1
|
Jozwik C, Eidelman O, Srivastava M. Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large-Scale, Targeted Antibody Microarray Platform. Methods Mol Biol 2023; 2660:219-233. [PMID: 37191800 DOI: 10.1007/978-1-0716-3163-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dynamic post-translational processes regulate protein expression in eukaryotic cells. However, the processes are difficult to assess on a proteomic scale because protein levels actually reflect the sum of individual biosynthesis and degradation rates. These rates are presently hidden from the conventional proteomic technologies. We present here a novel and dynamic, antibody microarray-based time-resolved approach to simultaneously measure not only the total protein changes but also the rates of biosynthesis of low abundance proteins in the proteome of lung epithelial cells. In this chapter, we describe the feasibility of this technique by investigating the complete proteomic kinetics of 507 low abundance proteins in cultured cystic fibrosis (CF) lung epithelial cells using 35[S] methionine or 32[P] and the consequences of repair by gene therapy with [wildtype] CFTR. This novel antibody microarray-based technology identifies relevant, hidden proteins whose regulation by the CF genotype would never have been detected by simple measurements of total proteomic masses.
Collapse
Affiliation(s)
- Catherine Jozwik
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Meera Srivastava
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA.
| |
Collapse
|
2
|
Immunoassays on thiol-ene synthetic paper generate a superior fluorescence signal. Biosens Bioelectron 2020; 163:112279. [PMID: 32421629 DOI: 10.1016/j.bios.2020.112279] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 11/23/2022]
Abstract
The fluorescence-based detection of biological complexes on solid substrates is widely used in microarrays and lateral flow tests. Here, we investigate thiol-ene micropillar scaffold sheets ("synthetic paper") as the solid substrate in such assays. Compared to state-of-the-art glass and nitrocellulose substrates, assays on synthetic paper provide a stronger fluorescence signal, similar or better reproducibility, lower limit of detection (LOD), and the possibility of working with lower immunoreagent concentrations. Using synthetic paper, we detected the antibiotic enrofloxacin in whole milk with a LOD of 1.64 nM, which is on par or better than the values obtained with other common tests, and much lower than the maximum level allowed by European Union regulations. The significance of these results lays in that they indicate that synthetically-derived microstructured substrate materials have the potential to improve the performance of diagnostic assays.
Collapse
|
3
|
Han XJ, Ma XL, Yang L, Wei YQ, Peng Y, Wei XW. Progress in Neoantigen Targeted Cancer Immunotherapies. Front Cell Dev Biol 2020; 8:728. [PMID: 32850843 PMCID: PMC7406675 DOI: 10.3389/fcell.2020.00728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 02/05/2023] Open
Abstract
Immunotherapies that harness the immune system to kill cancer cells have showed significant therapeutic efficacy in many human malignancies. A growing number of studies have highlighted the relevance of neoantigens in recognizing cancer cells by intrinsic T cells. Cancer neoantigens are a direct consequence of somatic mutations presenting on the surface of individual cancer cells. Neoantigens are fully cancer-specific and exempt from central tolerance. In addition, neoantigens are important targets for checkpoint blockade therapy. Recently, technological innovations have made neoantigen discovery possible in a variety of malignancies, thus providing an impetus to develop novel immunotherapies that selectively enhance T cell reactivity for the destruction of cancer cells while leaving normal tissues unharmed. In this review, we aim to introduce the methods of the identification of neoantigens, the mutational patterns of human cancers, related clinical trials, neoantigen burden and sensitivity to immune checkpoint blockade. Moreover, we focus on relevant challenges of targeting neoantigens for cancer treatment.
