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Andronis CE, Jacques S, Lopez-Ruiz FJ, Lipscombe R, Tan KC. Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem. J Proteomics 2024; 301:105181. [PMID: 38670258 DOI: 10.1016/j.jprot.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Phytopathogenic oomycetes constitute some of the most devastating plant pathogens and cause significant crop and horticultural yield and economic losses. The phytopathogen Phytophthora cinnamomi causes dieback disease in native vegetation and several crops. The most commonly used chemical to control P. cinnamomi is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it targets the pathogen, the host, or both. Resistance to phosphite is emerging in P. cinnamomi isolates and other oomycete phytopathogens. The mode of action of phosphite on phosphite-sensitive and resistant isolates of the pathogen and through a model host was investigated using label-free quantitative proteomics. In vitro treatment of sensitive P. cinnamomi isolates with phosphite hinders growth by interfering with metabolism, signalling and gene expression; traits that are not observed in the resistant isolate. When the model host Lupinus angustifolius was treated with phosphite, proteins associated with photosynthesis, carbon fixation and lipid metabolism in the host were enriched. Increased production of defence-related proteins was also observed in the plant. We hypothesise the multi-modal action of phosphite and present two models constructed using comparative proteomics that demonstrate mechanisms of pathogen and host responses to phosphite. SIGNIFICANCE: Phytophthora cinnamomi is a significant phytopathogenic oomycete that causes root rot (dieback) in a number of horticultural crops and a vast range of native vegetation. Historically, areas infected with phosphite have been treated with the oomyceticide phosphite despite its unknown mode of action. Additionally, overuse of phosphite has driven the emergence of phosphite-resistant isolates of the pathogen. We conducted a comparative proteomic study of a sensitive and resistant isolate of P. cinnamomi in response to treatment with phosphite, and the response of a model host, Lupinus angustifolius, to phosphite and its implications on infection. The present study has allowed for a deeper understanding of the bimodal action of phosphite, suggested potential biochemical factors contributing to chemical resistance in P. cinnamomi, and unveiled possible drivers of phosphite-induced host plant immunity to the pathogen.
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Affiliation(s)
- Christina E Andronis
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia; Proteomics International, Nedlands, WA, Australia.
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia
| | | | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.
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2
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Bruce JW, Park E, Magnano C, Horswill M, Richards A, Potts G, Hebert A, Islam N, Coon JJ, Gitter A, Sherer N, Ahlquist P. HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B. PLoS Pathog 2023; 19:e1011492. [PMID: 37459363 PMCID: PMC10374047 DOI: 10.1371/journal.ppat.1011492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 07/27/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
HIV-1 spreads efficiently through direct cell-to-cell transmission at virological synapses (VSs) formed by interactions between HIV-1 envelope proteins (Env) on the surface of infected cells and CD4 receptors on uninfected target cells. Env-CD4 interactions bring the infected and uninfected cellular membranes into close proximity and induce transport of viral and cellular factors to the VS for efficient virion assembly and HIV-1 transmission. Using novel, cell-specific stable isotope labeling and quantitative mass spectrometric proteomics, we identified extensive changes in the levels and phosphorylation states of proteins in HIV-1 infected producer cells upon mixing with CD4+ target cells under conditions inducing VS formation. These coculture-induced alterations involved multiple cellular pathways including transcription, TCR signaling and, unexpectedly, cell cycle regulation, and were dominated by Env-dependent responses. We confirmed the proteomic results using inhibitors targeting regulatory kinases and phosphatases in selected pathways identified by our proteomic analysis. Strikingly, inhibiting the key mitotic regulator Aurora kinase B (AURKB) in HIV-1 infected cells significantly increased HIV activity in cell-to-cell fusion and transmission but had little effect on cell-free infection. Consistent with this, we found that AURKB regulates the fusogenic activity of HIV-1 Env. In the Jurkat T cell line and primary T cells, HIV-1 Env:CD4 interaction also dramatically induced cell cycle-independent AURKB relocalization to the centromere, and this signaling required the long (150 aa) cytoplasmic C-terminal domain (CTD) of Env. These results imply that cytoplasmic/plasma membrane AURKB restricts HIV-1 envelope fusion, and that this restriction is overcome by Env CTD-induced AURKB relocalization. Taken together, our data reveal a new signaling pathway regulating HIV-1 cell-to-cell transmission and potential new avenues for therapeutic intervention through targeting the Env CTD and AURKB activity.
