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Torres-Sangiao E, Happonen L, Heusel M, Palm F, Gueto-Tettay C, Malmström L, Shannon O, Malmström J. Quantification of adaptive immune responses against protein binding interfaces in the streptococcal M1 protein. Mol Cell Proteomics 2024:100753. [PMID: 38527648 DOI: 10.1016/j.mcpro.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024] Open
Abstract
Bacterial or viral antigens can contain subdominant protein regions that elicit weak antibody responses upon vaccination or infection although there is accumulating evidence that antibody responses against subdominant regions can enhance the protective immune response. One proposed mechanism for subdominant protein regions is binding of host proteins that prevent antibody production against epitopes hidden within the protein binding interfaces. Here, we used affinity-purification combined with quantitative mass spectrometry (AP-MS) to examine the level of competition between antigen-specific antibodies and host-pathogen protein interaction networks using the M1 protein from Streptococcus pyogenes as a model system. As most humans have circulating antibodies against the M1 protein, we first used AP-MS to show that the M1 protein interspecies protein network formed with human plasma proteins is largely conserved in naïve mice. Immunizing mice with the M1 protein generated a time-dependent increase of anti-M1 antibodies. AP-MS analysis comparing the composition of the M1-plasma protein network from naïve and immunized mice showed a significant enrichment of 292 IgG peptides associated with 56 IgG chains in the immune mice. Despite the significant increase of bound IgGs, the levels of interacting plasma proteins were not significantly reduced in the immune mice. The results indicate that the antigen-specific polyclonal IgG against the M1 protein primarily targets epitopes outside the other plasma protein binding interfaces. In conclusion, this study demonstrates that AP-MS is a promising strategy to determine the relationship between antigen-specific antibodies and host-pathogen interaction networks that could be used to define subdominant protein regions of relevance for vaccine development.
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Affiliation(s)
- E Torres-Sangiao
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Health Research Institute of Santiago de Compostela (IDIS), Escherichia coli group. 15706 Santiago de Compostela, Spain; University Hospital Complex of Santiago de Compostela, Clinical Microbiology Lab. 15706 Santiago de Compostela, Spain.
| | - L Happonen
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - M Heusel
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Evosep ApS, Buchwaldsgade 35, Odense, Denmark
| | - F Palm
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - C Gueto-Tettay
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - L Malmström
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden
| | - O Shannon
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden; Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, 20506 Malmö, Sweden
| | - J Malmström
- Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine. BMC D13, SE-22184, Lund, Sweden.
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Carvalho SB, Profit L, Krishnan S, Gomes RA, Alexandre BM, Clavier S, Hoffman M, Brower K, Gomes-Alves P. SWATH-MS as a strategy for CHO host cell protein identification and quantification supporting the characterization of mAb purification platforms. J Biotechnol 2024; 384:1-11. [PMID: 38340900 DOI: 10.1016/j.jbiotec.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Host cell proteins (HCPs) are process-related impurities expressed by the host cells during biotherapeutics' manufacturing, such as monoclonal antibodies (mAbs). Some challenging HCPs evade clearance during the downstream processing and can be co-purified with the molecule of interest, which may impact product stability, efficacy, and safety. Therefore, HCP content is a critical quality attribute to monitor and quantify across the bioprocess. Here we explored a mass spectrometry (MS)-based proteomics tool, the sequential window acquisition of all theoretical fragment-ion spectra (SWATH) strategy, as an orthogonal method to traditional ELISA. The SWATH workflow was applied for high-throughput individual HCP identification and quantification, supporting characterization of a mAb purification platform. The design space of HCP clearance of two polishing resins was evaluated through a design of experiment study. Absolute quantification of high-risk HCPs was achieved (reaching 1.8 and 4.2 ppm limits of quantification, for HCP A and B respectively) using HCP-specific synthetic heavy labeled peptide calibration curves. Profiling of other HCPs was also possible using an average calibration curve (using labeled peptides from different HCPs). The SWATH approach is a powerful tool for HCP assessment during bioprocess development enabling simultaneous monitoring and quantification of different individual HCPs and improving process understanding of their clearance.
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Affiliation(s)
- Sofia B Carvalho
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2780-901, Portugal; ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. Da República, Oeiras 2780-157, Portugal
| | - Ludivine Profit
- Mammalian Platform, Global CMC Development, Sanofi R&D, Vitry-sur-Seine, France
| | - Sushmitha Krishnan
- Mammalian Platform, Global CMC Development, Sanofi R&D, Framingham, MA, USA
| | - Ricardo A Gomes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2780-901, Portugal; ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. Da República, Oeiras 2780-157, Portugal
| | - Bruno M Alexandre
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2780-901, Portugal; ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. Da República, Oeiras 2780-157, Portugal
| | - Severine Clavier
- BioAnalytics, Global CMC Development, Sanofi R&D, Vitry-sur-Seine, France
| | - Michael Hoffman
- Mammalian Platform, Global CMC Development, Sanofi R&D, Framingham, MA, USA
| | - Kevin Brower
- Mammalian Platform, Global CMC Development, Sanofi R&D, Framingham, MA, USA.
| | - Patrícia Gomes-Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2780-901, Portugal; ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. Da República, Oeiras 2780-157, Portugal.
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3
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Gonzalez-Martin R, de Castro P, Fernandez C, Quintana F, Quiñonero A, Ferrando M, Dominguez F. Proteomic Profiling Identifies Candidate Diagnostic Biomarkers of Hydrosalpinx in Endometrial Fluid: A Pilot Study. Int J Mol Sci 2024; 25:968. [PMID: 38256043 PMCID: PMC10816103 DOI: 10.3390/ijms25020968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Hydrosalpinx is a fluid occlusion and distension of the fallopian tubes, often resulting from pelvic inflammatory disease, which reduces the success of artificial reproductive technologies (ARTs) by 50%. Tubal factors account for approximately 25% of infertility cases, but their underlying molecular mechanisms and functional impact on other reproductive tissues remain poorly understood. This proteomic profiling study applied sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) to study hydrosalpinx cyst fluid and pre- and post-salpingectomy endometrial fluid. Among the 967 proteins identified, we found 19 and 17 candidate biomarkers for hydrosalpinx in pre- and post-salpingectomy endometrial fluid, respectively. Salpingectomy significantly affected 76 endometrial proteins, providing insights into the enhanced immune response and inflammation present prior to intervention, and enhanced coagulation cascades and wound healing processes occurring one month after intervention. These findings confirmed that salpingectomy reverses the hydrosalpinx-related functional impairments in the endometrium and set a foundation for further biomarker validation and the development of less-invasive diagnostic strategies for hydrosalpinx.
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Affiliation(s)
- Roberto Gonzalez-Martin
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (R.G.-M.); (P.d.C.); (A.Q.)
| | - Pedro de Castro
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (R.G.-M.); (P.d.C.); (A.Q.)
| | - Carmen Fernandez
- IVIRMA Global Research Alliance, IVI-RMA Bilbao, 48940 Bizkaia, Spain; (C.F.); (F.Q.); (M.F.)
| | - Fernando Quintana
- IVIRMA Global Research Alliance, IVI-RMA Bilbao, 48940 Bizkaia, Spain; (C.F.); (F.Q.); (M.F.)
| | - Alicia Quiñonero
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (R.G.-M.); (P.d.C.); (A.Q.)
| | - Marcos Ferrando
- IVIRMA Global Research Alliance, IVI-RMA Bilbao, 48940 Bizkaia, Spain; (C.F.); (F.Q.); (M.F.)
| | - Francisco Dominguez
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (R.G.-M.); (P.d.C.); (A.Q.)
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4
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Pandit AK, Misra S, Sengupta S, Chakraborty R, Singh P, Singh GP, Phuljhele S, Srivastava AK, Vibha D, Garg A, Shankar V, Mohania D, Shukla G, Prasad K. Cerebrospinal fluid proteins in idiopathic intracranial hypertension: An exploratory SWATH proteomics analysis. Proteomics Clin Appl 2024; 18:e2300021. [PMID: 37551060 DOI: 10.1002/prca.202300021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
PURPOSE The pathogenesis of idiopathic intracranial hypertension (IIH) is currently poorly understood. This exploratory study aimed to identify potential cerebrospinal fluid (CSF) biomarkers in IIH cases compared to controls using SWATH-MS proteomics approach. EXPERIMENTAL DESIGN CSF samples were collected prospectively from IIH cases and control subjects which were subjected to SWATH-MS based untargeted proteomics. Proteins with fold change > 1.5 or < 0.67 and p-value < 0.05 were considered significantly differentially expressed. Data are available via ProteomeXchange with identifier PXD027751. Statistical analysis was conducted in R version 3.6.2. RESULTS We included CSF samples from 33 subjects, consisting of 13 IIH cases and 20 controls. A total of 262 proteins were identified in Proteinpilot search. Through SWATH analysis, we quantified 232 proteins. We observed 37 differentially expressed proteins between the two groups with 24 upregulated and 13 downregulated proteins. There were two differential proteins among overweight versus non-overweight IIH cases. Network for 23 proteins was highly connected in the interaction analysis. CONCLUSIONS AND CLINICAL RELEVANCE Neurosecretory, neuroendocrine, and inflammatory proteins were predominantly involved in causing IIH. This exploratory study served as a platform to identify 37 differentially expressed proteins in IIH and also showed significant differences between overweight and non-overweight IIH patients.
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Affiliation(s)
- Awadh Kishor Pandit
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Shubham Misra
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Department of Neurology, Yale University, New Haven, USA
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rahul Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Gyaninder Pal Singh
- Department of Neuroanesthesiology and Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Phuljhele
- Department of Ophthalmology, Dr R.P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepti Vibha
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Garg
- Department of Neuroradiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Shankar
- Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India
| | - Dheeraj Mohania
- Dr R.P. Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Garima Shukla
- Department of Neurology (Epilepsy & Sleep Medicine), Department of Medicine, Queen's University, Kingston, Canada
| | - Kameshwar Prasad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Department of Neurology, Rajendra Institute of Medical Sciences, Ranchi, India
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5
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Babele P, Midha MK, Rao KVS, Kumar A. Temporal Profiling of Host Proteome against Different M. tuberculosis Strains Reveals Delayed Epigenetic Orchestration. Microorganisms 2023; 11:2998. [PMID: 38138142 PMCID: PMC10745383 DOI: 10.3390/microorganisms11122998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 12/24/2023] Open
Abstract
Apart from being preventable and treatable, tuberculosis is the deadliest bacterial disease afflicting humankind owing to its ability to evade host defence responses, many of which are controlled by epigenetic mechanisms. Here, we report the temporal dynamics of the proteome of macrophage-like host cells after infecting them for 6, 18, 30, and 42 h with two laboratory strains (H37Ra and H37Rv) and two clinical strains (BND433 and JAL2287) of Mycobacterium tuberculosis (MTB). Using SWATH-MS, the proteins characterized at the onset of infection broadly represented oxidative stress and cell cytoskeleton processes. Intermediary and later stages of infection are accompanied by a reshaping of the combination of proteins implicated in histone stability, gene expression, and protein trafficking. This study provides strain-specific and time-specific variations in the proteome of the host, which might further the development of host-directed therapeutics and diagnostic tools against the pathogen. Also, our findings accentuate the importance of proteomic tools in delineating the complex recalibration of the host defence enabled as an effect of MTB infection. To the best of our knowledge, this is the first comprehensive proteomic account of the host response to avirulent and virulent strains of MTB at different time periods of the life span of macrophage-like cells. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier PXD022352.
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Affiliation(s)
- Prabhakar Babele
- Translational Health Science and Technology Institute, Faridabad 121001, India; (P.B.); (K.V.S.R.)
| | | | - Kanury V. S. Rao
- Translational Health Science and Technology Institute, Faridabad 121001, India; (P.B.); (K.V.S.R.)
| | - Ajay Kumar
- Translational Health Science and Technology Institute, Faridabad 121001, India; (P.B.); (K.V.S.R.)
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6
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Álvarez S, Mullen AM, Álvarez C, Hamill RM, O'Neill E, Gagaoua M. Impact of sampling location and aging on the Longissimus thoracis et lumborum muscle proteome of dry-aged beef. Meat Sci 2023; 205:109315. [PMID: 37625354 DOI: 10.1016/j.meatsci.2023.109315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
This study aimed to explore the differences in the proteome and molecular pathways between two sampling locations (external, internal) of bovine Longissimus thoracis et lumborum (LTL) muscles at 0, 21, and 28 days of dry-aging (i.e. 3, 24, and 31 days post-mortem). It further assessed the impact of post-mortem aging on the meat proteome changes and the biological processes at interplay. Proteins related to defence response to bacterium and regulation of viral entry into host cell were identified to be more abundant on the external location before dry-aging, which may be associated to the oxidative conditions and microbial activity to which post-mortem muscle is exposed during dressing, chilling, and/or quartering of the carcasses. This highlights the relevance of sampling from interior tissues when searching for meat quality biomarkers. As dry-aging progressed, the meat proteome and related biological processes changed differently between sampling locations; proteins related to cell-cell adhesion and ATP metabolic processes pathways were revealed in the external location at 21 and 28 days, respectively. On the other hand, the impact of aging on the proteome of the interior meat samples, evidenced that muscle contraction and structure together with energy metabolism were the major pathways driving dry-aging. Additionally, aging impacted other pathways in the interior tissues, such as regulation of calcium import, neutrophil activation, and regeneration. Overall, the differences in the proteome allowed discriminating the three dry-aging times, regardless of the sampling location. Several proteins were proposed for validation as robust biomarkers to monitor the aging process (tenderization) of dry-aged beef: TTN, GRM4, EEF1A1, LDB3, CILP2, TNNT3, GAPDH, SERPINI1, and OMD.
