Recipient of the V Scholar PLUS Award, a third year of grant support for V Scholars who have made exceptional progress in year 1 and 2 of their original grant
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.
More children die from brain tumors than any other type of cancer, and the most common type of brain tumor in children is medulloblastoma. Children with medulloblastoma are treated with surgery, radiation, and chemotherapy, and more than 50% of patients survive into adulthood. However, the treatments used for medulloblastoma lead to many long-term side effects, including growth defects, hormone abnormalities, and impaired intelligence. Like all cancers, medulloblastoma is caused by uncontrolled cell growth. Approximately one-third of medulloblastoma cancers arise when a particular signal that tells brain cells to grow, called Hedgehog, gets stuck in the “on” position. We are interested in uncovering exactly how Hedgehog signals tell medulloblastoma cells to grow. To do so, we are investigating how the Hedgehog pathway is activated, and how Hedgehog activation regulates the expression of other signals to influence cell growth. In particular, we are using existing drugs to understand whether block critical mediators of Hedgehog effects blocks the growth of medulloblastoma. Understanding how Hedgehog signals cause cancer may show us how to turn off these signals, and potentially, lead to new therapies for medulloblastoma.
Funded by the 2015 Wine Celebration Fund a Need, including donations raised by the Dick Vitale Gala and Bristol-Myers Squibb
Recent research revealed that malignant gliomas in children often have common gene mutations in a molecule named H3.3, which is a component of the human genome. Approximately 30% of pediatric glioblastoma and 70% of diffuse intrinsic pontine glioma (DIPG) cases have the same mutation which causes a change in the H3.3 protein. The human immune system, such as T-lymphocytes (T-cells hereafter), do not normally react to normal proteins, but can recognize and attack cells that have abnormal proteins. Therefore, cancer-specific mutations can be suitable targets for cancer immunotherapy, such as cancer vaccines and adoptive T-cell transfer therapy (i.e., infusion of large number of T-cells). Indeed, immunotherapy using patients’ own T-cells that are engineered to recognize cancer cells have shown remarkable success in other cancers, such as acute lymphocytic leukemia in children. However, it is also important to ensure that those T-cells attack tumor cells but not normal cells. We recently found that the common mutation in H3.3 includes cytotoxic T cells which can kill glioma cells that have the mutation but not cells without the mutation. We are proposing two lines of translational studies. First, we will isolate genes for the T cell receptor which allows the specific recognition of mutated glioma cells. This will lead to a near future development of adoptive transfer immunotherapy. Concurrently, we will design and conduct a pilot vaccine trial using synthetic peptide for the mutated part of H3.3 in children with H3.3-mutated DIPG or high-grade glioma.
The last two decades have seen the development of increasingly effective cancer therapies that target different facets of transformed cells, including aberrant proliferation/survival, immune evasion, hyper-activated signaling pathways and dysregulated transcriptional programs. In a subset of cancers, including acute myeloid leukemia (AML) and non-small cell lung cancer with activating EGFR mutations, these therapies lead to dramatic clinical responses in a significant proportion of patients.
However, in the majority of AML and EGFR mutant lung cancer patients who respond to anti-cancer therapies, therapeutic relapse subsequently ensues, although often after a considerable interval, such that these responses do not lead to long-term cures. Often the relapsed tumors are infiltrated by adaptive immune cells (T cells). With the advances in immunotherapy, which utilize a patient’s own immune system to fight the cancer, it is possible to treat with immunotherapy after relapse. We are studying the T cell infiltrates before, during, and after relapse in both AML and NSCLC patients to determine if the response if the relapsed tumors have the characteristics of an immunogenic tum.
Tumors across different patients can be understood as independent evolutionary processes of clonal Darwinian evolution under distinct therapeutic evolutionary pressures. Different therapeutic strategies disrupt evolution in distinct ways allowing the inference of the order and co-mutation patterns specifically associated to these therapies. Inferring evolutionary patterns from large cross-sectional and longitudinal therapy specific cohorts will identify specific mechanisms of drug resistance, the genetic background of these mechanisms and will inform the dynamic model of the main routes of drug evasion.
First, using CAT(0) phylogenetic spaces, we will learn the statistics of phylogenetic processes associated specific drug mechanisms in breast cancer and melanoma. We conjecture that undisrupted evolutionary processes follow linear patterns and that specific therapies generate distinct branching patterns associated to number of alterations needed for relapse and effective size of the resistant population. Second, the highly branched processes associated to therapy allow to reconstruct the genetic alterations of ancestral clones allowing to order the genetic alterations. Combining cross-sectional information, one can elucidate the main routes of drug resistance, what alterations are selected under specific therapy and which is the mutational background in which they arise. As genomic data from clinical studies will be arriving we will generate first evolutionary models and integrate the results with the networks from dynamic modeling. By combining genomic data of longitudinal studies with state of the art network inference, we aim to uncover the main mechanisms of drug resistance and design combinatorial approaches.
