Abstract PR003: T cell receptor repertoire and diversity are prognostic markers in bladder cancer
Authors: Kristjánsdóttir Nanna , Kjær Asbjørn , Nordentoft Iver , Juul Randi I , Birkenkamp-Demtröder Karin , Ahrenfeldt Johanne , Strandgaard Trine , Radif Deema , Hodgson Darren , Abbosh Christopher , Aerts Hugo JWL , Agerbæk Mads , Jensen Jørgen B , Birkbak Nicolai J. , Dyrskjøt Lars 
Published: May 2024

Abstract
T cells represent essential effector cells in the intrinsic antitumor immune response. Cancer-specific T cells can recognize cancer neoantigens through their T cell receptors (TCRs). The expansion of these clones is believed to be an early response to malignancy. We hypothesized that the T cell landscape offers insights into immune competency. We aimed to characterize the TCR repertoire in patients with bladder cancer and explore correlations with disease outcomes. We analyzed the TCR landscape in a cohort of 119 patients with muscle-invasive bladder cancer (MIBC) treated with chemotherapy followed by radical cystectomy. Peripheral and tumor TCR repertoires were produced using ultradeep amplicon-based sequencing of the TCR beta chain. T cell fractions were inferred from whole exome sequencing data of blood DNA using TcellExTRECT. Latent viral DNA was investigated in plasma whole genome sequencing data using Kraken2. Antigen targets were estimated using GLIPH2. The T cell subtype compositions in tumor and blood were investigated in four patients with bladder cancer using the Chromium Single Cell Immune profiling kit from 10X Genomics. Low pre-treatment peripheral TCR diversity was associated with worse overall survival (HR = 2.3, p = 0.024, n = 119) in patients with MIBC, particularly when combined with a low fraction of circulating T cells (HR= 4.7, p = 0.00049, n = 67). We validated these findings in two independent cohorts of patients with MIBC (p = 0.01, n = 107; p = 0.042, n = 79). The low-diversity TCR repertoires were characterized by large expanded T cell clones that persisted over time. Longitudinal analysis indicated a potential adverse impact of treatment, evidenced by a reduction in TCR diversity and circulating T cells over time in patients with initially high-diversity repertoires. TCR target annotation revealed that expanded T cell clones disproportionately targeted latent viral infections and cytomegalovirus DNA detection was strongly associated with low TCR diversity (p = 5.3 × 10−5). We observed a notable disparity between tumor and peripheral blood TCR repertoires. Single-cell sequencing revealed that regulatory T cells were prevalent in the tumor, whereas a combination of cytotoxic and naïve T cells dominated the blood. More explicitly, expanded clones in the blood were commonly annotated as terminally differentiated effector memory T cells expressing high levels of cytotoxic and exhausted genes. Our results suggest that high peripheral TCR diversity and high T cell fraction are markers of general immune competence, reflecting the ability to eradicate cancer and other diseases. In contrast, the expanded persistent clones predominating the low peripheral TCR diversity repertoires are likely exhausted and less likely to exhibit tumor specificity or effective disease-fighting capabilities. Our findings underline the crucial role of the immune system in determining disease outcomes and highlight the potential for improving immune health as a promising approach for future treatment and prevention.
Citation Format: Nanna Kristjánsdóttir, Asbjørn Kjær, Iver Nordentoft, Randi I Juul, Karin Birkenkamp-Demtröder, Johanne Ahrenfeldt, Trine Strandgaard, Deema Radif, Darren Hodgson, Christopher Abbosh, Hugo JWL Aerts, Mads Agerbæk, Jørgen B Jensen, Nicolai J. Birkbak, Lars Dyrskjøt. T cell receptor repertoire and diversity are prognostic markers in bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr PR003.