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Stern L, McGuire HM, Avdic S, Blyth E, Gottlieb D, Patrick E, Abendroth A, Slobedman B. Circulating cytokine and chemokine patterns associated with cytomegalovirus reactivation after stem cell transplantation. Clin Transl Immunology 2023; 12:e16815. [PMID: 38034080 PMCID: PMC10684332 DOI: 10.1002/cti2.1473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/31/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Objectives Human cytomegalovirus (HCMV) reactivation is the leading viral complication after allogeneic haematopoietic stem cell transplantation (allo-HSCT). Understanding of circulating cytokine/chemokine patterns which accompany HCMV reactivation and correlate with HCMV DNAemia magnitude is limited. We aimed to characterise plasma cytokine/chemokine profiles in 36 allo-HSCT patients (21 with HCMV reactivation and 15 without HCMV reactivation) at four time-points in the first 100-day post-transplant. Methods The concentrations of 31 cytokines/chemokines in plasma samples were analysed using a multiplex bead-based immunoassay. Cytokine/chemokine concentrations were compared in patients with high-level HCMV DNAemia, low-level HCMV DNAemia or no HCMV reactivation, and correlated with immune cell frequencies measured using mass cytometry. Results Increased plasma levels of T helper 1-type cytokines/chemokines (TNF, IL-18, IP-10, MIG) were detected in patients with HCMV reactivation at the peak of HCMV DNAemia, relative to non-reactivators. Stem cell factor (SCF) levels were significantly higher before the detection of HCMV reactivation in patients who went on to develop high-level HCMV DNAemia (810-52 740 copies/mL) vs. low-level HCMV DNAemia (< 250 copies/mL). High-level HCMV reactivators, but not low-level reactivators, developed an elevated inflammatory cytokine/chemokine profile (MIP-1α, MIP-1β, TNF, LT-α, IL-13, IL-9, SCF, HGF) at the peak of reactivation. Plasma cytokine concentrations displayed unique correlations with circulating immune cell frequencies in patients with HCMV reactivation. Conclusion This study identifies distinct circulating cytokine/chemokine signatures associated with the magnitude of HCMV DNAemia and the progression of HCMV reactivation after allo-HSCT, providing important insight into immune recovery patterns associated with HCMV reactivation and viral control.
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Affiliation(s)
- Lauren Stern
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
| | - Helen M McGuire
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
| | - Selmir Avdic
- Westmead Institute for Medical ResearchThe University of SydneySydneyNSWAustralia
| | - Emily Blyth
- Westmead Institute for Medical ResearchThe University of SydneySydneyNSWAustralia
- Blood Transplant and Cell Therapies Program, Department of HaematologyWestmead HospitalSydneyNSWAustralia
- Faculty of Medicine and Health, Sydney Medical SchoolThe University of SydneySydneyNSWAustralia
| | - David Gottlieb
- Westmead Institute for Medical ResearchThe University of SydneySydneyNSWAustralia
- Blood Transplant and Cell Therapies Program, Department of HaematologyWestmead HospitalSydneyNSWAustralia
- Faculty of Medicine and Health, Sydney Medical SchoolThe University of SydneySydneyNSWAustralia
| | - Ellis Patrick
- Westmead Institute for Medical ResearchThe University of SydneySydneyNSWAustralia
- School of Mathematics and StatisticsThe University of SydneySydneyNSWAustralia
| | - Allison Abendroth
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
| | - Barry Slobedman
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
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Bowser BL, Patterson KL, Robinson RA. Evaluating cPILOT Data toward Quality Control Implementation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1741-1752. [PMID: 37459602 DOI: 10.1021/jasms.3c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Multiplexing enables the monitoring of hundreds to thousands of proteins in quantitative proteomics analyses and increases sample throughput. In most mass-spectrometry-based proteomics workflows, multiplexing is achieved by labeling biological samples with heavy isotopes via precursor isotopic labeling or isobaric tagging. Enhanced multiplexing strategies, such as combined precursor isotopic labeling and isobaric tagging (cPILOT), combine multiple technologies to afford an even higher sample throughput. Critical to enhanced multiplexing analyses is ensuring that analytical performance is optimal and that missingness of sample channels is minimized. Automation of sample preparation steps and use of quality control (QC) metrics can be incorporated into multiplexing analyses and reduce the likelihood of missing information, thus maximizing the amount of usable quantitative data. Here, we implemented QC metrics previously developed in our laboratory to evaluate a 36-plex cPILOT experiment that encompassed 144 mouse samples of various tissue types, time points, genotypes, and biological replicates. The evaluation focuses on the use of a sample pool generated from all samples in the experiment to monitor the daily instrument performance and to provide a means for data normalization across sample batches. Our results show that tracking QC metrics enabled the quantification of ∼7000 proteins in each sample batch, of which ∼70% had minimal missing values across up to 36 sample channels. Implementation of QC metrics for future cPILOT studies as well as other enhanced multiplexing strategies will help yield high-quality data sets.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã As Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory & Alzheimer's Center, Nashville, Tennessee 37212, United States
- Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Nashville, Tennessee 37232, United States
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3
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Hu WT, Nayyar A, Kaluzova M. Charting the Next Road Map for CSF Biomarkers in Alzheimer's Disease and Related Dementias. Neurotherapeutics 2023; 20:955-974. [PMID: 37378862 PMCID: PMC10457281 DOI: 10.1007/s13311-023-01370-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 06/29/2023] Open
Abstract
Clinical prediction of underlying pathologic substrates in people with Alzheimer's disease (AD) dementia or related dementia syndromes (ADRD) has limited accuracy. Etiologic biomarkers - including cerebrospinal fluid (CSF) levels of AD proteins and cerebral amyloid PET imaging - have greatly modernized disease-modifying clinical trials in AD, but their integration into medical practice has been slow. Beyond core CSF AD biomarkers (including beta-amyloid 1-42, total tau, and tau phosphorylated at threonine 181), novel biomarkers have been interrogated in single- and multi-centered studies with uneven rigor. Here, we review early expectations for ideal AD/ADRD biomarkers, assess these goals' future applicability, and propose study designs and performance thresholds for meeting these ideals with a focus on CSF biomarkers. We further propose three new characteristics: equity (oversampling of diverse populations in the design and testing of biomarkers), access (reasonable availability to 80% of people at risk for disease, along with pre- and post-biomarker processes), and reliability (thorough evaluation of pre-analytical and analytical factors influencing measurements and performance). Finally, we urge biomarker scientists to balance the desire and evidence for a biomarker to reflect its namesake function, indulge data- as well as theory-driven associations, re-visit the subset of rigorously measured CSF biomarkers in large datasets (such as Alzheimer's disease neuroimaging initiative), and resist the temptation to favor ease over fail-safe in the development phase. This shift from discovery to application, and from suspended disbelief to cogent ingenuity, should allow the AD/ADRD biomarker field to live up to its billing during the next phase of neurodegenerative disease research.
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Affiliation(s)
- William T Hu
- Department of Neurology, Rutgers Biomedical and Health Sciences, Rutgers-Robert Wood Johnson Medical School, 125 Paterson Street, Suite 6200, New Brunswick, NJ, 08901, USA.
- Center for Innovation in Health and Aging Research, Institute for Health, Health Care Policy, and Aging Research, Rutgers Biomedical and Health Sciences, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA.
| | - Ashima Nayyar
- Department of Neurology, Rutgers Biomedical and Health Sciences, Rutgers-Robert Wood Johnson Medical School, 125 Paterson Street, Suite 6200, New Brunswick, NJ, 08901, USA
| | - Milota Kaluzova
- Department of Neurology, Rutgers Biomedical and Health Sciences, Rutgers-Robert Wood Johnson Medical School, 125 Paterson Street, Suite 6200, New Brunswick, NJ, 08901, USA
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4
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Sabirov D, Ogurcov S, Baichurina I, Blatt N, Rizvanov A, Mukhamedshina Y. Molecular diagnostics in neurotrauma: Are there reliable biomarkers and effective methods for their detection? Front Mol Biosci 2022; 9:1017916. [PMID: 36250009 PMCID: PMC9557129 DOI: 10.3389/fmolb.2022.1017916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 12/05/2022] Open
Abstract
To date, a large number of studies are being carried out in the field of neurotrauma, researchers not only establish the molecular mechanisms of the course of the disorders, but are also involved in the search for effective biomarkers for early prediction of the outcome and therapeutic intervention. Particular attention is paid to traumatic brain injury and spinal cord injury, due to the complex cascade of reactions in primary and secondary injury that affect pathophysiological processes and regenerative potential of the central nervous system. Despite a wide range of methods available methods to study biomarkers that correlate with the severity and degree of recovery in traumatic brain injury and spinal cord injury, development of reliable test systems for clinical use continues. In this review, we evaluate the results of recent studies looking for various molecules acting as biomarkers in the abovementioned neurotrauma. We also summarize the current knowledge of new methods for studying biological molecules, analyzing their sensitivity and limitations, as well as reproducibility of results. In this review, we also highlight the importance of developing reliable and reproducible protocols to identify diagnostic and prognostic biomolecules.
