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Oliver N, Choi MJ, Arul AB, Whitaker MD, Robinson RAS. Establishing Quality Control Metrics for Large-Scale Plasma Proteomic Sample Preparation. ACS MEASUREMENT SCIENCE AU 2024; 4:442-451. [PMID: 39184360 PMCID: PMC11342454 DOI: 10.1021/acsmeasuresciau.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 08/27/2024]
Abstract
Large-scale plasma proteomics studies have been transformed due to the multiplexing and automation of sample preparation workflows. However, these workflows can suffer from reproducibility issues, a lack of standardized quality control (QC) metrics, and the assessment of variation before liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The incorporation of robust QC metrics in sample preparation workflows ensures better reproducibility, lower assay variation, and better-informed decisions for troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of patient samples (N = 808) using tandem mass tag (TMT) 16-plex batches (N = 58). The proteomic workflow consisted of protein depletion, protein digestion, TMT labeling, and fractionation. Five QC sample types (QCstd, QCdig, QCpool, QCTMT, and QCBSA) were created to measure the performance of sample preparation prior to the final LC-MS/MS analysis. We measured <10% CV for individual sample preparation steps in the proteomic workflow based on data from various QC sample steps. The establishment of robust measures for QC of sample preparation steps allowed for greater confidence in prepared samples for subsequent LC-MS/MS analysis. This study also provides recommendations for standardized QC metrics that can assist with future large-scale cohort sample preparation workflows.
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Affiliation(s)
- Nekesa
C. Oliver
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B. Arul
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D. Whitaker
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Memory and Alzheimer’s Center, Vanderbilt
University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Vanderbilt
Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Neurology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
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2
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Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Michel M, Plotkin DL, Mattingly ML, Mobley B, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. Aging (Albany NY) 2024; 16:6631-6651. [PMID: 38643460 PMCID: PMC11087122 DOI: 10.18632/aging.205751] [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: 06/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.
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Affiliation(s)
| | | | | | | | | | | | | | - Max Michel
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | | | - Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | - Andrew D. Fruge
- College of Nursing, Auburn University, Auburn, AL 36849, USA
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3
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Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Max Michel J, Plotkin DL, Mattingly ML, Brooks Mobley C, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543459. [PMID: 37333259 PMCID: PMC10274632 DOI: 10.1101/2023.06.02.543459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We examined the myofibrillar (MyoF) and non-myofibrillar (non-MyoF) proteomic profiles of the vastus lateralis (VL) muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6), and MA following eight weeks of knee extensor resistance training (RT, 2d/week). Shotgun/bottom-up proteomics in skeletal muscle typically yields wide protein abundance ranges that mask lowly expressed proteins. Thus, we adopted a novel approach whereby the MyoF and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS) analysis. A total of 10,866 proteins (4,421 MyoF and 6,445 non-MyoF) were identified. Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteome were evident between age cohorts. Further, most of these age-related non-MyoF proteins (447/543) were more enriched in MA versus Y. Several biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including (but not limited to) increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. Non-MyoF proteins associated with splicing and proteostasis were further interrogated, and in agreement with bioinformatics, alternative protein variants, spliceosome-associated proteins (snRNPs), and proteolysis-related targets were more abundant in MA versus Y. RT in MA non-significantly increased VL muscle cross-sectional area (+6.5%, p=0.066) and significantly increased knee extensor strength (+8.7%, p=0.048). However, RT modestly altered the MyoF (~0.3%, 11 upregulated and two downregulated proteins) and non-MyoF proteomes (~1.0%, 56 upregulated and eight downregulated proteins, p<0.01). Further, RT did not affect predicted biological processes in either fraction. Although participant numbers were limited, these preliminary results using a novel deep proteomic approach in skeletal muscle suggest that aging and RT predominantly affects protein abundances in the non-contractile protein pool. However, the marginal proteome adaptations occurring with RT suggest either: a) this may be an aging-associated phenomenon, b) more rigorous RT may stimulate more robust effects, or c) RT, regardless of age, subtly affects skeletal muscle protein abundances in the basal state.
