Following are public and technical abstracts for the Resistance to Immune Therapy project funded by the Department of Defense Kidney Cancer Research Program (KCRP) for 2017.
Principal Investigators: Catherine Wu and Michael Atkins (research partners)
Institutions: Dana-Farber Cancer Institute and Georgetown University
Funding Mechanism: Translational Research Partnership
Award Amounts: $837,705 and $194,963
Public Abstract
Kidney cancer (also known as renal cell cancer, or “RCC”) is one of the 10 most common cancers in the United States, and one of the 5 most commonly diagnosed cancers in the VA system. Each year, over 60,000 people are newly diagnosed with RCC and 14,000 patients die from the disease. One-third of patients either have at the time of diagnosis, or ultimately develop, disease spread to distant areas of the body (called “advanced” kidney cancer). While there have been many new therapies developed for patients with advanced kidney cancer over the past decade, still only 8% to 12% of patients with advanced kidney cancer live for 5 years or longer.
Recently, a new type of therapy, called immune checkpoint blockade (or “CPB”), has shown considerable success in the treatment of patients with advanced RCC. These therapies work by “removing the brakes” on the immune system, allowing a patient’s immune cells to recognize and, in some cases, eliminate kidney cancer cells throughout the body. One such therapy, called nivolumab (or “nivo”), is already approved as a second-line treatment (after a patient’s cancer has grown on another therapy), and the combination of nivo with another immune checkpoint blocking drug called ipilimumab (or “ipi”), is poised to become the dominant first-line treatment option for patients with advanced kidney cancer. This clinical progress raises several fundamental questions with direct impact on patient clinical care: (1) Can we identify in advance which patients will benefit from nivo therapy? (2) Can the combination of nivo + ipi work in patients who fail to respond to single agent nivo therapy and, if so, in which patients? To address these important questions we have launched a clinical trial of first-line nivo therapy, and if no response, then combination nivo + ipi, in patients with advanced RCC (the HCRN GU16-260 trial). This trial will also allow us to study each patient’s tumor in the laboratory, where we hope to identify features of the tumor (biomarkers) that will allow us to predict in advance which patients will benefit from single agent nivo therapy, which patients need the combination of nivo + ipi, and which patients will not benefit from either treatment.
However, despite the ability of CPB therapies to lengthen the lives of patients with kidney cancer, over half the patients have disease that is resistant to these treatments. Thus, in addition to identifying which patients will benefit from single agent and combinations of CPB drugs (like nivo and ipi), a fundamental challenge is to understand why certain patients’ tumors are resistant to treatment and then to design combinations of therapies to overcome this resistance so that more patients with RCC can benefit from CPB therapies.
Patients can be resistant to CPB therapies for many reasons, including the presence of individual resistant tumor cells, or dysfunction in the patient’s immune response to the tumor. Traditional laboratory methods for analyzing tumors average the effects of all cells (tumor and immune) together — meaning the effects of individual resistant tumor cells or dysfunctional immune cells are obscured in the analysis. This problem is particularly relevant to kidney cancer, which is characterized by remarkable variability in both its tumor cell and immune cell components. A new technology called single-cell RNA-sequencing (or “scRNA-seq”) can overcome this obstacle. ScRNA-seq provides a unique ability to define the composition and function of tumor and immune subpopulations within the tumor mass and understand the role individual cells play in response and resistance to CPB therapy.
In this grant proposal, we aim to use scRNA-seq to dissect and analyze individual tumor and immune cells using tumor samples collected from the HCRN GU16-260 clinical trial. We will integrate our analysis of individual cells with information about each patient’s response (or resistance) to nivo therapy. Through this analysis, we aim to discover how individual tumor and immune cell populations and/or their attributes contribute to response or resistance to CPB in kidney cancer and to thereby develop biomarkers for predicting patient outcomes and rationally choosing therapies for future patients. As this trial will complete patient recruitment in 2018, and will have results by 2020, we believe it provides our research team, which combines extensive expertise in kidney cancer biology and immunotherapy with similar expertise in tumor and immune system analysis, a unique and real-time opportunity to translate scientific discovery into clinical benefit for patients with kidney cancer over next few years.
