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Yang X, Yang Z, Wang Y, Zeng H, Wang B. Proteomics and metabolomics elucidate the biosynthetic pathway of acid stress-induced exopolysaccharides and its impact on growth phenotypes in Lactiplantibacillus plantarum HMX2. Food Chem 2025; 476:143431. [PMID: 39977986 DOI: 10.1016/j.foodchem.2025.143431] [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: 12/03/2024] [Revised: 02/07/2025] [Accepted: 02/13/2025] [Indexed: 02/22/2025]
Abstract
Lactiplantibacillus plantarum has been well acknowledged to produce exopolysaccharides (EPS) as a defense mechanism against acid stress. However, the complete biosynthetic pathway of EPS in L. plantarum and its impact on the cell growth and primary metabolism were still unclear. To fill these gaps, we carried out phenotypic, proteomic and metabolomics analysis of L. plantarum HMX2 cultured under different acidic conditions. Component and structure analysis showed that the repeating unit of EPS consisted of N-acetylmannosamine, N-acetylglucosamine, galactose, mannoses and glucoses. Multiomics analysis facilitated the curation and entablement of the complete EPS biosynthetic pathway ready for use in genome-scale metabolic models. Furthermore, proteomics and metabolomics data indicated that compared to the pH 6.5 condition, the acid stress at pH 4.5 significantly accelerated glycolysis and EPS biosynthesis processes while reduced the metabolic fluxes through the TCA cycle and the lactic acid fermentation, which suggested a trade-off between primary and secondary metabolism.
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Affiliation(s)
- Xinyu Yang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Zhijie Yang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Yanbo Wang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Hong Zeng
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China.
| | - Bei Wang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China.
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Mehta S, Wagner R, Do KT, Johnson JE, Yu F, Jubenville T, Richards K, Coleman S, Popescu FE, Nesvizhskii AI, Largaespada DA, Jagtap PD, Griffin TJ. A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.07.647596. [PMID: 40291680 PMCID: PMC12026984 DOI: 10.1101/2025.04.07.647596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
Background Characterizing peptide antigens, processed from tumor-specific proteoforms, and bound to the major histocompatibility complex, is critical for immuno-oncology research. Next-generation sequencing predicts candidate neoantigen peptides derived from DNA mutations and/or RNA transcripts coding proteoform sequences that differ from the reference proteome. Mass spectrometry (MS)-based immunopeptidomics identifies predicted, MHC-bound neoantigen peptides and other tumor antigens. This "immunopeptidogenomic" approach requires multi-omic software integration, challenging researchers with limited bioinformatics expertise and resources. As a solution, we developed the immunopeptidogenomic (iPepGen) pipeline in the Galaxy ecosystem. iPepGen is composed of five core workflow modules, available via publicly accessible, scalable Galaxy instances, accompanied by training resources to empower community adoption. Findings Using representative multi-omic data from malignant peripheral nerve sheath tumors, we demonstrate the operation of iPepGen modules with these functions: 1) Predict neoantigen candidates from sequencing data and generate customized protein sequence databases, including reference and non-reference neoantigen candidate sequences; 2) Discover neoantigen peptide candidates by sequence database searching of tandem mass spectrometry (MS/MS) immunopeptidomics data; 3) Verify discovered peptide candidates through a secondary peptide-centric evaluation method against the MS/MS dataset; 4) Visualize and classify the nature of verified neoantigen peptides encoded by the genome and/or transcriptome; 5) Prioritize neoantigens for further exploration and empirical validation. Conclusions We demonstrate the effectiveness of the iPepGen pipeline for candidate neoantigen discovery and characterization. With tools, workflows, and training resources available in the open Galaxy ecosystem, iPepGen should provide cancer researchers with a flexible and accessible informatics resource tailored to accelerating immuno-oncology studies.
