
| |
Collapse
|
41
|
Zhang G, Mou Z, Xue W, Liu H. Phosphorylated protein modification analysis on normal liver and Exo-celiac liver of Glyptosternum maculatum. J Fish Biol 2021; 99:1696-1707. [PMID: 34392541 DOI: 10.1111/jfb.14877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND This study aimed to reveal the biological function and molecular mechanism of phosphorylated proteins in the normal liver (NG) and Exo-celiac liver (WG) of Glyptosternum maculatum and potential plateau-adaption mechanisms of G. maculatum. METHODS A multivariate analysis was performed on proteomic quantitative data (label-free group) and phosphorylated proteome data (phosphorylation group) to reveal protein characteristics. The differentially expressed proteins (DEPs) between NG and WG in the two groups were analysed. Enrichment analysis of these DEPs was performed prior to the protein-protein interaction (PPI) analysis. Finally, an integrated interaction network was constructed to reveal the biological mechanism of the DEP-mediated signal transduction process. RESULT The NG and WG samples in the phosphorylation group were well distinguished compared to the label-free group. A total of 49 and 313 DEPs were identified in the label-free and phosphorylation groups, respectively. These DEPs, including LIM and calponin homology domains-containing protein 1 (LIMCH1) and DEAD(Asp-Glu-Ala-Asp)-Box Helicase 51 (DDX51), were mainly assembled in functions such as cell adhesion. Two PPI networks were constructed using DEPs in the two groups. Finally, an integrated interaction network was constructed using co-DEP Ferredoxin 1 (FDX1) and associated pathways, including RNA transport. CONCLUSION LIMCH1 and DDX51 might play important roles in the organogenesis of normal liver and Exo-celiac liver in G. maculatum via the cell adhesion function. Moreover, FXD1 might be associated with the plateau-adaption mechanisms of G. maculatum via participation in the RNA transport pathway.
Collapse
Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhenbo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Wenhua Xue
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| |
Collapse
|
42
|
Wu Q, Chen C, Wang X, Zhang Z, Yu F, Guy RD. Proteomic analysis of metabolic mechanisms associated with fatty acid biosynthesis during Styrax tonkinensis kernel development. J Sci Food Agric 2021; 101:6053-6063. [PMID: 33856056 DOI: 10.1002/jsfa.11262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/01/2021] [Accepted: 04/15/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Styrax tonkinensis is a white-flowered tree with considerable potential as a feedstock source for biodiesel production from the oily seed contained within its nutlike drupes. Transcriptome changes during oil accumulation have been previously reported, but not concurrent changes in the proteome. RESULTS Using proteomic analysis of samples collected at 50, 70, 100 and 130 days after flowering (DAF), we identified 1472 differentially expressed proteins (DEPs). Based on their expression patterns, we grouped the DEPs into nine clusters and analyzed the pathway enrichment. Proteins related to starch and sucrose metabolism were most abundant at 50 DAF. Proteins involved in fatty acid (FA) biosynthesis were mainly grouped into a cluster that peaked at 70 DAF. Proteins related to protein processing in endoplasmic reticulum had two major patterns, trending either upwards or downwards, while proteins involved in amino acid biosynthesis showed more complex relationships. We identified 42 key enzymes involved in lipid accumulation during kernel development, including the acetyl-CoA carboxylase complex (ACC) and the pyruvate dehydrogenase complex (PDC). One oil body membrane protein, oleosin, continuously increased during kernel development. CONCLUSION A regulatory network of oil accumulation processes was built based on protein and available transcriptome expression data, which were in good temporal agreement. This analysis placed ACC and PDC in the center of the network, suggesting that the glycolytic provision of substrate plays a central regulatory role in FA biosynthesis and oil accumulation. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Qikui Wu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, China
| | - Chen Chen
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
| | - Xiaojun Wang
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
| | - Zihan Zhang
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Tree Genetics and Breeding and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian, Beijing, China