Pancreatic ductal adenocarcinoma (PDAC) is a common and increasing cause of cancer death in the U.S.A. While attempts to harness the immune system to fight cancer has been successful in the treatment of many cancers, these strategies have to date been ineffective in PDAC. PDAC tumors contain not only cancer cells but a dense layer of fibrous tissue, called stroma. The stroma interferes with the immune systems ability to attack PDAC both by releasing substances that inhibit the immune system and by acting as a physical barrier to immune cells reaching the cancer cells. We have recently shown that Vitamin D can act on PDAC tumors to prevent the stroma from releasing immune inhibitory substances and to facilitate immune cell entry into tumors, potentially setting the stage for a more effective immune attack on PDAC. In this proposal, the post-doc/clinical fellow will work closely with a team of physicians, cancer immunologists, and computational biophysicists will work together to improve the effectiveness of immunotherapy for PDAC. The post-doc/clinical fellow will contribute toward the completion of two tightly coupled aims: first, novel theoretical and experimental tools will be used to characterize the patient-specific immunological environment of PDAC tumors; second, the detailed understanding of the immune environment in PDAC tumors will be used to develop novel immunotherapy strategies that will be tested in a new clinical trial. The clinical trial will use a combination of conventional chemotherapy, a potent Vitamin D analogue, a drug that activates immune cells, and surgery, in an effort to improve the outcomes of patients with pancreas cancer. The Penn post-doc will be the critical individual who supplies operative tissue to the diverse collaborators in the project, and correlates the different genomic and immunologic studies with patient outcomes. As such they will gain knowledge and experience in molecular phenotyping of tumors, immunotherapy, and clinical trials.
Pancreatic cancer is one of the most deadly diseases in the U.S. It is hard to diagnose early, and it does not respond to treatments when discovered late. Therefore, new methods for early diagnosis and prevention are critical. Currently, our approach to finding cancer biomarkers relies on technologies that lack spatial or temporal resolution for discriminating individual cells and tumor regions. In fact, much of our analyses are based on average measurements from the mixed population of different cell types within the tumor tissue. This means that each biomarker has to be validated in multiple experimental and pre-clinical settings through very time-consuming and expensive processes, severely hampering our ability to discover diagnostic or therapeutic biomarkers. We developed a novel method to image and sequence DNA and RNA genome-wide without extracting them from the tissue, and the nucleic acid sequence is visualized directly under the microscope. Therefore, we combine positional features associated with cancer progression and molecular or genetic features associated with cancer clonal evolution. Our proposal will determine genetic sequences associated with each pixel of cancer tissue images to generate a map of genetic alteration and biomarkers as a function of the tissue landscape. If successful, our proposal could signal a new approach to discovering genetic biomarkers using specific architectural hallmarks of cancer, rather than average gene expression differences between heterogeneous tissues.
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.
Breast cancer is the most common cancer in women. Despite advances in understanding how breast cancer develops, this has not translated into better therapies. The majority of breast cancers are positive for hormone receptors, such as the estrogen and progesterone receptor (PR), and are dependent on these receptors and their hormone ligands (estrogen and progesterone) for growth. However, as tumors progress they become hormone-independent, meaning they grow in the absence of hormones normally required for cell growth, perhaps due to unregulated hormone receptors. It was recently shown that women who were taking hormone replacement therapy that included progesterone had an increased risk of developing breast cancer, underscoring the importance of studying PR in breast cancer. Understanding PR action in the context of breast cancer is important to the development of better therapies.
PR is required during normal breast development and pregnancy, activating genes in the nucleus that stimulate cell growth. Recently, we identified that PR also regulates genes that drive inflammation, a normal cellular process that can function uncontrollably in cancer, generating mutations that may drive cancer growth. Decreasing inflammation has been shown to reduce the risk of developing breast cancer. The objective of the proposed experiments is to determine how PR regulates genes involved in inflammation, and if PR-dependent inflammation can be detected, and eventually blocked, in breast cancer. Understanding how PR regulates inflammation could lead to the development of a new area of therapies for breast cancer, combining currently existing hormone-based therapies with treatment aimed at reducing inflammation.
If detected early melanoma is usually curable with surgery. However, melanomas are often detected at later stages after cancer cells have metastasized and survival rates for patients with metastatic disease are less than 15%. Furthermore, some thin melanomas, even when detected early, lead to mortality. What defines this difference in outcome is largely unknown and suggests a need for new markers that can predict a patient’s risk. Recently, the cellular microenvironment that surrounds a tumor has gained significant attention as a critical regulator of tumor progression, response to therapy and resistance. Effective therapies that specifically target immune suppression by tumor microenvironments have been developed; however, our understanding of the specific way in which these therapies work is incomplete. A better understanding of which parts of the microenvironment suppress immune responses will not only allow for better prediction of patient prognosis but may also help enhance a patient’s response to new immune-based therapies. Lymphatic vessel growth in melanoma is correlated with poor prognosis and enhanced metastasis to lymph nodes, however, until now lymphatic vessels were largely ignored as players in host anti-tumor immune responses. Our recent work demonstrates for the first time that lymphatic vessels are immune suppressive in tumor microenvironments and impair therapy. This proposal will test the hypothesis that lymphatic vessels directly contribute to immune suppression and suggests they may be a novel marker both for risk stratification in melanoma patients and as a novel therapeutic target.