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Affiliation(s)
- Sara Álvarez
- Dept. of Food Quality and Sensory Science, Teagasc Food Research Centre Ashtown, Dublin D15 DY05, Ireland; School of Food and Nutritional Sciences, University College, Cork, Western Road, Cork T12 YN60, Ireland
| | - Anne Maria Mullen
- Dept. of Food Quality and Sensory Science, Teagasc Food Research Centre Ashtown, Dublin D15 DY05, Ireland
| | - Carlos Álvarez
- Dept. of Food Quality and Sensory Science, Teagasc Food Research Centre Ashtown, Dublin D15 DY05, Ireland
| | - Ruth M Hamill
- Dept. of Food Quality and Sensory Science, Teagasc Food Research Centre Ashtown, Dublin D15 DY05, Ireland
| | - Eileen O'Neill
- School of Food and Nutritional Sciences, University College, Cork, Western Road, Cork T12 YN60, Ireland
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7
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Li ZQ, Yin XL, Gu HW, Zou D, Ding B, Li Z, Chen Y, Long W, Fu H, She Y. Revealing the chemical differences and their application in the storage year prediction of Qingzhuan tea by SWATH-MS based metabolomics analysis. Food Res Int 2023; 173:113238. [PMID: 37803551 DOI: 10.1016/j.foodres.2023.113238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 10/08/2023]
Abstract
It's generally believed that the longer the storage, the better the quality of dark tea, but the chemical differences of Qingzhuan tea (QZT) with different storage years is still unclear. Herein, in this work, an untargeted metabolomic approach based on SWATH-MS was established to investigate the differential compounds of QZT with 0-9 years' storage time. These QZT samples were roughly divided into two categories by principal component analysis (PCA). After orthogonal projections to latent structures discriminant analysis (OPLS-DA), 18 differential compounds were putatively identified as chemical markers for the storage year variation of QZT. Heatmap visualization showed that the contents of catechins, fatty acids, and some phenolic acids significantly reduced, flavonoid glycosides, triterpenoids, and 8-C N-ethyl-2-pyrrolidinone-substituted flavan-3-ols (EPSFs) increased with the increase of storage time. Furthermore, these chemical markers were verified by the peak areas corresponding to MS2 ions from SWATH-MS. Based on the extraction chromatographic peak areas of MS and MS2 ions, a duration time prediction model was built for QZT with correlation coefficient R2 of 0.9080 and 0.9701, and RMSEP value of 0.85 and 1.24, respectively. This study reveals the chemical differences of QZT with different storage years and provides a theoretical basis for the quality evaluation of stored dark tea.
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Affiliation(s)
- Zhi-Quan Li
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Xiao-Li Yin
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China.
| | - Hui-Wen Gu
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Dan Zou
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Baomiao Ding
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Zhenshun Li
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Ying Chen
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Wanjun Long
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Haiyan Fu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Yuanbin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China.
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. Proteome Changes Resulting from Malting in Hordein-Reduced Barley Lines. J Agric Food Chem 2023; 71:14079-14091. [PMID: 37712129 PMCID: PMC10540200 DOI: 10.1021/acs.jafc.3c02292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/18/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Hordeum vulgare L., commonly known as barley, is primarily used for animal feed and malting. The major storage proteins in barley are hordeins, known triggers of celiac disease (CD). Here, sequential window acquisition of all theoretical mass spectra (SWATH)-MS proteomics was employed to investigate the proteome profile of grain and malt samples from the malting barley cultivar Sloop and single-, double-, and triple hordein-reduced lines bred in a Sloop background. Using a discovery proteomics approach, 2688 and 3034 proteins were detected from the grain and malt samples, respectively. By utilizing label-free relative quantitation through SWATH-MS, a total of 2654 proteins have been quantified from grain and malt. The comparative analyses between the barley grain and malt samples revealed that the C-hordein-reduced lines have a more significant impact on proteome level changes due to malting than B- and D-hordein-reduced lines. Upregulated proteins in C-hordein-reduced lines were primarily involved in the tricarboxylic acid cycle and fatty acid peroxidation processes to provide more energy for seed germination during malting. By applying proteomics approaches after malting in hordein-reduced barley lines, we uncovered additional changes in the proteome driven by the genetic background that were not apparent in the sound grain. Our findings offer valuable insights for barley breeders and maltsters seeking to understand and optimize the performance of gluten-free grains in malt products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
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9
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Hamzelou S, Belobrajdic D, Juhász A, Brook H, Bose U, Colgrave ML, Broadbent JA. Nutrition, allergenicity and physicochemical qualities of food-grade protein extracts from Nannochloropsis oculata. Food Chem 2023; 424:136459. [PMID: 37247596 DOI: 10.1016/j.foodchem.2023.136459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Microalgae offer an opportunity to act as a sustainable source of dietary protein. This study aimed to evaluate the impact of different protein extraction methods on the nutritional and physicochemical properties of Nannochloropsis oculata. Food-grade protein extracts were obtained by hypotonic osmotic shock using milli-Q water. Food grade (FG) and non-food grade (NFG) extraction buffers were compared along with three cell disruption methods including bead beating, probe sonication and a combination of both methods for protein extraction. Mass spectrometry was used for protein and putative allergen identification in FG extracts. Bead beating led to a slightly higher number of identifiable proteins in FG extracts compared to control condition. Putative allergenic proteins were identified in FG extracts of N. oculata using different in-silico methods. These findings support the need to further evaluate the potential allergenic proteins in microalgae including N. oculata such as immunoglobulin E (IgE) binding tests.
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Affiliation(s)
- Sara Hamzelou
- CSIRO Health & Biosecurity, Adelaide, SA 5000, Australia.
| | | | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Henri Brook
- CSIRO Health & Biosecurity, Adelaide, SA 5000, Australia
| | - Utpal Bose
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
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10
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Meng X, Liu D, Guan Y. Advances in the application of label-free quantitative proteomic techniques in malignancy research. Biomed Chromatogr 2023:e5667. [PMID: 37125667 DOI: 10.1002/bmc.5667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Proteomics is the scientific discipline that deals with the protein composition of cells, tissues, and organisms and their patterns of change. It is considered an invaluable tool for tackling many challenges faced in medicine and biology. Among the available approaches, label-free quantitative proteomic techniques are extensively used to study malignant tumors due to their low cost, simple operation, and short cycle time. As a result, it provides a novel approach to explore the pathogenesis, diagnostic markers, and targeted drugs of malignant tumors. Here, we summarize the research progress and potential of label-free quantitative proteomics and discuss the application of such techniques in the research of malignancies.
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Affiliation(s)
- Xiao Meng
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Dong Liu
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Yan Guan
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
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11
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Barik SK, Tripathy SP, Bisht D, Singh P, Chakraborty R, Patil SA, Singh TP, Varshney D, Jena S, Mohanty KK. SWATH-MS analysis of plasma proteins among Indian HIV-1 infected patients. Bioinformation 2023; 19:392-398. [PMID: 37822814 PMCID: PMC10563564 DOI: 10.6026/97320630019392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
The identification and characterization of plasma proteins in drug resistant and drug sensitive in HIV-1 infected/AIDS patients were carried out using the SWATH-MS protocol. In total, 204 proteins were identified and quantified, 57 proteins were differentially expressed, out of which 25 proteins were down regulated and 32 proteins were up regulated in drug resistant patients. Six proteins such as complement C4-A, immunoglobulin heavy variable 1-2, carboxylic ester hydrolase, fibulin-1, immunoglobulin lambda constant7, secreted phosphoprotein 24 were differentially expressed in individuals with drug resistant HIV as compared to individuals with drug sensitive HIV. Gene ontology of 57 differentially expressed proteins was analysed and documented.
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Affiliation(s)
- Sushanta Kumar Barik
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India-282004
| | - Srikanth Prasad Tripathy
- ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, Tamil Nadu, India-600031
| | - Deepa Bisht
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India-282004
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, CSIR, New Delhi-110025
| | - Rahul Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, CSIR, New Delhi-110025
| | - Shripad A Patil
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India-282004
| | - Tej Pal Singh
- Sarojini Naidu Medical College, Agra, Uttar-Pradesh, India-282003
| | - Deepika Varshney
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India-282004
| | - Srikanta Jena
- Ravenshaw University, Odisha, Cuttack, India - 753003
| | - Keshar Kunja Mohanty
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar-Pradesh, India-282004
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12
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Ramírez Medina CR, Ali I, Baricevic-Jones I, Odudu A, Saleem MA, Whetton AD, Kalra PA, Geifman N. Proteomic signature associated with chronic kidney disease (CKD) progression identified by data-independent acquisition mass spectrometry. Clin Proteomics 2023; 20:19. [PMID: 37076799 PMCID: PMC10116780 DOI: 10.1186/s12014-023-09405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/14/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Halting progression of chronic kidney disease (CKD) to established end stage kidney disease is a major goal of global health research. The mechanism of CKD progression involves pro-inflammatory, pro-fibrotic, and vascular pathways, but pathophysiological differentiation is currently lacking. METHODS Plasma samples of 414 non-dialysis CKD patients, 170 fast progressors (with ∂ eGFR-3 ml/min/1.73 m2/year or worse) and 244 stable patients (∂ eGFR of - 0.5 to + 1 ml/min/1.73 m2/year) with a broad range of kidney disease aetiologies, were obtained and interrogated for proteomic signals with SWATH-MS. We applied a machine learning approach to feature selection of proteins quantifiable in at least 20% of the samples, using the Boruta algorithm. Biological pathways enriched by these proteins were identified using ClueGo pathway analyses. RESULTS The resulting digitised proteomic maps inclusive of 626 proteins were investigated in tandem with available clinical data to identify biomarkers of progression. The machine learning model using Boruta Feature Selection identified 25 biomarkers as being important to progression type classification (Area Under the Curve = 0.81, Accuracy = 0.72). Our functional enrichment analysis revealed associations with the complement cascade pathway, which is relevant to CKD as the kidney is particularly vulnerable to complement overactivation. This provides further evidence to target complement inhibition as a potential approach to modulating the progression of diabetic nephropathy. Proteins involved in the ubiquitin-proteasome pathway, a crucial protein degradation system, were also found to be significantly enriched. CONCLUSIONS The in-depth proteomic characterisation of this large-scale CKD cohort is a step toward generating mechanism-based hypotheses that might lend themselves to future drug targeting. Candidate biomarkers will be validated in samples from selected patients in other large non-dialysis CKD cohorts using a targeted mass spectrometric analysis.
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Affiliation(s)
- Carlos R. Ramírez Medina
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Ibrahim Ali
- Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Salford, UK
| | - Ivona Baricevic-Jones
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH UK
| | - Aghogho Odudu
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, UK
| | - Moin A. Saleem
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH UK
| | - Philip A. Kalra
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH UK
| | - Nophar Geifman
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH UK
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Musiał N, Bogucka A, Tretiakow D, Skorek A, Ryl J, Czaplewska P. Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands. Clin Proteomics 2023; 20:11. [PMID: 36949424 PMCID: PMC10035263 DOI: 10.1186/s12014-023-09402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Salivary stones, also known as sialoliths, are formed in a pathological situation in the salivary glands. So far, neither the mechanism of their formation nor the factors predisposing to their formation are known despite several hypotheses. While they do not directly threaten human life, they significantly deteriorate the patient's quality of life. Although this is not a typical research material, attempts are made to apply various analytical tools to characterise sialoliths and search for the biomarkers in their proteomes. In this work, we used mass spectrometry and SWATH-MS qualitative and quantitative analysis to investigate the composition and select proteins that may contribute to solid deposits in the salivary glands. Twenty sialoliths, previously characterized spectroscopically and divided into the following groups: calcified (CAL), lipid (LIP) and mixed (MIX), were used for the study. Proteins unique for each of the groups were found, including: for the CAL group among them, e.g. proteins from the S100 group (S100 A8/A12 and P), mucin 7 (MUC7), keratins (KRT1/2/4/5/13), elastase (ELANE) or stomatin (STOM); proteins for the LIP group-transthyretin (TTR), lactotransferrin (LTF), matrix Gla protein (MPG), submandibular gland androgen-regulated protein 3 (SMR3A); mixed stones had the fewest unique proteins. Bacterial proteins present in sialoliths have also been identified. The analysis of the results indicates the possible role of bacterial infections, disturbances in calcium metabolism and neutrophil extracellular traps (NETs) in the formation of sialoliths.
