While immune checkpoint blockade elicits efficacious responses in many cancer patients, it also produces a diverse and unpredictable number of immune-related adverse events (IRAE). Mechanisms driving IRAE are generally unknown. Because CTLA-4 blockade leads to proliferation of circulating T cells, we examined in this study whether ipilimumab treatment leads to clonal expansion of tissue-reactive T cells. Rather than narrowing the T cell repertoire to a limited number of clones, ipilimumab induced greater diversification in the T cell repertoire in IRAE patients compared to patients without IRAE. Specifically, ipiliumumab triggered increases in the numbers of clonotypes, including newly detected clones and a decline in overall T cell clonality. Initial broadening in the repertoire occurred within 2 weeks of treatment, preceding IRAE onset. IRAE patients exhibited greater diversity of CD4+ and CD8+ T cells, but showed no differences in regulatory T cell numbers relative to patients without IRAE. PSA responses to ipilimumab were also associated with increased T cell diversity. Our results show how rapid diversification in the immune repertoire immediately after checkpoint blockade can be both detrimental and beneficial for cancer patients.

Sipuleucel-T is an autologous cellular therapy for asymptomatic, or minimally symptomatic, metastatic castrate-resistant prostate cancer, designed to stimulate an immune response against prostate cancer. In a recent clinical trial (NCT00715104), we found that neoadjuvant sipuleucel-T increased the number of activated T cells within the tumor microenvironment. The current analysis examined whether sipuleucel-T altered adaptive T-cell responses by expanding pre-existing T cells or by recruiting new T cells to prostate tissue.

BackgroundCancer immunotherapy has demonstrated significant clinical activity in different cancers. T cells represent a crucial component of the adaptive immune system and are thought to mediate anti-tumoral immunity. Antigen-specific recognition by T cells is via the T cell receptor (TCR) which is unique for each T cell. Next generation sequencing (NGS) of the TCRs can be used as a platform to profile the T cell repertoire. Though there are a number of software tools available for processing repertoire data by mapping antigen receptor segments to sequencing reads and assembling the clonotypes, most of them are not designed to track and examine the dynamic nature of the TCR repertoire across multiple time points or between different biologic compartments (e.g., blood and tissue samples) in a clinical context.ResultsWe integrated different diversity measures to assess the T cell repertoire diversity and examined the robustness of the diversity indices. Among those tested, Clonality was identified for its robustness as a key metric for study design and the first choice to measure TCR repertoire diversity. To evaluate the dynamic nature of T cell clonotypes across time, we utilized several binary similarity measures (such as Baroni-Urbani and Buser overlap index), relative clonality and Morisita’s overlap index, as well as the intraclass correlation coefficient, and performed fold change analysis, which was further extended to investigate the transition of clonotypes among different biological compartments. Furthermore, the application of differential testing enabled the detection of clonotypes which were significantly changed across time. By applying the proposed “3D” analysis pipeline to the real example of prostate cancer subjects who received sipuleucel-T, an FDA-approved immunotherapy, we were able to detect changes in TCR sequence frequency and diversity thus demonstrating that sipuleucel-T treatment affected TCR repertoire in blood and in prostate tissue. We also found that the increase in common TCR sequences between tissue and blood after sipuleucel-T treatment supported the hypothesis that treatment-induced T cell migrated into the prostate tissue. In addition, a second example of prostate cancer subjects treated with Ipilimumab and granulocyte macrophage colony stimulating factor (GM-CSF) was presented in the supplementary documents to further illustrate assessing the treatment-associated change in a clinical context by the proposed workflow.ConclusionsOur paper provides guidance to study the diversity and dynamics of NGS-based TCR repertoire profiling in a clinical context to ensure consistency and reproducibility of post-analysis. This analysis pipeline will provide an initial workflow for TCR sequencing data with serial time points and for comparing T cells in multiple compartments for a clinical study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1544-9) contains supplementary material, which is available to authorized users.

Background: Prostate cancer is one of leading causes of cancer death among men worldwide. Androgen deprivation therapy is a central part of the prostate cancer treatment algorithm, however, resistance to androgen deprivation commonly leads to disease progression. Mutations in the phosphoinositide-3-kinase pathway (PI3K) have been implicated in cancer progression and the development of castration-resistance. Thus, inhibitors of this pathway and its downstream signaling partners have been studied as potential therapeutic agents to treat metastatic castration resistant prostate cancer (mCRPC). In this article, we review recent clinical results for novel targeted therapies against the PI3K-AKT-mTOR pathway. Materials and Methods: Trials included in this systemic review were identified through conference abstracts, citations in review articles, PubMed, and ClinicalTrials.gov . Trial eligibility was independent of clinical setting or sample size. Results: A total of 13 prospective clinical trials between 2012 and 2020 were reviewed: Two trials for pan-PI3K inhibitors, 2 trials for selective PI3K inhibitors, 4 trials for AKT inhibitors, 5 trials for mTOR inhibitors, and 1 for a combined PI3K and mTOR inhibitor. All studies were phase I or II studies with primary outcomes of either safety and tolerability or efficacy. Conclusion: Overall, pan-PI3K inhibitors and selective-PI3K inhibitors have not demonstrated clinical efficacy and may have significant adverse effects. AKT inhibitors may have significant adverse effects, but showed some evidence of improved survival. mTORC1 inhibitors show modest efficacy and significant adverse effects.