1
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Zhen K, Hou W, Bai L, Wang M, Yue Z, Xu Z, Xiong D, Gao L, Ying W. An effective urobilin clearance strategy based on paramagnetic beads facilitates microscale proteomic analysis of urine. Analyst 2024; 149:3625-3635. [PMID: 38775334 DOI: 10.1039/d4an00312h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Urine provides an ideal source for disease biomarker discovery. High-adhesion contaminants such as urobilin, which are difficult to remove from urine, can severely interfere with urinary proteomic analysis. Here, we aimed to establish a strategy based on single-pot, solid-phase-enhanced sample preparation (SP3) technology to prepare samples for urinary proteomics analysis that almost completely eliminates the impact of urobilin. A systematic evaluation of the effects of two urinary protein precipitation methods, two types of protein lysis buffers, and different ratios of magnetic digestion beads on the identification and quantification of the microscale urinary proteome was conducted. Our results indicate that methanol-chloroform precipitation, coupled with efficient lysis facilitated by urea, and subsequent enzymatic digestion using a mix of hydrophilic and hydrophobic magnetic beads offers the best performance. Further applying this strategy to the urine of patients with benign prostatic hyperplasia, prostate cancer and healthy individuals, combined with a narrow window of data-independent acquisition, FGFR4, MYLK, ORM2, GOLM1, SPP1, CD55, CSF1, DLD and TIMP3 were identified as potential biomarkers to discriminate benign prostatic hyperplasia and prostate cancer patients.
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Affiliation(s)
- Kemiao Zhen
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Wenhao Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Lu Bai
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Mingchao Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zhan Yue
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zanxin Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Deyun Xiong
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Li Gao
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Govender IS, Mokoena R, Stoychev S, Naicker P. Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics. Proteomes 2023; 11:29. [PMID: 37873871 PMCID: PMC10594433 DOI: 10.3390/proteomes11040029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Urine provides a diverse source of information related to a patient's health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
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Affiliation(s)
- Ireshyn Selvan Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Rethabile Mokoena
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- School of Molecular and Cellular Biology, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
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Sakamoto K, Konami M, Kameda S, Satoh Y, Wakimoto H, Kitagawa Y, Gotoh B, Jiang DP, Hotta H, Itoh M. Suppression of viral RNA polymerase activity is necessary for persistent infection during the transformation of measles virus into SSPE virus. PLoS Pathog 2023; 19:e1011528. [PMID: 37494386 PMCID: PMC10406308 DOI: 10.1371/journal.ppat.1011528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/07/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] Open
Abstract
Subacute sclerosing panencephalitis (SSPE) is a fatal neurodegenerative disease caused by measles virus (MV), which typically develops 7 to 10 years after acute measles. During the incubation period, MV establishes a persistent infection in the brain and accumulates mutations that generate neuropathogenic SSPE virus. The neuropathogenicity is closely associated with enhanced propagation mediated by cell-to-cell fusion in the brain, which is principally regulated by hyperfusogenic mutations of the viral F protein. The molecular mechanisms underlying establishment and maintenance of persistent infection are unclear because it is impractical to isolate viruses before the appearance of clinical signs. In this study, we found that the L and P proteins, components of viral RNA-dependent RNA polymerase (RdRp), of an SSPE virus Kobe-1 strain did not promote but rather attenuated viral neuropathogenicity. Viral RdRp activity corresponded to F protein expression; the suppression of RdRp activity in the Kobe-1 strain because of mutations in the L and P proteins led to restriction of the F protein level, thereby reducing cell-to-cell fusion mediated propagation in neuronal cells and decreasing neuropathogenicity. Therefore, the L and P proteins of Kobe-1 did not contribute to progression of SSPE. Three mutations in the L protein strongly suppressed RdRp activity. Recombinant MV harboring the three mutations limited viral spread in neuronal cells while preventing the release of infectious progeny particles; these changes could support persistent infection by enabling host immune escape and preventing host cell lysis. Therefore, the suppression of RdRp activity is necessary for the persistent infection of the parental MV on the way to transform into Kobe-1 SSPE virus. Because mutations in the genome of an SSPE virus reflect the process of SSPE development, mutation analysis will provide insight into the mechanisms underlying persistent infection.