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Affiliation(s)
- Natalia Musiał
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland
- Institute of Biochemistry, Medical Faculty, Justus Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Dmitry Tretiakow
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Andrzej Skorek
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Jacek Ryl
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
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14
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Wang C, Zhao R, Zhao Z, Liu N, Cheng J, Guo M. Proteomic characterization and comparison of milk fat globule membrane proteins of Saanen goat milk from 3 habitats in China using SWATH-MS technique. J Dairy Sci 2023; 106:2289-2302. [PMID: 36870831 DOI: 10.3168/jds.2022-22393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/01/2022] [Indexed: 03/06/2023]
Abstract
Saanen goats are among the major dairy goats in China. In present study, variation of milk fat globule membrane proteins profile of Saanen goat milk caused by geographic location was investigated using sequential window acquisition of all theoretical fragment ions data-independent acquisition mass spectrometry based proteomic approach. A total of 1,001 proteins were quantified in goat milk collected from 3 habitats of China [Guangdong (GD); Inner Mongolia (IM); Shannxi (SX)]. Most of the proteins were found to act cellular process of biological process, cell of cellular component, binding of molecular function after Gene Ontology annotation and metabolic of pathway indicated by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Differentially expressed proteins (DEP) for GD versus IM, GD versus SX, IM versus SX were identified to be 81, 91, and 44, respectively. Gene Ontology enrichment analysis showed that the greatest DEP for 3 groups (GD vs. IM, GD vs. SX, IM vs. SX) were cellular process, cellular process and organonitrogen compound biosynthetic process/immune system process for biological process. For cellular component, the largest number of DEP for 3 comparison groups were organelle, organelle and organelle/intracellular. For molecular function, DEP of the 3 comparison groups were expressed most in structural molecule activity, binding and anion binding, respectively. Pathways with the majority of DEP were ribosome, systemic lupus erythematosus and primary immunodeficiency/systemic lupus erythematosus/amoebiasis/PI3K-Akt signaling pathway for GD versus IM, GD versus SX and IM versus SX, severally. Protein-protein interaction network analysis showed that DEP interacted most were 40S ribosomal protein S5, fibronectin and Cytochrome b-c1 complex subunit 2, mitochondrial for GD versus IM, GD versus SX and IM versus SX, separately. Data may give useful information for goat milk selection and milk authenticity in China.
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Affiliation(s)
- Cuina Wang
- Department of Food Science, Jilin University, Changchun, 130062, China
| | - Ru Zhao
- Department of Food Science, Jilin University, Changchun, 130062, China
| | - Zixuan Zhao
- Department of Food Science, Northeast Agriculture University, Harbin, 150030, China
| | - Ning Liu
- Department of Food Science, Northeast Agriculture University, Harbin, 150030, China
| | - Jianjun Cheng
- Department of Food Science, Northeast Agriculture University, Harbin, 150030, China
| | - Mingruo Guo
- Department of Nutrition and Food Sciences, College of Agriculture and Life Sciences, University of Vermont, Burlington 05405.
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Baichan P, Naicker P, Augustine TN, Smith M, Candy G, Devar J, Nweke EE. Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry. Clin Proteomics 2023; 20:8. [PMID: 36855072 PMCID: PMC9976386 DOI: 10.1186/s12014-023-09399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Gallbladder cancer (GBC) is a lethal cancer with a poor prognosis. The lack of specific and sensitive biomarkers results in delayed diagnosis with most patients presenting at late stages of the disease. Furthermore, there is little known about the molecular mechanisms associated with GBC, especially in patients of African ancestry. This study aimed to determine dysregulated proteins in South African GBC patients to identify potential mechanisms of the disease progression and plausible biomarkers. METHODS Tissues (27 GBC, 13 Gallstone disease, and 5 normal tissues) and blood plasma (54 GBC and 73 Benign biliary pathology) were obtained from consenting patients. Protein extraction was performed on all tissues and liquid chromatography-mass spectrometry was used for proteomic profiling. A project-specific spectral library was built using the Pulsar search algorithm. Principal component and Spearman's rank correlation analyses were performed using PAST (V4.07b). Pathway and Network analyses were conducted using REACTOME (v3.7) and stringAPP (v1.7.0), respectively. RESULTS In the tissue sample group, there were 62 and 194 dysregulated proteins in GBC compared to normal and gallstone groups, respectively. In the plasma group, there were 33 altered proteins in GBC compared to the benign biliary pathology group. We found 9 proteins (APOA1, APOA2, RET4, TTR, HEMO, HBB, HBA, PIGR, and APOE) to be commonly dysregulated in both tissue and plasma. Furthermore, a subset analysis demonstrated that 2 proteins, S100A8 and S100A9, were downregulated in GBC patients with GD history compared to those without. Pathway analysis showed that the dysregulated proteins in GBC patients were enriched in pathways involved in smooth muscle contraction, metabolism, ECM organization, and integrin cell surface interactions. CONCLUSION The identified dysregulated proteins help in understanding GBC molecular mechanisms in our patient group. Furthermore, the alteration of specific proteins in both tissue and plasma samples suggests their potential utility as biomarkers of GBC in this sample cohort.
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Affiliation(s)
- Pavan Baichan
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa
| | - Previn Naicker
- grid.7327.10000 0004 0607 1766Council for Scientific and Industrial Research, Pretoria, 0001 South Africa
| | - Tanya Nadine Augustine
- grid.11951.3d0000 0004 1937 1135School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193 South Africa
| | - Martin Smith
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa ,grid.414240.70000 0004 0367 6954Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Geoffrey Candy
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa
| | - John Devar
- grid.11951.3d0000 0004 1937 1135Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193 South Africa ,grid.414240.70000 0004 0367 6954Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Ekene Emmanuel Nweke
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa.
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Tang M, Li C, Zhang C, Cai Y, Zhang Y, Yang L, Chen M, Zhu F, Li Q, Li K. SWATH-MS-Based Proteomics Reveals the Regulatory Metabolism of Amaryllidaceae Alkaloids in Three Lycoris Species. Int J Mol Sci 2023; 24. [PMID: 36901927 DOI: 10.3390/ijms24054495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Alkaloids are a class of nitrogen-containing alkaline organic compounds found in nature, with significant biological activity, and are also important active ingredients in Chinese herbal medicine. Amaryllidaceae plants are rich in alkaloids, among which galanthamine, lycorine, and lycoramine are representative. Since the difficulty and high cost of synthesizing alkaloids have been the major obstacles in industrial production, particularly the molecular mechanism underlying alkaloid biosynthesis is largely unknown. Here, we determined the alkaloid content in Lycoris longituba, Lycoris incarnata, and Lycoris sprengeri, and performed a SWATH-MS (sequential window acquisition of all theoretical mass spectra)-based quantitative approach to detect proteome changes in the three Lycoris. A total of 2193 proteins were quantified, of which 720 proteins showed a difference in abundance between Ll and Ls, and 463 proteins showed a difference in abundance between Li and Ls. KEGG enrichment analysis revealed that differentially expressed proteins are distributed in specific biological processes including amino acid metabolism, starch, and sucrose metabolism, implicating a supportive role for Amaryllidaceae alkaloids metabolism in Lycoris. Furthermore, several key genes collectively known as OMT and NMT were identified, which are probably responsible for galanthamine biosynthesis. Interestingly, RNA processing-related proteins were also abundantly detected in alkaloid-rich Ll, suggesting that posttranscriptional regulation such as alternative splicing may contribute to the biosynthesis of Amaryllidaceae alkaloids. Taken together, our SWATH-MS-based proteomic investigation may reveal the differences in alkaloid contents at the protein levels, providing a comprehensive proteome reference for the regulatory metabolism of Amaryllidaceae alkaloids.
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Ekmekciu L, Hopfgartner G. Liquid chromatography and differential mobility spectrometry-data-independent mass spectrometry for comprehensive multidimensional separations in metabolomics. Anal Bioanal Chem 2023; 415:1905-1915. [PMID: 36820908 PMCID: PMC10050028 DOI: 10.1007/s00216-023-04602-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
The benefits of combining drift time ion mobility (DTIMS) with liquid chromatography-high-resolution mass spectrometry (HRMS) have been reported for metabolomics but the use of differential time mobility spectrometry (DMS) is less obvious due to the need for rapid scanning of the DMS cell. Drift DTIMS provides additional precursor ion selectivity and collisional cross-section information but the separation resolution between analytes remains cell- and component-dependent. With DMS, the addition of 2-propanol modifier can improve the selectivity but on cost of analyte MS response. In the present work, we investigate the liquid chromatography-mass spectrometry (LC-MS) analysis of a mix of 50 analytes, representative for urine and plasma metabolites, using scanning DMS with the single modifiers cyclohexane (Ch), toluene (Tol), acetonitrile (ACN), ethanol (EtOH), and 2-propanol (IPA), and a binary modifier mixture (cyclohexane/2-propanol) with emphasis on selectivity and signal sensitivity. 1.5% IPA in the N2 stream was found to suppress the signal of 50% of the analytes which could be partially recovered with the use of IPA to 0.05% as a Ch/IPA mixture. The potential to use the separation voltage/compensation voltage/modifier (SV/CoV/Mod) feature as an additional analyte identifier for qualitative analysis is also presented and applied to a data-independent LCxDMS-SWATH-MS workflow for the analysis of endogenous metabolites and drugs of abuse in human urine samples from traffic control.
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Affiliation(s)
- Lysi Ekmekciu
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, 1211, Geneva 4, Switzerland.
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Muazzam A, Spick M, Cexus ONF, Geary B, Azhar F, Pandha H, Michael A, Reed R, Lennon S, Gethings LA, Plumb RS, Whetton AD, Geifman N, Townsend PA. A Novel Blood Proteomic Signature for Prostate Cancer. Cancers (Basel) 2023; 15. [PMID: 36831393 DOI: 10.3390/cancers15041051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Prostate cancer is the most common malignant tumour in men. Improved testing for diagnosis, risk prediction, and response to treatment would improve care. Here, we identified a proteomic signature of prostate cancer in peripheral blood using data-independent acquisition mass spectrometry combined with machine learning. A highly predictive signature was derived, which was associated with relevant pathways, including the coagulation, complement, and clotting cascades, as well as plasma lipoprotein particle remodeling. We further validated the identified biomarkers against a second cohort, identifying a panel of five key markers (GP5, SERPINA5, ECM1, IGHG1, and THBS1) which retained most of the diagnostic power of the overall dataset, achieving an AUC of 0.91. Taken together, this study provides a proteomic signature complementary to PSA for the diagnosis of patients with localised prostate cancer, with the further potential for assessing risk of future development of prostate cancer. Data are available via ProteomeXchange with identifier PXD025484.
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Mu Y, Guo X, Yu J, Wang R, Liu Z, Hu K, Song J, Chen L, Song B, Du J. SWATH-MS based quantitative proteomics analysis reveals novel proteins involved in PAMP triggered immunity against potato late blight pathogen Phytophthora infestans. Front Plant Sci 2022; 13:1036637. [PMID: 36466288 PMCID: PMC9715588 DOI: 10.3389/fpls.2022.1036637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Potato is the most important non-grain food in the world, while late blight caused by Phytophthora infestans seriously threatens the production of potato. Since pathogen-associated molecular patterns (PAMPs) are relatively conserved, PAMP-triggered immunity (PTI) can provide durable resistance to late blight for potato. However, knowledge of the regulatory mechanisms of PTI against oomycete pathogens at protein levels remains limited due to the small number of identified proteins. In the present work, changes in the proteome profile of Nicotiana benthamiana leaves upon P. infestans PAMP induction were examined using the SWATH-MS (sequential windowed acquisition of all theoretical mass spectra) approach, which provides quantification of protein abundances and large-scale identification of PTI-related proteins. A total of 4401 proteins have been identified, of which 1429 proteins were differentially expressed at least at one time point of 8, 12, 24 and 48 h after PAMP induction, compared with the expression at 0 h when immediately after PAMP induction. They were further analyzed by expression clustering and gene ontology (GO) enrichment analysis. Through functional verification, six novel DEPs of 19 candidates were proved to be involved in PTI responses, including mitochondrial phosphate carrier protein (MPT) 3, vesicle-associated membrane protein (VAMP) 714, lysophospholipase (LysoPL) 2, ascorbate peroxidase (APX) 1, heat shock 70 kDa protein (HSP) 2 and peptidyl-prolyl cis-trans isomerase FKBP (FKBP) 15-1. Taken together, the time course approach and the resulting large-scale proteomic analyses have enlarged our understanding of PTI mechanisms and provided a valuable resource for the discovery of complex protein networks involved in the resistance response of potato to late blight.
