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Ivanov MV, Kopeykina AS, Gorshkov MV. Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38938158 DOI: 10.1021/jasms.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a method of choice for quantitative proteomic applications requiring high throughput analysis of large cohorts of samples. With the advent of the combination of high resolution mass spectrometry with an asymmetric track lossless analyzer, these DIA capabilities were further extended with the recent demonstration of quantitative analyses at the speed of up to hundreds of samples per day. In particular, the proteomic data for the brain samples related to multiple system atrophy disease were acquired using 7 and 28 min chromatography gradients (Guzman et al., Nat. Biotech. 2024). In this work, we applied the recently introduced DirectMS1 method to reanalysis of these data using only MS1 spectra. Both DirectMS1 and DIA results were matched against long gradient DDA analysis from the earlier study of the same sample cohort. While the quantitation efficiency of DirectMS1 was comparable with DIA on the same data sets, we found an additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples missed by the MS/MS-based quantitation methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in high-throughput quantitative proteomic studies.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna S Kopeykina
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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Xie Y, Li J, Tao Q, Wu Y, Liu Z, Chen Y, Zeng C. Identification of subclusters and prognostic genes based on GLS-associated molecular signature in ulcerative colitis. Sci Rep 2024; 14:13102. [PMID: 38849409 PMCID: PMC11161595 DOI: 10.1038/s41598-024-63891-2] [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: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic and recurrent inflammatory disease that affects the colon and rectum. The response to treatment varies among individuals with UC. Therefore, the aim of this study was to identify and explore potential biomarkers for different subtypes of UC and examine their association with immune cell infiltration. We obtained UC RNA sequencing data from the GEO database, which included the training set GSE92415 and the validation set GSE87473 and GSE72514. UC patients were classified based on GLS and its associated genes using consensus clustering analysis. We identified differentially expressed genes (DEGs) in different UC subtypes through a differential expression analysis of the training cohort. Machine learning algorithms, including Weighted Gene Co-Expression Network Analysis (WGCNA), Least Absolute Shrinkage and Selection Operator (LASSO), and Support Vector Machine Recursive Feature Elimination (SVM-RFE), were utilized to identify marker genes for UC. The CIBERSORT algorithm was used to determine the abundance of various immune cells in UC and their correlation with UC signature genes. Finally, we validated the expression of GLS through in vivo and ex vivo experiments. The expression of GLS was found to be elevated in patients with UC compared to normal patients. GLS and its related genes were able to classify UC patients into two subtypes, C1 and C2. The C1 subtype, as compared to the C2 subtype, showed a higher Mayo score and poorer treatment response. A total of 18 DEGs were identified in both subtypes, including 7 up-regulated and 11 down-regulated genes. Four UC signature genes (CWH43, HEPACAM2, IL24, and PCK1) were identified and their diagnostic value was validated in a separate cohort (AUC > 0.85). Furthermore, we found that UC signature biomarkers were linked to the immune cell infiltration. CWH43, HEPACAM2, IL24, and PCK1 may serve as potential biomarkers for diagnosing different subtypes of UC, which could contribute to the development of targeted molecular therapy and immunotherapy for UC.
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Affiliation(s)
- Yang Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jun Li
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qing Tao
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yonghui Wu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zide Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
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Nguyen TX, Agazzi A, McGill S, Weidt S, Han QH, Gelemanović A, McLaughlin M, Savoini G, Eckersall PD, Burchmore R. Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed Part II: Ileum proteomes. J Proteomics 2023; 270:104739. [PMID: 36174954 DOI: 10.1016/j.jprot.2022.104739] [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: 03/25/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/01/2023]
Abstract
This study evaluates how long-term dietary low ω6:ω3 ratio in sows and offspring's seaweed (SW) intake affects piglet intestinal function and growth through modifying ileum proteome. Sows were assigned to either control diet (CR, ω6:ω3 ratio = 13:1) or treatment diet (LR, ω6:ω3 = 4:1) during gestation and lactation (n = 8 each). The male weaned offspring were received a basal diet with or without SW powder supplementation (4 g/kg) for 21 days, denoted as SW and CT groups, respectively. In total, four groups of weaned piglets were formed following maternal and offspring's diets combination, represented by CRCT, CRSW, LRCT, and LRSW (n = 10 each). Piglet ileum tissue was collected on day 22 post-weaning and analysed using TMT-based quantitative proteomics. The differentially abundant proteins (n = 300) showed the influence of maternal LR diet on protein synthesis, cell proliferation, and cell cycle regulation. In contrast, the SW diet lowered the inflammation severity and promoted ileal tissue development in CRSW piglets but reduced the fat absorption capacity in LRSW piglets. These results uncovered the mechanism behind the anti-inflammation and intestinal-boosting effects of maternal LR diet in piglets supplemented with SW.
