Melanoma is a dangerous and potentially life-threatening skin cancer. While it is rare in children, pediatric melanoma often behaves very differently than adult melanoma, making it more difficult to recognize, diagnose, and treat. Certain types of melanomas are more common in children, particularly those that arise from congenital melanocytic nevi (moles present at birth) and Spitzoid tumors, which can appear benign but may, in rare cases, present as melanoma. Because the precursor lesions (spitzoid lesions or congenital nevi) often look non-threatening, the standard medical approach has been to monitor them over time rather than remove them or conduct advanced genetic testing. This proposal was inspired by one of my own patients—a child who had a mole biopsied at age four. Fortunately, the pathology was considered benign at the time, and no genetic testing was performed, which is in line with standard care. The mole was watched for years without significant change, but during puberty, it suddenly became ulcerated. When it was removed, it was diagnosed as melanoma. Genetic testing revealed serious mutations, and unfortunately, the disease progressed rapidly. Had we known earlier what was happening at the molecular level, it’s possible that a more proactive treatment plan could have been offered—one that might have changed the outcome. Today, genetic testing is typically only done for melanomas. As a result, we know little about the precursor lesions which may have early molecular changes or otherwise signal a higher risk for progression. This project aims to bridge that gap by studying preserved tumor tissue from pediatric patients who had congenital nevi, spitzoid lesions, or melanomas biopsied in the past—which were never genetically analyzed. Using advanced sequencing technologies, we will look for hidden genetic changes that could help distinguish between harmless and high-risk tumors. Our study will examine archived cases of pediatric melanoma that were never tested using modern genomic tools. We will also study Spitzoid tumors, which are often difficult to classify, to better understand whether certain genetic signatures are associated with more aggressive behavior or have recognized genetic patterns. Finally, we will analyze congenital moles to see whether some of them carry genetic markers that could guide future care, including earlier intervention or targeted therapies that are already showing promise in related conditions. By combining decades of carefully collected tissue samples with modern genetic techniques, this research seeks to change how we understand and manage pediatric melanocytic tumors. Rather than relying solely on how a tumor looks under the microscope, we hope to identify genetic information that can help doctors make more informed decisions—leading to earlier diagnoses, better treatments, and improved outcomes for children at risk of melanoma.  

The proposed research will develop an innovative and clinically relevant class of nanomaterials—DNA-based “dendritic” (branched) nanostructures—as immunotherapeutics for treating melanoma. Melanoma immunotherapies, where one seeks to harness the body’s natural immune system and reprogram it to attack melanoma tumor cells, are currently ineffective in most patients. New approaches are urgently needed to improve response rates and deliver long-lasting remissions. One promising avenue lies in utilizing a cell’s natural “alarm system,” the cGAS–STING pathway. This pathway, activated when DNA binds to the cGAS enzyme, triggers a cascade of signals that stimulates both innate and adaptive immune defenses against cancer. Clinical efforts to exploit this pathway with small molecule STING agonists have not succeeded clinically because these drugs are rapidly cleared from the body, do not enter cells efficiently, and vary in potency across patient populations.

Adding to the challenge, immune activation through cGAS-STING also increases levels of a checkpoint “brake” protein PD-L1 on tumor and immune cells, which in turn dampens tumor killing and exhausts the immune system. To overcome these hurdles, we will develop a new class of programmable DNA-based nanostructures that can carry and precisely deliver orthogonally complementary therapies: DNA sequences to activate the cGAS–STING pathway and separate short DNA sequences that block the production of PD-L1 surface protein. This proposed research innovatively develops these nanostructures as molecular platforms to structure these immunotherapeutic cues and deliver them in optimized architectures to cells. Due to the modularity of our system, we propose to harness this feature to evaluate specific structural parameters that lead to effective delivery of immune-stimulating cues as well as appropriate timing of the anti-tumor-evasion cues. Our research is a paradigm shift in the way in which melanoma treatments are developed, as it harnesses advances in chemistry and nanotechnology to expand our capabilities in immunology. With our approach, we have the opportunity to develop robust and longer-lasting melanoma immunotherapies that are effective across a wide population of patients. By uniting precise immune activation with reduced “immune brake protein” expression in a single, modular platform, this research aims to produce a versatile, next-generation immunotherapy to treat patients with melanoma.  

Melanoma is the most lethal skin cancer, and the success of current therapies remains limited. To better tailor melanoma treatments, we must understand the complexity of the tumor microenvironment (TME). Within the TME, many different types of cells interact with each other, including immune cells, tumor cells, and stromal cells. The stroma is composed of the structural components that support the tumor tissue. A key component of the stroma are cancer-associated fibroblasts (CAFs), which can control tumor growth, blood supply, protection from the immune system, or the ability to metastasize. However, these CAFs are complex and can display tumor-promoting or tumor-restraining functions. For example, inflammatory CAFs attract defective immune cells that can promote tumor growth, while myofibroblastic CAFs form barriers to tumor cell invasion and spread.

