1
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Takagi S, Suzuki N, Ishihama Y. Revisiting Protein Reversed-Phase Chromatography for Bottom-Up Proteomics. J Proteome Res 2024; 23:4704-4714. [PMID: 39293027 DOI: 10.1021/acs.jproteome.4c00642] [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: 09/20/2024]
Abstract
We revisited protein reversed-phase chromatography (RP), using state-of-the-art RP columns developed for biopharmaceuticals, such as monoclonal antibodies, in order to evaluate the suitability of this methodology as a prefractionation step for bottom-up proteomics. The protein RP prefractionation (Prot-RP) method was compared with two other widely used prefractionation methods, SDS-PAGE and high-pH peptide RP (Pept-RP) by using cell lysates as samples. The overlap between fractions of Prot-RP was comparable to that of SDS-PAGE, and the protein recovery was approximately 2-fold higher. On the other hand, the overlap between fractions of Prot-RP was slightly larger than that of Pept-RP, but Prot-RP was able to identify more protein termini and more isoform-specific peptides than Pept-RP. Our results indicate that the combination of highly efficient protein prefractionation with modern mass spectrometers is particularly effective for proteoform profiling from cellular samples.
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Affiliation(s)
- Shunsuke Takagi
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Analytical and Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., Hiratsuka, Kanagawa 254-0014, Japan
| | - Nobuyuki Suzuki
- Analytical and Quality Evaluation Research Laboratories, Daiichi Sankyo Co., Ltd., Hiratsuka, Kanagawa 254-0014, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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2
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Stopa V, Lileikyte G, Bakochi A, Agarwal P, Beske R, Stammet P, Hassager C, Årman F, Nielsen N, Devaux Y. Multiomic biomarkers after cardiac arrest. Intensive Care Med Exp 2024; 12:83. [PMID: 39331333 PMCID: PMC11436561 DOI: 10.1186/s40635-024-00675-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Cardiac arrest is a sudden cessation of heart function, leading to an abrupt loss of blood flow and oxygen to vital organs. This life-threatening emergency requires immediate medical intervention and can lead to severe neurological injury or death. Methods and biomarkers to predict neurological outcome are available but lack accuracy. Such methods would allow personalizing healthcare and help clinical decisions. Extensive research has been conducted to identify prognostic omic biomarkers of cardiac arrest. With the emergence of technologies allowing to combine different levels of omics data, and with the help of artificial intelligence and machine learning, there is a potential to use multiomic signatures as prognostic biomarkers after cardiac arrest. This review article delves into the current knowledge of cardiac arrest biomarkers across various omic fields and suggests directions for future research aiming to integrate multiple omics data layers to improve outcome prediction and cardiac arrest patient's care.
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Affiliation(s)
- Victoria Stopa
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg
| | - Gabriele Lileikyte
- Department of Clinical Sciences Lund, Anaesthesia and Intensive Care, Lund University, Helsingborg Hospital, Svart-brödragränden 3, 251 87, Helsingborg, Sweden
| | - Anahita Bakochi
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
- Department of Clinical Sciences Lund, Infection Medicine, Lund University, Lund, Sweden
| | - Prasoon Agarwal
- Science for Life Laboratory, Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden (NBIS), Lund University, 22362, Lund, Sweden
| | - Rasmus Beske
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Pascal Stammet
- Department of Anesthesia and Intensive Care Medicine, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg
| | - Christian Hassager
- Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Filip Årman
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Niklas Nielsen
- Department of Clinical Sciences Lund, Anaesthesia and Intensive Care, Lund University, Helsingborg Hospital, Svart-brödragränden 3, 251 87, Helsingborg, Sweden
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg.
