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Meisinger T, Vogt A, Kretz R, Hammer HS, Planatscher H, Poetz O. Mass spectrometry-based ligand binding assays in biomedical research. Expert Rev Proteomics 2025; 22:123-140. [PMID: 39964118 DOI: 10.1080/14789450.2025.2467263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 02/05/2025] [Accepted: 02/07/2025] [Indexed: 02/25/2025]
Abstract
INTRODUCTION Ligand binding assays combining immunoaffinity enrichment steps with mass spectrometry (MS) readout have gained attention as a highly specific and sensitive tool for protein quantification. These techniques typically combine enzymatic fragmentation of the sample or enriched protein with capture on the protein or peptide-level for quantification. Antibodies ensure specific target recognition, while MS offers quantitative accuracy with isotopically labeled internal standards. This dual approach supports a broad dynamic range, enabling protein measurements from picomolar to nanomolar levels. These methods have diverse applications, from quantifying signaling proteins in basic research to biomarker monitoring in clinical trials and analyzing the pharmacokinetics of therapeutic proteins. AREAS COVERED This review delves into the diverse workflows of immunoaffinity-MS, shedding light on the innovative strategies employed, their practical applications, efficacy, and inherent limitations in the realm of protein quantification. EXPERT OPINION Immunoaffinity-MS has transformed protein analysis, but widespread adoption is hindered by complex workflows, high instrument costs, and limited capture molecule availability. Efforts to enhance automation, standardize workflows, and advance technological innovation aim to overcome these barriers. Improvements in mass spectrometer sensitivity, advances in recombinant capture technologies, and support from public initiatives are poised to further improve the reliability and accessibility of this method.
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Affiliation(s)
| | | | | | | | | | - Oliver Poetz
- SIGNATOPE GmbH, Reutlingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
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2
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Gobena S, Admassu B, Kinde MZ, Gessese AT. Proteomics and Its Current Application in Biomedical Area: Concise Review. ScientificWorldJournal 2024; 2024:4454744. [PMID: 38404932 PMCID: PMC10894052 DOI: 10.1155/2024/4454744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Biomedical researchers tirelessly seek cutting-edge technologies to advance disease diagnosis, drug discovery, and therapeutic interventions, all aimed at enhancing human and animal well-being. Within this realm, proteomics stands out as a pivotal technology, focusing on extensive studies of protein composition, structure, function, and interactions. Proteomics, with its subdivisions of expression, structural, and functional proteomics, plays a crucial role in unraveling the complexities of biological systems. Various sophisticated techniques are employed in proteomics, including polyacrylamide gel electrophoresis, mass spectrometry analysis, NMR spectroscopy, protein microarray, X-ray crystallography, and Edman sequencing. These methods collectively contribute to the comprehensive understanding of proteins and their roles in health and disease. In the biomedical field, proteomics finds widespread application in cancer research and diagnosis, stem cell studies, and the diagnosis and research of both infectious and noninfectious diseases. In addition, it plays a pivotal role in drug discovery and the emerging frontier of personalized medicine. The versatility of proteomics allows researchers to delve into the intricacies of molecular mechanisms, paving the way for innovative therapeutic approaches. As infectious and noninfectious diseases continue to emerge and the field of biomedical research expands, the significance of proteomics becomes increasingly evident. Keeping abreast of the latest developments in proteomics applications becomes paramount for the development of therapeutics, translational research, and study of diverse diseases. This review aims to provide a comprehensive overview of proteomics, offering a concise outline of its current applications in the biomedical domain. By doing so, it seeks to contribute to the understanding and advancement of proteomics, emphasizing its pivotal role in shaping the future of biomedical research and therapeutic interventions.
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Affiliation(s)
- Semira Gobena
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Bemrew Admassu
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Mebrie Zemene Kinde
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Tesfaye Gessese
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
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FNU PIJ, Tanim-Al-Hassan M, Yaroshuk T, Ai Y, Chen H. Absolute Quantitation of Peptides and Proteins by Coulometric Mass Spectrometry After Derivatization. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117153. [PMID: 38009161 PMCID: PMC10673616 DOI: 10.1016/j.ijms.2023.117153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Peptide/protein quantitation using mass spectrometry (MS) is advantageous due to its high sensitivity. Traditional absolute peptide quantitation methods rely on making calibration curves using peptide standards or isotope-labelled peptide standards, which are expensive and take time to synthesize. A method which can eliminate the need for using standards would be beneficial. Recently, we developed coulometric mass spectrometry (CMS) which can be used to quantify peptides that are oxidizable (e.g., those containing tyrosine or tryptophan), without using peptide standard. The method is based on electrochemical oxidation of peptides followed by MS to measure the oxidation yield. However, it cannot be directly used to quantify peptides without oxidizable residues. To extend this method for quantifying peptides/proteins in general, in this study, we adopted a derivatization strategy, in which a target peptide is first tagged with an electroactive reagent such as monocarboxymethylene blue NHS ester (MCMB-NHS ester), followed with quantitation by CMS. To illustrate the power of this method, we have analyzed peptides MG and RPPGFSPFR. The quantification error was less than 5%. Using RPPGFSPFR as an example, the quantitation sensitivity of the technique was found to be 0.25 pmol. Furthermore, we also used the strategy to quantify proteins cytochrome C and β-casein with an error of 2-26%.
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Affiliation(s)
- Praneeth Ivan Joel FNU
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Md. Tanim-Al-Hassan
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Timothy Yaroshuk
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
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Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J. High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc 2023; 18:700-731. [PMID: 36494494 PMCID: PMC10673696 DOI: 10.1038/s41596-022-00780-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Robust, reliable quantification of large sample cohorts is often essential for meaningful clinical or pharmaceutical proteomics investigations, but it is technically challenging. When analyzing very large numbers of samples, isotope labeling approaches may suffer from substantial batch effects, and even with label-free methods, it becomes evident that low-abundance proteins are not reliably measured owing to unsufficient reproducibility for quantification. The MS1-based quantitative proteomics pipeline IonStar was designed to address these challenges. IonStar is a label-free approach that takes advantage of the high sensitivity/selectivity attainable by ultrahigh-resolution (UHR)-MS1 acquisition (e.g., 120-240k full width at half maximum at m/z = 200) which is now widely available on ultrahigh-field Orbitrap instruments. By selectively and accurately procuring quantitative features of peptides within precisely defined, very narrow m/z windows corresponding to the UHR-MS1 resolution, the method minimizes co-eluted interferences and substantially enhances signal-to-noise ratio of low-abundance species by decreasing noise level. This feature results in high sensitivity, selectivity, accuracy and precision for quantification of low-abundance proteins, as well as fewer missing data and fewer false positives. This protocol also emphasizes the importance of well-controlled, robust experimental procedures to achieve high-quality quantification across a large cohort. It includes a surfactant cocktail-aided sample preparation procedure that achieves high/reproducible protein/peptide recoveries among many samples, and a trapping nano-liquid chromatography-mass spectrometry strategy for sensitive and reproducible acquisition of UHR-MS1 peptide signal robustly across a large cohort. Data processing and quality evaluation are illustrated using an example dataset ( http://proteomecentral.proteomexchange.org ), and example results from pharmaceutical project and one clinical project (patients with acute respiratory distress syndrome) are shown. The complete IonStar pipeline takes ~1-2 weeks for a sample cohort containing ~50-100 samples.
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Affiliation(s)
- Shichen Shen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xue Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Xiaoyu Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Sailee Rasam
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Min Ma
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Shihan Huo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shuo Qian
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Miao Qu
- Department of Neurology, Xuanwu Hospital, Beijing, China
| | - Chenqi Hu
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Liang Jin
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Yu Tian
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Sanjay Sethi
- Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - David Poulsen
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Chengjian Tu
- BioProduction Group, Thermo Fisher Scientific, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
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Mirshahvaladi S, Topraggaleh TR, Bucak MN, Rahimizadeh P, Shahverdi A. Quantitative proteomics of sperm tail in asthenozoospermic patients: exploring the molecular pathways affecting sperm motility. Cell Tissue Res 2023:10.1007/s00441-023-03744-y. [PMID: 36847810 DOI: 10.1007/s00441-023-03744-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/23/2023] [Indexed: 02/28/2023]
Abstract
Asthenozoospermia, characterized by low sperm motility, is one of the most common causes of male infertility. While many intrinsic and extrinsic factors are involved in the etiology of asthenozoospermia, the molecular basis of this condition remains unclear. Since sperm motility results from a complex flagellar structure, an in-depth proteomic analysis of the sperm tail can uncover mechanisms underlying asthenozoospermia. This study quantified the proteomic profile of 40 asthenozoospermic sperm tails and 40 controls using TMT-LC-MS/MS. Overall, 2140 proteins were identified and quantified where 156 proteins have not been described earlier in sperm tail. There were 409 differentially expressed proteins (250 upregulated and 159 downregulated) in asthenozoospermia which by far is the highest number reported earlier. Further, bioinformatics analysis revealed several biological processes, including mitochondrial-related energy production, oxidative phosphorylation (OXPHOS), citric acid cycle (CAC), cytoskeleton, stress response, and protein metabolism altered in asthenozoospermic sperm tail samples. Collectively, our findings reveal the importance of mitochondrial energy production and induced stress response as potential mechanisms involved in the loss of sperm motility in asthenozoospermia.
