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Funded Research

Engaging the endogenous immune system with CAR T cells

Engaging the endogenous immune system with CAR T cells

Engaging the endogenous immune system with CAR T cells

Sarwish Rafiq, PhD, MA

Award Type Career Development Award
Institution Emory University

Metastatic melanoma is one of the most aggressive, and complex cancers with a 35% 5-year survival rate. Therapies using T cells that are genetically engineered to express tumor-recognizing molecules, known as chimeric antigen receptors (CAR), have shown promise against some blood cancers, but not in solid tumors like melanoma. The proposed study aims to engineer CAR T cells to overcome the suppressive tumor microenvironment and engage other immune cells to mount a more effective therapeutic response. This will be accomplished by creating combination immunotherapies through developing CAR T cells that produce drugs that engage other immune cells and help develop immunological memory to the tumor. The overall goal of our research is to develop optimized immune cell therapies for patients with melanoma by understanding how these treatments interact with the tumor environment and patients’ immune system.

Targeting PCBP2 to augment melanoma cell killing by CD4+ T cells

Targeting PCBP2 to augment melanoma cell killing by CD4+ T cells

Targeting PCBP2 to augment melanoma cell killing by CD4+ T cells

Korbinian Kropp, MD

Mentor Christopher Klebanoff, MD
Award Type Career Development Award
Institution Memorial Sloan Kettering Cancer Center

A major reason that T cell-based melanoma immunotherapies can fail, either initially or after a period of treatment, is due to mutations that result in CD8+ T cells being incapable of directly recognizing and killing tumor cells. Many melanomas, however, express HLA-II which enables tumor cells to be recognized and eliminated by an alternative lymphocyte subset called CD4+ T cells. Unlike tumor cell killing by CD8+ T cells, the molecular mechanisms governing response and resistance of tumor cells to CD4+ T cell killing have previously not been studied in a systematic and unbiased fashion. This gap in knowledge limits the rational application of CD4+ T cells as an effector population in melanoma immunotherapies. Using a genome-scale CRISPR screen I recently identified genes that confer enhanced sensitivity or resistance of melanoma cells to CD4+ cell killing. I discovered that loss of function of the RNA-binding protein PCBP2 led to enhanced killing of tumor cells by CD4+ T cells. The tumor-intrinsic role of PCBP2 in tumor immunology has previously not been studied. In my project, I seek to define the molecular mechanisms that control enhanced tumor-intrinsic sensitivity of PCBP2-deleted melanoma cells to immunologic attack by CD4+ T cells. These findings will inform a novel, mechanism-based immunotherapeutic approach that augments antitumor efficacy of CD4+ T cells in melanoma and other common cancers.

ADAR1 Inhibitor: Novel Therapeutic for Melanoma & Immunotherapy Resistance

ADAR1 Inhibitor: Novel Therapeutic for Melanoma & Immunotherapy Resistance

ADAR1 Inhibitor: Novel Therapeutic for Melanoma & Immunotherapy Resistance

Kazuko Nishikura, PhD,

Co-PI Jessie Villaneuva, PhD
Award Type Established Investigator Award
Institution Wistar Institute

The phenomenon of “RNA editing” is a relatively recent discovery with exciting implications. RNA editing is a process that modifies the sequence of RNA after it is copied from the DNA (the gene). One type of RNA editing converts adenosine (A) residues to inosine (I) specifically in double-stranded RNA (dsRNA), and this process is called A-to-I RNA editing. A-to-I RNA editing is carried out by a class of enzymes called ADARs (adenosine deaminases acting on RNA). To date, three ADAR enzymes (ADAR1, ADAR2, ADAR3) have been discovered in mammals. ADAR edits many RNA messages copied from “non-coding and repetitive sequences”. We identified ADAR1, the pioneer member of the ADAR gene family, and made major contributions to the development of the A-to-I RNA editing field.

Melanoma is one of the most commonly diagnosed cancers in the United States. There were an estimated 186,680 new cases of melanoma and 7,990 deaths in 2023. Despite the development of targeted therapies and immunotherapies, many melanomas eventually develop resistance to these treatments. Interestingly, recent studies have identified ADAR1 as a critical factor that regulates resistance to immunotherapy. ADAR1 mediated A-to-I editing of dsRNAs made from repetitive elements spread all over the human genome prevents these dsRNAs from activating interferons and inflammatory responses in tumors, which in turn dampens the responsiveness of tumors to immunotherapy. Furthermore, our own studies suggest that inhibition of ADAR1 enzymatic activity induces accumulation of aberrant R-loops (a form of RNA:DNA hybrid) at the chromosome ends and apoptosis specifically in cancer cells. These recent discoveries suggest that, if ADAR1 activity in tumors could be repressed, this might kill only cancer cells and allow the tumor to be more responsive to immunotherapy. However, no effective drugs to inhibit ADAR1 are currently available. To this end, we have recently identified an ADAR1 inhibitor compound, ADAR1i-124, by high-throughput molecular screening. In this proposal, we explore the potential of ADAR1i-124 as a novel therapeutic to treat melanoma and immunotherapy resistance.