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3
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Ward B, Pyr Dit Ruys S, Balligand JL, Belkhir L, Cani PD, Collet JF, De Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Lingurski M, Yombi JC, Vertommen D, Elens L. Deep Plasma Proteomics with Data-Independent Acquisition: Clinical Study Protocol Optimization with a COVID-19 Cohort. J Proteome Res 2024; 23:3806-3822. [PMID: 39159935 PMCID: PMC11385417 DOI: 10.1021/acs.jproteome.4c00104] [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: 08/21/2024]
Abstract
Plasma proteomics is a precious tool in human disease research but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional data-dependent acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and data-independent acquisition (DIA) to significantly improve proteome coverage and depth while remaining cost-efficient. Using human plasma collected from a 20-patient COVID-19 cohort, our method utilizes commonly available solutions for depletion, sample preparation, and fractionation, followed by 3 liquid chromatography-mass spectrometry/MS (LC-MS/MS) injections for a 360 min total DIA run time. We detect 1321 proteins on average per patient and 2031 unique proteins across the cohort. Differential analysis further demonstrates the applicability of this method for plasma proteomic research and clinical biomarker identification, identifying hundreds of differentially abundant proteins at biological concentrations as low as 47 ng/L in human plasma. Data are available via ProteomeXchange with the identifier PXD047901. In summary, this study introduces a streamlined, cost-effective approach to deep plasma proteome analysis, expanding its utility beyond classical research environments and enabling larger-scale multiomics investigations in clinical settings. Our comparative analysis revealed that fractionation, whether the samples were pooled or separate postfractionation, significantly improved the number of proteins quantified. This underscores the value of fractionation in enhancing the depth of plasma proteome analysis, thereby offering a more comprehensive landscape for biomarker discovery in diseases such as COVID-19.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr Dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean-Luc Balligand
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Leïla Belkhir
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Patrice D Cani
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean-François Collet
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Julien De Greef
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Joseph P Dewulf
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Vincent Haufroid
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Jodogne
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Benoît Kabamba
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Maxime Lingurski
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean Cyr Yombi
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Didier Vertommen
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
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4
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Pollé OG, Pyr Dit Ruys S, Lemmer J, Hubinon C, Martin M, Herinckx G, Gatto L, Vertommen D, Lysy PA. Plasma proteomics in children with new-onset type 1 diabetes identifies new potential biomarkers of partial remission. Sci Rep 2024; 14:20798. [PMID: 39242727 PMCID: PMC11379901 DOI: 10.1038/s41598-024-71717-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 08/30/2024] [Indexed: 09/09/2024] Open
Abstract
Partial remission (PR) occurs in only half of people with new-onset type 1 diabetes (T1D) and corresponds to a transient period characterized by low daily insulin needs, low glycemic fluctuations and increased endogenous insulin secretion. While identification of people with newly-onset T1D and significant residual beta-cell function may foster patient-specific interventions, reliable predictive biomarkers of PR occurrence currently lack. We analyzed the plasma of children with new-onset T1D to identify biomarkers present at diagnosis that predicted PR at 3 months post-diagnosis. We first performed an extensive shotgun proteomic analysis using Liquid Chromatography-Tandem-Mass-Spectrometry (LCMS/MS) on the plasma of 16 children with new-onset T1D and quantified 98 proteins significantly correlating with Insulin-Dose Adjusted glycated hemoglobin A1c score (IDAA1C). We next applied a series of both qualitative and statistical filters and selected protein candidates that were associated to pathophysiological mechanisms related to T1D. Finally, we translationally verified several of the candidates using single-shot targeted proteomic (PRM method) on raw plasma. Taken together, we identified plasma biomarkers present at diagnosis that may predict the occurrence of PR in a single mass-spectrometry run. We believe that the identification of new predictive biomarkers of PR and β-cell function is key to stratify people with new-onset T1D for β-cell preservation therapies.
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Affiliation(s)
- Olivier G Pollé
- Pôle PEDI, Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
- Specialized Pediatrics Service, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | | | - Julie Lemmer
- Pôle PEDI, Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Camille Hubinon
- Pôle PEDI, Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Manon Martin
- Computational Biology and Bioinformatics (CBIO) Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Gaetan Herinckx
- MASSPROT Platform, Institut de Duve, UCLouvain, Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics (CBIO) Unit, de Duve Institute, UCLouvain, Brussels, Belgium
| | - Didier Vertommen
- MASSPROT Platform, Institut de Duve, UCLouvain, Brussels, Belgium
| | - Philippe A Lysy
- Pôle PEDI, Institut de Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium.
- Specialized Pediatrics Service, Cliniques universitaires Saint-Luc, Brussels, Belgium.
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5
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Zhou Y, Zheng H, Tan Z, Kang E, Xue P, Li X, Guan F. Optimizing and integrating depletion and precipitation methods for plasma proteomics through data-independent acquisition-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1235:124046. [PMID: 38382157 DOI: 10.1016/j.jchromb.2024.124046] [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: 12/09/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
The application of plasma proteomics is a reliable approach for the discovery of biomarkers. However, the utilization of mass spectrometry-based proteomics in plasma encounters limitations due to the presence of high-abundant proteins (HAPs) and the vast dynamic range. To address this issue, we conducted an optimization and integration of depletion and precipitation strategies eliminating interference from HAPs. The optimized procedure involved utilizing 40 µL of beads for the removal of 1 µL of plasma, and maintaining a ratio of 1:1:1 between plasma, urea, and trichloroacetic acid for the precipitation of 50 µL of plasma. To facilitate high-throughput processing, experimental procedures were carried out utilizing 96-well plates. The depletion method identified a total of 1510 proteins, whereas the precipitated method yielded a total of 802 proteins. The integration of these methods yielded a total of 1794 proteins, including a wide concentration range spanning over 8 orders of magnitude. Furthermore, these approaches exhibited a commendable level of reproducibility, as indicated by median coefficients of variation of 14.7 % and 21.1 % for protein intensities, respectively. The integrative method was found to be effective in precisely quantifying yeast proteins that were intentionally spiked in plasma at predetermined rations of 5, 2, 0.5, and 0.2 with a high genuine positive recovery with a range of 71 % to 91 % of all yeast proteins. The use of a complementary and finely tuned approach involving depletion and precipitation demonstrates tremendous potential in the field of discovering protein biomarkers from large-scale cohort studies.