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Xu F, Luo S, Huang Z, Wang J, Li T, Zhong L, Si X. The Molecular Mechanisms of Bergapten Against Abdominal Aortic Aneurysm: Evidence From Network Pharmacology, Molecular Docking/Dynamics, and Experimental Validation. J Cell Biochem 2025; 126:e70029. [PMID: 40159385 DOI: 10.1002/jcb.70029] [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: 01/14/2025] [Revised: 03/02/2025] [Accepted: 03/16/2025] [Indexed: 04/02/2025]
Abstract
This study endeavors to assess the potential protective role of bergapten (BP) in mitigating abdominal aortic aneurysm (AAA) and to decipher the underlying mechanisms and molecular targets. Network pharmacology was utilized to search for potential targets of BP against AAA. Molecular docking and molecular dynamics simulations were utilized to validate the interaction of BP with core targets, and then the therapeutic effect and mechanism of BP on AAA were verified by using an elastase-induced AAA model. Network pharmacology analysis identified five pharmacological targets for BP, including EGFR, SRC, PIK3CA, PIK3CB, and JAK2. Molecular docking and molecular dynamics simulations further prioritized JAK2 as the most promising candidate for the potential treatment of AAA. The results of animal experiments demonstrated that BP significantly reduced the expression of inflammatory cytokines IL-6, TNF-α, and IL-1β in the aortic tissue of AAA mouse model, and inhibited the phosphorylation of JAK2 and STAT3. BP plays an important role in the treatment of AAA, and it may become a promising drug to combat AAA progression. The inhibitory effect of BP on AAA vascular progression and the attenuation of inflammatory cell infiltration may be related to the regulation of JAK2/STAT3 signaling pathway.
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Affiliation(s)
- Fujia Xu
- Guizhou Medical University, Guiyang, China
| | - Sihan Luo
- Guizhou Medical University, Guiyang, China
| | - Zhenhua Huang
- Department of Emergency Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Junfen Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tian Li
- Tianjin Key Laboratory of Acute Abdomen Disease-Associated Organ Injury and ITCWM Repair, Institute of Integrative Medicine of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Lintao Zhong
- Department of Cardiology, The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, China
| | - Xiaoyun Si
- Guizhou Medical University, Guiyang, China
- Department of Cardiology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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Zhu F, Qin R, Ma S, Zhou Z, Tan C, Yang H, Zhang P, Xu Y, Luo Y, Chen J, Pan P. Designing a multi-epitope vaccine against Pseudomonas aeruginosa via integrating reverse vaccinology with immunoinformatics approaches. Sci Rep 2025; 15:10425. [PMID: 40140433 PMCID: PMC11947098 DOI: 10.1038/s41598-025-90226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 02/11/2025] [Indexed: 03/28/2025] Open
Abstract
Pseudomonas aeruginosa is a typically opportunistic pathogen responsible for a wide range of nosocomial infections. In this study, we designed two multi-epitope vaccines targeting P. aeruginosa proteins, incorporating cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and linear B lymphocyte (LBL) epitopes identified using reverse vaccinology and immunoinformatics approaches. The vaccines exhibited favorable physicochemical properties, including stability, solubility, and optimal molecular weight, suggesting their potential as viable candidates for vaccine development. Molecular docking studies revealed strong binding affinity to Toll-like receptors 1 (TLR1) and 2 (TLR2). Furthermore, molecular dynamics simulations confirmed the stability of the vaccine-TLR complexes over time. Immune simulation analyses indicated that the vaccines could induce robust humoral and cellular immune responses, providing a promising new approach for combating P. aeruginosa infections, particularly in the face of increasing antibiotic resistance.
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Affiliation(s)
- Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
- FuRong Laboratory, Changsha, 410008, Hunan, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
- FuRong Laboratory, Changsha, 410008, Hunan, China.
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
- FuRong Laboratory, Changsha, 410008, Hunan, China.
