1
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Ramey-Ward AN, Walthall HP, Smith S, Barrows TH. Human keratin matrices promote wound healing by modulating skin cell expression of cytokines and growth factors. Wound Repair Regen 2024; 32:257-267. [PMID: 38111086 DOI: 10.1111/wrr.13137] [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: 06/30/2023] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
A wide variety of biomaterials has been developed to assist in wound healing, including acellular animal and human-derived protein matrices. However, millions of patients worldwide still suffer from non-healing chronic wounds, demonstrating a need for further innovation in wound care. To address this need, a novel biomaterial, the human keratin matrix (HKM), was developed, characterised, and tested in vitro and in vivo. HKM was found to be degradation-resistant, and a proteomics analysis showed it to be greater than 99% human keratin proteins. PCR revealed adult human epidermal keratinocytes (HEKa) grown in contact with HKM showed increased gene expression of keratinocyte activations markers such as Epidermal Growth Factor (EGF). Additionally, a cytokine microarray demonstrated culture on HKM increased the release of cytokines involved in wound inflammatory modulation by both HEKa cells and adult human dermal fibroblasts (HDFa). Finally, in a murine chronic wound model, full-thickness wounds treated weekly with HKM were smaller through the healing process than those treated with human amniotic membrane (AM), bovine dermis (BD), or porcine decellularized small intestinal submucosa (SIS). HKM-treated wounds also closed significantly faster than AM- and SIS-treated wounds. These data suggest that HKM is an effective novel treatment for chronic wounds.
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2
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Hernández ÁP, Iglesias-Anciones L, Vaquero-González JJ, Piñol R, Criado JJ, Rodriguez E, Juanes-Velasco P, García-Vaquero ML, Arias-Hidalgo C, Orfao A, Millán Á, Fuentes M. Enhancement of Tumor Cell Immunogenicity and Antitumor Properties Derived from Platinum-Conjugated Iron Nanoparticles. Cancers (Basel) 2023; 15:3204. [PMID: 37370813 DOI: 10.3390/cancers15123204] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
From chemistry design to clinical application, several approaches have been developed to overcome platinum drawbacks in antitumoral therapies. An in-depth understanding of intracellular signaling may hold the key to the relationship of both conventional drugs and nanoparticles. Within these strategies, first, nanotechnology has become an essential tool in oncotherapy, improving biopharmaceutical properties and providing new immunomodulatory profiles to conventional drugs mediated by activation of endoplasmic reticulum (ER) stress. Secondly, functional proteomics techniques based on microarrays have proven to be a successful method for high throughput screening of proteins and profiling of biomolecule mechanisms of action. Here, we conducted a systematic characterization of the antitumor profile of a platinum compound conjugated with iron oxide nanoparticles (IONPs). As a result of the nano-conjugation, cytotoxic and proteomics profiles revealed a significant improvement in the antitumor properties of the starting material, providing selectivity in certain tumor cell lines tested. Moreover, cell death patterns associated with immunogenic cell death (ICD) response have also been identified when ER signaling pathways have been triggered. The evaluation in several tumor cell lines and the analysis by functional proteomics techniques have shown novel perspectives on the design of new cisplatin-derived conjugates, the high value of IONPs as drug delivery systems and ICD as a rewarding approach for targeted oncotherapy and onco-immunotherapies.
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Affiliation(s)
- Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
- Department of Pharmaceutical Sciences, Organic Chemistry Section, Faculty of Pharmacy, University of Salamanca, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Laura Iglesias-Anciones
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - José Javier Vaquero-González
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Rafael Piñol
- Institute of Nanoscience and Materials of Aragon (INMA), CSIC-University of Zaragoza, 50009 Zaragoza, Spain
| | - Julio J Criado
- Department of Inorganic Chemistry, Faculty of Chemical Sciences, Plaza de los Caídos, s/n, 37008 Salamanca, Spain
| | - Emilio Rodriguez
- Department of Inorganic Chemistry, Faculty of Chemical Sciences, Plaza de los Caídos, s/n, 37008 Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Marina L García-Vaquero
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
| | - Ángel Millán
- Institute of Nanoscience and Materials of Aragon (INMA), CSIC-University of Zaragoza, 50009 Zaragoza, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno, s/n, 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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3
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Romano A, Rižner TL, Werner HMJ, Semczuk A, Lowy C, Schröder C, Griesbeck A, Adamski J, Fishman D, Tokarz J. Endometrial cancer diagnostic and prognostic algorithms based on proteomics, metabolomics, and clinical data: a systematic review. Front Oncol 2023; 13:1120178. [PMID: 37091170 PMCID: PMC10118013 DOI: 10.3389/fonc.2023.1120178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/09/2023] Open
Abstract
Endometrial cancer is the most common gynaecological malignancy in developed countries. Over 382,000 new cases were diagnosed worldwide in 2018, and its incidence and mortality are constantly rising due to longer life expectancy and life style factors including obesity. Two major improvements are needed in the management of patients with endometrial cancer, i.e., the development of non/minimally invasive tools for diagnostics and prognostics, which are currently missing. Diagnostic tools are needed to manage the increasing number of women at risk of developing the disease. Prognostic tools are necessary to stratify patients according to their risk of recurrence pre-preoperatively, to advise and plan the most appropriate treatment and avoid over/under-treatment. Biomarkers derived from proteomics and metabolomics, especially when derived from non/minimally-invasively collected body fluids, can serve to develop such prognostic and diagnostic tools, and the purpose of the present review is to explore the current research in this topic. We first provide a brief description of the technologies, the computational pipelines for data analyses and then we provide a systematic review of all published studies using proteomics and/or metabolomics for diagnostic and prognostic biomarker discovery in endometrial cancer. Finally, conclusions and recommendations for future studies are also given.