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Affiliation(s)
- Yang Mu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao Guo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ruxun Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kefan Hu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingyi Song
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Botao Song
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Juan Du
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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20
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Msheik Z, Durand S, Pinault E, Caillaud M, Vignaud L, Billet F, El Massry M, Desmouliere A. Charcot-Marie-Tooth-1A and sciatic nerve crush rat models: insights from proteomics. Neural Regen Res 2022; 18:1354-1363. [PMID: 36453423 PMCID: PMC9838138 DOI: 10.4103/1673-5374.357911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models: the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease. In this study, we sought to highlight and compare the protein signature of these two pathological situations. Indeed, the identification of protein profiles in diseases can play an important role in the development of pharmacological targets. In fact, Charcot-Marie-Tooth-1A rats develop motor impairments that are more severe in the hind limbs. Therefore, for the first time, protein expression in sciatic nerve of Charcot-Marie-Tooth-1A rats was examined. First, distal sciatic nerves were collected from Charcot-Marie-Tooth-1A and uninjured wild-type rats aged 3 months. After protein extraction, sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry was employed. 445 proteins mapped to Swiss-Prot or trEMBL Uniprot databases were identified and quantified. Of these, 153 proteins showed statistically significant differences between Charcot-Marie-Tooth-1A and wild-type groups. The majority of these proteins were overexpressed in Charcot-Marie-Tooth-1A. Hierarchical clustering and functional enrichment using Gene Ontology were used to group these proteins based on their biological effects concerning Charcot-Marie-Tooth-1A pathophysiology. Second, proteomic characterization of wild-type rats subjected to sciatic nerve crush was performed sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry. One month after injury, distal sciatic nerves were collected and analyzed as described above. Out of 459 identified proteins, 92 showed significant differences between sciatic nerve crush and the uninjured wild-type rats used in the first study. The results suggest that young adult Charcot-Marie-Tooth-1A rats (3 months old) develop compensatory mechanisms at the level of redox balance, protein folding, myelination, and axonogenesis. These mechanisms seem insufficient to hurdle the progress of the disease. Notably, response to oxidative stress appears to be a significant feature of Charcot-Marie-Tooth-1A, potentially playing a role in the pathological process. In contrast to the first experiment, the majority of the proteins that differed from wild-type were downregulated in the sciatic nerve crush group. Functional enrichment suggested that neurogenesis, response to axon injury, and oxidative stress were important biological processes. Protein analysis revealed an imperfect repair at this time point after injury and identified several distinguishable proteins. In conclusion, we suggest that peripheral neuropathies, whether of a genetic or traumatic cause, share some common pathological pathways. This study may provide directions for better characterization of these models and/or identifying new specific therapeutic targets.
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Affiliation(s)
- Zeina Msheik
- UR20218 NeurIT (NEURopathies périphériques et Innovation Thérapeutique), University of Limoges, Limoges, France
| | - Stephanie Durand
- BISCEm (Biologie Intégrative Santé Chimie Environnement) Platform, US 42 Inserm/UAR 2015 CNRS, University of Limoges, Limoges, France,UMR 1308 Inserm/CHU–CAPTuR (Contrôle de l’Activation cellulaire, Progression Tumorale et Résistance thérapeutique), University of Limoges, Limoges, France
| | - Emilie Pinault
- BISCEm (Biologie Intégrative Santé Chimie Environnement) Platform, US 42 Inserm/UAR 2015 CNRS, University of Limoges, Limoges, France
| | - Martial Caillaud
- Inserm UMR1235–TENS (The Enteric Nervous System in Gut and Brain Diseases), University of Nantes, Nantes, France
| | - Laetitia Vignaud
- UR20218 NeurIT (NEURopathies périphériques et Innovation Thérapeutique), University of Limoges, Limoges, France
| | - Fabrice Billet
- UR20218 NeurIT (NEURopathies périphériques et Innovation Thérapeutique), University of Limoges, Limoges, France
| | - Mohamed El Massry
- UR20218 NeurIT (NEURopathies périphériques et Innovation Thérapeutique), University of Limoges, Limoges, France
| | - Alexis Desmouliere
- UR20218 NeurIT (NEURopathies périphériques et Innovation Thérapeutique), University of Limoges, Limoges, France,Correspondence to: Alexis Desmoulière, .
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21
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Kumar S, Tripathi J, Maurya DK, Nuwad J, Gautam S. Anti-proliferative effect and underlying mechanism of ethoxy-substituted phylloquinone (vitamin K1 derivative) from Spinacia oleracea leaf and enhancement of its extractability using radiation technology. 3 Biotech 2022; 12:265. [PMID: 36091087 PMCID: PMC9452621 DOI: 10.1007/s13205-022-03264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/17/2022] [Indexed: 11/01/2022] Open
Abstract
In our previous studies, a novel antimutagenic compound, 2-ethoxy-3-(3,7,11,15-tetramethylhexadec-2-ethyl) naphthaquinone-1,4-dione (ethoxy-substituted phylloquinone; ESP) from spinach was characterized and mechanism contributing to its antimutagenicity was deduced. In the current study, anti-proliferative activity of ESP was assessed in lung cancer (A549) cells using MTT [3-(4,5-dimethylthiazole-2yl)-2,5-diphenyl tetrazolium bromide], clonogenic assays and cell cycle analysis. ESP treatment showed selective cytotoxicity against lung cancer cells and no cytotoxicity in normal lung (WI38) cells. Cell cycle analysis revealed that ESP treatment arrests A549 cell population in G2-M phase. In-silico analysis indicated positive drug-likeness features of ESP. Molecular docking showed H-bonding and hydrophobic interactions between ESP and B-DNA dodecamer residues at minor groove. SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) based proteomic analysis indicated down-regulation of proteins involved in EGFR signaling, NEDDylation and other metabolic pathways and up-regulation of tumor suppressor (STAT1 and NDRG1) proteins. Treatment of spinach powder with gamma radiation (5-20 kGy) from cobalt (Co-60) enhanced the extractability of ESP up to 4.4-fold at the highest dose of 20 kGy. Scanning electron microscopy of spinach powder displayed decrease in smoothness and compactness with increase in radiation dose attributing to its enhanced extractability. Increase in the extractability of ESP with increasing radiation doses as measured by fluorescence intensity and dry weight basis was strongly correlated. Nonetheless, radiation treatment did not affect the functionality of ESP in terms of anti-proliferative and antimutagenic activities. Current findings thus highlight broad spectrum bioactivity of ESP from spinach, its underlying mechanism and applicability of radiation technology in enhancing extractability. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03264-6.
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Affiliation(s)
- Sanjeev Kumar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085 India
| | - Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085 India
| | - Dharmendra K. Maurya
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 400 085 India
- Homi Bhabha National Institute, Mumbai, 400 094 India
| | - Jitendra Nuwad
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, 400 085 India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400 085 India
- Homi Bhabha National Institute, Mumbai, 400 094 India
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22
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Bahmani M, Juhász A, Broadbent J, Bose U, Nye-Wood MG, Edwards IB, Colgrave ML. Proteome Phenotypes Discriminate the Growing Location and Malting Traits in Field-Grown Barley. J Agric Food Chem 2022; 70:10680-10691. [PMID: 35981222 PMCID: PMC9449971 DOI: 10.1021/acs.jafc.2c03816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Barley is one of the key cereal grains for malting and brewing industries. However, climate variability and unprecedented weather events can impact barley yield and end-product quality. The genetic background and environmental conditions are key factors in defining the barley proteome content and malting characteristics. Here, we measure the barley proteome and malting characteristics of three barley lines grown in Western Australia, differing in genetic background and growing location, by applying liquid chromatography-mass spectrometry (LC-MS). Using data-dependent acquisition LC-MS, 1571 proteins were detected with high confidence. Quantitative data acquired using sequential window acquisition of all theoretical (SWATH) MS on barley samples resulted in quantitation of 920 proteins. Multivariate analyses revealed that the barley lines' genetics and their growing locations are strongly correlated between proteins and desired traits such as the malt yield. Linking meteorological data with proteomic measurements revealed how high-temperature stress in northern regions affects seed temperature tolerance during malting, resulting in a higher malt yield. Our results show the impact of environmental conditions on the barley proteome and malt characteristics; these findings have the potential to expedite breeding programs and malt quality prediction.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - James Broadbent
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
| | - Utpal Bose
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
| | - Mitchell G. Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd., SABC, Loneragan Building, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University,
School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Rd, St. Lucia, QLD 4067, Australia
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Chen L, Shi H, Li Z, Yang F, Zhang X, Xue Y, Zhang H, Xue C. Molecular mechanism of protein dynamic change in Pacific oyster (Crassostrea gigas) during depuration at different salinities uncovered by mass spectrometry-based proteomics combined with bioinformatics. Food Chem 2022; 394:133454. [PMID: 35753254 DOI: 10.1016/j.foodchem.2022.133454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/04/2022] [Accepted: 06/08/2022] [Indexed: 11/04/2022]
Abstract
Salinity stress during depuration of Pacific oysters (Crassostrea gigas) leads to degradation in quality; therefore, an understanding of the molecular mechanisms regulating dynamic changes during depuration is needed. Here, C. gigas was depurated for 72 h at salinities ranging from 26 to 38 g/L, a ± 10-20% fluctuation from that in the production area, and the gill proteomes were analyzed by sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS). Of the 1218 proteins analyzed, 241 were differentiating proteins (DPs). Salinity stress led to increased levels of DPs associated with glycolysis and the extracellular matrix-receptor interaction pathway, and decreased levels of DPs associated with the citric acid cycle, lipid metabolism, genetic information processing, and cell transformation, especially in oysters exposed to 38 g/L salinity (+20%). Controlling salinity fluctuation within ± 10% of the production area during depuration was conducive to maintaining quality in C. gigas.
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Affiliation(s)
- Lipin Chen
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Haohao Shi
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Zhaojie Li
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, PR China
| | - Fan Yang
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Xiaomei Zhang
- Food and Agricultural Products Testing Agency, Technology Center of Qingdao Customs District, Qingdao, Shandong Province, PR China
| | - Yong Xue
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Hongwei Zhang
- Food and Agricultural Products Testing Agency, Technology Center of Qingdao Customs District, Qingdao, Shandong Province, PR China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, No. 5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, PR China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for MarineScience and Technology (Qingdao), Qingdao 266237, Shandong Province, PR China.
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24
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Zhang J, Wu J, Lu D, To CH, Lam TC, Lin B. Retinal Proteomic Analysis in a Mouse Model of Endotoxin-Induced Uveitis Using Data-Independent Acquisition-Based Mass Spectrometry. Int J Mol Sci 2022; 23:ijms23126464. [PMID: 35742911 PMCID: PMC9223489 DOI: 10.3390/ijms23126464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Uveitis is a group of sight-threatening ocular inflammatory diseases, potentially leading to permanent vision loss in patients. However, it remains largely unknown how uveitis causes retinal malfunction and vision loss. Endotoxin-induced uveitis (EIU) in rodents is a good animal model to study uveitis and associated acute retinal inflammation. To understand the pathogenic mechanism of uveitis and screen potential targets for treatment, we analyzed the retinal proteomic profile of the EIU mouse model using a data-independent acquisition-based mass spectrometry (SWATH-MS). After systemic LPS administration, we observed activation of microglial cells accompanied with the elevation of pro-inflammatory mediators and visual function declines. In total, we observed 79 upregulated and 90 downregulated differentially expressed proteins (DEPs). Among the DEPs, we found that histone family members (histone H1, H2A, H2B) and blood proteins including haptoglobin (HP), hemopexin (HPX), and fibrinogen gamma chain (FGG) were dramatically increased in EIU groups relative to those in control groups. We identified phototransduction and synaptic vesicle cycle as the top two significant KEGG pathways. Moreover, canonical pathway analysis on DEPs using Ingenuity Pathway Analysis revealed top three most significant enriched pathways related to acute phase response signaling, synaptogenesis signaling, and eif2 signaling. We further confirmed upregulation of several DEPs associated with the acute phase response signaling including HP, HPX, and FGG in LPS-treated retinas by qPCR and Western blot. In summary, this study serves as the first report to detect retinal proteome changes in the EIU model. The study provides several potential candidates for exploring the mechanism and novel therapeutic targets for uveitis and other retinal inflammatory diseases.
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Affiliation(s)
- Jing Zhang
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
| | - Jiangmei Wu
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
| | - Daqian Lu
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
| | - Chi-Ho To
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Thomas Chuen Lam
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
- Correspondence: (T.C.L.); (B.L.)
| | - Bin Lin
- School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China; (J.Z.); (J.W.); (D.L.); (C.-H.T.)