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Affiliation(s)
- Davran Sabirov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Sergei Ogurcov
- Neurosurgical Department No. 2, Republic Clinical Hospital, Kazan, Russia
| | - Irina Baichurina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- *Correspondence: Irina Baichurina,
| | - Nataliya Blatt
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yana Mukhamedshina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Department of Histology, Cytology, and Embryology, Kazan State Medical University, Kazan, Russia
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5
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Rappold BA. Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part II-Operations. Ann Lab Med 2022; 42:531-557. [PMID: 35470272 PMCID: PMC9057814 DOI: 10.3343/alm.2022.42.5.531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/08/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022] Open
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is increasingly utilized in clinical laboratories because it has advantages in terms of specificity and sensitivity over other analytical technologies. These advantages come with additional responsibilities and challenges given that many assays and platforms are not provided to laboratories as a single kit or device. The skills, staff, and assays used in LC-MS/MS are internally developed by the laboratory, with relatively few exceptions. Hence, a laboratory that deploys LC-MS/MS assays must be conscientious of the practices and procedures adopted to overcome the challenges associated with the technology. This review discusses the post-development landscape of LC-MS/MS assays, including validation, quality assurance, operations, and troubleshooting. The content knowledge of LC-MS/MS users is quite broad and deep and spans multiple scientific fields, including biology, clinical chemistry, chromatography, engineering, and MS. However, there are no formal academic programs or specific literature to train laboratory staff on the fundamentals of LC-MS/MS beyond the reports on method development. Therefore, depending on their experience level, some readers may be familiar with aspects of the laboratory practices described herein, while others may be not. This review endeavors to assemble aspects of LC-MS/MS operations in the clinical laboratory to provide a framework for the thoughtful development and execution of LC-MS/MS applications.
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Affiliation(s)
- Brian A Rappold
- Laboratory Corporation of America Holdings, Research Triangle Park, NC, USA
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6
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Thomas SN, French D, Jannetto PJ, Rappold BA, Clarke WA. Liquid chromatography–tandem mass spectrometry for clinical diagnostics. NATURE REVIEWS. METHODS PRIMERS 2022; 2:96. [PMCID: PMC9735147 DOI: 10.1038/s43586-022-00175-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 12/13/2022]
Abstract
Mass spectrometry is a powerful analytical tool used for the analysis of a wide range of substances and matrices; it is increasingly utilized for clinical applications in laboratory medicine. This Primer includes an overview of basic mass spectrometry concepts, focusing primarily on tandem mass spectrometry. We discuss experimental considerations and quality management, and provide an overview of some key applications in the clinic. Lastly, the Primer discusses significant challenges for implementation of mass spectrometry in clinical laboratories and provides an outlook of where there are emerging clinical applications for this technology. Tandem mass spectrometry is increasingly utilized for clinical applications in laboratory medicine. In this Primer, Thomas et al. discuss experimental considerations and quality management for implementing clinical tandem mass spectrometry in the clinic with an overview of some key applications.
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Affiliation(s)
- Stefani N. Thomas
- grid.17635.360000000419368657Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN USA
| | - Deborah French
- grid.266102.10000 0001 2297 6811Laboratory Medicine, University of California San Francisco, San Francisco, CA USA
| | - Paul J. Jannetto
- grid.66875.3a0000 0004 0459 167XDepartment of Pathology & Laboratory Medicine, Mayo Clinic, Rochester, MN USA
| | - Brian A. Rappold
- grid.419316.80000 0004 0550 1859Research and Development, Labcorp, Burlington, NC USA
| | - William A. Clarke
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Prohászka Z, Frazer-Abel A. Complement multiplex testing: Concept, promises and pitfalls. Mol Immunol 2021; 140:120-126. [PMID: 34688958 DOI: 10.1016/j.molimm.2021.10.006] [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: 05/22/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Complement is a complex system. This complexity becomes more obvious when looking at complement analysis in health and disease, where one presentation can require a number of measurements to understand the full role of this cascade in the disease. The current state of clinical testing requires multiple tests to cover the whole of the complement cascade. There is a clear potential for multiplex testing to help address this need for comprehensive analysis of the state of complement deficiency, activation or inhibition. Fortunately, there are a number of potential methods for multiplex analysis, each with advantages and disadvantages that need to be considered in light of the intricacy of the complement cascade and its interconnection to other systems. Despite the complexities of such methods several groups have started utilizing multiplex analysis for research and even for diagnostic testing. The potential methods, current successes, and the type of testing that needs to be streamlined are reviewed in this text.
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Affiliation(s)
- Zoltán Prohászka
- Department of Internal Medicine and Haematology, Semmelweis University, and Research Group for Immunology and Haematology, Semmelweis University- EötvösLoránd Research Network (Office for Supported Research Groups), Budapest, Hungary
| | - Ashley Frazer-Abel
- Exsera BioLabs, University of Colorado School of Medicine, Aurora, CO, USA.
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8
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Liu BM, Martins TB, Peterson LK, Hill HR. Clinical significance of measuring serum cytokine levels as inflammatory biomarkers in adult and pediatric COVID-19 cases: A review. Cytokine 2021; 142:155478. [PMID: 33667962 PMCID: PMC7901304 DOI: 10.1016/j.cyto.2021.155478] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/29/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a rapidly evolving infectious/inflammatory disorder which has turned into a global pandemic. With severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as its etiologic agent, severe COVID-19 cases usually develop uncontrolled inflammatory responses and cytokine storm-like syndromes. Measuring serum levels of pro-inflammatory cytokines (e.g., IL-6 and others) as inflammatory biomarkers may have several potential applications in the management of COVID-19, including risk assessment, monitoring of disease progression, determination of prognosis, selection of therapy and prediction of response to treatment. This is especially true for pediatric patients with COVID-19 associated Kawasaki-like disease and similar syndromes. In this report, we review the current knowledge of COVID-19 associated cytokines, their roles in host immune and inflammatory responses, the clinical significance and utility of cytokine immunoassays in adult and pediatric COVID-19 patients, as well as the challenges and pitfalls in implementation and interpretation of cytokine immunoassays. Given that cytokines are implicated in different immunological disorders and diseases, it is challenging to interpret the multiplex cytokine data for COVID-19 patients. Also, it should be taken into consideration that biological and technical variables may affect the commutability of cytokine immunoassays and enhance complexity of cytokine immunoassay interpretation. It is recommended that the same method, platform and laboratory should be used when monitoring differences in cytokine levels between groups of individuals or for the same individual over time. It may be important to correlate cytokine profiling data with the SARS-CoV-2 nucleic acid amplification testing and imaging observations to make an accurate interpretation of the inflammatory status and disease progression in COVID-19 patients.
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Affiliation(s)
- Benjamin M Liu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Thomas B Martins
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA; ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Lisa K Peterson
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA; ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Harry R Hill
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA; ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA; Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA; Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.
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9
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Gilboa T, Maley AM, Ogata AF, Wu C, Walt DR. Sequential Protein Capture in Multiplex Single Molecule Arrays: A Strategy for Eliminating Assay Cross-Reactivity. Adv Healthc Mater 2021; 10:e2001111. [PMID: 32893488 PMCID: PMC8238389 DOI: 10.1002/adhm.202001111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/12/2020] [Indexed: 12/31/2022]
Abstract
Measurements of multiple biomolecules within the same biological sample are important for many clinical applications to enable accurate disease diagnosis or classification. These disease-related biomarkers often exist at very low levels in biological fluids, necessitating ultrasensitive measurement methods. Single-molecule arrays (Simoa), a bead-based digital enzyme-linked immunosorbent assay, is the current state of the art for ultrasensitive protein detection and can detect sub-femtomolar protein concentrations, but its ability to achieve high-order multiplexing without cross-reactivity remains a challenge. Here, a sequential protein capture approach for multiplex Simoa assays is implemented to eliminate cross-reactivity between binding reagents by sequentially capturing each protein analyte and then incubating each capture bead with only its corresponding detection antibody. This strategy not only reduces cross-reactivity to background levels and significantly improves measurement accuracies, but also enables higher-order multiplexing. As a proof of concept, the sequential multiplex Simoa assay is used to measure five different cytokines in plasma samples from Coronavirus Disease 2019 (COVID-19) patients. The ultrasensitive sequential multiplex Simoa assays will enable the simultaneous measurements of multiple low-abundance analytes in a time- and cost-effective manner and will prove especially critical in many cases where sample volumes are limited.
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Affiliation(s)
- Tal Gilboa
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Adam M Maley
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Alana F Ogata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Connie Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
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Martins RS, Oliani AH, Oliani DV, de Oliveira JM. Continuous endometrial volumetric analysis for endometrial receptivity assessment on assisted reproductive technology cycles. BMC Pregnancy Childbirth 2020; 20:663. [PMID: 33143675 PMCID: PMC7640386 DOI: 10.1186/s12884-020-03372-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/28/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Human implantation is a complex process requiring synchrony between a healthy embryo and a functionally competent or receptive endometrium. In order to assess endometrial receptivity in Assisted Reproductive Technology (ART) cycles serial evaluation of endometrial volumetric analysis may have a predictive value on a positive outcome. METHODS Serial 3D transvaginal ultrasound performed in women on ART cycle to evaluate embryo implantation predictors. Prospective case control study of 169 subjects were assessed. Endometrial pattern, thickness, volume and adjusted endometrial volume (ratio between endometrial volume and uterine volume) was performed to all subjects on a continuous process from baseline, during controlled ovarian stimulation, trigger day with human chorionic gonadotropin hormone (hCG) and at embryo transfer day. RESULTS Demographics and ART procedures and scores, was similar between the two groups. Endometrial morphology also showed no difference between the two groups. Endometrial volume and adjusted endometrial volume was significantly higher in the positive group as soon as day 6 of ovarian controlled stimulation. CONCLUSIONS Serial 3D endometrial volume and adjusted endometrial volumes provides a predicting clinical tool enhancing elective embryo transfers in fresh ART cycle. Thus providing a non-invasive continuous technique for endometrial receptivity assessment that reflects endometrial changes during ART procedures.
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Affiliation(s)
- Renato Silva Martins
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503, Covilha, Portugal.