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Affiliation(s)
- Andrea Romano
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Tea Lanišnik Rižner
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Henrica Maria Johanna Werner
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Andrzej Semczuk
- Department of Gynaecology, Lublin Medical University, Lublin, Poland
| | | | | | | | - Jerzy Adamski
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dmytro Fishman
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Janina Tokarz
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
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4
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Barpanda A, Tuckley C, Ray A, Banerjee A, Duttagupta SP, Kantharia C, Srivastava S. A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer. Proteomics Clin Appl 2023; 17:e2200062. [PMID: 36408811 DOI: 10.1002/prca.202200062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer. EXPERIMENTAL DESIGN The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease. RESULTS The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.
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Affiliation(s)
- Abhilash Barpanda
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arka Ray
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Siddhartha P Duttagupta
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Chetan Kantharia
- Department of surgical gastroenterology at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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5
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Mowoe MO, Garnett S, Lennard K, Talbot J, Townsend P, Jonas E, Blackburn JM. Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data. BMC Bioinformatics 2022; 23:534. [PMID: 36494629 PMCID: PMC9733281 DOI: 10.1186/s12859-022-05095-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The central role of proteins in diseases has made them increasingly attractive as therapeutic targets and indicators of cellular processes. Protein microarrays are emerging as an important means of characterising protein activity. Their accurate downstream analysis to produce biologically significant conclusions is largely dependent on proper pre-processing of extracted signal intensities. However, existing computational tools are not specifically tailored to the nature of these data and lack unanimity. RESULTS Here, we present the single-channel Protein Microarray Analysis Pipeline, a tailored computational tool for analysis of single-channel protein microarrays enabling biomarker identification, implemented in R, and as an interactive web application. We compared four existing background correction and normalization methods as well as three array filtering techniques, applied to four real datasets with two microarray designs, extracted using two software programs. The normexp, cyclic loess, and array weighting methods were most effective for background correction, normalization, and filtering respectively. CONCLUSIONS Thus, here we provided a versatile and effective pre-processing and differential analysis workflow for single-channel protein microarray data in form of an R script and web application ( https://metaomics.uct.ac.za/shinyapps/Pro-MAP/ .) for those not well versed in the R programming language.
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Affiliation(s)
- Metoboroghene Oluwaseyi Mowoe
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Katherine Lennard
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jade Talbot
- grid.5379.80000000121662407Manchester Cancer Research Centre, Division of Cancer Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Townsend
- grid.5475.30000 0004 0407 4824Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey UK
| | - Eduard Jonas
- grid.7836.a0000 0004 1937 1151Surgical Gastroenterology Unit, Division of General Surgery, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Jonathan Michael Blackburn
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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6
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Juanes‐Velasco P, García‐Vaquero ML, Landeira‐Viñuela A, Lopez‐Campos JL, Marín C, Lecrevisse Q, Arias‐Hidalgo C, Montalvillo E, Góngora R, Hernández Á, Fuentes M. Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS-CoV-2 infection as model. Proteomics Clin Appl 2022; 16:e2100100. [PMID: 36168869 PMCID: PMC9537801 DOI: 10.1002/prca.202100100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE Acute phase reactants (APRs) play a critical role in inflammation. The difference in their physiological functions or the different dynamic ranges of these proteins in plasma makes it difficult to detect them simultaneously and to use several of these proteins as a tool in clinical practice. EXPERIMENTAL DESIGN A novel multiplex assay has been designed and optimized to carry out a high-throughput and simultaneous screening of APRs, allowing the detection of each of them at the same time and in their corresponding dynamic range. RESULTS Using Sars-CoV-2 infection as a model, it has been possible to profile different patterns of acute phase proteins that vary significantly between healthy and infected patients. In addition, severity profiles (acute respiratory distress syndrome and sepsis) have been established. CONCLUSIONS AND CLINICAL RELEVANCE Differential profiles in acute phase proteins can serve as a diagnostic and prognostic tool, among patient stratification. The design of this new platform for their simultaneous detection paves the way for them to be more extensive use in clinical practice.