Collapse
|
4
|
Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes 2018; 11:156. [PMID: 29482592 PMCID: PMC5828362 DOI: 10.1186/s13104-018-3266-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. Electronic supplementary material The online version of this article (10.1186/s13104-018-3266-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jessica Da Gama Duarte
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Tumour Immunology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ryan W Goosen
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Peter J Lawry
- Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Blackburn Laboratory, N3.03, Wernher & Beit Building North, Institute of Infectious Disease & Molecular Medicine, UCT Faculty of Health Sciences, Observatory, Cape Town, 7925, South Africa
| |
Collapse
|
5
|
Meeusen E, Lim E, Mathivanan S. Secreted Tumor Antigens - Immune Biomarkers for Diagnosis and Therapy. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/29/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Els Meeusen
- Department of Biochemistry and Genetics; La Trobe Institute for Molecular Science; La Trobe University; Bundoora Victoria Australia
| | - Elgene Lim
- Garvan Institute of Medical Research; St. Vincent's Health; University of New South Wales; Darlinghurst NSW Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics; La Trobe Institute for Molecular Science; La Trobe University; Bundoora Victoria Australia
| |
Collapse
|
6
|
A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer. SENSORS 2015; 15:11972-87. [PMID: 26007739 PMCID: PMC4481930 DOI: 10.3390/s150511972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/14/2015] [Indexed: 11/17/2022]
Abstract
Levels of total human kallikrein 2 (hK2), a protein involved the pathology of prostate cancer (PCa), could be used as a biomarker to aid in the diagnosis of this disease. In this study, we report on a porous silicon antibody immunoassay platform for the detection of serum levels of total hK2. The surface of porous silicon has a 3-dimensional macro- and nanoporous structure, which offers a large binding capacity for capturing probe molecules. The tailored pore size of the porous silicon also allows efficient immobilization of antibodies by surface adsorption, and does not require chemical immobilization. Monoclonal hK2 capture antibody (6B7) was dispensed onto P-Si chip using a piezoelectric dispenser. In total 13 × 13 arrays (169 spots) were spotted on the chip with its single spot volume of 300 pL. For an optimization of capture antibody condition, we firstly performed an immunoassay of the P-Si microarray under a titration series of hK2 in pure buffer (PBS) at three different antibody densities (75, 100 and 145 µg/mL). The best performance of the microarray platform was seen at 100 µg/mL of the capture antibody concentration (LOD was 100 fg/mL). The platform then was subsequently evaluated for a titration series of serum-spiked hK2 samples. The developed platform utilizes only 15 µL of serum per test and the total assay time is about 3 h, including immobilization of the capture antibody. The detection limit of the hK2 assay was 100 fg/mL in PBS buffer and 1 pg/mL in serum with a dynamic range of 106 (10−4 to 102 ng/mL).
Collapse
|
7
|
Akbani R, Becker KF, Carragher N, Goldstein T, de Koning L, Korf U, Liotta L, Mills GB, Nishizuka SS, Pawlak M, Petricoin EF, Pollard HB, Serrels B, Zhu J. Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society. Mol Cell Proteomics 2014; 13:1625-43. [PMID: 24777629 DOI: 10.1074/mcp.o113.034918] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.
Collapse
Affiliation(s)
- Rehan Akbani
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Neil Carragher
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ted Goldstein
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
| | | | - Ulrike Korf
- **German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Gordon B Mills
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Michael Pawlak
- §§§The Natural and Medical Sciences Institute, Reutlingen, Germany
| | | | - Harvey B Pollard
- ¶¶Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Bryan Serrels
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jingchun Zhu
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
| |
Collapse
|
8
|
Androulakis IP, Kamisoglu K, Mattick JS. Topology and Dynamics of Signaling Networks: In Search of Transcriptional Control of the Inflammatory Response. Annu Rev Biomed Eng 2013; 15:1-28. [DOI: 10.1146/annurev-bioeng-071812-152425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ioannis P. Androulakis
