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Liang W, Zhu Z, Zheng C. Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:93-106. [PMID: 39192122 DOI: 10.1007/978-1-0716-4108-8_11] [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] [Indexed: 08/29/2024]
Abstract
As an interferon-stimulating factor protein, STING plays a role in the response and downstream liaison in antiviral natural immunity. Upon viral invasion, the immediate response of STING protein leads to a series of changes in downstream proteins, which ultimately leads to an antiviral immune response in the form of proinflammatory cytokines and type I interferons, thus triggering an innate immune response, an adaptive immune response in vivo, and long-term protection of the host. In the field of antiviral natural immunity, it is particularly important to rigorously and sequentially probe the dynamic changes in the antiviral natural immunity connector protein STING caused by the entire anti-inflammatory and anti-pathway mechanism and the differences in upstream and downstream proteins. Traditionally, proteomics technology has been validated by detecting proteins in a 2D platform, for which it is difficult to sensitively identify changes in the nature and abundance of target proteins. With the development of mass spectrometry (MS) technology, MS-based proteomics has made important contributions to characterizing the dynamic changes in the natural immune proteome induced by viral infections. MS analytical techniques have several advantages, such as high throughput, rapidity, sensitivity, accuracy, and automation. The most common techniques for detecting complex proteomes are liquid chromatography (LC) and mass spectrometry (MS). LC-MS (Liquid Chromatography-Mass Spectrometry), which combines the physical separation capability of LC and the mass analysis capability of MS, is a powerful technique mainly used for analyzing the proteome of cells, tissues, and body fluids. To explore the combination of traditional proteomics techniques such as Western blotting, Co-IP (co-Immunoprecipitation), and the latest LC-MS methods to probe the anti-inflammatory pathway and the differential changes in upstream and downstream proteins induced by the antiviral natural immune junction protein STING.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
| | - Zhenpeng Zhu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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Wei W, Xie Z, Yan J, Luo R, He J. Progress in research on induced sputum in asthma: a narrative review. J Asthma 2024:1-16. [PMID: 39290080 DOI: 10.1080/02770903.2024.2395383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/01/2024] [Accepted: 08/18/2024] [Indexed: 09/19/2024]
Abstract
OBJECTIVE To explore the clinical significance of induced sputum in asthma through a retrospective analysis of induced sputum in patients with asthma. DATA SOURCES The data and references cited in this article were obtained from PubMed, Sci-Hub, and Web of Science. STUDY SELECTION Observational studies with reliable data were selected. CONCLUSIONS The cytological count, -omics, and pathogen detection of induced sputum are helpful for the clinical diagnosis of asthma and in guiding medication choices.
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Affiliation(s)
- Wenjie Wei
- Department of Respiratory and Critical Care Medicine, Hunan University of Medicine General Hospital, Huaihua, People's Republic of China
| | - Zhihao Xie
- Pediatric Department, The First Affiliated Hospital of Hunan University of Medicine, Huaihua, People's Republic of China
| | - Jun Yan
- Pediatric Department, The First Affiliated Hospital of Hunan University of Medicine, Huaihua, People's Republic of China
| | - Renrui Luo
- Department of Respiratory and Critical Care Medicine, Hunan University of Medicine General Hospital, Huaihua, People's Republic of China
| | - Jianbin He
- Department of Respiratory and Critical Care Medicine, Hunan University of Medicine General Hospital, Huaihua, People's Republic of China
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Guo D, Dong Y, Li H, Li H, Yang B. Proteomics and digital subtraction angiography approaches reveal CDH18 as a potential target for therapy of moyamoya disease. Biol Direct 2024; 19:76. [PMID: 39238003 PMCID: PMC11378584 DOI: 10.1186/s13062-024-00522-w] [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: 05/30/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024] Open
Abstract
Moyamoya disease, characterized by basal cerebral artery obstruction, was studied for differential protein expression to elucidate its pathogenesis. Proteomic analysis of cerebrospinal fluid from 10 patients, categorized by postoperative angiography into good and poor prognosis groups, revealed 46 differentially expressed proteins. Notably, cadherin 18 (CDH18) was the most significantly upregulated in the good prognosis group. In addition, the expression of cadherin 18 (CDH18) and phenotypic transformation-related proteins were measured by qRT-PCR and western blot. The effects of CDH18 in vascular smooth muscle cells were detected by CCK-8, EdU, transwell and wound healing assays. The overexpression of CDH18 in vascular smooth muscle cells (VSMCs) was found to inhibit proliferation, migration, and phenotypic transformation. These findings suggest CDH18 as a potential therapeutic target in moyamoya disease.
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Affiliation(s)
- Dong Guo
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yang Dong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Hongbin Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hongwei Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.
| | - Bo Yang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.
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Huang R, Gong S, Xiong B, Yang X, Chen C, Song W, Wu R, Yang L, Yin J, Chen M. A classic prescription alleviates inflammation in CUMS model mice via modulating MYDGF/MAP4K4/NF-κB signaling pathway, verified through UPLC-HRMS and proteomics analysis. Heliyon 2024; 10:e34596. [PMID: 39114061 PMCID: PMC11305300 DOI: 10.1016/j.heliyon.2024.e34596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Background Xiaoyaosan (XYS), a renowned classical traditional Chinese medicinal formula utilized in addressing major depressive disorder (MDD), has garnered significant acclaim for its remarkable efficacy in clinical application. The onset of major depressive disorder (MDD) often correlates with chronic unpredictable mild stress (CUMS), a pivotal instigating factor in its development.Aim of the study: This study aims to clarify the potential anti-inflammatory mechanisms of XYS in treating CUMS model mice. Materials and methods Utilizing cutting-edge ultra high-performance liquid chromatography - high-resolution mass spectrometry (UPLC-HRMS), the active constituents of XYS were discerned, while employing proteomics analysis to delve into the potential mechanisms of its efficacy. Molecular docking studies, alongside subsequent in vivo experiments utilizing CUMS model mice, were conducted to corroborate the findings derived from the proteomics analysis. Results In vivo experiments demonstrated that XYS not only markedly ameliorated behavioral markers but also attenuated serum inflammatory markers and suppressed IL-6 and TNF-α expression within the brains of CUMS model mice. Proteomics analysis suggested that the pivotal anti-inflammatory mechanism of XYS against CUMS-induced damage might involve modulation of the MAPK signaling pathway. Utilizing UPLC-HRMS, the active constituents of XYS were successfully identified, while molecular docking investigations explored interactions between XYS and MYDGF, PKC, MAP4K4, P-p65, p65, P-IKBα, and IKBα. The findings revealed XYS's regulatory influence on the MYDGF/MAP4K4/NF-κB signaling cascade. Conclusions This study is the first to our knowledge to demonstrate that XYS can alleviate inflammation in CUMS model mice by modulating the MYDGF/MAP4K4/NF-κB signaling pathway.
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Affiliation(s)
- Ruolan Huang
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Shenzhen University General Hospital, Clinical Research Center for Neurological Diseases, Shenzhen University, Shenzhen, Guangdong, China
| | - Shenglan Gong
- Department of Cardiovascular Disease, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- Sixth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Bocheng Xiong
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Chongyang Chen
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, China
| | - Wei Song
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ruodai Wu
- Shenzhen University General Hospital, Clinical Research Center for Neurological Diseases, Shenzhen University, Shenzhen, Guangdong, China
| | - Li Yang
- Shenzhen University General Hospital, Clinical Research Center for Neurological Diseases, Shenzhen University, Shenzhen, Guangdong, China
| | - Jia Yin
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mingtai Chen
- Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao, China
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Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 PMCID: PMC11220622 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
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Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
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Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
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Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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7
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Yang J, Zhou Y, Wang T, Li N, Chao Y, Gao S, Zhang Q, Wu S, Zhao L, Dong X. A multi-omics study to monitor senescence-associated secretory phenotypes of Alzheimer's disease. Ann Clin Transl Neurol 2024; 11:1310-1324. [PMID: 38605603 DOI: 10.1002/acn3.52047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 04/13/2024] Open
Abstract
OBJECTIVE Alzheimer's disease (AD) is characterized by the progressive degeneration and damage of neurons in the brain. However, developing an accurate diagnostic assay using blood samples remains a challenge in clinic practice. The aim of this study was to explore senescence-associated secretory phenotypes (SASPs) in peripheral blood using mass spectrometry based multi-omics approach and to establish diagnostic assays for AD. METHODS This retrospective study included 88 participants, consisting of 29 AD patients and 59 cognitively normal (CN) individuals. Plasma and serum samples were examined using high-resolution mass spectrometry to identify proteomic and metabolomic profiles. Receiver operating characteristic (ROC) analysis was employed to screen biomarkers with diagnostic potential. K-nearest neighbors (KNN) algorithm was utilized to construct a multi-dimensional model for distinguishing AD from CN. RESULTS Proteomics analysis revealed upregulation of five plasma proteins in AD, including RNA helicase aquarius (AQR), zinc finger protein 587B (ZNF587B), C-reactive protein (CRP), fibronectin (FN1), and serum amyloid A-1 protein (SAA1), indicating their potential for AD classification. Interestingly, KNN-based three-dimensional model, comprising AQR, ZNF587B, and CRP, demonstrated its high accuracy in AD recognition, with evaluation possibilities of 0.941, 1.000, and 1.000 for the training, testing, and validation datasets, respectively. Besides, metabolomics analysis suggested elevated levels of serum phenylacetylglutamine (PAGIn) in AD. INTERPRETATION The multi-omics outcomes highlighted the significance of the SASPs, specifically AQR, ZNF587B, CRP, and PAGIn, in terms of their potential for diagnosing AD and suggested neuronal aging-associated pathophysiology.
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Affiliation(s)
- Jingzhi Yang
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Yinge Zhou
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Tianjiao Wang
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Na Li
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Yufan Chao
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Songyan Gao
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Qun Zhang
- Department of Internal Medicine, Shanghai Baoshan Elderly Nursing Hospital, Shanghai, 200435, China
| | - Shuo Wu
- Neurology Department, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China
| | - Liang Zhao
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China
| | - Xin Dong
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- School of Medicine, Shanghai University, Shanghai, 200444, China
- Suzhou Innovation Center of Shanghai University, Suzhou, 215000, Jiangsu, China
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Zhao X, Ma R, Abulikemu A, Qi Y, Liu X, Wang J, Xu K, Guo C, Li Y. Proteomics revealed composition- and size-related regulators for hepatic impairments induced by silica nanoparticles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:170584. [PMID: 38309355 DOI: 10.1016/j.scitotenv.2024.170584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
Along with the growing production and application of silica nanoparticles (SiNPs), increased human exposure and ensuing safety evaluation have progressively attracted concern. Accumulative data evidenced the hepatic injuries upon SiNPs inhalation. Still, the understanding of the hepatic outcomes resulting from SiNPs exposure, and underlying mechanisms are incompletely elucidated. Here, SiNPs of two sizes (60 nm and 300 nm) were applied to investigate their composition- and size-related impacts on livers of ApoE-/- mice via intratracheal instillation. Histopathological and biochemical analysis indicated SiNPs promoted inflammation, lipid deposition and fibrosis in the hepatic tissue, accompanied by increased ALT, AST, TC and TG. Oxidative stress was activated upon SiNPs stimuli, as evidenced by the increased hepatic ROS, MDA and declined GSH/GSSG. Of note, these alterations were more dramatic in SiNPs with a smaller size (SiNPs-60) but the same dosage. LC-MS/MS-based quantitative proteomics unveiled changes in mice liver protein profiles, and filtered out particle composition- or size-related molecules. Interestingly, altered lipid metabolism and oxidative damage served as two critical biological processes. In accordance with correlation analysis and liver disease-targeting prediction, a final of 10 differentially expressed proteins (DEPs) were selected as key potential targets attributable to composition- (4 molecules) and size-related (6 molecules) liver impairments upon SiNPs stimuli. Overall, our study provided strong laboratory evidence for a comprehensive understanding of the harmful biological effects of SiNPs, which was crucial for toxicological evaluation to ensure nanosafety.