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Affiliation(s)
- Kento Sakamoto
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Miho Konami
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Shinra Kameda
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Yuto Satoh
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Hiroshi Wakimoto
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Yoshinori Kitagawa
- Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Bin Gotoh
- Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Da-Peng Jiang
- Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
| | - Hak Hotta
- Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
| | - Masae Itoh
- Department of Microbiology, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
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Zedan H, Morimura K, Elguoshy A, Yamamoto T, Natsuka S. Microheterogeneity and Individual Differences of Human Urinary N-Glycome under Normal Physiological Conditions. Biomolecules 2023; 13:biom13050756. [PMID: 37238626 DOI: 10.3390/biom13050756] [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: 03/15/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Urine is considered an outstanding biological fluid for biomarker discovery, reflecting both systemic and urogenital physiology. However, analyzing the N-glycome in urine in detail has been challenging due to the low abundance of glycans attached to glycoproteins compared to free oligosaccharides. Therefore, this study aims to thoroughly analyze urinary N-glycome using LC-MS/MS. The N-glycans were released using hydrazine and labeled with 2-aminopyridine (PA), followed by anion-exchange fractionation before LC-MS/MS analysis. A total of 109 N-glycans were identified and quantified, of which 58 were identified and quantified repeatedly in at least 80% of samples and accounted for approximately 85% of the total urinary glycome signal. Interestingly, a comparison between urine and serum N-glycome revealed that approximately 50% of the urinary glycome could originate from the kidney and urinary tract, where they were exclusively identified in urine, while the remaining 50% were common in both. Additionally, a correlation was found between age/sex and the relative abundances of urinary N-glycome, with more age-related changes observed in women than men. The results of this study provide a reference for human urine N-glycome profiling and structural annotations.
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Affiliation(s)
- Hend Zedan
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kousuke Morimura
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Shunji Natsuka
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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Toma L, Vignali G, Maffioli E, Tambuzzi S, Giaccari R, Mattarozzi M, Nonnis S, Milioli M, Franceschetti L, Paredi G, Negri A, Riccardi B, Cattaneo C, Careri M, Tedeschi G, Bruno S. Mass spectrometry-based proteomic strategy for ecchymotic skin examination in forensic pathology. Sci Rep 2023; 13:6116. [PMID: 37059833 PMCID: PMC10104867 DOI: 10.1038/s41598-023-32520-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics has recently attracted the attention from forensic pathologists. This work is the first report of the development of a shotgun bottom-up proteomic approach based on rapid protein extraction and nano-liquid chromatography/high-resolution mass spectrometry applied to full-thickness human skin for the differential analysis of normal and ecchymotic tissues to identify new biomarkers for bruise characterization and dating. We identified around 2000 proteins from each pooled extract. The method showed excellent precision on independent replicates, with Pearson correlation coefficients always higher than 95%. Glycophorin A, a known biomarker of vital wounds from immunochemical studies, was identified only in ecchymotic tissues, as confirmed by Western blotting analysis. This finding suggests that this protein can be used as a MS-detectable biomarker of wound vitality. By focusing on skin samples from individuals with known wound dating, besides Glycophorin A, other proteins differentially expressed in ecchymotic samples and dependant on wound age were identified, although further analysis on larger datasets are needed to validate these findings. This study paves the way for an in-depth investigation of the potential of MS-based techniques for wound examination in forensic pathology, overcoming the limitations of immunochemical assays.
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Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Giulia Vignali
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Elisa Maffioli
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Stefano Tambuzzi
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Roberta Giaccari
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Simona Nonnis
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy.
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy.