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
- Biomedical Engineering Department, Rutgers University, Piscataway, New Jersey 08854
| | - Kubra Kamisoglu
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
| | - John S. Mattick
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
| |
Collapse
|
9
|
Lab-on-a-Chip, Micro- and Nanoscale Immunoassay Systems, and Microarrays. THE IMMUNOASSAY HANDBOOK 2013. [PMCID: PMC7152144 DOI: 10.1016/b978-0-08-097037-0.00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
10
|
|
11
|
Differentiating Branch Duct and Mixed IPMN in Endoscopically Collected Pancreatic Cyst Fluid via Cytokine Analysis. Gastroenterol Res Pract 2012; 2012:247309. [PMID: 23326260 PMCID: PMC3543798 DOI: 10.1155/2012/247309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 10/31/2012] [Accepted: 11/14/2012] [Indexed: 01/13/2023] Open
Abstract
Background. Differentiating branch duct from mixed intraductal papillary mucinous neoplasm (BD-IPMN) is problematic, but clinically important as mixed IPMNs are managed surgically, while some BD-IPMN may be followed. Inflammatory mediator proteins (IMPs) have been implicated in acute and chronic inflammatory and malignant pancreatic diseases. Aim. To compare IMP profile of pancreatic cyst fluid collected endoscopically from BD-IPMN and mixed IPMN. Methods. Pancreatic cyst fluid from ten patients (5 BD-IPMN and 5 mixed IPMN) was collected by endoscopic ultrasound-guided fine needle aspiration or endoscopic retrograde cholangiopancreatography. Concentrations of 89 IMPs in these samples were determined using a multiplexed bead-based microarray protein assay and compared between BD-IPMN and mixed IPMN. Results. Eighty-six of 89 IMPs were detected in at least one of the 10 samples. Fourteen IMPs were detected only in mixed IPMN, while none were only in BD-IPMN. Of these, TGF-β1 was most prevalent, present in 3 of 5 mixed IPMNs. Seventy-two IMPs were detected in both BD-IPMN and mixed IPMNs. Of these, only G-CSF (P < 0.05) was present in higher concentrations in mixed IPMNs. Conclusion. TGF-β1 and G-CSF detected in endoscopically collected pancreatic cyst fluid are potential diagnostic biomarkers capable of distinguishing mixed IPMN from BD-IPMN.
Collapse
|
12
|
Zheng J, Tan BH, Sugrue R, Tang K. Current approaches on viral infection: proteomics and functional validations. Front Microbiol 2012; 3:393. [PMID: 23162545 PMCID: PMC3499792 DOI: 10.3389/fmicb.2012.00393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022] Open
Abstract
Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way.
Collapse
Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University Singapore
| | | | | | | |
Collapse
|
13
|
Pitarch A, Jiménez A, Nombela C, Gil C. Serological proteome analysis to identify systemic candidiasis patients in the intensive care unit: Analytical, diagnostic and prognostic validation of anti-Candida enolase antibodies on quantitative clinical platforms. Proteomics Clin Appl 2012; 2:596-618. [PMID: 21136858 DOI: 10.1002/prca.200780039] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Systemic candidiasis (SC) is associated with high morbidity and mortality, because it generally affects patients with severe underlying diseases and its diagnosis is difficult and often delayed, resulting in delayed therapy. We used serological proteome analysis to screen serum anti-Candida IgG antibody-reactivity profiles in 24 patients under intensive care, 12 of which had confirmed SC (fungal cultures), and in 12 healthy subjects. A total of 15 immunogenic proteins from Candida albicans protoplast lysates were differentially immunorecognized by serum IgG antibodies from SC patients compared to controls. Two-way hierarchical clustering and principal-component analyses of these antibody-reactivity patterns accurately differentiated SC patients from controls. Anti-Eno1p IgG antibodies were found to be present at high abundance in SC patients and be an important molecular fingerprint in serum for SC diagnosis. Differential anti-Eno1p IgG antibody reactivity was further validated by a tag capture ELISA and a Western blot assay in 45 SC patients and 118 non-SC subjects. Both quantitative assays provided comparable analytical, diagnostic and prognostic performances, and verified initial proteomic-profiling results. If confirmed in prospective cohort studies, these anti-Eno1p IgG antibodies might be useful for SC diagnosis. However, these, at least as measured by these clinical platforms, appear to have limited prognostic value in SC patients.