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Affiliation(s)
- Xinying Zhao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Ru Ma
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Alimire Abulikemu
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yi Qi
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Xiaoying Liu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Ji Wang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Kun Xu
- School of Medicine, Hunan Normal University, Changsha, Hunan 410013, China
| | - Caixia Guo
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China; Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Yanbo Li
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
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Dai Q, Zhao S, Li W, Liu K, Tao X, Liu C, Yao H, Mu F, Chen S, Li J, Wei P, Gao F, Xi M. Pharmacodynamics and Mechanism of Astragali Radix and Anemarrhenae Rhizoma in Treating Chronic Heart Failure by Inhibiting Complement Activation. Rejuvenation Res 2024; 27:61-74. [PMID: 38386515 DOI: 10.1089/rej.2023.0068] [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] [Indexed: 02/24/2024] Open
Abstract
Astragali radix (AR) and anemarrhenae rhizoma (AAR) are used clinically in Chinese medicine for the treatment of chronic heart failure (CHF), but the exact therapeutic mechanism is unclear. In this study, a total of 60 male C57BL/6 mice were divided into 5 groups, namely sham, model, AR, AAR, and AR-AAR. In the sham group, the chest was opened without ligation. In the other groups, the chest was opened and the transverse aorta was ligated to construct the transverse aortic constriction model. After 8 weeks of feeding, mice were given medicines by gavage for 4 weeks. Left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) were detected by echocardiography. Heart weight index (HWI) and wheat germ agglutinin staining were used to evaluate cardiac hypertrophy. Hematoxylin-eosin staining was used to observe the pathological morphology of myocardial tissue. Masson staining was used to evaluate myocardial fibrosis. The content of serum brain natriuretic peptide (BNP) was detected by enzyme-linked immunosorbent assay kit. The content of serum immunoglobulin G (IgG) was detected by immunoturbidimetry. The mechanism of AR-AAR in the treatment of CHF was explored by proteomics. Western blot was used to detect the protein expressions of complement component 1s (C1s), complement component 9 (C9), and terminal complement complex 5b-9 (C5b-9). The results show that AR-AAR inhibits the expression of complement proteins C1s, C9, and C5b-9 by inhibiting the production of IgG antibodies from B cell activation, which further inhibits the complement activation, attenuates myocardial fibrosis, reduces HWI and cardiomyocyte cross-sectional area, improves cardiomyocyte injury, reduces serum BNP release, elevates LVEF and LVFS, improves cardiac function, and exerts myocardial protection.
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Affiliation(s)
- Qi Dai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
| | - Shi Zhao
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
| | - Weihong Li
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
- College of Life Sciences, Northwestern University, Xi'an, China
| | - Kedi Liu
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
| | - Xingru Tao
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chengzhao Liu
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
| | - Hong Yao
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
| | - Fei Mu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Sha Chen
- YouYi Clinical Laboratories of Shaanxi, Xi'an, China
| | - Jing Li
- YouYi Clinical Laboratories of Shaanxi, Xi'an, China
| | - Peifeng Wei
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
- National Drug Clinical Trial Institute, The Second Affiliated Hospital, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Feng Gao
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Miaomiao Xi
- TANK Medicinal Biology Institute of Xi'an, Xi'an, China
- National Drug Clinical Trial Institute, The Second Affiliated Hospital, Shaanxi University of Chinese Medicine, Xi'an, China
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Wang L, Tian S, Ruan S, Wei J, Wei S, Chen W, Hu H, Qin W, Li Y, Yuan H, Mao J, Xu Y, Xie J. Neuroprotective effects of cordycepin on MPTP-induced Parkinson's disease mice via suppressing PI3K/AKT/mTOR and MAPK-mediated neuroinflammation. Free Radic Biol Med 2024; 216:60-77. [PMID: 38479634 DOI: 10.1016/j.freeradbiomed.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024]
Abstract
Parkinson's disease (PD) is a prevalent progressive and multifactorial neurodegenerative disorder. Cordycepin is known to exhibit antitumor, anti-inflammatory, antioxidative stress, and neuroprotective effects; however, few studies have explored the neuroprotective mechanism of cordycepin in PD. Using a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model, we investigated the impact of cordycepin on PD and its underlying molecular mechanisms. The findings indicated that cordycepin significantly mitigated MPTP-induced behavior disorder and neuroapoptosis, diminished the loss of dopaminergic neurons in the striatum-substantia nigra pathway, elevated striatal monoamine levels and its metabolites, and inhibited the polarization of microglia and the expression of pro-inflammatory factors. Subsequent proteomic and phosphoproteomic analyses revealed the involvement of the MAPK, mTOR, and PI3K/AKT signaling pathways in the protective mechanism of cordycepin. Cordycepin treatment inhibited the activation of the PI3K/AKT/mTOR signaling pathway and enhanced the expression of autophagy proteins in the striatum and substantia nigra. We also demonstrated the in vivo inhibition of the ERK/JNK signaling pathway by cordycepin treatment. In summary, our investigation reveals that cordycepin exerts neuroprotective effects against PD by promoting autophagy and suppressing neuroinflammation and neuronal apoptosis by inhibiting the PI3K/AKT/mTOR and ERK/JNK signaling pathways. This finding highlights the favorable characteristics of cordycepin in neuroprotection and provides novel molecular insights into the neuroprotective role of natural products in PD.
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Affiliation(s)
- Linhai Wang
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China; Beijing Life Science Academy (BLSA), Beijing, China.
| | - Shu Tian
- Inner Mongolia Kunming Cigarette Limited Liability Company, Huhhot, Inner Mongolia Autonomous Region, China.
| | - Sisi Ruan
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China; Beijing Life Science Academy (BLSA), Beijing, China.
| | - Jingjing Wei
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China; Beijing Life Science Academy (BLSA), Beijing, China.
| | - Sijia Wei
- Xinxiang Central Hospital, Xinxiang, Hennan, China.
| | - Weiwei Chen
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Hangcui Hu
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Weiwei Qin
- Department of Neurology, State Key Clinical Specialty of the Ministry of Health for Neurology, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
| | - Yan Li
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China.
| | - Hang Yuan
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China.
| | - Jian Mao
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China; Beijing Life Science Academy (BLSA), Beijing, China.
| | - Yan Xu
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Jianping Xie
- Flavour Science Research Center, College of Chemistry, Zhengzhou University, Zhengzhou, China; Beijing Life Science Academy (BLSA), Beijing, China.
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11
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Jang B, Yoon D, Lee JY, Kim J, Hong J, Koo H, Sa JK. Integrative multi-omics characterization reveals sex differences in glioblastoma. Biol Sex Differ 2024; 15:23. [PMID: 38491408 PMCID: PMC10943869 DOI: 10.1186/s13293-024-00601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common and lethal primary brain tumor in adults, with limited treatment modalities and poor prognosis. Recent studies have highlighted the importance of considering sex differences in cancer incidence, prognosis, molecular disparities, and treatment outcomes across various tumor types, including colorectal adenocarcinoma, lung adenocarcinoma, and GBM. METHODS We performed comprehensive analyses of large-scale multi-omics data (genomic, transcriptomic, and proteomic data) from TCGA, GLASS, and CPTAC to investigate the genetic and molecular determinants that contribute to the unique clinical properties of male and female GBM patients. RESULTS Our results revealed several key differences, including enrichments of MGMT promoter methylation, which correlated with increased overall and post-recurrence survival and improved response to chemotherapy in female patients. Moreover, female GBM exhibited a higher degree of genomic instability, including aneuploidy and tumor mutational burden. Integrative proteomic and phosphor-proteomic characterization uncovered sex-specific protein abundance and phosphorylation activities, including EGFR activation in males and SPP1 hyperphosphorylation in female patients. Lastly, the identified sex-specific biomarkers demonstrated prognostic significance, suggesting their potential as therapeutic targets. CONCLUSIONS Collectively, our study provides unprecedented insights into the fundamental modulators of tumor progression and clinical outcomes between male and female GBM patients and facilitates sex-specific treatment interventions. Highlights Female GBM patients were characterized by increased MGMT promoter methylation and favorable clinical outcomes compared to male patients. Female GBMs exhibited higher levels of genomic instability, including aneuploidy and TMB. Each sex-specific GBM is characterized by unique pathway dysregulations and molecular subtypes. EGFR activation is prevalent in male patients, while female patients are marked by SPP1 hyperphosphorylation.
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Affiliation(s)
- Byunghyun Jang
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Dayoung Yoon
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Ji Yoon Lee
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Jiwon Kim
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Jisoo Hong
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Harim Koo
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, South Korea
- Department of Clinical Research, Research Institute and Hospital, National Cancer Center, Goyang, South Korea
| | - Jason K Sa
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, South Korea.
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea.
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12
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Qiao Z, Liao M, Xiao M, Luo S, Wang K, Niu M, Jiang H, Sun S, Xu G, Xu N, Xu Q, Liu Y. Ephrin B3 exacerbates colitis and colitis-associated colorectal cancer. Biochem Pharmacol 2024; 220:116004. [PMID: 38142837 DOI: 10.1016/j.bcp.2023.116004] [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: 08/07/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Ephrin B3, a member of Eph/ephrin family, contributes to embryogenesis and carcinogenesis, but few studies have suggested whether this ligand has regulatory effect on colitis. This study was to determine whether ephrin B3 played a role in colitis and colonic carcinogenesis. Dextran sodium sulfate (DSS)-induced colitis and azoxymethane (AOM)/DSS-induced colitis-associated carcinogenesis model was established in Efnb3-deficient (Efnb3-/-) mice. Label-free quantitative proteomics were performed to identify the Efnb3-regulated proteins. Our results showed that Efnb3 knock out reduced the symptoms of DSS-induced colitis, such as disease activity index (DAI), inflammatory factors release, and dysfunction of the intestinal barrier. Quantitative proteomics revealed that Efnb3 regulated 95 proteins which clustered in the platelet degranulation, response to elevated platelet cytosolic Ca2+, MAPK signaling for integrins such as ITGB4. Furthermore, ephrin B3 inactived ITGB4/AKT signal pathway and then promoted epithelial barrier dysfunction. Simultaneously, ephrin B3 promoted Gremlin-1/NF-κB signal pathway and thereby increased inflammatory factors release. In addition, the higher level of Efnb3 in colon cancer patients is correlated with worse survival. Efnb3-/- mice exhibited susceptibility to AOM/DSS-induced colorectal cancer. Our finding discovered that Efnb3 played an important role in the development of colitis and colitis-associated colorectal cancer. Efnb3 deficiency improved the intestinal barrier by ITGB4 and suppressed inflammation via Gremlin-1/NF-κB signal pathway, which may provide a novel therapeutic strategy for the treatment of colitis and colitis-associated colorectal cancer.