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Affiliation(s)
| | | | | | | | | | | | | | - J. Max Michel
- School of Kinesiology, Auburn University, Auburn, AL USA
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4
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Sriboonvorakul N, Hu J, Boriboonhirunsarn D, Ng LL, Tan BK. Proteomics Studies in Gestational Diabetes Mellitus: A Systematic Review and Meta-Analysis. J Clin Med 2022; 11:2737. [PMID: 35628864 PMCID: PMC9143836 DOI: 10.3390/jcm11102737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
Gestational Diabetes Mellitus (GDM) is the most common metabolic complication during pregnancy and is associated with serious maternal and fetal complications such as pre-eclampsia and stillbirth. Further, women with GDM have approximately 10 times higher risk of diabetes later in life. Children born to mothers with GDM also face a higher risk of childhood obesity and diabetes later in life. Early prediction/diagnosis of GDM leads to early interventions such as diet and lifestyle, which could mitigate the maternal and fetal complications associated with GDM. However, no biomarkers identified to date have been proven to be effective in the prediction/diagnosis of GDM. Proteomic approaches based on mass spectrometry have been applied in various fields of biomedical research to identify novel biomarkers. Although a number of proteomic studies in GDM now exist, a lack of a comprehensive and up-to-date meta-analysis makes it difficult for researchers to interpret the data in the existing literature. Thus, we undertook a systematic review and meta-analysis on proteomic studies and GDM. We searched MEDLINE, EMBASE, Web of Science and Scopus from inception to January 2022. We searched Medline, Embase, CINHAL and the Cochrane Library, which were searched from inception to February 2021. We included cohort, case-control and observational studies reporting original data investigating the development of GDM compared to a control group. Two independent reviewers selected eligible studies for meta-analysis. Data collection and analyses were performed by two independent reviewers. The PROSPERO registration number is CRD42020185951. Of 120 articles retrieved, 24 studies met the eligibility criteria, comparing a total of 1779 pregnant women (904 GDM and 875 controls). A total of 262 GDM candidate biomarkers (CBs) were identified, with 49 CBs reported in at least two studies. We found 22 highly replicable CBs that were significantly different (nine CBs were upregulated and 12 CBs downregulated) between women with GDM and controls across various proteomic platforms, sample types, blood fractions and time of blood collection and continents. We performed further analyses on blood (plasma/serum) CBs in early pregnancy (first and/or early second trimester) and included studies with more than nine samples (nine studies in total). We found that 11 CBs were significantly upregulated, and 13 CBs significantly downregulated in women with GDM compared to controls. Subsequent pathway analysis using Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics resources found that these CBs were most strongly linked to pathways related to complement and coagulation cascades. Our findings provide important insights and form a strong foundation for future validation studies to establish reliable biomarkers for GDM.
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Affiliation(s)
- Natthida Sriboonvorakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Jiamiao Hu
- Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou 100816, China;
| | - Dittakarn Boriboonhirunsarn
- Department of Obstetrics & Gynecology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Leong Loke Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK;
| | - Bee Kang Tan
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK;
- Diabetes Research Centre, Leicester General Hospital, Leicester LE5 4PW, UK
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5
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Langen B, Vorontsov E, Spetz J, Swanpalmer J, Sihlbom C, Helou K, Forssell-Aronsson E. Age and sex effects across the blood proteome after ionizing radiation exposure can bias biomarker screening and risk assessment. Sci Rep 2022; 12:7000. [PMID: 35487913 PMCID: PMC9055069 DOI: 10.1038/s41598-022-10271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Abstract
Molecular biomarkers of ionizing radiation (IR) exposure are a promising new tool in various disciplines: they can give necessary information for adaptive treatment planning in cancer radiotherapy, enable risk projection for radiation-induced survivorship diseases, or facilitate triage and intervention in radiation hazard events. However, radiation biomarker discovery has not yet resolved the most basic features of personalized medicine: age and sex. To overcome this critical bias in biomarker identification, we quantitated age and sex effects and assessed their relevance in the radiation response across the blood proteome. We used high-throughput mass spectrometry on blood plasma collected 24 h after 0.5 Gy total body irradiation (15 MV nominal photon energy) from male and female C57BL/6 N mice at juvenile (7-weeks-old) or adult (18-weeks-old) age. We also assessed sex and strain effects using juvenile male and female BALB/c nude mice. We showed that age and sex created significant effects in the proteomic response regarding both extent and functional quality of IR-induced responses. Furthermore, we found that age and sex effects appeared non-linear and were often end-point specific. Overall, age contributed more to differences in the proteomic response than sex, most notably in immune responses, oxidative stress, and apoptotic cell death. Interestingly, sex effects were pronounced for DNA damage and repair pathways and associated cellular outcome (pro-survival vs. pro-apoptotic). Only one protein (AHSP) was identified as a potential general biomarker candidate across age and sex, while GMNN, REG3B, and SNCA indicated some response similarity across age. This low yield advocated that unisex or uniage biomarker screening approaches are not feasible. In conclusion, age- and sex-specific screening approaches should be implemented as standard protocol to ensure robustness and diagnostic power of biomarker candidates. Bias-free molecular biomarkers are a necessary progression towards personalized medicine and integral for advanced adaptive cancer radiotherapy and risk assessment.