Collapse
Affiliation(s)
- Aida Pitarch
- Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
| | | | | | | |
Collapse
|
14
|
Ruktanonchai U, Nuchuchua O, Charlermroj R, Pattarakankul T, Karoonuthaisiri N. Signal amplification of microarray-based immunoassay by optimization of nanoliposome formulations. Anal Biochem 2012; 429:142-7. [DOI: 10.1016/j.ab.2012.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 07/03/2012] [Accepted: 07/07/2012] [Indexed: 10/28/2022]
|
15
|
Järås K, Adler B, Tojo A, Malm J, Marko-Varga G, Lilja H, Laurell T. Porous silicon antibody microarrays for quantitative analysis: measurement of free and total PSA in clinical plasma samples. Clin Chim Acta 2012; 414:76-84. [PMID: 22921878 DOI: 10.1016/j.cca.2012.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
Abstract
The antibody microarrays have become widespread, but their use for quantitative analyses in clinical samples has not yet been established. We investigated an immunoassay based on nanoporous silicon antibody microarrays for quantification of total prostate-specific-antigen (PSA) in 80 clinical plasma samples, and provide quantitative data from a duplex microarray assay that simultaneously quantifies free and total PSA in plasma. To further develop the assay the porous silicon chips was placed into a standard 96-well microtiter plate for higher throughput analysis. The samples analyzed by this quantitative microarray were 80 plasma samples obtained from men undergoing clinical PSA testing (dynamic range: 0.14-44 ng/ml, LOD: 0.14 ng/ml). The second dataset, measuring free PSA (dynamic range: 0.40-74.9 ng/ml, LOD: 0.47 ng/ml) and total PSA (dynamic range: 0.87-295 ng/ml, LOD: 0.76 ng/ml), was also obtained from the clinical routine. The reference for the quantification was a commercially available assay, the ProStatus PSA Free/Total DELFIA. In an analysis of 80 plasma samples the microarray platform performs well across the range of total PSA levels. This assay might have the potential to substitute for the large-scale microtiter plate format in diagnostic applications. The duplex assay paves the way for a future quantitative multiplex assay, which analyzes several prostate cancer biomarkers simultaneously.
Collapse
Affiliation(s)
- Kerstin Järås
- Dept. of Laboratory Medicine, Div. of Clinical Chemistry, Lund University, Skåne University Hospital, 205 02, Malmö, Sweden.,Dept. of Measurement Technology and Industrial Electrical Engineering, Div. Nanobiotechnology, Lund University, 223 63, Lund, Sweden
| | - Belinda Adler
- Dept. of Measurement Technology and Industrial Electrical Engineering, Div. Nanobiotechnology, Lund University, 223 63, Lund, Sweden
| | - Axel Tojo
- Dept. of Measurement Technology and Industrial Electrical Engineering, Div. Nanobiotechnology, Lund University, 223 63, Lund, Sweden
| | - Johan Malm
- Dept. of Laboratory Medicine, Div. of Clinical Chemistry, Lund University, Skåne University Hospital, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Dept. of Measurement Technology and Industrial Electrical Engineering, Div. Nanobiotechnology, Lund University, 223 63, Lund, Sweden
| | - Hans Lilja
- Dept. of Laboratory Medicine, Div. of Clinical Chemistry, Lund University, Skåne University Hospital, 205 02, Malmö, Sweden.,Departments of Laboratory Medicine, Surgery, and Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.,Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Thomas Laurell
- Dept. of Measurement Technology and Industrial Electrical Engineering, Div. Nanobiotechnology, Lund University, 223 63, Lund, Sweden.,Department of Biomedical Engineering, Dongguk University, Seoul, South Korea
| |
Collapse
|
16
|
Lee LS, Banks PA, Bellizzi AM, Sainani NI, Kadiyala V, Suleiman S, Conwell DL, Paulo JA. Inflammatory protein profiling of pancreatic cyst fluid using EUS-FNA in tandem with cytokine microarray differentiates between branch duct IPMN and inflammatory cysts. J Immunol Methods 2012; 382:142-149. [PMID: 22683544 DOI: 10.1016/j.jim.2012.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/29/2012] [Accepted: 05/30/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Diagnosis of pancreatic cystic neoplasms remains problematic. We hypothesize that inflammatory mediator proteins in pancreatic cyst fluid can differentiate branch duct intraductal papillary mucinous neoplasms (BD-IPMNs) and pancreatic inflammatory cysts. We aim to 1) detect inflammatory mediator proteins (IMPs) using a multiplexed IMP-targeted microarray in pancreatic cyst fluid obtained during endoscopic ultrasound fine needle aspiration (EUS-FNA) and 2) compare IMP profiles in pancreatic cyst fluid from BD-IPMNs and inflammatory cysts. Pancreatic cyst fluid from ten patients (5 BD-IPMN and 5 inflammatory cysts) was obtained by EUS-FNA and analyzed directly with a multiplexed microarray assay to determine concentrations of 89 IMPs. Statistical analysis was performed using non-parametric methods. RESULTS Eighty-three of the 89 assayed IMPs were detected in at least one of the 10 patient samples. Seven IMPs were detected in BD-IPMN but not inflammatory cysts, while eleven IMPs were identified in inflammatory cysts but not BD-IPMN. Notably, granulocyte-macrophage colony-stimulating factor (GM-CSF) expression was present in all five inflammatory cyst samples. Hepatocyte growth factor (HGF) was present in significantly higher concentrations in inflammatory cysts compared to BD-IPMN. CONCLUSION Our exploratory analysis reveals that GM-CSF and HGF in EUS-FNA-collected pancreatic cyst fluid can distinguish between BD-IPMN and inflammatory cyst. Coupling microarray molecular techniques to EUS-FNA may represent a major step forward to our understanding complex pancreatic disease.