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Affiliation(s)
- James W. Bruce
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Eunju Park
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Chris Magnano
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mark Horswill
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Alicia Richards
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Gregory Potts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Alexander Hebert
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Nafisah Islam
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Anthony Gitter
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, United States of America
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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3
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Alghanem B, Mansour FA, Shaibah H, Almuhalhil K, Almourfi F, Alamri HS, Alajmi H, Rashid M, Alroqi F, Jalouli M, Harrath AH, Boudjellal M, Barhoumi T. Quantitative proteomics analysis of COVID-19 patients: Fetuin-A and tetranectin as potential modulators of innate immune responses. Heliyon 2023; 9:e15224. [PMID: 37064481 PMCID: PMC10082967 DOI: 10.1016/j.heliyon.2023.e15224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/26/2023] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Treatment of severe cases of coronavirus disease 2019 (COVID-19) is extremely important to minimize death and end-organ damage. Here we performed a proteomic analysis of plasma samples from mild, moderate and severe COVID-19 patients. Analysis revealed differentially expressed proteins and different therapeutic potential targets related to innate immune responses such as fetuin-A, tetranectin (TN) and paraoxonase-1 (PON1). Furthermore, protein changes in plasma showed dysregulation of complement and coagulation cascades in COVID-19 patients compared to healthy controls. In conclusion, our proteomics data suggested fetuin-A and TN as potential targets that might be used for diagnosis as well as signatures for a better understanding of the pathogenesis of COVID-19 disease.
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Affiliation(s)
- Bandar Alghanem
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Fatmah A Mansour
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hayat Shaibah
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Khawlah Almuhalhil
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Feras Almourfi
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hassan S Alamri
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hala Alajmi
- Saudi Biobank, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Mamoon Rashid
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Fayhan Alroqi
- Department of Pediatrics, King Abdulaziz Medical City, King Abdullah Specialized Children's Hospital, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Maroua Jalouli
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Abdel Halim Harrath
- King Saud University, Department of Zoology, College of Sciences, Riyadh, 11451, Saudi Arabia
| | - Mohammad Boudjellal
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Tlili Barhoumi
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene. Commun Biol 2023; 6:156. [PMID: 36750726 PMCID: PMC9904262 DOI: 10.1038/s42003-023-04433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2023] [Indexed: 02/09/2023] Open
Abstract
Global control of the tuberculosis epidemic is threatened by increasing prevalence of drug resistant M. tuberculosis isolates. Many genome-wide studies focus on SNP-associated drug resistance mechanisms, but drug resistance in 5-30% of M. tuberculosis isolates (varying with antibiotic) appears unrelated to reported SNPs, and alternative drug resistance mechanisms involving variation in gene/protein expression are not well-studied. Here, using an omics approach, we identify 388 genes with lineage-related differential expression and 68 candidate drug resistance-associated gene pairs/clusters in 11 M. tuberculosis isolates (variable lineage/drug resistance profiles). Structural, mutagenesis, biochemical and bioinformatic studies on Rv3094c from the Rv3093c-Rv3095 gene cluster, a gene cluster selected for further investigation as it contains a putative monooxygenase/repressor pair and is associated with ethionamide resistance, provide insights on its involvement in ethionamide sulfoxidation, the initial step in its activation. Analysis of the structure of Rv3094c and its complex with ethionamide and flavin mononucleotide, to the best of our knowledge the first structures of an enzyme involved in ethionamide activation, identify key residues in the flavin mononucleotide and ethionamide binding pockets of Rv3094c, and F221, a gate between flavin mononucleotide and ethionamide allowing their interaction to complete the sulfoxidation reaction. Our work broadens understanding of both lineage- and drug resistance-associated gene/protein expression perturbations and identifies another player in mycobacterial ethionamide metabolism.
