How can we see our immune system?

20 January 2015
By Rachael Bashford-Rogers

The B-cell sequence networks for a patient with chronic lymphocytic leukemia (i) prior to and (ii) after second cycle of treatment. Credit: DOI: 10.1101/gr.154815.113

The B-cell sequence networks for a patient with chronic lymphocytic leukaemia (i) prior to and (ii) after second cycle of treatment. Credit: DOI: 10.1101/gr.154815.113

Humans are constantly surrounded (and outnumbered) by bacteria, viruses and other potentially harmful entities. One of the main lines of defence against such infectious agents are special proteins, known as antibodies, produced by specialised immune cells, known as B-cells.

Therefore, understanding B-cell biology and population dynamics are of considerable clinical importance. But, how can we see B-cell populations?

With the advent of high-throughput sequencing, we have been able to develop methods of sequencing unique sections of DNA from individual B-cells. B-cells are continually being generated in our bone-marrow during which each maturing B-cell undergoes DNA recombination, such that each B-cell genome generates new antibodies. This means that each B-cell clone (i.e. a collection of related B-cells) has a unique DNA sequence encoding for its antibody, like a cellular barcode.

We have recently developed fast, reproducible methods for sequencing and analysing these antibody sequences from B-cell populations, such as from a simple sample of blood. These methods give us an insight into the workings of the immune system in health and disease. So, what can we see in these B-cell populations?

As we expected, analysis of the sequence data shows us that healthy individuals have very diverse B-cell populations and low numbers of related antibody sequences. When a B-cell is stimulated to multiply (i.e. making many copies of itself by dividing, known as B-cell clonal expansion), such as during infection or in B-cell blood cancers, we can observe a massive increase in clonality in the B-cell antibody repertoire (i.e. lots of B-cells producing the same antibody sequence).

We have been able to, for the first time, use antibody sequence networks to quantify population differences between different diseases, accurately assess the population changes over time within individuals, thus providing a valuable tool to immunologists for seeing immune responses.

These exciting tools have many implications in both immunology and patient care. We have shown that antibody sequencing has higher sensitivity for detecting cancer B-cells than currently used clinical methods. Therefore these methods may be used by clinicians for better monitoring of patients with cancer or other blood disorders, deciding treatment strategies, and, potentially, for patient disease diagnosis.

In addition, antibodies generated in response to infection may be used to develop highly effective therapeutics. This is particularly important in the field of emerging infectious diseases, such as MERS and Ebola, where there are no current effective treatments or vaccines. Indeed, in our lab, we have used antibody sequencing to characterise novel antibodies that can effectively bind and neutralise multiple HIV strains.

Antibody sequencing is only in its infancy with many exciting avenues of exploration, and with great potential to improve therapies and patient outcomes. So, what we will see next in our immune system?

Rachael Bashford-Rogers has just completed a PhD where she worked under the supervision of Prof. Allan Bradley and Prof. Paul Kellem on the development of novel, robust and sensitive experimental and computational approaches for analysing B-cell and T-cell populations and dynamics using high-throughput B- and T-cell receptor sequencing respectively, thus revealing insights into the immunology and disease biology.

References

  • Bashford-Rogers RJM, et al (2014). Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods. BMC ImmunologyDOI:10.1186/s12865-014-0029-0
  • Bashford-Rogers RJM, et al (2015). Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. Genome ResearchDOI:10.1101/gr.154815.113
  • Cotten M, et al (2013). Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. The LancetDOI:10.1016/S0140-6736(13)61887-5
  • McCoy L, et al (2014). Molecular Evolution of Broadly Neutralizing Llama Antibodies to the CD4-Binding Site of HIV-1. PLOS PathogensDOI:10.1371/journal.ppat.1004552

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