- Centro Investigação Ciências da Saúde - Faculdade Ciências da Saúde, Universidade da Beira Interior, Alameda Infante D, Henrique, 6200 506, Covilha, Portugal.
| | - António Helio Oliani
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503, Covilha, Portugal
| | - Denise Vaz Oliani
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503, Covilha, Portugal
| | - José Martinez de Oliveira
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503, Covilha, Portugal
- Centro Investigação Ciências da Saúde - Faculdade Ciências da Saúde, Universidade da Beira Interior, Alameda Infante D, Henrique, 6200 506, Covilha, Portugal
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11
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Silva Martins R, Helio Oliani A, Vaz Oliani D, Martinez de Oliveira J. Subendometrial resistence and pulsatility index assessment of endometrial receptivity in assisted reproductive technology cycles. Reprod Biol Endocrinol 2019; 17:62. [PMID: 31375113 PMCID: PMC6676512 DOI: 10.1186/s12958-019-0507-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 07/25/2019] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To evaluate Subendometrial and Uterine artery resistance and pulsatility index continuous analysis as a predictor of Endometrial receptivity in Assisted Reproductive Technology (ART) Cycles. DESIGN Serial 2D transvaginal coloured power doppler ultrasound performed in women on ART cycle to evaluate a pattern that better predicts implantation rates. One hundred sixty-nine subjects on a prospective case control study were assessed. Uterine artery and Subendometrial resistance and pulsatility index was performed to all subjects at baseline (prior to ovarian controlled stimulation), at day 6, 8 and 10 of controlled ovarian stimulation, at trigger day and at embryo transfer day. Also the ratio of fluxometric parameters between Subendometrial blood flow and uterine artery was measured. RESULTS No statistical difference was noted between two groups in terms of demographics and ART procedures and scores. Uterine artery resistance and pulsatility index showed statistical difference between the two groups (implantation versus non-implantation group). Also statistical significance was obtained between two groups in terms of Subendometrial vascularization. Ratio between Subendometrial and Uterine artery showed lower values of fluxometric parameters in all range for the Subendometrial territory. CONCLUSIONS Serial Subendometrial and Uterine artery fluxometry may be a useful tool for clinicians in predicting endometrial receptivity enhancing elective embryo transfers in the same ART cycle.
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Affiliation(s)
- R. Silva Martins
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503 Covilha, Portugal
- 0000 0001 2220 7094grid.7427.6Centro Investigação Ciências da Saúde – Faculdade Ciências da Saúde, Universidade da Beira Interior, Alameda Infante D, Henrique, 6200 506 Covilha, Portugal
| | - A. Helio Oliani
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503 Covilha, Portugal
| | - D. Vaz Oliani
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503 Covilha, Portugal
| | - J. Martinez de Oliveira
- Centro Hospitalar Universitário Cova da Beira EPE, Quinta do Alvito, 6200 503 Covilha, Portugal
- 0000 0001 2220 7094grid.7427.6Centro Investigação Ciências da Saúde – Faculdade Ciências da Saúde, Universidade da Beira Interior, Alameda Infante D, Henrique, 6200 506 Covilha, Portugal
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12
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Grawe RW, Knotts TA. The effects of tether placement on antibody stability on surfaces. J Chem Phys 2018; 146:215102. [PMID: 28576081 DOI: 10.1063/1.4983705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.
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Affiliation(s)
- Rebecca W Grawe
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
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Erkens T, Goeminne N, Kegels A, Byloos M, Vinken P. Analytical performance of a commercial multiplex Luminex-based cytokine panel in the rat. J Pharmacol Toxicol Methods 2018; 91:43-49. [PMID: 29371052 DOI: 10.1016/j.vascn.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 11/20/2017] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Multiplex immunoassays are an important tool in biomarker research during preclinical drug development. However, information regarding analytical performance of commercial multiplex assays for animal species is often limited. To be able to correctly interpret study results, a fit-for-purpose validation approach is recommended. The objective of our study was to provide a realistic example of what level of validation can be expected from this type of assay, using a rat cytokine panel. METHODS The analytical performance of a commercial Luminex-based multiplex assay comprising IFN-γ, IL-6, IL-10, IL-12p70, IP-10 and TNF-α was evaluated in Sprague-Dawley rat plasma and serum. Calibration curve, working range, precision, accuracy, selectivity, parallelism, dilutional linearity, prozone effect and sample stability were assessed. RESULTS Analytical performance in plasma and serum was comparable. Precision and accuracy results for all analytes were acceptable with coefficient of variation (CV) and relative error (RE) often below 15%, except for serum IL-6. Selectivity results varied per analyte with several cytokines showing CV>30% and no single minimum required dilution (MRD) could be identified. In addition, some striking differences between recombinant and endogenous protein results were observed. A pronounced prozone effect was detected for IP-10. Analytes in samples stored at -70°C were stable (RE<30%) from 1 up to 6months depending on the analyte. DISCUSSION The results illustrate the challenges encountered during validation of commercial animal Luminex-based multiplex assays, revealing analytical limitations such as matrix and prozone effects. The Milliplex rat cytokine panel under investigation was deemed suitable for relative quantification of exploratory type biomarkers.
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Affiliation(s)
- Tim Erkens
- Mechanistic and Investigative Toxicology, Preclinical Development & Safety, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, Belgium.
| | - Nick Goeminne
- Mechanistic and Investigative Toxicology, Preclinical Development & Safety, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, Belgium
| | - Ann Kegels
- Mechanistic and Investigative Toxicology, Preclinical Development & Safety, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, Belgium
| | - Martine Byloos
- Mechanistic and Investigative Toxicology, Preclinical Development & Safety, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, Belgium
| | - Petra Vinken
- Mechanistic and Investigative Toxicology, Preclinical Development & Safety, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, Belgium
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Vasquez MM, Hu C, Roe DJ, Halonen M, Guerra S. Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available. Stat Methods Med Res 2017; 28:670-680. [PMID: 29166842 DOI: 10.1177/0962280217734241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Measurement of serum biomarkers by multiplex assays may be more variable as compared to single biomarker assays. Measurement error in these data may bias parameter estimates in regression analysis, which could mask true associations of serum biomarkers with an outcome. The Least Absolute Shrinkage and Selection Operator (LASSO) can be used for variable selection in these high-dimensional data. Furthermore, when the distribution of measurement error is assumed to be known or estimated with replication data, a simple measurement error correction method can be applied to the LASSO method. However, in practice the distribution of the measurement error is unknown and is expensive to estimate through replication both in monetary cost and need for greater amount of sample which is often limited in quantity. We adapt an existing bias correction approach by estimating the measurement error using validation data in which a subset of serum biomarkers are re-measured on a random subset of the study sample. We evaluate this method using simulated data and data from the Tucson Epidemiological Study of Airway Obstructive Disease (TESAOD). We show that the bias in parameter estimation is reduced and variable selection is improved.
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Affiliation(s)
- Monica M Vasquez
- 1 Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA.,2 Asthma and Airway Disease Research Center, The University of Arizona, Tucson, AZ, USA
| | - Chengcheng Hu
- 1 Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA
| | - Denise J Roe
- 1 Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA
| | - Marilyn Halonen
- 2 Asthma and Airway Disease Research Center, The University of Arizona, Tucson, AZ, USA
| | - Stefano Guerra
- 2 Asthma and Airway Disease Research Center, The University of Arizona, Tucson, AZ, USA.,3 ISGlobal, CREAL, Barcelona, Spain
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15
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Aygun U, Avci O, Seymour E, Urey H, Ünlü MS, Ozkumur AY. Label-Free and High-Throughput Detection of Biomolecular Interactions Using a Flatbed Scanner Biosensor. ACS Sens 2017; 2:1424-1429. [PMID: 28929734 DOI: 10.1021/acssensors.7b00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence based microarray detection systems provide sensitive measurements; however, variation of probe immobilization and poor repeatability negatively affect the final readout, and thus quantification capability of these systems. Here, we demonstrate a label-free and high-throughput optical biosensor that can be utilized for calibration of fluorescence microarrays. The sensor employs a commercial flatbed scanner, and we demonstrate transformation of this low cost (∼100 USD) system into an Interferometric Reflectance Imaging Sensor through hardware and software modifications. Using this sensor, we report detection of DNA hybridization and DNA directed antibody immobilization on label-free microarrays with a noise floor of ∼30 pg/mm2, and a scan speed of 5 s (50 s for 10 frames averaged) for a 2 mm × 2 mm area. This novel system may be used as a standalone label-free sensor especially in low-resource settings, as well as for quality control and calibration of microarrays in existing fluorescence-based DNA and protein detection platforms.
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Affiliation(s)
- Ugur Aygun
- Electrical
and Electronics Engineering Department, Koç University, 34450, Sariyer, Istanbul, Turkey
| | | | - Elif Seymour
- Biotechnology
Research Program Department, ASELSAN Research Center, Ankara, 06370, Turkey
| | - Hakan Urey
- Electrical
and Electronics Engineering Department, Koç University, 34450, Sariyer, Istanbul, Turkey
| | | | - Ayca Yalcin Ozkumur
- Department
of Electrical and Electronics Engineering, Bahcesehir University, Istanbul, 34349, Turkey
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16
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The association between cigarette smoking and inflammation: The Genetic Epidemiology Network of Arteriopathy (GENOA) study. PLoS One 2017; 12:e0184914. [PMID: 28922371 PMCID: PMC5602636 DOI: 10.1371/journal.pone.0184914] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/01/2017] [Indexed: 01/30/2023] Open
Abstract
To inform the study and regulation of emerging tobacco products, we sought to identify sensitive biomarkers of tobacco-induced subclinical cardiovascular damage by testing the cross-sectional associations of smoking with 17 biomarkers of inflammation in 2,702 GENOA study participants belonging to sibships ascertained on the basis of hypertension. Cigarette smoking was assessed by status, intensity (number of cigarettes per day), burden (pack-years of smoking), and time since quitting. We modeled biomarkers as geometric mean (GM) ratios using generalized estimating equations (GEE). The mean age of participants was 61 ±10 years; 64.5% were women and 54.4% African American. The prevalence of smoking was 12.2%. After adjusting for potential confounders, 6 of 17 biomarkers were significantly higher among current smokers at a Bonferroni adjusted p-value threshold (p<0.003). High sensitivity C-reactive protein was the most elevated biomarker among current smokers when compared to never smokers [GM ratio = 1.39 (95% CI: 1.23, 1.57); p <0.001]. Among former smokers, each pack-year of cigarettes smoked was associated with a 0.4% higher serum level of hsCRP [GM ratio = 1.004 (95% CI: 1.001, 1.006); p = 0.002] and each 5-year lapsed since quitting was associated with a 4% lower serum level of hsCRP [GM ratio = 0.96 (95% CI: 0.93, 0.99); p = 0.006]. However, we found no significant association of smoking intensity or burden with biomarkers of inflammation among current smokers. HsCRP appears to be the most sensitive biomarker of inflammation associated with cigarette smoking of those investigated, and could be a useful biomarker of smoking-related injury for the study and regulation of emerging tobacco products.