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Affiliation(s)
- Zhen Qiao
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Min Liao
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Mingyue Xiao
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Saiyan Luo
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kexin Wang
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Mengxin Niu
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Honglv Jiang
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Suya Sun
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Anatomy, Histology and Embryology, Neuroscience Division, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guoqiang Xu
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - NanJie Xu
- Department of Anatomy, Histology and Embryology, Neuroscience Division, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qiongming Xu
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yanli Liu
- Department of Pharmacognosy, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
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13
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Shi Y, Chen J, Cai L, Zhang X, Chen Z, Yang J, Jiang Y, Lu Y. Uncovering the Hidden World of Aqueous Humor Proteins for Discovery of Biomarkers for Marfan Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303161. [PMID: 38088571 PMCID: PMC10853735 DOI: 10.1002/advs.202303161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Ectopia lentis is a hallmark of Marfan syndrome (MFS), a genetic connective tissue disorder affecting 1/5000 to 1/10 000 individuals worldwide. Early detection in ophthalmology clinics and timely intervention of cardiovascular complications can be lifesaving. In this study, a modified proteomics workflow with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based data-independent acquisition (DIA) and field asymmetric ion mobility spectrometry (FAIMS) to profile the proteomes of aqueous humor (AH) and lens tissue from MFS children with ectopia lentis is utilized. Over 2300 and 2938 comparable proteins are identified in AH and the lens capsule, respectively. Functional enrichment analyses uncovered dysregulation of complement and coagulation-related pathways, collagen binding, and cell adhesion in MFS. Through weighted correlation network analysis (WGCNA) and machine learning, distinct modules associated with clinical traits are constructed and a unique biomarker panel (Q14376, Q99972, P02760, Q07507; gene names: GALE, MYOC, AMBP, DPT) is defined. These biomarkers are further validated using advanced parallel reaction monitoring (PRM) in an independent patient cohort. The results provide novel insights into the proteome characterization of ectopia lentis and offer a promising approach for developing a valuable biomarker panel to aid in the early diagnosis of Marfan syndrome via AH proteome.
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Affiliation(s)
- Yumeng Shi
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jiahui Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Lei Cai
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Xueling Zhang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Zexu Chen
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Jin Yang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yongxiang Jiang
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
| | - Yi Lu
- Eye Institute and Department of Ophthalmology, Eye and ENT HospitalFudan UniversityShanghai200031China
- NHC Key Laboratory of MyopiaFudan UniversityShanghai200031China
- Key Laboratory of MyopiaChinese Academy of Medical SciencesShanghai200031China
- Shanghai Key Laboratory of Visual Impairment and RestorationShanghai200031China
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14
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Meng XL, Yuan PB, Wang XJ, Hang J, Shi XM, Zhao YY, Wei Y. The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1246-1259. [PMID: 37121272 PMCID: PMC11082409 DOI: 10.1016/j.gpb.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 05/02/2023]
Abstract
In perinatal medicine, intrauterine growth restriction (IUGR) is one of the greatest challenges. The etiology of IUGR is multifactorial, but most cases are thought to arise from placental insufficiency. However, identifying the placental cause of IUGR can be difficult due to numerous confounding factors. Selective IUGR (sIUGR) would be a good model to investigate how impaired placentation affects fetal development, as the growth discordance between monochorionic twins cannot be explained by confounding genetic or maternal factors. Herein, we constructed and analyzed the placental proteomic profiles of IUGR twins and normal cotwins. Specifically, we identified a total of 5481 proteins, of which 233 were differentially expressed (57 up-regulated and 176 down-regulated) in IUGR twins. Bioinformatics analysis indicates that these differentially expressed proteins (DEPs) are mainly associated with cardiovascular system development and function, organismal survival, and organismal development. Notably, 34 DEPs are significantly enriched in angiogenesis, and diminished placental angiogenesis in IUGR twins has been further elaborately confirmed. Moreover, we found decreased expression of metadherin (MTDH) in the placentas of IUGR twins and demonstrated that MTDH contributes to placental angiogenesis and fetal growth in vitro. Collectively, our findings reveal the comprehensive proteomic signatures of placentas for sIUGR twins, and the DEPs identified may provide in-depth insights into the pathogenesis of placental dysfunction and subsequent impaired fetal growth.
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Affiliation(s)
- Xin-Lu Meng
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Peng-Bo Yuan
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Xue-Ju Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Beijing 100191, China
| | - Xiao-Ming Shi
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yang-Yu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.
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15
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Zhang X, Li X, Xiong X. Applying proteomics in metabolic dysfunction-associated steatotic liver disease: From mechanism to biomarkers. Clin Res Hepatol Gastroenterol 2023; 47:102230. [PMID: 37931846 DOI: 10.1016/j.clinre.2023.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD), which represents the most common cause of liver disease, is emerging as a major health problem around the world. However, the molecular events that underline the pathogenesis and the progression of MASLD remain to be fully elucidated. Advanced stages of MASLD is strongly associated with liver-related outcomes and overall mortality. Despite this, highly accurate, sensitive, and non-invasive diagnostic tools are currently not aviailable, yet no FDA approved drugs for MASLD. The advance of proteomics has enable the study of protein expression, post-translational modifications (PTMs), subcellular distribution, and interactions. In this review, we discuss insights gained from the recent proteomics studies that shed new light on the pathogenesis, diagnosis and potential theraputic targets of MASLD.
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Affiliation(s)
- Xiaofu Zhang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, 180 Fenlin Road, Xuhui District, Shanghai 200032, China
| | - Xiaoying Li
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, 180 Fenlin Road, Xuhui District, Shanghai 200032, China
| | - Xuelian Xiong
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, 180 Fenlin Road, Xuhui District, Shanghai 200032, China.
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16
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Wang Y, Sun Y, Wang Y, Jia S, Qiao Y, Zhou Z, Shao W, Zhang X, Guo J, Zhang B, Niu X, Wang Y, Peng D. Identification of novel diagnostic panel for mild cognitive impairment and Alzheimer's disease: findings based on urine proteomics and machine learning. Alzheimers Res Ther 2023; 15:191. [PMID: 37925455 PMCID: PMC10625308 DOI: 10.1186/s13195-023-01324-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Alzheimer's disease is a prevalent disease with a heavy global burden. Proteomics is the systematic study of proteins and peptides to provide comprehensive descriptions. Aiming to obtain a more accurate and convenient clinical diagnosis, researchers are working for better biomarkers. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels. METHODS We firstly enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples, and conducted an LC-MS/MS analysis. In parallel, clinical data were collected, and clinical examinations were performed. After statistical and bioinformatics analyses, significant risk factors and differential urinary proteins were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM. RESULTS Fifty-seven AD patients, 43 MCI patients, and 62 CN subjects were enrolled. A total of 3366 proteins were identified, and 608 urine proteins were finally included in the analysis. There were 33 significantly differential proteins between the AD and CN groups and 15 significantly differential proteins between the MCI and CN groups. AD diagnostic panel included DDC, CTSC, EHD4, GSTA3, SLC44A4, GNS, GSTA1, ANXA4, PLD3, CTSH, HP, RPS3, CPVL, age, and APOE ε4 with an AUC of 0.9989 in the training test and 0.8824 in the test set while MCI diagnostic panel included TUBB, SUCLG2, PROCR, TCP1, ACE, FLOT2, EHD4, PROZ, C9, SERPINA3, age, and APOE ε4 with an AUC of 0.9985 in the training test and 0.8143 in the test set. Besides, diagnostic proteins were weakly correlated with cognitive functions. CONCLUSIONS In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN.
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Affiliation(s)
- Yuye Wang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Sun
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Shuhong Jia
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yanan Qiao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zhi Zhou
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Wen Shao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiangfei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Guo
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Bin Zhang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaoqian Niu
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dantao Peng
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China.
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
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17
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Gao C, Ni B, Lu X, Guo C, Wei G. An integrated investigation of 16S rRNA gene sequencing and proteomics to elucidate the mechanism of Corydalis bungeana Turcz. on dextran sulfate sodium-induced colitis. Biomed Pharmacother 2023; 167:115550. [PMID: 37741254 DOI: 10.1016/j.biopha.2023.115550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023] Open
Abstract
Corydalis bungeana Turcz. (CBT) is frequently used to treat inflammatory illnesses, the mechanisms underlying its use to ulcerative colitis (UC) remain unclear. A dextran sulfate sodium (DSS)-induced UC mice model was established. The disease activity index (DAI), colonic length, histological inspection by hematoxylin-eosin staining, the cytokines levels in the colon, proteomics and intestinal flora in mice were investigated to evaluate the effect of CBT. The results showed that CBT can significantly reduce the DAI, increase the length of colon, improve the pathological injury of colon tissue, decrease the level of TNF-α, IL-6, IL-1β and increase the level of IL-10 in UC mice. Gut microbe sequencing showed that CBT could enhance the abundance of the intestinal microbiome, decrease possibly harmful bacteria and promote potentially helpful microbes. Proteomics investigation showed that 20 overlapping differentially expressed proteins (DEPs) were discovered in the control, model, and CBT administration groups. The DEPs in the CBT administration group were connected to biological procedures mainly involving detoxification. Extracellular matrix (ECM) receptor-associated proteins such as Col6a1 and CD36 may be important targets for CBT treatment of UC. Overall, this integrated methodology identified a comprehensive multi-omics network, composed of a certain set of gut microbiota and proteins, which may be potential targets for CBT treatment with UC.
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Affiliation(s)
- Chang Gao
- Department of pharmacy, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, Jiangxi, China; Ganzhou Key Laboratory of Immunotherapeutic Drugs Developing for Childhood Leukemia, Ganzhou 341000, Jiangxi, China; Ganzhou Key Laboratory of Antitumor Drugs Developing of Natural Drugs, Ganzhou 341000, Jiangxi, China.
| | - Bin Ni
- Department of pharmacy, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, Jiangxi, China
| | - Xiaolu Lu
- Gannan Medical University, Ganzhou 341000, Jiangxi, China
| | - Chunyu Guo
- Department of pharmacy, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, Jiangxi, China
| | - Guilin Wei
- Department of pharmacy, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, Jiangxi, China.
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18
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Yang L, Xie F, Li Y, Lu Y, Li B, Hong S, Tang J, Liu J, Cheng J, He Y, Zhang Z, Zhang S, Chen M, Li L, Yao L, Yan S, Cai J, Hong L. Chitin-based hydrogel loaded with bFGF and SDF-1 for inducing endogenous mesenchymal stem cells homing to improve stress urinary incontinence. Carbohydr Polym 2023; 319:121144. [PMID: 37567701 DOI: 10.1016/j.carbpol.2023.121144] [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: 02/14/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 08/13/2023]
Abstract
Nonoperative treatments for Stress Urinary Incontinence (SUI) represent an ideal treatment method. Mesenchymal stem cell (MSCs) treatment is a new modality, but there is a lack of research in the field of gynecological pelvic floor and no good method to induce internal MSC homing to improve SUI. Herein, we develop an injectable and self-healing hydrogel derived from β-chitin which consists of an amino group of quaternized β-chitin (QC) and an aldehyde group of oxidized dextran (OD) between the dynamic Schiff base linkage.it can carry bFGF and SDF-1a and be injected into the vaginal forearm of mice in a non-invasive manner. It provides sling-like physical support to the anterior vaginal wall in the early stages. In the later stage, it slowly releasing factors and promoting the homing of MSCs in vivo, which can improve the local microenvironment, increase collagen deposition, repair the tissue around urethra and finally improve SUI (Scheme 1). This is the first bold attempt in the field of pelvic floor using hydrogel mechanical support combined with MSCs homing and the first application of chitin hydrogel in gynecology. We think the regenerative medicine approach based on bFGF/SDF-1/chitin hydrogel may be an effective non-surgical approach to combat clinical SUI.