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Affiliation(s)
- Pablo Juanes‐Velasco
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Marina L. García‐Vaquero
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Alicia Landeira‐Viñuela
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - José Luis Lopez‐Campos
- Unidad Médico‐Quirúrgica de Enfermedades Respiratorias. Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del Rocío/Universidad de SevillaSpain,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Carmen Marín
- Instituto de Biomedicina de Sevilla (IBiS)Hospital Universitario Virgen del RocíoSevillaSpain
| | - Quentin Lecrevisse
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Carlota Arias‐Hidalgo
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Enrique Montalvillo
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain
| | - Ángela‐Patricia Hernández
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain,Department of Pharmaceutical Sciences: Organic Chemistry; Faculty of PharmacyUniversity of Salamanca, CIETUS, IBSALSalamanca37007Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service‐Nucleus, CIBERONCCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)SalamancaSpain,Proteomics UnitCancer Research Centre (IBMCC/CSIC/USAL/IBSAL)Salamanca37007Spain
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7
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Kfoury-Beaumont N, Prakasam R, Pondugula S, Lagas JS, Matkovich S, Gontarz P, Yang L, Yano H, Kim AH, Rubin JB, Kroll KL. The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential. BMC Biol 2022; 20:124. [PMID: 35637482 PMCID: PMC9153095 DOI: 10.1186/s12915-022-01324-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders increase brain tumor risk, suggesting that normal brain development may have protective properties. Mutations in epigenetic regulators are common in pediatric brain tumors, highlighting a potentially central role for disrupted epigenetic regulation of normal brain development in tumorigenesis. For example, lysine 27 to methionine mutation (H3K27M) in the H3F3A gene occurs frequently in Diffuse Intrinsic Pontine Gliomas (DIPGs), the most aggressive pediatric glioma. As H3K27M mutation is necessary but insufficient to cause DIPGs, it is accompanied by additional mutations in tumors. However, how H3K27M alone increases vulnerability to DIPG tumorigenesis remains unclear. RESULTS Here, we used human embryonic stem cell models with this mutation, in the absence of other DIPG contributory mutations, to investigate how H3K27M alters cellular proliferation and differentiation. We found that H3K27M increased stem cell proliferation and stem cell properties. It interfered with differentiation, promoting anomalous mesodermal and ectodermal gene expression during both multi-lineage and germ layer-specific cell specification, and blocking normal differentiation into neuroectoderm. H3K27M mutant clones exhibited transcriptomic diversity relative to the more homogeneous wildtype population, suggesting reduced fidelity of gene regulation, with aberrant expression of genes involved in stem cell regulation, differentiation, and tumorigenesis. These phenomena were associated with global loss of H3K27me3 and concordant loss of DNA methylation at specific genes in H3K27M-expressing cells. CONCLUSIONS Together, these data suggest that H3K27M mutation disrupts normal differentiation, maintaining a partially differentiated state with elevated clonogenicity during early development. This disrupted response to early developmental cues could promote tissue properties that enable acquisition of additional mutations that cooperate with H3K27M mutation in genesis of DMG/DIPG. Therefore, this work demonstrates for the first time that H3K27M mutation confers vulnerability to gliomagenesis through persistent clonogenicity and aberrant differentiation and defines associated alterations of histone and DNA methylation.
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Affiliation(s)
- N. Kfoury-Beaumont
- Department of Neurosurgery, University of California in San Diego, La Jolla, CA USA
| | - R. Prakasam
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO USA
| | - S. Pondugula
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO USA
| | - J. S. Lagas
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO USA
| | - S. Matkovich
- Center for Cardiovascular Research, Department of Medicine, Washington University School of Medicine, St Louis, MO USA
| | - P. Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO USA
| | - L. Yang
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO USA
| | - H. Yano
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO USA
| | - A. H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO USA
- The Brain Tumor Center, Washington University School of Medicine, Siteman Cancer Center, St. Louis, MO USA
| | - J. B. Rubin
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO USA
- The Brain Tumor Center, Washington University School of Medicine, Siteman Cancer Center, St. Louis, MO USA
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO USA
| | - K. L. Kroll
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO USA
- The Brain Tumor Center, Washington University School of Medicine, Siteman Cancer Center, St. Louis, MO USA
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8
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Subramanian D, Natarajan J. Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data. Crit Rev Microbiol 2022; 49:391-413. [PMID: 35468027 DOI: 10.1080/1040841x.2022.2065905] [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: 11/03/2022]
Abstract
Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.