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17
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Richter KR, Nasr AN, Mexas AM. Cytokine Concentrations Measured by Multiplex Assays in Canine Peripheral Blood Samples. Vet Pathol 2017; 55:53-67. [PMID: 28812527 DOI: 10.1177/0300985817725388] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cytokines are known to play important roles in a wide range of pathologic conditions spanning all organ systems in every species studied. As our knowledge of the physiology of individual cytokines expands and our ability to measure multiple cytokines in smaller biological samples increases, we gain more insight into the significance and function of each cytokine and the importance of cytokine networks. Previous studies that reported measurements of cytokine concentrations from serum or plasma in dogs with infectious, autoimmune, metabolic, endocrine, and neoplastic diseases yield an appreciation for the complexity of cytokine control and potential applications for cytokine measurements in the diagnosis, prognosis, and therapy of a variety of disease conditions. In this review, we highlight the benefits of multiplex cytokine analysis, summarize clinical and experimental reports that have used this technology in dogs, and discuss the strengths and limitations of data analysis for the interpretation of results in these studies. We describe how differences in technical acuity, data reporting tactics, statistical analysis, study population selection criteria, and cross-sectional experimental design methods may affect interpretation of results from this technology. We also suggest methods for analysis in future studies, such as reporting median fluorescence intensity values, analyzing the proportion of patients above population medians, and performing longitudinal studies.
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Affiliation(s)
- Kristen R Richter
- 1 College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Amirah N Nasr
- 1 College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Angela M Mexas
- 1 College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
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18
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Chen J, Guest PC, Schwarz E. The Utility of Multiplex Assays for Identification of Proteomic Signatures in Psychiatry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:131-138. [DOI: 10.1007/978-3-319-52479-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Chen J, Schwarz E. Opportunities and Challenges of Multiplex Assays: A Machine Learning Perspective. Methods Mol Biol 2017; 1546:115-122. [PMID: 27896760 DOI: 10.1007/978-1-4939-6730-8_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Multiplex assays that allow the simultaneous measurement of multiple analytes in small sample quantities have developed into a widely used technology. Their implementation spans across multiple assay systems and can provide readouts of similar quality as the respective single-plex measures, albeit at far higher throughput. Multiplex assay systems are therefore an important element for biomarker discovery and development strategies but analysis of the derived data can face substantial challenges that may limit the possibility of identifying meaningful biological markers. This chapter gives an overview of opportunities and challenges of multiplexed biomarker analysis, in particular from the perspective of machine learning aimed at identification of predictive biological signatures.
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Affiliation(s)
- Junfang Chen
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, J 5, Mannheim, 68159, Germany
| | - Emanuel Schwarz
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, J 5, Mannheim, 68159, Germany.
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20
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Schmidt MF, Freeman KB, Windham BG, Griswold ME, Kullo IJ, Turner ST, Mosley TH. Associations Between Serum Inflammatory Markers and Hippocampal Volume in a Community Sample. J Am Geriatr Soc 2016; 64:1823-9. [PMID: 27549073 DOI: 10.1111/jgs.14283] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To quantify associations between inflammatory biomarkers and hippocampal volume (HV) and to examine effect modification according to sex, race, and age. DESIGN Cross-sectional analyses using generalized estimating equations to account for familial clustering; standardized β-coefficients adjusted for age, sex, race, and education. SETTING Community cohorts in Jackson, Mississippi and Rochester, Minnesota. PARTICIPANTS The Genetic Epidemiology Network of Arteriopathy study. MEASUREMENTS C-reactive protein (CRP), interleukin-6 (IL-6), and soluble tumor necrosis factor receptors 1 (sTNFR-1) and 2 (sTNFR-2) from peripheral blood were measured in a sample of 773 non-Hispanic whites (61% women, aged 60.2 ± 9.8) and 514 African Americans (70% women, aged 63.9 ± 8.1) who also underwent brain magnetic resonance imaging. Biomarkers were standardized and compared according to sex, race and age with HV. RESULTS In the full sample, higher sTNFR-1 and sTNFR-2 were associated with smaller HV. Each standard deviation (SD) increase in sTNFR-1 was associated with 59.1 mm(3) (95% confidence interval (CI) = -101.4 to -16.7 mm(3) ) smaller HV and each SD increase in sTNFR-2 associated with 48.8 mm(3) (95% CI = -92.2 to -5.3 mm(3) ) smaller HV. Relationships were stronger for sTNFR-2 in men (HV = -116.6 mm(3) for each SD increase, 95% CI = -201.0 to -32.1) than women (HV = -26.0 per SD increase, 95% CI = -72.4-20.5) and sTNFR-1 in non-Hispanic whites (HV = -84.7 mm(3) per SD increase, 95% CI = -142.2 to -27.1) than African Americans (HV = -14.1 mm(3) per SD increase, 95% CI = -78.3-50.1). Associations between IL-6 or CRP and HV were not supported. CONCLUSION Higher levels of sTNFRs were associated cross-sectionally with smaller hippocampi. Longitudinal data are needed to determine whether these biomarkers may help to identify risk of late-life cognitive impairment.
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Affiliation(s)
- Mike F Schmidt
- Program in Neuroscience, University of Mississippi Medical Center, Jackson, Mississippi.,Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi
| | - Kevin B Freeman
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, Mississippi
| | - Beverly G Windham
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi
| | - Michael E Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi.
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Marrero A, Lawrence S, Wilsker D, Voth AR, Kinders RJ. Translating pharmacodynamic biomarkers from bench to bedside: analytical validation and fit-for-purpose studies to qualify multiplex immunofluorescent assays for use on clinical core biopsy specimens. Semin Oncol 2016; 43:453-63. [PMID: 27663477 PMCID: PMC5065024 DOI: 10.1053/j.seminoncol.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Multiplex pharmacodynamic (PD) assays have the potential to increase sensitivity of biomarker-based reporting for new targeted agents, as well as revealing significantly more information about target and pathway activation than single-biomarker PD assays. Stringent methodology is required to ensure reliable and reproducible results. Common to all PD assays is the importance of reagent validation, assay and instrument calibration, and the determination of suitable response calibrators; however, multiplex assays, particularly those performed on paraffin specimens from tissue blocks, bring format-specific challenges adding a layer of complexity to assay development. We discuss existing multiplex approaches and the development of a multiplex immunofluorescence assay measuring DNA damage and DNA repair enzymes in response to anti-cancer therapeutics and describe how our novel method addresses known issues.
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Affiliation(s)
- Allison Marrero
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Scott Lawrence
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Deborah Wilsker
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Andrea Regier Voth
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert J Kinders
- Pharmacodynamics Assay Development and Implementation Section, Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD.
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22
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Aldo P, Marusov G, Svancara D, David J, Mor G. Simple Plex(™) : A Novel Multi-Analyte, Automated Microfluidic Immunoassay Platform for the Detection of Human and Mouse Cytokines and Chemokines. Am J Reprod Immunol 2016; 75:678-93. [PMID: 27170460 PMCID: PMC5084752 DOI: 10.1111/aji.12512] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/21/2016] [Indexed: 01/19/2023] Open
Abstract
Problem Quantitative measurement of proteins in bodily fluids or cellular preparations is critical for the evaluation of biomarkers or the study of complex cellular processes. While immunoassays are the most common quantitative approach used so far, they are not practical for the evaluation of multiple proteins. Microfluidic technology allows a fine spatial control in immobilizing proteins and biomolecules inside microchannels, eliminating cross‐reactivity between competing analytes, and allowing rapid and sensitive detection of targeted antigens for multiple applications. We report the characterization and validation of the Simple Plex™ platform for the detection and quantification of cytokines and chemokines from human and mouse samples. Method Cytokine and chemokine expression levels were determined using Simple Plex cartridges from ProteinSimple. Serum samples were obtained from the Yale Biorepository. Results Our data demonstrate an excellent correlation between the results obtained with Simple Plex and conventional immunoassays such as ELISA and Luminex. Conclusion We describe the characterization and validation of Simple Plex, a novel multi‐analyte, automated microfluidic platform that allows the evaluation of cytokines and chemokines from human and mice biological samples. Simple Plex showed significant advantages over traditional approaches in terms of low sample volume requirements, sensitivity and dynamic range, coefficient of variation, and reproducibility.