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Affiliation(s)
- Lian Yang
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Fang Xie
- College of Chemistry & Molecular Sciences, Wuhan University, Hubei Engineering Center of Natural Polymers-based Medical Materials, Wuhan, 430072, People's Republic of China
| | - Yang Li
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Yiwen Lu
- College of Chemistry & Molecular Sciences, Wuhan University, Hubei Engineering Center of Natural Polymers-based Medical Materials, Wuhan, 430072, People's Republic of China
| | - Bingshu Li
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Shasha Hong
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Jianming Tang
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Jianfeng Liu
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Jianhong Cheng
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Yong He
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Zihui Zhang
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Shufei Zhang
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Mao Chen
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Lu Li
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Lichao Yao
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Sisi Yan
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China
| | - Jie Cai
- College of Chemistry & Molecular Sciences, Wuhan University, Hubei Engineering Center of Natural Polymers-based Medical Materials, Wuhan, 430072, People's Republic of China.
| | - Li Hong
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, Hubei Province 430060, People's Republic of China.
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Ji S, Liu Y, Yan L, Zhang Y, Li Y, Zhu Q, Xia W, Ge S, Zhang J. DIA-based analysis of the menstrual blood proteome identifies association between CXCL5 and IL1RN and endometriosis. J Proteomics 2023; 289:104995. [PMID: 37657716 DOI: 10.1016/j.jprot.2023.104995] [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: 02/16/2023] [Revised: 07/23/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
Endometriosis is a gynecological disease related to menstruation that affects nearly 10% of reproductive-age women. However, so far, there are no reliable diagnostic biomarkers for endometriosis, causing a delay in diagnosis of 6.7 ± 6.2 years. Menstrual blood is a non-invasive source of endometrial tissue that can be analyzed for biomarkers of endometriosis. In this study, menstrual blood samples were collected from women with (n = 8) and without (n = 8) endometriosis. Data Independent Acquisition (DIA)-based mass spectrometry and bioinformatic analysis were used to quantify and identify differentially expressed proteins (DEPs) using the thresholds of fold change >1.5 and P value <0.05. A total of 95 DEPs were identified in menstrual blood from women with endometriosis compared to women without endometriosis, of which 64 were up-regulated and 31 were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to functionally annotate DEPs. Protein-protein interaction (PPI) network analysis was then conducted to identify hub genes and the MCODE plugin placed CXCL1, CXCL3, CXCL5, CCL18, and IL1RN in the most significant cluster network. The expression of the above candidate proteins was confirmed by enzyme-linked immunosorbent assay (ELISA), among which CXCL5 and IL1RN protein expression was increased in patients with endometriosis, indicating that CXCL5 and IL1RN in menstrual blood may be useful biomarkers to diagnose endometriosis from non-invasive samples. SIGNIFICANCE: Endometriosis is a common gynecological disease that causes discomfort in many women. Unfortunately, the diagnosis of endometriosis is frequently delayed due to a lack of reliable non-invasive biomarkers. To our knowledge, this is the first time that DIA-MS was used to characterize the proteome and identify the differentially expressed proteins in menstrual blood from women with endometriosis. The results, as confirmed by ELISA, showed that CXCL5 and IL1RN protein expression is significantly increased in patients with endometriosis, indicating that these proteins can be used as biomarkers for endometriosis. This study contributes to the identification of putative endometriosis biomarkers from non-invasive samples and lays the groundwork for future research into the roles of CXCL5 and IL1RN in the pathogenesis of endometriosis.
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Affiliation(s)
- Sifan Ji
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Yuan Liu
- Department of Pathology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China
| | - Li Yan
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Yiqin Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Yamei Li
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Qian Zhu
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Wei Xia
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China
| | - Shunna Ge
- Department of Central Laboratory, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China.
| | - Jian Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No. 910, Hengshan Rd, Shanghai 200030, China; Shanghai Municipal Key Clinical Specialty, Shanghai 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China.
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20
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Fabregat-Cid G, Cedeño DL, Harutyunyan A, Rodríguez-López R, Monsalve-Dolz V, Mínguez-Martí A, Hernández-Cádiz MJ, Escrivá-Matoses N, Villanueva-Pérez V, Asensio Samper JM, De Andrés J, Vallejo R. Effect of Conventional Spinal Cord Stimulation on Serum Protein Profile in Patients With Persistent Spinal Pain Syndrome: A Case-Control Study. Neuromodulation 2023; 26:1441-1449. [PMID: 37516956 DOI: 10.1016/j.neurom.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/30/2023] [Accepted: 05/30/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Spinal cord stimulation (SCS) provides pain relief for most patients with persistent spinal pain syndrome type 2 (PSPS 2). Evidence is mounting on molecular changes induced by SCS as one of the mechanisms to explain pain improvement. We report the SCS effect on serum protein expression in vivo in patients with PSPS 2. MATERIALS AND METHODS Serum proteins were identified and quantified using mass spectrometry. Proteins with significantly different expression among patients with PSPS 2 relative to controls, responders, and nonresponders to SCS, or significantly modulated by SCS relative to baseline, were identified. Those most correlated with the presence and time course of pain were selected using multivariate discriminant analysis. Bioinformatic tools were used to identify related biological processes. RESULTS Thirty patients with PSPS 2, of whom 23 responded to SCS, were evaluated, together with 14 controls with no pain who also had undergone lumbar spinal surgery. A significant improvement in pain intensity, disability, and quality of life was recorded among responders. Five proteins differed significantly at baseline between patients with PSPS 2 and controls, with three proteins, mostly involved in immune processes and inflammation, being downregulated and two, mostly involved in vitamin metabolism, synaptic transmission, and restorative processes, being upregulated. In addition, four proteins, mostly related to immune processes and inflammation, decreased significantly, and three, mostly related to iron metabolism and containment of synaptic sprouting, increased significantly during SCS. CONCLUSION This study identifies various biological processes that may underlie PSPS 2 pain and SCS therapeutic effects, including the modulation of neuroimmune response and inflammation, synaptic sprouting, vitamin and iron metabolism, and restorative processes.
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Affiliation(s)
- Gustavo Fabregat-Cid
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain; Surgery Department, Medical School, University of Valencia, Valencia, Spain.
| | | | - Anushik Harutyunyan
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain
| | | | - Vicente Monsalve-Dolz
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain
| | - Ana Mínguez-Martí
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain
| | | | | | | | - Juan Marcos Asensio Samper
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain; Surgery Department, Medical School, University of Valencia, Valencia, Spain
| | - José De Andrés
- Multidisciplinary Pain Management Department, University General Hospital, Valencia, Spain; Surgery Department, Medical School, University of Valencia, Valencia, Spain
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Qin G, Wang B, Zhang G, Wu L, Zhu P, Zhang Q. Bikunin: A Promising Prognostic Biomarker for Acute-on-Chronic Liver Failure in Patients with Viral Hepatitis B. Infect Drug Resist 2023; 16:5765-5775. [PMID: 37670978 PMCID: PMC10476654 DOI: 10.2147/idr.s417472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
Purpose To screen out potential prognostic biomarkers for HBV-related acute-on-chronic liver failure (HBV-ACLF). Patients and Methods Peripheral blood samples of HBV-ACLF patients (n=56) and normal controls (n=15) from the Affiliated Hospital of Southwest Medical University from January 2021 to April 2022 were collected, 5 normal patients and 10 patients with ACLF were randomly selected for Data independent acquisition (DIA) mass spectrometry analysis, and the potential core proteins were screened out via bioinformatics. All samples were validated by Enzyme linked immunosorbent assays (ELISA) technology, and the survival curve was constructed based on the patient's 90-day survival time. Results A total of 247 differentially expressed proteins (DEPs) were screened, of which 148 were upregulated and 99 were down-regulated. The DEPs were mainly enriched in high-density lipoprotein particle remodeling, coagulation, and hemostasis and participated in signaling pathways such as cholesterol metabolism, coagulation cascades, and PPAR signaling pathway. Finally, bikunin was selected for further study and validated via the ELISA, compared with the normal group, bikunin was poorly expressed in the HBV-ACLF group, the difference was statistically significant (P < 0.0001), the area under the curve (AUC) for Receiver operating characteristic (ROC) analysis was 0.917. Furthermore, compared with the non-survival group, bikunin was highly expressed in the HBV-ACLF survival group, the difference was statistically significant (P=0.0015), and the survival curve showed a positive correlation with patient survival (P=0.0063). Conclusion The level of plasma bikunin in HBV-ACLF is down-regulated, which is positively correlated with the survival of the patients with HBV-ACLF, and is expected to become a new prognostic biomarker.
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Affiliation(s)
- Gang Qin
- Department of Gastroenterology, Suining First People's Hospital, Suining, People’s Republic of China
| | - Bo Wang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
| | - Geng Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
| | - Lili Wu
- Department of Gastroenterology, Suining First People's Hospital, Suining, People’s Republic of China
| | - Peng Zhu
- Department of Gastroenterology, Suining First People's Hospital, Suining, People’s Republic of China
| | - Qian Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
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Li Y, Tam WW, Yu Y, Zhuo Z, Xue Z, Tsang C, Qiao X, Wang X, Wang W, Li Y, Tu Y, Gao Y. The application of Aptamer in biomarker discovery. Biomark Res 2023; 11:70. [PMID: 37468977 DOI: 10.1186/s40364-023-00510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Biomarkers are detectable molecules that can reflect specific physiological states of cells, organs, and organisms and therefore be regarded as indicators for specific diseases. And the discovery of biomarkers plays an essential role in cancer management from the initial diagnosis to the final treatment regime. Practically, reliable clinical biomarkers are still limited, restricted by the suboptimal methods in biomarker discovery. Nucleic acid aptamers nowadays could be used as a powerful tool in the discovery of protein biomarkers. Nucleic acid aptamers are single-strand oligonucleotides that can specifically bind to various targets with high affinity. As artificial ssDNA or RNA, aptamers possess unique advantages compared to conventional antibodies. They can be flexible in design, low immunogenicity, relative chemical/thermos stability, as well as modifying convenience. Several SELEX (Systematic Evolution of Ligands by Exponential Enrichment) based methods have been generated recently to construct aptamers for discovering new biomarkers in different cell locations. Secretome SELEX-based aptamers selection can facilitate the identification of secreted protein biomarkers. The aptamers developed by cell-SELEX can be used to unveil those biomarkers presented on the cell surface. The aptamers from tissue-SELEX could target intracellular biomarkers. And as a multiplexed protein biomarker detection technology, aptamer-based SOMAScan can analyze thousands of proteins in a single run. In this review, we will introduce the principle and workflow of variations of SELEX-based methods, including secretome SELEX, ADAPT, Cell-SELEX and tissue SELEX. Another powerful proteome analyzing tool, SOMAScan, will also be covered. In the second half of this review, how these methods accelerate biomarker discovery in various diseases, including cardiovascular diseases, cancer and neurodegenerative diseases, will be discussed.
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Affiliation(s)
- Yongshu Li
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
| | - Winnie Wailing Tam
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhenjian Zhuo
- State Key Laboratory of Chemical Oncogenomic, Peking University Shenzhen Graduate School, Shenzhen, China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhichao Xue
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Chiman Tsang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Qiao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaokang Wang
- Department of Pharmacy, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Weijing Wang
- Shantou University Medical College, Shantou, China
| | - Yongyi Li
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yanyang Tu
- Research Center, Huizhou Central People's Hospital, Guangdong Medical University, Huizhou City, China.