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Affiliation(s)
- Britta Langen
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Section of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Egor Vorontsov
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johan Spetz
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - John Swanpalmer
- Department of Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, Gothenburg, Sweden
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6
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Ravuri HG, Noor Z, Mills PC, Satake N, Sadowski P. Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes 2022; 10:9. [PMID: 35324581 PMCID: PMC8953371 DOI: 10.3390/proteomes10010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/22/2022] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry-based plasma proteomics offers a major advance for biomarker discovery in the veterinary field, which has traditionally been limited to quantification of a small number of proteins using biochemical assays. The development of foundational data and tools related to sequential window acquisition of all theoretical mass spectra (SWATH)-mass spectrometry has allowed for quantitative profiling of a significant number of plasma proteins in humans and several animal species. Enabling SWATH in dogs enhances human biomedical research as a model species, and significantly improves diagnostic and disease monitoring capability. In this study, a comprehensive peptide spectral library specific to canine plasma proteome was developed and evaluated using SWATH for protein quantification in non-depleted dog plasma. Specifically, plasma samples were subjected to various orthogonal fractionation and digestion techniques, and peptide fragmentation data corresponding to over 420 proteins was collected. Subsequently, a SWATH-based assay was introduced that leveraged the developed resource and that enabled reproducible quantification of 400 proteins in non-depleted plasma samples corresponding to various disease conditions. The ability to profile the abundance of such a significant number of plasma proteins using a single method in dogs has the potential to accelerate biomarker discovery studies in this species.
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Affiliation(s)
- Halley Gora Ravuri
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Zainab Noor
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Paul C. Mills
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Nana Satake
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Bertholim L, Chaves AFA, Oliveira AK, Menezes MC, Asega AF, Tashima AK, Zelanis A, Serrano SMT. Systemic Effects of Hemorrhagic Snake Venom Metalloproteinases: Untargeted Peptidomics to Explore the Pathodegradome of Plasma Proteins. Toxins (Basel) 2021; 13:toxins13110764. [PMID: 34822548 PMCID: PMC8622078 DOI: 10.3390/toxins13110764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 01/15/2023] Open
Abstract
Hemorrhage induced by snake venom metalloproteinases (SVMPs) is a complex phenomenon that involves capillary disruption and blood extravasation. HF3 (hemorrhagic factor 3) is an extremely hemorrhagic SVMP of Bothrops jararaca venom. Studies using proteomic approaches revealed targets of HF3 among intracellular and extracellular proteins. However, the role of the cleavage of plasma proteins in the context of the hemorrhage remains not fully understood. The main goal of this study was to analyze the degradome of HF3 in human plasma. For this purpose, approaches for the depletion of the most abundant proteins, and for the enrichment of low abundant proteins of human plasma, were used to minimize the dynamic range of protein concentration, in order to assess the proteolytic activity of HF3 on a wide spectrum of proteins, and to detect the degradation products using mass spectrometry-based untargeted peptidomics. The results revealed the hydrolysis products generated by HF3 and allowed the identification of cleavage sites. A total of 61 plasma proteins were identified as cleaved by HF3. Some of these proteins corroborate previous studies, and others are new HF3 targets, including proteins of the coagulation cascade, of the complement system, proteins acting on the modulation of inflammation, and plasma proteinase inhibitors. Overall, the data indicate that HF3 escapes inhibition and sculpts the plasma proteome by degrading key proteins and generating peptides that may act synergistically in the hemorrhagic process.
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Affiliation(s)
- Luciana Bertholim
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
| | - Alison F. A. Chaves
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
| | - Ana K. Oliveira
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
| | - Milene C. Menezes
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
| | - Amanda F. Asega
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo 04023-901, SP, Brazil;
| | - Andre Zelanis
- Functional Proteomics Laboratory, Department of Science and Technology, Federal University of São Paulo (UNIFESP), 330 Talim St., São José dos Campos 12231-280, SP, Brazil;
| | - Solange M. T. Serrano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signalig, CeTICS, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.B.); (A.F.A.C.); (A.K.O.); (M.C.M.); (A.F.A.)
- Correspondence:
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8
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Khan T, Dasgupta S, Ghosh N, Chaudhury K. Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers. Mol Omics 2021; 17:43-58. [PMID: 33073811 DOI: 10.1039/d0mo00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a debilitating chronic progressive and fibrosing lung disease that culminates in the destruction of alveolar integrity and dismal prognosis. Its etiology is unknown and pathophysiology remains unclear. While great advances have been made in elucidating the pathogenesis mechanism, considerable gaps related to information on pathogenetic pathways and key protein targets involved in the clinical course of the disease exist. These issues need to be addressed for better clinical management of this highly challenging disease. Omics approach has revolutionized the entire area of disease understanding and holds promise in its translation to clinical biomarker discovery. This review outlines the contribution of proteomics towards identification of important biomarkers in IPF in terms of their clinical utility, i.e. prognosis, differential diagnosis, disease progression and treatment monitoring. The major dysregulated pathways associated with IPF are also discussed. Based on numerous proteomics studies on human and animal models, it is proposed that IPF pathogenesis involves complex interactions of several pathways such as oxidative stress, endoplasmic reticulum stress, unfolded protein response, coagulation system, inflammation, abnormal wounding, fibroblast proliferation, fibrogenesis and deposition of extracellular matrix. These pathways and their key path-changing mediators need further validation in large well-planned multi-centric trials at various geographical locations for successful development of clinical biomarkers of this confounding disease.