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Zhang Z, Rao C, Hu M, Yan W, Du Z. Highly expressed GCN1 is associated with cancer progression and poor prognosis in hepatocellular carcinoma patients. Cancer Cell Int 2025; 25:107. [PMID: 40114124 PMCID: PMC11927180 DOI: 10.1186/s12935-025-03732-y] [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: 07/21/2024] [Accepted: 03/06/2025] [Indexed: 03/22/2025] Open
Abstract
BACKGROUND General control non-derepressible protein 1 (GCN1), a ribosome-binding protein, has been implicated in the development and progression of multiple cancers. However, the potential role of GCN1 in hepatocellular carcinoma (HCC) has not yet been investigated. METHODS The expression of GCN1 in HCC was analyzed using multiple databases. Bioinformatics analysis was employed to investigate the correlation of GCN1 expression with clinical significance and immune infiltration in HCC. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene set enrichment analysis (GSEA), and in vitro experiments were conducted to study the function and potential mechanisms of GCN1 in HCC. RESULTS GCN1 was significantly upregulated in HCC, which was associated with worse clinicopathological features and poorer prognosis of the patients. GCN1 expression was closely associated with immune cell infiltration in HCC. GSEA analysis showed that GCN1 was involved in several tumor-related signaling pathways, including cell cycle, DNA replication, and Wnt signaling pathway. Knockdown of GCN1 inhibited the proliferation, invasion and migration of HCC cells, and also down-regulated the expression levels of cell cycle protein cyclin B1 (CCNB1), cyclin D1 (CCND1), and Wnt signaling pathway-related proteins Wnt3A and β-catenin. CONCLUSION GCN1 overexpression was associated with HCC progression and poor prognosis, and GCN1 knockdown could suppress the proliferation, migration and invasion ability of HCC cells by regulating Wnt signaling pathway, suggesting the potential of GCN1 as a prognostic and therapeutic target for HCC.
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Affiliation(s)
- Zhongchao Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430000, China
| | - Caijun Rao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingcun Hu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yan
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430000, China.
| | - Zhipeng Du
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430000, China.
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Hernandez R, Garcia-Rodriguez NS, Arriaga MA, Perez R, Bala AA, Leandro AC, Diego VP, Almeida M, Parsons JG, Manusov EG, Galan JA. The hepatocellular model of fatty liver disease: from current imaging diagnostics to innovative proteomics technologies. Front Med (Lausanne) 2025; 12:1513598. [PMID: 40109726 PMCID: PMC11919916 DOI: 10.3389/fmed.2025.1513598] [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: 10/18/2024] [Accepted: 02/06/2025] [Indexed: 03/22/2025] Open
Abstract
Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent chronic liver condition characterized by lipid accumulation and inflammation, often progressing to severe liver damage. We aim to review the pathophysiology, diagnostics, and clinical care of MASLD, and review highlights of advances in proteomic technologies. Recent advances in proteomics technologies have improved the identification of novel biomarkers and therapeutic targets, offering insight into the molecular mechanisms underlying MASLD progression. We focus on the application of mass spectrometry-based proteomics including single cell proteomics, proteogenomics, extracellular vesicle (EV-omics), and exposomics for biomarker discovery, emphasizing the potential of blood-based panels for noninvasive diagnosis and personalized medicine. Future research directions are presented to develop targeted therapies and improve clinical outcomes for MASLD patients.
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Affiliation(s)
- Renee Hernandez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Natasha S Garcia-Rodriguez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marco A Arriaga
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Ricardo Perez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Auwal A Bala
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Ana C Leandro
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Vince P Diego
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marcio Almeida
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Jason G Parsons
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Eron G Manusov
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Jacob A Galan
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
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7
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Orchard SE. What have Data Standards ever done for us? Mol Cell Proteomics 2025:100933. [PMID: 40024375 DOI: 10.1016/j.mcpro.2025.100933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025] Open
Abstract
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies for both the field of molecular interaction and that of mass spectrometry for more than 20 years. This review explores some of the ways that the proteomics community has benefitted from the development of community standards and takes a look at some of the tools and resources that have been improved or developed as a result of the work of the HUPO-PSI.