Collapse
Affiliation(s)
- Linda S Lee
- Center for Pancreatic Disease, Division of Gastroenterology Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Peter A Banks
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA
| | - Nisha I Sainani
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Vivek Kadiyala
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Shadeah Suleiman
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Darwin L Conwell
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| | - Joao A Paulo
- Department of Pathology, Children's Hospital Boston, Boston, MA Proteomics Center at Children's Hospital Boston, Boston, MA Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA
| |
Collapse
|
17
|
Kim D, Karns K, Tia SQ, He M, Herr AE. Electrostatic Protein Immobilization Using Charged Polyacrylamide Gels and Cationic Detergent Microfluidic Western Blotting. Anal Chem 2012; 84:2533-40. [DOI: 10.1021/ac3000013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dohyun Kim
- Department of Bioengineering, University of California, Berkeley, 342 Stanley Hall,
Berkeley, California 94720, United States
| | - Kelly Karns
- The UC Berkeley − UCSF Graduate Program in Bioengineering, Berkeley,
California 94720, United States
| | - Samuel Q. Tia
- The UC Berkeley − UCSF Graduate Program in Bioengineering, Berkeley,
California 94720, United States
| | - Mei He
- Department of Bioengineering, University of California, Berkeley, 342 Stanley Hall,
Berkeley, California 94720, United States
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, 342 Stanley Hall,
Berkeley, California 94720, United States
- The UC Berkeley − UCSF Graduate Program in Bioengineering, Berkeley,
California 94720, United States
| |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Catherine E Jozwik
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Bethesda, MD, USA.
| | | | | | | | | | | | | |
Collapse
|
19
|
Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assay. J Immunol Methods 2011; 369:98-107. [PMID: 21569776 DOI: 10.1016/j.jim.2011.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 04/18/2011] [Accepted: 04/25/2011] [Indexed: 02/08/2023]
Abstract
Cytokines are secreted immunomodulating proteins involved in pancreatic stellate cell activation and propagation of fibrosis in chronic pancreatitis. We aim to show that cytokines can be identified from pancreatic fluid by (1) collecting pancreatic fluid with the ePFT method, (2) processing the fluid for cytokine-targeted microarray analysis, and (3) comparing cytokine profiles in pancreatic fluid of chronic pancreatitis (CP) patients and of chronic abdominal pain (CAP) controls. We endoscopically collected pancreatic fluid from patients with CP and those with CAP using the ePFT method. This fluid was subjected directly to a multiplexed cytokine protein microarray assay. Six patients (3 CP, 3 CAP) underwent a secretin-stimulated ePFT. The mean peak bicarbonate concentrations [meq/L] of the CP and CAP patients were 43 and 97, respectively. Statistically significant decreases in the cytokine concentrations of EGF, IP-10, eotaxin, IL-3, MIP-1a, IL-15, PDGF-AB/BB, and IL-1a were observed in the CP specimens (p<0.05). We have successfully identified differences in the abundance of cytokines in ePFT-collected pancreatic fluid with a multiplexed microarray assay comparing CP and CAP controls. Further targeted investigation of cytokines in ePFT-collected fluid will broaden our knowledge of pancreatic immune response and pathogenesis in chronic pancreatitis.