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
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Zhou GYJ, Zhao DY, Yin TF, Wang QQ, Zhou YC, Yao SK. Proteomics-based identification of proteins in tumor-derived exosomes as candidate biomarkers for colorectal cancer. World J Gastrointest Oncol 2023; 15:1227-1240. [PMID: 37546562 PMCID: PMC10401461 DOI: 10.4251/wjgo.v15.i7.1227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/28/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the second leading cause of cancer-related death, with high morbidity worldwide. There is an urgent need to find reliable diagnostic biomarkers of CRC and explore the underlying molecular mechanisms. Exosomes are involved in intercellular communication and participate in multiple pathological processes, serving as an important part of the tumor microenvironment.
AIM To investigate the proteomic characteristics of CRC tumor-derived exosomes and to identify candidate exosomal protein markers for CRC.
METHODS In this study, 10 patients over 50 years old who were diagnosed with moderately differentiated adenocarcinoma were recruited. We paired CRC tissues and adjacent normal intestinal tissues (> 5 cm) to form the experimental and control groups. Purified exosomes were extracted separately from each tissue sample. Data-independent acquisition mass spectrometry was implemented in 8 matched samples of exosomes to explore the proteomic expression profiles, and differentially expressed proteins (DEPs) were screened by bioinformatics analysis. Promising exosomal proteins were verified using parallel reaction monitoring (PRM) analysis in 10 matched exosome samples.
RESULTS A total of 1393 proteins were identified in the CRC tissue group, 1304 proteins were identified in the adjacent tissue group, and 283 proteins were significantly differentially expressed between them. Enrichment analysis revealed that DEPs were involved in multiple biological processes related to cytoskeleton construction, cell movement and migration, immune response, tumor growth and telomere metabolism, as well as ECM-receptor interaction, focal adhesion and mTOR signaling pathways. Six differentially expressed exosomal proteins (NHP2, OLFM4, TOP1, SAMP, TAGL and TRIM28) were validated by PRM analysis and evaluated by receiver operating characteristic curve (ROC) analysis. The area under the ROC curve was 0.93, 0.96, 0.97, 0.78, 0.75, and 0.88 (P < 0.05) for NHP2, OLFM4, TOP1, SAMP, TAGL, and TRIM28, respectively, indicating their good ability to distinguish CRC tissues from adjacent intestinal tissues.
CONCLUSION In our study, comprehensive proteomic profiles were obtained for CRC tissue exosomes. Six exosomal proteins, NHP2, OLFM4, TOP1, SAMP, TAGL and TRIM28, may be promising diagnostic markers and effective therapeutic targets for CRC, but further experimental investigation is needed.
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Affiliation(s)
- Ge-Yu-Jia Zhou
- Department of Gastroenterology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Beijing 100029, China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Dong-Yan Zhao
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Teng-Fei Yin
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Qian-Qian Wang
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Yuan-Chen Zhou
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Shu-Kun Yao
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, China
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Gao Z, Zhao Q, Xu Y, Wang L. Improving the efficacy of combined radiotherapy and immunotherapy: focusing on the effects of radiosensitivity. Radiat Oncol 2023; 18:89. [PMID: 37226275 DOI: 10.1186/s13014-023-02278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/08/2023] [Indexed: 05/26/2023] Open
Abstract
Cancer treatment is gradually entering an era of precision, with multitude studies in gene testing and immunotherapy. Tumor cells can be recognized and eliminated by the immune system through the expression of tumor-associated antigens, but when the cancer escapes or otherwise suppresses immunity, the balance between cancer cell proliferation and immune-induced cancer cell killing may be interrupted, resulting in tumor proliferation and progression. There has been significant attention to combining conventional cancer therapies (i.e., radiotherapy) with immunotherapy as opposed to treatment alone. The combination of radio-immunotherapy has been demonstrated in both basic research and clinical trials to provide more effective anti-tumor responses. However, the absolute benefits of radio-immunotherapy are dependent on individual characteristics and not all patients can benefit from radio-immunotherapy. At present, there are numerous articles about exploring the optimal models for combination radio-immunotherapy, but the factors affecting the efficacy of the combination, especially with regard to radiosensitivity remain inconclusive. Radiosensitivity is a measure of the response of cells, tissues, or individuals to ionizing radiation, and various studies have shown that the radiosensitivity index (RSI) will be a potential biomarker for predicting the efficacy of combination radio-immunotherapy. The purpose of this review is to focus on the factors that influence and predict the radiosensitivity of tumor cells, and to evaluate the impact and predictive significance of radiosensitivity on the efficacy of radio-immunotherapy combination.
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Affiliation(s)
- Zhiru Gao
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Qian Zhao
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430064, China
| | - Yiyue Xu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Linlin Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
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Rike WA, Stern S. Proteins and Transcriptional Dysregulation of the Brain Extracellular Matrix in Parkinson's Disease: A Systematic Review. Int J Mol Sci 2023; 24:ijms24087435. [PMID: 37108598 PMCID: PMC10138539 DOI: 10.3390/ijms24087435] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The extracellular matrix (ECM) of the brain is a dynamic structure made up of a vast network of bioactive macromolecules that modulate cellular events. Structural, organizational, and functional changes in these macromolecules due to genetic variation or environmental stressors are thought to affect cellular functions and may result in disease. However, most mechanistic studies to date usually focus on the cellular aspects of diseases and pay less attention to the relevance of the processes governing the dynamic nature of the extracellular matrix in disease pathogenesis. Thus, due to the ECM's diversified biological roles, increasing interest in its involvement in disease, and the lack of sufficient compiled evidence regarding its relationship with Parkinson's disease (PD) pathology, we aimed to compile the existing evidence to boost the current knowledge on the area and provide refined guidance for the future research. Here, in this review, we gathered postmortem brain tissue and induced pluripotent stem cell (iPSC)-related studies from PubMed and Google Scholar to identify, summarize and describe common macromolecular alterations in the expression of brain ECM components in Parkinson's disease (PD). A literature search was conducted up until 10 February 2023. The overall hits from the database and manual search for proteomic and transcriptome studies were 1243 and 1041 articles, respectively. Following a full-text review, 10 articles from proteomic and 24 from transcriptomic studies were found to be eligible for inclusion. According to proteomic studies, proteins such as collagens, fibronectin, annexins, and tenascins were recognized to be differentially expressed in Parkinson's disease. Transcriptomic studies displayed dysregulated pathways including ECM-receptor interaction, focal adhesion, and cell adhesion molecules in Parkinson's disease. A limited number of relevant studies were accessed from our search, indicating that much work remains to be carried out to better understand the roles of the ECM in neurodegeneration and Parkinson's disease. However, we believe that our review will elicit focused primary studies and thus support the ongoing efforts of the discovery and development of diagnostic biomarkers as well as therapeutic agents for Parkinson's disease.
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Affiliation(s)
- Wote Amelo Rike
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
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Lim MJ, Yagnik G, Henkel C, Frost SF, Bien T, Rothschild KJ. MALDI HiPLEX-IHC: multiomic and multimodal imaging of targeted intact proteins in tissues. Front Chem 2023; 11:1182404. [PMID: 37201132 PMCID: PMC10187789 DOI: 10.3389/fchem.2023.1182404] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/20/2023] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is one of the most widely used methods for imaging the spatial distribution of unlabeled small molecules such as metabolites, lipids and drugs in tissues. Recent progress has enabled many improvements including the ability to achieve single cell spatial resolution, 3D-tissue image reconstruction, and the precise identification of different isomeric and isobaric molecules. However, MALDI-MSI of high molecular weight intact proteins in biospecimens has thus far been difficult to achieve. Conventional methods normally require in situ proteolysis and peptide mass fingerprinting, have low spatial resolution, and typically detect only the most highly abundant proteins in an untargeted manner. In addition, MSI-based multiomic and multimodal workflows are needed which can image both small molecules and intact proteins from the same tissue. Such a capability can provide a more comprehensive understanding of the vast complexity of biological systems at the organ, tissue, and cellular levels of both normal and pathological function. A recently introduced top-down spatial imaging approach known as MALDI HiPLEX-IHC (MALDI-IHC for short) provides a basis for achieving this high-information content imaging of tissues and even individual cells. Based on novel photocleavable mass-tags conjugated to antibody probes, high-plex, multimodal and multiomic MALDI-based workflows have been developed to image both small molecules and intact proteins on the same tissue sample. Dual-labeled antibody probes enable multimodal mass spectrometry and fluorescent imaging of targeted intact proteins. A similar approach using the same photocleavable mass-tags can be applied to lectin and other probes. We detail here several examples of MALDI-IHC workflows designed to enable high-plex, multiomic and multimodal imaging of tissues at a spatial resolution as low as 5 µm. This approach is compared to other existing high-plex methods such as imaging mass cytometry, MIBI-TOF, GeoMx and CODEX. Finally, future applications of MALDI-IHC are discussed.
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Affiliation(s)
- Mark J. Lim
- AmberGen, Inc., Billerica, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
| | | | | | | | - Tanja Bien
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Kenneth J. Rothschild
- AmberGen, Inc., Billerica, MA, United States
- Department of Physics and Photonics Center, Boston University, Boston, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
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27
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Ni J, Tian S, Bai L, Lv Q, Liu J, Liu J, Fang Y, Zhai Y, Shen Q, Rao J, Ding C, Xu H. Comparative proteomic analysis of children FSGS FFPE tissues. BMC Pediatr 2022; 22:707. [PMID: 36503536 PMCID: PMC9743561 DOI: 10.1186/s12887-022-03764-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In children, focal segmental glomerulosclerosis (FSGS) is the main cause of steroid resistant nephrotic syndrome (SRNS). To identify specific candidates and the mechanism of steroid resistance, we examined the formalin-fixed paraffin embedded (FFPE) renal tissue protein profiles via liquid chromatography tandem mass spectrometry (LC-MS/MS). METHODS Renal biopsies from seven steroid-sensitive (SS) and eleven steroid-resistant (SR) children FSGS patients were obtained. We examined the formalin-fixed paraffin embedded (FFPE) renal tissue protein profiles via liquid chromatography tandem mass spectrometry (LC-MS/MS). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) analysis, as well as the construction of protein-protein interaction (PPI) network were performed. Two proteins were further valiadated by immunohistochemistry staining in FSGS patients and mice models. RESULTS In total, we quantified more than 4000 proteins, of which 325 were found to be differentially expressed proteins (DEPs) between the SS and SR group (foldchange ≥2, P<0.05). The results of GO revealed that the most significant up-regulated proteins were primarily related to protein transportation, regulation of the complement activation process and cytolysis. Moreover, clustering analysis showed differences in the pathways (lysosome, terminal pathway of complement) between the two groups. Among these potential candidates, validation analyses for LAMP1 and ACSL4 were conducted. LAMP1 was observed to have a higher expression in glomerulus, while ACSL4 was expressed more in tubular epithelial cells. CONCLUSIONS In this study, the potential mechanism and candidates related to steroid resistance in children FSGS patients were identified. It could be helpful in identifying potential therapeutic targets and predicting outcomes with these proteomic changes for children FSGS patients.