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Affiliation(s)
- Yue Zhou
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Helong Zheng
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Zengqi Tan
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Enci Kang
- Xi'an Gaoxin No.1 High School International Division, Xi'an, Shaanxi, China
| | - Peng Xue
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Xiang Li
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Feng Guan
- College of Life Science, Northwest University, Xi'an, Shaanxi, China.
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6
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Ulanova M, Gloag L, Kim CK, Bongers A, Kim Duong HT, Gooding JJ, Tilley RD, Sachdev PS, Braidy N. Biocompatibility and proteomic profiling of DMSA-coated iron nanocubes in a human glioblastoma cell line. Nanomedicine (Lond) 2024; 19:303-323. [PMID: 38270934 DOI: 10.2217/nnm-2023-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Background: Superparamagnetic iron core iron oxide shell nanocubes have previously shown superior performance in magnetic resonance imaging T2 contrast enhancement compared with spherical nanoparticles. Methods: Iron core iron oxide shell nanocubes were synthesized, stabilized with dimercaptosuccinic acid (DMSA-NC) and physicochemically characterized. MRI contrast enhancement and biocompatibility were assessed in vitro. Results: DMSA-NC showed a transverse relaxivity of 122.59 mM-1·s-1 Fe. Treatment with DMSA-NC did not induce cytotoxicity or oxidative stress in U-251 cells, and electron microscopy demonstrated DMSA-NC localization within endosomes and lysosomes in cells following internalization. Global proteomics revealed dysregulation of iron storage, transport, transcription and mRNA processing proteins. Conclusion: DMSA-NC is a promising T2 MRI contrast agent which, in this preliminary investigation, demonstrates favorable biocompatibility with an astrocyte cell model.
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Affiliation(s)
- Marina Ulanova
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Lucy Gloag
- School of Mathematical & Physical Science, Faculty of Science, University of Technology Sydney, Sydney, New South Wales, 2007, Australia
| | - Chul-Kyu Kim
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Andre Bongers
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, 2052, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, 2052, Australia
- National Imaging Facility, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hong Thien Kim Duong
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Justin Gooding
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Richard D Tilley
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, 2052, Australia
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, 2052, Australia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, New South Wales, 2031, Australia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, 2052, Australia
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7
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Peng M, Zhou Y, Wang Y, Yi Z, Li S, Wan C. Identified Small Open Reading Frame-Encoded Peptides in Human Serum with Nanoparticle Protein Coronas. J Proteome Res 2024; 23:368-376. [PMID: 38006349 DOI: 10.1021/acs.jproteome.3c00608] [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: 11/27/2023]
Abstract
The low-molecular-weight proteins (LMWP) in serum and plasma are related to various human diseases and can be valuable biomarkers. A small open reading frame-encoded peptide (SEP) is one kind of LMWP, which has been found to function in many bioprocesses and has also been found in human blood, making it a potential biomarker. The detection of LMWP by a mass spectrometry (MS)-based proteomic assay is often inhibited by the wide dynamic range of serum/plasma protein abundance. Nanoparticle protein coronas are a newly emerging protein enrichment method. To analyze SEPs in human serum, we have developed a protocol integrated with nanoparticle protein coronas and liquid chromatography (LC)/MS/MS. With three nanoparticles, TiO2, Fe3O4@SiO2, and Fe3O4@SiO2@TiO2, we identified 164 new SEPs in the human serum sample. Fe3O4@SiO2 and a nanoparticle mixture obtained the maximum number and the largest proportion of identified SEPs, respectively. Compared with acetonitrile-based extraction, nanoparticle protein coronas can cover more small proteins and SEPs. The magnetic nanoparticle is also fit for high-throughput parallel protein separation before LC/MS. This method is fast, efficient, reproducible, and easy to operate in 96-well plates and centrifuge tubes, which will benefit the research on SEPs and biomarkers.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yi Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Zi Yi
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Shenglan Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
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8
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Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH. Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues. Commun Biol 2024; 7:6. [PMID: 38168632 PMCID: PMC10762018 DOI: 10.1038/s42003-023-05687-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada.
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Andrea L Kinnear
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Pallab Bhowmick
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto, ON, Canada
- Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
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9
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Bennike TB. Advances in proteomics: characterization of the innate immune system after birth and during inflammation. Front Immunol 2023; 14:1254948. [PMID: 37868984 PMCID: PMC10587584 DOI: 10.3389/fimmu.2023.1254948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Proteomics is the characterization of the protein composition, the proteome, of a biological sample. It involves the large-scale identification and quantification of proteins, peptides, and post-translational modifications. This review focuses on recent developments in mass spectrometry-based proteomics and provides an overview of available methods for sample preparation to study the innate immune system. Recent advancements in the proteomics workflows, including sample preparation, have significantly improved the sensitivity and proteome coverage of biological samples including the technically difficult blood plasma. Proteomics is often applied in immunology and has been used to characterize the levels of innate immune system components after perturbations such as birth or during chronic inflammatory diseases like rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). In cancers, the tumor microenvironment may generate chronic inflammation and release cytokines to the circulation. In these situations, the innate immune system undergoes profound and long-lasting changes, the large-scale characterization of which may increase our biological understanding and help identify components with translational potential for guiding diagnosis and treatment decisions. With the ongoing technical development, proteomics will likely continue to provide increasing insights into complex biological processes and their implications for health and disease. Integrating proteomics with other omics data and utilizing multi-omics approaches have been demonstrated to give additional valuable insights into biological systems.