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Affiliation(s)
- Shahab Mirshahvaladi
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Tohid Rezaei Topraggaleh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
- Department of Anatomical Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | - Mustafa Numan Bucak
- Department of Reproduction and Artificial Insemination, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Pegah Rahimizadeh
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Division of Experimental Surgery, McGill University, Montreal, QC, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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Liu N, Wang J, Wang X, Qiu S, Zhang M. Bilirubin level is decreased in patients with allergic rhinitis. J Proteomics 2023; 272:104787. [PMID: 36470582 DOI: 10.1016/j.jprot.2022.104787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/07/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND There are limitations in detecting methods for early diagnosis and screening of allergic rhinitis. Considering the anti-inflammatory and anti-oxidative effects of bilirubin, this study aims to explore the relationship between bilirubin and allergic rhinitis and to identify bilirubin-related candidate urinary protein biomarkers associated with allergic rhinitis. METHODS 63 allergic rhinitis patients (AR group) and 86 healthy controls (NC group) were enrolled. Venous blood was obtained to measure serum total IgE levels and bilirubin parameters. Patients in the AR group were then classified into the AR1 group (IgE > 125 IU/mL) and the AR2 group (IgE ≤ 125 IU/mL). After randomly selecting ten urine samples from the AR1 group, ten samples were chosen from the AR2 and the NC groups, respectively, according to age and gender matching. We employed a Tandem Mass Tag-Based liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) proteomics approach and targeted parallel-reaction monitoring(PRM) to identify and validate urinary biomarkers for allergic rhinitis. RESULTS Compared with the NC group, the bilirubin levels of the AR group, AR1 group, and AR2 group were significantly lower. Although the bilirubin level of the AR1 group was lower than that of the AR2 group, the difference was not significant. Further urinary proteomics analysis found that the expression levels of proteins related to bilirubin metabolism and transportation in the AR1 and AR2 groups, including ABCC1, GSTA1, GSTO1, GSTM3, GSTM5, and BLVRB, were significantly higher than those in the NC group. By PRM-based quantification, GSTA1 and GSTO1 showed significant differences in different degrees of Allergic Rhinitis groups and healthy controls. The AUC of the combined diagnosis of GSTA1 and GSTO1 was 0.79 (95% CI 0.583-0.997, P = 0.007), and the sensitivity and specificity were 100% and 60.0%, respectively. CONCLUSIONS Bilirubin levels are associated with allergic rhinitis. Our study revealed that urine proteomics has a specific value for exploring the pathophysiological mechanism of bilirubin changes in AR patients and screening possible biomarkers.
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Affiliation(s)
- Na Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Jitu Wang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Xueyan Wang
- Department of Allergy, Beijing Shijitan Hospital,Capital Medical University, Beijing, China
| | - Sainan Qiu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China.
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Aragoneses-Cazorla G, Machuca A, Buendia-Nacarino MP, Anunciação DS, Garcia-Calvo E, Luque-Garcia JL. Super-SILAC Quantitative Proteome Profiling of Zebrafish Larvae. Methods Mol Biol 2023; 2603:199-207. [PMID: 36370281 DOI: 10.1007/978-1-0716-2863-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The super-SILAC approach enables the quantitative proteome profiling of highly complex samples such as biological tissues or whole organisms. In this approach, a super-SILAC mix consisting of heavy isotope-labeled cells representative of the tissue or organism to be analyzed is mixed with the unlabeled samples of interest, such that the labeled proteins act as a spike-in standard, thus allowing the relative quantification of proteins between the samples of interest. In this chapter, we thoroughly describe the protocol to carry out the super-SILAC approach using a common in vivo model such as zebrafish larvae.
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Affiliation(s)
| | - Andres Machuca
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - M Pilar Buendia-Nacarino
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - Daniela S Anunciação
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Estefania Garcia-Calvo
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
| | - Jose L Luque-Garcia
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
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Dar MA, Arafah A, Bhat KA, Khan A, Khan MS, Ali A, Ahmad SM, Rashid SM, Rehman MU. Multiomics technologies: role in disease biomarker discoveries and therapeutics. Brief Funct Genomics 2022; 22:76-96. [PMID: 35809340 DOI: 10.1093/bfgp/elac017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/21/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Medical research has been revolutionized after the publication of the full human genome. This was the major landmark that paved the way for understanding the biological functions of different macro and micro molecules. With the advent of different high-throughput technologies, biomedical research was further revolutionized. These technologies constitute genomics, transcriptomics, proteomics, metabolomics, etc. Collectively, these high-throughputs are referred to as multi-omics technologies. In the biomedical field, these omics technologies act as efficient and effective tools for disease diagnosis, management, monitoring, treatment and discovery of certain novel disease biomarkers. Genotyping arrays and other transcriptomic studies have helped us to elucidate the gene expression patterns in different biological states, i.e. healthy and diseased states. Further omics technologies such as proteomics and metabolomics have an important role in predicting the role of different biological molecules in an organism. It is because of these high throughput omics technologies that we have been able to fully understand the role of different genes, proteins, metabolites and biological pathways in a diseased condition. To understand a complex biological process, it is important to apply an integrative approach that analyses the multi-omics data in order to highlight the possible interrelationships of the involved biomolecules and their functions. Furthermore, these omics technologies offer an important opportunity to understand the information that underlies disease. In the current review, we will discuss the importance of omics technologies as promising tools to understand the role of different biomolecules in diseases such as cancer, cardiovascular diseases, neurodegenerative diseases and diabetes. SUMMARY POINTS
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Zhang H, Situ C, Guo X. Recent progress of proteomic analysis on spermatogenesis. Biol Reprod 2022; 107:109-117. [DOI: 10.1093/biolre/ioac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Testis, the only organ responsible for generating sperm, is by far the organ with the largest variety of proteins and tissue-specific proteins in humans. In testis, spermatogenesis is a multi-step complex process well-accepted that protein and mRNA are decoupled in certain stages of spermatogenesis. With the fast development of mass spectrometry-based proteomics, it is possible to systemically study protein abundances and modifications in testis and sperm to help us understand the molecular mechanisms of spermatogenesis. This review provides an overview of the recent progress of proteomics analysis on spermatogenesis, including protein expression and multiple PTMs, such as phosphorylation, glycosylation, ubiquitylation, and acetylation.
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Affiliation(s)
- Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
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Zhu Y, Bian JF, Lu DQ, To CH, Lam CSY, Li KK, Yu FJ, Gong BT, Wang Q, Ji XW, Zhang HM, Nian H, Lam TC, Wei RH. Alteration of EIF2 Signaling, Glycolysis, and Dopamine Secretion in Form-Deprived Myopia in Response to 1% Atropine Treatment: Evidence From Interactive iTRAQ-MS and SWATH-MS Proteomics Using a Guinea Pig Model. Front Pharmacol 2022; 13:814814. [PMID: 35153787 PMCID: PMC8832150 DOI: 10.3389/fphar.2022.814814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose: Atropine, a non-selective muscarinic antagonist, effectively slows down myopia progression in human adolescents and several animal models. However, the underlying molecular mechanism is unclear. The current study investigated retinal protein changes of form-deprived myopic (FDM) guinea pigs in response to topical administration of 1% atropine gel (10 g/L). Methods: At the first stage, the differentially expressed proteins were screened using fractionated isobaric tags for a relative and absolute quantification (iTRAQ) approach, coupled with nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) (n = 24, 48 eyes) using a sample pooling technique. At the second stage, retinal tissues from another cohort with the same treatment (n = 12, 24 eyes) with significant ocular changes were subjected to label-free sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics for orthogonal protein target confirmation. The localization of Alpha-synuclein was verified using immunohistochemistry and confocal imaging. Results: A total of 1,695 proteins (8,875 peptides) were identified with 479 regulated proteins (FC ≥ 1.5 or ≤0.67) found from FDM eyes and atropine-treated eyes receiving 4-weeks drug treatment using iTRAQ-MS proteomics. Combining the iTRAQ-MS and SWATH-MS datasets, a total of 29 confident proteins at 1% FDR were consistently quantified and matched, comprising 12 up-regulated and 17 down-regulated proteins which differed between FDM eyes and atropine treated eyes (iTRAQ: FC ≥ 1.5 or ≤0.67, SWATH: FC ≥ 1.4 or ≤0.71, p-value of ≤0.05). Bioinformatics analysis using IPA and STRING databases of these commonly regulated proteins revealed the involvement of the three commonly significant pathways: EIF2 signaling; glycolysis; and dopamine secretion. Additionally, the most significantly regulated proteins were closely connected to Alpha-synuclein (SNCA). Using immunostaining (n = 3), SNCA was further confirmed in the inner margin of the inner nuclear layer (INL) and spread throughout the inner plexiform layer (IPL) of the retina of guinea pigs. Conclusion: The molecular evidence using next-generation proteomics (NGP) revealed that retinal EIF2 signaling, glycolysis, and dopamine secretion through SNCA are implicated in atropine treatment of myopia in the FDM-induced guinea pig model.