Technical Abstract
Renal cell carcinoma (RCC) is one of the ten most common cancers in the United States, and one of the five most commonly diagnosed cancers in the VA system. Nearly one-third of patients with RCC present with or ultimately develop metastatic disease and, despite important advances in the treatment of advanced RCC, the 5-year survival rate for these patients is only 8% to 12%. Immune checkpoint blockade (CPB) has shown considerable success in the treatment of metastatic RCC; however, many patients do not respond to single agent or even combination CPB. The fundamental challenges ahead are to identify which patients will benefit from CPB and to understand and eventually overcome mechanisms of resistance to CPB. To begin to address these challenges, we have launched a prospective multi-center phase 2 clinical trial of front-line nivolumab (nivo) monotherapy followed by salvage nivo + ipilimumab, if no response, in patients with advanced RCC (HCRN GU16-260/NCT03117309), which includes (already funded) immunohistochemical (IHC) and bulk genomic (WES) and transcriptomic (RNA-seq) correlative analyses to provide more robust predictive biomarkers of response and resistance.
While the study of bulk cell populations can provide important insights, such analyses average effects over a population and can therefore obscure important signals from heterogeneity that drive therapeutic response or resistance, including to CPB. Intratumoral heterogeneity has been found to be a particularly important feature of RCC, where such heterogeneity may lead to the emergence of subclones that are associated with poor prognosis. Consequently, efforts to develop predictive markers of immune response and identify mechanisms of immune resistance using only bulk tumor analyses (IHC, WES, and RNA-seq) may be particularly problematic in RCC. Single-cell transcriptomics technology (scRNA-seq) enables comprehensive and unbiased profiling of the tumor and immune microenvironment and is already transforming our understanding of cancer biology and providing insight into mechanisms of therapeutic resistance in several cancer types. Because of the extensive intratumoral heterogeneity in RCC, scRNAseq is uniquely suited to define the composition and transcriptional state of tumor and immune subpopulations and help us understand the role they play in response and resistance to CPB in RCC.
We hypothesize that the co-evolution of tumor and its immune microenvironment in the setting of therapeutic exposure drives resistance to immunotherapy. To this end, we will simultaneously dissect both tumor and immune microenvironment heterogeneity using our established robust workflows for scRNA-seq.
Aim 1: Define the composition, transcriptional state, and evolution of gene expression programs of tumor cells and tumor-infiltrating immune cells that drive primary resistance to nivo. Using paired pre-treatment and post-nivo resistance fresh tumor samples, we will use scRNA-seq to examine tumoral transcriptional heterogeneity and to provide a comprehensive, unbiased phenotyping of immune populations, enabling better understanding of cellular heterogeneity in the RCC microenvironment and its relationship to treatment response.
Aim 2: Determine the number, state, and specificity of tumor-infiltrating T cell clones in patients receiving nivo. We will perform paired alpha-beta scTCR sequencing, cloning, reconstruction, and neoantigen specificity testing to understand T cell-related mechanisms of resistance to CPB, with the goal of ultimately being able to design therapies to overcome these resistance mechanisms.
Aim 3: Validate immune or tumor subpopulations and transcriptional signatures associated with response and resistance to nivo. We will validate gene expression signatures and protein markers of response and resistance in the larger HCRN GU16-260 cohort through interrogation of bulk RNA-seq data and novel IHC stains.
ScRNA-seq analysis will allow us to fully characterize the tumor and immune subpopulations and determine the specificity and functional state of tumor-infiltrating T cells in baseline and nivo-resistant RCC specimens. Combining this data with the unique clinical information, IHC, and bulk genomic and transcriptomic analyses from the HCRN GU16-260 trial will enable us to identify biomarkers of response and mechanisms of resistance to CPB. Understanding the mechanisms of intrinsic resistance to nivo should enable the rational application of personalized combination regimens necessary to successfully unleash the potential of immunotherapy for the majority of patients with advanced RCC.