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Qiao S, Zhang WY, Xie YF, Li HY, Cui CS, Tao SX, Xin T, Liu QJ. Diagnostic signatures and immune cell infiltration characteristics in anti-GABA BR encephalitis. J Neuroimmunol 2024; 388:578296. [PMID: 38309225 DOI: 10.1016/j.jneuroim.2024.578296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/16/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
PURPOSE Anti-gamma-aminobutyric acid B receptor (GABABR) encephalitis is an uncommon form of autoimmune encephalitis associated with a poor prognosis and a high fatality rate. We aim to find diagnostic markers for anti- GABABR encephalitis as well as the effects of immune cell infiltration on this pathology. METHODS For quantitative proteomic analysis, isobaric tags for relative and absolute quantitation were used in conjunction with LC-MS/MS analysis. To conduct functional correlation analyses, differentially expressed proteins (DEPs) were identified. Following that, we used bioinformatics analysis to screen for and determine the diagnostic signatures of anti- GABABR encephalitis. ROC curves were used to evaluate the diagnostic values. To assess the inflammatory status of anti- GABABR encephalitis, we used cell-type identification by estimating relative subsets of the RNA transcript (CIBERSORT) and explored the link between diagnostic markers and infiltrating immune cells. RESULTS Overall, 108 robust DEPs (47 upregulated and 61 downregulated) were identified, of which 11 were immune related. The most impressively enriched pathways were complemented and coagulation cascades, actin cytoskeleton regulation, and cholesterol metabolism; GSEA revealed that the enriched pathways were considerably differentially connected to immune modulation. Eleven immune-related DEPs were chosen for further investigation. We developed a novel diagnostic model based on CSF1R and AZGP1 serum levels using ROC analysis (area under the ROC curve = 1). M1 macrophages and activated natural killer cells are likely to play a role in course of anti- GABABR encephalitis. CONCLUSION We identified CSF1R and AZGP1 are possible anti-GABABR encephalitis diagnostic indicators, and immune cell infiltration may have a significant impact on the development and occurrence of anti- GABABR encephalitis.
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Affiliation(s)
- Shan Qiao
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China; Key Laboratory for Experimental Teratology, Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Wen-Yu Zhang
- Department of Clinical Research, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Yun-Fang Xie
- Key Laboratory for Experimental Teratology, Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hai-Yun Li
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Cai-San Cui
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
| | - Shu-Xin Tao
- Department of Neurology, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Tao Xin
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China; Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
| | - Qi-Ji Liu
- Key Laboratory for Experimental Teratology, Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
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Quality Control—A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome. Biomolecules 2023; 13:biom13030491. [PMID: 36979426 PMCID: PMC10046854 DOI: 10.3390/biom13030491] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Proteomic studies using mass spectrometry (MS)-based quantification are a main approach to the discovery of new biomarkers. However, a number of analytical conditions in front and during MS data acquisition can affect the accuracy of the obtained outcome. Therefore, comprehensive quality assessment of the acquired data plays a central role in quantitative proteomics, though, due to the immense complexity of MS data, it is often neglected. Here, we address practically the quality assessment of quantitative MS data, describing key steps for the evaluation, including the levels of raw data, identification and quantification. With this, four independent datasets from cerebrospinal fluid, an important biofluid for neurodegenerative disease biomarker studies, were assessed, demonstrating that sample processing-based differences are already reflected at all three levels but with varying impacts on the quality of the quantitative data. Specifically, we provide guidance to critically interpret the quality of MS data for quantitative proteomics. Moreover, we provide the free and open source quality control tool MaCProQC, enabling systematic, rapid and uncomplicated data comparison of raw data, identification and feature detection levels through defined quality metrics and a step-by-step quality control workflow.
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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] [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.