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
- Correspondence: (T.C.L.); (B.L.)
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25
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Masoomi‐Aladizgeh F, Kamath KS, Haynes PA, Atwell BJ. Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat. Plant Cell Environ 2022; 45:1242-1256. [PMID: 35092006 PMCID: PMC9415111 DOI: 10.1111/pce.14268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
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Affiliation(s)
| | | | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Brian J. Atwell
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
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Masoomi-Aladizgeh F, McKay MJ, Asar Y, Haynes PA, Atwell BJ. Patterns of gene expression in pollen of cotton (Gossypium hirsutum) indicate downregulation as a feature of thermotolerance. Plant J 2022; 109:965-979. [PMID: 34837283 DOI: 10.1111/tpj.15608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Reproductive performance in plants is impaired as maximum temperatures consistently approach 40°C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses during pollen maturation in cotton to investigate the vulnerability to high temperature. Tetrads (TEs), uninucleate and binucleate microspores, and mature pollen were subjected to SWATH-MS and RNA-seq analyses after exposure to 38/28°C (day/night) for 5 days. The results indicated that molecular signatures were downregulated progressively in response to heat during pollen development. This was even more evident in leaves, where three-quarters of differentially changed proteins decreased in abundance during heat. Functional analysis showed that translation of genes increased in TEs after exposure to heat; however, the reverse pattern was observed in mature pollen and leaves. For example, proteins involved in transport were highly abundant in TEs whereas in later stages of pollen formation and leaves, heat suppressed synthesis of proteins involved in cell-to-cell communication. Moreover, a large number of heat shock proteins were identified in heat-affected TEs, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of TE cells to heat is related to high rates of translation targeted to pathways that might not be essential for thermotolerance. Molecular signatures during stages of pollen development after heatwaves could provide markers for future genetic improvement.
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Affiliation(s)
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, NSW, Australia
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27
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Pérez-Sánchez R, Carnero-Morán A, Luz Valero M, Oleaga A. A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva. Parasit Vectors 2022; 15:1. [PMID: 34980218 PMCID: PMC8722417 DOI: 10.1186/s13071-021-05118-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The argasid tick Ornithodoros erraticus is the main vector of tick-borne human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin. The prevention and control of these diseases would greatly benefit from the elimination of O. erraticus populations, and anti-tick vaccines are envisaged as an effective and sustainable alternative to chemical acaricide usage for tick control. Ornithodoros erraticus saliva contains bioactive proteins that play essential functions in tick feeding and host defence modulation, which may contribute to host infection by tick-borne pathogens. Hence, these proteins could be candidate antigen targets for the development of vaccines aimed at the control and prevention of O. erraticus infestations and the diseases this tick transmits. The objective of the present work was to obtain and characterise the proteome of the saliva of O. erraticus adult ticks as a means to identify and select novel salivary antigen targets. METHODS A proteomics informed by transcriptomics (PIT) approach was applied to analyse samples of female and male saliva separately using the previously obtained O. erraticus sialotranscriptome as a reference database and two different mass spectrometry techniques, namely liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data-dependent acquisition mode and sequential window acquisition of all theoretical fragment ion spectra MS (SWATH-MS). RESULTS Up to 264 and 263 proteins were identified by LC-MS/MS in the saliva of O. erraticus female and male ticks, respectively, totalling 387 non-redundant proteins. Of these, 224 were further quantified by SWATH-MS in the saliva of both male and female ticks. Quantified proteins were classified into 23 functional categories and their abundance compared between sexes. Heme/iron-binding proteins, protease inhibitors, proteases, lipocalins and immune-related proteins were the categories most abundantly expressed in females, while glycolytic enzymes, protease inhibitors and lipocalins were the most abundantly expressed in males. Ninety-seven proteins were differentially expressed between the sexes, of which 37 and 60 were overexpressed in females and males, respectively. CONCLUSIONS The PIT approach demonstrated its usefulness for proteomics studies of O. erraticus, a non-model organism without genomic sequences available, allowing the publication of the first comprehensive proteome of the saliva of O. erraticus reported to date. These findings confirm important quantitative differences between sexes in the O. erraticus saliva proteome, unveil novel salivary proteins and functions at the tick-host feeding interface and improve our understanding of the physiology of feeding in O. erraticus ticks. The integration of O. erraticus sialoproteomic and sialotranscriptomic data will drive a more rational selection of salivary candidates as antigen targets for the development of vaccines aimed at the control of O. erraticus infestations and the diseases it transmits.
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Affiliation(s)
- Ricardo Pérez-Sánchez
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Angel Carnero-Morán
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - M. Luz Valero
- Proteomics Section, Central Service for Experimental Research, University of Valencia, Carrer del Dr. Moliner, 50, 46100 Burjassot, Spain
| | - Ana Oleaga
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
- Proteomics Section, Central Service for Experimental Research, University of Valencia, Carrer del Dr. Moliner, 50, 46100 Burjassot, Spain
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28
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Gonzalez-Rodriguez M, Villar-Conde S, Astillero-Lopez V, Villanueva-Anguita P, Ubeda-Banon I, Flores-Cuadrado A, Martinez-Marcos A, Saiz-Sanchez D. Neurodegeneration and Astrogliosis in the Human CA1 Hippocampal Subfield Are Related to hsp90ab1 and bag3 in Alzheimer's Disease. Int J Mol Sci 2021; 23:165. [PMID: 35008592 PMCID: PMC8745315 DOI: 10.3390/ijms23010165] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD), the most prevalent neurodegenerative disorder, is characterized by executive dysfunction and memory impairment mediated by the accumulation of extracellular amyloid-β peptide (Aβ) and intracellular hyperphosphorylated tau protein. The hippocampus (HIPP) is essential for memory formation and is involved in early stages of disease. In fact, hippocampal atrophy is used as an early biomarker of neuronal injury and to evaluate disease progression. It is not yet well-understood whether changes in hippocampal volume are due to neuronal or glial loss. The aim of the study was to assess hippocampal atrophy and/or gliosis using unbiased stereological quantification and to obtain hippocampal proteomic profiles related to neurodegeneration and gliosis. Hippocampal volume measurement, stereological quantification of NeuN-, Iba-1- and GFAP-positive cells, and sequential window acquisition of all theoretical mass spectrometry (SWATH-MS) analysis were performed in AD and non-AD cases. Reduced hippocampal volume was identified using the Cavalieri probe, particularly in the CA1 region, where it correlated with neuronal loss and astrogliosis. A total of 102 downregulated and 47 upregulated proteins were identified in the SWATH-MS analysis after restrictive filtering based on an FC > 1.5 and p value < 0.01. The Hsp90 family of chaperones, particularly BAG3 and HSP90AB1, are closely related to astrocytes, indicating a possible role in degrading Aβ and tau through chaperone-mediated autophagy.
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Affiliation(s)
| | | | | | | | | | | | - Alino Martinez-Marcos
- CRIB, Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, University of Castilla-La Mancha, 13071 Ciudad Real, Spain; (M.G.-R.); (S.V.-C.); (V.A.-L.); (P.V.-A.); (I.U.-B.); (A.F.-C.)
| | - Daniel Saiz-Sanchez
- CRIB, Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, University of Castilla-La Mancha, 13071 Ciudad Real, Spain; (M.G.-R.); (S.V.-C.); (V.A.-L.); (P.V.-A.); (I.U.-B.); (A.F.-C.)
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Wang S, Wang X, Yang X, Liu F, Li J, Li W, Bai Z, Wang H, Mao J, Li T, He K, Wang H. Comprehensive kinomic study via a chemical proteomic approach reveals kinome reprogramming in hepatocellular carcinoma tissues. Proteomics 2021; 22:e2100141. [PMID: 34932872 DOI: 10.1002/pmic.202100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 11/07/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Kinases are attractive therapeutic targets since they are commonly altered in cancers. Here, to identify kinases of potential therapeutic interest in HCC, a quantitative kinomic study of tumour and adjacent non-tumour liver tissues was performed using a chemical proteomics approach. In total, 124 kinases were found differentially expressed and they were distributed over all nine kinase groups. Exploration of The Cancer Genome Atlas (TCGA) data showed that the dysregulation of 45 kinases was correlated with poor prognosis in HCC patients. We then tested 11 inhibitors targeting 12 crucial protein kinases alone or in combination for their ability to inhibit cell growth in Hep3B and PLC/PRF/5 cell lines. Six inhibitors significantly reduced viability in both cell lines. Combination inhibition of polo-like kinase 1 (PLK1) and casein kinase 1 epsilon (CSNK1E) significantly induced growth arrest in both cell lines synergistically. In summary, our analysis presents the most complete view of kinome reprogramming in HCC and provides novel insight into crucial kinases in HCC and potential therapeutic targets for HCC treatment. Moreover, the identification of hundreds of differentially expressed kinases forms a rich resource for novel drug targets or diagnostic biomarker discovery. Data are available via ProteomeXchange (identifier PXD023806).
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Affiliation(s)
- Shufeng Wang
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Xinzheng Wang
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Xin Yang
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Feng Liu
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jin Li
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Weihua Li
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Zhaofang Bai
- Department of Liver Disease, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China
| | - Hongbo Wang
- Department of Hepatobiliary Surgery Center, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, 100039, China
| | - Jie Mao
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Tingting Li
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Kun He
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Hongxia Wang
- National Center of Biomedical Analysis, Beijing, 100850, China
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Sun X, Zhu L, Qi X, Zhang H, Wu L, Wang J, Hou H. Cleavage sites and non-enzymatic self-degradation mechanism of ready-to-eat sea cucumber during storage. Food Chem 2021; 375:131722. [PMID: 34922275 DOI: 10.1016/j.foodchem.2021.131722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 02/07/2023]
Abstract
The non-enzymatic degradation of ready-to-eat sea cucumber (RSC) was closely related to the quality of sea cucumber products. When stored at 37 °C for 0-30 d, the hardness of RSC decreased by 86.7% and the proportion of free water increased by 12.71%. The content of free hydroxyproline increased from 8.33 μg/g to 24.12 μg/g. Label-free quantitative proteomics analysis showed that protein was prone to break at the sites of G, Q, N, D, and L, and the peptide bonds in QI, DL, NL, RI, EF and SY were much more liable to break. Edman degradation method showed that the breakage sites of RSC were at S, D, H, E, and V. NL, NA and NG calculated by B3LYP/6-31G(d) showed that the relative free energies in the initial cyclization step were 53.20, 143.53 and 78.10 kcal/mol, respectively, which may be the rate-determining step for peptide bond cleavage.
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Affiliation(s)
- Xiao Sun
- College of Food Science and Engineering, Ocean University of China, No.5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Lulu Zhu
- College of Food Science and Engineering, Ocean University of China, No.5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Xin Qi
- College of Food Science and Engineering, Ocean University of China, No.5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Hongwei Zhang
- Technology Center of Qingdao Customs, No. 83, Xinyue Road, Qingdao, Shandong Province 266109, PR China
| | - Ling Wu
- Wuhu Midea Smart Kitchen Appliance Manufacturing Co., Ltd, Wuhu, Anhui Province 241012, PR China
| | - Jinhua Wang
- Wuhu Midea Smart Kitchen Appliance Manufacturing Co., Ltd, Wuhu, Anhui Province 241012, PR China
| | - Hu Hou
- College of Food Science and Engineering, Ocean University of China, No.5, Yu Shan Road, Qingdao, Shandong Province 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266237, PR China.
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Chien HJ, Huang YH, Zheng YF, Wang WC, Kuo CY, Wei GJ, Lai CC. Proteomics for species authentication of cod and corresponding fishery products. Food Chem 2021; 374:131631. [PMID: 34838403 DOI: 10.1016/j.foodchem.2021.131631] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022]
Abstract
Seafood substitutions is a global problem and come under the spotlight in recent years. In Taiwan, Greenland halibut is usually substituted for the cod because of its lower price. Nowadays, DNA technology is widely used for fish species identifications; however, it still has concern about the DNA of processed fishery products might be destroyed. This study was designed to develop a proteomic-based method for fish and fishery product authentication by using ultra performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) with Sequential window acquisition of all theoretical fragment ion spectra (SWATH). The protein biomarkers from the meat of Alaska pollock, Atlantic cod, and Greenland halibut were identified and validated for species authentication of cod and corresponding fishery products, which might prevent consumer substitutions and fish product mislabeling. Besides, the E. coli proteins can be measured from existing SWATH-MS data though retrospective analysis successfully, it might present the quality of fish meat.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Yu-Han Huang
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Yi-Feng Zheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Guor-Jien Wei
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan; Metabolomics-Proteomics Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Graduate Institute of Chinese Medical Science, China Medical University, Taichung 40402, Taiwan.