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Xu XJ, Liu BY, Dong JQ, Ge QQ, Lu SH, Yang MS, Zhuang Y, Zhang B, Niu F. Tandem Mass Tag-based proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model. Neural Regen Res 2023. [PMID: 35799536 PMCID: PMC9241417 DOI: 10.4103/1673-5374.343886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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7
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Ahmadzai H, Tee LBG, Crowe A. Are active efflux transporters contributing to infant drug exposure via breastmilk? A longitudinal study. Basic Clin Pharmacol Toxicol 2022; 131:487-499. [PMID: 36130042 PMCID: PMC9827846 DOI: 10.1111/bcpt.13794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 01/12/2023]
Abstract
Although most drugs are considered safe and compatible with breastfeeding, cases of toxic drug exposure have been reported. Active efflux transporters have been implicated as a mechanism in the transfer of drugs from mother to baby via breastmilk. Using breastmilk as a source of human mammary epithelial cells, this novel longitudinal study investigated the expression of four active transporters, namely, MDR1, MRP1, MRP2 and BCRP in the lactating human breast. BCRP gene was found to be strongly overexpressed with levels peaking at 5 months postpartum, potentially indicating a time where a breastfed infant may be at risk of inadvertent exposure to BCRP substrates. Serum albumin, a major component of human breastmilk was increasingly downregulated as lactation progresses. Xanthine oxidase/dehydrogenase, an enzyme in breastmilk attributed to a reduced risk of gastroenteritis caused by Escherichia coli and Salmonella enteritides, was downregulated. Lysozyme and fatty acid synthase are progressively upregulated. This study also shows that breastmilk-derived epithelial cells, when propagated in culture, exhibit characteristics significantly different to those derived directly from breastmilk. This serves to warn that in vitro studies are not a true representation of in vivo processes in the lactating breast; hence, application of in vitro data should be conducted with caution.
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Affiliation(s)
- Hilai Ahmadzai
- Curtin Medical SchoolCurtin UniversityBentleyWestern AustraliaAustralia,Pharmacy DepartmentSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - Lisa B. G. Tee
- Curtin Medical SchoolCurtin UniversityBentleyWestern AustraliaAustralia
| | - Andrew Crowe
- Curtin Medical SchoolCurtin UniversityBentleyWestern AustraliaAustralia
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Upadhya SR, Ryan CJ. Experimental reproducibility limits the correlation between mRNA and protein abundances in tumor proteomic profiles. CELL REPORTS METHODS 2022; 2:100288. [PMID: 36160043 PMCID: PMC9499981 DOI: 10.1016/j.crmeth.2022.100288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022]
Abstract
Large-scale studies of human proteomes have revealed only a moderate correlation between mRNA and protein abundances. It is unclear to what extent this moderate correlation reflects post-transcriptional regulation and to what extent it reflects measurement error. Here, by analyzing replicate profiles of tumors and cell lines, we show that there is considerable variation in the reproducibility of measurements of transcripts and proteins from individual genes. Proteins with more reproducible measurements tend to have a higher mRNA-protein correlation, suggesting that measurement reproducibility accounts for a substantial fraction of the unexplained variation between mRNA and protein abundances. The reproducibility of individual proteins is somewhat consistent across studies, and we exploit this to develop an aggregate reproducibility score that explains a substantial amount of the variation in mRNA-protein correlations across multiple studies. Finally, we show that pathways previously reported to have a higher-than-average mRNA-protein correlation may simply contain members that can be more reproducibly quantified.