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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
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Wang J, Wang X, Li J, Xia Y, Gao M, Zhang X, Huang LH. A novel hydrophilic MOFs-303-functionalized magnetic probe for the highly efficient analysis of N-linked glycopeptides. J Mater Chem B 2022; 10:2011-2018. [PMID: 35244662 DOI: 10.1039/d1tb02827h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effective analysis of glycoproteomics in clinical complex samples is of vital importance for the diagnosis and therapy of diseases. In this study, a hydrophilic MOFs-303-functionalized magnetic probe (GO@Fe3O4@MOF-303) is designed and fabricated to profile N-linked glycopeptides. Owing to its strong magnetic property, large surface area (845 m2 g-1), excellent hydrophilicity and suitable porous structure, the GO@Fe3O4@MOF-303 probe exhibits an ultralow detection limit (0.1 fmol μL-1), perfect size-exclusion effect (HRP digests/BSA protein/HRP protein, 1 : 1000 : 1000, w/w/w), a high binding capacity (200 mg g-1) and excellent reusability in the capture of standard N-linked glycopeptides. More excitingly, the GO@Fe3O4@MOF-303 probe also shows remarkable performance in practical applications, where 274 N-linked glycopeptides from 101 glycoproteins were identified in total for healthy controls, while a total of 265 N-linked glycopeptides from 102 glycoproteins were identified in serum (1 μL) with hepatocellular carcinoma (HCC). In addition, we discovered 4 up-regulated and 19 down-regulated serum glycoproteins in HCC patients by the hierarchical clustering heatmap. All results demonstrated that the reusable GO@Fe3O4@MOF-303 probe has great potential in profiling different N-linked glycopeptides in complex clinical samples. This study not only developed a novel probe for the highly effective capture of N-linked glycopeptides but also contributed to further understanding the mechanism of HCC and provides guidance for the development of novel clinical diagnostic methods.
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Affiliation(s)
- Jiaxi Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China. .,Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Xinmei Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Jie Li
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Yan Xia
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Mingxia Gao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Xiangmin Zhang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Li-Hao Huang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
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Xie S, Zhang C, Zhao J, Li D, Chen J. Exposure to concentrated ambient PM 2.5 (CAPM) induces intestinal disturbance via inflammation and alternation of gut microbiome. ENVIRONMENT INTERNATIONAL 2022; 161:107138. [PMID: 35176574 DOI: 10.1016/j.envint.2022.107138] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 05/21/2023]
Abstract
Air pollution causes a great disease burden worldwide. Recent evidences suggested that PM2.5 contributes to intestinal disease. The objective of present study was to investigate the influence of ambient PM2.5 on intestinal tissue and microbiome via whole-body inhalation exposure. The results showed that high levels and prolonged periods exposure to concentrated ambient PM2.5 (CAPM) could destroy the mucous layer of the colon, and significantly alter the mRNA expression of tight junction (Occludin and ZO-1) and inflammation-related (IL-6, IL-10 and IL-1β) genes in the colon, comparing with exposure to the filtered air (FA). The composition of intestinal microbiome at the phylum and genus levels also varied along with the exposure time and PM2.5 levels. At the phylum level, Bacteroidetes was greatly decreased, while Proteobacteria was increased after exposure to CAPM, comparing with exposure to FA. At the genus level, Clostridium XlVa, Akkermansia and Acetatifactor, were significantly elevated exposure to CAPM, comparing with exposure to FA. Our results also indicated that high levels and prolonged periods exposure to CAPM altered metabolic functional pathways. The correlation analysis showed that the intestinal inflammation was related to the alteration of gut microbiome induced by CAPM exposure, which may be a potential mechanism that elucidates PM2.5-induced intestinal diseases. These results extend our knowledge on the toxicology and health effects of ambient PM2.5.
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Affiliation(s)
- Shanshan Xie
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Caihong Zhang
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Jinzhuo Zhao
- Department of Environmental Health, School of Public Health and the Key Laboratory of Public Health Safety, Fudan University, Shanghai 200032, China.
| | - Dan Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Institute of Atmospheric Sciences, Fudan University, Shanghai, China.
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
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