| | - Fangyuan Yu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University, Nanjing, China
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
| |
Collapse
|
43
|
Wang Y, Chen H, Zhang J, Lam TP, Hung ALH, Cheng JCY, Lee WYW. Potential Muscle-Related Biomarkers in Predicting Curve Progression to the Surgical Threshold in Adolescent Idiopathic Scoliosis-A Pilot Proteomic Study Comparing Four Non-Progressive vs. Four Progressive Patients vs. A Control Cohort. J Clin Med 2021; 10:4927. [PMID: 34768447 DOI: 10.3390/jcm10214927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/17/2021] [Accepted: 10/17/2021] [Indexed: 11/17/2022] Open
Abstract
Previous studies have reported abnormal muscle morphology and functions in patients with adolescent idiopathic scoliosis (AIS). To answer whether such abnormalities could be reflected in their circulation and their clinical implication for predicting curve progression to the surgical threshold, this preliminary study explored the presence of baseline muscle-related proteins and their association with curve progression. Plasma samples were collected at the first clinical visit for AIS, with patients divided into non-progressive or progressive groups (N = four and four) according to their Cobb angle in six-year follow-ups, with age- and sex-matched healthy subjects (N = 50). Then, the samples were subjected to isobaric tags for relative and absolute quantitation (iTRAQ) for global comparison of untargeted protein expression. Seventy-one differentially expressed proteins (DEPs) were found elevated in progressive AIS. Functional analysis showed that 18 of these are expressed in muscles and play an essential role in muscle activities. Among the muscle-related DEPs, α-actin had the highest fold change in progressive/non-progressive groups. This preliminary study firstly suggested higher circulating levels of muscle structural proteins in progressive AIS, indicating the likelihood of structural damage at the microscopic level and its association with progression to the surgical threshold. Further studies with larger sample sizes are warranted to validate these novel candidates for early diagnosis and predicting progression.
Collapse
|
44
|
Jia Z, Liu L, Zhang S, Zhao X, Luo L, Tang Y, Shen B, Chen M. Proteomics changes after negative pressure wound therapy in diabetic foot ulcers. Mol Med Rep 2021; 24:834. [PMID: 34608502 PMCID: PMC8503750 DOI: 10.3892/mmr.2021.12474] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023] Open
Abstract
Label-free quantitative mass spectrometry was used to analyze the differences in the granulation tissue protein expression profiles of patients with diabetic foot ulcers (DFUs) before and after negative-pressure wound therapy (NPWT) to understand how NPWT promotes the healing of diabetic foot wounds. A total of three patients with DFUs hospitalized for Wagner grade 3 were enrolled. The patients received NPWT for one week. The granulation tissue samples of the patients prior to and following NPWT for one week were collected. The protein expression profiles were analyzed with label-free quantitative mass spectrometry and the differentially expressed proteins (DEPs) in the DFU patients prior to and following NPWT for one week were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were conducted to annotate the DEPs and DEP-associated signaling pathways. Western blotting and ELISA were performed to validate the results. By comparing the differences in the protein profiles of granulation tissue samples prior to and following NPWT for one week, 36 proteins with significant differences were identified (P<0.05); 33 of these proteins were upregulated and three proteins were downregulated. NPWT altered proteins mainly associated with antioxidation and detoxification, the cytoskeleton, regulation of the inflammatory response, complement and coagulation cascades and lipid metabolism. The functional validation of the DEPs demonstrated that the levels of cathepsin S in peripheral blood and granulation tissue were significantly lower than those prior to NPWT (P<0.05), while the levels of protein S isoform 1, inter α-trypsin inhibitor heavy chain H4 and peroxiredoxin-2 in peripheral blood and granulation tissue were significantly higher than those prior to NPWT (P<0.05). The present study identified multiple novel proteins altered by NPWT and laid a foundation for further studies investigating the mechanism of action of NPWT.