Collapse
|
20
|
Reverse phase protein microarray technology in traumatic brain injury. J Neurosci Methods 2010; 192:96-101. [DOI: 10.1016/j.jneumeth.2010.07.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Revised: 07/12/2010] [Accepted: 07/21/2010] [Indexed: 11/17/2022]
|
21
|
Eidelman O, Jozwik C, Huang W, Srivastava M, Rothwell SW, Jacobowitz DM, Ji X, Zhang X, Guggino W, Wright J, Kiefer J, Olsen C, Adimi N, Mueller GP, Pollard HB. Gender dependence for a subset of the low-abundance signaling proteome in human platelets. HUMAN GENOMICS AND PROTEOMICS : HGP 2010; 2010:164906. [PMID: 20981232 PMCID: PMC2958630 DOI: 10.4061/2010/164906] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 01/05/2010] [Indexed: 11/23/2022]
Abstract
The incidence of cardiovascular diseases is ten-times higher in males than females, although the biological basis for this gender disparity is not known. However, based on the fact that antiplatelet drugs are the mainstay for prevention and therapy, we hypothesized that the signaling proteomes in platelets from normal male donors might be more activated than platelets from normal female donors. We report here that platelets from male donors express significantly higher levels of signaling cascade proteins than platelets from female
donors. In silico connectivity analysis shows that the 24 major hubs in platelets from male donors focus on pathways associated with megakaryocytic expansion and platelet activation. By contrast, the 11 major hubs in platelets from female donors were found to be either negative or neutral for platelet-relevant processes. The difference may suggest a biological mechanism for gender discrimination in cardiovascular disease.
Collapse
Affiliation(s)
- Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, USU Center for Medical Proteomics, Uniformed Services University, School of Medicine, USUHS, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Kim YH, Kim YS. Effect of Nanoparticles in Protein Separation by Capillary Electrophoresis. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.02.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
23
|
Abstract
BACKGROUND Over the last 10 years, DNA microarrays have achieved a robust analytical performance, enabling their use for analyzing the whole transcriptome or for screening thousands of single-nucleotide polymorphisms in a single experiment. DNA microarrays allow scientists to correlate gene expression signatures with disease progression, to screen for disease-specific mutations, and to treat patients according to their individual genetic profiles; however, the real key is proteins and their manifold functions. It is necessary to achieve a greater understanding of not only protein function and abundance but also their role in the development of diseases. Protein concentrations have been shown to reflect the physiological and pathologic state of an organ, tissue, or cells far more directly than DNA, and proteins can be profiled effectively with protein microarrays, which require only a small amount of sample material. CONTENT Protein microarrays have become well-established tools in basic and applied research, and the first products have already entered the in vitro diagnostics market. This review focuses on protein microarray applications for biomarker discovery and validation, disease diagnosis, and use within the area of personalized medicine. SUMMARY Protein microarrays have proved to be reliable research tools in screening for a multitude of parameters with only a minimal quantity of sample and have enormous potential in applications for diagnostic and personalized medicine.
Collapse
Affiliation(s)
- Xiaobo Yu
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | | | | |
Collapse
|
24
|
Avens HJ, Bowman CN. Development of fluorescent polymerization-based signal amplification for sensitive and non-enzymatic biodetection in antibody microarrays. Acta Biomater 2010; 6:83-9. [PMID: 19508906 DOI: 10.1016/j.actbio.2009.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Antibody microarrays are a critical tool for proteomics, requiring broad, highly sensitive detection of numerous low abundance biomarkers. Fluorescent polymerization-based amplification (FPBA) is presented as a novel, non-enzymatic signal amplification method that takes advantage of the chain-reaction nature of radical polymerization to achieve a highly amplified fluorescent response. A streptavidin-eosin conjugate localizes eosin photoinitiators for polymerization on the chip where biotinylated target protein is bound. The chip is contacted with acrylamide as a monomer, N-methyldiethanolamine as a coinitiator and yellow/green fluorescent nanoparticles (NPs) which, upon initiation, combine to form a macroscopically visible and highly fluorescent film. The rapid polymerization kinetics and the presence of cross-linker favor entrapment of the fluorescent NPs in the polymer, enabling highly sensitive fluorescent biodetection. This method is demonstrated as being appropriate for antibody microarrays and is compared to detection approaches which utilize streptavidin-fluorescein isothiocyanate (SA-FITC) and streptavidin-labeled yellow/green NPs (SA-NPs). It is found that FPBA is able to detect 0.16 + or - 0.01 biotin-antibody microm(-2) (or 40 zmol surface-bound target molecules), while SA-FITC has a limit of detection of 31 + or - 1 biotin-antibody microm(-2) and SA-NPs fail to achieve any significant signal under the conditions evaluated here. Further, FPBA in conjunction with fluorescent stereomicroscopy yields equal or better sensitivity compared to fluorescent detection of SA-eosin using a much more costly microarray scanner. By facilitating highly sensitive detection, FPBA is expected to enable detection of low abundance antigens and also make possible a transition towards less expensive fluorescence detection instrumentation.
