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The Wistar Institute Scientists Discover New Weapon to Fight Treatment-Resistant Melanoma

PRESS RELEASE

PHILADELPHIA — (February 5, 2025) —The lab of The Wistar Institute’s Jessie Villanueva, Ph.D., has identified a new strategy for attacking treatment-resistant melanoma: inhibiting the gene S6K2. The team published their findings in the paper, “Selective abrogation of S6K2 identifies lipid homeostasis as a survival vulnerability in MAPKi-resistant NRASMUT melanoma,” from the journal Science Translational Medicine.

“This work shows that, even in the face of notoriously treatment-resistant melanoma, targeting S6K2 is a viable strategy for improving therapeutic outcomes,” said Dr. Villanueva, associate professor in Wistar’s Ellen and Ronald Caplan Cancer Center. “We’re excited to see where further research will lead us in the continued fight to reduce deaths from melanoma.”

Melanoma is the deadliest skin cancer, and it is also on the rise. Since 2000, the number of melanoma cases per 100,000 Americans has increased from roughly 18 to 24, which scientists suspect to be at least partially caused by increased exposure to UV radiation from sources like time spent without protection in sunlight or the use of tanning beds. In general, cancer tends to be a disease correlated with age, but melanoma is notable as one of the most common cancers diagnosed in people under 30, with cases on the rise in that age cohort as well. Although significant progress has been made in treating melanoma, drug resistance remains a daunting challenge, and many patients do not respond to current treatments.

As part of The Wistar Institute’s Melanoma Research Center, the Villanueva lab pursues new ways to overcome the challenge of melanoma drug resistance. In this paper, the group took aim at melanomas with a mutation in the NRAS gene (abbreviated as NRASMUT melanoma).

NRASMUT melanoma accounts for about 30% of all melanoma cases, which has made it a priority of melanoma researchers. Previous research has indicated that MAPK inhibitors could be a potential therapy for NRASMUT melanoma. However, on their own, MAPK inhibitors fail in about 80% of cases and don’t extend patient survival with any significant improvement.

By analyzing the downstream molecular and genetic impact of MAPK inhibition in NRASMUT melanomas, the Villanueva team identified the gene S6K2 as a possible target. Once they assessed melanoma patient data, Dr. Villanueva and lab found that expression of S6K2 was correlated with worse patient outcomes and MAPK-treatment resistance in patients with NRASMUT melanoma.

The team tested their hypothesis in the lab by silencing the S6K2 gene, which successfully killed NRASMUT melanoma cell lines known to resist MAPK inhibition. Further analysis revealed that S6K2 inhibition killed these cancer cells by disrupting an important lipid metabolism process.

The Villanueva lab’s discovery of S6K2 inhibition’s anti-melanoma potential also led to their identification of yet another angle of attack against melanoma resistant to treatment with MAPK inhibition. When they silenced S6K2, the team noticed that it had an effect on another gene called PPARα. After refining their understanding of PPARα’s effects on NRASMUT melanomas, the researchers capitalized on this finding by using a combination treatment of two compounds, fenofibrate (which activates PPARα) and DHA (also known as Omega-3), to successfully induce cell death in melanomas that were known to resist treatment with MAPK inhibitors.

“Our findings suggest a clear path forward for more preclinical research on these treatment options,” said co-first author, Brittany Lipchick, Ph.D., associate staff scientist in the Villanueva lab. “Not only did our treatments work in the lab — they also appear to be quite safe. Some of the drugs we tested, like fenofibrate, are already safely used in humans for other purposes, so the road ahead is well-lit.”

Fellow co-first author Adam Guterres, Ph.D., Villanueva lab associate staff scientist, agreed: “Before this paper, we knew that certain treatments could theoretically work against melanomas that resist treatment with MAPK inhibitors, but they were a non-starter because they were incredibly toxic. Our work shows that we can still fight this stubborn melanoma without a prohibitively toxic treatment, which is exciting news for where this work takes us.”

Co-authors: Brittany Lipchick1, Adam N. Guterres1, Hsin-Yi Chen1, Delaine M. Zundell1, Segundo Del Aguila1, Patricia I. Reyes-Uribe1, Yulissa Tirado1, Subhasree Basu1, Xiangfan Yin1, Andrew V. Kossenkov1, Yiling Lu2, Gordon B. Mills3, Qin Liu1, Aaron R. Goldman1, Maureen E. Murphy1, David W. Speicher1, and Jessie Villanueva1

1The Wistar Institute, Philadelphia, Pennsylvania 19104
2The University of Texas MD Anderson Cancer Center
3Knight Cancer Institute, Oregon Health & Sciences University

Work supported by: This work was supported by National Institutes of Health grants P30CA010815, S10OD023586S10, CA016672, P01CA114046, P50CA174523, R01CA268510, U54CA224070, T32GM008275, and T32CA009171; Department of Defense grant HT94252310914; and Pennsylvania Department of Health SAP# 4100083104. Additional funding support was provided by Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, The Melanoma Research Alliance, the V Foundation for Cancer Research, The Wistar Science Accelerator Award, and The Goldblum Family Healthcare Fund.

Publication information: “Selective abrogation of S6K2 maps lipid homeostasis as a survival vulnerability in MAPKi-resistant NRASMUT melanoma,” from Science Translational Medicine.

