DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma.

Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.

Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy.

Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.

Effects of Regulatory T Cell Depletion in BALB/c Mice Infected with Low Doses of Borrelia burgdorferi.

We previously demonstrated that a depletion of regulatory T (Treg) cells in Lyme arthritis-resistant C57BL/6 mice leads to pathological changes in the tibiotarsal joints following infection with Borrelia burgdorferi. Here, we assessed the effects of Treg cells on the response to B. burgdorferi infection in BALB/c mice, which exhibit infection-dose-dependent disease and a different sequence of immune events than C57BL/6 mice. The depletion of Treg cells prior to infection with 1 × 102, but not 5 × 103, organisms led to increased swelling of the tibiotarsal joints. However, Treg cell depletion did not significantly affect the development of histopathology at these low doses of infection. BALB/c mice depleted of Treg cells before infection with 1 × 103 spirochetes harbored a higher borrelial load in the hearts and exhibited higher levels of serum interleukin-10 five weeks later. These results indicate that Treg cells regulate certain aspects of the response to B. burgdorferi in a mouse strain that may display a range of disease severities. As the presentation of Lyme disease may vary among humans, it is necessary to consider multiple animal models to obtain a complete picture of the various means by which Treg cells affect the host response to B. burgdorferi.