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Affiliation(s)
- Tue Bjerg Bennike
- Medical Microbiology and Immunology, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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10
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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11
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Ulanova M, Gloag L, Bongers A, Kim CK, Duong HTK, Kim HN, Gooding JJ, Tilley RD, Biazik J, Wen W, Sachdev PS, Braidy N. Evaluation of Dimercaptosuccinic Acid-Coated Iron Nanoparticles Immunotargeted to Amyloid Beta as MRI Contrast Agents for the Diagnosis of Alzheimer's Disease. Cells 2023; 12:2279. [PMID: 37759500 PMCID: PMC10527350 DOI: 10.3390/cells12182279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Nanoparticle-based magnetic contrast agents have opened the potential for magnetic resonance imaging (MRI) to be used for early non-invasive diagnosis of Alzheimer's disease (AD). Accumulation of amyloid pathology in the brain has shown association with cognitive decline and tauopathy; hence, it is an effective biomarker for the early detection of AD. The aim of this study was to develop a biocompatible magnetic nanoparticle targeted to amyloid beta (Aβ) plaques to increase the sensitivity of T2-weighted MRI for imaging of amyloid pathology in AD. We presented novel iron core-iron oxide nanoparticles stabilized with a dimercaptosuccinic acid coating and functionalized with an anti-Aβ antibody. Nanoparticle biocompatibility and cellular internalization were evaluated in vitro in U-251 glioblastoma cells using cellular assays, proteomics, and transmission electron microscopy. Iron nanoparticles demonstrated no significant in vitro cytotoxicity, and electron microscopy results showed their movement through the endocytic cycle within the cell over a 24 h period. In addition, immunostaining and bio-layer interferometry confirmed the targeted nanoparticle's binding affinity to amyloid species. The iron nanoparticles demonstrated favourable MRI contrast enhancement; however, the addition of the antibody resulted in a reduction in the relaxivity of the particles. The present work shows promising preliminary results in the development of a targeted non-invasive method of early AD diagnosis using contrast-enhanced MRI.
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Affiliation(s)
- Marina Ulanova
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, NSW 2052, Australia; (M.U.); (C.-K.K.); (W.W.); (P.S.S.)
| | - Lucy Gloag
- Faculty of Science, School of Mathematical and Physical Science, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Andre Bongers
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia; (A.B.); (R.D.T.); (J.B.)
- Faculty of Medicine, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Chul-Kyu Kim
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, NSW 2052, Australia; (M.U.); (C.-K.K.); (W.W.); (P.S.S.)
| | - Hong Thien Kim Duong
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (H.T.K.D.); (J.J.G.)
| | - Ha Na Kim
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia;
| | - John Justin Gooding
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (H.T.K.D.); (J.J.G.)
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Richard D. Tilley
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia; (A.B.); (R.D.T.); (J.B.)
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (H.T.K.D.); (J.J.G.)
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Joanna Biazik
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia; (A.B.); (R.D.T.); (J.B.)
| | - Wei Wen
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, NSW 2052, Australia; (M.U.); (C.-K.K.); (W.W.); (P.S.S.)
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, NSW 2052, Australia; (M.U.); (C.-K.K.); (W.W.); (P.S.S.)
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, NSW 2052, Australia; (M.U.); (C.-K.K.); (W.W.); (P.S.S.)
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12
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Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer. J Proteome Res 2023; 22:2525-2537. [PMID: 37294184 PMCID: PMC11060334 DOI: 10.1021/acs.jproteome.3c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide molecular ions by the electrospray source. To maximize the transfer of peptides from the liquid to gaseous phase and allow molecular ions to enter the mass spectrometer at microspray flow rates, an efficient electrospray process is required. Here we describe the superior performance of newly design vacuum insulated probe heated electrospray ionization (VIP-HESI) source coupled to a Bruker timsTOF PRO mass spectrometer operated in microspray mode. VIP-HESI significantly improves chromatography signals in comparison to electrospray ionization (ESI) and nanospray ionization using the captivespray (CS) source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient of variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that the Slice-PASEF VIP-HESI mode is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with microflow rate chromatography achieves a higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications. Data and spectral libraries are available via ProteomeXchange (PXD040497).