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Affiliation(s)
- Swathi Ramachandra Upadhya
- School of Computer Science, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J. Ryan
- School of Computer Science, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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Abstract
Mass spectrometry (MS)-based proteomics is currently the most successful approach to measure and compare peptides and proteins in a large variety of biological samples. Modern mass spectrometers, equipped with high-resolution analyzers, provide large amounts of data output. This is the case of shotgun/bottom-up proteomics, which consists in the enzymatic digestion of protein into peptides that are then measured by MS-instruments through a data dependent acquisition (DDA) mode. Dedicated bioinformatic tools and platforms have been developed to face the increasing size and complexity of raw MS data that need to be processed and interpreted for large-scale protein identification and quantification. This chapter illustrates the most popular bioinformatics solution for the analysis of shotgun MS-proteomics data. A general description will be provided on the data preprocessing options and the different search engines available, including practical suggestions on how to optimize the parameters for peptide search, based on hands-on experience.
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Affiliation(s)
- Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Federica Marini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy.
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Du J, Shen T, Xiong Q, Zhu C, Peng X, He X, Fu J, Ouyang L, Bian J, Hu L, Sun X, Zhou D, He H, Zhong L, Chen X. Combined proteomics, metabolomics and physiological analyses of rice growth and grain yield with heavy nitrogen application before and after drought. BMC PLANT BIOLOGY 2020; 20:556. [PMID: 33302870 PMCID: PMC7731554 DOI: 10.1186/s12870-020-02772-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/02/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrogen application can effectively mitigate the damage to crop growth and yield caused by drought. However, the efficiency of heavy nitrogen application before drought (NBD) and heavy nitrogen application after drought (NAD) to regulate rice response to drought stress remains controversial. In this study, we profiled physiology, proteomics and metabolomics in rice variety Wufengyou 286 of two nitrogen management modes (NBD and NAD) to investigate their yield formation and the mechanism of nitrogen regulation for drought resistance. RESULTS Results revealed that the yield of NBD and NAD decreased significantly when it was subjected to drought stress at the stage of young panicle differentiation, while the yield of NBD was 33.85 and 36.33% higher than that of NAD in 2017 and 2018, reaching significant levels. Under drought conditions, NBD increased chlorophyll content and net photosynthetic rate in leaves, significantly improved the activities of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase and catalase, and decreased malondialdehyde (MDA) content compared with NAD. NBD promoted nitrogen assimilation in leaves, which was characterized by increased activities of nitrate reductase (NR) and glutamine synthetase (GS). In addition, NBD significantly increased the contents of osmotic regulatory substances such as soluble sugar, soluble protein and free proline. Gene ontology and KEGG enrichment analysis of 234 differentially expressed proteins and 518 differential metabolites showed that different nitrogen management induced strong changes in photosynthesis pathway, energy metabolism pathway, nitrogen metabolism and oxidation-reduction pathways. CONCLUSION Different nitrogen management methods have significant differences in drought resistance of rice. These results suggest that heavy nitrogen application before drought may be an important pathway to improve the yield and stress resistance of rice, and provide a new ecological perspective on nitrogen regulation in rice.
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Affiliation(s)
- Jie Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Tianhua Shen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Qiangqiang Xiong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Xiaotang Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China
| | - Lei Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China.
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Jiangxi, 330045, China.