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Affiliation(s)
- Thi Xuan Nguyen
- Università degli Studi di Milano, Via dell'Università, 6, 26900 Lodi, Italy; University of Glasgow, Bearsden Rd, G61 1QH, United Kingdom; Vietnam National University of Agriculture, Hanoi, Viet Nam.
| | - Alessandro Agazzi
- Università degli Studi di Milano, Via dell'Università, 6, 26900 Lodi, Italy
| | - Suzanne McGill
- University of Glasgow, Bearsden Rd, G61 1QH, United Kingdom
| | - Stefan Weidt
- University of Glasgow, Bearsden Rd, G61 1QH, United Kingdom
| | - Quang Hanh Han
- University of Glasgow, Bearsden Rd, G61 1QH, United Kingdom; Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Andrea Gelemanović
- Mediterranean Institute for Life Sciences (MedILS), Meštrovićevo šetalište 45, 21000 Split, Croatia
| | | | - Giovanni Savoini
- Università degli Studi di Milano, Via dell'Università, 6, 26900 Lodi, Italy
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Zhang Y, Zhang Q, Li H, Cong H, Qu Y. In vitro and in vivo anti−Toxoplasma activities of HDAC inhibitor Panobinostat on experimental acute ocular toxoplasmosis. Front Cell Infect Microbiol 2022; 12:1002817. [PMID: 36171756 PMCID: PMC9510647 DOI: 10.3389/fcimb.2022.1002817] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
Ocular toxoplasmosis (OT) is retinochoroiditis caused by Toxoplasma gondii infection, which poses a huge threat to vision. However, most traditional oral drugs for this disease have multiple side effects and have difficulty crossing the blood-retinal barrier, so the new alternative strategy is required to be developed urgently. Histone deacetylases (HDAC) inhibitors, initially applied to cancer, have attracted considerable attention as potential anti-Toxoplasma gondii drugs. Here, the efficacy of a novel HDAC inhibitor, Panobinostat (LBH589), against T. gondii has been investigated. In vitro, LBH589 inhibited the proliferation and activity of T. gondii in a dose-dependent manner with low toxicity to retinal pigment epithelial (RPE) cells. In vivo, optical coherence tomography (OCT) examination and histopathological studies showed that the inflammatory cell infiltration and the damage to retinal architecture were drastically reduced in C57BL/6 mice upon treatment with intravitreal injection of LBH589. Furthermore, we have found the mRNA expression levels of inflammatory cytokines were significantly decreased in LBH589–treated group. Collectively, our study demonstrates that LBH589 holds great promise as a preclinical candidate for control and cure of ocular toxoplasmosis.
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Affiliation(s)
- Yu Zhang
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Qingqing Zhang
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Haiming Li
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Hua Cong
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Hua Cong, ; Yi Qu,
| | - Yi Qu
- Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Hua Cong, ; Yi Qu,
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Moreira-Silva F, Henrique R, Jerónimo C. From Therapy Resistance to Targeted Therapies in Prostate Cancer. Front Oncol 2022; 12:877379. [PMID: 35686097 PMCID: PMC9170957 DOI: 10.3389/fonc.2022.877379] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is the second most common malignancy among men worldwide. Although early-stage disease is curable, advanced stage PCa is mostly incurable and eventually becomes resistant to standard therapeutic options. Different genetic and epigenetic alterations are associated with the development of therapy resistant PCa, with specific players being particularly involved in this process. Therefore, identification and targeting of these molecules with selective inhibitors might result in anti-tumoral effects. Herein, we describe the mechanisms underlying therapy resistance in PCa, focusing on the most relevant molecules, aiming to enlighten the current state of targeted therapies in PCa. We suggest that selective drug targeting, either alone or in combination with standard treatment options, might improve therapeutic sensitivity of resistant PCa. Moreover, an individualized analysis of tumor biology in each PCa patient might improve treatment selection and therapeutic response, enabling better disease management.
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Affiliation(s)
- Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences of the University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences of the University of Porto (ICBAS-UP), Porto, Portugal
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Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
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Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
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