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Affiliation(s)
- S E Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
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Wu P, Zhao L, Du Y, Lu J, He Y, Shu Q, Peng H, Wang X. Melatonin protects retinal pigment epithelium cells against ferroptosis in AMD via the PI3K/AKT/MDM2/P53 pathway. Front Pharmacol 2025; 16:1543575. [PMID: 40083383 PMCID: PMC11903707 DOI: 10.3389/fphar.2025.1543575] [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: 12/11/2024] [Accepted: 01/21/2025] [Indexed: 03/16/2025] Open
Abstract
Introduction Oxidative stress-prompted degeneration of the retinal pigment epithelium (RPE) notably contributes to the onset of age-related macular degeneration (AMD). However, the pathways leading to RPE deterioration and possible preventative strategies are not yet completely comprehended. Methods Ferroptosis was assayed through the evaluation of lipid peroxidation (C11-BODIPY and MDA), reactive oxygen species (ROS), transmission electron microscopy (TEM), iron content measurement, q-PCR, western blotting, and immunofluorescence. To assess the structure and retinal function of RPE in mice, ERG (electroretinography), OCT (optical coherence tomography), and H&E (hematoxylin and eosin) staining were employed. Network pharmacology methods were utilized to elucidate the potential mechanisms underlying melatonin's protective effects against ferroptosis in RPE cells in AMD. Genetic engineering techniques were applied to investigate the regulatory relationships among phosphatidylinositol 3-kinase (PI3K), protein kinase-B (AKT), murine double minute-2 (MDM2), protein 53 (P53), and solute carrier family 7 member 11 (SLC7A11). In vitro knockdown experiments of MDM2 were conducted to explore its regulatory role in ferroptosis within RPE cells. Results Aβ1-40 can trigger ferroptosis in RPE cells. Melatonin can inhibit the oxidative stress and ferroptosis induced by Aβ1-40 in RPE cells. Melatonin exhibits a protective effect on Aβ1-40-induced AMD, significantly improving the structure of the mouse retina and RPE layer, and facilitating the restoration of visual function. Network pharmacology methods revealed that the potential targets of melatonin in AMD are closely related to ferroptosis, and indicated that the predominant pathways are significantly associated with the PI3K/AKT/MDM2/P53 signaling pathway. Knocking down the specific expression of MDM2 can significantly weaken the inhibitory effect of melatonin on oxidative stress and ferroptosis. Discussion Melatonin can suppress cell death by ferroptosis in RPE via the PI3K/AKT/MDM2/P53 pathway, thereby preventing and decelerating the progression of AMD.
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Affiliation(s)
- Ping Wu
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, Chongqing Aier Eye Hospital, Chongqing, China
| | - Long Zhao
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Du
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Lu
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxia He
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinxin Shu
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Peng
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xing Wang
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Huang R, Xia H, Meng T, Fan Y, Tang X, Li Y, Zhang T, Deng J, Yao B, Huang Y, Yang Y. Construction of human pluripotent stem cell-derived testicular organoids and their use as humanized testis models for evaluating the effects of semaglutide. Theranostics 2025; 15:2597-2623. [PMID: 39990223 PMCID: PMC11840739 DOI: 10.7150/thno.104523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 01/15/2025] [Indexed: 02/25/2025] Open
Abstract
Background: The generation of human testicular organoids from human induced pluripotent stem cells (hiPSCs) presents exciting opportunities for gonadal developmental biology, and reproductive disease modeling. However, creating organoids that closely mimic the tissue structure of testes remains challenging. Methods: In this study, we established a method for generating testicular organoids (TOs) from hiPSCs using a stepwise differentiation approach and a combination of hanging drop and rotational culture systems. The capability of hiPSC-derived precursor testicular cells to self-assemble into organoids was confirmed by detection of morphology, single-cell RNA-sequencing, and protein profiles. The reliability of testicular organoids as a drug evaluation model was assessed by the measurements of transcriptome signatures and functional features, including hormone responsiveness and blood-testis barrier (BTB) formation, and drug sensitivity assessment by recording cell viability and BTB integrity in organoids exposed to reproductive toxicants. Finally, we applied testicular organoids to evaluate the effects of semaglutide, a glucagon-like peptide-1 receptor agonist (GLP-1 RA), on testicular function, thereby underscoring their utility as a model for drug evaluation. Results: These organoids exhibited testicular cord-like structures and BTB function. RNA sequencing and functional assays confirmed that testicular organoids possess gene expression profiles and endocrine functions regulated by gonadotropins, closely resembling those of testicular tissue. Notably, these organoids displayed sensitivity to semaglutide. Treatment with semaglutide resulted in reduced testosterone levels and downregulation of INHBB expression, aligning with previous clinical observations. Conclusions: These findings introduced a method for generating testicular organoids from human pluripotent stem cells, highlighting their potential as valuable models for studying testicular function, drug toxicity, and the effects of compounds like semaglutide on testicular health.