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Wang H, Chen J, Gao C, Chen W, Chen G, Zhang M, Luo C, Wang T, Chen X, Tao L. TMT-based proteomics analysis to screen potential biomarkers of acute-phase TBI in rats. Life Sci 2020; 264:118631. [PMID: 33131748 DOI: 10.1016/j.lfs.2020.118631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/09/2020] [Accepted: 10/17/2020] [Indexed: 01/19/2023]
Abstract
AIMS Traumatic brain injury (TBI) is a common nervous system injury. However, the detailed mechanisms about functional dysregulation and dignostic biomarkers post-TBI are still unclear. So we aimed to identify potential differentially expressed proteins and genes in TBI for clinical diagnosis and therapeutic purposes. MAIN METHODS Rat TBI model was established by the weight-drop method. First, through TMT-proteomics, we screened for the change in the proteins expression profile acute phase post-TBI. The DAVID and Reactome databases were used to analyze and visualize the dysregulation proteins. Then, using publicly available microarray datasets GSE45997, differentially expressed genes (DGEs) were identified for the 24 h post-TBI stage. Also, the proteomic data were compared with microarray data to analyze the similarity. KEY FINDINGS We found significant proteomics and transcriptomic changes in post-TBI samples. 989, 881, 832, 1057 proteins were quantitated at 1 h, 6 h, 24 h, and 3 d post-injury correspondingly. Concerning proteomics findings, oxygen transport, acute-phase response, and negative regulation of endopeptidase activity were influenced throughout the acute phrase of TBI. Also, pathways related to scavenging of heme from plasma, binding, and uptake of ligands by scavenger receptors were highly enriched in all time-points of TBI samples. SIGNIFICANCE We noticed that the interaction-networks trend to get complicated with more node connections following the progression of TBI. We inferred that Hk-1, PRKAR2A, and MBP could be novel candidate biomarkers related to time-injury in acute-phase TBI. Also, Ceruloplasmin and Complement C3 were found to be important proteins and genes are involved in the TBI.
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Affiliation(s)
- Haochen Wang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
| | - Jie Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Cheng Gao
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Wei Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Guang Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Mingyang Zhang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Chengliang Luo
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Tao Wang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Xiping Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
| | - Luyang Tao
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
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13
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Du H, Zhou L, Lu Z, Bie X, Zhao H, Niu YD, Lu F. Transcriptomic and proteomic profiling response of methicillin-resistant Staphylococcus aureus (MRSA) to a novel bacteriocin, plantaricin GZ1-27 and its inhibition of biofilm formation. Appl Microbiol Biotechnol 2020; 104:7957-7970. [PMID: 32803295 DOI: 10.1007/s00253-020-10589-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/09/2020] [Accepted: 03/25/2020] [Indexed: 01/14/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become a worrisome superbug, due to its wide distribution and multidrug resistance. To characterize effects of a newly identified plantaricin GZ1-27 on MRSA, transcriptomic and proteomic profiling of MRSA strain ATCC43300 was performed in response to sub-MIC (16 μg/mL) plantaricin GZ1-27 stress. In total, 1090 differentially expressed genes (padj < 0.05) and 418 differentially expressed proteins (fold change > 1.2, p < 0.05) were identified. Centralized protein expression clusters were predicted in biological functions (biofilm formation, DNA replication and repair, and heat-shock) and metabolic pathways (purine metabolism, amino acid metabolism, and biosynthesis of secondary metabolites). Moreover, a capacity of inhibition MRSA biofilm formation and killing biofilm cells were verified using crystal violet staining, scanning electron microscopy, and confocal laser-scanning microscopy. These findings yielded comprehensive new data regarding responses induced by plantaricin and could inform evidence-based methods to mitigate MRSA biofilm formation.
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Affiliation(s)
- Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Libang Zhou
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Yan D Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, T2N 4Z6, Canada
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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14
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Reduction of Allergenic Potential in Bread Wheat RNAi Transgenic Lines Silenced for CM3, CM16 and 0.28 ATI Genes. Int J Mol Sci 2020; 21:ijms21165817. [PMID: 32823634 PMCID: PMC7461106 DOI: 10.3390/ijms21165817] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Although wheat is used worldwide as a staple food, it can give rise to adverse reactions, for which the triggering factors have not been identified yet. These reactions can be caused mainly by kernel proteins, both gluten and non-gluten proteins. Among these latter proteins, α-amylase/trypsin inhibitors (ATI) are involved in baker’s asthma and realistically in Non Celiac Wheat Sensitivity (NCWS). In this paper, we report characterization of three transgenic lines obtained from the bread wheat cultivar Bobwhite silenced by RNAi in the three ATI genes CM3, CM16 and 0.28. We have obtained transgenic lines showing an effective decrease in the activity of target genes that, although showing a higher trypsin inhibition as a pleiotropic effect, generate a lower reaction when tested with sera of patients allergic to wheat, accounting for the important role of the three target proteins in wheat allergies. Finally, these lines show unintended differences in high molecular weight glutenin subunits (HMW-GS) accumulation, involved in technological performances, but do not show differences in terms of yield. The development of new genotypes accumulating a lower amount of proteins potentially or effectively involved in allergies to wheat and NCWS, not only offers the possibility to use them as a basis for the production of varieties with a lower impact on adverse reaction, but also to test if these proteins are actually implicated in those pathologies for which the triggering factor has not been established yet.