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Affiliation(s)
- Jiajia Ni
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Sha Tian
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lin Bai
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Qianying Lv
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jialu Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jiaojiao Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Ye Fang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Yihui Zhai
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Qian Shen
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jia Rao
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Chen Ding
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Hong Xu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
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Chen H, Lai X, Zhu Y, Huang H, Zeng L, Zhang L. Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis. Clin Proteomics 2022; 19:44. [PMID: 36404333 PMCID: PMC9677906 DOI: 10.1186/s12014-022-09381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 11/06/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Lung cancer (LC) is a common malignant tumor with a high incidence and poor prognosis. Early LC could be cured, but the 5-year-survival rate for patients advanced is extremely low. Early screening of tumor biomarkers through plasma could allow more LC to be detected at an early stage, leading to a earlier treatment and a better prognosis. METHODS This study was based on total proteomic analysis and parallel reaction monitoring validation of peripheral blood from 20 lung adenocarcinoma patients and 20 healthy individuals. Furthermore, differentially expressed proteins closely related to prognosis were analysed using Kaplan-Meier Plotter and receiver operating characteristic curve (ROC) curve analysis. RESULTS The candidate proteins GAPDH and RAC1 showed the highest connectivity with other differentially expressed proteins between the lung adenocarcinoma group and the healthy group using STRING. Kaplan-Meier Plotter analysis showed that lung adenocarcinoma patients with positive ATCR2, FHL1, RAB27B, and RAP1B expression had observably longer overall survival than patients with negative expression (P < 0.05). The high expression of ARPC2, PFKP, PNP, RAC1 was observably negatively correlated with prognosis (P < 0.05). 17 out of 27 proteins showed a high area under the curve (> 0.80) between the lung adenocarcinoma and healthy plasma groups. Among those proteins, UQCRC1 had an area under the curve of 0.960, and 5 proteins had an area under the curve from 0.90 to 0.95, suggesting that these hub proteins might have discriminatory potential in lung adenocarcinoma, P < 0.05. CONCLUSIONS These findings provide UQCRC1, GAPDH, RAC1, PFKP have potential as novel biomarkers for the early screening of lung adenocarcinoma.
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Affiliation(s)
- Hongyu Chen
- grid.13291.380000 0001 0807 1581Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Xiaoqin Lai
- grid.412901.f0000 0004 1770 1022Day Surgery Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yihan Zhu
- grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hong Huang
- grid.412901.f0000 0004 1770 1022Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Lingyan Zeng
- grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Li Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
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Larrey EK, Pathak R. Radiation-Induced Intestinal Normal Tissue Toxicity: Implications for Altered Proteome Profile. Genes (Basel) 2022; 13:2006. [PMID: 36360243 PMCID: PMC9689954 DOI: 10.3390/genes13112006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 09/12/2023] Open
Abstract
Radiation-induced toxicity to healthy/normal intestinal tissues, especially during radiotherapy, limits the radiation dose necessary to effectively eradicate tumors of the abdomen and pelvis. Although the pathogenesis of intestinal radiation toxicity is highly complex, understanding post-irradiation alterations in protein profiles can provide crucial insights that make radiotherapy safer and more efficient and allow for increasing the radiation dose during cancer treatment. Recent preclinical and clinical studies have advanced our current understanding of the molecular changes associated with radiation-induced intestinal damage by assessing changes in protein expression with mass spectrometry-based approaches and 2-dimensional difference gel electrophoresis. Studies by various groups have demonstrated that proteins that are involved in the inflammatory response, the apoptotic pathway, reactive oxygen species scavenging, and cell proliferation can be targeted to develop effective radiation countermeasures. Moreover, altered protein profiles serve as a crucial biomarkers for intestinal radiation damage. In this review, we present alterations in protein signatures following intestinal radiation damage as detected by proteomics approaches in preclinical and clinical models with the aim of providing a better understanding of how to accomplish intestinal protection against radiation damage.
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Affiliation(s)
- Enoch K. Larrey
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR 72205, USA
- Department of Information Science, University of Arkansas at Little Rock, 2801 S University Ave, Little Rock, AR 72204, USA
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR 72205, USA
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Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. J Transl Med 2022; 102:1170-1181. [PMID: 36775443 PMCID: PMC9362039 DOI: 10.1038/s41374-022-00830-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/15/2022] Open
Abstract
Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other 'omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.
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Affiliation(s)
- Miao Cui
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Mount Sinai West, New York, NY, USA
| | - Chao Cheng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA. .,Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
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31
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Ling B, Zhang Z, Xiang Z, Cai Y, Zhang X, Wu J. Advances in the application of proteomics in lung cancer. Front Oncol 2022; 12:993781. [PMID: 36237335 PMCID: PMC9552298 DOI: 10.3389/fonc.2022.993781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Although the incidence and mortality of lung cancer have decreased significantly in the past decade, it is still one of the leading causes of death, which greatly impairs people’s life and health. Proteomics is an emerging technology that involves the application of techniques for identifying and quantifying the overall proteins in cells, tissues and organisms, and can be combined with genomics, transcriptomics to form a multi-omics research model. By comparing the content of proteins between normal and tumor tissues, proteomics can be applied to different clinical aspects like diagnosis, treatment, and prognosis, especially the exploration of disease biomarkers and therapeutic targets. The applications of proteomics have promoted the research on lung cancer. To figure out potential applications of proteomics associated with lung cancer, we summarized the role of proteomics in studies about tumorigenesis, diagnosis, prognosis, treatment and resistance of lung cancer in this review, which will provide guidance for more rational application of proteomics and potential therapeutic strategies of lung cancer.
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Affiliation(s)
- Bai Ling
- Department of Pharmacy, The Yancheng Clinical College of Xuzhou Medical University, The First people’s Hospital of Yancheng, Yancheng, China
| | - Zhengyu Zhang
- Nanjing Medical University School of Medicine, Nanjing, China
| | - Ze Xiang
- Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqi Cai
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyue Zhang
- Stomatology Hospital, School of stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Jian Wu
- Department of Clinical Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- *Correspondence: Jian Wu,
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Bian W, Jiang H, Feng S, Chen J, Wang W, Li X. Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. STAR Protoc 2022; 3:101569. [PMID: 35874475 PMCID: PMC9304681 DOI: 10.1016/j.xpro.2022.101569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Identification of protein interactors is fundamental to understanding their functions. Here, we describe a modified protocol for tandem affinity purification coupled with mass spectrometry (TAP/MS), which includes two-step purification. We detail the S-, 2×FLAG-, and Streptavidin-Binding Peptide (SBP)- tandem tags (SFB-tag) system for protein purification. This protocol can be used to identify protein interactors and establish a high-confidence protein-protein interaction network based on computational models. This is particularly useful for identifying bona fide interacting proteins for subsequent functional studies. For complete details on the use and execution of this protocol, please refer to Bian et al. (2021).
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Affiliation(s)
- Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Hua Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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33
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Wu J, Liu H, Wang H, Wang Y, Cheng Q, Zhao R, Gao H, Fang L, Zhu F, Xue B. iTRAQ-based quantitative proteomic analysis of the liver regeneration termination phase after partial hepatectomy in mice. J Proteomics 2022; 267:104688. [PMID: 35914716 DOI: 10.1016/j.jprot.2022.104688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/09/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023]
Abstract
Liver regeneration (LR) is an important biological process after liver injury. As the "brake" in the process of LR, the termination phase of LR not only suppresses the continuous increase in liver volume but also effectively promotes the recovery of liver function. However, the mechanisms underlying the termination phase of LR are still not clear. In our study, we used isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic analysis to determine the protein expression profiles of livers in the termination phase of mouse LR after partial hepatectomy (PH). We found that the expression of 197 proteins increased gradually during LR; in addition, 187 proteins were upregulated and 264 proteins were downregulated specifically in the termination phase of LR. The GO analysis of the proteins revealed the upregulation of "cell-cell adhesion" and "translation" and the downregulation of the "oxidation-reduction process". The KEGG pathway analysis showed that "biosynthesis of antibiotics" and "ribosomes" were significantly upregulated, while "metabolic pathways" were significantly downregulated. These analyses indicated that the termination phase of LR mainly focuses on restoring cellular structure and function. Differentially expressed proteins such as SNX5 were also screened out from biological processes. SIGNIFICANCE: The key regulatory factors in the termination phase of LR were studied by iTRAQ-based proteomics to lay a foundation for further study of the molecular mechanism and biomarkers of the termination phase of LR. This study will guide the clinical perioperative management of patients after hepatectomy.
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Affiliation(s)
- Jing Wu
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - He Liu
- General surgery Department, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Haiquan Wang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China
| | - Yuqi Wang
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Qi Cheng
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China
| | - Ruochen Zhao
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Hongliang Gao
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China.
| | - Feng Zhu
- General surgery Department, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China.
| | - Bin Xue
- Core Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166, China.
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A Protocol for the Acquisition of Comprehensive Proteomics Data from Single Cases Using Formalin-Fixed Paraffin Embedded Sections. Methods Protoc 2022; 5:mps5040057. [PMID: 35893583 PMCID: PMC9326557 DOI: 10.3390/mps5040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
The molecular analysis of small or rare patient tissue samples is challenging and often limited by available technologies and resources, such as reliable antibodies against a protein of interest. Although targeted approaches provide some insight, here, we describe the workflow of two complementary mass spectrometry approaches, which provide a more comprehensive and non-biased analysis of the molecular features of the tissue of interest. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) generates spatial intensity maps of molecular features, which can be easily correlated with histology. Additionally, liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify and quantify proteins of interest from a consecutive section of the same tissue. Here, we present data from concurrent precancerous lesions from the endometrium and fallopian tube of a single patient. Using this complementary approach, we monitored the abundance of hundreds of proteins within the precancerous and neighboring healthy regions. The method described here represents a useful tool to maximize the number of molecular data acquired from small sample sizes or even from a single case. Our initial data are indicative of a migratory phenotype in these lesions and warrant further research into their malignant capabilities.
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Pan J, Wang R, Shang F, Ma R, Rong Y, Zhang Y. Functional Micropeptides Encoded by Long Non-Coding RNAs: A Comprehensive Review. Front Mol Biosci 2022; 9:817517. [PMID: 35769907 PMCID: PMC9234465 DOI: 10.3389/fmolb.2022.817517] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/24/2022] [Indexed: 12/03/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) were originally defined as non-coding RNAs (ncRNAs) which lack protein-coding ability. However, with the emergence of technologies such as ribosome profiling sequencing and ribosome-nascent chain complex sequencing, it has been demonstrated that most lncRNAs have short open reading frames hence the potential to encode functional micropeptides. Such micropeptides have been described to be widely involved in life-sustaining activities in several organisms, such as homeostasis regulation, disease, and tumor occurrence, and development, and morphological development of animals, and plants. In this review, we focus on the latest developments in the field of lncRNA-encoded micropeptides, and describe the relevant computational tools and techniques for micropeptide prediction and identification. This review aims to serve as a reference for future research studies on lncRNA-encoded micropeptides.
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Affiliation(s)
- Jianfeng Pan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rong Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- *Correspondence: Yanjun Zhang,
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Vizuet-de-Rueda JC, Montero-Vargas JM, Galván-Morales MÁ, Porras-Gutiérrez-de-Velasco R, Teran LM. Current Insights on the Impact of Proteomics in Respiratory Allergies. Int J Mol Sci 2022; 23:ijms23105703. [PMID: 35628512 PMCID: PMC9144092 DOI: 10.3390/ijms23105703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Respiratory allergies affect humans worldwide, causing extensive morbidity and mortality. They include allergic rhinitis (AR), asthma, pollen food allergy syndrome (PFAS), aspirin-exacerbated respiratory disease (AERD), and nasal polyps (NPs). The study of respiratory allergic diseases requires new technologies for early and accurate diagnosis and treatment. Omics technologies provide the tools required to investigate DNA, RNA, proteins, and other molecular determinants. These technologies include genomics, transcriptomics, proteomics, and metabolomics. However, proteomics is one of the main approaches to studying allergic disorders' pathophysiology. Proteins are used to indicate normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. In this field, the principal goal of proteomics has been to discover new proteins and use them in precision medicine. Multiple technologies have been applied to proteomics, but that most used for identifying, quantifying, and profiling proteins is mass spectrometry (MS). Over the last few years, proteomics has enabled the establishment of several proteins for diagnosing and treating respiratory allergic diseases.