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Affiliation(s)
- Paulomi Aldo
- Division of Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine. New Haven, CT, USA
| | | | | | | | - Gil Mor
- Division of Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine. New Haven, CT, USA
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A First Tetraplex Assay for the Simultaneous Quantification of Total α-Synuclein, Tau, β-Amyloid42 and DJ-1 in Human Cerebrospinal Fluid. PLoS One 2016; 11:e0153564. [PMID: 27116005 PMCID: PMC4846093 DOI: 10.1371/journal.pone.0153564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/31/2016] [Indexed: 01/17/2023] Open
Abstract
The quantification of four distinct proteins (α-synuclein, β-amyloid1-42, DJ-1, and total tau) in cerebrospinal fluid (CSF) has been proposed as a laboratory-based platform for the diagnosis of Parkinson’s disease (PD) and Alzheimer’s disease (AD). While there is some clinical utility in measuring these markers individually, their usage in routine clinical testing remains challenging, in part due to substantial overlap of concentrations between healthy controls and diseased subjects. In contrast, measurement of different analytes in a single sample from individual patients in parallel appears to considerably improve the accuracy of AD or PD diagnosis. Here, we report the development and initial characterization of a first, electrochemiluminescence-based multiplex immunoassay for the simultaneous quantification of all four proteins (‘tetraplex’) in as little as 50 μl of CSF. In analytical performance experiments, we assessed its sensitivity, spike-recovery rate, parallelism and dilution linearity as well as the intra- and inter-assay variability. Using our in-house calibrators, we recorded a lower limit of detection for α-synuclein, β-amyloid42, DJ-1, and t-tau of 1.95, 1.24, 5.63, and 4.05 pg/ml, respectively. The corresponding, linear concentration range covered >3 orders of magnitude. In diluted CSF samples (up to 1:4), spike-recovery rates ranged from a low of 55% for β-amyloid42 to a high of 98% for DJ-1. Hillslopes ranged from 1.03 to 1.30, and inter-assay variability demonstrated very high reproducibility. Our newly established tetraplex assay represents a significant technical advance for fluid-based biomarker studies in neurodegenerative disorders allowing the simultaneous measurement of four pivotal makers in single CSF specimens. It provides exceptional sensitivity, accuracy and speed.
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Tighe PJ, Ryder RR, Todd I, Fairclough LC. ELISA in the multiplex era: potentials and pitfalls. Proteomics Clin Appl 2015; 9:406-22. [PMID: 25644123 PMCID: PMC6680274 DOI: 10.1002/prca.201400130] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/08/2014] [Accepted: 01/19/2015] [Indexed: 12/20/2022]
Abstract
Multiplex immunoassays confer several advantages over widely adopted singleplex immunoassays including increased efficiency at a reduced expense, greater output per sample volume ratios and higher throughput predicating more resolute, detailed diagnostics and facilitating personalised medicine. Nonetheless, to date, relatively few protein multiplex immunoassays have been validated for in vitro diagnostics in clinical/point-of-care settings. This review article will outline the challenges, which must be ameliorated prior to the widespread integration of multiplex immunoassays in clinical settings: (i) biomarker validation; (ii) standardisation of immunoassay design and quality control (calibration and quantification); (iii) availability, stability, specificity and cross-reactivity of reagents; (iv) assay automation and the use of validated algorithms for transformation of raw data into diagnostic results. A compendium of multiplex immunoassays applicable to in vitro diagnostics and a summary of the diagnostic products currently available commercially are included, along with an analysis of the relative states of development for each format (namely planar slide based, suspension and planar/microtitre plate based) with respect to the aforementioned issues.
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Affiliation(s)
- Patrick J Tighe
- School of Life Sciences, The University of Nottingham, Nottingham, UK
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25
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Windham BG, Simpson BN, Lirette S, Bridges J, Bielak L, Peyser PA, Kullo I, Turner S, Griswold ME, Mosley TH. Associations between inflammation and cognitive function in African Americans and European Americans. J Am Geriatr Soc 2015; 62:2303-10. [PMID: 25516026 DOI: 10.1111/jgs.13165] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES To examine associations between specific inflammatory biomarkers and cognitive function in African Americans (AAs) and European Americans (EAs) with prevalent vascular risk factors. DESIGN Cross-sectional analysis using generalized estimating equations to account for familial clustering; standardized β-coefficients, adjusted for age, sex, and education are reported. SETTING Community cohort study in Jackson, Mississippi, and Rochester, Minnesota. PARTICIPANTS Genetic Epidemiology Network of Arteriopathy (GENOA)-Genetics of Microangiopathic Brain Injury (GMBI) Study participants. MEASUREMENTS Associations between inflammation (high-sensitivity C-reactive protein (CRP), interleukin (IL)-6, soluble tumor necrosis factor (TNF) receptor 1 and 2 (sTNFR1, sTNFR2)) and cognitive function (global, processing speed, language, memory, and executive function) were examined in AAs and EAs (N = 1,965; aged 26-95, 64% women, 52% AA, 75% with hypertension). RESULTS In AAs, higher sTNFR2 was associated with poorer cognition in all domains (global: -0.11, P = .009; processing speed: -0.11, P < .001; language: -0.08, P = .002; memory: -0.09, P = .008; executive function: -0.07, P = .03); sTNFR1 was associated with slower processing speed (-0.08, P < .001) and poorer executive function (-0.08, P = .008); higher CRP was associated with slower processing speed (-0.04, P = .024), and higher IL6 was associated with poorer executive function (-0.07, P = .02). In EA, only higher sTNFR1 was associated with slower processing speed (-0.05, P = .007). Associations were not found between cognition and sTNFR2, CRP, or IL6 in EA. CONCLUSION In a population with high vascular risk, adverse associations between inflammation and cognitive function were especially apparent in AAs, primarily involving markers of TNFα activity.
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Affiliation(s)
- B Gwen Windham
- Division of Geriatric Medicine, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi
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26
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Development and validation of protein microarray technology for simultaneous inflammatory mediator detection in human sera. Mediators Inflamm 2014; 2014:820304. [PMID: 25382942 PMCID: PMC4213990 DOI: 10.1155/2014/820304] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 09/08/2014] [Accepted: 09/08/2014] [Indexed: 12/26/2022] Open
Abstract
Biomarkers, including cytokines, can help in the diagnosis, prognosis, and prediction of treatment response across a wide range of disease settings. Consequently, the recent emergence of protein microarray technology, which is able to quantify a range of inflammatory mediators in a large number of samples simultaneously, has become highly desirable. However, the cost of commercial systems remains somewhat prohibitive. Here we show the development, validation, and implementation of an in-house microarray platform which enables the simultaneous quantitative analysis of multiple protein biomarkers. The accuracy and precision of the in-house microarray system were investigated according to the Food and Drug Administration (FDA) guidelines for pharmacokinetic assay validation. The assay fell within these limits for all but the very low-abundant cytokines, such as interleukin- (IL-) 10. Additionally, there were no significant differences between cytokine detection using our microarray system and the “gold standard” ELISA format. Crucially, future biomarker detection need not be limited to the 16 cytokines shown here but could be expanded as required. In conclusion, we detail a bespoke protein microarray system, utilizing well-validated ELISA reagents, that allows accurate, precise, and reproducible multiplexed biomarker quantification, comparable with commercial ELISA, and allowing customization beyond that of similar commercial microarrays.
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27
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Lau CY, Zahidi AAA, Liew OW, Ng TW. A direct heating model to overcome the edge effect in microplates. J Pharm Biomed Anal 2014; 102:199-202. [PMID: 25289516 DOI: 10.1016/j.jpba.2014.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/10/2014] [Accepted: 09/13/2014] [Indexed: 11/25/2022]
Abstract
Array-based tests in a microplate format are complicated by the regional variation in results of the outer against the inner wells of the plate. Analysis of the evaporation mechanics of sessile drops showed that evaporation rate increase with temperature was due to changes in the heat of vaporization, density and diffusion coefficient. In simulations of direct bottom heating of standard microplates, considerable heat transfer via conduction from the side walls was found to be responsible for lower temperatures in the liquid in wells close to the edge. Applying a two temperature heating mode, 304 K at the side compared to 310 K at the bottom, allowed for a more uniform temperature distribution. Transparency microplates were found to inherently possess immunity to the edge effect problem due to the presence of air between the liquid and solid wall.
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Affiliation(s)
- Chun Yat Lau
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Alifa Afiah Ahmad Zahidi
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Oi Wah Liew
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Tuck Wah Ng
- Laboratory for Optics and Applied Mechanics, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, Victoria 3800, Australia.
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Frampton JP, White JB, Simon AB, Tsuei M, Paczesny S, Takayama S. Aqueous two-phase system patterning of detection antibody solutions for cross-reaction-free multiplex ELISA. Sci Rep 2014; 4:4878. [PMID: 24786974 PMCID: PMC4007081 DOI: 10.1038/srep04878] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/16/2014] [Indexed: 12/22/2022] Open
Abstract
Accurate disease diagnosis, patient stratification and biomarker validation require the analysis of multiple biomarkers. This paper describes cross-reactivity-free multiplexing of enzyme-linked immunosorbent assays (ELISAs) using aqueous two-phase systems (ATPSs) to confine detection antibodies at specific locations in fully aqueous environments. Antibody cross-reactions are eliminated because the detection antibody solutions are co-localized only to corresponding surface-immobilized capture antibody spots. This multiplexing technique is validated using plasma samples from allogeneic bone marrow recipients. Patients with acute graft versus host disease (GVHD), a common and serious condition associated with allogeneic bone marrow transplantation, display higher mean concentrations for four multiplexed biomarkers (HGF, elafin, ST2 and TNFR1) relative to healthy donors and transplant patients without GVHD. The antibody co-localization capability of this technology is particularly useful when using inherently cross-reactive reagents such as polyclonal antibodies, although monoclonal antibody cross-reactivity can also be reduced. Because ATPS-ELISA adapts readily available antibody reagents, plate materials and detection instruments, it should be easily transferable into other research and clinical settings.