| | - Marco Milioli
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Lorenzo Franceschetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Gianluca Paredi
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Armando Negri
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
| | - Benedetta Riccardi
- Department of Pharmacokinetic, Biochemistry and Metabolism, Global Research and Preclinical Development, Chiesi Farmaceutici Spa, 43122, Parma, Italy
| | - Cristina Cattaneo
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133, Milan, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science, University of Milan, 26900, Lodi, Italy
- CRC Innovation for Well-Being and Environment (I-WE), University of Milan, 20133, Milan, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
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Watanabe Y, Hirao Y, Kasuga K, Kitamura K, Nakamura K, Yamamoto T. Urinary proteome profiles associated with cognitive decline in community elderly residents—A pilot study. Front Neurol 2023; 14:1134976. [PMID: 37006491 PMCID: PMC10061132 DOI: 10.3389/fneur.2023.1134976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Non-invasive and simple methods enabling easy identification of individuals at high risk of cognitive decline are needed as preventive measures against dementia. This pilot study aimed to explore protein biomarkers that can predict cognitive decline using urine, which can be collected non-invasively. Study subjects were selected from participants in a cohort study of middle-aged and older community-dwelling adults who underwent cognitive testing using the Mini-Mental State Examination and provided spot urine samples at two time points with an interval of approximately 5 years. Seven participants whose cognitive function declined 4 or more points from baseline (Group D) and 7 sex- and age-matched participants whose cognitive function remained within the normal range during the same period (Group M) were selected. Urinary proteomics using mass spectrometry was performed and discriminant models were created using orthogonal partial least squares-discriminant analysis (OPLS-DA). OPLS-DA yielded two models that significantly discriminated between the two groups at baseline and follow-up. Both models had ORM1, ORM2, and SERPINA3 in common. A further OPLS-DA model using baseline ORM1, ORM2, and SERPINA3 data showed similar predictive performance for data at follow-up as it did for baseline data (sensitivity: 0.85, specificity: 0.85), with the receiver operating characteristic curve analysis yielding an area under the curve of 0.878. This prospective study demonstrated the potential for using urine to identify biomarkers of cognitive decline.
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Affiliation(s)
- Yumi Watanabe
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- *Correspondence: Yumi Watanabe
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kaori Kitamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazutoshi Nakamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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Melkonian K, Stolze SC, Harzen A, Nakagami H. miniTurbo-based interactomics of two plasma membrane-localized SNARE proteins in Marchantia polymorpha. THE NEW PHYTOLOGIST 2022; 235:786-800. [PMID: 35396742 DOI: 10.1111/nph.18151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Marchantia polymorpha is a model liverwort and its overall low genetic redundancy is advantageous for dissecting complex pathways. Proximity-dependent in vivo biotin-labelling methods have emerged as powerful interactomics tools in recent years. However, interactomics studies applying proximity labelling are currently limited to angiosperm species in plants. Here, we established and evaluated a miniTurbo-based interactomics method in M. polymorpha using MpSYP12A and MpSYP13B, two plasma membrane-localized SNARE proteins, as baits. We show that our method yields a manifold of potential interactors of MpSYP12A and MpSYP13B compared to a coimmunoprecipitation approach. Our method could capture specific candidates for each SNARE. We conclude that a miniTurbo-based method is a feasible tool for interactomics in M. polymorpha and potentially applicable to other model bryophytes. Our interactome dataset on MpSYP12A and MpSYP13B will be a useful resource to elucidate the evolution of SNARE functions.
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Affiliation(s)
- Katharina Melkonian
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Anne Harzen
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
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8
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Sakamoto K, Satoh Y, Takahashi KI, Wakimoto H, Kitagawa Y, Gotoh B, Ayata M, Itoh M. Upregulation of viral RNA polymerase activity promotes adaptation of SSPE virus to neuronal cells. Virology 2022; 573:1-11. [DOI: 10.1016/j.virol.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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Sim YE, Kim JW, Ko BJ, Kim JY. Rapid and simple LC–MS/MS determination of urinary ethyl glucuronide, naltrexone, 6β-naltrexol, chlordiazepoxide, and norchlordiazepoxide for monitoring alcohol abuse. J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00315-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractIn this study, a liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed to detect ethyl glucuronide (EtG), which is a biomarker for monitoring alcohol consumption, and naltrexone (NTX), 6β-naltrexol (6βNTX), chlordiazepoxide (CDP), and norchlordiazepoxide (norCDP), which are analyzed to confirm the presence of medications for alcohol dependence treatment. The protein precipitation method was conducted to rapidly prepare samples. LC–MS/MS analysis was performed in the multiple-reaction monitoring mode. The analytes were separated using a Scherzo SM-C18 (2.0 × 100 mm, 3 µm) column. The calibration ranges were 5–1000 ng/mL for EtG, 6βNTX, CDP, and norCDP, and 1–100 ng/mL for NTX, with the correlation coefficients (r) being ≥ 0.994, and the weighting factor being 1/x2. The lower limit of quantification was 1–5 ng/mL. The method was also validated for precision, accuracy, selectivity, dilution integrity, recovery, matrix effect, and stability. The developed method was successfully applied for the determination of EtG, NTX, 6βNTX, CDP, and norCDP in urine samples obtained from 49 probationers who received alcohol dependence treatment orders. The method developed herein can be used to monitor the drug-based treatment of alcohol abuse and alcohol consumption during the treatment of individuals under probation.