Collapse
Affiliation(s)
- Zeguo Jia
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Lei Liu
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Shiqian Zhang
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Xiaotong Zhao
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Li Luo
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Yizhong Tang
- Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Mingwei Chen
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| |
Collapse
|
45
|
Li M, Qi Y, Wang G, Bu S, Chen M, Yu J, Luo T, Meng L, Dai A, Zhou Y, Liu S, Huo X. Proteomic profiling of saliva reveals association of complement system with primary Sjögren's syndrome. Immun Inflamm Dis 2021; 9:1724-1739. [PMID: 34516718 PMCID: PMC8589410 DOI: 10.1002/iid3.529] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION To compare the saliva proteomes of experimental Sjögren's syndrome (ESS) model mice and healthy controls to identify potential diagnostic biomarkers for primary Sjögren's syndrome (pSS). METHODS Proteins were extracted from the saliva of three ESS and three normal control mice using the data-independent acquisition technique. R language was used to identify the differentially expressed proteins (DEPs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to functionally annotate the DEPs. The protein-protein interaction (PPI) network was constructed and the core proteins were identified with the STRING website and Cytoscape software. The concentrations of Serpin family G member 1 (SERPING1), C3, complement factor H (CFH), fibrinogen alpha (FGA), and fibrinogen gamma (FGG) in saliva were determined by ELISA. RESULTS A total of 1722 DEPs were identified in the saliva of the ESS mice relative to the controls, of which 50 showed significantly different expression levels between the two groups. SERPING1, C3, CFH, FGA, and FGG were significantly downregulated, and keratin 4 (Krt4) and transglutaminase 3 (TGM3) were upregulated in the saliva of ESS mice. The PPI network showed that SERPING1, C3, FGG, FGA, TGM3, and hemopexin (HPX) were the core proteins. ELISA results showed that the expression of C3, CFH, FGA, and SERPING1 were significantly downregulated in the saliva of ESS mice. However, the expression of FGG was a little downregulated but with no significant difference. SERPING1, FGG, and FGA may downregulate the complement C3 by inhibiting immune complement system, thereby promoting pSS progression. CONCLUSIONS The salivary proteome of ESS mice was markedly different from that of healthy controls, suggesting that salivary proteomics is a promising noninvasive diagnostic tool for pSS. SERPING1, C3, CFH, FGA, and FGG are potential biomarkers of pSS.
Collapse
Affiliation(s)
- Mingde Li
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Anesthesiology, Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Yajun Qi
- Department of Traditional Chinese Medicine, College of Acupuncture and Massage, Anhui University of traditional Chinese Medicine, Hefei, Anhui, China
| | - Guizhen Wang
- Department of Rheumatology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Su Bu
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Ming Chen
- Department of Anesthesiology, Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Jiahui Yu
- Department of Traditional Chinese Pharmacology, College of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Tianyang Luo
- Department of Anesthesiology, Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Lulu Meng
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Anran Dai
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yong Zhou
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Shuai Liu
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xingxing Huo
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| |
Collapse
|
46
|
Shi Y, Ding Y, Li G, Wang L, Osman RA, Sun J, Qian L, Zheng G, Zhang G. Discovery of Novel Biomarkers for Diagnosing and Predicting the Progression of Multiple Sclerosis Using TMT-Based Quantitative Proteomics. Front Immunol 2021; 12:700031. [PMID: 34489947 PMCID: PMC8417809 DOI: 10.3389/fimmu.2021.700031] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/05/2021] [Indexed: 01/18/2023] Open
Abstract
Objective Here, we aimed to identify protein biomarkers that could rapidly and accurately diagnose multiple sclerosis (MS) using a highly sensitive proteomic immunoassay. Methods Tandem mass tag (TMT) quantitative proteomic analysis was performed to determine the differentially expressed proteins (DEPs) in cerebrospinal fluid (CSF) samples collected from 10 patients with MS and 10 non-inflammatory neurological controls (NINCs). The DEPs were analyzed using bioinformatics tools, and the candidate proteins were validated using the ELISA method in another cohort comprising 160 samples (paired CSF and plasma of 40 patients with MS, CSF of 40 NINCs, and plasma of 40 healthy individuals). Receiver operating characteristic (ROC) curves were used to determine the diagnostic potential of this method. Results Compared to NINCs, we identified 83 CSF-specific DEPs out of a total of 343 proteins in MS patients. Gene ontology (GO) enrichment analysis revealed that these DEPs are mainly involved in platelet degranulation, negative regulation of proteolysis, and post-translational protein modification. Pathway enrichment analysis revealed that the complement and coagulation cascades, Ras signaling pathway, and PI3K-Akt signaling pathway are the main components. Insulin-like growth factor-binding protein 7 (IGFBP7), insulin-like growth factor 2 (IGF2), and somatostatin (SST) were identified as the potential proteins with high scores, degree, and centrality in the protein-protein interaction (PPI) network. We validated the expression of these three proteins using ELISA. Compared to NINCs, the level of CSF IGFBP7 was significantly upregulated, and the level of CSF SST was significantly downregulated in the MS group. Conclusion Our results suggest that SST and IGFBP7 might be associated with the pathogenesis of MS and would be helpful in diagnosing MS. Since IGFBP7 was used to classify relapsing remitting MS (RRMS) and secondary progressive MS (SPMS) patients, therefore, it may act as a potential key marker and therapeutic target in MS.