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Affiliation(s)
- Tila Khan
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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9
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Garay-Baquero DJ, White CH, Walker NF, Tebruegge M, Schiff HF, Ugarte-Gil C, Morris-Jones S, Marshall BG, Manousopoulou A, Adamson J, Vallejo AF, Bielecka MK, Wilkinson RJ, Tezera LB, Woelk CH, Garbis SD, Elkington P. Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis. JCI Insight 2020; 5:137427. [PMID: 32780727 PMCID: PMC7526553 DOI: 10.1172/jci.insight.137427] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDTuberculosis (TB) kills more people than any other infection, and new diagnostic tests to identify active cases are required. We aimed to discover and verify novel markers for TB in nondepleted plasma.METHODSWe applied an optimized quantitative proteomics discovery methodology based on multidimensional and orthogonal liquid chromatographic separation combined with high-resolution mass spectrometry to study nondepleted plasma of 11 patients with active TB compared with 10 healthy controls. Prioritized candidates were verified in independent UK (n = 118) and South African cohorts (n = 203).RESULTSWe generated the most comprehensive TB plasma proteome to date, profiling 5022 proteins spanning 11 orders-of-magnitude concentration range with diverse biochemical and molecular properties. We analyzed the predominantly low-molecular weight subproteome, identifying 46 proteins with significantly increased and 90 with decreased abundance (peptide FDR ≤ 1%, q ≤ 0.05). Verification was performed for novel candidate biomarkers (CFHR5, ILF2) in 2 independent cohorts. Receiver operating characteristics analyses using a 5-protein panel (CFHR5, LRG1, CRP, LBP, and SAA1) exhibited discriminatory power in distinguishing TB from other respiratory diseases (AUC = 0.81).CONCLUSIONWe report the most comprehensive TB plasma proteome to date, identifying novel markers with verification in 2 independent cohorts, leading to a 5-protein biosignature with potential to improve TB diagnosis. With further development, these biomarkers have potential as a diagnostic triage test.FUNDINGColciencias, Medical Research Council, Innovate UK, NIHR, Academy of Medical Sciences, Program for Advanced Research Capacities for AIDS, Wellcome Centre for Infectious Diseases Research.
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Affiliation(s)
- Diana J Garay-Baquero
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA
| | - Cory H White
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Naomi F Walker
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Tebruegge
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom.,Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Hannah F Schiff
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Cesar Ugarte-Gil
- TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Instituto de Medicina Tropical Alexander von Humboldt, School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stephen Morris-Jones
- Department of Microbiology, University College London Hospitals NHS Trust, London, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben G Marshall
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
| | | | - John Adamson
- Pharmacology Core, Africa Health Research Institute (AHRI), Durban, South Africa
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | | | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Liku B Tezera
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Spiros D Garbis
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA.,Cancer Sciences Division, Faculty of Medicine, University of Southampton, United Kingdom
| | - Paul Elkington
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
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10
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Garcia-Rosa S, Carvalho BS, Guest PC, Steiner J, Martins-de-Souza D. Blood plasma proteomic modulation induced by olanzapine and risperidone in schizophrenia patients. J Proteomics 2020; 224:103813. [DOI: 10.1016/j.jprot.2020.103813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/27/2020] [Accepted: 05/05/2020] [Indexed: 12/29/2022]
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11
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Cao TH, Jones DJ, Voors AA, Quinn PA, Sandhu JK, Chan DC, Parry HM, Mohan M, Mordi IR, Sama IE, Anker SD, Cleland JG, Dickstein K, Filippatos G, Hillege HL, Metra M, Ponikowski P, Samani NJ, Van Veldhuisen DJ, Zannad F, Lang CC, Ng LL. Plasma proteomic approach in patients with heart failure: insights into pathogenesis of disease progression and potential novel treatment targets. Eur J Heart Fail 2020; 22:70-80. [PMID: 31692186 PMCID: PMC7028019 DOI: 10.1002/ejhf.1608] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
AIMS To provide insights into pathogenesis of disease progression and potential novel treatment targets for patients with heart failure by investigation of the plasma proteome using network analysis. METHODS AND RESULTS The plasma proteome of 50 patients with heart failure who died or were rehospitalised were compared with 50 patients with heart failure, matched for age and sex, who did not have an event. Peptides were analysed on two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D LC ESI-MS/MS) in high definition mode (HDMSE). We identified and quantified 3001 proteins, of which 51 were significantly up-regulated and 46 down-regulated with more than two-fold expression changes in those who experienced death or rehospitalisation. Gene ontology enrichment analysis and protein-protein interaction networks of significant differentially expressed proteins discovered the central role of metabolic processes in clinical outcomes of patients with heart failure. The findings revealed that a cluster of proteins related to glutathione metabolism, arginine and proline metabolism, and pyruvate metabolism in the pathogenesis of poor outcome in patients with heart failure who died or were rehospitalised. CONCLUSIONS Our findings show that in patients with heart failure who died or were rehospitalised, the glutathione, arginine and proline, and pyruvate pathways were activated. These pathways might be potential targets for therapies to improve poor outcomes in patients with heart failure.