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Affiliation(s)
- Devika Subramanian
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
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9
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Juanes-Velasco P, Landeira-Viñuela A, García-Vaquero ML, Lecrevisse Q, Herrero R, Ferruelo A, Góngora R, Corrales F, Rivas JDL, Lorente JA, Hernández ÁP, Fuentes M. SARS-CoV-2 Infection Triggers Auto-Immune Response in ARDS. Front Immunol 2022; 13:732197. [PMID: 35154090 PMCID: PMC8831226 DOI: 10.3389/fimmu.2022.732197] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/06/2022] [Indexed: 12/15/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a severe pulmonary disease, which is one of the major complications in COVID-19 patients. Dysregulation of the immune system and imbalances in cytokine release and immune cell activation are involved in SARS-CoV-2 infection. Here, the inflammatory, antigen, and auto-immune profile of patients presenting COVID-19-associated severe ARDS has been analyzed using functional proteomics approaches. Both, innate and humoral responses have been characterized through acute-phase protein network and auto-antibody signature. Severity and sepsis by SARS-CoV-2 emerged to be correlated with auto-immune profiles of patients and define their clinical progression, which could provide novel perspectives in therapeutics development and biomarkers of COVID-19 patients. Humoral response in COVID-19 patients’ profile separates with significant differences patients with or without ARDS. Furthermore, we found that this profile can be correlated with COVID-19 severity and results more common in elderly patients.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina L García-Vaquero
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Quentin Lecrevisse
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Raquel Herrero
- Department of Critical Care Medicine, Hospital Universitario de Getafe, Madrid, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Investigación Carlos III, Madrid, Spain.,Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain
| | - Antonio Ferruelo
- Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,PROTEORED-ISCIII, Red Nacional de Laboratorios de Proteomica-ISCIII, Madrid, Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas & University of Salamanca, Salamanca, Spain
| | - Jose A Lorente
- Department of Critical Care Medicine, Hospital Universitario de Getafe, Madrid, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Investigación Carlos III, Madrid, Spain.,Fundación de Investigación Biomédica del Hospital Universitario de Getafe, Madrid, Spain.,Universidad Europea de Madrid, Madrid, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,PROTEORED-ISCIII, Red Nacional de Laboratorios de Proteomica-ISCIII, Madrid, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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10
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Bérubé S, Kobayashi T, Wesolowski A, Norris DE, Ruczinski I, Moss WJ, Louis TA. A pre-processing pipeline to quantify, visualize, and reduce technical variation in protein microarray studies. Proteomics 2021; 22:e2100033. [PMID: 34668656 DOI: 10.1002/pmic.202100033] [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: 02/05/2021] [Revised: 07/13/2021] [Accepted: 10/07/2021] [Indexed: 11/07/2022]
Abstract
Technical variation, or variation from non-biological sources, is present in most laboratory assays. Correcting for this variation enables analysts to extract a biological signal that informs questions of interest. However, each assay has different sources and levels of technical variation, and the choice of correction methods can impact downstream analyses. Compared to similar assays such as DNA microarrays, relatively few methods have been developed and evaluated for protein microarrays, a versatile tool for measuring levels of various proteins in serum samples. Here, we propose a pre-processing pipeline to correct for some common sources of technical variation in protein microarrays. The pipeline builds upon an existing normalization method by using controls to reduce technical variation. We evaluate our method using data from two protein microarray studies and by simulation. We demonstrate that pre-processing choices impact the fluorescent-intensity based ranks of proteins, which in turn, impact downstream analysis.
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Affiliation(s)
- Sophie Bérubé
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Douglas E Norris
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - William J Moss
- Department of Epidemiology, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA.,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Thomas A Louis
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
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11
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Usategui-Martín R, Puertas-Neyra K, García-Gutiérrez MT, Fuentes M, Pastor JC, Fernandez-Bueno I. Human Mesenchymal Stem Cell Secretome Exhibits a Neuroprotective Effect over In Vitro Retinal Photoreceptor Degeneration. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:1155-1166. [PMID: 32514411 PMCID: PMC7267685 DOI: 10.1016/j.omtm.2020.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Retinal photoreceptor degeneration occurs frequently in several neurodegenerative retinal diseases such as age-related macular degeneration, retinitis pigmentosa, or genetic retinal diseases related to the photoreceptors. Despite the impact on daily life and the social and economic consequences, there is no cure for these diseases. Considering this, cell-based therapy may be an optimal therapeutic option. This study evaluated the neuroprotective in vitro potential of a secretome of human bone marrow mesenchymal stem cells (MSCs) for retinal photoreceptors in vitro. We analyzed the photoreceptor morphologic changes and the paracrine factors secreted by human bone marrow MSCs in a physically separated co-culture with degenerated neuroretinas, using organotypic neuroretinal cultures. The results showed that the secretome of human bone marrow MSCs had a neuroprotective effect over the neuroretinal general organization and neuropreserved the photoreceptors from degeneration probably by secretion of neuroprotective proteins. The study of the expression of 1,000 proteins showed increased paracrine factors secreted by MSCs that could be crucial in the neuroprotective effect of the stem cell secretome over in vitro retinal degeneration. The current results reinforce the hypothesis that the paracrine effect of the human bone marrow MSCs may slow photoreceptor neurodegeneration and be a therapeutic option in retinal photoreceptor degenerative diseases.
