The precision oncology approach to the treatment of cancer bases treatment decisions on the biology of an individual’s cancer, most often using genetic alterations or mutations to inform therapy. This approach has been successful in a few cancer types, including lung cancer, melanoma, and chronic myelogenous leukemia where oral targeted therapies have led to both improved patient outcomes and fewer side effects compared to standard chemotherapy. However, this approach has not yet realized its full potential in these or other cancer types. In this proposal we plan to study new cancer-causing gene mutations involving the NTRK1, NTRK2 and NTRK3 genes, which are found in numerous types of cancer. We have already demonstrated that tumor cells treated with targeted therapies against this gene family can kill cancer cells in the laboratory. We have also observed early and dramatic tumor shrinkage in patients with different tumor types that share mutations in these NTRK genes. This proposal will focus on determining additional mutations of NTRK genes that may respond to therapy. The proposal will also study how cancer cells become resistant to targeted therapies and develop new laboratory models of NTRK+ cancer to develop new therapies for these cancers.
One of the most exciting frontiers in cancer treatment is the field of immunotherapy where beneficial effects have been observed in a broad range of cancers. The major goal of our project is to identify the determinants of immunotherapy success in patients with head and neck cancers. We are performing a novel clinical trial with an immunotherapy-targeted agent that allows the patient’s own immune system to control their cancer. Using samples from this trial, our goal is to understand why some patients do or do not respond to immunotherapy. We have assembled a multi-disciplinary team that will use genetic and immunologic tests on patient samples to clarify which patients may actually benefit from this powerful approach. These data will allow us to define a precision approach to immunotherapy and in addition will provide an improved biologic understanding of the mechanism of immunotherapeutic modalities.
Lung cancer is the top cancer killer in the United States and worldwide, claiming over 1.5 million lives in 2012, according to the World Health Organization. The purpose of our research project is to understand how patients’ genetic ancestry contributes to the likelihood of acquiring specific harmful changes in DNA (“mutations”) in lung cells that lead to lung cancer. Mutations in the EGFR gene are important because EGFR mutations often cause lung cancer, especially in non-smokers. Significantly, patients whose lung cancers have EGFR mutations benefit from drugs targeting mutant EGFR, including gefitinib, erlotinib, and afatinib. Mutations in EGFR occur more frequently in lung cancer patients of East Asian or Latin American origin but the basis for this observation is a mystery, especially because these mutations are not inherited but arise after birth. Here, we propose to analyze DNA from 1500 Latin American lung cancer patients, to understand whether and how their genetic makeup leads to increased risk of developing EGFR-mutant lung cancer.
By defining the basis of increased risk of EGFR mutant lung cancer in Latin American populations, we could enable the use of effective existing treatments in this population. Additionally, if we can find a genetic marker for susceptibility to EGFR mutation, we could facilitate the screening, early detection and early EGFR-targeted therapy of lung cancer in at-risk populations. We therefore believe that our research plan could lead not only to an improved intellectual understanding of lung cancer but to improved outcomes for lung cancer patients from susceptible populations.
The global burden of cancer, severe pathology bottlenecks in underserved regions, and evolving medical knowledge increase the need for inexpensive and rapid diagnostic approaches for point-of-care use. We developed a low-cost imaging module (D3), mountable onto standard smartphones, that exploits holography to detect and profile tumors using scant clinical samples. Cells are decorated with plastic beads coated with antibodies against various cancer markers. Recorded holograms (inherently noisy and undecipherable images) are transmitted wirelessly to a remote server via a secure, encrypted cloud service. Results are rapidly reconstructed and returned to the end user’s smartphone screen along with a diagnostic readout. Pilot testing of human biopsies demonstrated protein profiling capabilities comparable to gold standard methods and excellent diagnostic accuracies compared to expert pathology interpretation. To render the platform poised for global field testing, we propose to optimize D3 to achieve simultaneous, multiple marker testing along a spectrum of field conditions using scant samples. We will then inaugurate this next generation platform and pilot its global oncology reach by tackling a key unmet need – early breast cancer detection in Botswana. Testing for key markers in breast cancer specimens is universal practice in developed regions yet rarely performed elsewhere due to highly inadequate resources. Instead, empiric treatment with anti-estrogens occurs leading to over/under treatment and significant drug-drug interactions (e.g. reduced HIV medication levels). D3 could position itself as a key early detection tool in global regions, enabling judicious and personalized treatment and increased biological insight.