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Affiliation(s)
- Rufei Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Huan Xia
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Tao Meng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yufei Fan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Xun Tang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yifang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Tiantian Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jingxian Deng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Bing Yao
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Yadong Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Yan Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
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10
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The UniProt Consortium, Bateman A, Martin MJ, Orchard S, Magrane M, Adesina A, Ahmad S, Bowler-Barnett EH, Bye-A-Jee H, Carpentier D, Denny P, Fan J, Garmiri P, Gonzales LJDC, Hussein A, Ignatchenko A, Insana G, Ishtiaq R, Joshi V, Jyothi D, Kandasaamy S, Lock A, Luciani A, Luo J, Lussi Y, Marin JSM, Raposo P, Rice DL, Santos R, Speretta E, Stephenson J, Totoo P, Tyagi N, Urakova N, Vasudev P, Warner K, Wijerathne S, Yu CWH, Zaru R, Bridge AJ, Aimo L, Argoud-Puy G, Auchincloss AH, Axelsen KB, Bansal P, Baratin D, Batista Neto TM, Blatter MC, Bolleman JT, Boutet E, Breuza L, Gil BC, Casals-Casas C, Echioukh KC, Coudert E, Cuche B, de Castro E, Estreicher A, Famiglietti ML, Feuermann M, Gasteiger E, Gaudet P, Gehant S, Gerritsen V, Gos A, Gruaz N, Hulo C, Hyka-Nouspikel N, Jungo F, Kerhornou A, Mercier PL, Lieberherr D, Masson P, Morgat A, Paesano S, Pedruzzi I, Pilbout S, Pourcel L, Poux S, Pozzato M, Pruess M, Redaschi N, Rivoire C, Sigrist CJA, Sonesson K, Sundaram S, Sveshnikova A, Wu CH, Arighi CN, Chen C, Chen Y, Huang H, Laiho K, Lehvaslaiho M, McGarvey P, Natale DA, Ross K, Vinayaka CR, Wang Y, Zhang J. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Res 2025; 53:D609-D617. [PMID: 39552041 PMCID: PMC11701636 DOI: 10.1093/nar/gkae1010] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/14/2024] [Accepted: 10/16/2024] [Indexed: 11/19/2024] Open
Abstract
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe ongoing changes to our production pipeline to limit the sequences available in UniProtKB to high-quality, non-redundant reference proteomes. We continue to manually curate the scientific literature to add the latest functional data and use machine learning techniques. We also encourage community curation to ensure key publications are not missed. We provide an update on the automatic annotation methods used by UniProtKB to predict information for unreviewed entries describing unstudied proteins. Finally, updates to the UniProt website are described, including a new tab linking protein to genomic information. In recognition of its value to the scientific community, the UniProt database has been awarded Global Core Biodata Resource status.
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11
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Marzano V, Levi Mortera S, Putignani L. Insights on Wet and Dry Workflows for Human Gut Metaproteomics. Proteomics 2024:e202400242. [PMID: 39740098 DOI: 10.1002/pmic.202400242] [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: 07/16/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/02/2025]
Abstract
The human gut microbiota (GM) is a community of microorganisms that resides in the gastrointestinal (GI) tract. Recognized as a critical element of human health, the functions of the GM extend beyond GI well-being to influence overall systemic health and susceptibility to disease. Among the other omic sciences, metaproteomics highlights additional facets that make it a highly valuable discipline in the study of GM. Indeed, it allows the protein inventory of complex microbial communities. Proteins with associated taxonomic membership and function are identified and quantified from their constituent peptides by liquid chromatography coupled to mass spectrometry analyses and by querying specific databases (DBs). The aim of this review was to compile comprehensive information on metaproteomic studies of the human GM, with a focus on the bacterial component, to assist newcomers in understanding the methods and types of research conducted in this field. The review outlines key steps in a metaproteomic-based study, such as protein extraction, DB selection, and bioinformatic workflow. The importance of standardization is emphasized. In addition, a list of previously published studies is provided as hints for researchers interested in investigating the role of GM in health and disease states.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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12