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Affiliation(s)
- Ricardo Usategui-Martín
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Retina Group, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Kevin Puertas-Neyra
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Retina Group, Universidad de Valladolid, 47011 Valladolid, Spain
| | - María-Teresa García-Gutiérrez
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Retina Group, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Manuel Fuentes
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC), University of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain.,Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC), University of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - José Carlos Pastor
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Retina Group, Universidad de Valladolid, 47011 Valladolid, Spain.,Department of Ophthalmology, Hospital Clínico Universitario de Valladolid, 47003 Valladolid, Spain.,Centro en Red de Medicina Regenerativa y Terapia Celular de Castilla y León, 47011 Valladolid, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Oftared, Instituto de Salud Carlos III, 47011 Valladolid, Spain
| | - Ivan Fernandez-Bueno
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Retina Group, Universidad de Valladolid, 47011 Valladolid, Spain.,Centro en Red de Medicina Regenerativa y Terapia Celular de Castilla y León, 47011 Valladolid, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Oftared, Instituto de Salud Carlos III, 47011 Valladolid, Spain
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12
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Gallardo-Vara E, Ruiz-Llorente L, Casado-Vela J, Ruiz-Rodríguez MJ, López-Andrés N, Pattnaik AK, Quintanilla M, Bernabeu C. Endoglin Protein Interactome Profiling Identifies TRIM21 and Galectin-3 as New Binding Partners. Cells 2019; 8:cells8091082. [PMID: 31540324 PMCID: PMC6769930 DOI: 10.3390/cells8091082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/07/2019] [Accepted: 09/07/2019] [Indexed: 12/15/2022] Open
Abstract
Endoglin is a 180-kDa glycoprotein receptor primarily expressed by the vascular endothelium and involved in cardiovascular disease and cancer. Heterozygous mutations in the endoglin gene (ENG) cause hereditary hemorrhagic telangiectasia type 1, a vascular disease that presents with nasal and gastrointestinal bleeding, skin and mucosa telangiectases, and arteriovenous malformations in internal organs. A circulating form of endoglin (alias soluble endoglin, sEng), proteolytically released from the membrane-bound protein, has been observed in several inflammation-related pathological conditions and appears to contribute to endothelial dysfunction and cancer development through unknown mechanisms. Membrane-bound endoglin is an auxiliary component of the TGF-β receptor complex and the extracellular region of endoglin has been shown to interact with types I and II TGF-β receptors, as well as with BMP9 and BMP10 ligands, both members of the TGF-β family. To search for novel protein interactors, we screened a microarray containing over 9000 unique human proteins using recombinant sEng as bait. We find that sEng binds with high affinity, at least, to 22 new proteins. Among these, we validated the interaction of endoglin with galectin-3, a secreted member of the lectin family with capacity to bind membrane glycoproteins, and with tripartite motif-containing protein 21 (TRIM21), an E3 ubiquitin-protein ligase. Using human endothelial cells and Chinese hamster ovary cells, we showed that endoglin co-immunoprecipitates and co-localizes with galectin-3 or TRIM21. These results open new research avenues on endoglin function and regulation.
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Affiliation(s)
- Eunate Gallardo-Vara
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain; (E.G.-V.); (L.R.-L.)
| | - Lidia Ruiz-Llorente
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain; (E.G.-V.); (L.R.-L.)
| | - Juan Casado-Vela
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III and Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Leganés, 28911 Madrid, Spain;
| | | | - Natalia López-Andrés
- Cardiovascular Translational Research, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain;
| | - Asit K. Pattnaik
- School of Veterinary Medicine and Biomedical Sciences, and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Miguel Quintanilla
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC), and Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
- Correspondence: (M.Q.); (C.B.)
| | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain; (E.G.-V.); (L.R.-L.)
- Correspondence: (M.Q.); (C.B.)
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13
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A Systematic Analysis Workflow for High-Density Customized Protein Microarrays in Biomarker Screening. Methods Mol Biol 2019; 1871:107-122. [PMID: 30276735 DOI: 10.1007/978-1-4939-8814-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
High-density protein microarrays constitute a promising high-throughput platform for the characterization of protein expression patterns, biomarker discovery, and validation. Different types of protein microarrays have been described according to several features (such as content, format, and detection system) presenting advantages and disadvantages which are relevant for the specific application and purposes. Therefore, an experimental design is key for any screening based on protein microarrays assays; in fact, the data analysis strategy is directly related to the experimental design, type of protein microarray and consequently the final outcome, the data and results interpretation, is also directly linked. Here, it is proposed a systematic workflow for biomarker discovery based on tailor-made protein microarrays platforms which obtain comprehensively info for the functional protein characterization in high-throughput format.
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14
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Abstract
The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new, and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent progress in genomics and mass spectrometry have led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel-based, array-based, mass spectrometry-based, DNA-based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of protein antigens targeted by the immune system during disease.
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Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabel Baltat
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada.
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15
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Wang Z, Huang X, Cheng Z. Automatic Spot Identification Method for High Throughput Surface Plasmon Resonance Imaging Analysis. BIOSENSORS 2018; 8:E85. [PMID: 30217054 PMCID: PMC6163621 DOI: 10.3390/bios8030085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
An automatic spot identification method is developed for high throughput surface plasmon resonance imaging (SPRi) analysis. As a combination of video accessing, image enhancement, image processing and parallel processing techniques, the method can identify the spots in SPRi images of the microarray from SPRi video data. In demonstrations of the method, SPRi video data of different protein microarrays were processed by the method. Results show that our method can locate spots in the microarray accurately regardless of the microarray pattern, spot-background contrast, light nonuniformity and spotting defects, but also can provide address information of the spots.