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Affiliation(s)
- John P Frampton
- Department of Biomedical Engineering, University of Michigan
| | - Joshua B White
- Department of Biomedical Engineering, University of Michigan
| | - Arlyne B Simon
- Department of Macromolecular Science and Engineering, University of Michigan
| | - Michael Tsuei
- Department of Biomedical Engineering, University of Michigan
| | - Sophie Paczesny
- Department of Pediatrics, Indiana University School of Medicine
| | - Shuichi Takayama
- 1] Department of Biomedical Engineering, University of Michigan [2] Department of Macromolecular Science and Engineering, University of Michigan
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Bastarache JA, Koyama T, Wickersham NE, Ware LB. Validation of a multiplex electrochemiluminescent immunoassay platform in human and mouse samples. J Immunol Methods 2014; 408:13-23. [PMID: 24768796 DOI: 10.1016/j.jim.2014.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/31/2014] [Accepted: 04/14/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Despite the widespread use of multiplex immunoassays, there are very few scientific reports that test the accuracy and reliability of a platform prior to publication of experimental data. Our laboratory has previously demonstrated the need for new assay platform validation prior to use of biologic samples from large studies in order to optimize sample handling and assay performance. METHODS In this study, our goal was to test the accuracy and reproducibility of an electrochemiluminescent multiplex immunoassay platform (Meso Scale Discovery, MSD®) and compare this platform to validated, singleplex immunoassays (R&D Systems®) using actual study subject (human plasma and mouse bronchoalveolar lavage fluid (BAL) and plasma) samples. RESULTS We found that the MSD platform performed well on intra- and inter-assay comparisons, spike and recovery and cross-platform comparisons. The mean intra-assay CV% and range for MSD were 3.49 (0.0-10.4) for IL-6 and 2.04 (0.1-7.9) for IL-8. The correlation between values for identical samples measured on both MSD and R&D was R=0.97 for both analytes. The mouse MSD assay had a broader range of CV% with means ranging from 9.5 to 28.5 depending on the analyte. The range of mean CV% was similar for single plex ELISAs at 4.3-23.7 depending on the analyte. Regardless of species or sample type, CV% was more variable at lower protein concentrations. CONCLUSIONS In conclusion, we validated a multiplex electrochemiluminescent assay system and found that it has superior test characteristics in human plasma compared to mouse BALF and plasma. Both human and MSD assays compared favorably to well-validated singleplex ELISAs.
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Affiliation(s)
- J A Bastarache
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN 37232-2650, United States.
| | - T Koyama
- Department of Biostatistics, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN 37232-2650, United States
| | - N E Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN 37232-2650, United States
| | - L B Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN 37232-2650, United States
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Cretich M, Damin F, Chiari M. Protein microarray technology: how far off is routine diagnostics? Analyst 2014; 139:528-42. [DOI: 10.1039/c3an01619f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Hagan S, Tomlinson A. Tear Fluid Biomarker Profiling: A Review of Multiplex Bead Analysis. Ocul Surf 2013; 11:219-35. [DOI: 10.1016/j.jtos.2013.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 04/19/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
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Edgell TA, Rombauts LJF, Salamonsen LA. Assessing receptivity in the endometrium: the need for a rapid, non-invasive test. Reprod Biomed Online 2013; 27:486-96. [PMID: 23933033 DOI: 10.1016/j.rbmo.2013.05.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/30/2013] [Accepted: 05/30/2013] [Indexed: 01/11/2023]
Abstract
Successful implantation of an embryo into the uterus requires synchrony between the blastocyst and the endometrium. Endometrial preparedness, or receptivity, occurs only for a very short time during the mid-secretory phase of the menstrual cycle in fertile women. Failure to achieve receptivity results in infertility and is a rate-limiting step for IVF success. Frozen embryo transfer in non-stimulation cycles is already improving live birth rates. However, an important tool that is missing in the armoury of reproductive specialists is a means to rapidly assess endometrial receptivity, either during initial assessment or immediately prior to embryo transfer. The development of a wealth of omics technologies now opens the way for identifying potential receptivity markers, although validation of these is still a major issue. This review assesses the current state of the field and the requirements to proceed to a valid clinical test.
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Affiliation(s)
- Tracey A Edgell
- Prince Henry's Institute of Medical Research, P.O. Box 5152, Clayton, Victoria 3168, Australia.
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Eckels J, Nathe C, Nelson EK, Shoemaker SG, Nostrand EV, Yates NL, Ashley VC, Harris LJ, Bollenbeck M, Fong Y, Tomaras GD, Piehler B. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics 2013; 14:145. [PMID: 23631706 PMCID: PMC3671158 DOI: 10.1186/1471-2105-14-145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 03/27/2013] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. RESULTS The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. CONCLUSIONS Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.
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Affiliation(s)
| | | | | | - Sara G Shoemaker
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Nicole L Yates
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Vicki C Ashley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Linda J Harris
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark Bollenbeck
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
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Browne RW, Kantarci A, LaMonte MJ, Andrews CA, Hovey KM, Falkner KL, Cekici A, Stephens D, Genco RJ, Scannapieco FA, Van Dyke TE, Wactawski-Wende J. Performance of multiplex cytokine assays in serum and saliva among community-dwelling postmenopausal women. PLoS One 2013; 8:e59498. [PMID: 23577067 PMCID: PMC3618114 DOI: 10.1371/journal.pone.0059498] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/14/2013] [Indexed: 11/24/2022] Open
Abstract
Multiplexing arrays increase the throughput and decrease sample requirements for studies employing multiple biomarkers. The goal of this project was to examine the performance of Multiplex arrays for measuring multiple protein biomarkers in saliva and serum. Specimens from the OsteoPerio ancillary study of the Women’s Health Initiative Observational Study were used. Participants required the presence of at least 6 teeth and were excluded based on active cancer and certain bone issues but were not selected on any specific condition. Quality control (QC) samples were created from pooled serum and saliva. Twenty protein markers were measured on five multiplexing array panels. Sample pretreatment conditions were optimized for each panel. Recovery, lower limit of quantification (LLOQ) and imprecision were determined for each analyte. Statistical adjustment at the plate level was used to reduce imprecision estimates and increase the number of usable observations. Sample pre-treatment improved recovery estimates for many analytes. The LLOQ for each analyte agreed with manufacturer specifications except for MMP-1 and MMP-2 which were significantly higher than reported. Following batch adjustment, 17 of 20 biomarkers in serum and 9 of 20 biomarkers in saliva demonstrated acceptable precision, defined as <20% coefficient of variation (<25% at LLOQ). The percentage of cohort samples having levels within the reportable range for each analyte varied from 10% to 100%. The ratio of levels in saliva to serum varied from 1∶100 to 28∶1. Correlations between saliva and serum were of moderate positive magnitude and significant for CRP, MMP-2, insulin, adiponectin, GM-CSF and IL-5. Multiplex arrays exhibit high levels of analytical imprecision, particularly at the batch level. Careful sample pre-treatment can enhance recovery and reduce imprecision. Following statistical adjustments to reduce batch effects, we identified biomarkers that are of acceptable quality in serum and to a lesser degree in saliva using Multiplex arrays.
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Affiliation(s)
- Richard W Browne
- Department of Biotechnical and Clinical Laboratory Sciences, University at Buffalo, Buffalo, New York, USA.
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Cretich M, Monroe MR, Reddington A, Zhang X, Daaboul GG, Damin F, Sola L, Unlu MS, Chiari M. Interferometric silicon biochips for label and label-free DNA and protein microarrays. Proteomics 2012; 12:2963-77. [PMID: 22930463 DOI: 10.1002/pmic.201200202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/12/2022]
Abstract
Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics. Traditional microarray applications employ labeled detection strategies based on the use of fluorescent and chemiluminescent secondary antibodies. However, the development of high throughput, sensitive, label-free detection techniques is attracting attention as they do not require labeled reactants and provide quantitative information on binding kinetics. In this article, we will provide an overview of the recent author's work in label and label-free sensing platforms employing silicon/silicon oxide (Si/SiO(2)) substrates for interferometric and/or fluorescence detection of microarrays. The review will focus on applications of Si/SiO(2) with controlled oxide layers to (i) enhance the fluorescence intensity by optical interferences, (ii) quantify with sub-nanometer accuracy the axial locations of fluorophore-labeled probes tethered to the surface, and (iii) detect protein-protein interactions label free. Different methods of biofunctionalization of the sensing surface will be discussed. In particular, organosilanization reactions for monodimensional coatings and polymeric coatings will be extensively reviewed. Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
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Microfluidic strategies applied to biomarker discovery and validation for multivariate diagnostics. Bioanalysis 2012; 3:2233-51. [PMID: 21985417 DOI: 10.4155/bio.11.224] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Complex diseases are caused by combinatorial genetic, environmental and lifestyle factors. The emergence of multibiomarker tests to define these diseases and to identify the early, presymptomatic stages offers several advantages to the conventional use of single marker tests. The development of multibiomarker protein-based tests remains constrained by technological and operational limitations in assaying hundreds to thousands of proteins in thousands of samples. In order to develop a multibiomarker test that stratifies risk for Type 2 diabetes, we took a candidate-driven immunoassay approach utilizing a microfluidics platform to analyze 89 candidate proteins in thousands of samples, which allowed us to move from discovery to a commercial test in 2 years. Future multibiomarker test development will be enhanced by advancements in the number of proteins that can be analyzed, analytical sensitivity and throughput, and sample volume requirements, all of which depend on the further advancement of microfluidics, detection technologies and affinity-based reagents.
