Literature DB >> 23843942

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

Federica Villanova1, 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.   

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.

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Year:  2013        PMID: 23843942      PMCID: PMC3701052          DOI: 10.1371/journal.pone.0065485

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


  28 in total

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Journal:  Clin Pharmacol Ther       Date:  2001-03       Impact factor: 6.875

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Authors:  Jeffrey K Aronson
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3.  Development of a cross-platform biomarker signature to detect renal transplant tolerance in humans.

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Journal:  J Clin Invest       Date:  2010-05-24       Impact factor: 14.808

4.  Functional T cell responses to tumor antigens in breast cancer patients have a distinct phenotype and cytokine signature.

Authors:  Margaret Inokuma; Corazon dela Rosa; Charles Schmitt; Perry Haaland; Janet Siebert; Douglas Petry; Mengxiang Tang; Maria A Suni; Smita A Ghanekar; Daiva Gladding; John F Dunne; Vernon C Maino; Mary L Disis; Holden T Maecker
Journal:  J Immunol       Date:  2007-08-15       Impact factor: 5.422

5.  flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding.

Authors:  Yongchao Ge; Stuart C Sealfon
Journal:  Bioinformatics       Date:  2012-05-17       Impact factor: 6.937

6.  Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.

Authors:  Nima Aghaeepour; Pratip K Chattopadhyay; Anuradha Ganesan; Kieran O'Neill; Habil Zare; Adrin Jalali; Holger H Hoos; Mario Roederer; Ryan R Brinkman
Journal:  Bioinformatics       Date:  2012-02-29       Impact factor: 6.937

Review 7.  Biomarkers in cardiovascular clinical trials: past, present, future.

Authors:  Sharif A Halim; L Kristin Newby; E Magnus Ohman
Journal:  Clin Chem       Date:  2012-01       Impact factor: 8.327

Review 8.  Computational analysis of high-throughput flow cytometry data.

Authors:  J Paul Robinson; Bartek Rajwa; Valery Patsekin; Vincent Jo Davisson
Journal:  Expert Opin Drug Discov       Date:  2012-06-18       Impact factor: 6.098

Review 9.  Biomarkers in psoriasis and psoriatic arthritis.

Authors:  Federica Villanova; Paola Di Meglio; Frank O Nestle
Journal:  Ann Rheum Dis       Date:  2013-04       Impact factor: 19.103

10.  Performance of plate-based cytokine flow cytometry with automated data analysis.

Authors:  Maria A Suni; Holli S Dunn; Patricia L Orr; Rian de Laat; Elizabeth Sinclair; Smita A Ghanekar; Barry M Bredt; John F Dunne; Vernon C Maino; Holden T Maecker
Journal:  BMC Immunol       Date:  2003-09-02       Impact factor: 3.615

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  9 in total

Review 1.  Immune biomarkers: the promises and pitfalls of personalized medicine.

Authors:  Joanna C D Willis; Graham M Lord
Journal:  Nat Rev Immunol       Date:  2015-03-27       Impact factor: 53.106

2.  Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data.

Authors:  Kieran O'Neill; Adrin Jalali; Nima Aghaeepour; Holger Hoos; Ryan R Brinkman
Journal:  Bioinformatics       Date:  2014-01-08       Impact factor: 6.937

3.  CytoML for cross-platform cytometry data sharing.

Authors:  Greg Finak; Wenxin Jiang; Raphael Gottardo
Journal:  Cytometry A       Date:  2018-12       Impact factor: 4.355

4.  High throughput automated analysis of big flow cytometry data.

Authors:  Albina Rahim; Justin Meskas; Sibyl Drissler; Alice Yue; Anna Lorenc; Adam Laing; Namita Saran; Jacqui White; Lucie Abeler-Dörner; Adrian Hayday; Ryan R Brinkman
Journal:  Methods       Date:  2017-12-27       Impact factor: 3.608

5.  Correlation of corneal immune cell changes with clinical severity in dry eye disease: An in vivo confocal microscopy study.

Authors:  Shruti Aggarwal; Ahmad Kheirkhah; Bernardo M Cavalcanti; Andrea Cruzat; Arsia Jamali; Pedram Hamrah
Journal:  Ocul Surf       Date:  2020-06-03       Impact factor: 5.033

6.  Characterization of innate lymphoid cells in human skin and blood demonstrates increase of NKp44+ ILC3 in psoriasis.

Authors:  Federica Villanova; Barry Flutter; Isabella Tosi; Katarzyna Grys; Hemawtee Sreeneebus; Gayathri K Perera; Anna Chapman; Catherine H Smith; Paola Di Meglio; Frank O Nestle
Journal:  J Invest Dermatol       Date:  2013-11-11       Impact factor: 8.551

7.  A Semi-automated Approach to Preparing Antibody Cocktails for Immunophenotypic Analysis of Human Peripheral Blood.

Authors:  Yoshinobu Koguchi; Iliana L Gonzalez; Tanisha L Meeuwsen; William L Miller; Daniel P Haley; Alice N Tanibata-Branham; Keith S Bahjat
Journal:  J Vis Exp       Date:  2016-02-08       Impact factor: 1.355

8.  Flow cytometry bioinformatics.

Authors:  Kieran O'Neill; Nima Aghaeepour; Josef Spidlen; Ryan Brinkman
Journal:  PLoS Comput Biol       Date:  2013-12-05       Impact factor: 4.475

9.  Immune cell phenotyping in low blood volumes for assessment of cardiovascular disease risk, development, and progression: a pilot study.

Authors:  Yvonne Baumer; Cristhian A Gutierrez-Huerta; Ankit Saxena; Pradeep K Dagur; Steven D Langerman; Kosuke Tamura; Joniqua N Ceasar; Marcus R Andrews; Valerie Mitchell; Billy S Collins; Quan Yu; Heather L Teague; Martin P Playford; Christopher K E Bleck; Nehal N Mehta; J Philip McCoy; Tiffany M Powell-Wiley
Journal:  J Transl Med       Date:  2020-01-17       Impact factor: 5.531

  9 in total

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