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Affiliation(s)
- Zhiyou Wang
- School of Electronic and Communication, Changsha University, Changsha 410003, China.
| | - Xiaoqing Huang
- School of Electronic and Communication, Changsha University, Changsha 410003, China.
| | - Zhiqiang Cheng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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16
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Arévalo-Pinzón G, González-González M, Suárez CF, Curtidor H, Carabias-Sánchez J, Muro A, LaBaer J, Patarroyo MA, Fuentes M. Self-assembling functional programmable protein array for studying protein-protein interactions in malaria parasites. Malar J 2018; 17:270. [PMID: 30016987 PMCID: PMC6050706 DOI: 10.1186/s12936-018-2414-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
Background Plasmodium vivax is the most widespread malarial species, causing significant morbidity worldwide. Knowledge is limited regarding the molecular mechanism of invasion due to the lack of a continuous in vitro culture system for these species. Since protein–protein and host–cell interactions play an essential role in the microorganism’s invasion and replication, elucidating protein function during invasion is critical when developing more effective control methods. Nucleic acid programmable protein array (NAPPA) has thus become a suitable technology for studying protein–protein and host–protein interactions since producing proteins through the in vitro transcription/translation (IVTT) method overcomes most of the drawbacks encountered to date, such as heterologous protein production, stability and purification. Results Twenty P. vivax proteins on merozoite surface or in secretory organelles were selected and successfully cloned using gateway technology. Most constructs were displayed in the array expressed in situ, using the IVTT method. The Pv12 protein was used as bait for evaluating array functionality and co-expressed with P. vivax cDNA display in the array. It was found that Pv12 interacted with Pv41 (as previously described), as well as PvMSP142kDa, PvRBP1a, PvMSP8 and PvRAP1. Conclusions NAPPA is a high-performance technique enabling co-expression of bait and query in situ, thereby enabling interactions to be analysed rapidly and reproducibly. It offers a fresh alternative for studying protein–protein and ligand–receptor interactions regarding a parasite which is difficult to cultivate (i.e. P. vivax). Electronic supplementary material The online version of this article (10.1186/s12936-018-2414-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela Arévalo-Pinzón
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 # 26-20, Bogotá, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - María González-González
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.,Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Carlos Fernando Suárez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 # 26-20, Bogotá, Colombia.,Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A.), Calle 222 # 55-37, Bogotá, Colombia
| | - Hernando Curtidor
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 # 26-20, Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | | | - Antonio Muro
- Unidad de Investigación Enfermedades Infecciosas y Tropicales (e-INTRO), Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (IBSAL-CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Universitario Miguel de Unamuno s/n, 37007, Salamanca, Spain
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Manuel Alfonso Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 # 26-20, Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Manuel Fuentes
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain. .,Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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17
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León IE, Díez P, Baran EJ, Etcheverry SB, Fuentes M. Decoding the anticancer activity of VO-clioquinol compound: the mechanism of action and cell death pathways in human osteosarcoma cells. Metallomics 2018; 9:891-901. [PMID: 28581009 DOI: 10.1039/c7mt00068e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Vanadium compounds were studied in recent years by considering them as a representative of a new class of non-platinum metal anticancer drugs. However, a few challenges still remain in the discovery of new molecular targets of these new metallodrugs. Studies on cell signaling pathways related to vanadium compounds have scarcely been reported and so far this information is highly critical for identifying novel targets that play a key role in the antitumor actions of vanadium complexes. This research deals with the alterations in the intracellular signaling pathways promoted by an oxovanadium(iv) complex with the clioquinol (5-chloro-7-iodo-8-quinolinol), VO(CQ)2, on a human osteosarcoma cell line (MG-63). Herein are reported, for the first time, the antitumor properties of VO(CQ)2 and the relative abundance of 224 proteins (which are involved in most of the common intracellular pathways) to identify novel targets of the studied complex. Besides, full-length human recombinant AKT1 kinase was produced by using an IVTT system to evaluate the variation of relative tyrosin-phosphorylation levels caused by this compound. The results of the differential protein expression levels reveal several up-regulated proteins such as CASP3, CASP6, CASP7, CASP10, CASP11, Bcl-x, DAPK and down-regulated ones, such as PKB/AKT, DIABLO, among others. Moreover, cell signaling pathways involved in several altered pathways related to the PKC and AP2 family have been identified in both treatments (2.5 and 10 μM) suggesting the crucial antitumoral role of VO(CQ)2. Finally, it has been demonstrated that this compound (10 μM, 6 h) triggers a decrease of 2-fold in in situ AKT1 expression.
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Affiliation(s)
- Ignacio E León
- Chair of Patologic Biochemistry, Exact School Sciences, National University of La Plata, 47 y 115, 1900 La Plata, Argentina.