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Affiliation(s)
- Mukul K Midha
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - David H Baxter
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Seamus R Morrone
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Timothy J Prokop
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
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13
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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [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: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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14
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Ubaida-Mohien C, Tanaka T, Tian Q, Moore Z, Moaddel R, Basisty N, Simonsick EM, Ferrucci L. Blood Biomarkers for Healthy Aging. Gerontology 2023; 69:1167-1174. [PMID: 37166337 PMCID: PMC11137618 DOI: 10.1159/000530795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 05/12/2023] Open
Abstract
Measuring the abundance of biological molecules and their chemical modifications in blood and tissues has been the cornerstone of research and medical diagnoses for decades. Although the number and variety of molecules that can be measured have expanded exponentially, the blood biomarkers routinely assessed in medical practice remain limited to a few dozen, which have not substantially changed over the last 30-40 years. The discovery of novel biomarkers would allow, for example, risk stratification or monitoring of disease progression or the effectiveness of treatments and interventions, improving clinical practice in myriad ways. In this review, we combine the biomarker discovery concept with geroscience. Geroscience bridges aging research and translation to clinical applications by combining the framework of medical gerontology with high-technology medical research. With the development of geroscience and the rise of blood biomarkers, there has been a paradigm shift from disease prevention and cure to promoting health and healthy aging. New -omic technologies have played a role in the development of blood biomarkers, including epigenetic, proteomic, metabolomic, and lipidomic markers, which have emerged as correlates or predictors of health status, from disease to exceptional health.
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Affiliation(s)
- Ceereena Ubaida-Mohien
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Qu Tian
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Ruin Moaddel
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Nathan Basisty
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Eleanor M Simonsick
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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15
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Midha MK, Kapil C, Maes M, Baxter DH, Morrone SR, Prokop TJ, Moritz RL. Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528699. [PMID: 36824828 PMCID: PMC9949110 DOI: 10.1101/2023.02.15.528699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide ions by the electrospray source. To maximize the transfer of peptides from liquid to a gaseous phase to allow molecular ions to enter the mass spectrometer at micro-spray flow rates, an efficient electrospray process is required. Here we describe superior performance of new Vacuum-Insulated-Probe-Heated-ElectroSpray-Ionization source (VIP-HESI) coupled with micro-spray flow rate chromatography and Bruker timsTOF PRO mass spectrometer. VIP-HESI significantly improves chromatography signals in comparison to nano-spray ionization using the CaptiveSpray source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient-of-variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that Slice-PASEF mode with VIP-HESI setup is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with micro-flow-rate chromatography achieves higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications.
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16
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Mosavi Z, Bashi Zadeh Fakhar H, Rezaei-Tavirani M, Akbari ME, Rostami F. Proteome profiling of ductal carcinoma in situ. Breast Dis 2023; 41:513-520. [PMID: 36641653 DOI: 10.3233/bd-220017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND AIM DCIS is the most common type of non-invasive breast cancer, accounting for about 15 to 30%. Proteome profile is used to detect biomarkers in the tissues of breast cancer patients by mass spectrometry. This study aimed to obtain the expression profile of DCIS proteome, and the expression profile of invasive biomarkers, and finally to introduce a dedicated biomarker panel to facilitate the prognosis and early detection for in situ breast cancer patients. METHODS AND MATERIALS In this study, 10 patients with breast cancer (DCIS) were studied. Benign (marginal) and cancerous tissue samples were obtained from patients for proteomics experiments. Initially, all tissue proteins were extracted using standard methods, and the proteins were separated using two-dimensional electrophoresis. Then, the expression amount of the extracted proteins was determined by ITRAQ. The data were analysed by R software, and gene ontology was utilised for describing the protein in detail. RESULTS 30 spots on gel electrophoresis were found in the tumor tissue group (sample), and 15 spots in the margin group (control) with P < 0.05. Healthy and cancerous tissue gels showed that 5 spots had different expression. VWF, MMP9, ITGAM, MPO and PLG protein spots were identified using the site www.ebi.ac.uk/IPI. Finally, protein biomarkers for breast tumor tissue with margin were introduced with the names of P04406, P49915, P05323, P06733, and P02768. DISCUSSION There are 5 critical proteins in inducing cancer pathways especially complement and coagulation cascades. The hall markers of a healthy cell to be cancerous are proliferation, invasion, angiogenesis, and changes in the immune system. Hence, regulation of protein plays a key role in developing recurrence to breast cancer in margins.
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Affiliation(s)
- Zeinb Mosavi
- Department of Medical Science, Islamic Azad University, Chalus Branch, Chalous, Iran
| | - Haniyeh Bashi Zadeh Fakhar
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Laboratory Science, Islamic Azad University, Chalous Branch, Chalous, Iran
| | | | - Mohamd Esmaeel Akbari
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Forouzan Rostami
- Department of Nursing, Faculty of Nursing and Midwifery, Islamic Azad University, Chalous, Iran
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17
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Poljak A, Raftery M, Polly P. Evaluating Cellular Viability by iTRAQ Proteomic Profiling. Methods Mol Biol 2023; 2644:193-209. [PMID: 37142923 DOI: 10.1007/978-1-0716-3052-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Cellular health, functionality, response to environment, and other variables affecting cell, tissue, or organ viability are reflected in the cellular proteomes and metabolomes. These "omic" profiles are in constant flux even during normal cellular functioning, to maintain cellular homeostasis, in response to small environmental changes and maintenance of optimal cell viability. However proteomic "fingerprints" can also provide insight into cellular ageing, response to disease, adjustment to environmental changes, and other variables that impact cellular viability. A variety of proteomic methods can be used to determine qualitative and quantitative proteomic change. In this chapter, we will focus on a labeling method called isobaric tags for relative and absolute quantification (iTRAQ), which is frequently used to identify and quantify proteomic expression changes in cells and tissues.