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Minor changes in serum levels of cytokines after removal of amalgam restorations. Toxicol Lett 2012; 211:120-5. [PMID: 22475563 DOI: 10.1016/j.toxlet.2012.03.769] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/18/2012] [Accepted: 03/20/2012] [Indexed: 01/08/2023]
Abstract
Dental amalgam restorations release mercury and silver which is absorbed and distributed in the body. Animal studies have shown that both elements may interfere with the host by activation of the immune system in genetically susceptible strains at exposure levels relevant to those from dental amalgam restorations. The aim of this study was to test the hypothesis of no change over time in concentrations of a number of immune mediators in serum after removal of all dental amalgam restorations in patients with health complaints attributed to their amalgam restorations and compare with a healthy reference group. Twenty patients previously examined at a specialty unit for health complaints attributed to dental materials were included in a clinical trial and had all amalgam restorations replaced with other dental restorative materials. Serum samples were collected before amalgam removal and 3 and 12 months after the removal was finished. Twenty blood donors matched for age and gender were used as comparison group. A fluorescent bead-based (Luminex) immunoassay kit was used to measure cytokines, chemokines and growth factors in serum. At baseline, the patient group had slightly higher values for GM-CSF, IL-6, IL-2R, IFN-alpha, IL-7, and IL-12p40/p70 compared with the reference group. After amalgam removal a decrease towards the median value of the reference group was found for GM-CSF, IL-8, and IL-7. In conclusion, removal of all dental amalgam restorations and replacement with other dental restorative materials was associated with decreased concentrations of Th1-type proinflammatory markers in serum.
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Pre-analytical effects of blood sampling and handling in quantitative immunoassays for rheumatoid arthritis. J Immunol Methods 2012; 378:72-80. [PMID: 22366959 DOI: 10.1016/j.jim.2012.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 02/08/2012] [Indexed: 01/20/2023]
Abstract
Variability in pre-analytical blood sampling and handling can significantly impact results obtained in quantitative immunoassays. Understanding the impact of these variables is critical for accurate quantification and validation of biomarker measurements. Particularly, in the design and execution of large clinical trials, even small differences in sample processing and handling can have dramatic effects in analytical reliability, results interpretation, trial management and outcome. The effects of two common blood sampling methods (serum vs. plasma) and two widely-used serum handling methods (on the clot with ambient temperature shipping, "traditional", vs. centrifuged with cold chain shipping, "protocol") on protein and autoantibody concentrations were examined. Matched serum and plasma samples were collected from 32 rheumatoid arthritis (RA) patients representing a wide range of disease activity status. Additionally, a set of matched serum samples with two sample handling methods was collected. One tube was processed per manufacturer's instructions and shipped overnight on cold packs (protocol). The matched tube, without prior centrifugation, was simultaneously shipped overnight at ambient temperatures (traditional). Upon delivery, the traditional tube was centrifuged. All samples were subsequently aliquoted and frozen prior to analysis of protein and autoantibody biomarkers. Median correlation between paired serum and plasma across all autoantibody assays was 0.99 (0.98-1.00) with a median % difference of -3.3 (-7.5 to 6.0). In contrast, observed protein biomarker concentrations were significantly affected by sample types, with median correlation of 0.99 (0.33-1.00) and a median % difference of -10 (-55 to 23). When the two serum collection/handling methods were compared, the median correlation between paired samples for autoantibodies was 0.99 (0.91-1.00) with a median difference of 4%. In contrast, significant increases were observed in protein biomarker concentrations among certain biomarkers in samples processed with the 'traditional' method. Autoantibody quantification appears robust to both sample type (plasma vs. serum) and pre-analytical sample collection/handling methods (protocol vs. traditional). In contrast, for non-antibody protein biomarker concentrations, sample type had a significant impact; plasma samples generally exhibit decreased protein biomarker concentrations relative to serum. Similarly, sample handling significantly impacted the variability of protein biomarker concentrations. When biomarker concentrations are combined algorithmically into a single test score such as a multi-biomarker disease activity test for rheumatoid arthritis (MBDA), changes in protein biomarker concentrations may result in a bias of the score. These results illustrate the importance of characterizing pre-analytical methodology, sample type, sample processing and handling procedures for clinical testing in order to ensure test accuracy.
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Henderson MPA, Pond GR, Kavsak PA. Statistical and analytical approaches for assessing biomarkers: new approaches, new technologies, with the same-old rigor for evaluation. Clin Biochem 2012; 45:187-8. [PMID: 22300592 DOI: 10.1016/j.clinbiochem.2012.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 09/10/2011] [Accepted: 09/14/2011] [Indexed: 11/19/2022]
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Jozwik CE, Pollard HB, Srivastava M, Eidelman O, Fan Q, Darling TN, Zeitlin PL. Antibody microarrays: analysis of cystic fibrosis. Methods Mol Biol 2012; 823:179-200. [PMID: 22081346 DOI: 10.1007/978-1-60327-216-2_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cystic fibrosis (CF) is the most common autosomal recessive disease in the USA and Europe, whose life-limiting phenotype is manifest on epithelial cells throughout the body. The principal cause of morbidity and mortality is a massively proinflammatory condition in the lung. The mutation responsible for most cases of CF is [ΔF508]CFTR. However, the penetrance of the disease is quite variable, and adverse events leading to hospitalization cannot be easily predicted. Thus, there is a strong need for prognostic endpoints that might serve to identify impending clinical problems long before they happen. Our approach has been to search for proteomic signatures in easily accessed biological fluids that might identify the molecular basis for adverse events. We describe here a workflow that begins with patient-derived bronchial brush biopsies and progresses to analysis of serum and plasma from patients on antibody microarrays.
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Affiliation(s)
- Catherine E Jozwik
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Bethesda, MD, USA.
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Whiteaker JR, Zhao L, Lin C, Yan P, Wang P, Paulovich AG. Sequential multiplexed analyte quantification using peptide immunoaffinity enrichment coupled to mass spectrometry. Mol Cell Proteomics 2011; 11:M111.015347. [PMID: 22203691 DOI: 10.1074/mcp.m111.015347] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Peptide immunoaffinity enrichment coupled to selected reaction monitoring (SRM) mass spectrometry (immuno-SRM) has emerged as a technology with great potential for quantitative proteomic assays. One advantage over traditional immunoassays is the tremendous potential for concurrent quantification of multiple analytes from a given sample (i.e. multiplex analysis). We sought to explore the capacity of the immuno-SRM technique for analyzing large numbers of analytes by evaluating the multiplex capabilities and demonstrating the sequential analysis of groups of peptides from a single sample. To evaluate multiplex analysis, immuno-SRM assays were arranged in groups of 10, 20, 30, 40, and 50 peptides using a common set of reagents. The multiplex immuno-SRM assays were used to measure synthetic peptides added to plasma covering several orders of magnitude concentration. Measurements made in large multiplex groups were highly correlated (r(2) ≥ 0.98) and featured good agreement (bias ≤ 1%) compared with single-plex assays or a 10-plex configuration. The ability to sequentially enrich sets of analyte peptides was demonstrated by enriching groups of 10 peptides from a plasma sample in a sequential fashion. The data show good agreement (bias ≤ 1.5%) and similar reproducibility regardless of enrichment order. These significant advancements demonstrate the utility of immuno-SRM for analyzing large numbers of analytes, such as in large biomarker verification experiments or in pathway-based targeted analysis.
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Monroe MR, Reddington AP, Collins AD, LaBoda C, Cretich M, Chiari M, Little FF, Unlü MS. Multiplexed method to calibrate and quantitate fluorescence signal for allergen-specific IgE. Anal Chem 2011; 83:9485-91. [PMID: 22060132 PMCID: PMC3395232 DOI: 10.1021/ac202212k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Using a microarray platform for allergy diagnosis allows for testing of specific IgE sensitivity to a multitude of allergens, while requiring only small volumes of serum. However, variation of probe immobilization on microarrays hinders the ability to make quantitative, assertive, and statistically relevant conclusions necessary in immunodiagnostics. To address this problem, we have developed a calibrated, inexpensive, multiplexed, and rapid protein microarray method that directly correlates surface probe density to captured labeled secondary antibody in clinical samples. We have identified three major technological advantages of our calibrated fluorescence enhancement (CaFE) technique: (i) a significant increase in fluorescence emission over a broad range of fluorophores on a layered substrate optimized specifically for fluorescence; (ii) a method to perform label-free quantification of the probes in each spot while maintaining fluorescence enhancement for a particular fluorophore; and (iii) a calibrated, quantitative technique that combines fluorescence and label-free modalities to accurately measure probe density and bound target for a variety of antibody-antigen pairs. In this paper, we establish the effectiveness of the CaFE method by presenting the strong linear dependence of the amount of bound protein to the resulting fluorescence signal of secondary antibody for IgG, β-lactoglobulin, and allergen-specific IgEs to Ara h 1 (peanut major allergen) and Phl p 1 (timothy grass major allergen) in human serum.
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Affiliation(s)
- Margo R Monroe
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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Pla-Roca M, Leulmi RF, Tourekhanova S, Bergeron S, Laforte V, Moreau E, Gosline SJC, Bertos N, Hallett M, Park M, Juncker D. Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. Mol Cell Proteomics 2011; 11:M111.011460. [PMID: 22171321 PMCID: PMC3322566 DOI: 10.1074/mcp.m111.011460] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA microarrays were rapidly scaled up from 256 to 6.5 million targets, and although antibody microarrays were proposed earlier, sensitive multiplex sandwich assays have only been scaled up to a few tens of targets. Cross-reactivity, arising because detection antibodies are mixed, is a known weakness of multiplex sandwich assays that is mitigated by lengthy optimization. Here, we introduce (1) vulnerability as a metric for assays. The vulnerability of multiplex sandwich assays to cross-reactivity increases quadratically with the number of targets, and together with experimental results, substantiates that scaling up of multiplex sandwich assays is unfeasible. We propose (2) a novel concept for multiplexing without mixing named antibody colocalization microarray (ACM). In ACMs, both capture and detection antibodies are physically colocalized by spotting to the same two-dimensional coordinate. Following spotting of the capture antibodies, the chip is removed from the arrayer, incubated with the sample, placed back onto the arrayer and then spotted with the detection antibodies. ACMs with up to 50 targets were produced, along with a binding curve for each protein. The ACM was validated by comparing it to ELISA and to a small-scale, conventional multiplex sandwich assay (MSA). Using ACMs, proteins in the serum of breast cancer patients and healthy controls were quantified, and six candidate biomarkers identified. Our results indicate that ACMs are sensitive, robust, and scalable.
