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Microarrays
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Antibody Microarrays in Clinical Proteomics
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Antibody Microarrays in Clinical Proteomics

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (15 September 2015) | Viewed by 32039

Special Issue Editors

Prof. Carl A. K. Borrebaeck

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Guest Editor
Department of Immunotechnology and CREATE Health, Lund University, Medicon Village Scheelevägen 8, 223 81 Lund, Sweden
Interests: cancer; biomarkers; personalized medicine; affinity proteomics; therapeutic antibodies; antibody microarray; early diagnostics
Prof. Christer Wingren

E-Mail Website
Guest Editor
Department of Immunotechnology and CREATE Health, Lund University, Medicon Village Scheelevägen 8, 223 81 Lund, Sweden
Interests: affinity proteomics; antibody microarray; antibody design; disease proteomics; biomarkers; cancer; autoimmunity; diagnosis; prognosis
Dr. Ulrika Andreasson

E-Mail Website
Guest Editor
Department of Immunotechnology and CREATE Health, Lund University, Medicon Village Scheelevägen 8, 223 81 Lund, Sweden
Interests: cancer; lymphomas; biomarkers; personalized medicine; antibody microarray; proteomics; phage display

Special Issue Information

Dear Colleagues,

High throughput proteomic analysis provides powerful tools for the discovery of novel biomarkers, which could be used in the diagnosis and/or prognosis of diseases. Consequently, protein microarrays have been widely used for profiling biomarkers related with disease development and progression. The advantage of microarrays is that they allow for high throughput screening of large numbers of biomarkers, using minute amount of samples. This special issue will summarize the utilization of antibody microarrays and their implication in clinical settings. The focus will be both on recent technology developments in this field as well as the usefulness of this technique to demonstrate clinical utility and unmet medical needs, such as early diagnosis, patient stratification and evidence therapy selection.

Prof.Carl A. K. Borrebaeck
Prof. Christer Wingren
Dr. Ulrika Andreasson
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • antibody microarray
  • clinical utility

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Published Papers (4 papers)

