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Wang C, Huyan T, Guo W, Shu Q, Li Q, Shi J. NTCdb: Single-cell transcriptome database of human inflammatory-associated diseases. Comput Struct Biotechnol J 2024; 23:1978-1989. [PMID: 38765608 PMCID: PMC11098674 DOI: 10.1016/j.csbj.2024.04.057] [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: 01/15/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
With both the advancement of technology and the decline in costs, single-cell transcriptomics sequencing has become widespread in the biomedical area in recent years. It can facilitate the pathogenic characteristics at the single-cell level, which will assist clinical researchers in exploring the mechanism of diseases. As a result, single-cell transcriptome data based on clinical samples grew exponentially. However, there is still a lack of a comprehensive database about immunocytes in inflammatory-associated diseases. To address this deficiency, we propose a human inflammatory-associated disease-based single-cell transcriptome database, NTCdb (www.ntcdb.org.cn). NTCdb integrates the open-source data of 1,023,166 cells derived from 11 tissues of 17 inflammatory-associated diseases in a uniform pipeline. It provides a set of analyzing results, including cell communication analysis, enrichment analysis, and Pseudo-Time analysis, to obtain various characteristics of immune cells in inflammatory-associated disease. Taking COVID-19 as a case study, NTCdb displays important information including potentially significant functions of certain cells, genes, and signaling pathways, as well as the commonalities of specific immunocytes between different inflammatory-associated disease.
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Affiliation(s)
| | | | - Wuli Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Qi Shu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | | | - Jianyu Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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Sommella E, Capaci V, Aloisio M, Salviati E, Campiglia P, Molinario G, Licastro D, Di Lorenzo G, Romano F, Ricci G, Monasta L, Ura B. A Label-Free Proteomic Approach for the Identification of Biomarkers in the Exosome of Endometrial Cancer Serum. Cancers (Basel) 2022; 14:6262. [PMID: 36551747 PMCID: PMC9776976 DOI: 10.3390/cancers14246262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Endometrial cancers (ECs) are mostly adenocarcinomas arising from the inner part of the uterus. The identification of serum biomarkers, either soluble or carried in the exosome, may be useful in making an early diagnosis. We used label-free quantification mass spectrometry (LFQ-MS)-based proteomics to investigate the proteome of exosomes in the albumin-depleted serum from 12 patients with EC, as compared to 12 healthy controls. After quantification and statistical analysis, we found significant changes in the abundance (p < 0.05) of 33 proteins in EC vs. control samples, with a fold change of ≥1.5 or ≤0.6. Validation using Western blotting analysis in 36 patients with EC as compared to 36 healthy individuals confirmed the upregulation of APOA1, HBB, CA1, HBD, LPA, SAA4, PF4V1, and APOE. A multivariate logistic regression model based on the abundance of these proteins was able to separate the controls from the EC patients with excellent sensitivity levels, particularly for stage 1 ECs. The results show that using LFQ-MS to explore the specific proteome of serum exosomes allows for the identification of biomarkers in EC. These observations suggest that PF4V1, CA1, HBD, and APOE represent biomarkers that are able to reach the clinical stage, after a validation phase.
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Affiliation(s)
- Eduardo Sommella
- Department of Pharmacy, University of Salerno, 84084 Salerno, Italy
| | - Valeria Capaci
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | | | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Salerno, Italy
| | | | | | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | - Federico Romano
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | - Giuseppe Ricci
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | - Blendi Ura
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy
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Deng B, Liu W, Pu L, Wang X, Duan R, Wang T, Wang Z, Du L, Gao Z, Chen Z. Quantitative Proteomics Reveals the Effects of Resveratrol on High-Altitude Polycythemia Treatment. Proteomics 2020; 20:e1900423. [PMID: 32468662 DOI: 10.1002/pmic.201900423] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/18/2020] [Indexed: 12/17/2022]
Abstract
High-altitude polycythemia (HAPC) is a common plateau chronic disease in which red blood cells are compensatory hyperproliferative due to high altitude hypoxic environment. HAPC severely affects the physical and mental health of populations on the plateau. However, the pathogenesis and treatment of HAPC has been rarely investigated. Here, the hypoxia-induced HAPC model of rat is established, in which hemoglobin concentration significantly increases and platelets clearly decrease. The effect of resveratrol upon hypoxia enables HAPC remission and makes hemoglobin and platelet tend to a normal level. Furthermore, quantitative proteomics is applied to investigate the plasma proteome variation and the underlying molecular regulation during HAPC occurrence and treatment with resveratrol. Hypoxia promotes erythrocyte developing and differentiating and disrupts cytoskeleton organization. Notably, the resveratrol administration reverses the proteome change pattern due to hypoxia and contributes to plateau adaption. Quantitative verification of differentially expressed proteins confirms the roles of resveratrol in HAPC. Resveratrol is expected to be useful for HAPC treatment.
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Affiliation(s)
- Bingnan Deng
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Weili Liu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Lingling Pu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Xinxing Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Ruifeng Duan
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tianhui Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zirou Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Lianqun Du
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhixian Gao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhaoli Chen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
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Biological Effects of Korean Red Ginseng Polysaccharides in Aged Rat Using Global Proteomic Approach. Molecules 2020; 25:molecules25133019. [PMID: 32630349 PMCID: PMC7412055 DOI: 10.3390/molecules25133019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/20/2020] [Accepted: 06/29/2020] [Indexed: 01/07/2023] Open
Abstract
Much has been written on the physiological benefits of Korean Red Ginseng (KRG). Among its various components, ginsenosides have been widely investigated for their various pharmacological effects. However, polysaccharides are a major KRG component that has not received scrutiny similar to that of ginsenosides. The present study aims to fill that gap in the existing literature and to investigate the possible functions of polysaccharide in KRG. The researchers evaluated proteomic changes in non-saponin fractions with rich polysaccharides (NFP) in KRG. Based on the serum analysis, proteomics analysis of the liver and the spleen was additionally conducted to identify related functions. We validated the suggested functions of NFP with the galactosamine-induced liver injury model and the cyclophosphamide-induced immunosuppression model. Then, we evaluated the antimetastatic potential of NFP in the lungs. Further proteomics analysis of the spleen and liver after ingestion confirmed functions related to immunity, cancer, hepatoprotection, and others. Then, we validated the suggested corresponding functions of the NFP in vivo model. NFP showed immune-enhancing effects, inhibited melanoma cell metastasis in the lung, and decreased liver damage. The results show that using the proteomic approach uncovers the potential effects of polysaccharides in KRG, which include enhancing the immune system and protecting the liver.
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Herráez-Albendea MM, González-Real E, Martínez-Fernández M. Hemoglobin Yuda: First case reported in Spain. Med Clin (Barc) 2018; 151:503-504. [PMID: 29496239 DOI: 10.1016/j.medcli.2018.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 11/20/2022]
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