Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery

Federica Villanova; Paola Di Meglio; Margaret Inokuma; Nima Aghaeepour; Esperanza Perucha; Jennifer Mollon; Laurel Nomura; Maria Hernandez Fuentes; Andrew Cope; A Toby Prevost; Susanne Heck; Vernon Maino; Graham Lord; Ryan R Brinkman; Frank O Nestle

doi:10.1371/journal.pone.0065485

Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery

Federica Villanova, Paola Di Meglio, Margaret Inokuma, Nima Aghaeepour, Esperanza Perucha, Jennifer Mollon, Laurel Nomura, Maria Hernandez Fuentes, Andrew Cope, A Toby Prevost, Susanne Heck, Vernon Maino, Graham Lord, Ryan R Brinkman, Frank O Nestle

Research output: Contribution to journal › Article › peer-review

14 Citations (Scopus)

Abstract

Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases.

Original language	English
Article number	e65485
Number of pages	8
Journal	PLoS ONE
Volume	8
Issue number	7
DOIs	https://doi.org/10.1371/journal.pone.0065485
Publication status	Published - 3 Jul 2013

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Villanova, F., Di Meglio, P., Inokuma, M., Aghaeepour, N., Perucha, E., Mollon, J., Nomura, L., Hernandez Fuentes, M., Cope, A., Prevost, A. T., Heck, S., Maino, V., Lord, G., Brinkman, R. R., & Nestle, F. O. (2013). Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery. PLoS ONE, 8(7), Article e65485. https://doi.org/10.1371/journal.pone.0065485

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title = "Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery",

abstract = "Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases.",

author = "Federica Villanova and {Di Meglio}, Paola and Margaret Inokuma and Nima Aghaeepour and Esperanza Perucha and Jennifer Mollon and Laurel Nomura and {Hernandez Fuentes}, Maria and Andrew Cope and Prevost, {A Toby} and Susanne Heck and Vernon Maino and Graham Lord and Brinkman, {Ryan R} and Nestle, {Frank O}",

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Villanova, F , Di Meglio, P, Inokuma, M, Aghaeepour, N, Perucha, E , Mollon, J, Nomura, L, Hernandez Fuentes, M , Cope, A , Prevost, AT, Heck, S, Maino, V, Lord, G, Brinkman, RR & Nestle, FO 2013, 'Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery', PLoS ONE, vol. 8, no. 7, e65485. https://doi.org/10.1371/journal.pone.0065485

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T1 - Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery

AU - Villanova, Federica

AU - Di Meglio, Paola

AU - Inokuma, Margaret

AU - Aghaeepour, Nima

AU - Perucha, Esperanza

AU - Mollon, Jennifer

AU - Nomura, Laurel

AU - Hernandez Fuentes, Maria

AU - Cope, Andrew

AU - Prevost, A Toby

AU - Heck, Susanne

AU - Maino, Vernon

AU - Lord, Graham

AU - Brinkman, Ryan R

AU - Nestle, Frank O

PY - 2013/7/3

Y1 - 2013/7/3

N2 - Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases.

AB - Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases.

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DO - 10.1371/journal.pone.0065485

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JO - PLoS ONE

JF - PLoS ONE

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Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery

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