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Affiliation(s)
- Thong H. Cao
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
| | - Donald J.L. Jones
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
- Leicester Cancer Research Centre, Leicester Royal InfirmaryUniversity of LeicesterLeicesterUK
| | - Adriaan A. Voors
- Department of CardiologyUniversity of GroningenGroningenThe Netherlands
| | - Paulene A. Quinn
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
| | - Jatinderpal K. Sandhu
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
| | - Daniel C.S. Chan
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
| | - Helen M. Parry
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | - Mohapradeep Mohan
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | - Ify R. Mordi
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | - Iziah E. Sama
- Department of CardiologyUniversity of GroningenGroningenThe Netherlands
| | - Stefan D. Anker
- Division of Cardiology and Metabolism; Department of Cardiology (CVK)Center for Regenerative Therapies (BCRT); German Centre for Cardiovascular Research (DZHK) partner site Berlin; Charité Universitätsmedizin BerlinBerlinGermany
| | - John G. Cleland
- Robertson Centre for BiostatisticsInstitute of Health and Wellbeing, University of Glasgow, Glasgow Royal InfirmaryGlasgowUK
| | | | - Gerasimos Filippatos
- Department of Cardiology, Heart Failure Unit, Athens University Hospital Attikon, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Hans L. Hillege
- Department of CardiologyUniversity of GroningenGroningenThe Netherlands
| | - Marco Metra
- Institute of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences and Public HealthUniversity of BresciaBresciaItaly
| | - Piotr Ponikowski
- Department of Heart DiseasesWroclaw Medical University and Cardiology Department, Military HospitalWroclawPoland
| | - Nilesh J. Samani
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
| | | | - Faiez Zannad
- Inserm CIC 1433Université de LorraineNancyFrance
| | - Chim C. Lang
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical SchoolUniversity of DundeeDundeeUK
| | - Leong L. Ng
- Department of Cardiovascular SciencesUniversity of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUK
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12
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Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. J Proteome Res 2019; 18:4085-4097. [PMID: 31573204 DOI: 10.1021/acs.jproteome.9b00503] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.
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Affiliation(s)
- Vera Ignjatovic
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia.,Department of Paediatrics , The University of Melbourne , Parkville , VIC 3052 , Australia
| | - Philipp E Geyer
- NNF Center for Protein Research, Faculty of Health Sciences , University of Copenhagen , 2200 Copenhagen , Denmark.,Department of Proteomics and Signal Transduction , Max Planck Institute of Biochemistry , 82152 Martinsried , Germany
| | - Krishnan K Palaniappan
- Freenome , 259 East Grand Avenue , South San Francisco , California 94080 , United States
| | - Jessica E Chaaban
- Haematology Research , Murdoch Children's Research Institute , Parkville , VIC 3052 , Australia
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Human Genetics, and Internal Medicine and School of Public Health , University of Michigan , 100 Washtenaw Avenue , Ann Arbor , Michigan 48109-2218 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , 75 Talavera Road , North Ryde , NSW 2109 , Australia
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab , KTH Royal Institute of Technology , 171 65 Stockholm , Sweden
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13
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Mass Spectrometry-Based Biomarkers in Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:435-449. [PMID: 31347063 DOI: 10.1007/978-3-030-15950-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increases the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
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14
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Pietrowska M, Wlosowicz A, Gawin M, Widlak P. MS-Based Proteomic Analysis of Serum and Plasma: Problem of High Abundant Components and Lights and Shadows of Albumin Removal. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:57-76. [PMID: 31236839 DOI: 10.1007/978-3-030-12298-0_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Blood serum or plasma proteome is a gold mine of disease biomarkers. However, complexity and a huge dynamic range of their components, combined with multiple mechanisms of degradation and posttranslational modifications, further complicated by the presence of lipids, salts, and other metabolites, represent a real challenge for analytical sensitivity, resolution, and reproducibility. This problem exists particularly in the case of potential disease-specific markers, most typically represented by low-abundant proteins (LAPs), whose detection is usually impaired by the dominance of albumins, immunoglobulins, and other high-abundant serum/plasma proteins (HAPs). Hence, analysis of biomarker candidates in serum/plasma samples frequently requires separation of their components, usually including depletion of albumin in a fraction of interest. Such "preprocessing" of serum/plasma specimens is critical in proteomic analysis based on mass spectrometry. This approach is very potent; nevertheless a wide range of protein concentrations in serum/plasma represents a particular challenge, since high-abundant proteins (mostly albumin) dominate in a sample subjected to mass spectrometry and suppress peptide ions originating from low-abundant proteins, thus limiting probability and reliability of their detection. An emerging approach in serum-/plasma-based biomarker-oriented studies is the proteome component of exosomes - nanovesicles secreted by cells and involved in multiple aspects of intercellular communication. However, the presence of albumin, frequent contaminant of exosomes isolated from human serum/plasma, represents a real challenge also in this type of study. A similar problem is encountered in proteomic studies based on exosomes obtained in in vitro experiments where culture media are normally supplemented with fetal bovine serum containing growth factors and hormones. In this case exosomes are frequently contaminated with bovine serum albumin and other bovine serum proteins which should be removed before proteomic analysis of exosome cargo.