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Muazzam A, Chiasserini D, Kelsall J, Geifman N, Whetton AD, Townsend PA. A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification. Cancers (Basel) 2021; 13:5580. [PMID: 34771740 DOI: 10.3390/cancers13215580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Prostate cancer is the third most frequent cancer in men worldwide, with a notable increase in prevalence over the past two decades. The PSA is the only well-established protein biomarker for prostate cancer diagnosis, staging, and surveillance. It frequently leads to inaccurate diagnosis and overtreatment since it is an organ-specific biomarker rather than a tumour-specific biomarker. As a result, one of the primary goals of prostate cancer proteome research is to identify novel biomarkers that can be used with or instead of PSA, particularly in non-invasive blood samples. Thousands of peptides or assays were detected in blood samples from patients with low- to high-grade prostate cancer and healthy individuals, allowing data processing of sequential window acquisition of all theoretical mass spectra (SWATH-MS). By assisting in the detection of prostate cancer biomarkers in blood samples, this useful resource will improve our understanding of the role of proteomics in prostate cancer diagnosis and risk assessment. Abstract Prostate cancer is the most frequent form of cancer in men, accounting for more than one-third of all cases. Current screening techniques, such as PSA testing used in conjunction with routine procedures, lead to unnecessary biopsies and the discovery of low-risk tumours, resulting in overdiagnosis. SWATH-MS is a well-established data-independent (DI) method requiring prior knowledge of targeted peptides to obtain valuable information from SWATH maps. In response to the growing need to identify and characterise protein biomarkers for prostate cancer, this study explored a spectrum source for targeted proteome analysis of blood samples. We created a comprehensive prostate cancer serum spectral library by combining data-dependent acquisition (DDA) MS raw files from 504 patients with low, intermediate, or high-grade prostate cancer and healthy controls, as well as 304 prostate cancer-related protein in silico assays. The spectral library contains 114,684 transitions, which equates to 18,479 peptides translated into 1227 proteins. The robustness and accuracy of the spectral library were assessed to boost confidence in the identification and quantification of prostate cancer-related proteins across an independent cohort, resulting in the identification of 404 proteins. This unique database can facilitate researchers to investigate prostate cancer protein biomarkers in blood samples. In the real-world use of the spectrum library for biomarker detection, using a signature of 17 proteins, a clear distinction between the validation cohort’s pre- and post-treatment groups was observed. Data are available via ProteomeXchange with identifier PXD028651.
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Yan Y, Wang J, Dong X, Cai Y, Wang Y, Ren L, Zhang C, Tao M, Luo K, Zeng Y, Liu S. Quantitative proteomic analysis of hepatic tissue in allotetraploid hybridized from red crucian carp and common carp identified crucial proteins and pathways associated with metabolism and growth rate. Proteomics 2021; 22:e2100115. [PMID: 34713569 DOI: 10.1002/pmic.202100115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023]
Abstract
Allotetraploid is a new species produced by distant hybridization between red crucian carp (Carassius auratus red var., abbreviated as RCC) and common carp (Cyprinus carpio L., abbreviated as CC). There is a significant difference in growth rate between allotetraploid and its parents. However, the underlying molecular mechanism is largely unknown. In this study, to find direct evidence associated with metabolism and growth rate in protein level, we performed quantitative proteomics analysis on liver tissues between allotetraploid and its parents. A total of 2502 unique proteins were identified and quantified by SWATH-MS in our proteomics profiling. Subsequently, comprehensive bioinformatics analyses including gene ontology enrichment analysis, pathway and network analysis, and protein-protein interaction analysis (PPI) were conducted based on differentially expressed proteins (DEPs) between allotetraploid and its parents. The results revealed several significant DEPs involved in metabolism pathways in liver. More specifically, the integrative analysis highlighted that the DEPs ACSBG1, OAT, and LDHBA play vital roles in metabolism pathways including "pentose phosphate pathway," "TCA cycle," and "glycolysis and gluconeogenesis." These could directly affect the growth rate in fresh water fishes by regulating the metabolism, utilization, and exchange of substance and energy. Since the liver is the central place for metabolism activity in animals, we firstly established the comprehensive and quantitative proteomics knowledge base for liver tissue from freshwater fishes, our study may serve as an irreplaceable reference for further studies regarding fishes' culture and growth.
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Affiliation(s)
- Yujie Yan
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Junting Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yisheng Cai
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yude Wang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Li Ren
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Chun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Min Tao
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Kaikun Luo
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Yong Zeng
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
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Fachim HA, Iqbal Z, Gibson JM, Baricevic-Jones I, Campbell AE, Geary B, Syed AA, Whetton A, Soran H, Donn RP, Heald AH. Relationship between the Plasma Proteome and Changes in Inflammatory Markers after Bariatric Surgery. Cells 2021; 10:cells10102798. [PMID: 34685777 PMCID: PMC8534496 DOI: 10.3390/cells10102798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/25/2022] Open
Abstract
Severe obesity is a disease associated with multiple adverse effects on health. Metabolic bariatric surgery (MBS) can have significant effects on multiple body systems and was shown to improve inflammatory markers in previous short-term follow-up studies. We evaluated associations between changes in inflammatory markers (CRP, IL6 and TNFα) and circulating proteins after MBS. Methods: Sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics was performed on plasma samples taken at baseline (pre-surgery) and 6 and 12 months after MBS, and concurrent analyses of inflammatory/metabolic parameters were carried out. The change in absolute abundances of those proteins, showing significant change at both 6 and 12 months, was tested for correlation with the absolute and percentage (%) change in inflammatory markers. Results: We found the following results: at 6 months, there was a correlation between %change in IL-6 and fold change in HSPA4 (rho = −0.659; p = 0.038) and in SERPINF1 (rho = 0.714, p = 0.020); at 12 months, there was a positive correlation between %change in IL-6 and fold change in the following proteins—LGALS3BP (rho = 0.700, p = 0.036), HSP90B1 (rho = 0.667; p = 0.05) and ACE (rho = 0.667, p = 0.05). We found significant inverse correlations at 12 months between %change in TNFα and the following proteins: EPHX2 and ACE (for both rho = −0.783, p = 0.013). We also found significant inverse correlations between %change in CRP at 12 months and SHBG (rho = −0.759, p = 0.029), L1CAM (rho = −0.904, p = 0.002) and AMBP (rho = −0.684, p = 0.042). Conclusion: Using SWATH-MS, we identified several proteins that are involved in the inflammatory response whose levels change in patients who achieve remission of T2DM after bariatric surgery in tandem with changes in IL6, TNFα and/or CRP. Future studies are needed to clarify the underlying mechanisms in how MBS decreases low-grade inflammation.
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Affiliation(s)
- Helene A. Fachim
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Salford Royal Foundation Trust, Department of Endocrinology, Diabetes and Metabolism, Salford M6 8HD, UK
- Correspondence: (H.A.F.); (A.H.H.); Tel.: +44-161-206-0108 (A.H.H.)
| | - Zohaib Iqbal
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Salford Royal Foundation Trust, Department of Endocrinology, Diabetes and Metabolism, Salford M6 8HD, UK
| | - J. Martin Gibson
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Salford Royal Foundation Trust, Department of Endocrinology, Diabetes and Metabolism, Salford M6 8HD, UK
| | - Ivona Baricevic-Jones
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Amy E. Campbell
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Bethany Geary
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Akheel A. Syed
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Salford Royal Foundation Trust, Department of Endocrinology, Diabetes and Metabolism, Salford M6 8HD, UK
| | - Antony Whetton
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester National Institute for Health Research Biomedical Research Centre, Manchester M13 9WL, UK
| | - Handrean Soran
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
| | - Rachelle P. Donn
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
| | - Adrian H. Heald
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (I.B.-J.); (A.E.C.); (B.G.); (A.A.S.); (A.W.); (H.S.); (R.P.D.)
- Salford Royal Foundation Trust, Department of Endocrinology, Diabetes and Metabolism, Salford M6 8HD, UK
- Correspondence: (H.A.F.); (A.H.H.); Tel.: +44-161-206-0108 (A.H.H.)
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Duan YF, Zhang C, Zhang M, Ye Y, Zhang KL, Chen MX, Chen L, Wang XR, Zhu FY. SWATH-MS based quantitive proteomics reveal regulatory metabolism and networks of androdioecy breeding system in Osmanthus fragrans. BMC Plant Biol 2021; 21:468. [PMID: 34645403 PMCID: PMC8513349 DOI: 10.1186/s12870-021-03243-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/30/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND The fragrant flower plant Osmanthus fragrans has an extremely rare androdioecious breeding system displaying the occurrence of males and hermaphrodites in a single population, which occupies a crucial intermediate stage in the evolutionary transition between hermaphroditism and dioecy. However, the molecular mechanism of androdioecy plant is very limited and still largely unknown. RESULTS Here, we used SWATH-MS-based quantitative approach to study the proteome changes between male and hermaphroditic O. fragrans pistils. A total of 428 proteins of diverse functions were determined to show significant abundance changes including 210 up-regulated and 218 down-regulated proteins in male compared to hermaphroditic pistils. Functional categorization revealed that the differentially expressed proteins (DEPs) primarily distributed in the carbohydrate metabolism, secondary metabolism as well as signaling cascades. Further experimental analysis showed the substantial carbohydrates accumulation associated with promoted net photosynthetic rate and water use efficiency were observed in purplish red pedicel of hermaphroditic flower compared with green pedicel of male flower, implicating glucose metabolism serves as nutritional modulator for the differentiation of male and hermaphroditic flower. Meanwhile, the entire upregulation of secondary metabolism including flavonoids, isoprenoids and lignins seem to protect and maintain the male function in male flowers, well explaining important feature of androdioecy that aborted pistil of a male flower still has a male function. Furthermore, nine selected DEPs were validated via gene expression analysis, suggesting an extra layer of post-transcriptional regulation occurs during O. fragrans floral development. CONCLUSION Taken together, our findings represent the first SWATH-MS-based proteomic report in androdioecy plant O. fragrans, which reveal carbohydrate metabolism, secondary metabolism and post-transcriptional regulation contributing to the androdioecy breeding system and ultimately extend our understanding on genetic basis as well as the industrialization development of O. fragrans.
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Affiliation(s)
- Yi-Fan Duan
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Cheng Zhang
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Min Zhang
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Ye
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Kai-Lu Zhang
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Mo-Xian Chen
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Lin Chen
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xian-Rong Wang
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China.
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Fu-Yuan Zhu
- College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, China.
- College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Brandi J, Robotti E, Manfredi M, Barberis E, Marengo E, Novelli E, Cecconi D. Kohonen Artificial Neural Network and Multivariate Analysis in the Identification of Proteome Changes during Early and Long Aging of Bovine Longissimus dorsi Muscle Using SWATH Mass Spectrometry. J Agric Food Chem 2021; 69:11512-11522. [PMID: 34523341 PMCID: PMC8485349 DOI: 10.1021/acs.jafc.1c03578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 06/13/2023]
Abstract
To study proteomic changes involved in tenderization of Longissimus dorsi, Charolais heifers and bulls muscles were sampled after early and long aging (12 or 26 days). Sensory evaluation and instrumental tenderness measurement were performed. Proteins were analyzed by gel-free proteomics. By pattern recognition (principal component analysis and Kohonen's self-organizing maps) and classification (partial least squares-discriminant analysis) tools, 58 and 86 dysregulated proteins were detected after 12 and 26 days of aging, respectively. Tenderness was positively correlated mainly with metabolic enzymes (PYGM, PGAM2, TPI1, PGK1, and PFKM) and negatively with keratins. Downregulation in hemoglobin subunits and carbonic anhydrase 3 levels was relevant after 12 days of aging, while mimecan and collagen chains levels were reduced after 26 days of aging. Bioinformatics indicated that aging involves a prevalence of metabolic pathways after late and long periods. These findings provide a deeper understanding of changes involved in aging of beef and indicate a powerful method for future proteomics studies.