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Affiliation(s)
- Anne Poljak
- Bioanalytical Mass Spectrometry Facility (BMSF), Mark Wainwright Analytical Centre (MWAC), University of New South Wales, Sydney, NSW, Australia
| | - Mark Raftery
- Bioanalytical Mass Spectrometry Facility (BMSF), Mark Wainwright Analytical Centre (MWAC), University of New South Wales, Sydney, NSW, Australia
| | - Patsie Polly
- Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
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18
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Rice SJ, Belani CP. Optimizing data-independent acquisition (DIA) spectral library workflows for plasma proteomics studies. Proteomics 2022; 22:e2200125. [PMID: 35708973 DOI: 10.1002/pmic.202200125] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022]
Abstract
Traditional data-independent acquisition (DIA) workflows employ off-column fractionation with data-dependent acquisition (DDA) to generate spectral libraries for data extraction. Recent advances have led to the establishment of library-independent approaches for DIA analyses. The selection of a DIA workflow may affect the outcome of plasma proteomics studies. Here, we establish a gas-phase fractionation (GPF) workflow to create DIA libraries for DIA with parallel accumulation and serial fragmentation (diaPASEF). This workflow along with three other workflows, fractionated DDA libraries, fractionated DIA libraries, and predicted spectra libraries, were evaluated on 20 plasma samples from nonsmall cell lung cancer patients with low or high levels of IL-6. We sought to optimize protein identification and total experiment time. The novel GPF workflow for diaPASEF outperformed the traditional ddaPASEF workflow in the number of identified and quantified proteins. A library-independent workflow based on predicted spectra identified and quantified the most proteins in our experiment at the cost of computational power. Overall, the choice of DIA library workflow seemed to have a limited effect on the overall outcome of a plasma proteomics experiment, but it can affect the number of proteins identified and the total experiment time.
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Affiliation(s)
- Shawn J Rice
- Penn State Cancer Institute, Hershey, Pennsylvania, USA
| | - Chandra P Belani
- Penn State Cancer Institute, Hershey, Pennsylvania, USA.,Department of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
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19
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Neset L, Takayidza G, Berven FS, Hernandez-Valladares M. Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography-Mass Spectrometry Analysis of Human Cells and Plasma. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113390. [PMID: 35684327 PMCID: PMC9181984 DOI: 10.3390/molecules27113390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/16/2022] [Accepted: 05/21/2022] [Indexed: 12/02/2022]
Abstract
The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phase-enhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins.
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Affiliation(s)
- Lasse Neset
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Gracious Takayidza
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Frode S. Berven
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
| | - Maria Hernandez-Valladares
- The Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (L.N.); (G.T.); (F.S.B.)
- Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5021 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: ; Tel.: +47-555-863-68
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20
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Tognetti M, Sklodowski K, Müller S, Kamber D, Muntel J, Bruderer R, Reiter L. Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area. J Proteome Res 2022; 21:1718-1735. [PMID: 35605973 PMCID: PMC9251764 DOI: 10.1021/acs.jproteome.2c00122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The plasma proteome
has the potential to enable a holistic analysis
of the health state of an individual. However, plasma biomarker discovery
is difficult due to its high dynamic range and variability. Here,
we present a novel automated analytical approach for deep plasma profiling
and applied it to a 180-sample cohort of human plasma from lung, breast,
colorectal, pancreatic, and prostate cancers. Using a controlled quantitative
experiment, we demonstrate a 257% increase in protein identification
and a 263% increase in significantly differentially abundant proteins
over neat plasma. In the cohort, we identified 2732 proteins. Using
machine learning, we discovered biomarker candidates such as STAT3
in colorectal cancer and developed models that classify the diseased
state. For pancreatic cancer, a separation by stage was achieved.
Importantly, biomarker candidates came predominantly from the low
abundance region, demonstrating the necessity to deeply profile because
they would have been missed by shallow profiling.