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Chen M, Chen X, Chen Q, Chu C, Yang S, Wu C, You Y, Hung A, Yang AWH, Sun X, Zhou L, Zhao X, Li H, Liu Y. Potential candidates from a functional food Zanthoxyli Pericarpium (Sichuan pepper) for the management of hyperuricemia: high-through virtual screening, network pharmacology and dynamics simulations. Front Endocrinol (Lausanne) 2024; 15:1436360. [PMID: 39722812 PMCID: PMC11668583 DOI: 10.3389/fendo.2024.1436360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 11/22/2024] [Indexed: 12/28/2024] Open
Abstract
Introduction Hyperuricemia (HUA) is a metabolic syndrome caused by purine metabolism disorders. Zanthoxyli Pericarpium (ZP) is a medicinal and food homologous plant, and its ripe peel is used to treat diseases and as a spice for cooking. Some studies have shown that ZP can inhibit the formation of xanthine oxidase and reduce the production of uric acid. Methods Through network pharmacology, ZP's potential targets and mechanisms for HUA treatment were identified. Databases like TCMSP, UniProt, and Swiss Target Prediction were utilized for ZP's active ingredients and targets. HUA-related targets were filtered using GeneCards, Drugbank, and Open Targets. Core targets for ZP's HUA treatment were mapped in a PPI network and analyzed with Cytoscape. GO and KEGG pathway enrichments were conducted on intersected targets via DAVID. Molecular docking and virtual screening were performed to find optimal binding pockets, and ADMET screening assessed compound safety. Molecular dynamics simulations confirmed compound stability in binding sites. Results We identified 81 ZP active ingredient targets, 140 HUA-related targets, and 6 drug targets, with xanthine dehydrogenase (XDH) as the top core target. Molecular docking revealed ZP's active ingredients had strong binding to XDH. Virtual screening via Protein plus identified 48 compounds near the optimal binding pocket, with 2'-methylacetophenone, ledol, beta-sitosterol, and ethyl geranate as the most promising. Molecular dynamics simulations confirmed binding stability, suggesting ZP's potential in HUA prevention and the need for further experimental validation. Conclusion Our study provides foundations for exploring the mechanism of the lowering of uric acid by ZP and developing new products of ZP. The role of ZP in the diet may provide a new dietary strategy for the prevention of HUA, and more experimental studies are needed to confirm our results in the future.
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Affiliation(s)
- Meilin Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Xiaomei Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qinghong Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Chenyang Chu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Shuxuan Yang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Chuanghai Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Yanting You
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Angela Wei Hong Yang
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, VIC, Australia
| | - Xiaomin Sun
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Lin Zhou
- Endocrinology Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoshan Zhao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Traditional Chinese Medicine Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hong Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Yanyan Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Traditional Chinese Medicine Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
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13
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Arıkan M, Atabay B. Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases. J Proteome Res 2024; 23:5250-5262. [PMID: 39449618 DOI: 10.1021/acs.jproteome.4c00665] [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: 10/26/2024]
Abstract
In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availability of well-curated reference databases and tools for custom database construction is essential to enhance the performance of metaproteomics analyses. In this review, we first provide an overview of metaproteomics by presenting a concise historical background, outlining a typical experimental and bioinformatics workflow, emphasizing the crucial step of constructing a protein sequence database for metaproteomics. We then delve into the current tools available for building such databases, highlighting their individual approaches, utility, and advantages and limitations. Next, we examine existing protein sequence databases, detailing their scope and relevance in metaproteomics research. Then, we provide practical recommendations for constructing protein sequence databases for metaproteomics, along with an overview of the current challenges in this area. We conclude with a discussion of anticipated advancements, emerging trends, and future directions in the construction of protein sequence databases for metaproteomics.