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18
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Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes 2018; 11:156. [PMID: 29482592 PMCID: PMC5828362 DOI: 10.1186/s13104-018-3266-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. Electronic supplementary material The online version of this article (10.1186/s13104-018-3266-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Da Gama Duarte
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Tumour Immunology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ryan W Goosen
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Peter J Lawry
- Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Blackburn Laboratory, N3.03, Wernher & Beit Building North, Institute of Infectious Disease & Molecular Medicine, UCT Faculty of Health Sciences, Observatory, Cape Town, 7925, South Africa
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19
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Jara-Acevedo R, Díez P, González-González M, Dégano RM, Ibarrola N, Góngora R, Orfao A, Fuentes M. Screening Phage-Display Antibody Libraries Using Protein Arrays. Methods Mol Biol 2018; 1701:365-380. [PMID: 29116516 DOI: 10.1007/978-1-4939-7447-4_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phage-display technology constitutes a powerful tool for the generation of specific antibodies against a predefined antigen. The main advantages of phage-display technology in comparison to conventional hybridoma-based techniques are: (1) rapid generation time and (2) antibody selection against an unlimited number of molecules (biological or not). However, the main bottleneck with phage-display technology is the validation strategies employed to confirm the greatest number of antibody fragments. The development of new high-throughput (HT) techniques has helped overcome this great limitation. Here, we describe a new method based on an array technology that allows the deposition of hundreds to thousands of phages by micro-contact on a unique nitrocellulose surface. This setup comes in combination with bioinformatic approaches that enables simultaneous affinity screening in a HT format of antibody-displaying phages.
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Affiliation(s)
- Ricardo Jara-Acevedo
- ImmunoStep SL. Edificio Centro de Investigación del Cáncer. Avda. Coimbra s/n, 37007, Salamanca, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rosa María Dégano
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain.
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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20
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León IE, Díez P, Etcheverry SB, Fuentes M. Deciphering the effect of an oxovanadium(iv) complex with the flavonoid chrysin (VOChrys) on intracellular cell signalling pathways in an osteosarcoma cell line. Metallomics 2017; 8:739-49. [PMID: 27175625 DOI: 10.1039/c6mt00045b] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vanadium complexes were studied during recent years and considered as a representative of a new class of non-platinum metal antitumor agents in combination with their low toxicity. However, a few challenges still remain in the discovery of new molecular targets for these novel metal-based drugs. The study of cell signaling pathways related to vanadium drugs, which is highly critical for identifying specific targets that play an important role in the antitumor activity of vanadium compounds, is scarce. This research deals with the alterations in intracellular signaling pathways promoted by an oxovanadium(iv) complex with the flavonoid chrysin [VO(chrysin)2EtOH]2 (VOChrys) in a human osteosarcoma cell line (MG-63). Herein we report for the first time the effect of [VO(chrysin)2EtOH]2 on the relative abundance of 224 proteins, which are involved in the most common intracellular pathways. Besides, full-length human recombinant (FAK and AKT1) kinases are produced using an in situ IVTT system and then we have evaluated the variation of relative tyrosine-phosphorylation levels caused by the [VO(chrysin)2EtOH]2 compound. The results of the differential protein expression levels reveal that several proteins such as PKB/AKT, PAK, DAPK, Cdk 4, 6 and 7, FADD, AP2, NAK, and JNK, among others, were altered. Moreover, cell signaling pathways related to the PTK2B, FAK, PKC families suggests an important role associated with the antitumor activity of [VO(chrysin)2EtOH]2 was demonstrated. Finally, the effect of this compound on in situ expressed FAK and AKT1 is validated by determining the phosphorylation level, which decreased in the former and increased in the latter.
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Affiliation(s)
- Ignacio E León
- Chair of Patologic Biochemistry, Exact School Sciences, National University of La Plata, 47 y 115, 1900 La Plata, Argentina. and Inorganic Chemistry Center (CEQUINOR, CONICET), Exact School Sciences, National University of La Plata, 47 y 115, 1900 La Plata, Argentina
| | - Paula Díez
- Cancer Research Center, University of Salamanca-CSIC, IBSAL, Department of Medicine, Servicio General de Citometría-Nucleus, Campus Miguel de Unamuno S/N, 37007 Salamanca, Spain and Proteomics Unit, Cancer Research Center, IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno S/N, 37007 Salamanca, Spain
| | - Susana B Etcheverry
- Chair of Patologic Biochemistry, Exact School Sciences, National University of La Plata, 47 y 115, 1900 La Plata, Argentina. and Inorganic Chemistry Center (CEQUINOR, CONICET), Exact School Sciences, National University of La Plata, 47 y 115, 1900 La Plata, Argentina
| | - Manuel Fuentes
- Cancer Research Center, University of Salamanca-CSIC, IBSAL, Department of Medicine, Servicio General de Citometría-Nucleus, Campus Miguel de Unamuno S/N, 37007 Salamanca, Spain and Proteomics Unit, Cancer Research Center, IBSAL, University of Salamanca-CSIC, Campus Miguel de Unamuno S/N, 37007 Salamanca, Spain
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Sierra-Sánchez Á, Garrido-Martín D, Lourido L, González-González M, Díez P, Ruiz-Romero C, Sjöber R, Droste C, De Las Rivas J, Nilsson P, Blanco F, Fuentes M. Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies. J Proteome Res 2017; 16:1890-1899. [DOI: 10.1021/acs.jproteome.6b00980] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Lucía Lourido
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
| | | | | | - Cristina Ruiz-Romero
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
| | - Ronald Sjöber
- Affinity
Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), SE-17165 Stockholm, Sweden
| | | | | | - Peter Nilsson
- Affinity
Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), SE-17165 Stockholm, Sweden
| | - Francisco Blanco
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
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Khalilpour A, Kilic T, Khalilpour S, Álvarez MM, Yazdi IK. Proteomic-based biomarker discovery for development of next generation diagnostics. Appl Microbiol Biotechnol 2016; 101:475-491. [PMID: 28013407 DOI: 10.1007/s00253-016-8029-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/09/2023]
Abstract
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers. This review covers a selection of widely used proteomic technologies for biomarker discovery. In addition, we describe the most commonly used approaches for diagnosis based on proteomic biomarkers and further discuss trends and critical challenges during development of cost-effective rapid diagnostic tests and microfluidic diagnostic systems based on proteomic biomarkers.