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15
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Differential Expression of Multiple Disease-Related Protein Groups Induced by Valproic Acid in Human SH-SY5Y Neuroblastoma Cells. Brain Sci 2020; 10:brainsci10080545. [PMID: 32806546 PMCID: PMC7465595 DOI: 10.3390/brainsci10080545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022] Open
Abstract
Valproic acid (VPA) is a multifunctional medication used for the treatment of epilepsy, mania associated with bipolar disorder, and migraine. The pharmacological effects of VPA involve a variety of neurotransmitter and cell signaling systems, but the molecular mechanisms underlying its clinical efficacy is to date largely unknown. In this study, we used the isobaric tags for relative and absolute quantitation shotgun proteomic analysis to screen differentially expressed proteins in VPA-treated SH-SY5Y cells. We identified changes in the expression levels of multiple proteins involved in Alzheimer’s disease, Parkinson’s disease, chromatin remodeling, controlling gene expression via the vitamin D receptor, ribosome biogenesis, ubiquitin-mediated proteolysis, and the mitochondrial oxidative phosphorylation and electron transport chain. Our data indicate that VPA may modulate the differential expression of proteins involved in mitochondrial function and vitamin D receptor-mediated chromatin transcriptional regulation and proteins implicated in the pathogenesis of neurodegenerative diseases.
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16
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Proteomic profiling of developing wheat heads under water-stress. Funct Integr Genomics 2020; 20:695-710. [PMID: 32681185 DOI: 10.1007/s10142-020-00746-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
A replicated iTRAQ (isobaric tags for relative and absolute quantification) study on developing wheat heads from two doubled haploid (DH) lines identified from a cross between cv Westonia x cv Kauz characterized the proteome changes influenced by reproductive stage water-stress. All lines were exposed to 10 days of water-stress from early booting (Zadok 40), with sample sets taken from five head developmental stages. Two sample groups (water-stressed and control) account for 120 samples that required 18 eight-plex iTRAQ runs. Based on the IWGSC RefSeq v1 wheat assembly, among the 4592 identified proteins, a total of 132 proteins showed a significant response to water-stress, including the down-regulation of a mitochondrial Rho GTPase, a regulator of intercellular fundamental biological processes (7.5 fold) and cell division protein FtsZ at anthesis (6.0 fold). Up-regulated proteins included inosine-5'-monophosphate dehydrogenase (3.83 fold) and glycerophosphodiester phosphodiesterase (4.05 fold). The Pre-FHE and FHE stages (full head emerged) of head development were differentiated by 391 proteins and 270 proteins differentiated the FHE and Post-FHE stages. Water-stress during meiosis affected seed setting with 27% and 6% reduction in the progeny DH105 and DH299 respectively. Among the 77 proteins that differentiated between the two DH lines, 7 proteins were significantly influenced by water-stress and correlated with the seed set phenotype response of the DH lines to water-stress (e.g. the up-regulation of a subtilisin-like protease in DH 299 relative to DH 105). This study provided unique insights into the biological changes in developing wheat head that occur during water-stress.