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Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica-molecular background revealed by quantitative proteomics. Appl Microbiol Biotechnol 2021; 106:349-367. [PMID: 34913994 PMCID: PMC8720085 DOI: 10.1007/s00253-021-11731-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022]
Abstract
Abstract In this research, we were interested in answering a question whether subjecting a Yarrowia lipolytica strain overproducing a recombinant secretory protein (rs-Prot) to pre-optimized stress factors may enhance synthesis of the rs-Prot. Increased osmolarity (3 Osm kg−1) was the primary stress factor implemented alone or in combination with decreased temperature (20 °C), known to promote synthesis of rs-Prots. The treatments were executed in batch bioreactor cultures, and the cellular response was studied in terms of culture progression, gene expression and global proteomics, to get insight into molecular bases underlying an awaken reaction. Primarily, we observed that hyperosmolarity executed by high sorbitol concentration does not enhance synthesis of the rs-Prot but increases its transcription. Expectedly, hyperosmolarity induced synthesis of polyols at the expense of citric acid synthesis and growth, which was severely limited. A number of stress-related proteins were upregulated, including heat-shock proteins (HSPs) and aldo–keto reductases, as observed at transcriptomics and proteomics levels. Concerted downregulation of central carbon metabolism, including glycolysis, tricarboxylic acid cycle and fatty acid synthesis, highlighted redirection of carbon fluxes. Elevated abundance of HSPs and osmolytes did not outbalance the severe limitation of protein synthesis, marked by orchestrated downregulation of translation (elongation factors, several aa-tRNA synthetases), amino acid biosynthesis and ribosome biogenesis in response to the hyperosmolarity. Altogether we settled that increased osmolarity is not beneficial for rs-Prots synthesis in Y. lipolytica, even though some elements of the response could assist this process. Insight into global changes in the yeast proteome under the treatments is provided. Key points • Temp enhances, but Osm decreases rs-Prots synthesis by Y. lipolytica. • Enhanced abundance of HSPs and osmolytes is overweighted by limited translation. • Global proteome under Osm, Temp and Osm Temp treatments was studied. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11731-y.
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Immunization with a Bacterial Lipoprotein Establishes an Immuno-Protective Response with Upregulation of Effector CD4+ T Cells and Neutrophils Against Methicillin-Resistant Staphylococcus aureus Infection. Pathogens 2020; 9:pathogens9020138. [PMID: 32093163 PMCID: PMC7169464 DOI: 10.3390/pathogens9020138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a commensal bacterium in the human body; however, the bacterium frequently generates serious inflammation and infectious diseases. Some strains of S. aureus, such as methicillin-resistant Staphylococcus aureus (MRSA), are still a serious problem in public health facilities. Thus, an effective protection strategy is eagerly expected for the prevention and cure of MRSA infection. Here, we report that a specific fraction of an S. aureus lipoprotein (SA-LP) established a protective response against MRSA infection. The fractionated S. aureus lipoprotein SA-LP-F2, which is contained in 30–50 kDa of crude S. aureus lipoprotein (SA-LP-C), effectively activated dendritic cells (DCs) and the SA-LP-F2-pulsed DCs generated IFN-γ+CD4+ T (Th1) and IL-17A+CD4+ T (Th17) cells by in vitro antigen presentation. The SA-LP-F2 immunization upregulated the Th1 and Th17 populations so that MRSA colonization on the skin was suppressed during the challenge phase with MRSA. By following the effector T cell upregulation, the neutrophil function, which was a substantial effector cell against MRSA, was also enhanced in the SA-LP-F2-immunized mice. Finally, we found that the protective effect of SA-LP-F2 immunization was maintained for at least 90 days because the immunized mice continued to show a protective response during the MRSA challenge period. In the MRSA challenge, reactivated Th1 and Th17 populations were maintained in the SA-LP-F2-immunized mice as compared to naive mice. In addition, the neutrophil population was also upregulated in the mice. The memory CD4+ T cell (central memory T; TCM and effector memory T; TEM) population was established by SA-LP-F2 immunization and was maintained at higher levels than usual. Taken together, our findings may provide a breakthrough in the establishment of an immunization strategy against MRSA infection.
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Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS. Nat Commun 2020; 11:157. [PMID: 31919466 PMCID: PMC6952431 DOI: 10.1038/s41467-019-13973-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications. Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.
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