Collapse
|
25
|
Weinrich D, Jonkheijm P, Niemeyer CM, Waldmann H. Applications of protein biochips in biomedical and biotechnological research. Angew Chem Int Ed Engl 2009; 48:7744-51. [PMID: 19757463 PMCID: PMC7159567 DOI: 10.1002/anie.200901480] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Progress in the development of protein‐immobilization strategies and methods has made protein biochips increasingly accessible. The integration of these assay and analysis platforms into biomedical and biotechnological research has substantially expanded the repertoire of methods available for proteomics and biomarker research and for drug development. This Minireview highlights selected developments in the application of protein biochips in these fields.
Collapse
Affiliation(s)
- Dirk Weinrich
- Max-Planck-Institut für molekulare Physiologie and Technische Universität Dortmund, Fachbereich Chemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | | | | | | |
Collapse
|
26
|
Ikonomou G, Samiotaki M, Panayotou G. Proteomic methodologies and their application in colorectal cancer research. Crit Rev Clin Lab Sci 2009; 46:319-42. [DOI: 10.3109/10408360903375277] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
27
|
Chandra H, Srivastava S. Cell-free synthesis-based protein microarrays and their applications. Proteomics 2009; 10:717-30. [DOI: 10.1002/pmic.200900462] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
28
|
Weinrich D, Jonkheijm P, Niemeyer C, Waldmann H. Proteinbiochips in der Biomedizin und Biotechnologie. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901480] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
29
|
Agoston DV, Gyorgy A, Eidelman O, Pollard HB. Proteomic biomarkers for blast neurotrauma: targeting cerebral edema, inflammation, and neuronal death cascades. J Neurotrauma 2009; 26:901-11. [PMID: 19397421 DOI: 10.1089/neu.2008.0724] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteomics for blast traumatic brain injury (bTBI) research represents an exciting new approach that can greatly help to address the complex pathology of this condition. Antibody-based platforms, antibody microarrays (AbMA), and reverse capture protein microarrays (RCPM) can complement the classical methods based on 2D gel electrophoresis and mass spectrometry (2DGE/MS). These new technologies can address problematic issues, such as sample complexity, sensitivity, quantitation, reproducibility, and analysis time, which are typically associated with 2DGE/MS. Combined with bioinformatics analysis and interpretation of primary microarray data, these methods will generate a new level of understanding about bTBI at the level of systems biology. As biological and clinical knowledge and the availability of these systems become more widely established, we expect that AbMA and RCPM will be used routinely in clinical diagnostics, and also for following therapeutic progress. At the technical level, we anticipate that these platforms will evolve to accommodate comprehensive, high-speed, label-free analysis on a human proteome-wide scale.
Collapse
Affiliation(s)
- Denes V Agoston
- Department of Anatomy, Physiology and Genetics, Program in Neuroscience, Neurosurgery Program National Capital Consortium, Uniformed Services University School of Medicine (USU), 4301 Jones Bridge Road, Bethesda, MD 20814, USA.
