Therapy Resistance Mechanisms for Cancer

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

We are harnessing a comprehensive suite of next-generation technologies-including whole-exome sequencing, bulk and single-cell RNA sequencing, and epigenetic profiling-to uncover how cancer cells evolve resistance to cutting-edge treatments such as small molecule inhibitors and adoptive cell therapies. Our focus is to understand, at a molecular level, how and why certain cancers escape targeted therapies and to design new interventions that can overcome or prevent such resistance. Medullary thyroid carcinoma (MTC) is a rare but aggressive form of thyroid cancer. While surgical removal of the thyroid (thyroidectomy) remains the cornerstone of treatment, its curative potential is limited by the fact that many patients are diagnosed at advanced stages. Nearly 50% of patients present with stage III or IV disease at diagnosis, where long-term survival drops dramatically-71% at 10 years for stage III and just 21% for stage IV. Even with the advent of targeted therapies such as RET inhibitors, approximately 10% of patients eventually develop metastatic disease, underscoring the urgent need for more effective strategies. Over the past decade, several tyrosine kinase inhibitors (TKIs) targeting the RET signaling pathway have been evaluated for advanced MTC. Among these, vandetanib and cabozantinib have received approval from both the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA). Vandetanib inhibits RET, EGFR, and VEGFR kinases, while cabozantinib targets RET, c-MET, and VEGFR. These drugs can produce meaningful tumor responses and delay disease progression. However, not all patients benefit, and those who do may eventually develop drug resistance-often accompanied by significant side effects that limit long-term tolerability. Our research is focused on understanding how resistance to these RET-targeted therapies develops, with the goal of designing smarter, more durable treatment combinations. By analyzing tumor DNA, RNA, and chromatin state over time, we are identifying the precise genetic and epigenetic changes that allow cancer cells to escape RET inhibition. For example, we have found that some MTC cells develop resistance through gene amplifications that increase mutant RET expression, or by acquiring secondary mutations (like the clinically observed p.G810S mutation) that directly block drug binding. In other cases, resistance arises not from the RET pathway itself but through alternative survival pathways, such as the RAS/MAPK signaling axis. These "bypass" mechanisms represent important vulnerabilities that we can target in combination with RET inhibitors. To address these challenges, we are developing and testing combination therapies that target RET alongside downstream effectors such as MEK, a key component of the RAS/MAPK pathway. In preclinical models, the combination of the selective RET inhibitor selpercatinib with the MEK inhibitor trametinib shows strong synergy-even in models that are already resistant to RET inhibition. This dual-therapy approach may offer a path forward for patients whose tumors have become refractory to current standard-of-care treatments. Beyond small molecule resistance, we are also deeply investigating resistance mechanisms to adoptive cell therapies, particularly Chimeric Antigen Receptor (CAR) T cell therapies. These therapies, which engineer a patient's own T cells to recognize and attack tumor cells, have shown promise in blood cancers but have performed poorly in solid tumors. The main challenges include heterogeneous expression of tumor-associated antigens (TAAs) across tumor cells, limited T cell persistence, and T cell exhaustion-a state in which immune cells lose their ability to function over time. To improve CAR T cell therapies for solid tumors, we focus on two targets: glypican-2 (GPC2) and CD276 (also known as B7-H3). These proteins are frequently-but inconsistently-expressed in neuroblastoma (NB), a deadly pediatric cancer. Rather than committing to a single antigen, we are developing bicistronic "OR" CARs (BiCisCARs) that allow a single T cell to attack any tumor cell expressing either GPC2 or CD276. This strategy reduces the risk of tumor escape due to antigen loss. To optimize CAR design, we use an advanced screening platform known as Pooled Competitive Optimization of CARs by CITE-seq (P-COCC). This technology allows us to evaluate CAR T cells at single-cell resolution, measuring both their surface protein expression and gene expression profiles simultaneously. Using this data, we identify the most potent CARs-those that kill tumor cells effectively while maintaining long-term fitness. We then validate these CARs in cytotoxicity assays, testing their ability to eliminate tumor cells. The top candidates are combined into a BiCisCAR, which is expected to demonstrate not only greater cytotoxicity but also resistance to exhaustion and prolonged persistence compared to single-antigen CARs. Early results suggest this approach significantly improves T cell function and durability-two of the most critical factors for success in solid tumor immunotherapy. To further understand what makes tumors resistant-or sensitive-to BiCisCARs, we are also employing CRISPR-based genome-wide knockout and activation screens in neuroblastoma cells. These functional genomics tools help us pinpoint the genes and pathways that tumors use to evade CAR T cells. Ultimately, this will allow us to design even more effective CAR constructs and combination strategies. Taken together, our research bridges precision oncology and immunotherapy, providing a comprehensive roadmap to overcome therapeutic resistance in both targeted and cell-based cancer treatments. By understanding the adaptive strategies of cancer cells, we aim to stay one step ahead-developing therapies that are not only effective at first use but remain durable over time.