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Affiliation(s)
- M Pla-Roca
- Biomedical Engineering Department, McGill University, Montreal, Quebec, Canada
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Circulating cytokine concentrations in dogs with different degrees of myxomatous mitral valve disease. Vet J 2011; 192:106-11. [PMID: 21696985 DOI: 10.1016/j.tvjl.2011.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 05/05/2011] [Accepted: 05/07/2011] [Indexed: 12/18/2022]
Abstract
Cytokines have been associated with the progression of congestive heart failure (CHF) in humans and may be implicated in the pathophysiology of myxomatous mitral valve disease (MMVD) in dogs. The aim of this study was to determine the serum concentrations of cytokines in dogs with MMVD. The study included 16 Cairn terriers with no or minimal mitral regurgitation (MR), 41 Cavalier King Charles Spaniels (CKCS) with different degrees of MR and 11 dogs of different breeds with CHF due to MMVD. Granulocyte-macrophage colony-stimulating factor, interferon-γ, interleukin (IL)-2, IL-6, IL-7, IL-8, IL-10, IL-15, IL-18, keratinocyte-derived chemokine, interferon-γ-induced protein and monocyte chemoattractant protein-1 (MCP-1) were measured using a canine-specific multiplex immunoassay. CHF dogs had significantly higher MCP-1 concentrations than dogs with no or minimal MR. Among the CKCS, IL-2 and IL-7 decreased with increasing left atrial size and IL-7 also decreased with increasing MR. IL-8 decreased with increasing left ventricular end-systolic internal dimensions. MCP-1 was increased in CHF dogs compared to healthy control dogs and IL-2, IL-7 and IL-8 decreased with increasing indices of disease severity. The results suggest a role for these cytokines in canine MMVD and CHF.
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Accuracy and reproducibility of a multiplex immunoassay platform: a validation study. J Immunol Methods 2011; 367:33-9. [PMID: 21277854 DOI: 10.1016/j.jim.2011.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 01/17/2011] [Accepted: 01/17/2011] [Indexed: 01/17/2023]
Abstract
BACKGROUND Multiplex immunoassays offer many advantages over singleplex assays for the analysis of multiple analytes in a single sample. We sought to validate a specific multiplex cytokine immunoassay (Human 9-plex cytokine array on the Searchlight® platform by Thermoscientific) prior to use in a large clinical study. METHODS We compared spike and recovery of recombinant proteins on the Searchlight® platform to singleplex immunoassays purchased from R&D Systems, measured identical patient samples on the two different platforms, and measured identical patient samples on different days to measure intra- and inter-assay variability. RESULTS Assays using the Searchlight® platform had inefficient recovery of spiked recombinant proteins compared to R&D Systems singleplex assays. Assaying identical patients samples on different days on the Searchlight platform had acceptable intra-assay variability (intra-assay coefficient of variation (CV%) range for all analytes of 9.1-13.7) but unacceptably high inter-assay variability (CV% range for all analytes 16.7-119.3) suggesting plate-to plate variability. Similar assays for individual cytokines on the R&D platform had an intra-assay CV% range of 1.6-6.4 and an inter-assay CV% range of 3.8-7.1. Some deficiencies in Searchlight® assay performance may be due to irregularities in spotting of capture antibodies during manufacturing. CONCLUSIONS We conclude that the Searchlight® multiplex immunoassay platform would require extensive additional assay optimization prior to widespread clinical research use.
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Phan K, Sohn KY, Hill SA, Worster A, You J, Oremus M, Devereaux PJ, Jaffe AS, Kavsak PA. Multiplex protein assay performance/evaluation and the requirement for precision and correlation to clinical assays. Clin Chem Lab Med 2011; 49:1915-8. [DOI: 10.1515/cclm.2011.683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lippa KA, Duewer DL, Salit ML, Game L, Causton HC. Exploring the use of internal and externalcontrols for assessing microarray technical performance. BMC Res Notes 2010; 3:349. [PMID: 21189145 PMCID: PMC3020182 DOI: 10.1186/1756-0500-3-349] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/28/2010] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. RESULTS A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics. CONCLUSIONS These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.
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Affiliation(s)
- Katrice A Lippa
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - David L Duewer
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - Marc L Salit
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - Laurence Game
- MRC Clinical Sciences Centre (CSC) Imperial College Microarray Centre Hammersmith Hospital Campus London W12 0NN, UK
| | - Helen C Causton
- MRC Clinical Sciences Centre (CSC) Imperial College Microarray Centre Hammersmith Hospital Campus London W12 0NN, UK
- Department of Biological Sciences Columbia University New York, NY 10027 USA
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Tarrant JM. Blood cytokines as biomarkers of in vivo toxicity in preclinical safety assessment: considerations for their use. Toxicol Sci 2010; 117:4-16. [PMID: 20447938 PMCID: PMC2923281 DOI: 10.1093/toxsci/kfq134] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In the drive to develop drugs with well-characterized and clinically monitorable safety profiles, there is incentive to expand the repertoire of safety biomarkers for toxicities without routine markers or premonitory detection. Biomarkers in blood are pursued because of specimen accessibility, opportunity for serial monitoring, quantitative measurement, and the availability of assay platforms. Cytokines, chemokines, and growth factors (here referred to collectively as cytokines) show robust modulation in proximal events of inflammation, immune response, and repair. These are key general processes in many toxicities; therefore, cytokines are commonly identified during biomarker discovery studies. In addition, multiplexed cytokine immunoassays are easily applied to biomarker discovery and routine toxicity studies to measure blood cytokines. However, cytokines pose several challenges as safety biomarkers because of a short serum half-life; low to undetectable baseline levels; lack of tissue-specific or toxicity-specific expression; complexities related to cytokine expression with multiorgan involvement; and species, strain, and interindividual differences. Additional challenges to their application are caused by analytical, methodological, and study design-related variables. A final consideration is the strength of the relationship between changes in cytokine levels and the development of phenotypic or functional manifestations of toxicity. These factors should inform the integrated judgment-based qualification of novel biomarkers in preclinical, and potentially clinical, risk assessment. The dearth of robust, predictive cytokine biomarkers for specific toxicities is an indication of the significant complexity of these challenges. This review will consider the current state of the science and recommendations for appropriate application of cytokines in preclinical safety assessment.
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Abstract
Coronary heart disease (CHD) will soon become the leading cause of death and morbidity in the world. Early detection and treatment of CHD is thus imperative to improve global health. Atherosclerosis of the coronary arteries is a complex multifactorial disease process involving multiple pathways that can be influenced by both genetic and environmental factors. With the recent advances in genomics and proteomics, many new risk factors with small-to-moderate effects are likely to be identified. Additionally, individualized risk stratification and targeted therapy may become feasible; each individual could potentially be assessed with a panel of tests for genomic and proteomic markers and, on the basis of the individual's composite risk profile, preventive and therapeutic steps could then be undertaken. With a multimarker approach, it may also be possible to identify alterations in pathways involved in atherogenesis, rather than focus on individual risk factors. In this article, we use the specific example of atherosclerosis to discuss the role of genomics and proteomics in cardiovascular risk assessment.
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Kim CX, Bailey KR, Klee GG, Ellington AA, Liu G, Mosley TH, Rehman H, Kullo IJ. Sex and ethnic differences in 47 candidate proteomic markers of cardiovascular disease: the Mayo Clinic proteomic markers of arteriosclerosis study. PLoS One 2010; 5:e9065. [PMID: 20140090 PMCID: PMC2816715 DOI: 10.1371/journal.pone.0009065] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 11/20/2009] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) susceptibility differs between men and women and varies with ethnicity. This variability is not entirely explained by conventional CVD risk factors. We examined differences in circulating levels of 47 novel protein markers of CVD in 2561 men and women of African-American (AA) and non-Hispanic White (NHW) ethnicity, enrolled at geographically distinct sites. METHODOLOGY/PRINCIPAL FINDINGS Participants (1,324 AAs, mean age 63.5 y, 71% women; 1,237 NHWs, mean age 58.9 y, 57% women) belonged to sibships ascertained on the basis of hypertension. Solid-phase immunoassays and immunoturbidometric, clot-based, chromogenic, and electrophoretic assays were used to measure the 47 protein markers in plasma or serum. Marker levels were log transformed and outliers were adjusted to within 4 SD. To identify markers independently associated with sex or ethnicity, we employed multivariable regression analyses that adjusted for conventional risk factors, prior history of CVD, medication use and lifestyle factors (physical activity, alcohol consumption and education). Generalized estimating equations were used to correct for intrafamilial correlations. After adjustment for the above covariates, female sex was associated with higher levels of 29 markers and lower levels of 6 markers. Female sex was independently associated with higher levels of several inflammatory markers as well as lipoproteins, adipokines, natriuretic peptides, vasoconstrictor peptides and markers of calcification and thrombosis. AA ethnicity was associated with higher levels of 19 markers and lower levels of 6 markers, including higher levels of several inflammatory makers, higher leptin and lower adiponectin levels, lower levels of vasodilator-natriuretic peptides, higher levels of vasoconstrictor-antidiuretic peptides and markers of calcification and thrombosis. CONCLUSIONS/SIGNIFICANCE Plasma levels of several novel protein markers of CVD differ significantly in the context of sex and ethnicity. These results have implications for individualized CVD risk assessment.
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Affiliation(s)
- Charles X. Kim
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kent R. Bailey
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - George G. Klee
- Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Guanghui Liu
- Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Hamid Rehman
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Iftikhar J. Kullo
- Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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