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Affiliation(s)
| | | | | | | | - Jan Muntel
- Biognosys, Schlieren, Zurich 8952, Switzerland
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21
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Cummins TD, Powell DW, Wilkey DW, Brady MP, Benz FW, Barati MT, Caster DJ, Klein JB, Merchant ML. Quantitative Mass Spectrometry Normalization in Urine Biomarker Analysis in Nephrotic Syndrome. GLOMERULAR DISEASES 2022; 2:121-131. [PMID: 36199623 PMCID: PMC9529004 DOI: 10.1159/000522217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chronic kidney disease (CKD) affects 30 million adults, costs ~$79 billion dollars (2016) in Medicare expenditures, and is the ninth leading cause of death in the United States. The disease is silent or undiagnosed in almost half of people with severely reduced kidney function. Urine provides an ideal biofluid that is accessible to high-sensitivity mass spectrometry-based proteomic interrogation and is an indicator of renal homeostasis. While the accurate and precise diagnosis and better disease management of CKD can be aided using urine biomarkers, their discovery in excessive protein or nephrotic urine samples can present challenges. In this work we present a mass spectrometry-based method utilizing multiplex tandem mass tag (TMT) quantification and improved protein quantification using reporter ion normalization to urinary creatinine to analyze urinary proteins from patients with a form of nephrotic syndrome (FSGS). A comparative analysis was performed for urine from patients in remission versus active disease flare. Two-dimensional LC-MS/MS TMT quantitative analysis identified over 1058 urine proteins, 580 proteins with 2 peptides or greater and quantifiable. Normalization of TMT abundance values to creatinine per ml of urine concentrated reduced variability in 2D-TMT-LC-MS/MS experiments. Univariate and multivariate analyses showed that 27 proteins were significantly increased in proteinuric disease flare. Hierarchical heatmap clustering showed that SERPINA1 and ORM1 were >1.5 fold increased in active disease versus remission urine samples. ELISA validation of SERPINA1 and ORM1 abundance agreed with our quantitative TMT proteomics analysis. These findings provide support for the utility of this method for identification of novel diagnostic markers of CKD and identify SERPINA1 and ORM1 as promising candidate diagnostic markers for FSGS.
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Affiliation(s)
- Timothy D. Cummins
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA,*Timothy D. Cummins,
| | - David W. Powell
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Makayla P. Brady
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Fredrick W. Benz
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Michelle T. Barati
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Dawn J. Caster
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Jon B. Klein
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
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22
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Recent Developments in Clinical Plasma Proteomics—Applied to Cardiovascular Research. Biomedicines 2022; 10:biomedicines10010162. [PMID: 35052841 PMCID: PMC8773619 DOI: 10.3390/biomedicines10010162] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 01/27/2023] Open
Abstract
The human plasma proteome mirrors the physiological state of the cardiovascular system, a fact that has been used to analyze plasma biomarkers in routine analysis for the diagnosis and monitoring of cardiovascular diseases for decades. These biomarkers address, however, only a very limited subset of cardiovascular diseases, such as acute myocardial infarct or acute deep vein thrombosis, and clinical plasma biomarkers for the diagnosis and stratification cardiovascular diseases that are growing in incidence, such as heart failure and abdominal aortic aneurysm, do not exist and are urgently needed. The discovery of novel biomarkers in plasma has been hindered by the complexity of the human plasma proteome that again transforms into an extreme analytical complexity when it comes to the discovery of novel plasma biomarkers. This complexity is, however, addressed by recent achievements in technologies for analyzing the human plasma proteome, thereby facilitating the possibility for novel biomarker discoveries. The aims of this article is to provide an overview of the recent achievements in technologies for proteomic analysis of the human plasma proteome and their applications in cardiovascular medicine.
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23
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Andersen LAC, Palstrøm NB, Diederichsen A, Lindholt JS, Rasmussen LM, Beck HC. Determining Plasma Protein Variation Parameters as a Prerequisite for Biomarker Studies-A TMT-Based LC-MSMS Proteome Investigation. Proteomes 2021; 9:proteomes9040047. [PMID: 34941812 PMCID: PMC8707687 DOI: 10.3390/proteomes9040047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/03/2022] Open
Abstract
Specific plasma proteins serve as valuable markers for various diseases and are in many cases routinely measured in clinical laboratories by fully automated systems. For safe diagnostics and monitoring using these markers, it is important to ensure an analytical quality in line with clinical needs. For this purpose, information on the analytical and the biological variation of the measured plasma protein, also in the context of the discovery and validation of novel, disease protein biomarkers, is important, particularly in relation to for sample size calculations in clinical studies. Nevertheless, information on the biological variation of the majority of medium-to-high abundant plasma proteins is largely absent. In this study, we hypothesized that it is possible to generate data on inter-individual biological variation in combination with analytical variation of several hundred abundant plasma proteins, by applying LC-MS/MS in combination with relative quantification using isobaric tagging (10-plex TMT-labeling) to plasma samples. Using this analytical proteomic approach, we analyzed 42 plasma samples prepared in doublets, and estimated the technical, inter-individual biological, and total variation of 265 of the most abundant proteins present in human plasma thereby creating the prerequisites for power analysis and sample size determination in future clinical proteomics studies. Our results demonstrated that only five samples per group may provide sufficient statistical power for most of the analyzed proteins if relative changes in abundances >1.5-fold are expected. Seventeen of the measured proteins are present in the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Biological Variation Database, and demonstrated remarkably similar biological CV’s to the corresponding CV’s listed in the EFLM database suggesting that the generated proteomic determined variation knowledge is useful for large-scale determination of plasma protein variations.
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Affiliation(s)
| | - Nicolai Bjødstrup Palstrøm
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense, Denmark; (N.B.P.); (L.M.R.)
