When the T cell repertoire sets an example for integration and diversity

From the Robins lab, Human Biology Division

February 18, 2019 • By —By NR Chuvin

More than half of the people in the US have been infected by the cytomegalovirus (CMV) by the age of forty. Most infected people do not present any symptoms although the virus stays in the body for the remainder of their lives. However, CMV can create a life-threatening condition upon re-activation in immunodeficient patients or pregnant women. Additionally, in the elderly (after seventy), CMV infection is associated with increased mortality due to the weakening of the immune system. On one hand, it is thought that the ability of the immune system to mount a specific T cell response against CMV partially determines the outcome in older patients. On the other hand, some studies suggest that, following CMV reactivation, the expansion of T cell clones that are CMV-specific may alter the overall T cell repertoire. The T cell repertoire behaves like a databank of T cell clones, each of which is specific for an antigen. Hence, the broader the repertoire is, the more likely is the body able to mount an efficient response against any new pathogens. First author of a recent publication by the Robins lab on this topic, Dr. Paul Lindau explains: “We know that CMV chronically stimulates the immune system leading to incredibly large antigen-specific T cell clones. These massive clones have been hypothesized to expel smaller T cell clones from the T cell repertoire in order to maintain homeostasis, thereby reducing T cell repertoire diversity and the overall ability of the immune system to clear new infections”. However, the tools used so far by the researchers to track this repertoire lacked in specificity and sensitivity.

Recently, Dr. Harlan Robins, head of the Herbold Computational Biology Program and member of the Human Biology division, started a company, Adaptive Biotechnologies, based on his postdoctoral research at the Fred Hutchinson Cancer Research Center to commercialize a new technique to study T cell repertoire: the immunosequencing of the T Cell Receptor-b chain (TCRb). TCRb is the molecule responsible for specific antigen recognition within the TCR complex in T cells. This antigen specificity is so high that two T cells bearing the same TCRb are necessarily issued from the same original clone that proliferated in response to antigen recognition. Thus, quantitatively sequencing all the TCRbs allows to determine the number of T cells bearing each singular TCRb, leading to the calculation of the so-called clonality. The higher the clonality (closer to one), the lower the diversity of the repertoire. High clonality can be reached through specific expansion of few clones specific to a limited number of foreign antigens. To study the quality of the repertoire in different T cell subsets in response to CMV infection, Lindau and colleagues combined this sequencing method with cell sorting via flow cytometry and published their results in the Journal of Immunology.

The authors first examined, by TCRb immunosequencing, the T cell repertoire of 543 CMV-positive and CMV-negative patients from a previous study and analyzed the data comparing different age ranges. They focused on the overall proportion of the top 0.1% biggest clones in the CMV+ population (the 0.1% clones with the more T cells). The higher the proportion, the more the CMV-specific T cells have expanded. Confirming previous reports, this proportion was higher in CMV-positive compared to CMV-negative patients. Interestingly, the researchers observed an increase in the 0.1% most numerous T cells clones in the CMV-positive population older than 20 compared to younger ages. However, this increase stabilized in older age ranges, meaning that reactive T cell clones do not accumulate with increasing age.

Schematic representation of the different possible evolutions of the T cell repertoire following CMV-specific T cell expansion. Either non-reactive cells are expelled from the repertoire to maintain the same repertoire size (Model 1). Or the repertoire size increases to accommodate the expanded clones without compromising the overall repertoire diversity (Model 2). Illustration provided by Dr. Paul Lindau, adapted from publication by NR Chuvin.

To further understand these results, Lindau and colleagues performed the same analysis on a different T cell population sorted by flow cytometry, from five CMV-positive and three CMV-negative patients between the ages of 70 and 74. They could demonstrate that the CMV-specific clones were exclusively present in the CD8 memory and CD8 effector memory populations (antigen-experienced), but not in naïve cells. Moreover, when challenged with CMV antigens, these most numerous T cell clones were also the most reactive as assessed by the activation marker CD137. When assessing clonality of the different T cell subsets, the authors confirmed the results obtained in the previous larger cohort: although there is no difference in clonality of naïve T cells between CMV-positive and CMV-negative patients, the clonality of memory and effector memory CD8 T cells is increased in CMV-positive patients. Most surprisingly, when assessing the distribution of T cell clones in the naïve compartment, the authors observed the same results independently of the CMV infection status. In addition, they observed a dramatic increase of the CD8 T cell count in CMV-positive compared to CMV-negative patients. Lindau explains: “We found that T cell repertoire diversity is the same between elderly people with and without CMV and that the number of T cells in the body increases to maintain overall T cell repertoire diversity. This result is impactful because it demonstrates that the capacity of the T cell repertoire to recognize new infections is not diminished despite extreme perturbation by a lifelong infection. Furthermore, our work suggests that immune repertoire diversity is relatively stable despite a lifetime of pathogenic exposures.” Their results lead to the proposition of a new model for pathogen-specific T cell expansion and its influence on the repertoire (see figure). There are now two possibilities: “the ‘crowding out’ model where [non-specific] clones are expelled from the repertoire (second panel) and the ‘accommodation’ model where the repertoire simply grows in size (third panel)”, said Lindau.

If the repertoire diversity is maintained after CMV exposure even in the elderly, how should we account for the increased mortality CMV-positive patients after 70? Lindau proposes: “The diversity of T cell receptors is maintained indicating that the potential to recognize a novel pathogen is maintained; however, overall physiologic cellular fitness is maybe reduced due to cellular aging. The immune system is then unable to eliminate the pathogen despite recognition, which could account for the conventional wisdom that we are more prone to infection as we age.”

This work was supported by the Ellison Medical Foundation.

Fred Hutch/UW Cancer Consortium faculty members Drs Harlan Robins, Cameron Turtle, Stanley Riddell, and Edus Warren contributed to this research.

Lindau P, Mukherjee R, Gutschow MV, Vignali M, Warren EH, Riddell SR, Makar KW, Turtle CJ, Robins HS. 2019. Cytomegalovirus Exposure in the Elderly Does Not Reduce CD8 T Cell Repertoire Diversity. J Immunol. 202 (2) 476-483. DOI: https://doi.org/10.4049/jimmunol.1800217.