Review
Meeting the challenges of measuring human immune regulation

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Abstract

Data is now emerging that many human diseases not previously considered immune diseases have an immunological basis. As such human immunology is in need of more standardized systems-wide methods for monitoring immune regulation. Despite significant advances in basic immunology research, thousands of patients visiting health practitioners daily still have no reliable immunological metrics by which to assess the status of their immune health beyond the standard blood count. Further investigations are costly, time consuming and often don't offer significant insights into the mechanics of immune deviation or regulation. The immune system meets many criteria of complex biological networks and therefore systems-wide approaches are highly suitable to determining the emergent properties of immune responses. Standardization of immune monitoring, the development of new technology and integrated informatics approaches are needed in order to identify useful hematological and serological markers that are informative for immune health. This brief review outlines some of the more promising developments in systems immunology.

Introduction

Effective immune regulation is critical to human health, and there is growing recognition that dysregulation of the immune system underlies many human diseases. Aberrant immune responses are thought to be a common risk factor for the development of many complex diseases, including diabetes, autoimmunity, allergy, cancer and atherosclerotic disease (Prescott, 2013). Until recently, our knowledge of the determinants of immune homeostasis and their relationship with the development of complex diseases has been limited. Much of this can be attributed to conventional reductionist methods for assessing immune function, which do not often give a complete picture of the immune network (Shen-Orr, 2012). As with genomics, the field of immunology is evolving with regard to new methodologies that now enable researchers to take a systems approach toward a more comprehensive understanding of immune homeostasis in the development of complex diseases. Capitalizing on the strengths of these applications is likely to require a shift in the way research is done. As these new approaches become more affordable and standardized there will be a significant opportunity for the development of new therapeutics and diagnostics relating to the immune system, how it functions as a network and how it is regulated. In this article we explore the emerging technologies that are likely to significantly contribute to achieving this goal.

Section snippets

The problem of increasing complexity and the need for systems immunology

The human immune system is a rich and complex network of highly compartmentalized, local tissue immune processes interconnected via circulating immune cells in the periphery. We know a lot about the individual components of the immune network, but know very little about how these components coordinately regulate the emergent properties of the system, and its response to the environment. The level of complexity in the immune network in terms of the cellular and functional heterogeneity among

Phenotyping the entire cellular immune network using flow cytometry

Flow cytometry is the current gold-standard technique for cellular immune phenotyping. In flow, properties of cells are resolved on the basis of characteristic markers, which can be targeted using fluorescently labeled monoclonal antibodies in a highly specific and sensitive manner. Immune phenotyping is commonly performed on a variety of biological specimens, including blood, bone marrow, serous cavity fluids, cerebrospinal fluid, urine, and more recently solid tissues with techniques focussed

Beyond flourophores to ionization: mass cytometry

Mass cytometry is an emerging alternative technology for immune phenotyping that is more scalable than flow, as it can incorporate more information without data accuracy compromise (Ornatsky et al., 2010, Bendall et al., 2012). In mass cytometry cell markers (cell surface and signaling proteins) are targeted by antibodies conjugated to metal ion tags rather than flourophores. Labeled cells are individually ionized and the resulting atomic ion cloud from each cell is captured using time of

Standardized platforms for monitoring immune protein networks in patient specimens

Evaluating immune function by means of sera antibody and protein analyte screening has useful applications for autoimmune disorders, allergy testing, evaluating infectious disease and vaccine responses. The ELISA has traditionally been the workhorse assay used to measure immune function from a serological sample, however, these low throughput approaches have now been scaled up into multiplexed bead assays that allow higher throughput, reduced sample volume and lower costs. Luminex™ xMAP bead

Monitoring the network of antigen-specific receptor diversity

Monitoring the changing diversity of antigen-specific receptors provides information about the specificity of the immune network at the genomic level. Dysregulation in complex and tightly regulated process of T- and B-cell gene rearrangement can result in inappropriate immune responses and subsequent disease. Traditionally Southern-blot and PCR have been used to quantify immune receptor diversity and proliferation assays have provided robust measures of antigen-specificity. These techniques are

Microfluidics and single-cell technologies

Measuring the specific properties of individual immune cells as opposed to measuring the average response of a heterogeneous cell population has many advantages. Single-cell analysis is gaining momentum and is likely to yield a new understanding of the polyclonal and polyfunctional nature of immune cells. Several technologies are emerging which mostly rely on the fabrication of picoliter-scale micro channel systems that permit precise handling of very small clinical samples such as cytobrushes

The genomics revolution

The application of ‘omics’ technology in human immunology has provided the opportunity to define immune cells on the basis of ‘transcriptomes’, ‘genomes’ and ‘epigenomes’ (Northrup, 2011). Sequencing technology and chromatin immunoprecipitation techniques now provide a global view of how transcription-factor networks coordinate with DNA on a genome-scale and determine cell fate decisions (Samstein et al., 2012). These technologies have expanded our view of T-cell differentiation beyond

Systems wide data analysis

As with any high-throughput technology, significant gains in data quantity come at the expense of significant investments in data analysis time. This shifts the bottleneck in research from data acquisition to data processing and analysis. Integrative data analysis strategies that incorporate the various components of the immune system discussed here will yield large amounts of comprehensive data. These data will inevitably be extremely useful for determining the extent to which changes in one

Summary

Immunology has yet to enjoy the technological advances that have catalyzed the measurement of single variables to high-dimensional data space. Metabolomics and lipidomics are relatively new players in this field joining more established methods in genomics and proteomics. The potential rewards are huge, yet the challenges are equally formidable since the dynamic range over which the immune system is regulated is enormous (mucosal tissue immune responses, circulating cellular immune responses,

Conflict of interest

The authors declare no conflicts of interest.

References (33)

  • P.D. Baum et al.

    Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors

    Eur. J. Immunol.

    (2012)
  • S.C. Bendall

    Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum

    Science

    (2011)
  • Dmitry A. Bolotin

    Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms

    Eur. J. Immunol.

    (2012)
  • Dmitriy A. Bolotin

    MiTCR: software for T-cell receptor sequencing data analysis

    Nat. Methods

    (2013)
  • U.M. Braga-Neto et al.

    From functional genomics to functional immunomics: new challenges, old problems, big rewards

    PLoS Comput. Biol.

    (2006)
  • C.M. Britten

    Toward the harmonization of immune monitoring in clinical trials: quo vadis?

    Cancer Immunol. Immunother.

    (2007)
  • Cited by (0)

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    Both authors contributed equally to this work.

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