| | | | | | | |
Collapse
|
30
|
Agoston DV, Gyorgy A, Eidelman O, Pollard HB. Proteomic Biomarkers for Blast Neurotrauma: Targeting Cerebral Edema, Inflammation, and Neuronal Death Cascades. J Neurotrauma 2009. [DOI: 10.1089/neu.2008.0724 [doi]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Denes V. Agoston
- Department of Anatomy, Physiology and Genetics, School of Medicine
| | - Andrea Gyorgy
- Department of Anatomy, Physiology and Genetics, School of Medicine
| | - Ofer Eidelman
- Center for Medical Proteomics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Harvey B. Pollard
- Center for Medical Proteomics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| |
Collapse
|
31
|
Bearinger JP, Stone G, Dugan LC, El Dasher B, Stockton C, Conway JW, Kuenzler T, Hubbell JA. Porphyrin-based photocatalytic nanolithography: a new fabrication tool for protein arrays. Mol Cell Proteomics 2009; 8:1823-31. [PMID: 19406753 DOI: 10.1074/mcp.m800585-mcp200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nanoarray fabrication is a multidisciplinary endeavor encompassing materials science, chemical engineering, and biology. We formed nanoarrays via a new technique, porphyrin-based photocatalytic nanolithography. The nanoarrays, with controlled features as small as 200 nm, exhibited regularly ordered patterns and may be appropriate for (a) rapid and parallel proteomics screening of immobilized biomolecules, (b) protein-protein interactions, and/or (c) biophysical and molecular biology studies involving spatially dictated ligand placement. We demonstrated protein immobilization utilizing nanoarrays fabricated via photocatalytic nanolithography on silicon substrates where the immobilized proteins are surrounded by a non-fouling polymer background.
Collapse
Affiliation(s)
- Jane P Bearinger
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Ellington AA, Kullo IJ, Bailey KR, Klee GG. Measurement and quality control issues in multiplex protein assays: a case study. Clin Chem 2009; 55:1092-9. [PMID: 19372187 DOI: 10.1373/clinchem.2008.120717] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Multiplex arrays are increasingly used for measuring protein biomarkers. Advantages of this approach include specimen conservation, limited sample handling, and decreased time and cost, but the challenges of optimizing assay format for each protein, selecting common dilution factors, and establishing robust quality control algorithms are substantial. Here, we use measurements of 15 protein biomarkers from a large study to illustrate processing, analytic, and quality control issues with multiplexed immunoassays. METHODS We contracted with ThermoScientific for duplicate measurements of 15 proteins in 2322 participants from a community-based cohort, a plasma control, and recombinant protein controls using 2 custom planar microarrays with 6 (panel A) or 9 (panel B) capture antibodies printed in each well. We selected constituent analytes in each panel based on endogenous concentrations and assay availability. Protocols were standardized for sample processing, storage, and freeze-thaw exposures. We analyzed data for effects of deviations from processing protocols, precision, and bias. RESULTS Measurements were within reportable ranges for each of the assays; however, concentrations for 7 of the 15 proteins were not centered on the dose-response curves. An additional freeze-thaw cycle and erroneous sample dilution for a subset of samples produced significantly different results. Measurements with large differences between duplicates were seen to cluster by analyte, plate, and participant. Conventional univariate quality control algorithms rejected many plates. Plate-specific medians of cohort and plasma control data significantly covaried, an observation important for development of alternative quality control algorithms. CONCLUSIONS Multiplex measurements present difficult challenges that require further analytical and statistical developments.
Collapse
|
33
|
Challenges in cancer research and multifaceted approaches for cancer biomarker quest. FEBS Lett 2009; 583:1772-84. [DOI: 10.1016/j.febslet.2009.03.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 03/18/2009] [Accepted: 03/18/2009] [Indexed: 12/15/2022]
|
34
|
Progress in fabricating arrays of soft spherical vessels on mesoscale with spatial control. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-008-0485-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
35
|
Seidel M, Niessner R. Automated analytical microarrays: a critical review. Anal Bioanal Chem 2008; 391:1521-44. [PMID: 18504563 PMCID: PMC7080066 DOI: 10.1007/s00216-008-2039-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/25/2008] [Accepted: 02/28/2008] [Indexed: 11/24/2022]
Abstract
Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications.
Collapse
Affiliation(s)
- Michael Seidel
- Chair for Analytical Chemistry and Institute of Hydrochemistry, Technische Universität München, Marchioninistrasse 17, 81377, München, Germany.
| | | |
Collapse
|
36
|
From Our Sister Journal: Proteomics 20/2007. Proteomics 2007. [DOI: 10.1002/pmic.200790084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|