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17
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Comparative Proteomic Investigation of Plasma Reveals Novel Potential Biomarker Groups for Acute Aortic Dissection. DISEASE MARKERS 2020; 2020:4785068. [PMID: 32256857 PMCID: PMC7106916 DOI: 10.1155/2020/4785068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/03/2022]
Abstract
Acute aortic dissection (AAD) is a catastrophic cardiovascular disease with high disability and mortality due to multiple fatal complications. However, the molecular changes of the serum proteome after AAD are not very clear. Here, we performed isobaric tags for relative and absolute quantitation- (iTRAQ-) based comparative proteomic analysis to investigate the proteome profile changes after AAD by collecting plasma samples from 20 AAD patients and 20 controls. Out of the 345 identified proteins, 266 were considered as high-quality quantified proteins (95%confident peptides ≥ 2), of which 25 proteins were accumulated and 12 were reduced in AAD samples. Gene ontology enrichment analysis showed that the 25 AAD-accumulated proteins were enriched in high-density lipoprotein particles for the cellular component category and protein homodimerization acidity for the molecular function category. Protein-protein interaction network analysis showed that serum amyloid A proteins (SAAs), complement component proteins, and carboxypeptidase N catalytic chain proteins (CPNs) possessed the key nodes of the network. The expression levels of six selected AAD-accumulated proteins, B2-GP1, CPN1, F9, LBP, SAA1, and SAA2, were validated by ELISA. Moreover, ROC analysis showed that the AUCs of B2-GP1 and CPN1 were 0.808 and 0.702, respectively. Our data provide insights into molecular change profiles in proteome levels after AAD and indicate that B2-GP1 and CPN1 are potential biomarkers for AAD.
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18
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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19
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Yugandhar K, Gupta S, Yu H. Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J 2019; 17:805-811. [PMID: 31316724 PMCID: PMC6611912 DOI: 10.1016/j.csbj.2019.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 01/06/2023] Open
Abstract
Studying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize the down-stream computational strategies for identification and quantification of interactions from those techniques. Finally, we highlight the challenges and limitations of current computational pipelines in eliminating false positive interactors, followed by a summary of the innovative algorithms to address these issues, along with the scope for future improvements.
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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Shagun Gupta
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
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20
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Lee J, Shin J, Jeong M, Youn M, Noh J, Kang J, Cho W. Glycoproteomics Method to Discover Reliable Biomarkers from Human Plasma of Lung Cancer Patients for MS‐based Clinical Studies. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jinwook Lee
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Jihoon Shin
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Miseon Jeong
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Min‐Gyu Youn
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Joohyeong Noh
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Junghoon Kang
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
| | - Wonryeon Cho
- Department of ChemistryWonkwang University Iksan 54538 Republic of Korea
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21
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Callaghan NI, Hadipour-Lakmehsari S, Lee SH, Gramolini AO, Simmons CA. Modeling cardiac complexity: Advancements in myocardial models and analytical techniques for physiological investigation and therapeutic development in vitro. APL Bioeng 2019; 3:011501. [PMID: 31069331 PMCID: PMC6481739 DOI: 10.1063/1.5055873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/31/2018] [Indexed: 02/06/2023] Open
Abstract
Cardiomyopathies, heart failure, and arrhythmias or conduction blockages impact millions of patients worldwide and are associated with marked increases in sudden cardiac death, decline in the quality of life, and the induction of secondary pathologies. These pathologies stem from dysfunction in the contractile or conductive properties of the cardiomyocyte, which as a result is a focus of fundamental investigation, drug discovery and therapeutic development, and tissue engineering. All of these foci require in vitro myocardial models and experimental techniques to probe the physiological functions of the cardiomyocyte. In this review, we provide a detailed exploration of different cell models, disease modeling strategies, and tissue constructs used from basic to translational research. Furthermore, we highlight recent advancements in imaging, electrophysiology, metabolic measurements, and mechanical and contractile characterization modalities that are advancing our understanding of cardiomyocyte physiology. With this review, we aim to both provide a biological framework for engineers contributing to the field and demonstrate the technical basis and limitations underlying physiological measurement modalities for biologists attempting to take advantage of these state-of-the-art techniques.
