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Seasonal Allergic Rhinitis and Systems Biology-Oriented Biomarker Discovery

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General Methods in Biomarker Research and their Applications

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Abstract

There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems that are studied: all levels of structural and functional complexity, explicitly including the supracellular domain; their systems behavior or phenotypes; their networks with relationships that interact with the genome, the environment, and the phenotype; and their multifactorial processes involved in maintaining homeostasis and the breakdown of homeostasis within the system. This shift from a more reductionist to a more holistic approach on both the epistemological (theoretical) and the methodological level is also important for the conceptualization and the development of biomarkers.

Based on the dataset of a randomized controlled trial on the effects of a treatment of seasonal allergic rhinitis, using five different methods of permuted stepwise regression, three systems biology-oriented immunological pattern variables (biomarkers) were developed that demonstrated larger CV correct values than the separate cytokines with regard to the classification of cytokine samples in baseline (before treatment) and post-baseline (after treatment).

This example demonstrates that a systems biological approach in both the conceptualization and development of biomarkers is promising. However, more empirical studies with larger datasets are necessary to confirm the positive results of the presented study.

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Abbreviations

A2M:

Alpha-2-Macroglobulin

C:

Celsius

CD4:

Cluster of Differentiation 4

ConeLasso:

A Rescaled Version of Lasso

CV Correct:

Cross-Validated Correct Rate of Classification

DNA:

Deoxyribonucleic Acid

IFN-γ:

Interferon Gamma

IG:

Immunoglobulin

IL:

Interleukin

Lasso:

Least Absolute Shrinkage and Selection Operator

mL:

Milliliters

NL:

The Netherlands

OMP:

Orthogonal Matching Pursuit

PBMC:

Peripheral Blood Mononuclear Cell Fraction

Phl p 1:

Phleum Pretense

PStR:

Permuted Stepwise Regression

R2 :

R Squared

RAST:

Radioallergosorbent Testing

RNA:

Ribonucleic Acid

SAR:

Seasonal Allergic Rhinitis

StepwiseForwardP:

Forward Stepwise Selection

StepwiseP:

Stepwise Selection

TGF-β:

Transforming Growth Factor Beta

Th Cells:

T-Helper Cells

TNF-α:

Tumor Necrosis Factor Alpha

Treg Cells:

Regulatory T Cells

μg:

Microgram

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Acknowledgments

Parts of the text of this article concerning the development of the systems biological biomarkers are previously published in Baars et al. (2012).

Author information

Authors and Affiliations

  1. University of Applied Sciences Leiden, Zernikedreef 11, NL-2333 CK, Leiden, The Netherlands

    Erik W. Baars

  2. Louis Bolk Institute, Hoofdstraat 24, NL-3972 LA, Driebergen, The Netherlands

    Erik W. Baars

  3. Muvara, Tijmtuin 8, 2353 PH, Leiderdorp, The Netherlands

    Andreas F. M. Nierop

  4. Cell Biology and Immunology Group, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, The Netherlands

    Huub F. J. Savelkoul

Authors
  1. Erik W. Baars
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  2. Andreas F. M. Nierop
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  3. Huub F. J. Savelkoul
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Correspondence to Erik W. Baars .

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Editors and Affiliations

  1. Department of Nutrition and Dietetics, Division of Diabetes & Nutritional Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom

    Victor R. Preedy

  2. Faculty of Science & Technology, Department of Biomedical Sciences, University of Westminster, London, United Kingdom

    Vinood B. Patel

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Baars, E.W., Nierop, A.F.M., Savelkoul, H.F.J. (2015). Seasonal Allergic Rhinitis and Systems Biology-Oriented Biomarker Discovery. In: Preedy, V., Patel, V. (eds) General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7696-8_33

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