In this MRF 2024 Request for Proposals (RFP) – Established Investigator Awards (EIA) application, we focus on the area of emphasis: Therapy and Resistance and will develop novel therapeutic strategies for the treatment of melanoma and prevention of immunotherapy resistance.

Our objective is to prove our hypothesis that ADAR1 inhibitors hold promise as future therapeutics to treat melanoma and immunotherapy resistance. The outcome of this proposal will have a significant impact on the future treatment of melanoma patients. We expect that these studies will truly have a transformative impact on the management of melanoma for patients impacted by this devasting disease, and their family members as well.

Assessment of Uveal Melanoma Using Machine Learning

Assessment of Uveal Melanoma Using Machine Learning

Assessment of Uveal Melanoma Using Machine Learning

Michael Heiferman, MD

Mentor Xincheng Yao, PhD, MEng
Award Type Career Development Award
Institution University of Illinois at Chicago

Uveal Melanoma (UM), a deadly cancer arising in the eye, is the most common eye cancer in adults. Early detection of UM is important due to the cancer’s ability to spread to the rest of the body early and because effective treatments are available to reduce its spread. Despite the availability of effective treatments, more than half of patients’ cancer spreads to the rest of the body, suggesting that UM may spread before the time of treatment. Choroidal nevi are benign tumors that are commonly seen in patients’ eyes and rarely can turn into cancer. Choroidal nevi can look like UM, which makes the diagnosis of these eye tumors challenging. Therefore, there is a need to identify and treat small UM to minimize the number of tumors that are observed and subsequently grow during the observation period. However, current screening methods face inherent limitations, particularly in regions with limited access to specialized eye cancer doctors. Machine learning (ML) is a field of study in artificial intelligence that can be used to assist in disease diagnosis. ML offers a promising approach to improve the identification and evaluation of eye tumors, thereby providing a potential tool for eye doctors both in the community and who specialize in eye cancer. Despite the significant research being done with ML in medical imaging, few studies have worked towards an ML tool for eye tumors like choroidal nevi and UM. Our previous work used ML to screen images of patients’ eyes to successfully find choroidal nevi and UM. We also used ML to evaluate images and ultrasound of patients’ eyes to assess choroidal nevi and UM for their ability to spread to the rest of the body. The objective of this proposed project is to assess the ability of ML to diagnose choroidal nevi and UM. We will use a large collection of images from the University of Illinois Chicago, which includes multiple different types of images taken of many patients with choroidal nevi and UM. We propose to develop and then improve ML tools for the screening and diagnosis of choroidal nevi and UM. We will use additional information about the patient’s medical history to help the tools perform better. We will also annotate the images before providing them to the ML tools to see if this improves the performance in screening and diagnosing choroidal nevi and UM. After identifying the best-performing ML tool in this research study, we will test this tool to perform other tasks related to the choroidal nevi and UM. We will test the ML tool’s performance in predicting the likelihood that a choroidal nevus will grow and the likelihood that a UM will spread to the rest of the body. We expect these results to provide a better understanding of how ML can be developed into a clinically useful tool to inform and guide management decisions for choroidal nevi and UM in community eye clinics and eye cancer specialist clinics to potentially save patient lives.

Targeting EGFR in NF1 mutant melanoma

Targeting EGFR in NF1 mutant melanoma

Targeting EGFR in NF1 mutant melanoma

Milad Ibrahim

Mentor Iman Osman, MD
Award Type Resident Fellow Award
Institution New York University Grossman School of Medicine
Donor Support In honor of Richard Draeger

Melanoma can be classified according to TCGA into 4 genetic subtypes: BRAF, NRAS, NF1 mutants or triple wild type. A lot of research focused on BRAF and NRAS mutant melanoma and limited research was focused on understanding NF1 mutant melanoma despite having worse prognosis compared to all other melanoma subtypes. Our preliminary results from analyzing 33 melanoma cell lines that were isolated from patients, identified EGFR to be upregulated in NF1 mutant melanoma. Moreover, testing independent patients for their EGFR expression by histochemical analysis  showed similar results. This is a novel finding as EGFR is target in other cancer types like colorectal and lung cancer but not in melanoma. Our proposal aims at understanding the mechanism by which NF1 loss leads to EGFR activation and test if EGFR inhibition will prove a successful approach to be used as a treatment for NF1 mutant melanoma. This can lead to a fast transition to clinical use as EGFR inhibitors are already available and are used to treat other cancer types.