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Affiliation(s)
- Ying Zhu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Jing Fang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Da Qian Lu
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Chi Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- 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
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- 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
| | - King Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Feng Juan Yu
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Bo Teng Gong
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiong Wang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xiao Wen Ji
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Mei Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Nian
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- 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
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- *Correspondence: Rui Hua Wei, ; Thomas Chuen Lam,
| | - Rui Hua Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
- *Correspondence: Rui Hua Wei, ; Thomas Chuen Lam,
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Jelusic M, Sestan M, Giani T, Cimaz R. New Insights and Challenges Associated With IgA Vasculitis and IgA Vasculitis With Nephritis-Is It Time to Change the Paradigm of the Most Common Systemic Vasculitis in Childhood? Front Pediatr 2022; 10:853724. [PMID: 35372148 PMCID: PMC8965283 DOI: 10.3389/fped.2022.853724] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 12/29/2022] Open
Abstract
What are the challenges ahead and how have we responded so far when it comes to the non-granulomatous systemic vasculitis, characterized mainly by deposits of IgA immune complexes in the endothelium of small blood vessels-IgA vasculitis (IgAV)? That is the question to which we tried to answer. We summarized existing knowledge about epidemiology, pathogenesis, genetics, diagnostic tests and therapy in this somewhat neglected entity in pediatric rheumatology. Since etiopathogenesis of IgA vasculitis is complex, with factors other than galactose-deficient IgA1-containing immune complexes also being important, and may involve numerous interactions between environmental and genetic factors, genomics alone cannot explain the entirety of the risk for the disease. The incidence of IgAV and nephritis varies worldwide and may be a consequence of overlapping genetic and environmental factors. In addition to the role of the HLA class II genes, some studies have pointed to the importance of non-HLA genes, and modern geostatistical research has also indicated a geospatial risk distribution, which may suggest the strong influence of different environmental factors such as climate, pathogen load, and dietary factors. The application of modern geostatistical methods until recently was completely unknown in the study of this disease, but thanks to the latest results it has been shown that they can help us a lot in understanding epidemiology and serve as a guide in generating new hypotheses considering possible environmental risk factors and identification of potential genetic or epigenetic diversity. There is increasing evidence that an integrative approach should be included in the understanding of IgA vasculitis, in terms of the integration of genomics, proteomics, transcriptomics, and epigenetics. This approach could result in the discovery of new pathways important for finding biomarkers that could stratify patients according to the risk of complications, without an invasive kidney biopsy which is still the gold standard to confirm a diagnosis of nephritis, even if biopsy findings interpretation is not uniform in clinical practice. Ultimately, this will allow the development of new therapeutic approaches, especially important in the treatment of nephritis, for which there is still no standardized treatment.
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Affiliation(s)
- Marija Jelusic
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mario Sestan
- Department of Paediatrics, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Teresa Giani
- Department of Clincial Sciences and Community Health, University of Milan, Milan, Italy
| | - Rolando Cimaz
- Department of Clincial Sciences and Community Health, University of Milan, Milan, Italy.,ASST Pini-CTO, Milan, Italy
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Ferragut Cardoso AP, Banerjee M, Al-Eryani L, Sayed M, Wilkey DW, Merchant ML, Park JW, States JC. Temporal Modulation of Differential Alternative Splicing in HaCaT Human Keratinocyte Cell Line Chronically Exposed to Arsenic for up to 28 Wk. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:17011. [PMID: 35072517 PMCID: PMC8785870 DOI: 10.1289/ehp9676] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Chronic arsenic exposure via drinking water is associated with an increased risk of developing cancer and noncancer chronic diseases. Pre-mRNAs are often subject to alternative splicing, generating mRNA isoforms encoding functionally distinct protein isoforms. The resulting imbalance in isoform species can result in pathogenic changes in critical signaling pathways. Alternative splicing as a mechanism of arsenic-induced toxicity and carcinogenicity is understudied. OBJECTIVE This study aimed to accurately profile differential alternative splicing events in human keratinocytes induced by chronic arsenic exposure that might play a role in carcinogenesis. METHODS Independent quadruplicate cultures of immortalized human keratinocytes (HaCaT) were maintained continuously for 28 wk with 0 or 100 nM sodium arsenite. RNA-sequencing (RNA-Seq) was performed with poly(A) RNA isolated from cells harvested at 7, 19, and 28 wk with subsequent replicate multivariate analysis of transcript splicing (rMATS) analysis to detect and quantify differential alternative splicing events. Reverse transcriptase-polymerase chain reaction (RT-PCR) for selected alternative splicing events was performed to validate RNA-Seq predictions. Functional enrichment was performed by gene ontology (GO) analysis of the differential alternative splicing event data set at each time point. RESULTS At least 600 differential alternative splicing events were detected at each time point tested, comprising all the five main types of alternative splicing and occurring in both open reading frames (ORFs) and untranslated regions (UTRs). Based on functional relevance ELK4, SHC1, and XRRA1 were selected for validation of predicted alternative splicing events at 7 wk by RT-PCR. Densitometric analysis of RT-PCR data corroborated the rMATS predicted alternative splicing for all three events. Protein expression validation of the selected alternative splicing events was challenging given that very few isoform-specific antibodies are available. GO analysis demonstrated that the enriched terms in differential alternatively spliced mRNAs changed dynamically with the time of exposure. Notably, RNA metabolism and splicing regulation pathways were enriched at the 7-wk time point, when the greatest number of differentially alternatively spliced mRNAs are detected. Our preliminary proteomic analysis demonstrated that the expression of the canonical isoforms of the splice regulators DDX42, RMB25, and SRRM2 were induced upon chronic arsenic exposure, corroborating the splicing predictions. DISCUSSION These results using cultures of HaCaT cells suggest that arsenic exposure disrupted an alternative splice factor network and induced time-dependent genome-wide differential alternative splicing that likely contributed to the changing proteomic landscape in arsenic-induced carcinogenesis. However, significant challenges remain in corroborating alternative splicing data at the proteomic level. https://doi.org/10.1289/EHP9676.
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Affiliation(s)
- Ana P. Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Laila Al-Eryani
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mohammed Sayed
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Juw W. Park
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - J. Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
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13
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Huo S, Wang H, Yan M, Xu P, Song T, Li C, Tian R, Chen X, Bao K, Xie Y, Xu P, Zhu W, Liu F, Mao W, Shao C. Urinary Proteomic Characteristics of Hyperuricemia and Their Possible Links with the Occurrence of Its Concomitant Diseases. ACS OMEGA 2021; 6:9500-9508. [PMID: 33869930 PMCID: PMC8047722 DOI: 10.1021/acsomega.0c06229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Hyperuricemia (HUA), a chronic disease caused by metabolic disorders of purine, is often accompanied by other diseases such as gout, type 2 diabetes mellitus (T2DM), and hyperlipidemia. However, little is known about the relationship between HUA and these diseases on the protein level. We performed label-free liquid chromatography MS/MS spectrometry analysis of urine samples from 26 HUA patients and 25 healthy controls, attempting to establish the possible protein links between HUA and these diseases by profiling urine proteome. A total of 2119 proteins were characterized in sample proteomes. Among them, 11 were found decreased and 2 were found increased in HUA samples. Plausible pathways found by enrichment analysis of these differentially expressed proteins (DEPs) include the processes for insulin receptor recycling and lipid metabolism, suggesting potential links between HUA and T2DM and hyperlipidemia. The abundance changes of three key proteins (VATB1, CFAD, and APOC3) involved in these processes were validated by enzyme-linked immunosorbent assay (ELISA). In conclusion, our result provides proteomic evidence, for the first time, that the aberrant pathways enriched by described key DEPs are closely related to the incidence of HUA and its concomitant diseases.
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Affiliation(s)
- Shuai Huo
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Henan Provincial People’s
Hospital, Department of Nephrology of Central China Fuwai Hospital, Zhengzhou, Henan 450003, China
| | - Hongxin Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
- Key
Laboratory of Zoological Systematics and Application of Hebei Province,
College of Life Sciences, Hebei University, Baoding 071002, China
| | - Meixia Yan
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
| | - Peng Xu
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Guangdong Provincial Hospital
of Chinese Medicine, Guangzhou 510120, China
- Guangdong
Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, China
- Guangdong
Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment
of Refractory Chronic Diseases, Department of Pediatrics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120, China
| | - Tingting Song
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Chuang Li
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Guangdong Provincial Hospital
of Chinese Medicine, Guangzhou 510120, China
- Guangdong
Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, China
- Guangdong
Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment
of Refractory Chronic Diseases, Department of Pediatrics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120, China
| | - Ruimin Tian
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Guangdong Provincial Hospital
of Chinese Medicine, Guangzhou 510120, China
- Guangdong
Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, China
- Guangdong
Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment
of Refractory Chronic Diseases, Department of Pediatrics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120, China
| | - Xiaoling Chen
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
| | - Kun Bao
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Guangdong Provincial Hospital
of Chinese Medicine, Guangzhou 510120, China
- Guangdong
Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, China
- Guangdong
Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment
of Refractory Chronic Diseases, Department of Pediatrics, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120, China
| | - Ying Xie
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China
| | - Ping Xu
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
- Key
Laboratory of Zoological Systematics and Application of Hebei Province,
College of Life Sciences, Hebei University, Baoding 071002, China
| | - Weimin Zhu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
| | - Fengsong Liu
- Key
Laboratory of Zoological Systematics and Application of Hebei Province,
College of Life Sciences, Hebei University, Baoding 071002, China
| | - Wei Mao
- State
Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University
of Chinese Medicine, Guangzhou 510120, China
- The
Second Clinical Medical College, Guangzhou
University of Chinese Medicine,Guangzhou 510405, China
- Department
of Nephrology, Guangdong Provincial Hospital
of Chinese Medicine, Guangzhou 510120, China
- Guangdong
Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, China
| | - Chen Shao
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, Beijing 102206, China
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Dong Z, Coates D. Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration. J Proteome Res 2021; 20:2167-2181. [PMID: 33769828 DOI: 10.1021/acs.jproteome.1c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.
