Neoantigen vaccines stimulate the T cell recognition of novel antigens (neoantigens) commonly found in tumors and, as such, are seen as valuable tools in helping the immune system instigate tumor suppression. However, these treatments affect only a portion of those treated. A recent study by Neon Therapeutics suggests that the secret to which patients will respond may lie within their native T cells.
Using immune sequencing, they identified signatures of patient samples with progression-free survival 9 months post-therapy (PFS-9), demonstrated vaccine efficacy, and revealed surprising parallels between PFS-9 patients and chronic viral infection.
Establishing a baseline: TCR diversity as a biomarker of therapy response
Cancer is the result of the accumulation of mutations that lead to the rampant and uncontrolled growth of aberrant cells. Our immune system is the first and foremost defender in the fight to contain these tumors. Research has shown that somatic mutations in tumor cells lead to the presentation of neoantigens, which may be exploited to trigger T cell mediated tumor suppression. The challenge is determining which T cells are likely to respond.
Several recent studies suggest that repertoire diversity –– the relative abundance of different B and T cell clonotypes –– is associated with favorable outcomes in patients with cancer1-4.
Researchers at Neon Therapeutics sought to determine if this pattern holds true for neoantigen treatment response. Further, they developed a predictive model based on the combined analysis of peripheral blood TCR repertoires and frequencies of T and B cell subpopulations during pre-treatment with the goal of linking TCR repertoire diversity to long-term survivability5.
To accomplish this, they sequenced the immune repertoire of peripheral blood mononuclear cells (PBMCs) at each timepoint prior to combination therapy with an immune checkpoint inhibitor (nivolumab) and a novel neoantigen vaccine (NEO-PV-01). Their findings 1) indicate that samples from patients with PFS-9 have a significantly increased proportion of high-frequency clones and 2) suggest that TCR clonality could be used as a minimally invasive (from PBMC’s) biomarker for predicting response to the combination therapy.
Here’s what happens to the T cell repertoire of patients treated with a neoantigen cancer vaccine
The premise behind neoantigen vaccines is to present neoantigens –– such as those associated with tumors –– to activate T cells and encourage their attack of tumor cells. If neoantigen therapy works, we should be able to identify the activated T cells and measure changes in abundance following treatment for patients who respond. That’s exactly what the authors of this study did, using a combination of immune repertoire and single cell sequencing.
Neoantigen vaccines are commonly used alongside immune checkpoint inhibitors, which typically target checkpoint mediators that, when working properly, prevent T cell mediated killing of other cells. One such checkpoint mediator is PD-1, the target of nivolumab.
Poran et al. extracted T cells and RNA from 21 patients over the age of 18 with histologically or cytologically-confirmed unresectable or metastatic melanoma. PBMC samples were taken at three timepoints: before treatment with nivolumab (week 0), before treatment with the neoantigen vaccine NEO-PV-01 (10 weeks), and after treatment with nivolumab and the neoantigen vaccine (20 weeks). TCR repertoire profiling was done on each sample and assigned into groups representing the relative frequency of each TCR-beta CDR3 clone.
Using iRepertoire’s iR-Profile Reagent System, Poran et al. saw a strong relationship between the frequency of persistent clones and the frequency of CD8+ and CD4+ T cells across all patients. Conversely, there was a strong negative relationship between naive T cells and CTLA-4-expressing T cells.
Interestingly, when comparing pre-vaccination with post-vaccination turnover (relative to pre-treatment with nivolumab) in patients with PFS-9, no difference was observed. Likewise, the turnover of TCR clones in patients without PFS-9 increased from pre-vaccination to post-vaccination. TCR-alpha sequencing results matched those of TCR-beta, showing a higher incidence of increased frequency clones in PFS-9 patients than in those without PFS-9.
Poran et al. then went on to further characterize and validate particular TCRs associated with antigen activation. Using iRepertoire’s iPair single cell sequencing, the researchers found that four of the validated TCRs only expanded following vaccination, which suggests a potential benefit to using a neoantigen vaccine in combination therapies. Taken together, the findings suggest that patients with high, stable TCR clonal frequency respond better to treatment.
Surprising parallels with chronic viral infection
Interestingly, the increased clonality of peripheral TCR repertoires seen in PSF-9 patients resembles those who have a chronic viral infection. A comparable enrichment of effector T cells has been previously reported in patients with chronic viral infections6. More research should be done to elucidate this potential relationship as it could suggest that there are similarities in the immune phenotypes of patients with PFS-9 and those with a chronic viral infection.
Using TCR repertoires to prognose and customize cancer treatment
Having a diverse and stable TCR repertoire has been shown to relate to better patient response to clinical therapies. However, previous research has been inconsistent in tying this to patient response to immunotherapy. Poran et al. has demonstrated a clear relationship between increased, stable clonal baseline TCR repertoires and increased PFS, providing strong evidence of a prognostic relationship between a patient’s TCR repertoire and their outcome following immunotherapy.
These findings indicate that PFS in metastatic melanoma patients can be predicted with pre-treatment peripheral blood samples, which strongly suggests a pre-existing immune state that is amenable to immune modulation through immune checkpoint inhibitors and/or neoantigen therapy. Additionally, in some patients, metastatic cancer leads to changes in the peripheral blood immune repertoire, rendering these patients more likely to respond to immunotherapy. Using minimally invasive PBMC collection to examine the patient immune repertoire could offer a simple, safe approach to determining patient prognosis to immunotherapy in metastatic cancer.
TCR repertoire analysis offers a pragmatic clinical approach to assess patients’ immune state and to direct therapeutic decision-making therein. iRepertoire supports this by offering complementary technologies for sequencing paired chains in single cells and bulk immune repertoires for any or all BCR and TCR chains. Ultimately, immune profiling using iRepertoire’s technology could assist in the development of customized prognostic insight for an in-depth, personalized medical approach.
References
- Postow MA, Manuel M, Wong P, Yuan J, Dong Z, Liu C, et al. Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma. Journal for ImmunoTherapy of Cancer. 2015;3(1).
- Hopkins AC, Yarchoan M, Durham JN, Yusko EC, Rytlewski JA, Robins HS, et al. T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma. JCI Insight. 2018;3(13).
- Hosoi A, Takeda K, Nagaoka K, Iino T, Matsushita H, Ueha S, et al. Increased diversity with reduced “diversity evenness” of tumor infiltrating T-cells for the successful cancer immunotherapy. Sci Rep. 2018;8(1):1058.
- Topalian SL, Drake CG, Pardoll DM. Immune checkpoint blockade: a common denominator approach to cancer therapy. Cancer Cell. 2015;27(4):450-61.
- Poran A, Scherer J, Bushway ME, Besada R, Balogh KN, Wanamaker A, et al. Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1. Cell Reports Medicine. 2020;1(8).
- Lindau P, Mukherjee R, Gutschow MV, Vignali M, Warren EH, Riddell SR, et al. Cytomegalovirus Exposure in the Elderly Does Not Reduce CD8 T Cell Repertoire Diversity. J Immunol. 2019;202(2):476-83.