Collapse
Affiliation(s)
- Yijun Shi
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yaowei Ding
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guoge Li
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijuan Wang
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,NMPA Key Laboratory for Quality Control of In Vitro Diagnostics , Beijing, China.,Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
| | - Rasha Alsamani Osman
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jialu Sun
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lingye Qian
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guanghui Zheng
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,NMPA Key Laboratory for Quality Control of In Vitro Diagnostics , Beijing, China.,Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
| | - Guojun Zhang
- Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,NMPA Key Laboratory for Quality Control of In Vitro Diagnostics , Beijing, China.,Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
| |
Collapse
|
47
|
Song Y, Liu J, Wang J, Liu F. Growth, Stoichiometry, and Palatability of Suaeda salsa From Different Habitats Are Demonstrated by Differentially Expressed Proteins and Their Enriched Pathways. Front Plant Sci 2021; 12:733882. [PMID: 34539722 PMCID: PMC8440984 DOI: 10.3389/fpls.2021.733882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Suaeda salsa (L.) Pall., a medicinal and edible plant, has green and red-violet ecotypes that exhibit different phenotypes, tastes, and growth characteristics. However, few studies have focused on these differences from the aspect of differentially expressed proteins under the conditions of different habitats in the field. In this study, two ecotypes of S. salsa from the intertidal (control) and supratidal (treatment) habitats of the Yellow River Delta were selected. A total of 30 individual leaves were mixed into six samples (three biological replicates for each) and subjected to protein extraction by using tandem mass tag-labeled quantitative proteomic technology. A total of 4771 proteins were quantitated. They included 317 differentially expressed proteins (2.0-fold change, p < 0.05), among which 143 were upregulated and the remaining 174 were downregulated. These differentially expressed proteins mainly participated in biological processes, such as response to stimulus, stress, and biotic stimulus; in molecular functions, such as methyltransferase activity, transferase activity, one-C group transfer, and tetrapyrrole binding; and in cell components, such as non-membrane-bound organelles, intracellular non-membrane-bound organelles, chromosomes, and photosystems. The differentially expressed proteins were mainly enriched in eight pathways, among which the ribosome, phenylpropanoid biosynthesis, and photosynthesis pathways had higher protein numbers than the other pathways. The upregulation of differentially expressed proteins related to the ribosome and photosynthesis increased the relative growth rate and reduced the N:P ratio of S. salsa from the supratidal habitat, thereby improving its palatability. By contrast, most of the differentially expressed proteins involved in phenylpropanoid biosynthesis were downregulated in S. salsa from the intertidal habitat. This result indicated that S. salsa from the intertidal habitat might accumulate flavonoids, lignin, and other secondary metabolites in its leaves that confer a bitter taste. However, these secondary metabolites might increase the medicinal value of S. salsa from the intertidal habitat. This work could provide a theoretical basis and data support for the sustainable and high-value utilization of medicinal and edible plants from coastal wetlands.
Collapse
Affiliation(s)
- Ye Song
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Co-Operatives, Jinan, China
| | - Jiayuan Liu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, China
| | - Jianzhong Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Fude Liu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, China
| |
Collapse
|
48
|
Xiao K, Song L, Bai Y, Liu P, Liu Y, Xie F, Xie L. Decipering the Molecular Mechanism of ACE2 Regulating A549 Cells. Front Genet 2021; 12:653725. [PMID: 34354732 PMCID: PMC8329961 DOI: 10.3389/fgene.2021.653725] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is an aminopeptidase that functions as a part of the renin-angiotensin system (RAS). The RAS pathway plays a crucial role in regulating the local blood flow within a tissue. As a consequence, the role of ACE2 in regulating vasculature properties has been widely appreciated. Additionally, ACE2 has also been reported to show anti-tumorigenic activity. However, the mechanistic basis of this function has remained largely unexplored. In the current study, using a lentivirus-based expression system in lung cancer cells (A549), we show that ACE2 overexpression reduces the viability and migratory potential of cancer cells, highlighting the robust anti-tumorigenic effects of ACE2 function. Moreover, a quantitative proteome-level comparison between ACE2 overexpressed (OE) and empty vector-controlled (NC) cells reveals a large number (227) of differentially expressed proteins (DEPs) that may have contributed to this phenomenon. Functional enrichment of these DEPs has uncovered that most of them perform binding activities and enzymatic reactions associated with metabolic pathways and various post-transcriptional gene expression regulatory mechanisms. Besides, cellular component analysis reveals that the DEPs function across a range of compartments within a cell with a relatively heterogeneous distribution. Our study, therefore, supports the previously established anti-tumorigenic effects of ACE2 overexpression in lung cancer cells. An analysis based on comprehensive, unbiased, and quantitative proteomics, we have provided a rigorous mechanistic explanation for its functions.