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Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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15
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Simultaneous and quantitative monitoring transcription factors in human embryonic stem cell differentiation using mass spectrometry-based targeted proteomics. Anal Bioanal Chem 2021; 413:2081-2089. [PMID: 33655347 DOI: 10.1007/s00216-021-03160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/15/2020] [Accepted: 01/06/2021] [Indexed: 11/27/2022]
Abstract
Human embryonic stem cells (hESCs) can be self-propagated indefinitely in culture while holding the capacity to generate almost all cell types. Although this powerful differentiation ability of hESCs has become a potential source of cell replacement therapies, application of stem cells in clinical practice relies heavily on the exquisite control of their developmental fate. In general, an essential first step in differentiation is to exit the pluripotent state, which is precariously balanced and depends on a variety of factors, mainly centering on the core transcriptional mechanism. To date, much evidence has indicated that transcription factors such as Sox2, Oct4, and Nanog control the self-renewal and pluripotency of hESCs. Their expression displays a restricted spatial-temporal pattern and their small changes in level can significantly affect directed differentiation and the cell type derived. So far, few assays have been developed to monitor this process. Herein, we provided a mass spectrometry (MS)-based approach for simultaneous and quantitative monitoring of these transcription factors, in an attempt to provide insight into their contributions in hESC differentiation.
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16
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Vinaiphat A, Low JK, Yeoh KW, Chng WJ, Sze SK. Application of Advanced Mass Spectrometry-Based Proteomics to Study Hypoxia Driven Cancer Progression. Front Oncol 2021; 11:559822. [PMID: 33708620 PMCID: PMC7940826 DOI: 10.3389/fonc.2021.559822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the largest contributors to the burden of chronic disease in the world and is the second leading cause of death globally. It is associated with episodes of low-oxygen stress (hypoxia or ischemia/reperfusion) that promotes cancer progression and therapeutic resistance. Efforts have been made in the past using traditional proteomic approaches to decipher oxygen deprivation stress-related mechanisms of the disease initiation and progression and to identify key proteins as a therapeutic target for the treatment and prevention. Despite the potential benefits of proteomic in translational research for the discovery of new drugs, the therapeutic outcome with this approach has not met expectations in clinical trials. This is mainly due to the disease complexity which possess a multifaceted molecular pathology. Therefore, novel strategies to identify and characterize clinically important sets of modulators and molecular events for multi-target drug discovery are needed. Here, we review important past and current studies on proteomics in cancer with an emphasis on recent pioneered labeling approaches in mass spectrometry (MS)-based systematic quantitative analysis to improve clinical success. We also discuss the results of the selected innovative publications that integrate advanced proteomic technologies (e.g. MALDI-MSI, pSILAC/SILAC/iTRAQ/TMT-LC-MS/MS, MRM-MS) for comprehensive analysis of proteome dynamics in different biosystems, including cell type, cell species, and subcellular proteome (i.e. secretome and chromatome). Finally, we discuss the future direction and challenges in the application of these technological advancements in mass spectrometry within the context of cancer and hypoxia.
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Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jee Keem Low
- Department of Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kheng Wei Yeoh
- Department of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res 2020; 30:1593-1604. [PMID: 33060172 PMCID: PMC7605251 DOI: 10.1101/gr.255224.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic, and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified 15 loci with potential pleiotropic effects on the proteome. We showed that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein coexpression network, and a reprogramming of the genetic control of the abundance of many proteins, including those involved in stress response. Colocalizations between pQTLs and QTLs for ecophysiological traits, found mostly in the water deficit condition, indicated that this reprogramming may also affect the phenotypic level. Finally, we identified several candidate genes that are potentially responsible for both the coexpression of stress response proteins and the variations of ecophysiological traits under water deficit. Taken together, our findings provide novel insights into the molecular mechanisms of drought tolerance and suggest some pathways for further research and breeding.
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Kumar S, Koehn JT, Gonzalez-Juarrero M, Crans DC, Crick DC. Mycobacterium tuberculosis Survival in J774A.1 Cells Is Dependent on MenJ Moonlighting Activity, Not Its Enzymatic Activity. ACS Infect Dis 2020; 6:2661-2671. [PMID: 32866371 DOI: 10.1021/acsinfecdis.0c00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenJ, a flavoprotein oxidoreductase, is responsible for the saturation of the β-isoprene unit of mycobacterial menaquinone, resulting in the conversion of menaquinone with nine isoprene units (MK-9) to menaquinone with nine isoprene units where the double bond in the second unit is reduced [MK-9(II-H2)]. The hydrogenation of MK-9 increases the efficiency of the mycobacterial electron transport system, whereas the deletion of MenJ results in decreased survival of the bacteria inside J774A.1 macrophage-like cells but is not required for growth in culture. Thus, it was suggested that MenJ may represent a contextual drug target in M. tuberculosis, that is, a drug target that is valid only in the context of an infected macrophage. However, it was unclear if the conversion of MK-9 to MK-9(II-H2) or the MenJ protein itself was responsible for bacterial survival. In order to resolve this issue, a plasmid expressing folded, full-length, inactive MenJ was engineered. Primary sequence analysis data revealed that MenJ shares conserved FAD binding, NADH binding, and catalytic and C-terminal motifs with archaeal geranylgeranyl reductases. A MenJ mutant deficient in any one of these motifs is devoid of reductase activity. Therefore, point mutations of highly conserved amino acids in the conserved motifs were generated and the recombinant proteins were monitored for conformational changes by circular dichroism and oxidoreductase activity. The mutational analysis indicates that amino acids tryptophan 215 (W215) and cysteine 46 (C46) of M. tuberculosis MenJ, conserved in known archaeal geranylgeranyl reductases and putative menaquinone saturases, are essential to the hydrogenation of MK-9. The mutation of either C46 to serine (C46S) or W215 to leucine (W215L) in MenJ completely abolishes the catalytic activity in vitro, and menJ knockout strains of M. tuberculosis expressing either the C46S or W215L mutant protein are unable to convert MK-9 to MK-9(II-H2) but survive inside the J774A.1 cells. Thus, surprisingly, the survival of M. tuberculosis in J774A.1 cells is dependent on the expression of MenJ rather than its oxidoreductase activity, the conversion of MK-9 to MK-9(II-H2) as previously hypothesized. Overall, the current data suggest that MenJ is a moonlighting protein.
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Abstract
Multidrug resistance (MDR) is a vital issue in cancer treatment. Drug resistance can be developed through a variety of mechanisms, including increased drug efflux, activation of detoxifying systems and DNA repair mechanisms, and escape of drug-induced apoptosis. Identifying the exact mechanism related in a particular case is a difficult task. Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. In recent years, comparative proteomic methods have been performed to analyze MDR mechanisms in drug-selected model cancer cell lines. In this paper, we review the recent developments and progresses by comparative proteomic approaches to identify potential MDR mechanisms in drug-selected model cancer cell lines, which may help understand and design chemical sensitizers.
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Abstract
Extracellular vesicles (EVs) play an important role in intercellular communication in normal cellular process and pathological conditions by facilitating the transport of cellular content from one cell to another. EVs as conveyors of various biological molecules with their ability to redirect effects on a target cell physiological function in cell type-specific manner makes EVs an excellent candidate for drug delivery vehicle in disease therapy. Moreover, unique characteristics and contents of EVs which differ depends on cellular origin and physiological state make them a valuable source of diagnostic biomarker. Herein, we review the current progress in extracellular vesicle (EV) analysis, its transition from biomedical research to advancing therapy, and recent pioneered approaches to characterize and quantify EVs' subclasses with an emphasis on the integration of advanced technologies for both qualitative and quantitative analysis of EVs in different clinical tissue/body fluid samples.