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Affiliation(s)
- Jessica Brandi
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, Verona 37134, Italy
| | - Elisa Robotti
- Department
of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria 15121, Italy
| | - Marcello Manfredi
- Department
of Translational Medicine and Center for Translational Research on
Autoimmune Diseases, University of Piemonte
Orientale, Novara 28100, Italy
- Department
of Translational Medicine, University of
Piemonte Orientale, Novara 28100, Italy
| | - Elettra Barberis
- Department
of Translational Medicine and Center for Translational Research on
Autoimmune Diseases, University of Piemonte
Orientale, Novara 28100, Italy
- Department
of Translational Medicine, University of
Piemonte Orientale, Novara 28100, Italy
| | - Emilio Marengo
- Department
of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria 15121, Italy
| | - Enrico Novelli
- Department
of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua 35122, Italy
| | - Daniela Cecconi
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, Verona 37134, Italy
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Wu H, Wang D, Zheng Q, Xu Z. Integrating SWATH-MS proteomics and transcriptome analysis to preliminarily identify three DEGs as biomarkers for proliferative diabetic retinopathy. Proteomics Clin Appl 2021; 16:e2100016. [PMID: 34528762 DOI: 10.1002/prca.202100016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 11/05/2022]
Abstract
PURPOSE We intended to preliminarily find differentially expressed proteins that play crucial roles in proliferative diabetic retinopathy (PDR), and lay the foundation for subsequent further research on the mechanism. EXPERIMENTAL DESIGN Here, we developed a new strategy integrated the sequential windowed acquisition of all theoretical fragment ion (SWATH) mass spectra (MS) with multi-dataset joint analysis to screen for the PDR plasma biomarker. The annotation of the given gene list was performed with ClueGO function analysis. Additionally, the protein-protein interaction relationship was also revealed by the STRING database. RESULTS In SWATH-MS assays, we identified 23 upregulated and 13 downregulated proteins in PDR plasma. In the mRNA database analysis, 375 genes were identified as differentially expressed genes in GSE102485. Only three genes (FCGR3A, DPEP2, and ADGRF5) were characterized as upregulated in both the dataset and the SWATH-MS list. The area under the ROC curve (AUC) of FCGR3A, DPEP2, and ADGRF5 in distinguishing PDR from others was 0.739, 0.770, and 0.739. CONCLUSIONS AND CLINICAL RELEVANCE We provide a novel strategy for biomarker screening and identified plasma FCGR3A, DPEP2, and ADGRF5 as potential biomarkers for patients with PDR. Identifying the key molecules of the disease is essential for the development of new therapeutic molecules and new uses of existing drugs.
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Affiliation(s)
- Haijian Wu
- Department of Ophthalmology, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Dongguo Wang
- Department of Central Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Qianyin Zheng
- Department of Ophthalmology, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Zhiwei Xu
- Department of Ophthalmology, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
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Gómez BB, López-Cortés R, Casas-Nebra FJ, Vázquez-Estévez S, Pérez-Fentes D, Chantada-Vázquez MDP, Bravo SB, Núñez C. Detection of Circulating Serum Protein Biomarkers of Non-Muscle Invasive Bladder Cancer after Protein Corona-Silver Nanoparticles Analysis by SWATH-MS. Nanomaterials (Basel) 2021; 11:2384. [PMID: 34578700 DOI: 10.3390/nano11092384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022]
Abstract
Because cystoscopy is expensive and invasive, a new method of detecting non-invasive muscular bladder cancer (NMIBC) is needed. This study aims to identify potential serum protein markers for NMIBC to improve diagnosis and to find treatment approaches that avoid disease progression to a life-threatening phenotype (muscle-invasive bladder cancer, MIBC). Here, silver nanoparticles (AgNPs, 9.73 ± 1.70 nm) as a scavenging device together with sequential window acquisition of all theoretical mass spectra (SWATH-MS) were used to quantitatively analyze the blood serum protein alterations in two NMIBC subtypes, T1 and Ta, and they were compared to normal samples (HC). NMIBC’s analysis of serum samples identified three major groups of proteins, the relative content of which is different from the HC content: proteins implicated in the complement and coagulation cascade pathways and apolipoproteins. In conclusion, many biomarker proteins were identified that merit further examination to validate their useful significance and utility within the clinical management of NMIBC patients.
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Bose U, Juhász A, Yu R, Bahmani M, Byrne K, Blundell M, Broadbent JA, Howitt CA, Colgrave ML. Proteome and Nutritional Shifts Observed in Hordein Double-Mutant Barley Lines. Front Plant Sci 2021; 12:718504. [PMID: 34567030 PMCID: PMC8458801 DOI: 10.3389/fpls.2021.718504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements; proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Ronald Yu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | | | | | | | - Michelle L. Colgrave
- CSIRO Agriculture and Food, St Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA, Australia
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Shen CC, Chen MX, Xiao T, Zhang C, Shang J, Zhang KL, Zhu FY. Global proteome response to Pb(II) toxicity in poplar using SWATH-MS-based quantitative proteomics investigation. Ecotoxicol Environ Saf 2021; 220:112410. [PMID: 34126303 DOI: 10.1016/j.ecoenv.2021.112410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 05/07/2023]
Abstract
Lead (Pb) toxicity is a growing serious environmental pollution that threatens human health and crop productivity. Poplar, as an important economic and ecological forest species, has the characteristics of fasting growth and accumulating heavy metals, which is a powerful model plant for phytoremediation. Here, a novel label-free quantitative proteomic platform of SWATH-MS was applied to detect proteome changes in poplar seedling roots following Pb treatment. In total 4388 unique proteins were identified and quantified, among which 542 proteins showed significant abundance changes upon Pb(II) exposure. Functional categorizations revealed that differentially expressed proteins (DEPs) primarily distributed in specialized biological processes. Particularly, lignin and flavonoid biosynthesis pathway were strongly activated upon Pb exposure, implicating their potential roles for Pb detoxification in poplar. Furthermore, hemicellulose and pectin related cell wall proteins exhibited increased abundances, where may function as a sequestration reservoir to reduce Pb toxicity in cytoplasm. Simultaneously, up-regulation of glutathione metabolism may serve as a protective role for Pb-induced oxidative damages in poplar. Further correlation investigation revealed an extra layer of post-transcriptional regulation during Pb response in poplar. Overall, our work represents multiply potential regulators in mediating Pb tolerance in poplar, providing molecular targets and strategies for phytoremediation.
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Affiliation(s)
- Cong-Cong Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tian Xiao
- Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
| | - Cheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China; International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jun Shang
- SpecAlly Life Technology Co., Ltd and Wuhan Institute of Biotechnology, Wuhan, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China; International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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Iqbal Z, Fachim HA, Gibson JM, Baricevic-Jones I, Campbell AE, Geary B, Donn RP, Hamarashid D, Syed A, Whetton AD, Soran H, Heald AH. Changes in the Proteome Profile of People Achieving Remission of Type 2 Diabetes after Bariatric Surgery. J Clin Med 2021; 10:3659. [PMID: 34441954 PMCID: PMC8396849 DOI: 10.3390/jcm10163659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Bariatric surgery (BS) results in metabolic pathway recalibration. We have identified potential biomarkers in plasma of people achieving type 2 diabetes mellitus (T2DM) remission after BS. Longitudinal analysis was performed on plasma from 10 individuals following Roux-en-Y gastric bypass (n = 7) or sleeve gastrectomy (n = 3). Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) was done on samples taken at 4 months before (baseline) and 6 and 12 months after BS. Four hundred sixty-seven proteins were quantified by SWATH-MS. Principal component analysis resolved samples from distinct time points after selection of key discriminatory proteins: 25 proteins were differentially expressed between baseline and 6 months post-surgery; 39 proteins between baseline and 12 months. Eight proteins (SHBG, TF, PRG4, APOA4, LRG1, HSPA4, EPHX2 and PGLYRP) were significantly different to baseline at both 6 and 12 months post-surgery. The panel of proteins identified as consistently different included peptides related to insulin sensitivity (SHBG increase), systemic inflammation (TF and HSPA4-both decreased) and lipid metabolism (APOA4 decreased). We found significant changes in the proteome for eight proteins at 6- and 12-months post-BS, and several of these are key components in metabolic and inflammatory pathways. These may represent potential biomarkers of remission of T2DM.
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Affiliation(s)
- Zohaib Iqbal
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
| | - Helene A. Fachim
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
| | - J. Martin Gibson
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
| | - Ivona Baricevic-Jones
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (I.B.-J.); (A.E.C.); (B.G.); (A.D.W.)
| | - Amy E. Campbell
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (I.B.-J.); (A.E.C.); (B.G.); (A.D.W.)
| | - Bethany Geary
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (I.B.-J.); (A.E.C.); (B.G.); (A.D.W.)
| | - Rachelle P. Donn
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
| | - Dashne Hamarashid
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
| | - Akheel Syed
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (I.B.-J.); (A.E.C.); (B.G.); (A.D.W.)
- Manchester National Institute for Health Research Biomedical Research Centre, Manchester M13 9WL, UK
| | - Handrean Soran
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
| | - Adrian H. Heald
- The School of Medicine and Manchester Academic Health Sciences Centre, Manchester University, Manchester M13 9PL, UK; (Z.I.); (J.M.G.); (R.P.D.); (H.S.)
- Department of Endocrinology, Diabetes and Metabolism, Salford Royal Foundation Trust, Salford M6 8HD, UK; (D.H.); (A.S.)
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Serrano-Blesa E, Porter A, Lendrem DW, Pitzalis C, Barton A, Treumann A, Isaacs JD. Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach. Clin Proteomics 2021; 18:20. [PMID: 34384350 PMCID: PMC8359389 DOI: 10.1186/s12014-021-09323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that method to Sequential Window Acquisition of all Theoretical Spectra Mass Spectroscopy (SWATH-MS). Methods We used a sequential quality by design approach exploiting a fractional screening design to first identify critical SWATH-MS parameters, then using response surface methods to identify a robust operating window with good reproducibility, before validating those settings in a separate validation study. Results The screening experiment identified two critical SWATH-MS parameters. We modelled the number of proteins and reproducibility as a function of those parameters identifying an operating window permitting robust maximization of the number of proteins quantified in human serum. In a separate validation study, these settings were shown to give good proteome-wide coverage and high quantification reproducibility. Conclusions Using design of experiments permits identification of a robust operating window for SWATH-MS. The method gives a good understanding of proteomics assays and greater data-driven confidence in SWATH-MS performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09323-z.
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Affiliation(s)
- Edith Serrano-Blesa
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Porter
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - Dennis W Lendrem
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, Queen Mary University of London, London, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre,, The University of Manchester, Manchester, UK
| | - Achim Treumann
- Newcastle University Protein and Proteome Facility, Newcastle upon Tyne, UK
| | - John D Isaacs
- National Institute of Health Research Newcastle Biomedical Research Centre and the Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. .,Musculoskeletal Unit, Freeman Hospital, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK.
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Oleaga A, Carnero-Morán A, Valero ML, Pérez-Sánchez R. Proteomics informed by transcriptomics for a qualitative and quantitative analysis of the sialoproteome of adult Ornithodoros moubata ticks. Parasit Vectors 2021; 14:396. [PMID: 34380568 PMCID: PMC8356541 DOI: 10.1186/s13071-021-04892-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023] Open
Abstract
Background The argasid tick Ornithodoros moubata is the main vector in mainland Africa of African swine fever virus and the spirochete Borrelia duttoni, which causes human relapsing fever. The elimination of populations of O. moubata would contribute to the prevention and control of these two serious diseases. Anti-tick vaccines are an eco-friendly and sustainable means of eliminating tick populations. Tick saliva forms part of the tick-host interface, and knowledge of its composition is key to the identification and selection of vaccine candidate antigens. The aim of the present work is to increase the body of data on the composition of the saliva proteome of adult O. moubata ticks, particularly of females, since in-depth knowledge of the O. moubata sialome will allow the identification and selection of novel salivary antigens as targets for tick vaccines. Methods We analysed samples of female and male saliva using two different mass spectrometry (MS) approaches: data-dependent acquisition liquid chromatography-tandem MS (LC–MS/MS) and sequential window acquisition of all theoretical fragment ion spectra–MS (SWATH-MS). To maximise the number of proteins identified, a proteomics informed by transcriptomics analysis was applied using the O. moubata salivary transcriptomic dataset previously obtained by RNA-Seq. Results SWATH-MS proved to be superior to LC–MS/MS for the study of female saliva, since it identified 61.2% more proteins than the latter, the reproducibility of results was enhanced with its use, and it provided a quantitative picture of salivary components. In total, we identified 299 non-redundant proteins in the saliva of O. moubata, and quantified the expression of 165 of these in both male and female saliva, among which 13 were significantly overexpressed in females and 40 in males. These results indicate important quantitative differences in the saliva proteome between the sexes. Conclusions This work expands our knowledge of the O. moubata sialome, particularly that of females, by increasing the number of identified novel salivary proteins, which have different functions at the tick–host feeding interface. This new knowledge taken together with information on the O. moubata sialotranscriptome will allow a more rational selection of salivary candidates as antigen targets for tick vaccine development. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04892-2.