Collapse
Affiliation(s)
- Kun Xiao
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Licheng Song
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Ying Bai
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Pengfei Liu
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yuhong Liu
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Fei Xie
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lixin Xie
- Center of Pulmonary and Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| |
Collapse
|
49
|
Qu S, Song C, Tan X, Wang G, Ling F. Comparative proteomic analysis provides insight into the key proteins as potential targets underlying the effect of malachite green against Ichthyophthirius multifiliis. J Fish Dis 2021; 44:881-892. [PMID: 33560558 DOI: 10.1111/jfd.13346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Target identification is important for drug discovery. Unfortunately, no drug targets have been found in Ichthyophthirius multifiliis until now and further limited development of the novel drug for Ichthyophthiriasis. In this study, an iTRAQ-based quantitative proteomic analysis was used to find the target of malachite green (MG), exhibiting greater efficacy than the existing drugs, against I. multifiliis trophonts in situ. We also verified the proteomic results by RT-qPCR, TEM and cell apoptosis assay. Our results showed that major variations in protein abundance were found among many of the ribosome proteins, indicating ribosome might be a candidate target. Furthermore, GO and KEGG pathway analyses of differentially expressed proteins (DEPs) revealed that ribosome and PI3K-Akt signalling pathway were remarkably enriched. Taken together, the above DEPs were also verified by RT-qPCR and morphological observations. This study provides insights into the key proteins enriched in PI3K-Akt signal pathway and ribosome pathway as potential targets of MG killing I. multifiliis, which could be served as targets for other less toxic drugs and be tested as potential treatments for I. multifiliis.
Collapse
Affiliation(s)
- Shenye Qu
- Northwest A&F University, Yangling, Shaanxi, China
| | - Chenguang Song
- Northwest A&F University, Yangling, Shaanxi, China
- National Fishery Technology Extension Center, China Society of Fisheries, Peking, China
| | - Xiaoping Tan
- Northwest A&F University, Yangling, Shaanxi, China
| | - Gaoxue Wang
- Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Ling
- Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
50
|
Pierzchała D, Liput K, Korwin-Kossakowska A, Ogłuszka M, Poławska E, Nawrocka A, Urbański P, Ciepłoch A, Juszczuk-Kubiak E, Lepczyński A, Ślaska B, Kowal K, Te Pas MFW, Śmiech M, Leszczyński P, Taniguchi H, Fraser L, Sobiech P, Sachajko M, Herudzinska M, Pareek CS, Pierzchała M. Molecular Characterisation of Uterine Endometrial Proteins during Early Stages of Pregnancy in Pigs by MALDI TOF/TOF. Int J Mol Sci 2021; 22:6720. [PMID: 34201586 DOI: 10.3390/ijms22136720] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023] Open
Abstract
The molecular mechanism underlying embryonic implantation is vital to understand the correct communications between endometrium and developing conceptus during early stages of pregnancy. This study’s objective was to determine molecular changes in the uterine endometrial proteome during the preimplantation and peri-implantation between 9 days (9D), 12 days (12D), and 16 days (16D) of pregnant Polish Large White (PLW) gilts. 2DE-MALDI-TOF/TOF and ClueGOTM approaches were employed to analyse the biological networks and molecular changes in porcine endometrial proteome during maternal recognition of pregnancy. A total of sixteen differentially expressed proteins (DEPs) were identified using 2-DE gels and MALDI-TOF/TOF mass spectrometry. Comparison between 9D and 12D of pregnancy identified APOA1, CAPZB, LDHB, CCT5, ANXA4, CFB, TTR upregulated DEPs, and ANXA5, SMS downregulated DEPs. Comparison between 9D and 16D of pregnancy identified HP, APOA1, ACTB, CCT5, ANXA4, CFB upregulated DEPs and ANXA5, SMS, LDHB, ACTR3, HP, ENO3, OAT downregulated DEPs. However, a comparison between 12D and 16D of pregnancy identified HP, ACTB upregulated DEPs, and CRYM, ANXA4, ANXA5, CAPZB, LDHB, ACTR3, CCT5, ENO3, OAT, TTR down-regulated DEPs. Outcomes of this study revealed key proteins and their interactions with metabolic pathways involved in the recognition and establishment of early pregnancy in PLW gilts.
Collapse
|