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Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Sun X, Li H, Thapa S, Reddy Sangireddy S, Pei X, Liu W, Jiang Y, Yang S, Hui D, Bhatti S, Zhou S, Yang Y, Fish T, Thannhauser TW. Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene. HORTICULTURE RESEARCH 2020; 7:43. [PMID: 32257229 PMCID: PMC7109090 DOI: 10.1038/s41438-020-0264-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
Glyoxalase I (Gly I) is the first enzyme in the glutathionine-dependent glyoxalase pathway for detoxification of methylglyoxal (MG) under stress conditions. Transgenic tomato 'Money Maker' plants overexpressing tomato SlGlyI gene (tomato unigene accession SGN-U582631/Solyc09g082120.3.1) were generated and homozygous lines were obtained after four generations of self-pollination. In this study, SlGlyI-overepxressing line (GlyI), wild type (WT, negative control) and plants transformed with empty vector (ECtr, positive control), were subjected to Al-treatment by growing in Magnavaca's nutrient solution (pH 4.5) supplemented with 20 µM Al3+ ion activity. After 30 days of treatments, the fresh and dry weight of shoots and roots of plants from Al-treated conditions decreased significantly compared to the non-treated conditions for all the three lines. When compared across the three lines, root fresh and dry weight of GlyI was significant higher than WT and ECtr, whereas there was no difference in shoot tissues. The basal 5 mm root-tips of GlyI plants expressed a significantly higher level of glyoxalase activity under both non-Al-treated and Al-treated conditions compared to the two control lines. Under Al-treated condition, there was a significant increase in MG content in ECtr and WT lines, but not in GlyI line. Quantitative proteomics analysis using tandem mass tags mass spectrometry identified 4080 quantifiable proteins and 201 Al-induced differentially expressed proteins (DEPs) in root-tip tissues from GlyI, and 4273 proteins and 230 DEPs from ECtr. The Al-down-regulated DEPs were classified into molecular pathways of gene transcription, RNA splicing and protein biosynthesis in both GlyI and ECtr lines. The Al-induced DEPs in GlyI associated with tolerance to Al3+ and MG toxicity are involved in callose degradation, cell wall components (xylan acetylation and pectin degradation), oxidative stress (antioxidants) and turnover of Al-damaged epidermal cells, repair of damaged DNA, epigenetics, gene transcription, and protein translation. A protein-protein association network was constructed to aid the selection of proteins in the same pathway but differentially regulated in GlyI or ECtr lines. Proteomics data are available via ProteomeXchange with identifiers PXD009456 under project title '25Dec2017_Suping_XSexp2_ITAG3.2' for SlGlyI-overexpressing tomato plants and PXD009848 under project title '25Dec2017_Suping_XSexp3_ITAG3.2' for positive control ECtr line transformed with empty vector.
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Affiliation(s)
- Xudong Sun
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
- College of Horticulture, Shandong Agricultural University, Taian, Shandong P.R. China
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Santosh Thapa
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Sasikiran Reddy Sangireddy
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Xiaobo Pei
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Wei Liu
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Yuping Jiang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Shaolan Yang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Dafeng Hui
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Sarabjit Bhatti
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209 USA
| | - Yong Yang
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Tara Fish
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Theodore W. Thannhauser
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
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22
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Liu X, Cui Y, Li X, Yang H. In-depth transcriptomic and proteomic analyses of the hippocampus and cortex in a rat model after cerebral ischemic injury and repair by Shuxuetong (SXT) injection. JOURNAL OF ETHNOPHARMACOLOGY 2020; 249:112362. [PMID: 31676400 DOI: 10.1016/j.jep.2019.112362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/29/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND There is a lack of systematic descriptions and characterization of strokes and their effects in both the cerebral hippocampus and cortex. Shuxuetong (SXT) injection was reported to have good therapeutic effects in the clinic; therefore, it was selected as a drug intervention method for cerebral ischemia repair in rat models. The aim of this study was to understand the features of molecules and pathways and to reveal key processes of SXT repair. MATERIALS AND METHODS Evaluation of neurological deficit and infarct volume measurement was used to estimate the pharmacological effects of SXT injection on Ischemia-reperfusion(I/R) model rats. LC-MS/MS and RNA-Seq analysis were used to analyze the proteins and mRNA expression in the cerebral hippocampus and cortex 6 h and 24 h after ischemic injury and repair. A label-free approach (IBAQ) for proteomics analysis and FPKM based on gene read count for transcriptomics analysis were used to quantify the differences among the three experimental groups (Sham, Model and SXT-treated groups). Transcriptomics and proteomics analyses were verified by RT-qPCR and western blotting. RESULTS By combining LC-MS/MS and RNA-Seq, eight larger datasets (two time points and two tissues) were confidently identified in more than three biological replicates. An average of 4500 unique proteins and 8200 protein-coding genes were confidently identified. By combining the subcellular localization, hierarchical clustering, pathway enrichment analysis in the injury and repair phase, six core proteins and related genes that were significantly expressed were verified as candidates for cerebral ischemic injury by western blotting and quantitative real-time PCR. Meanwhile, the results indicated that there was better expression in the 6 h group by significant proteomics analysis during the development and progression of cerebral ischemia. Two primary co-enriched pathways, the PI3K-AKT and MAPK signaling pathways, and six related core candidates may play key roles in molecular mechanisms related to cerebral ischemic injury and repair by SXT injection. CONCLUSION Our data not only identified six core candidates and two key signaling pathways for cerebral ischemic injury and verification but also provided evidence for the explanation, prevention and treatment of cerebral ischemia by SXT injection. The results of the present study provide evidence for the explanation, prevention and treatment of cerebral ischemia by SXT injection.
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Affiliation(s)
- Xin Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Yiran Cui
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China.
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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23
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Paul P, Antonydhason V, Gopal J, Haga SW, Hasan N, Oh JW. Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. Int J Mol Sci 2020; 21:E961. [PMID: 32024005 PMCID: PMC7038205 DOI: 10.3390/ijms21030961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomics are highlighted in this review. The need for more attention and input from bioinformaticians is highlighted, so that progressive achievements and releases can be made. With just a handful of existing tools for renal and urinary proteomic research available, this review identifies a gap worth targeting by protein chemists and bioinformaticians. The probable causes for the lack of enthusiasm in this area are also speculated upon in this review. This is the first review that consolidates the bioinformatics applications specifically for renal and urinary proteomics.
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Affiliation(s)
- Piby Paul
- St. Jude Childrens Cancer Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Vimala Antonydhason
- Department of Microbiology and Immunology, Institute for Biomedicine, Gothenburg University, 413 90 Gothenburg, Sweden;
| | - Judy Gopal
- Department of Environmental Health Sciences, Konkuk University, Seoul 143-701, Korea;
| | - Steve W. Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung 804, Taiwan;
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
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24
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Wu C, Maley AM, Walt DR. Single-molecule measurements in microwells for clinical applications. Crit Rev Clin Lab Sci 2019:1-21. [PMID: 31865834 DOI: 10.1080/10408363.2019.1700903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to detect and analyze proteins, nucleic acids, and other biomolecules is critical for clinical diagnostics and for understanding the underlying mechanisms of disease. Current detection methods in clinical and research laboratories rely upon bulk measurement techniques such as immunoassays, polymerase chain reaction, and mass spectrometry to detect these biomarkers. However, many potentially useful protein or nucleic acid biomarkers in blood, saliva, or other biofluids exist at concentrations well below the detection limits of current methods, necessitating the development of more sensitive technologies. Single-molecule measurements are poised to address this challenge, vastly improving sensitivity for detecting low abundance biomarkers and rare events within a population. Microwell arrays have emerged as a powerful tool for single-molecule measurements, enabling ultrasensitive detection of disease-relevant biomolecules in easily accessible biofluids. This review discusses the development, fundamentals, and clinical applications of microwell-based single-molecule methods, as well as challenges and future directions for translating these methods to the clinic.
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Affiliation(s)
- Connie Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Adam M Maley
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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25
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Wang X, Shen S, Rasam SS, Qu J. MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts. MASS SPECTROMETRY REVIEWS 2019; 38:461-482. [PMID: 30920002 PMCID: PMC6849792 DOI: 10.1002/mas.21595] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/28/2019] [Indexed: 05/04/2023]
Abstract
The rapidly-advancing field of pharmaceutical and clinical research calls for systematic, molecular-level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large-cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large-cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false-positive discovery of altered proteins when sample size increases. MS1 ion current-based methods, which have become an important class of label-free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1-based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high-resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post-feature-generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1-based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
| | - Shichen Shen
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
| | - Sailee Suryakant Rasam
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
| | - Jun Qu
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
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26
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Andrei V, Copolovici D, Munteanu FD, Ngounou Wetie AG, Mihai I, Darie CC, Vasilescu A. Detection of Biomedically Relevant Stilbenes from Wines by Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:665-684. [PMID: 31347078 DOI: 10.1007/978-3-030-15950-4_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Stilbenes represent a class of compounds with a common 1,2-diphenylethylene backbone that have shown extraordinary potential in the biomedical field. As the most well-known example, resveratrol proved to have anti-aging effects and significant potential in the fight against cardiovascular diseases and some types of cancer. Mass spectrometry is an analytical method of critical importance in all studies related to stilbenes that are important in the biomedical field. From the discovery of new natural compounds and mapping the grape metabolome up to advanced investigations of stilbenes' potential for the protection of human health in clinical studies, mass spectrometry has provided critical analytical information. In this review we focus on various approaches related to mass spectrometry for the detection of stilbenes-such as coupling with chromatographic separation methods and direct infusion-with presentation of some illustrative applications. Clearly, the potential of mass spectrometry for assisting in the discovery of new stilbenes of biomedical importance, elucidating their mechanisms of action and quantifying minute quantities in complex matrices is far from being exhausted.