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Affiliation(s)
- Monika Pietrowska
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Agata Wlosowicz
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Marta Gawin
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland.
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15
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Abundant plasma protein depletion using ammonium sulfate precipitation and Protein A affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1089:43-59. [PMID: 29758408 DOI: 10.1016/j.jchromb.2018.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/10/2018] [Accepted: 04/26/2018] [Indexed: 11/23/2022]
Abstract
Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protein concentrations, a tandem depletion technique consisting of ammonium sulfate precipitation and Protein A affinity chromatography was developed. Using this method, 50% of albumin, together with other high abundant proteins such as alpha-1-antitrypsin, was depleted from the plasma sample at 20% to 40% ammonium sulfate saturation levels. In combination with immunoglobulin removal using a Protein A column, this technique delivered up to 40 new low- to medium abundance protein identifications when performing a shotgun mass spectrometry analysis. Compared to non-depleted plasma, 270 additional protein spots were observed during 2D-PAGE analysis. These results illustrate that this tandem depletion method is equivalent to commercial kits which are based on immune-affinity chromatography. Moreover, this method using Protein A immunoglobulin depletion was shown to be highly reproducible and a minimal amount of non-target proteins was depleted. The combination of ammonium sulfate precipitation and Protein A affinity chromatography offers a low cost, efficient, straightforward and reproducible alternative to commercial kits, with proteins remaining in native conformation, allowing protein activity and protein interaction studies.
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16
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Henry M, Meleady P. Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems. Methods Mol Biol 2017; 1485:375-388. [PMID: 27730564 DOI: 10.1007/978-1-4939-6412-3_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin based depletion column followed by either protein In-gel enzymatic digestion or protein in-solution enzymatic digestion and then analysis by one-dimensional reverse-phase chromatography or two-dimensional strong cation exchange (SCX)-reverse-phase chromatography (RPC).
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Affiliation(s)
- Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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17
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Limonier F, Van Steendam K, Waeterloos G, Brusselmans K, Sneyers M, Deforce D. An application of mass spectrometry for quality control of biologicals: Highly sensitive profiling of plasma residuals in human plasma-derived immunoglobulin. J Proteomics 2017; 152:312-320. [DOI: 10.1016/j.jprot.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 01/02/2023]
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18
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Wölter M, Röwer C, Koy C, Rath W, Pecks U, Glocker M. Proteoform profiling of peripheral blood serum proteins from pregnant women provides a molecular IUGR signature. J Proteomics 2016; 149:44-52. [DOI: 10.1016/j.jprot.2016.04.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/23/2016] [Accepted: 04/20/2016] [Indexed: 12/15/2022]
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19
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Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry. Anal Chim Acta 2015; 904:65-75. [PMID: 26724764 DOI: 10.1016/j.aca.2015.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
Human plasma is a readily available clinical sample that reflects the status of the body in normal physiological and disease states. Although the wide dynamic range and immense complexity of plasma proteins are obstacles, comprehensive proteomic analysis of human plasma is necessary for biomarker discovery and further verification. Various methods such as immunodepletion, protein equalization and hyper fractionation have been applied to reduce the influence of high-abundance proteins (HAPs) and to reduce the high level of complexity. However, the depth at which the human plasma proteome has been explored in a relatively short time frame has been limited, which impedes the transfer of proteomic techniques to clinical research. Development of an optimal strategy is expected to improve the efficiency of human plasma proteome profiling. Here, five three-dimensional strategies combining HAP depletion (the 1st dimension) and protein fractionation (the 2nd dimension), followed by LC-MS/MS analysis (the 3rd dimension) were developed and compared for human plasma proteome profiling. Pros and cons of the five strategies are discussed for two issues: HAP depletion and complexity reduction. Strategies A and B used proteome equalization and tandem Seppro IgY14 immunodepletion, respectively, as the first dimension. Proteome equalization (strategy A) was biased toward the enrichment of basic and low-molecular weight proteins and had limited ability to enrich low-abundance proteins. By tandem removal of HAPs (strategy B), the efficiency of HAP depletion was significantly increased, whereas more off-target proteins were subtracted simultaneously. In the comparison of complexity reduction, strategy D involved a deglycosylation step before high-pH RPLC separation. However, the increase in sequence coverage did not increase the protein number as expected. Strategy E introduced SDS-PAGE separation of proteins, and the results showed oversampling of HAPs and identification of fewer proteins. Strategy C combined single Seppro IgY14 immunodepletion, high-pH RPLC fractionation and LC-MS/MS analysis. It generated the largest dataset, containing 1544 plasma protein groups and 258 newly identified proteins in a 30-h-machine-time analysis, making it the optimum three-dimensional strategy in our study. Further analysis of the integrated data from the five strategies showed identical distribution patterns in terms of sequence features and GO functional analysis with the 1929-plasma-protein dataset, further supporting the reliability of our plasma protein identifications. The characterization of 20 cytokines in the concentration range from sub-nanograms/milliliter to micrograms/milliliter demonstrated the sensitivity of the current strategies.