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37
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Canto AM, Godoi AB, Matos AHB, Geraldis JC, Rogerio F, Alvim MKM, Yasuda CL, Ghizoni E, Tedeschi H, Veiga DFT, Henning B, Souza W, Rocha CS, Vieira AS, Dias EV, Carvalho BS, Gilioli R, Arul AB, Robinson RAS, Cendes F, Lopes-Cendes I. Benchmarking the proteomic profile of animal models of mesial temporal epilepsy. Ann Clin Transl Neurol 2022; 9:454-467. [PMID: 35238489 PMCID: PMC8994989 DOI: 10.1002/acn3.51533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We compared the proteomic signatures of the hippocampal lesion induced in three different animal models of mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE+HS): the systemic pilocarpine model (PILO), the intracerebroventricular kainic acid model (KA), and the perforant pathway stimulation model (PPS). METHODS We used shotgun proteomics to analyze the proteomes and find enriched biological pathways of the dorsal and ventral dentate gyrus (DG) isolated from the hippocampi of the three animal models. We also compared the proteomes obtained in the animal models to that from the DG of patients with pharmacoresistant MTLE+HS. RESULTS We found that each animal model presents specific profiles of proteomic changes. The PILO model showed responses predominantly related to neuronal excitatory imbalance. The KA model revealed alterations mainly in synaptic activity. The PPS model displayed abnormalities in metabolism and oxidative stress. We also identified common biological pathways enriched in all three models, such as inflammation and immune response, which were also observed in tissue from patients. However, none of the models could recapitulate the profile of molecular changes observed in tissue from patients. SIGNIFICANCE Our results indicate that each model has its own set of biological responses leading to epilepsy. Thus, it seems that only using a combination of the three models may one replicate more closely the mechanisms underlying MTLE+HS as seen in patients.
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Affiliation(s)
- Amanda M Canto
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Alexandre B Godoi
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Alexandre H B Matos
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Jaqueline C Geraldis
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Fabio Rogerio
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marina K M Alvim
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Clarissa L Yasuda
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Enrico Ghizoni
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Helder Tedeschi
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Diogo F T Veiga
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Barbara Henning
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Welliton Souza
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Cristiane S Rocha
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - André S Vieira
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Elayne V Dias
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rovilson Gilioli
- Laboratory of Animal Quality Control, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Fernando Cendes
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
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Luan W, Li M, Wu C, Shen X, Sun Z. Proteomic dissimilarities of primary microglia and BV2 cells under stimuli. Eur J Neurosci 2022; 55:1709-1723. [PMID: 35239205 DOI: 10.1111/ejn.15637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/01/2022]
Abstract
Microglia are the static resident cells possessing the phagocytic properties in the central nervous system (CNS). In many relevant studies, the immortalized murine microglial cell line BV2 has been used as a tool in primary microglia (PM) relevant studies. Microglia participate in neuroinflammation by converting into M1- and M2-like phenotypes. In this study, we established M1- and M2-like phenotype response models by exposing PM and BV2 cells to lipopolysaccharides (LPS) and interlukin-4 (IL-4), respectively, and discovered the proteomic differences between the two types of microglia. It turned out that the BV2 cells responses to LPS and IL-4 were narrower and weaker than that of PM. In addition, irradiation, which has been shown to activate microglia and induces neuroinflammation, was also used as a treatment in this study. The results showed that BV2 cells have stronger capacity of DNA damage repair. Besides, irradiation had a negative effect on the regulation of KEGG pathways such as proteasome, ribosome, oxidative phosphorylation and TCA cycle in both cells. Furthermore, the KEGG pathways including cell cycle and DNA replication (significantly down-regulated), and antigen processing and presentation and FC γ R mediated phagocytosis (significantly up-regulated) were only found in irradiated PM. These data demonstrate that PM is more fragile to irradiation. Results in this study indicate that BV2 cells only partially model PM and thus using BV2 in microglia related studies should be carefully considered.
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Affiliation(s)
- Wenhui Luan
- Neurology department EEG Room, Yantai Yuhuangding Hospital, Yantai, China
| | - Min Li
- Department of Neurology, Yantai Yuhuangding Hospital, Yantai, China
| | - Chunmei Wu
- Neurology department EEG Room, Yantai Yuhuangding Hospital, Yantai, China
| | - Xiaoqian Shen
- Department of Neurology Intensive Care Unit, Yantai Yuhuangding Hospital, Yantai, China
| | - Zhongwen Sun
- Department of Neurology, Yantai Yuhuangding Hospital, Yantai, China
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39
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Yu CT, Chen T, Lu S, Hu W, Zhang Q, Tan J, Sun D, Li L, Sun X, Xu C, Lai Y, Fan M, Shen Z, Shen W, Cheng H. Identification of Significant Modules and Targets of Xian-Lian-Jie-Du Decoction Based on the Analysis of Transcriptomics, Proteomics and Single-Cell Transcriptomics in Colorectal Tumor. J Inflamm Res 2022; 15:1483-1499. [PMID: 35256851 PMCID: PMC8898059 DOI: 10.2147/jir.s344861] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/31/2021] [Indexed: 12/14/2022] Open
Abstract
Purpose Colorectal cancer (CRC) remains the third most common tumor worldwide. Ulcerative colitis (UC) could cause chronic inflammation and ulcers in the colon and rectum. UC is a risk factor for a high incidence of CRC, and the incidence of UC-associated CRC (UC-CRC) is still increasing. Chinese medicine prescription, Xian-Lian-Jie-Du decoction (XLJDD), has been proven its efficacy in some UC-CRC patients. However, the mechanism of XLJDD in treating UC-CRC remains unknown. This study aimed to investigate the mechanism of XLJDD in treating UC-CRC. Methods We constructed an AOM/DSS mouse model that could simulate the various stages of UC-CRC in humans. XLJDD and its 5 main components are used to treat the AOM/DSS model, respectively. With the power of high-throughput sequencing technology, we described the mechanism of XLJDD from transcriptomics, proteomics, and single-cell transcriptomics. Results Our results showed that XLJDD could effectively suppress the occurrence and development of colorectal tumors. Using the weighted correlation network analysis (WGCNA), several mRNA and protein modules that respond to XLJDD have been identified. Moreover, two essential genes, Mfsd2a and Ccdc85c, were caught our attention. They were prognostic markers in CRC patients, and their expression could be significantly modulated by XLJDD, showing their potential as effective targets of XLJDD. In addition, we also discovered that XLJDD could affect the cell composition of the colorectal tumor environment, especially in the infiltration of B cells. Conclusion We demonstrated that XLJDD could prevent the initiation and development of colorectal tumors by modulating the expression of Mfsd2a and Ccdc85c and reducing the infiltration of B cells in the tumor microenvironment of colorectal tumor.
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Affiliation(s)
- Cheng-Tao Yu
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Tongqing Chen
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Sicheng Lu
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Wenlong Hu
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Qinchang Zhang
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jiani Tan
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Dongdong Sun
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Liu Li
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Xin Sun
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Changliang Xu
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Yueyang Lai
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Minmin Fan
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Zhengjie Shen
- Medical Oncology Department, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Weixing Shen
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
- Correspondence: Weixing Shen; Haibo Cheng, The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China, Tel +86 13815857118, Fax +86 2585811006, Email ;
| | - Haibo Cheng
- The First Clinical Medical College, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
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40
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Xie Y, Zhang H, Huang T. Quantitative proteomics reveal three potential biomarkers for risk assessment of acute myocardial infarction. Bioengineered 2022; 13:4939-4950. [PMID: 35156527 PMCID: PMC8973584 DOI: 10.1080/21655979.2022.2037365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Acute myocardial infarction (AMI) is the one of the main cause of death worldwide. Exosomes carry important information about intercellular communication and could be diagnostic marker for many diseases. Here, we aimed to find potential key proteins for the early diagnosis of AMI. A label free proteomics strategy was used to identify the differentially expressed proteins (DEPs) of AMI patients’ plasma exosome. By bioinformatics analysis and enzyme-linked immunosorbent assay to validate the candidate proteins. Compared to healthy control plasma exosome, we totally identified 72 differentially expressed proteins (DEPs) in AMI patients. Also, we found that complement and coagulation cascades was activated by KEGG analysis and GSEA. PLG, C8B and F2 were selected as candidate molecules for further study, and then validated another 40 plasma samples using enzyme-linked immunosorbent assay. Finally, we found that the expression levels of these three proteins (PLG, C8B and F2) were significantly higher than those of healthy controls (P < 0.05). ROC analysis revealed that PLG, C8B and F2 had potential value for AMI early diagnosis. In conclusion, our study identified three potential biomarkers for AMI diagnosis. But there remains a need to further study the mechanism of the biomarkers.
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Affiliation(s)
| | | | - Tieqiu Huang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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41
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Corda PO, Silva JV, Pereira SC, Barros A, Alves MG, Fardilha M. Bioinformatic Approach to Unveil Key Differentially Expressed Proteins in Human Sperm After Slow and Rapid Cryopreservation. Front Cell Dev Biol 2022; 9:759354. [PMID: 35145967 PMCID: PMC8821918 DOI: 10.3389/fcell.2021.759354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/23/2021] [Indexed: 11/25/2022] Open
Abstract
Currently, two conventional freezing techniques are used in sperm cryopreservation: slow freezing (SF) and rapid freezing (RF). Despite the protocolar improvements, cryopreservation still induces significant alterations in spermatozoon that are poorly understood. Here, available proteomic data from human cryopreserved sperm was analyzed through bioinformatic tools to unveil key differentially expressed proteins (DEPs) that can be used as modulation targets or quality markers. From the included proteomic studies, 160 and 555 DEPs were collected for SF and RF groups, respectively. For each group, an integrative network was constructed using gene ontology and protein-protein interaction data to identify key DEPs. Among them, arylsulfatase A (ARSA) was highlighted in both freezing networks, and low ARSA levels have been associated with poor-sperm quality. Thus, ARSA was selected for further experimental investigation and its levels were assessed in cryopreserved samples by western blot. ARSA levels were significantly decreased in RF and SF samples (∼31.97 and ∼39.28%, respectively). The bioinformatic analysis also revealed that the DEPs were strongly associated with proteasomal and translation pathways. The purposed bioinformatic approach allowed the identification of potential key DEPs in freeze-thawed human spermatozoa. ARSA has the potential to be used as a marker to assess sperm quality after cryopreservation.