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Affiliation(s)
- Muzaffer Arıkan
- Biotechnology Division, Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Türkiye
| | - Başak Atabay
- Department of Biomedical Engineering, School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul 34810, Türkiye
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14
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Zhu Y, Shi J, Wang Q, Zhu Y, Li M, Tian T, Shi H, Shang K, Yin Z, Zhang F. Novel dual-pathogen multi-epitope mRNA vaccine development for Brucella melitensis and Mycobacterium tuberculosis in silico approach. PLoS One 2024; 19:e0309560. [PMID: 39466745 PMCID: PMC11515988 DOI: 10.1371/journal.pone.0309560] [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: 07/05/2024] [Accepted: 08/13/2024] [Indexed: 10/30/2024] Open
Abstract
Brucellosis and Tuberculosis, both of which are contagious diseases, have presented significant challenges to global public health security in recent years. Delayed treatment can exacerbate the conditions, jeopardizing patient lives. Currently, no vaccine has been approved to prevent these two diseases simultaneously. In contrast to traditional vaccines, mRNA vaccines offer advantages such as high efficacy, rapid development, and low cost, and their applications are gradually expanding. This study aims to develop multi-epitope mRNA vaccines argeting Brucella melitensis and Mycobacterium tuberculosis H37Rv (L4 strain) utilizing immunoinformatics approaches. The proteins Omp25, Omp31, MPT70, and MPT83 from the specified bacteria were selected to identify the predominant T- and B-cell epitopes for immunological analysis. Following a comprehensive evaluation, a vaccine was developed using helper T lymphocyte epitopes, cytotoxic T lymphocyte epitopes, linear B-cell epitopes, and conformational B-cell epitopes. It has been demonstrated that multi-epitope mRNA vaccines exhibit increased antigenicity, non-allergenicity, solubility, and high stability. The findings from molecular docking and molecular dynamics simulation revealed a robust and enduring binding affinity between multi-epitope peptides mRNA vaccines and TLR4. Ultimately, Subsequently, following the optimization of the nucleotide sequence, the codon adaptation index was calculated to be 1.0, along with an average GC content of 54.01%. This indicates that the multi-epitope mRNA vaccines exhibit potential for efficient expression within the Escherichia coli(E. coli) host. Analysis through immune modeling indicates that following administration of the vaccine, there may be variation in immunecell populations associated with both innate and adaptive immune reactions. These types encompass helper T lymphocytes (HTL), cytotoxic T lymphocytes (CTL), regulatory T lymphocytes, natural killer cells, dendritic cells and various immune cell subsets. In summary, the results suggest that the newly created multi-epitope mRNA vaccine exhibits favorable attributes, offering novel insights and a conceptual foundation for potential progress in vaccine development.
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Affiliation(s)
- Yuejie Zhu
- Department of Reproductive Assistance, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Juan Shi
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Yun Zhu
- Xinjiang Uygur Autonomous Region Disease Prevention Control Center, Urumqi, Xinjiang, China
| | - Min Li
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Tingting Tian
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Huidong Shi
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Kaiyu Shang
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhengwei Yin
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
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15
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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16
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Zhou Z, Zhu F, Ma S, Tan C, Yang H, Zhang P, Xu Y, Qin R, Luo Y, Chen J, Pan P. Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method. Med Mycol 2024; 62:myae080. [PMID: 39122658 DOI: 10.1093/mmy/myae080] [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: 03/23/2024] [Revised: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024] Open
Abstract
Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.
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Affiliation(s)
- Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
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Zheng X, Shen J, Jiang H, Tian M, Wang Q, Guo K, Chen R, Xia Q, Yan Q, Du L, Duan S. Exploring the multifaceted role of GCN1: Implications in cellular responses and disease pathogenesis. Biomed Pharmacother 2024; 175:116681. [PMID: 38705128 DOI: 10.1016/j.biopha.2024.116681] [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: 02/04/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024] Open
Abstract
GCN1 is a highly conserved protein present widely across eukaryotes. As an upstream activator of protein kinase GCN2, GCN1 plays a pivotal role in integrated stress responses, such as amino acid starvation and oxidative stress. Through interaction with GCN2, GCN1 facilitates the activation of GCN2, thus initiating downstream signaling cascades in response to cellular stressors. In these contexts, the activation of GCN2 necessitates the presence and action of GCN1. Notably, GCN1 also operates as a ribosome collision sensor, contributing significantly to the translation quality control pathway. These discoveries offer valuable insights into cellular responses to internal stresses, vital for maintaining cellular homeostasis. Additionally, GCN1 exhibits the ability to regulate the cell cycle and suppress inflammation, among other processes, independently of GCN2. Our review outlines the structural characteristics and biological functions of GCN1, shedding light on its significant involvement in the onset and progression of various cancer and non-cancer diseases. Our work underscores the role of GCN1 in the context of drug therapeutic effects, hinting at its potential as a promising drug target. Furthermore, our work delves deep into the functional mechanisms of GCN1, promising innovative avenues for the diagnosis and treatment of diseases in the future. The exploration of GCN1's multifaceted roles not only enhances our understanding of its mechanisms but also paves the way for novel therapeutic interventions. The ongoing quest to unveil additional functions of GCN1 holds the promise of further enriching our comprehension of its mode of action.
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Affiliation(s)
- Xinying Zheng
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Hongting Jiang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Mei Tian
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China; Geriatric Medicine Center, Department of Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Kailin Guo
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Ruixiu Chen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Qing Xia
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Qibin Yan
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China
| | - Lihua Du
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang 310015, China.
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18
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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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