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Affiliation(s)
| | - Dana Copolovici
- Faculty of Food Engineering, Tourism and Environmental Protection, "Aurel Vlaicu" University of Arad, Arad, Romania
| | - Florentina-Daniela Munteanu
- Faculty of Food Engineering, Tourism and Environmental Protection, "Aurel Vlaicu" University of Arad, Arad, Romania
| | - Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Iuliana Mihai
- International Centre of Biodynamics, Bucharest, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
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27
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Bisht D, Sharma D, Sharma D, Singh R, Gupta VK. Recent insights into Mycobacterium tuberculosis through proteomics and implications for the clinic. Expert Rev Proteomics 2019; 16:443-456. [PMID: 31032653 DOI: 10.1080/14789450.2019.1608185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/12/2019] [Indexed: 01/25/2023]
Abstract
This review aimed at providing an update on the application of proteomics-based approaches to gain recent insights of Mycobacterium tuberculosis (M.tb) and its relevance to clinic. Proteomics and bioinformatics approaches helped in the identification and characterization of novel proteins. Studying M.tb, causative agent of tuberculosis (TB), at the proteomic level can contribute to the identification of proteins which can be considered as potential targets for developed drugs and can help us in better understanding the pathogen physiology. Areas covered: In this review we have presented a comprehensive literature pertaining to role of proteomics in understanding M.tb. We have also focused on how the development and advancement in technology in the field of proteomics has augmented the research and played a pivotal role in answering many unexplored questions. Lastly, the application of proteomics to clinic has also been discussed. Expert commentary: We envisage that proteomics has gained remarkable momentum over the years. Proteomics can play an important role in the discovery of biomarkers for TB and other diseases. Also, it can aid in development of effective vaccines and simple, rapid and cost-effective test for the diagnosis of TB which is crucial for the management and control of the disease.
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Affiliation(s)
- Deepa Bisht
- a Department of Biochemistry , National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR) , Agra , India
| | - Devesh Sharma
- a Department of Biochemistry , National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR) , Agra , India
| | - Divakar Sharma
- b Medical Microbiology and Molecular Biology Laboratory , Interdisciplinary Biotechnology Unit, Aligarh Muslim University , Aligarh , India
| | - Rananjay Singh
- a Department of Biochemistry , National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR) , Agra , India
| | - Vivek Kumar Gupta
- a Department of Biochemistry , National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR) , Agra , India
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28
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Pfammatter S, Bonneil E, McManus FP, Thibault P. Accurate Quantitative Proteomic Analyses Using Metabolic Labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). J Proteome Res 2019; 18:2129-2138. [DOI: 10.1021/acs.jproteome.9b00021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Kesse S, Boakye-Yiadom KO, Ochete BO, Opoku-Damoah Y, Akhtar F, Filli MS, Asim Farooq M, Aquib M, Maviah Mily BJ, Murtaza G, Wang B. Mesoporous Silica Nanomaterials: Versatile Nanocarriers for Cancer Theranostics and Drug and Gene Delivery. Pharmaceutics 2019; 11:E77. [PMID: 30781850 PMCID: PMC6410079 DOI: 10.3390/pharmaceutics11020077] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Mesoporous silica nanomaterials (MSNs) have made remarkable achievements and are being thought of by researchers as materials that can be used to effect great change in cancer therapies, gene delivery, and drug delivery because of their optically transparent properties, flexible size, functional surface, low toxicity profile, and very good drug loading competence. Mesoporous silica nanoparticles (MSNPs) show a very high loading capacity for therapeutic agents. It is well known that cancer is one of the most severe known medical conditions, characterized by cells that grow and spread rapidly. Thus, curtailing cancer is one of the greatest current challenges for scientists. Nanotechnology is an evolving field of study, encompassing medicine, engineering, and science, and it has evolved over the years with respect to cancer therapy. This review outlines the applications of mesoporous nanomaterials in the field of cancer theranostics, as well as drug and gene delivery. MSNs employed as therapeutic agents, as well as their importance and future prospects in the ensuing generation of cancer theranostics and drug and therapeutic gene delivery, are discussed herein. Thus, the use of mesoporous silica nanomaterials can be seen as using one stone to kill three birds.
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Affiliation(s)
- Samuel Kesse
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Kofi Oti Boakye-Yiadom
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Belynda Owoya Ochete
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Yaw Opoku-Damoah
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
| | - Fahad Akhtar
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Mensura Sied Filli
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Muhammad Asim Farooq
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Md Aquib
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Bazezy Joelle Maviah Mily
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Ghulam Murtaza
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus 54600, Pakistan.
| | - Bo Wang
- Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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30
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Abstract
"Making the Case for Functional Proteomics" first differentiates the Functional Proteome from the products of genetic protein expression. Qualitatively, the prevalence of posttranslational modifications (PTMs) virtually insures that individual, functional proteins do not equate to their genetic expression counterparts. Quantitatively, considering the frequency of PTMs and a conservative estimate of the number of functional entities arising from protein interactions, the size of the Functional Proteome exceeds that of the human genome by at least two orders of magnitude. The human genome does not, cannot, map the Functional Proteome. Further, the collective genome of the human microbiome dwarfs the human genome. With these facts established, "Making the Case…" proceeds to examine Functional Proteomics (of which both "gene expression" and "epigenetics" are but parts of a larger whole) within the context of Systems Biology, concluding that functionally related networks comprise the dominant motif for biological activity. Creating just such a network focus is essential in not only expanding basic knowledge but also in applying that knowledge in the pragmatic efforts of drug and biomarker development. Outlines for development of drugs and biomarkers, as well as the realization of precision medicine, within a functional proteomics-based, network motif are provided. The chapter proceeds to asses both the knowledge base and the tools to fully embrace Functional Proteomics. Given the decades-long infatuation with the reductionism of genomics, it is not surprising that both the proteomics knowledge base and tools are assessed as poor to fair. However, even a minor shift in research funding and a renewed challenge to methods developers will rapidly improve the current situation. Adoption of the included "Roadmap" will realistically make the twenty-first century the century of a long-awaited revolution in biology.
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Affiliation(s)
- Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
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31
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Li X, Zhang C, Gong T, Ni X, Li J, Zhan D, Liu M, Song L, Ding C, Xu J, Zhen B, Wang Y, Qin J. A time-resolved multi-omic atlas of the developing mouse stomach. Nat Commun 2018; 9:4910. [PMID: 30464175 PMCID: PMC6249217 DOI: 10.1038/s41467-018-07463-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023] Open
Abstract
The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.
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Affiliation(s)
- Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chunchao Zhang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tongqing Gong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jianming Xu
- Department of Gastrointestinal Oncology, Affiliated Hospital Cancer Center, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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32
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Upadhyay A, Kumar S, Rooker SA, Koehn JT, Crans DC, McNeil MR, Lott JS, Crick DC. Mycobacterial MenJ: An Oxidoreductase Involved in Menaquinone Biosynthesis. ACS Chem Biol 2018; 13:2498-2507. [PMID: 30091899 DOI: 10.1021/acschembio.8b00402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
MenJ, annotated as an oxidoreductase, was recently demonstrated to catalyze the reduction (saturation) of a single double bond in the isoprenyl side-chain of mycobacterial menaquinone. This modification was shown to be essential for bacterial survival in J774A.1 macrophage-like cells, suggesting that MenJ may be a conditional drug target in Mycobacterium tuberculosis and other pathogenic mycobacteria. Recombinant protein was expressed in a heterologous host, and the activity was characterized. Although highly regiospecific in vivo, the activity is not absolutely regiospecific in vitro; in addition, the enzyme is not specific for naphthoquinones vs benzoquinones. Coenzyme Q-1 (a benzoquinone, UQ-1) was used as the lipoquinone substrate, and NADH oxidation was followed spectrophotometrically as the activity readout. NADPH could not be substituted for NADH in the reaction mixture. The enzyme contains a FAD binding site that was 72% occupied in the purified recombinant protein. Enzyme activity was maximal at 37 °C and pH 7.0; addition of divalent cations, EDTA, and reducing agents such as dithiothreitol to the reaction mixture had no effect on activity. The addition of detergents did not stimulate activity, and addition of saturating levels of FAD had relatively little effect on the observed kinetic parameters. These properties allowed the development of a facile assay needed to study this potential drug target, which is also amenable to high throughput screening. The Km values for UQ-1 using recombinant MenJ from Mycobacterium smegmatis or M. tuberculosis without saturating concentrations of FAD were found to be 52 ± 9.6 and 44 ± 4.8 μM, respectively, while the KmNADH values were determined to be 59 ± 14 and 64 ± 15 μM. The Km for MK-1, the menaquinone analogue of UQ-1, using recombinant MenJ from M. tuberculosis without saturating concentrations of FAD but in the presence of 0.5% Tween 80 was shown to be 30 ± 2.9 μM. Thus, this is the first report of a kinetic characterization of a member of the geranylgeranyl reductase family of enzymes.