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Affiliation(s)
- Pedro O Corda
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Joana Vieira Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal.,Department of Chemistry, QOPNA and LAQV, University of Aveiro, Aveiro, Portugal.,Clinical and Experimental Endocrinology, Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Sara C Pereira
- Clinical and Experimental Endocrinology, Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Alberto Barros
- Department of Chemistry, QOPNA and LAQV, University of Aveiro, Aveiro, Portugal.,Centre for Reproductive Genetics A. Barros, Porto, Portugal.,Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Marco G Alves
- Clinical and Experimental Endocrinology, Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Margarida Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
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Wilson S, Steele S, Adeli K. Innovative technological advancements in laboratory medicine: Predicting the lab of the future. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2011413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Affiliation(s)
- Siobhan Wilson
- Clinical Biochemistry, Pediatric Laboratory Medicine and Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shannon Steele
- Clinical Biochemistry, Pediatric Laboratory Medicine and Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Khosrow Adeli
- Clinical Biochemistry, Pediatric Laboratory Medicine and Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Artificial Intelligence for Precision Oncology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:249-268. [DOI: 10.1007/978-3-030-91836-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Proteomics and Schizophrenia: The Evolution of a Great Partnership. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1400:129-138. [DOI: 10.1007/978-3-030-97182-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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45
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Kouter K, Videtic Paska A. 'Omics' of suicidal behaviour: A path to personalised psychiatry. World J Psychiatry 2021; 11:774-790. [PMID: 34733641 PMCID: PMC8546767 DOI: 10.5498/wjp.v11.i10.774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 08/30/2021] [Indexed: 02/06/2023] Open
Abstract
Psychiatric disorders, including suicide, are complex disorders that are affected by many different risk factors. It has been estimated that genetic factors contribute up to 50% to suicide risk. As the candidate gene approach has not identified a gene or set of genes that can be defined as biomarkers for suicidal behaviour, much is expected from cutting edge technological approaches that can interrogate several hundred, or even millions, of biomarkers at a time. These include the '-omic' approaches, such as genomics, transcriptomics, epigenomics, proteomics and metabolomics. Indeed, these have revealed new candidate biomarkers associated with suicidal behaviour. The most interesting of these have been implicated in inflammation and immune responses, which have been revealed through different study approaches, from genome-wide single nucleotide studies and the micro-RNA transcriptome, to the proteome and metabolome. However, the massive amounts of data that are generated by the '-omic' technologies demand the use of powerful computational analysis, and also specifically trained personnel. In this regard, machine learning approaches are beginning to pave the way towards personalized psychiatry.
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Affiliation(s)
- Katarina Kouter
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Alja Videtic Paska
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana SI-1000, Slovenia
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46
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Xu P, Yi Y, Luo Y, Liu Z, Xu Y, Cai J, Zeng Z, Liu A. Radiation‑induced dysfunction of energy metabolism in the heart results in the fibrosis of cardiac tissues. Mol Med Rep 2021; 24:842. [PMID: 34633055 PMCID: PMC8524410 DOI: 10.3892/mmr.2021.12482] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Thoracic radiotherapy increases the risk of radiation‑induced heart damage (RIHD); however, the molecular mechanisms underlying these changes are not fully understood. The aim of the present study was to investigate the effects of radiation on the mouse heart using high‑throughput proteomics. Male C57BL/6J mice were used to establish a model of RIHD by exposing the entire heart to 16 Gy high‑energy X‑rays, and cardiac injuries were verified using a cardiac echocardiogram, as well as by measuring serum brain natriuretic peptide levels and conducting H&E and Masson staining 5 months after irradiation. Proteomics experiments were performed using the heart apex of 5‑month irradiated mice and control mice that underwent sham‑irradiation. The most significantly differentially expressed proteins were enriched in 'cardiac fibrosis' and 'energy metabolism'. Next, the cardiac fibrosis and changes to energy metabolism were confirmed using immunohistochemistry staining and western blotting. Extracellular matrix proteins, such as collagen type 1 α 1 chain, collagen type III α 1 chain, vimentin and CCCTC‑binding factor, along with metabolism‑related proteins, such as fatty acid synthase and solute carrier family 25 member 1, exhibited upregulated expression following exposure to ionizing radiation. Additionally, the myocardial mitochondria inner membranes were injured, along with a decrease in ATP levels and the accumulation of lactic acid in the irradiated heart tissues. These results suggest that the high doses of ionizing radiation used lead to structural remodeling, functional injury and fibrotic alterations in the mouse heart. Radiation‑induced mitochondrial damage and metabolic alterations of the cardiac tissue may thus be a pathogenic mechanism of RIHD.
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Affiliation(s)
- Peng Xu
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yali Yi
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yijing Luo
- Department of Clinical Medicine, The First Clinical College of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Zhicheng Liu
- Department of Clinical Medicine, The First Clinical College of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Yilin Xu
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jing Cai
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhimin Zeng
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Anwen Liu
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Abstract
PURPOSE The proteome during lipopolysaccharide (LPS)-induced acute lung injury (ALI) in mice is unclear. MATERIALS AND METHODS In this study, eight-week-old male C57BL/6 mice were intraperitoneally injected with LPS and sacrificed 18 hours after LPS administration to identify protein expression levels in lung tissue using tandem mass tag (TMT) analysis for relative quantification. Hematoxylin-eosin (HE) staining was used to evaluate lung injury in mice. Immunohistochemical staining was used to calculate the production of myeloperoxidase (MPO) and TUNEL staining was performed to detect apoptosis. GO functional clustering and KEGG pathway enrichment analyses were performed to determine functions of differentially expressed proteins (DEPs) and transduction pathways. Domain annotation and subcellular localization analysis of the DEPs were also performed. Furthermore, parallel reaction monitoring (PRM) analysis was used to verify the top 30 DEPs. RESULTS A total of 5188 proteins were found to be expressed in lung tissues from LPS- and saline-treated mice. Among these proteins, 293 were differentially expressed between the two groups; 255 proteins were upregulated in the LPS-treated ALI mice, while 38 were downregulated. GO analysis showed that the DEPs are mainly extracellular, and KEGG analysis suggested that the DEPs are mainly enriched in the NOD-like receptor signaling pathway, complement and coagulation cascades and natural killer cell-mediated cytotoxicity. Enrichment of the DEPs is mainly peptidase S1A, serine proteases, peptidase S1, and the serpin domain. 26.6% of the DEPs are in the nucleus, 24.6% are in the cytosol, 19.1% are in the extracellular space, and 18.8% are in the plasma membrane. PRM validation showed that the trend of 30 DEPs was same with TMT analysis. Among these, Cytochrome b-245 heavy chain (Cybb), Monocyte differentiation antigen CD14 (Cd14) and Neutrophil gelatinase-associated lipocalin (NGAL) were the most obvious change. CONCLUSIONS Our results may help to identify markers and therapeutic targets for LPS-induced ALI.
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Affiliation(s)
- Shengsong Chen
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
| | - Qingyuan Zhan
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing , P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Beijing, P. R. China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, Beijing, P. R. China
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Tribe AK, McConnell MJ, Teesdale-Spittle PH. The Big Picture of Glioblastoma Malignancy: A Meta-Analysis of Glioblastoma Proteomics to Identify Altered Biological Pathways. ACS OMEGA 2021; 6:24535-24544. [PMID: 34604635 PMCID: PMC8482494 DOI: 10.1021/acsomega.1c02991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 05/08/2023]
Abstract
Glioblastoma is a highly malignant cancer with no effective treatment. It is vital to elucidate the mechanisms which drive glioblastoma in order to identify therapeutic targets. The differences in protein expression between glioblastoma, grade I-III glioma, and normal brain tissue reflect the functional alterations driving malignancy. However, proteomic analysis of glioblastoma has been hampered by the heterogeneity of glioblastoma and the variety of methodology used in its study. To reduce these inconsistencies, we performed a meta-analysis of the literature published since 2015, including 14 datasets from eight papers comparing the whole proteome of glioblastoma to normal brain or grade I-III glioma. We found that 154 proteins were commonly upregulated and 116 proteins were commonly downregulated in glioblastoma compared to normal brain. Meanwhile, 240 proteins were commonly upregulated and 125 proteins were commonly downregulated in glioblastoma compared to grade I-III glioma. Functional enrichment analysis revealed upregulation of proteins involved in mRNA splicing and the immune system and downregulation of proteins involved in synaptic signaling and glucose and glutamine metabolism. The identification of these altered biological pathways provides a basis for deeper investigation in the pursuit of an effective treatment for glioblastoma.
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Yun S, Lee D, Kang S, Kim DW, Kim Y, Cho JY, Seo K. Proteomic analysis of aqueous humor in canine primary angle-closure glaucoma in American Cocker Spaniel dogs. Vet Ophthalmol 2021; 24:520-532. [PMID: 34558166 DOI: 10.1111/vop.12937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To analyze proteomic profiles of the aqueous humor (AH) of canines with primary angle-closure glaucoma (PACG) and identify associated protein alterations. ANIMALS STUDIED Six American Cocker Spaniels with PACG and six American Cocker Spaniels without ocular diseases. METHODS Aqueous humor samples were collected from six American Cocker Spaniels with PACG at Seoul National University, VMTH, and six healthy Cocker Spaniels without ocular disease at Irion Animal Hospital. For the PACG group, AH samples were obtained by anterior chamber paracentesis prior to glaucoma treatment. For the AH control group, AH samples were collected from patients anesthetized for other reasons. Total AH protein concentration was determined by the bicinchoninic acid (BCA) assay. AH protein samples were quantified by liquid chromatography-mass spectrometry (LC-MS/MS). Raw MS spectra were processed using MaxQuant software 30, and the Gene Ontology (GO) enrichment analysis was performed using ClueGO. RESULTS The AH protein concentration in the PACG group (10.49 ± 17.98 µg/µl) was significantly higher than that of the control group (0.45 ± 0.11 µg/µl; p < .05). A total of 758 proteins were identified in the AH. Several proteins both significantly increased (n = 69) and decreased (n = 252) in the PACG group compared to those in the control group. GO enrichment analysis showed that the "response to wounding," "negative regulation of endopeptidase activity," and "cell growth" pathways were the most enriched terms in the PACG group compared to the control group. The top 5 proteins that were significantly increased in the AH of the PACG group were secreted phosphoprotein 1 (SPP1), peptidoglycan recognition proteins 2 (PGLYRP2), tyrosine 3-monooxygenase (YWHAE), maltase-glucoamylase (MGAM), and vimentin (VIM). CONCLUSIONS Gene Ontology enrichment analysis using the proteomic data showed that proteins and pathways related to inflammation were significantly upregulated in the various stage of PACG. Proteomic analysis of the AH from the PACG may provide valuable insights into PACG pathogenesis.
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Affiliation(s)
- Seongjin Yun
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea.,Irion animal hospital, Seoul, Korea
| | - Dabin Lee
- Department of Veterinary Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Seonmi Kang
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Dong Wook Kim
- Department of Veterinary Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Youngsam Kim
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Je-Yoel Cho
- Department of Veterinary Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Kangmoon Seo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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Ye M, Lin Y, Pan S, Wang ZW, Zhu X. Applications of Multi-omics Approaches for Exploring the Molecular Mechanism of Ovarian Carcinogenesis. Front Oncol 2021; 11:745808. [PMID: 34631583 PMCID: PMC8497990 DOI: 10.3389/fonc.2021.745808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. The molecular mechanisms of ovarian carcinogenesis need to be explored in order to identify effective clinical therapies for ovarian cancer. Recently, multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (metabolites) levels. Multi-omics approaches can identify some diagnostic and prognostic biomarkers and therapeutic targets for ovarian cancer, and these molecular signatures are beneficial for clarifying the development and progression of ovarian cancer. Moreover, the discovery of molecular signatures and targeted therapy strategies could noticeably improve the prognosis of ovarian cancer patients.
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Affiliation(s)
| | | | | | - Zhi-wei Wang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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