Why sequence the immune repertoire?

“Our immune system is the smartest and best doctor around, and if we can learn from the best, we can be better.”

Dr. Jian Han, founder and CSO of iRepertoire

Key questions: 

  1. What is the immune repertoire? In short, it is the collection of individual clonotypes produced by all B and T cells in the body.  
  1. Why is immune repertoire sequencing important? Sequencing the expressed T and B cell receptor genes in the immune repertoire provides a detailed picture of a person’s health.  

The importance of immune sequencing

The amount of diversity in the immune repertoire reflects the body’s ability to respond to disease. Immune profiles are clinically and diagnostically relevant because people with and without given diseases and with differing disease severity can exhibit distinct profile patterns.  

For instance, specific disease prognoses can lead to the evolution of similar or identical CDR3s in different patients. CDR3 sequencing can thus potentially be used for diagnosis. For a given patient, their immune repertoire may also be predictive of how they will respond to treatment or serve as a measure of treatment efficacy over time. 

At iRepertoire, we are deeply entrenched in the immunology field, and the technology we developed – from which our services are derived – was one of the first publications describing immune repertoire characterization with next generation sequencing (NGS). Immune repertoire sequencing has unique advantages compared to the more common diagnostic and prognostic techniques that predate it.  

Prior to the expansion of NGS, the secrets of the immune system were probed by analyzing proteins; however, protein-based diagnostic methods provide far less breadth and depth. The advantage of NGS-based methods is that the entire collection of T cell receptors (TCRs) and B cell receptors (BCRs) in a given patient can be probed simultaneously at the researcher’s depth of choice.  

Click here to learn more about iRepertoire’s immune sequencing technology

Advantages of immune repertoire sequencing

  • Clinically and diagnostically relevant
  • Helps predict treatment response
  • Increased breadth and depth compared to proteomics data
  • Simultaneously probe B and T cell receptors 
 

Case studies in immune repertoire sequencing 

Over the last decade, dozens of papers each year have demonstrated the potential of immune repertoire sequencing for investigating critical questions in health and medicine. A small sampling of these are described below.  

Clinical monitoring of T cell therapy using immune repertoire sequencing1 

There is a growing need for therapeutics for patients with HPV16+ malignancies. While previous vaccine and T cell therapeutic methods have been met with limited success, Quayle et al. describe a new and promising approach that utilizes a novel fusion protein, CUE-101, to act as a treatment for HPV16- driven tumors by enhancing tumor antigen-specific T cell activation. TCR library sequencing data was in part used to demonstrate that CUE-101 has the capacity to launch an effective antitumor immune response through selective activation and expansion of specific T cells. These findings show great potential for effective clinical trial use.  

Immune repertoire signatures of COVID-19 disease response and recovery2 

Detailed information about the immune response in COVID-19 patients is necessary to evaluate therapeutic options and assess vaccinations. Niu et al. utilized longitudinal analysis of T and B cell receptor transcripts to provide insight into the dynamic nature of the immune repertoire over the course of infection. This was made possible through technology that allowed for visualization of the full immune repertoire, and their findings suggest that while the immune response is dynamic, it follows a clear pattern. Their findings provide insight not only on infection response but also on how to assess clinical treatments.  

Immune repertoire signatures of H7N9 (bird flu) infection3 

In an attempt to identify protective antibodies against H7N9 infection, Huo et al. sequenced the BCR-heavy and TCR-beta chain libraries for patients that had been infected with the flu. They identified patterns in the immune repertoire associated with a positive prognosis and found that patients that ultimately survived the infection exhibited higher B cell diversity and lower T cell diversity. Hou et al. also identified a handful of potentially protective TCR and BCR clonotypes that were shared by survivors but were absent in non-survivors. 

Identifying B cell immune repertoire changes in response to gastric tumors4 

Katoh et al. examined the gastric tumor microenvironment to identify tumor-infiltrating immune cells (also known as tumor-infiltrating lymphocytes, or TILs). They found a wealth of infiltrating B cells, but limited T cell infiltration. Because little is known about the role of B cell immunity in cancer, they profiled the TIL repertoire and compared it with the composition of circulating immune cells. They found that IgG subtypes dominated in tumors, while IgA subtypes, which are usually associated with mucosal immunity, dominated in the GI mucosa. Tumor-infiltrating IgG’s also exhibited more clonal expansion than non-infiltrating IgG’s. Signatures suggesting B cell activation independent of T cells and a role for somatic hypermutation were also observed. Finally, they identified candidates for cancer therapeutics in the form of growth-suppressive B cell antibodies and their functional antigens. 

Probing the effect of a vegetarian diet on immune repertoire diversity5 

Diet has been shown to have effects on the immune system both directly, through nutrient and fat composition, and indirectly by shifting the composition of the microbiome. Zhang et al. profiled the immune repertoire of healthy volunteers both before and after switching to a 3-month lacto-ovo-vegetarian diet as well as long-term vegetarians to see if they could detect changes to the immune system based on animal product consumption. While there were no significant changes to the immune system in the short term, long-term vegetarians did show lower T cell diversity and higher B cell diversity compared to controls.  

Immune repertoire sequencing sheds light on T cell fate determination6 

Wang et al. sequenced T cell receptors to evaluate two competing hypotheses: 1) T cell fate is independent of TCR specificity, or 2) T cell fate is initiated through specific TCR-mediated interactions with a major histocompatibility complex. To determine if individual TCRs cluster within particular lineages (supporting hypothesis #2), they followed lineage-specific antibody pull-downs with TCR sequencing. They observed clonally expanded T cells of different fates, which suggests cell fate is determined downstream of TCR expression. 

Immune repertoire analysis in twins teases apart effects of heredity and disease7 

There is some evidence that the immune repertoire depends largely on environmental factors, not genetics. Even studies comparing fraternal and identical twins have suggested that environmental factors, such as whether or not someone is vaccinated for the flu, play a much more important role in the state of the immune system than genetic background. However, the effect of genetics on response to a continuous viral infection had not been previously explored. Jiang et al. sequenced TCRs of twins that had acquired HBV infections at birth. Immune repertoire signatures were highly concordant within twin pairs, and some – particularly V gene expression of beta chains – were shared by twins regardless of the consistency of infection. The similarity of immune repertoires between twins may help to explain the clinical observation that twins infected with HBV seem to have similar phenotypes.  

References

1. Quayle, S. et al. CUE-101, a Novel E7-pHLA-IL2-Fc Fusion Protein, Enhances Tumor Antigen-Specific T-Cell Activation for the Treatment of HPV16-Driven Malignancies. Clin. Cancer Res. 8, 1953-1964 (2020). 

2. Niu, X. et al. Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients. Front. Immunol. 11, 1–9 (2020). 

3. Hou, D. et al. Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients. Sci. Rep. 6, (2016). 

4. Katoh, H. et al. Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B Cell Antigens in Human Malignancies. Cell Rep. 20, 1073–1087 (2017). 

5. Zhang, C. et al. Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire. Front. Immunol. 9, (2018). 

6. Wang, C. et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc. Natl. Acad. Sci. U. S. A. 107, 1518–1523 (2010). 

7. Jiang, Q. et al. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochem. Biophys. Res. Commun. 497, 153–159 (2018).