- Center for Clinical Proteomics (CCP), Odense University Hospital, DK-5000 Odense, Denmark
| | - Axel Diederichsen
- Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense, Denmark; (A.D.); (J.S.L.)
- Department of Cardiology, Odense University Hospital, DK-5000 Odense, Denmark
| | - Jes Sanddal Lindholt
- Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense, Denmark; (A.D.); (J.S.L.)
- Department of Cardiothoracic and Vascular Surgery, Odense University Hospital, DK-5000 Odense, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense, Denmark; (N.B.P.); (L.M.R.)
- Center for Clinical Proteomics (CCP), Odense University Hospital, DK-5000 Odense, Denmark
- Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense, Denmark; (A.D.); (J.S.L.)
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense, Denmark; (N.B.P.); (L.M.R.)
- Center for Clinical Proteomics (CCP), Odense University Hospital, DK-5000 Odense, Denmark
- Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, DK-5000 Odense, Denmark; (A.D.); (J.S.L.)
- Correspondence: ; Tel.: +45-29-647-470
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24
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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25
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Cao X, Sandberg A, Araújo JE, Cvetkovski F, Berglund E, Eriksson LE, Pernemalm M. Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma. J Proteome Res 2021; 20:4610-4620. [PMID: 34320313 PMCID: PMC8419864 DOI: 10.1021/acs.jproteome.1c00378] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
High abundant protein depletion is a common strategy applied to increase analytical depth in global plasma proteomics experiment setups. The standard strategies for depletion of the highest abundant proteins currently rely on multiple-use HPLC columns or multiple-use spin columns. Here we evaluate the performance of single-use spin columns for plasma depletion and show that the single-use spin reduces handling time by allowing parallelization and is easily adapted to a nonspecialized lab environment without reducing the high plasma proteome coverage and reproducibility. In addition, we evaluate the effect of viral heat inactivation on the plasma proteome, an additional step in the plasma preparation workflow that allows the sample preparation of SARS-Cov2-infected samples to be performed in a BSL3 laboratory, and report the advantage of performing the heat inactivation postdepletion. We further show the possibility of expanding the use of the depletion column cross-species to macaque plasma samples. In conclusion, we report that single-use spin columns for high abundant protein depletion meet the requirements for reproducibly in in-depth plasma proteomics and can be applied on a common animal model while also reducing the sample handling time.
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Affiliation(s)
- Xiaofang Cao
- Cancer Proteomics Mass Spectrometry, Scilifelab, Department of Oncology and Pathology, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - AnnSofi Sandberg
- Cancer Proteomics Mass Spectrometry, Scilifelab, Department of Oncology and Pathology, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - José Eduardo Araújo
- Cancer Proteomics Mass Spectrometry, Scilifelab, Department of Oncology and Pathology, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Filip Cvetkovski
- Research and Development, ITB-Med AB, SE-113 66 Stockholm, Sweden
| | - Erik Berglund
- Section of Endocrine and Sarcoma Surgery, Department of Molecular Medicine and Surgery; Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Transplantation, Surgery, Karolinska Institute, SE-141 86 Stockholm, Sweden
| | - Lars E Eriksson
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.,Medical Unit Infectious Diseases, Karolinska University Hospital, SE-141 86 Huddinge, Sweden.,School of Health Sciences, City University of London, London EC1 V 0HB, United Kingdom
| | - Maria Pernemalm
- Cancer Proteomics Mass Spectrometry, Scilifelab, Department of Oncology and Pathology, Karolinska Institutet, SE-141 86 Stockholm, Sweden
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26
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Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
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Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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27
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Solanki SS, Singh P, Kashyap P, Sansi MS, Ali SA. Promising role of defensins peptides as therapeutics to combat against viral infection. Microb Pathog 2021; 155:104930. [PMID: 33933603 PMCID: PMC8084285 DOI: 10.1016/j.micpath.2021.104930] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Antimicrobial peptides (AMPs) are ubiquitously present small peptides, which play a critical function in the innate immune system. The defensin class of AMPs represented an evolutionarily ancient family containing cationic cysteine residue and frequently expressed in epithelial or neutrophils cells. It plays myriad functions in host innate immune responses against various infection. Defensin has a broad spectrum of antimicrobial activities, including anti-bacteria, anti-viruses (AVPs), anti-fungi, anti-cancers, and also overcoming bacterial drug resistance. In this review, we compiled the progress on defensin, particularly incorporating the mechanism of action, their application as an antiviral agent, prospects in different areas, and limitations to be solved as an antiviral peptide. Defensins were explored, in particular, their capacity to stimulate innate and adaptive immunity by trigging as anti-coronavirus (COVID-19) peptides. The present review summarised its immunomodulatory and immunoenhancing properties and predominantly focused on its promising therapeutic adjuvant choices for combat against viral infection.
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Affiliation(s)
| | - Parul Singh
- Cell Biology and Proteomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Poonam Kashyap
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | - Manish Singh Sansi
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, Haryana, India; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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