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Affiliation(s)
- Akbar Khalilpour
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA. .,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Tugba Kilic
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620, Izmir, Turkey.,Department of Biotechnology, Institute of Science, Ege University, 35100, Izmir, Turkey
| | - Saba Khalilpour
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Mario Moisés Álvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Iman K Yazdi
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02139, USA
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23
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Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases. INTERNATIONAL JOURNAL OF PROTEOMICS 2015; 2015:782798. [PMID: 26693351 PMCID: PMC4677025 DOI: 10.1155/2015/782798] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022]
Abstract
Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.
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Díez P, Jara-Acevedo R, González-González M, Casado-Vela J, Dasilva N, Lécrevisse Q, Bartolomé R, Claros JC, González A, López R, Orfao A, Fuentes M. High-throughgput phage-display screening in array format. Enzyme Microb Technol 2015; 79-80:34-41. [DOI: 10.1016/j.enzmictec.2015.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 06/26/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022]
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25
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Matei C, Tampa M, Caruntu C, Ion RM, Georgescu SR, Dumitrascu GR, Constantin C, Neagu M. Protein microarray for complex apoptosis monitoring of dysplastic oral keratinocytes in experimental photodynamic therapy. Biol Res 2015; 47:33. [PMID: 25204017 PMCID: PMC4125699 DOI: 10.1186/0717-6287-47-33] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Photodynamic therapy is an alternative treatment of muco-cutaneous tumors that uses a light source able to photoactivate a chemical compound that acts as a photosensitizer. The phthalocyanines append to a wide chemical class that encompasses a large range of compounds; out of them aluminium-substituted disulphonated phthalocyanine possesses a good photosensitizing potential. Results The destructive effects of PDT with aluminium-substituted disulphonated phthalocyanine are achieved by induction of apoptosis in tumoral cells as assessed by flow cytometry analysis. Using protein microarray we evaluate the possible molecular pathways by which photodynamic therapy activates apoptosis in dysplastic oral keratinocytes cells, leading to the tumoral cells destruction. Among assessed analytes, Bcl-2, P70S6K kinase, Raf-1 and Bad proteins represent the apoptosis related biomolecules that showed expression variations with the greatest amplitude. Conclusions Up to date, the intimate molecular apoptotic mechanisms activated by photodynamic therapy with this type of phthalocyanine in dysplastic human oral keratinocytes are not completely elucidated. With protein microarray as high-throughput proteomic approach a better understanding of the manner in which photodynamic therapy leads to tumoral cell destruction can be obtained, by depicting apoptotic molecules that can be potentially triggered in future anti-tumoral therapies.
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González-González M, Bartolome R, Jara-Acevedo R, Casado-Vela J, Dasilva N, Matarraz S, García J, Alcazar JA, Sayagues JM, Orfao A, Fuentes M. Evaluation of homo- and hetero-functionally activated glass surfaces for optimized antibody arrays. Anal Biochem 2014; 450:37-45. [PMID: 24440232 DOI: 10.1016/j.ab.2014.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/07/2014] [Indexed: 11/17/2022]
Abstract
Antibody arrays hold great promise for biomedical applications, but they are typically manufactured using chemically functionalized surfaces that still require optimization. Here, we describe novel hetero-functionally activated glass surfaces favoring oriented antibody binding for improved performance in protein microarray applications. Antibody arrays manufactured in our facility using the functionalization chemistries described here proved to be reproducible and stable and also showed good signal intensities. As a proof-of-principle of the glass surface functionalization protocols described in this article, we built antibody-based arrays functionalized with different chemistries that enabled the simultaneous detection of 71 human leukocyte membrane differentiation antigens commonly found in peripheral blood mononuclear cells. Such detection is specific and semi-quantitative and can be performed in a single assay under native conditions. In summary, the protocol described here, based on the use of antibody array technology, enabled the concurrent detection of a set of membrane proteins under native conditions in a specific, selective, and semi-quantitative manner and in a single assay.
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Affiliation(s)
- María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Raquel Bartolome
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | | | - Juan Casado-Vela
- Spanish National Research Council (CSIC)-Spanish National Biotechnology Centre (CNB), 28049 Madrid, Spain
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Jacinto García
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J A Alcazar
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J M Sayagues
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
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27
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Casado-Vela J, Fuentes M, Franco-Zorrilla JM. Screening of Protein–Protein and Protein–DNA Interactions Using Microarrays. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:231-81. [DOI: 10.1016/b978-0-12-800453-1.00008-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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