In spite of tremendous advances in the treatment of estrogen receptor-positive (ER+) breast cancer using therapies directed against the estrogen receptor (ER), patients frequently develop resistance to these therapies. These resistant tumors remain the most common cause of breast cancer death, yet mechanisms by which this resistance develops are poorly understood. Much more work is required to fully understand all of the clinically relevant resistance mechanisms in breast cancer patients treated with ER-directed therapies. Moreover, there is an urgent need to develop new therapies for patients who no longer respond to these therapies. The goal of this project is to improve our understanding of resistant ER+ breast cancer by using cutting-edge genomic technology to directly characterize tumor samples from patients who have developed resistant breast cancer, as well as systematic pre-clinical approaches in breast cancer cell lines. First, we will use next-generation sequencing technology to comprehensively characterize the genomic and molecular alterations from breast tumor samples obtained from 50 patients who have developed resistance to the drug fulvestrant, an FDA-approved therapy that directly targets the estrogen receptor. At the same time, we will conduct a systematic pre-clinical study in breast cancer cell lines to identify genes that might contribute to resistance to fulvestrant. Once completed, this work should help us understand how ER+ breast cancers develop resistance to ER-targeted therapies, as well as identify new targets and therapeutic strategies in resistant breast cancer.
Funded by the Stuart Scott Memorial Cancer Research Fund, with Partial Funding in Year Two From The Ewing Sarcoma Fund
Ewing sarcoma is the second most common bone cancer in children and has a low rate of survival compared to other pediatric cancers. Genetically, Ewing sarcoma is characterized by a fusion protein known as EWS-FLI1 that is essential for the growth and survival of tumor cells. EWS-FLI1 operates by binding DNA and changing the expression levels of many genes and we believe that studying its mechanisms of action in detail may reveal new opportunities for therapy. We recently analyzed EWS-FLI1 mediated events at thousands of sites across the genome and identified genes that are highly responsive to the fusion protein. Among these genes we found VRK1, a kinase that is involved in coordinating cell proliferation and that represents an attractive therapeutic target. Our experiments show that EWS-FLI1 controls VRK1 expression directly and that Ewing sarcoma cells are highly sensitive to downregulation of VRK1. We now plan to characterize the function of VRK1 in Ewing sarcoma to learn about VRK1 dependent mechanisms in this tumor type and to test the potential of VRK1 and related pathways as therapeutic targets.
Funded in Collaboration With Stand Up To Cancer (SU2C)
The last two decades have seen the development of increasingly effective cancer therapies that target different aspects of tumors cells, including uncontrolled growth/survival, evasion of the immune system, hyper-activated signaling pathways and dysregulated gene expression programs. In a subset of cancers, including non-small cell lung cancer (NSCLC) with mutations in the epidermal growth factor receptor (EGFR), these therapies can lead to dramatic tumor regressions in a significant number of patients. However, in the majority of EGFR mutant lung cancer patients who respond to anti-cancer therapies, relapse usually occurs preventing long-term cures. We propose to investigate the reasons why cancer cells become resistant to treatment. We believe a tumor is made up of a number of different types of cells that can each respond differently to treatment. We hope to uncover and understand these differences by looking at genomic data taken from patients who are biopsied before treatment, during response to treatment, and when resistance emerges. We are also interested in understanding the role the immune system plays during cancer treatment. We’d like to understand if the tumor has developed ways to evade the immune system, and how we can promote the patient’s own immune system to fight back against the cancer. It is our hope that combining traditional drug treatment with newer immunotherapies will provide greater tumor regressions. Our goal is to create a deeper understanding of the make-up of a tumor in order to identify novel therapies to expand the survival of patients with NSCLC.
Funded in Collaboration With Stand Up To Cancer (SU2C)
Pancreatic ductal adenocarcinoma (PDAC) is a frequent cause of cancer death in the United States; it currently is the fourth most common cause of cancer death and is expected to become the second most common cause of cancer death within the next five years. Unlike virtually all other major cancers, pancreas cancer is both increasing in incidence and has shown essentially no improvement in five year survival over the past two decades. The exceptional lethality of pancreas cancer is multifactorial, resulting from an intrinsically aggressive biology, lack of effective means of early detection, and poor responsiveness to systemic chemotherapy. Clearly novel approaches to this disease are needed.
Although there have been anecdotal reports of responses to immune-based therapies in pancreas cancer, activation of cellular immunity using checkpoint inhibitors, vaccine strategies and transfer of genetically modified T cells has not been shown to be generally effective. We have assembled a team of physicians, cancer immunobiologists, computational biophysicists, and engineers to better understand the unique immunological microenvironment of pancreatic cancer, develop the technologies needed to take advantage of therapeutic vulnerabilities, and to form a multi-institutional clinical consortium to readily implement these strategies to help change the course of this deadly disease.
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