It remains unclear how these different types of CAFs develop from normal skin fibroblasts and how CAF identity and functionality is shaped.   Despite the growing importance of CAFs in tumor biology, our understanding of their ‘epigenetic’ regulation is extremely limited. Epigenetics is the study of the processes that control how and when genes are turned on or off and is critical for shaping cellular identity. Here, we will use cutting-edge high-resolution approaches to study the epigenetic features that control CAF identity. Using mouse models of melanoma that mimic the complexity of the TME, we will use spatially resolved approaches to ‘observe’ cellular interactions and behaviors within the tumor as the melanoma develops. We will focus on inflammatory CAFs, which we showed can lead to an impaired anti-tumor immune response and increased tumor growth in mice. Our proposed work could reveal the presence of CAFs that inhibit immune function and indicate approaches to dampen their pro-tumor features, as some epigenetic regulators can be effectively targeted with drugs. Thus, a deeper understanding of the tumor stroma can lead to novel therapeutic approaches for melanoma patients.

Analysis of large families with more disease than expected has been shown to be a powerful way to identify cancer predisposition genes. We have used this approach in Utah to identify the major cancer genes BRCA1, BRCA2, as well as CDKN2A (identified in Utah and Texas cutaneous malignant melanoma (CMM) pedigrees). We have used the Utah high-risk pedigree approach more recently to identify genes for many cancers, including GOLM1 for CMM, as well as genes for other cancers (colon cancer, breast cancer, prostate and bladder cancer) and other disorders (e.g. Chiari malformations, osteoporosis, and Alzheimer’s). We propose to efficiently use this same approach here for an available resource of melanoma cases who died from their melanoma (lethal melanoma) and who belong to high-risk Utah melanoma pedigrees. In our Genetic Epidemiology Biorepository, we have 904 stored germline DNA samples from melanoma cases who are members of extended Utah pedigrees with a significant excess of melanoma (high-risk pedigrees). Among these sampled Utah cases there are 55 who have a linked Utah death certificate showing that melanoma was a contributing cause of death (lethal melanoma). Three of the pedigrees include 3 related affected sampled melanoma cases; the other 14 pedigrees include 2 related affected sampled melanoma cases.

We will perform whole genome sequencing (WGS) on these samples. We will apply a unique approach that includes analysis of the genetic sequence data to identify the rare genetic variants that are shared among these related Lethal melanoma cases; this will identify a set of strong candidate predisposition genes/variants for lethal melanoma. We will validate our candidates by testing for association with melanoma risk in publicly available data for independent populations of melanoma cases and controls (e.g. UKBiobank, VHA MVP, AllofUs). We will identify our top 10 candidate variants. We will assay the best candidates in the set of additional previously sampled and melanoma affected relatives of the affected cousin carriers (from our Biorepository) to confirm segregation in pedigrees. Identification of additional genes and variants responsible for lethal melanoma will improve identification of those people at most risk, will expand our understanding of the causes of lethal melanoma, and will allow the application of powerful screening and prevention strategies for this deadly cancer. 

While immunotherapy has greatly improved the survival for patients with melanoma of the sun-exposed skin, especially for those with advanced disease, at least half of the patients receiving this form of treatment still do not benefit. In addition, patients with forms of melanoma that are not caused by sun exposure, such as melanoma on the palms, soles, or under the nails, melanoma of the eyes, and melanoma of our mucosal membranes of for instance nose, mouse, or throat, respond poorly to current immunotherapies. Especially for the latter, an important reason for treatment failure is that the patient’s immune systems only weakly respond to these forms of melanoma. This happens presumably since these melanoma lack the wide-spread DNA damage that is caused by ultraviolet light and that would allow immune cells, especially so-called T cells, to “see”, infiltrate, and destroy the cancer cells. An important recent insight has been that in many forms of cancer, the majority of infiltrating T cells do not recognize the cancer but are so-called bystander T cells. Many of these bystander T cells were activated during past or ongoing common viral infections, circulate in the bloodstream, and are unspecifically recruited to the tumors, where they however do not unfold any activity since they don’t “see” the virus. It would be highly desirable to direct the activity of these bystander cells against the cancer cells, especially in poorly immunogenic forms of melanoma, which could lead to the destruction of these cancers. Our lab is working on a novel antibody-based therapy that aims to deliver small protein fragment of viruses(‘peptides’) to the surface of cancer cells in order to ‘trick’ antiviral bystander T cells into attacking the cancer cells as if they were infected by viruses.