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Affiliation(s)
| | | | | | | | - Craig A. Simmons
- Author to whom correspondence should be addressed: . Present address: Ted Rogers Centre for Heart
Research, 661 University Avenue, 14th Floor Toronto, Ontario M5G 1M1, Canada. Tel.:
416-946-0548. Fax: 416-978-7753
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22
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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23
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Smith BJ, Martins-de-Souza D, Fioramonte M. A Guide to Mass Spectrometry-Based Quantitative Proteomics. Methods Mol Biol 2019; 1916:3-39. [PMID: 30535679 DOI: 10.1007/978-1-4939-8994-2_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Affiliation(s)
- Bradley J Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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24
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Chen M, Yan G, Wang X, Huang Z, Shao X, Wu D, Zhang X, Liu B. Investigating the proteomic expression profile of tobacco (Nicotiana tabacum) leaves during four growth stages using the iTRAQ method. Anal Bioanal Chem 2019; 411:403-411. [PMID: 30478513 DOI: 10.1007/s00216-018-1453-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Despite the importance of tobacco (Nicotiana tabacum) in agriculture and model organism investigations, the proteomic changes that occur in the tobacco leaf as it matures remain to be explored. In this study, an isobaric tags for relative and absolute quantification (iTRAQ) strategy was applied to investigate the proteomic profiles of K326 and Honghua Dajinyuan (HD) tobacco leaves at four growth stages. The proteomic profile varied with growth stage in both K326 and HD. Gene ontology (GO) classification was used to identify the biological processes that showed the greatest changes in protein expression between growth stages of HD and K326. Moreover, the number of differentially expressed proteins was greater in HD than in K326, especially during the rosette growth stage and the fast-growing stage. The galactose metabolism and glycosphingolipid biosynthesis-globo series pathways appeared only during the rosette growth stage of HD. It therefore appears that these pathways may be correlated with tobacco mosaic disease. The identification of these pathways should prove useful in investigations of the pathogenesis of tobacco mosaic virus. Graphical abstract ᅟ.
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Affiliation(s)
- Min Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xuantang Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zhi Huang
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Xi Shao
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Da Wu
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Xiangmin Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Baizhan Liu
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China.
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25
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Shang P, Wang Z, Chamba Y, Zhang B, Zhang H, Wu C. A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes. J Cell Biochem 2018; 120:5277-5286. [PMID: 30302803 DOI: 10.1002/jcb.27802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The growth of pigs is an important economic trait that involves multiple genes and coordinated regulatory mechanisms. The growth rate and potential of skeletal muscles are largely decided by embryonic myofiber development. Tibetan pig (TP) that is a mini-type breed has a divergent phenotype in growth rate and adult body weight with Wujin pig (WJ) and large White pig (LW). In the current study, the transcriptome (using RNA-seq) and proteome (using the isobaric tag for relative and absolute quantification [iTRAQ]) data from the prenatal muscle tissues were analyzed to identify the genes related to postnatal growth rate and growth potential in pigs. In the RNA-seq experiment, 19 626 genes were detected in the embryonic muscle tissues, and 3626 unique differentially expressed genes (DEGs) were identified in TP in comparison to that in LW and WJ. In the iTRAQ experiment, 2474 proteins were detected, and 735 unique differentially expressed proteins (DEPs) were identified in TP in comparison to that in LW and WJ. Combining the DEGs and DEPs, 209 genes were found to be differentially expressed, consistently at both the messenger RNA and protein levels, between TP and the other two breeds; these are mainly involved in 2-oxocarboxylic acid metabolism, citrate cycle, and biosynthesis of amino acids. Of these, 20 genes that were related to myoblast differentiation and muscle fiber formation might have important roles in determining the postnatal growth rate and potential body weight in pigs. Our results provide new candidate genes and insights into the molecular mechanisms involved muscle growth traits in pigs.
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Affiliation(s)
- Peng Shang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.,Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
| | - Zhixiu Wang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.,Department of Animal Genetics and Breeding, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yangzom Chamba
- Department of animal husbandry, College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
| | - Bo Zhang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hao Zhang
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Changxin Wu
- Laboratory National Engineering For Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
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