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Affiliation(s)
- Ashutosh Upadhyay
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Santosh Kumar
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Steven A. Rooker
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Jordan T. Koehn
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Debbie C. Crans
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Michael R. McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - J. Shaun Lott
- Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Dean C. Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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Employing proteomics to understand the effects of nutritional intervention in cancer treatment. Anal Bioanal Chem 2018; 410:6371-6386. [PMID: 29974151 DOI: 10.1007/s00216-018-1219-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 12/22/2022]
Abstract
Lifestyle optimizations are implementable changes that can have an impact on health and disease. Nutrition is a lifestyle optimization that has been shown to be of great importance in cancer initiation, progression, and metastasis. Dozens of clinical trials are currently in progress that focus on the nutritional modifications that cancer patients can make prior to and during medical care that increase the efficacy of treatment. In this review, we discuss various nutritional inventions for cancer patients and the analytical approaches to characterize the downstream molecular effects. We first begin by briefly explaining the many different forms of nutritional intervention currently being used in cancer treatment as well as their motivating biology. The forms of nutrient modulation described in this review include calorie restriction, the different practices of fasting, and carbohydrate restriction. The review then shifts to explain how proteomics is used to determine biomarkers of cancer and how it can be utilized in the future to determine the metabolic phenotype of a tumor, and inform physicians if nutritional intervention should be recommended for a cancer patient. Nutrigenomics aims to understand the relationship of nutrients and gene expression and can be used to understand the downstream molecular effects of nutrition restriction, partially through proteomic analysis. Proteomics is just beginning to be used as cancer diagnostic and predictive tools. However, these approaches have not been used to their full potential to understand nutritional intervention in cancer. Graphical abstract ᅟ.
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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Otzen M, Palacio C, Janssen DB. Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics. Appl Microbiol Biotechnol 2018; 102:6699-6711. [PMID: 29850960 PMCID: PMC6061476 DOI: 10.1007/s00253-018-9073-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 01/04/2023]
Abstract
Some bacterial cultures are capable of growth on caprolactam as sole carbon and nitrogen source, but the enzymes of the catabolic pathway have not been described. We isolated a caprolactam-degrading strain of Pseudomonas jessenii from soil and identified proteins and genes putatively involved in caprolactam metabolism using quantitative mass spectrometry-based proteomics. This led to the discovery of a caprolactamase and an aminotransferase that are involved in the initial steps of caprolactam conversion. Additionally, various proteins were identified that likely are involved in later steps of the pathway. The caprolactamase consists of two subunits and demonstrated high sequence identity to the 5-oxoprolinases. Escherichia coli cells expressing this caprolactamase did not convert 5-oxoproline but were able to hydrolyze caprolactam to form 6-aminocaproic acid in an ATP-dependent manner. Characterization of the aminotransferase revealed that the enzyme deaminates 6-aminocaproic acid to produce 6-oxohexanoate with pyruvate as amino acceptor. The amino acid sequence of the aminotransferase showed high similarity to subgroup II ω-aminotransferases of the PLP-fold type I proteins. Finally, analyses of the genome sequence revealed the presence of a caprolactam catabolism gene cluster comprising a set of genes involved in the conversion of caprolactam to adipate.
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Affiliation(s)
- Marleen Otzen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Cyntia Palacio
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dick B Janssen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Schmit PO, Vialaret J, Wessels HJ, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics 2018; 175:12-26. [DOI: 10.1016/j.jprot.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
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Meerstein-Kessel L, van der Lee R, Stone W, Lanke K, Baker DA, Alano P, Silvestrini F, Janse CJ, Khan SM, van de Vegte-Bolmer M, Graumans W, Siebelink-Stoter R, Kooij TWA, Marti M, Drakeley C, Campo JJ, van Dam TJP, Sauerwein R, Bousema T, Huynen MA. Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites. Sci Rep 2018; 8:410. [PMID: 29323249 PMCID: PMC5765010 DOI: 10.1038/s41598-017-18840-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 12/02/2022] Open
Abstract
Plasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available 'omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated "gold standards" of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes. To illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia.
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Affiliation(s)
- Lisette Meerstein-Kessel
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Will Stone
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kjerstin Lanke
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Baker
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Pietro Alano
- Dipartimento Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy
| | | | - Chris J Janse
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Shahid M Khan
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Wouter Graumans
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Rianne Siebelink-Stoter
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Taco W A Kooij
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Matthias Marti
- Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Chris Drakeley
- Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Robert Sauerwein
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Teun Bousema
- Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands.
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Pandey A, Ding SL, Qin QM, Gupta R, Gomez G, Lin F, Feng X, Fachini da Costa L, Chaki SP, Katepalli M, Case ED, van Schaik EJ, Sidiq T, Khalaf O, Arenas A, Kobayashi KS, Samuel JE, Rivera GM, Alaniz RC, Sze SH, Qian X, Brown WJ, Rice-Ficht A, Russell WK, Ficht TA, de Figueiredo P. Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection. Cell Host Microbe 2017; 21:637-649.e6. [PMID: 28494245 DOI: 10.1016/j.chom.2017.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 03/12/2017] [Accepted: 04/24/2017] [Indexed: 12/26/2022]
Abstract
Cryptococcus neoformans (Cn) is a deadly fungal pathogen whose intracellular lifestyle is important for virulence. Host mechanisms controlling fungal phagocytosis and replication remain obscure. Here, we perform a global phosphoproteomic analysis of the host response to Cryptococcus infection. Our analysis reveals numerous and diverse host proteins that are differentially phosphorylated following fungal ingestion by macrophages, thereby indicating global reprogramming of host kinase signaling. Notably, phagocytosis of the pathogen activates the host autophagy initiation complex (AIC) and the upstream regulatory components LKB1 and AMPKα, which regulate autophagy induction through their kinase activities. Deletion of Prkaa1, the gene encoding AMPKα1, in monocytes results in resistance to fungal colonization of mice. Finally, the recruitment of AIC components to nascent Cryptococcus-containing vacuoles (CnCVs) regulates the intracellular trafficking and replication of the pathogen. These findings demonstrate that host AIC regulatory networks confer susceptibility to infection and establish a proteomic resource for elucidating host mechanisms that regulate fungal intracellular parasitism.
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Affiliation(s)
- Aseem Pandey
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA; Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Sheng Li Ding
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA; Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA; Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, Henan, China
| | - Qing-Ming Qin
- College of Plant Sciences, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, Jilin, China
| | - Rahul Gupta
- Health and Engineering Group, Leidos Inc., 2295 Parklake Drive, Atlanta, GA 30345, USA
| | - Gabriel Gomez
- Texas A&M Veterinary Medical Diagnostic Laboratory, Texas A&M University, College Station, Texas 77843, USA
| | - Furong Lin
- Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA
| | - Xuehuan Feng
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA; Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA
| | - Luciana Fachini da Costa
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA; Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Sankar P Chaki
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Madhu Katepalli
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Elizabeth D Case
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Erin J van Schaik
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Tabasum Sidiq
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Omar Khalaf
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Angela Arenas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Koichi S Kobayashi
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - James E Samuel
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Gonzalo M Rivera
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - Sing-Hoi Sze
- Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, Texas 77843, USA; Department of Computer Science and Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, Texas 77843, USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Xiaoning Qian
- Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, Texas 77843, USA; Department of Electrical and Computer Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - William J Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Allison Rice-Ficht
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, Texas 77843, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Thomas A Ficht
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA.
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas 77843, USA; Norman Borlaug Center, Texas A&M University, College Station, Texas 77843, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA.
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Ourradi K, Sharif M. Opportunities and challenges for the discovery and validation of proteomic biomarkers for common arthritic diseases. Biomark Med 2017; 11:877-892. [PMID: 28976778 DOI: 10.2217/bmm-2016-0374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Osteoarthritis (OA) and rheumatoid arthritis (RA) are most prevalent among all the rheumatic diseases, and currently, there are no reliable biochemical measures for early diagnosis or for predicting who is likely to progress. Early diagnosis is important for making decisions on treatment options and for better management of patients. This narrative review highlights the first-generation biomarkers identified over the last two decades and focuses on the discovery and validation of candidate OA biomarkers from recent mass-spectrometry-based proteomic studies for diagnosis and monitoring disease outcomes in human. It discusses the challenges and opportunities for discovery of novel biomarkers and progress in the development of techniques for measuring biomarkers, and provides directions for future discovery and validation of biomarkers for OA and rheumatoid arthritis.