We have already found in a mouse model of head and neck cancer that this form of immunotherapy is highly effective even in tumors that do not respond at all to conventional immunotherapies. Here we propose to develop these so-called antibody peptideepitope conjugates (APECs) for the treatment of those melanoma that fail to respond to current immunotherapies. APECs consist of antibodies that bind to the cancer cell surface and that are loaded with viral peptides. These peptides need to be released from the antibody by cancer cell-expressed enzymes called proteases. A critical aspect of designing APECs for a particular form of cancer is therefore to examine which proteases this cancer expresses. The first part of this project seeks to characterize the proteases active in melanoma, and especially in those forms of melanoma that are not caused by sun exposure and pose the greatest challenge to treatment. In the second part of the project, we will build APECs based on an improved design that will be easier to manufacture for future clinical use and test their therapeutic potential in a mouse model of melanoma, guided by knowledge of the proteases active in this melanoma model. 

The use of immunotherapies has revolutionized treatment for late-stage melanoma patients. These therapies have extended survival for many patients who would have previously succumbed to their disease. Unfortunately, resistance to immunotherapies is common, evident either at the outset of treatment or after some time when portions of the original tumor grow and expand in spite of treatment. Resistance is commonly characterized by poor immunogenicity of tumor cells, in that they fail to elicit a response by the T cells that are unleashed by immunotherapies. Addressing this resistance can be done by using supplementary therapies that target immunotherapy-resistant melanoma cells through immune-independent mechanisms or by using enhancement therapies that can augment immunotherapy responsiveness and block emergent resistance. My laboratory previously discovered a vulnerability of melanoma cells that is rooted in their use of bone morphogenetic protein (BMP) signaling. This is a cell-cell communication pathway that is turned on when one cell secretes a signaling ligand protein, which is then bound by receptors on receiving cells, leading to BMP pathway activation in the receiving cell. A normal function of BMP signaling is to prevent melanocyte differentiation during embryonic development. Melanomas reawaken this pathway by inappropriately expressing a BMP ligand called GDF6. GDF6 then activates BMP signaling in the tumor and keeps melanoma cells in an undifferentiated state that enables their continued, unrestrained cell division. When we disable GDF6-driven BMP signaling in melanoma cells it causes them to differentiate and then die.  

About 75% of human melanomas have active GDF6-driven BMP signaling, making it a therapeutic target that could impact a large fraction of melanoma patients. To target this pathway, we have created a monoclonal antibody that binds to and inhibits GDF6. This antibody kills melanoma cells in culture and blunts the growth of human melanoma tumors in mice. Thus far we have targeted melanoma cells and tumors that are naïve to immunotherapy. As part of this proposal our first aim will test whether inhibition of GDF6-driven BMP signaling can target immunotherapy-resistant cells and tumors without the involvement of the immune system. Additionally, we have discovered that treatment with anti-GDF6 antibody potentially makes melanoma cells more visible to the immune system. For this reason our second aim will test whether anti-GDF6 therapy could augment immunotherapies. Taken together, inhibition of GDF6-driven BMP signaling has the potential to be effective against a large fraction of melanomas through one mechanism that is independent of the immune system and another mechanism that cooperates with immunotherapies. Both mechanisms have the potential to blunt the resistance that is often seen with melanoma immunotherapy. 

Melanoma is an aggressive type of skin cancer with a low survival rate when it metastasizes. Melanoma originates mainly in sun-exposed areas, likely due to damage from sun ultraviolet (UV) irradiation. Sun UV radiation is a well-known human carcinogen that can damage DNA, and melanoma often originates in melanocytes with sun-damaged DNA. We have identified a new way that UV might contribute to melanoma formation, independent of direct DNA mutations in melanocytes. Our preliminary studies showed that the UV-induced environment in which melanocytes exist in the skin could change their behavior and even promote melanoma formation. We showed that epidermal cells, the neighboring cells of melanocytes in the skin, play a crucial role in setting up this environment. We identified that, upon exposure to UV irradiation, epidermal cells start to express and secrete proteins that alter the behavior of melanocytes. We showed that expression of these secreted proteins is typically inhibited by a complex of proteins called the Polycomb repressor complex, which functions to prevent melanocyte activation and suppress melanoma formation. UV irradiation, however, leads to the loss of Polycomb expression in epidermal cells resulting in the expression of secreted proteins that promote atypical melanocyte behavior. Interestingly, by studying human melanoma samples, we were able to detect the reduction of the Polycomb complex in the epidermis near melanoma sites.  Based on our preliminary studies, we propose a paradigm-shifting hypothesis that UV induces changes in epidermal cells to create an environment that promotes melanoma formation. We will test this hypothesis by addressing two specific aims. In Aim 1, we will use mouse models of melanoma to explore how losing Polycomb in the epidermis affects melanoma tumor formation and progression. These studies will establish the connection between Polycomb function in the epidermis and melanoma tumorigenesis. In Aim 2, we will use human primary melanoma samples to perform cellular studies to uncover the secreted proteins that alter melanocyte behavior and lead to melanoma. These studies will identify the signaling pathways by which the epidermis cross-talks with melanocytes during melanoma formation. In the long term, our discoveries will open new possibilities for preventative research focused on targeting epidermal cells.

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.

Established Investigator Award – Pere Puigserver, PhD

Established Investigator Award – Kari Kendra, MD, PhD