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Research

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1788 KiB  
Article
Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays
by Martin Sill, Christoph Schröder, Ying Shen, Aseel Marzoq, Radovan Komel, Jörg D. Hoheisel, Henrik Nienhüser, Thomas Schmidt and Damjana Kastelic
Microarrays 2016, 5(3), 19; https://doi.org/10.3390/microarrays5030019 - 8 Jul 2016
Cited by 4 | Viewed by 6432
Abstract
In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative [...] Read more.
In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much fewer molecules than the numbers usually identified in studies comparing tumor to healthy control tissues. Insulin-like growth factor-binding protein 7 (IGFBP7), S100 calcium binding protein A9 (S100A9), interleukin-10 (IL‐10) and mucin 6 (MUC6) exhibited the most profound variations. For an evaluation of the proteins’ capacity for discriminating gastric cancer, a Receiver Operating Characteristic curve analysis was performed, yielding an accuracy (area under the curve) value of 89.2% for distinguishing tumor from non-tumorous tissue. For confirmation, immunohistological analyses were done on tissue slices prepared from another cohort of patients with gastric cancer. The utility of the 17 marker proteins, and particularly the four molecules with the highest specificity for gastric adenocarcinoma, is discussed for them to act as candidates for diagnosis, even in serum, and targets for therapeutic approaches. Full article
(This article belongs to the Special Issue Antibody Microarrays in Clinical Proteomics)
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4262 KiB  
Article
Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays
by Anna S. Gerdtsson, Linda Dexlin-Mellby, Payam Delfani, Erica Berglund, Carl A. K. Borrebaeck and Christer Wingren
Microarrays 2016, 5(2), 16; https://doi.org/10.3390/microarrays5020016 - 8 Jun 2016
Cited by 10 | Viewed by 6872
Abstract
Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the [...] Read more.
Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the antibodies and the solid surfaces plays a central role. In this study, we have taken on the first comprehensive view and evaluated the overall impact of solid surfaces on the recombinant antibody microarray design. The results clearly demonstrated the importance of the surface-antibody interaction and showed the effect of the solid supports on the printing process, the array format of planar arrays (slide- and well-based), the assay performance (spot features, reproducibility, specificity and sensitivity) and assay processing (degree of automation). In the end, two high-end recombinant antibody microarray technology platforms were designed, based on slide-based (black polymer) and well-based (clear polymer) arrays, paving the way for future large-scale protein expression profiling efforts. Full article
(This article belongs to the Special Issue Antibody Microarrays in Clinical Proteomics)
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1217 KiB  
Article
Retrospective Proteomic Analysis of Cellular Immune Responses and Protective Correlates of p24 Vaccination in an HIV Elite Controller Using Antibody Arrays
by Suneth S. Perera, Bin Wang, Arturo Damian, Wayne Dyer, Li Zhou, Viviane Conceicao and Nitin K. Saksena
Microarrays 2016, 5(2), 14; https://doi.org/10.3390/microarrays5020014 - 2 Jun 2016
Cited by 4 | Viewed by 5889
Abstract
Background: HIV p24 is an extracellular HIV antigen involved in viral replication. Falling p24 antibody responses are associated with clinical disease progression and their preservation with non-progressive disease. Stimulation of p24 antibody production by immunization to delay progression was the basis of discontinued [...] Read more.
Background: HIV p24 is an extracellular HIV antigen involved in viral replication. Falling p24 antibody responses are associated with clinical disease progression and their preservation with non-progressive disease. Stimulation of p24 antibody production by immunization to delay progression was the basis of discontinued p24 vaccine. We studied a therapy-naive HIV+ man from Sydney, Australia, infected in 1988. He received the HIV-p24-virus like particle (VLP) vaccine in 1993, and continues to show vigorous p24 antigen responses (>4% p24-specific CD4+ T cells), coupled with undetectable plasma viremia. We defined immune-protective correlates of p24 vaccination at the proteomic level through parallel retrospective analysis of cellular immune responses to p24 antigen in CD4+ and CD8+ T cells and CD14+ monocytes at viremic and aviremic phases using antibody-array. We found statistically significant coordinated up-regulation by all three cell-types with high fold-changes in fractalkine, ITAC, IGFBP-2, and MIP-1α in the aviremic phase. TECK and TRAIL-R4 were down-regulated in the viremic phase and up-regulated in the aviremic phase. The up-regulation of fractalkine in all three cell-types coincided with protective effect, whereas the dysfunction in anti-apoptotic chemokines with the loss of immune function. This study highlights the fact that induction of HIV-1-specific helper cells together with coordinated cellular immune response (p < 0.001) might be important in immunotherapeutic interventions and HIV vaccine development. Full article
(This article belongs to the Special Issue Antibody Microarrays in Clinical Proteomics)
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Review

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2772 KiB  
Review
Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery
by Astrid Wachter, Stephan Bernhardt, Tim Beissbarth and Ulrike Korf
Microarrays 2015, 4(4), 520-539; https://doi.org/10.3390/microarrays4040520 - 3 Nov 2015
Cited by 9 | Viewed by 12116
Abstract
Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics. In 2001, reverse phase protein arrays (RPPA) were added to the repertoire of existing immunoassays, which, for the first time, allowed a profiling of [...] Read more.
Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics. In 2001, reverse phase protein arrays (RPPA) were added to the repertoire of existing immunoassays, which, for the first time, allowed a profiling of minute amounts of tumor lysates even after microdissection. A characteristic feature of RPPA is its outstanding sample capacity permitting the analysis of thousands of samples in parallel as a routine task. Until today, the RPPA approach has matured to a robust and highly sensitive high-throughput platform, which is ideally suited for biomarker discovery. Concomitant with technical advancements, new bioinformatic tools were developed for data normalization and data analysis as outlined in detail in this review. Furthermore, biomarker signatures obtained by different RPPA screens were compared with another or with that obtained by other proteomic formats, if possible. Options for overcoming the downside of RPPA, which is the need to steadily validate new antibody batches, will be discussed. Finally, a debate on using RPPA to advance personalized medicine will conclude this article. Full article
(This article belongs to the Special Issue Antibody Microarrays in Clinical Proteomics)
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