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Affiliation(s)
- Khadija Ourradi
- Musculoskeletal Research Unit, Translational Health Sciences Bristol Medical School, University of Bristol, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Mohammed Sharif
- Musculoskeletal Research Unit, Translational Health Sciences Bristol Medical School, University of Bristol, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
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Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics. Mol Diagn Ther 2017; 22:11-23. [DOI: 10.1007/s40291-017-0298-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Mourad FH, Yau Y, Wasinger VC, Leong RW. Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models. Dig Dis Sci 2017; 62:2266-2276. [PMID: 28717845 DOI: 10.1007/s10620-017-4673-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/04/2017] [Indexed: 12/14/2022]
Abstract
Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies. Our aim is to review the information and lessons acquired so far from the use of proteomics in animal models of colitis. These studies helped understand the importance of different proteins at different stages of the disease and unraveled the different pathways that are activated or inhibited during the inflammatory process. Expressed proteins related to inflammation, cellular structure, endoplasmic reticulum stress, and energy depletion advanced the knowledge about the reaction of intestinal cells to inflammation and repair. The role of mesenteric lymphocytes, exosomes, and the intestinal mucosal barrier was emphasized in the inflammatory process. In addition, studies in animal models revealed mechanisms of the beneficial effects of some therapeutic interventions and foods or food components on intestinal inflammation by monitoring changes in protein expression and paved the way for some new possible inflammatory pathways to target in the future. Advances in proteomics technology will further clarify the interaction between intestinal microbiota and IBD pathogenesis and investigate the gene-environmental axis of IBD etiology.
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Affiliation(s)
- Fadi H Mourad
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box 113-6044, Hamra, Beirut, 110 32090, Lebanon. .,Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia.
| | - Yunki Yau
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of NSW Australia, Kensington, NSW, 2052, Australia
| | - Rupert W Leong
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
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Jung HJ. Chemical Proteomic Approaches Targeting Cancer Stem Cells: A Review of Current Literature. Cancer Genomics Proteomics 2017; 14:315-327. [PMID: 28870999 PMCID: PMC5611518 DOI: 10.21873/cgp.20042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/24/2022] Open
Abstract
Cancer stem cells (CSCs) have been proposed as central drivers of tumor initiation, progression, recurrence, and therapeutic resistance. Therefore, identifying stem-like cells within cancers and understanding their properties is crucial for the development of effective anticancer therapies. Recently, chemical proteomics has become a powerful tool to efficiently determine protein networks responsible for CSC pathophysiology and comprehensively elucidate molecular mechanisms of drug action against CSCs. This review provides an overview of major methodologies utilized in chemical proteomic approaches. In addition, recent successful chemical proteomic applications targeting CSCs are highlighted. Future direction of potential CSC research by integrating chemical genomic and proteomic data obtained from a single biological sample of CSCs are also suggested in this review.
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Affiliation(s)
- Hye Jin Jung
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asan, Republic of Korea
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Hu H, Khatri K, Zaia J. Algorithms and design strategies towards automated glycoproteomics analysis. MASS SPECTROMETRY REVIEWS 2017; 36:475-498. [PMID: 26728195 PMCID: PMC4931994 DOI: 10.1002/mas.21487] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/30/2015] [Indexed: 05/09/2023]
Abstract
Glycoproteomics involves the study of glycosylation events on protein sequences ranging from purified proteins to whole proteome scales. Understanding these complex post-translational modification (PTM) events requires elucidation of the glycan moieties (monosaccharide sequences and glycosidic linkages between residues), protein sequences, as well as site-specific attachment of glycan moieties onto protein sequences, in a spatial and temporal manner in a variety of biological contexts. Compared with proteomics, bioinformatics for glycoproteomics is immature and many researchers still rely on tedious manual interpretation of glycoproteomics data. As sample preparation protocols and analysis techniques have matured, the number of publications on glycoproteomics and bioinformatics has increased substantially; however, the lack of consensus on tool development and code reuse limits the dissemination of bioinformatics tools because it requires significant effort to migrate a computational tool tailored for one method design to alternative methods. This review discusses algorithms and methods in glycoproteomics, and refers to the general proteomics field for potential solutions. It also introduces general strategies for tool integration and pipeline construction in order to better serve the glycoproteomics community. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:475-498, 2017.
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Affiliation(s)
- Han Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Kshitij Khatri
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
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Cui Y, Liu X, Li X, Yang H. In-Depth Proteomic Analysis of the Hippocampus in a Rat Model after Cerebral Ischaemic Injury and Repair by Danhong Injection (DHI). Int J Mol Sci 2017; 18:ijms18071355. [PMID: 28672812 PMCID: PMC5535848 DOI: 10.3390/ijms18071355] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/17/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023] Open
Abstract
Stroke is the second most common cause of death worldwide. A systematic description and characterization of the strokes and the effects induced in the hippocampus have not been performed so far. Here, we analysed the protein expression in the hippocampus 24 h after cerebral ischaemic injury and repair. Drug intervention using Danhong injection (DHI), which has been reported to have good therapeutic effects in a clinical setting, was selected for our study of cerebral ischaemia repair in rat models. A larger proteome dataset and total 4091 unique proteins were confidently identified in three biological replicates by combining tissue extraction for rat hippocampus and LC-MS/MS analysis. A label-free approach was then used to quantify the differences among the four experimental groups (Naive, Sham, middle cerebral artery occlusion (MCAO) and MCAO + DHI groups) and showed that about 2500 proteins on average were quantified in each of the experiment group. Bioinformatics analysis revealed that in total 280 unique proteins identified above were differentially expressed (P < 0.05). By combining the subcellular localization, hierarchical clustering and pathway information with the results from injury and repair phase, 12 significant expressed proteins were chosen and verified with respect to their potential as candidates for cerebral ischaemic injury by Western blot. The primary three signalling pathways of the candidates related may be involved in molecular mechanisms related to cerebral ischaemic injury. In addition, a glycogen synthase kinase-3β (Gsk-3β) inhibitor of the candidates with the best corresponding expression trends between western blotting (WB) and label-free quantitative results were chosen for further validation. The results of Western blot analysis of protein expression and 2,3,5- chloride three phenyl tetrazole (TTC) staining of rat brains showed that DHI treatment and Gsk-3β inhibitor are both able to confer protection against ischaemic injury in rat MCAO model. The observations of the present study provide a novel understanding regarding the regulatory mechanism of cerebral ischaemic injury.
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Affiliation(s)
- Yiran Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Xin Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China.
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El Bairi K, Amrani M, Kandhro AH, Afqir S. Prediction of therapy response in ovarian cancer: Where are we now? Crit Rev Clin Lab Sci 2017; 54:233-266. [PMID: 28443762 DOI: 10.1080/10408363.2017.1313190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/27/2017] [Indexed: 02/08/2023]
Abstract
Therapy resistance is a major challenge in the management of ovarian cancer (OC). Advances in detection and new technology validation have led to the emergence of biomarkers that can predict responses to available therapies. It is important to identify predictive biomarkers to select resistant and sensitive patients in order to reduce important toxicities, to reduce costs and to increase survival. The discovery of predictive and prognostic biomarkers for monitoring therapy is a developing field and provides promising perspectives in the era of personalized medicine. This review article will discuss the biology of OC with a focus on targetable pathways; current therapies; mechanisms of resistance; predictive biomarkers for chemotherapy, antiangiogenic and DNA-targeted therapies, and optimal cytoreductive surgery; and the emergence of liquid biopsy using recent studies from the Medline database and ClinicalTrials.gov.
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Affiliation(s)
- Khalid El Bairi
- a Faculty of Medicine and Pharmacy , Mohamed Ist University , Oujda , Morocco
| | - Mariam Amrani
- b Equipe de Recherche ONCOGYMA, Faculty of Medicine, Pathology Department , National Institute of Oncology, Université Mohamed V , Rabat , Morocco
| | - Abdul Hafeez Kandhro
- c Department of Biochemistry , Healthcare Molecular and Diagnostic Laboratory , Hyderabad , Pakistan
| | - Said Afqir
- d Department of Medical Oncology , Mohamed VI University Hospital , Oujda , Morocco
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Tubulin Beta-3 Chain as a New Candidate Protein Biomarker of Human Skin Aging: A Preliminary Study. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017. [PMID: 28626498 PMCID: PMC5463169 DOI: 10.1155/2017/5140360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Skin aging is a complex process, and a lot of efforts have been made to identify new and specific targets that could help to diagnose, prevent, and treat skin aging. Several studies concerning skin aging have analyzed the changes in gene expression, and very few investigations have been performed at the protein level. Moreover, none of these proteomic studies has used a global quantitative labeled proteomic offgel approach that allows a more accurate description of aging phenotype. We applied such an approach on human primary keratinocytes obtained from sun-nonexposed skin biopsies of young and elderly women. A total of 517 unique proteins were identified, and 58 proteins were significantly differentially expressed with 40 that were downregulated and 18 upregulated with aging. Gene ontology and pathway analysis performed on these 58 putative biomarkers of skin aging evidenced that these dysregulated proteins were mostly involved in metabolism and cellular processes such as cell cycle and signaling pathways. Change of expression of tubulin beta-3 chain was confirmed by western blot on samples originated from several donors. Thus, this study suggested the tubulin beta-3 chain has a promising biomarker in skin aging.
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50
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Zhang L, Wan S, Jiang Y, Wang Y, Fu T, Liu Q, Cao Z, Qiu L, Tan W. Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology. J Am Chem Soc 2017; 139:2532-2540. [PMID: 28121431 PMCID: PMC5519284 DOI: 10.1021/jacs.6b10646] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Shuo Wan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Yanyue Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Zhijuan Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
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