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20
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Rice SJ, Liu X, Miller B, Joshi M, Zhu J, Caruso C, Gilbert C, Toth J, Reed M, Rassaei N, Das A, Barochia A, El-Bayoumy K, Belani CP. Proteomic profiling of human plasma identifies apolipoprotein E as being associated with smoking and a marker for squamous metaplasia of the lung. Proteomics 2015; 15:3267-77. [DOI: 10.1002/pmic.201500029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/23/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Shawn J. Rice
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Xin Liu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Bruce Miller
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Monika Joshi
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Junjia Zhu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Carla Caruso
- Department of Pathology; Penn State College of Medicine; Hershey PA USA
| | - Chris Gilbert
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Jennifer Toth
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Michael Reed
- Penn State Heart and Vascular Institute and Cardiothoracic Surgery; Penn State College of Medicine; Hershey PA USA
| | - Negar Rassaei
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Arun Das
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Amit Barochia
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Chandra P. Belani
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
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21
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Norris L, Malkar A, Horner-Glister E, Hakimi A, Ng LL, Gescher AJ, Creaser C, Sale S, Jones DJL. Search for novel circulating cancer chemopreventive biomarkers of dietary rice bran intervention in ApcMin
mice model of colorectal carcinogenesis, using proteomic and metabolic profiling strategies. Mol Nutr Food Res 2015; 59:1827-36. [DOI: 10.1002/mnfr.201400818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Leonie Norris
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Aditya Malkar
- Centre for Analytical Science; Department of Chemistry; Loughborough University; Loughborough Leicestershire UK
| | - Emma Horner-Glister
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Amirmansoor Hakimi
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Leong L. Ng
- Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit; Glenfield Hospital; Leicester UK
| | - Andreas J. Gescher
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Colin Creaser
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Stewart Sale
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
| | - Donald J. L. Jones
- Department of Cancer Studies and Molecular Medicine; Leicester Royal Infirmary; University of Leicester; Leicester UK
- Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit; Glenfield Hospital; Leicester UK
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22
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Hassis ME, Niles RK, Braten MN, Albertolle ME, Ewa Witkowska H, Hubel CA, Fisher SJ, Williams KE. Evaluating the effects of preanalytical variables on the stability of the human plasma proteome. Anal Biochem 2015; 478:14-22. [PMID: 25769420 PMCID: PMC4492164 DOI: 10.1016/j.ab.2015.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/19/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
High quality clinical biospecimens are vital for biomarker discovery, verification, and validation. Variations in blood processing and handling can affect protein abundances and assay reliability. Using an untargeted LC-MS approach, we systematically measured the impact of preanalytical variables on the plasma proteome. Time prior to processing was the only variable that affected the plasma protein levels. LC-MS quantification showed that preprocessing times <6h had minimal effects on the immunodepleted plasma proteome, but by 4 days significant changes were apparent. Elevated levels of many proteins were observed, suggesting that in addition to proteolytic degradation during the preanalytical phase, changes in protein structure are also important considerations for protocols using antibody depletion. As to processing variables, a comparison of single- vs double-spun plasma showed minimal differences. After processing, the impact ⩽3 freeze-thaw cycles was negligible regardless of whether freshly collected samples were processed in short succession or the cycles occurred during 14-17 years of frozen storage (-80 °C). Thus, clinical workflows that necessitate modest delays in blood processing times or employ different centrifugation steps can yield valuable samples for biomarker discovery and verification studies.