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Affiliation(s)
- Ana Oleaga
- Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Salamanca, Spain.
| | - Angel Carnero-Morán
- Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Salamanca, Spain
| | - M Luz Valero
- Proteomics Section, Central Service for Experimental Research, University of Valencia, Valencia, Spain
| | - Ricardo Pérez-Sánchez
- Parasitology Laboratory, Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Salamanca, Spain
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Macur K, Zieschang S, Lei S, Morsey B, Jaquet S, Belshan M, Fox HS, Ciborowski P. SWATH-MS and MRM: Quantification of Ras-related proteins in HIV-1 infected and methamphetamine-exposed human monocyte-derived macrophages (hMDM). Proteomics 2021; 21:e2100005. [PMID: 34051048 PMCID: PMC9977323 DOI: 10.1002/pmic.202100005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022]
Abstract
HIV-1 infection of macrophages is a multistep and multifactorial process that has been shown to be enhanced by exposure to methamphetamine (Meth). In this study, we sought to identify the underlying mechanisms of this effect by quantifying the effect of Meth on the proteome of HIV-1-infected macrophages using sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) approach. The analyses identified several members of the Rab family of proteins as being dysregulated by Meth treatment, which was confirmed by bioinformatic analyses that indicated substantial alteration of vesicular transport pathways. Validation of the SWATH-MS was performed using an MRM based approach, which confirmed that Meth exposure affects expression of the Rab proteins. However, the pattern of expression changes were highly dynamic, and displayed high donor-to-donor variability. Surprisingly a similar phenomenon was observed for Actin. Our results demonstrate that Meth affects vesicular transport pathways, suggesting a possible molecular mechanism underlying its effect on HIV infection hMDM and a potential broader effect of Meth on cellular homeostasis.
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Affiliation(s)
- Katarzyna Macur
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE,Core Facility Laboratories, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Poland
| | - Sarah Zieschang
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Shulei Lei
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Brenda Morsey
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Spencer Jaquet
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE
| | - Howard S. Fox
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE,Corresponding author: Dr. Pawel Ciborowski, Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985800 University of Nebraska Medical Center, Omaha, NE 68198-5800, phone +1 (402) 559-3733, fax +1 (402) 559-7495
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Tahmasian A, Broadbent JA, Juhász A, Nye-Wood M, Le TT, Bose U, Colgrave ML. Evaluation of protein extraction methods for in-depth proteome analysis of narrow-leafed lupin (Lupinus angustifolius) seeds. Food Chem 2021; 367:130722. [PMID: 34375893 DOI: 10.1016/j.foodchem.2021.130722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023]
Abstract
Lupin is slated as a potential contributor towards future food security. Lupin possesses several nutritional and nutraceutical attributes, many linked to seed proteins. For in-depth characterisation of the lupin proteome, liquid chromatography-tandem mass spectrometry was used to evaluate four protein extraction procedures. The proteomes of three narrow-leafed lupin were qualitatively evaluated using protein/peptide identifications and further quantitatively assessed by data-independent proteome measurement. Each extraction buffer led to unique protein identifications; altogether yielding 2,760 protein identifications from lupin varieties. The analysis of protein abundance data highlighted distinct differences between Tris-HCl and urea extracted proteomes, while also revealing variation amongst the cultivar proteomes with the wild accession (P27255) distinctly different from the domesticated cultivars (Tanjil, Unicrop). The extraction buffer used influenced the proteome coverage, downstream functional annotation results and consequently the biological interpretation demonstrating the need to optimise and understand the impact of protein extraction conditions.
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Affiliation(s)
- Arineh Tahmasian
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Mitchell Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Thao T Le
- School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
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Njoku K, Chiasserini D, Geary B, Pierce A, Jones ER, Whetton AD, Crosbie EJ. Comprehensive Library Generation for Identification and Quantification of Endometrial Cancer Protein Biomarkers in Cervico-Vaginal Fluid. Cancers (Basel) 2021; 13:3804. [PMID: 34359700 DOI: 10.3390/cancers13153804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Endometrial cancer is the most common cancer of the female reproductive tract, and its incidence is rising. Early diagnosis has the potential to improve survival as women can receive care at the earliest possible stage when curative treatment is likely. Current tests for endometrial cancer diagnosis are sequentially invasive with low patient acceptability. A detection tool based on minimally invasive samples such as cervico-vaginal fluid would be a major advance in the field. This study focuses on the potential of detecting endometrial cancer based on the proteins and peptides expressed in cervico-vaginal fluid. Using Sequential window acquisition of all theoretical mass spectra (SWATH-MS), we present a spectral library of thousands of proteins in the cervico-vaginal fluid of women with or at risk of endometrial cancer. This important resource will enable the identification of endometrial cancer biomarkers in cervico-vaginal fluid and advances our knowledge of the role of proteomics in endometrial cancer detection. Abstract Endometrial cancer is the most common gynaecological malignancy in high-income countries and its incidence is rising. Early detection, aided by highly sensitive and specific biomarkers, has the potential to improve outcomes as treatment can be provided when it is most likely to effect a cure. Sequential window acquisition of all theoretical mass spectra (SWATH-MS), an accurate and reproducible platform for analysing biological samples, offers a technological advance for biomarker discovery due to its reproducibility, sensitivity and potential for data re-interrogation. SWATH-MS requires a spectral library in order to identify and quantify peptides from multiplexed mass spectrometry data. Here we present a bespoke spectral library of 154,206 transitions identifying 19,394 peptides and 2425 proteins in the cervico-vaginal fluid of postmenopausal women with, or at risk of, endometrial cancer. We have combined these data with a library of over 6000 proteins generated based on mass spectrometric analysis of two endometrial cancer cell lines. This unique resource enables the study of protein biomarkers for endometrial cancer detection in cervico-vaginal fluid. Data are available via ProteomeXchange with unique identifier PXD025925.
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Lewandowska AE, Fel A, Thiel M, Czaplewska P, Łukaszuk K, Wiśniewski JR, Ołdziej S. Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid. Int J Mol Sci 2021; 22:7415. [PMID: 34299044 PMCID: PMC8304916 DOI: 10.3390/ijms22147415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
We present two separate label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups, which are termed after the utilized instrument: Quad-Orbitrap (nano-LC) and Triple Quad-TOF (micro-LC) and their directed adaptation toward the analysis of human follicular fluid proteome. We identified about 1000 proteins in each distinct workflow using various sample preparation methods. With assistance of the Total Protein Approach, we were able to obtain absolute protein concentrations for each workflow. In a pilot study of twenty samples linked to diverse oocyte quality status from four donors, 455 and 215 proteins were quantified by the Quad-Orbitrap and Triple Quad-TOF workflows, respectively. The concentration values obtained from both workflows correlated to a significant degree. We found reasonable agreement of both workflows in protein fold changes between tested groups, resulting in unified lists of 20 and 22 proteins linked to oocyte maturity and blastocyst development, respectively. The Quad-Orbitrap workflow was best suited for an in-depth analysis without the need of extensive fractionation, especially of low abundant proteome, whereas the Triple Quad-TOF workflow allowed a more robust approach with a greater potential to increase in effectiveness with the growing number of analyzed samples after the initial effort of building a comprehensive spectral library.
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Affiliation(s)
- Aleksandra E. Lewandowska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Anna Fel
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Marcel Thiel
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
| | - Krzysztof Łukaszuk
- INVICTA Fertility and Reproductive Center, Polna 64, 81-740 Sopot, Poland;
- Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Jacek R. Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland; (A.F.); (M.T.); (P.C.)
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Chen H, Williams KE, Kwan EY, Kapidzic M, Puckett KA, Aburajab RK, Robinson JF, Fisher SJ. Global proteomic analyses of human cytotrophoblast differentiation/invasion. Development 2021; 148:dev199561. [PMID: 34121116 PMCID: PMC8276980 DOI: 10.1242/dev.199561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
During human pregnancy, cytotrophoblasts (CTBs) from the placenta differentiate into specialized subpopulations that play crucial roles in proper fetal growth and development. A subset of these CTBs differentiate along an invasive pathway, penetrating the decidua and anchoring the placenta to the uterus. A crucial hurdle in pregnancy is the ability of these cells to migrate, invade and remodel spiral arteries, ensuring adequate blood flow to nourish the developing fetus. Although advances continue in describing the molecular features regulating the differentiation of these cells, assessment of their global proteomic changes at mid-gestation remain undefined. Here, using sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which is a data-independent acquisition strategy, we characterized the protein repertoire of second trimester human CTBs during their differentiation towards an invasive phenotype. This mass spectrometry-based approach allowed identification of 3026 proteins across four culture time points corresponding to sequential stages of differentiation, confirming the expression dynamics of established molecules and offering new information into other pathways involved. The availability of a SWATH CTB global spectral library serves as a beneficial resource for hypothesis generation and as a foundation for further understanding CTB differentiation dynamics.
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Affiliation(s)
- Hao Chen
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, CA 94143, USA
| | - Katherine E. Williams
- Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, CA 94143, USA
| | - Elaine Y. Kwan
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Mirhan Kapidzic
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Kenisha A. Puckett
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Rayyan K. Aburajab
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Joshua F. Robinson
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Susan J. Fisher
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, CA 94143, USA
- Division of Maternal Fetal Medicine, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Human Embryonic Stem Cell Program, University of California, San Francisco, CA 94143, USA
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Belshan M, Holbrook A, George JW, Durant HE, Callahan M, Jaquet S, West JT, Siedlik J, Ciborowski P. Discovery of candidate HIV-1 latency biomarkers using an OMICs approach. Virology 2021; 558:86-95. [PMID: 33735754 PMCID: PMC10171037 DOI: 10.1016/j.virol.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 11/19/2022]
Abstract
Infection with HIV-1 remains uncurable due to reservoirs of latently infected cells. Any potential cure for HIV will require a mechanism to identify and target these cells in vivo. We created a panel of Jurkat cell lines latently infected with the HIV DuoFlo virus to identify candidate biomarkers of latency. SWATH mass spectrometry was used to compare the membrane proteomes of one of the cell lines to parental Jurkat cells. Several candidate proteins with significantly altered expression were identified. The differential expression of several candidates was validated in multiple latently infected cell lines. Three factors (LAG-3, CD147,CD231) were altered across numerous cell lines, but the expression of most candidate biomarkers was variable. These results confirm that phenotypic differences in latently infected cells exists and identify additional novel biomarkers. The variable expression of biomarkers across different cell clones suggests universal antigen-based detection of latently infected cells may require a multiplex approach.
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Affiliation(s)
- Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA.
| | - Alexander Holbrook
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Joseph W George
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Hannah E Durant
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Michael Callahan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Spencer Jaquet
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - John T West
- Department of Biochemistry, And the Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
| | - Jacob Siedlik
- Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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Rivera-Egea R, Sota N, González-Martín R, Meseguer M, Remohí J, Garrido N, Dominguez F. Differential sperm proteomic profiles according to pregnancy achievement in intracytoplasmic sperm injection cycles: a pilot study. J Assist Reprod Genet 2021; 38:1507-1521. [PMID: 33835370 PMCID: PMC8266945 DOI: 10.1007/s10815-021-02098-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/01/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE To describe the proteomic profiles in semen samples and define the differences in sperm proteomic profiles among samples that ultimately achieved pregnancy (P) via intracytoplasmic sperm injection (ICSI) in an oocyte donation program and those that were unsuccessful (NP). METHODS Prospective, analytical, observational nested case and control study evaluating the proteomic profile of spermatozoa from patients' ejaculates where pregnancies were (group pregnant (P), n= 4) or were not (group non-pregnant (NP), n=4) achieved after ICSI in an oocyte donation program aiming to standardize female factor. Proteins were separated and analyzed by means of SWATH-MS) and compared between P/NP groups to identify sperm biomarkers of fertility/infertility. Proteins are available via ProteomeXchange. RESULTS We identified and quantified 2228 proteins, with 37 significantly higher in the P group and 16 higher in NP. Enrichment analysis revealed that the increased proteins in P group sperm were related to motility, anaerobic metabolism, and protein biosynthesis functions, while the increased proteins in the NP group were involved in protein biosynthesis, protein folding, aerobic metabolism, and signal transduction, all of which are functions not previously described as influencing sperm success. Some proteins identified (e.g., SLC2A3, or CD81) are located in the cell membrane and thus may be employed to select spermatozoa by magnetic-activated cell sorting (MACS). CONCLUSION(S) This work revealed differences in the proteomic profiles of sperm samples successful in achieving pregnancy and those that were not, expanding our understanding of sperm function and infertility-related molecular markers, and enabling the future development of male fertility diagnostic tools and therapies.
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Affiliation(s)
- Rocio Rivera-Egea
- Andrology Laboratory and Sperm Bank, IVIRMA Valencia, Plaza de la Policía Local, 3, 46015 Valencia, Spain
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
| | - Nerea Sota
- Andrology Laboratory and Sperm Bank, IVIRMA Valencia, Plaza de la Policía Local, 3, 46015 Valencia, Spain
| | - Roberto González-Martín
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
| | - Marcos Meseguer
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
- IVF Laboratory, IVIRMA Valencia, Plaza de la Policía Local, 3, 46015 Valencia, Spain
| | - Jose Remohí
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
- Reproductive Medicine Department, IVIRMA Valencia, Plaza de la Policía Local, 3, 46015 Valencia, Spain
| | - Nicolas Garrido
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
| | - Francisco Dominguez
- IVI Foundation, Health Research Institute La Fe, Edificion Biopolo-La Fe, Avenida Fernando Abril Martorell, 106-Torre A, Planta 1ª, 46026 Valencia, Spain
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