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Affiliation(s)
- Maria E Hassis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard K Niles
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA
| | - Miles N Braten
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew E Albertolle
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Carl A Hubel
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Katherine E Williams
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143, USA; Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
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23
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Sok Hwee Cheow E, Hwan Sim K, de Kleijn D, Neng Lee C, Sorokin V, Sze SK. Simultaneous Enrichment of Plasma Soluble and Extracellular Vesicular Glycoproteins Using Prolonged Ultracentrifugation-Electrostatic Repulsion-hydrophilic Interaction Chromatography (PUC-ERLIC) Approach. Mol Cell Proteomics 2015; 14:1657-71. [PMID: 25862729 DOI: 10.1074/mcp.o114.046391] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 12/16/2022] Open
Abstract
Plasma glycoproteins and extracellular vesicles represent excellent sources of disease biomarkers, but laboratory detection of these circulating structures are limited by their relatively low abundance in complex biological fluids. Although intensive research has led to the development of effective methods for the enrichment and isolation of either plasma glycoproteins or extracellular vesicles from clinical materials, at present it is not possible to enrich both structures simultaneously from individual patient sample, a method that affords the identification of biomarker combinations from both entities for the prediction of clinical outcomes will be clinically useful. We have therefore developed an enrichment method for use in mass spectrometry-based proteomic profiling that couples prolonged ultracentrifugation with electrostatic repulsion-hydrophilic interaction chromatography, to facilitate the recovery of both glycoproteins and extracellular vesicles from nondepleted human plasma. Following prolonged ultracentrifugation, plasma glycoproteins and extracellular vesicles were concentrated as a yellow suspension, and simultaneous analyses of low abundant secretory and vesicular glycoproteins was achieved in a single LC-MS/MS run. Using this systematic prolonged ultracentrifugation-electrostatic repulsion-hydrophilic interaction chromatography approach, we identified a total of 127 plasma glycoproteins at a high level of confidence (FDR ≤ 1%), including 48 glycoproteins with concentrations ranging from pg to ng/ml. The novel enrichment method we report should facilitate future human plasma-based proteome and glycoproteome that will identify novel biomarkers, or combinations of secreted and vesicle-derived biomarkers, that can be used to predict clinical outcomes in human patients.
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Affiliation(s)
- Esther Sok Hwee Cheow
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Kae Hwan Sim
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Dominique de Kleijn
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ¶Experimental Cardiology Laboratory, Cardiology, University Medical Center Utrecht, the Netherlands & Interuniversity Cardiovascular Institute of the Netherlands, Utrecht, the Netherlands
| | - Chuen Neng Lee
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ‖National University Heart Centre, Department of Cardiac, Thoracic and Vascular Surgery, Singapore 119228; **Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Vitaly Sorokin
- §Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, and Cardiovascular Research Institute, Singapore 119228; ‖National University Heart Centre, Department of Cardiac, Thoracic and Vascular Surgery, Singapore 119228; **Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551;
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24
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Boschetti E, Righetti PG. Mixed-bed affinity chromatography: principles and methods. Methods Mol Biol 2015; 1286:131-158. [PMID: 25749952 DOI: 10.1007/978-1-4939-2447-9_12] [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: 06/04/2023]
Abstract
Mixed-bed chromatography is far from being a well-established technology within the panoply of bioseparation tools. Composed of an assembly of distinct sorbents that are mixed in a single bed, they have been mostly developed in the last decade for the reduction of dynamic concentration range where they allowed discovering many low-copy proteins within very complex proteomes. Other interesting preparative applications of mixed-bed chromatography have since been developed. In this chapter the basic concepts first and then detailed application recipes are described for (1) the reduction of protein dynamic concentration range, (2) the removal of impurity traces at the last stage of a biopurification process, and (3) the selection and use of sorbents as mixed bed in protein purification.
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Affiliation(s)
- Egisto Boschetti
- JAM-Conseil, 9-11 rue Boutard, 92200, Neuilly sur Seine, France,
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25
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Kim SW, Min CW, Gupta R, Jo IH, Bang KH, Kim YC, Kim KH, Kim ST. Proteomics Analysis of Early Salt-Responsive Proteins in Ginseng (Panax ginseng C. A. Meyer) Leaves. ACTA ACUST UNITED AC 2014. [DOI: 10.7783/kjmcs.2014.22.5.398] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Distler U, Kuharev J, Tenzer S. Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics. Expert Rev Proteomics 2014; 11:675-84. [DOI: 10.1586/14789450.2014.971114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics. Anal Chem 2014; 87:293-305. [DOI: 10.1021/ac502171b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
| | - Giovanni Candiano
- Laboratory on Pathophysiology of Uremia
and Department of Nephrology, Istituto Giannina Gaslini, Genova, Italy
| | - Attilio Citterio
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
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28
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Biomarkers in Alzheimer's disease analysis by mass spectrometry-based proteomics. Int J Mol Sci 2014; 15:7865-82. [PMID: 24806343 PMCID: PMC4057708 DOI: 10.3390/ijms15057865] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/03/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023] Open
Abstract
Alzheimer’s disease (AD) is a common chronic and destructive disease. The early diagnosis of AD is difficult, thus the need for clinically applicable biomarkers development is growing rapidly. There are many methods to biomarker discovery and identification. In this review, we aim to summarize Mass spectrometry (MS)-based proteomics studies on AD and discuss thoroughly the methods to identify candidate biomarkers in cerebrospinal fluid (CSF) and blood. This review will also discuss the potential research areas on biomarkers.
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29
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Mass spectrometry-based biomarkers in drug development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:341-59. [PMID: 24952191 DOI: 10.1007/978-3-319-06068-2_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance, and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement, and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increase the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
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