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ABOUT THE WISTAR INSTITUTE:

The Wistar Institute is the nation’s first independent nonprofit institution devoted exclusively to foundational biomedical research and training. Since 1972, the Institute has held National Cancer Institute (NCI)-designated Cancer Center status. Through a culture and commitment to biomedical collaboration and innovation, Wistar science leads to breakthrough early-stage discoveries and life science sector start-ups. Wistar scientists are dedicated to solving some of the world’s most challenging problems in the field of cancer and immunology, advancing human health through early-stage discovery and training the next generation of biomedical researchers. wistar.org


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Wistar Melanoma Researchers Discuss Risks and Solutions for Melanoma Awareness Month

Three of The Wistar Institute’s foremost melanoma researchers: professor Meenhard Herlyn, D.V.M., D.Sc.; associate professor Jessie Villanueva, Ph.D.; and assistant professor Noam Auslander, Ph.D. discussed the progress and potential in melanoma research. Each brings their own distinct expertise to the field of melanoma research with decades of combined experience, and in reflecting on the state of the field, Drs. Herlyn, Villanueva, and Auslander covered both how they came to melanoma research and how they continue to tackle the challenge of this disease every single day at Wistar.

There are a lot of cancers out there. What brought you to melanoma?

Dr. Noam Auslander: As someone who works on the computational side of things, I was attracted to melanoma research mainly because of the quantity of data. In science generally but in computational science in particular, more data is better — because that allows researchers to design high-fidelity models, which, with cancer, can lead to all sorts of benefits, like predictions of who will respond to what therapy, or which genetic patterns are implicated in a cancer.

I can access and analyze melanoma data in large batches simply because there’s a lot of it. Part of that is because it’s a common cancer — which isn’t a good thing — but because it’s both common and a subject of study for more than 40 years, that allows my team and I to improve our models.

Dr. Jessie Villanueva: For me, melanoma research began as pure scientific interest. Melanoma is an aggressive cancer, and when I started as a postdoctoral fellow, there were no approved targeted therapies or immunotherapies; if chemotherapy, radiation, and surgery all failed, there really weren’t other options.

That problem attracted me to the field as a scientist who wants to solve problems, and shortly afterward, the professional interest became a personal one: a childhood friend whom I’d known since kindergarten was diagnosed with melanoma, and not long after that, so was my uncle. Unfortunately, my uncle passed away, but my friend survived, and that combination of loss and hope solidified melanoma as something I wanted to dedicate myself toward working against.

Dr. Meenhard Herlyn: My story is not so inspiring. I was young — so I suppose it was something like a hundred years ago — but my boss told me to help him with a melanoma project, and that was that. But I was very lucky, because that project involved a man named Wallace Clark: a great pathologist of the disease, whose research laid the foundation for much of what we know today about melanoma. Much of his work was characterizing these melanoma cells under a microscope — a necessary first step — and thinking of stories in his mind about how they might behave. Characterizing and theorizing. So as a young scientist, I thought to myself, “we must find a way to fill in these stories with real data.” And I’ve followed that ever since.

There are other skin cancers; melanoma is just a subtype. What makes it so dangerous?

J.V.: Melanoma comes from cells that originally have an innate level of pluripotency (the ability to transform into different cell types); they have remarkable migratory abilities; and they give rise to a diverse array of cell types throughout the body. When those cells become cancerous, they are highly plastic and skilled at adapting to their environment. This plasticity also allows melanoma to evade treatment and become drug-resistant. Drug resistance is a big problem in the field; often when using drugs targeting one pathway, the tumors find an alternative pathway to exploit.

By collectively studying all the inner workings of melanoma — like its genetics (the kind of mutations it collects), epigenetics (how genes are turned on or off), and signaling pathways (controlling processes like cell growth, proliferation, and survival) — we aim to develop strategies that prevent tumors from evading treatment. We’ve made great progress treating melanoma, but tumors still develop strategies to bypass therapies. This ongoing challenge drives our relentless search for innovative and effective solutions, fueled by the hope of achieving cures and improving the lives of melanoma patients.

N.A.: Melanoma is associated with an unusually high inter- and intra-tumor heterogeneity; the mutational profile is exceptionally complex between different melanoma cells and even within melanoma cells. That’s why large-scale data analysis of melanoma with computational models isn’t just important but necessary — patterns that can help us fight this cancer exist, but distinguishing between patterns and noise both within a tumor and between tumors requires the help of advanced computational techniques.

Meenhard has talked about how we need to listen to cells, and that’s how I try to help Meenhard & Jessie’s work: by fine-tuning computer systems to listen for signals amid the chaos in cancer.

M.H.: We also have to remember that the cells that become melanoma are highly mobile by their very nature. As Jessie said, melanocytes have a certain amount of innate plasticity, which contributes to the cancer’s aggression once a melanocyte goes from normal to cancerous.

But that wouldn’t necessarily be as big a problem if it weren’t for these cells’ motility. When you have aggressive cancer cells moving throughout the body, that creates a situation that lends itself to metastasis. A skin cancer that isn’t melanoma doesn’t present as much danger because it’s probably more localized; I’m not saying that’s not serious, but a non-metastatic tumor on the skin is a lot easier to treat — at the simplest level, you just cut it off. With melanoma, once that diagnosis comes, the clock is ticking to stop the cancer before the metastatic impulse gets out of control.

More people are getting melanoma, with U.S. incidence up by more than 50% since 1999. Why do you think that is, and how can people protect themselves?

J.V.: The short answer is that we don’t yet know for sure — there are several ongoing epidemiological studies which we expect will provide clear answers. Lifestyle is a big part of it. Outdoor activity can be healthy; however, being outdoors means more sun & UV exposure. Anecdotally, since the pandemic, we’ve noticed more people spending more time outdoors. And that’s a risk factor.

We’re seeing a sharp increase in melanoma for young people, particularly young women. Cancer tends to be correlated with age — the older we get, the higher the probability of having cancer — but melanoma is the most frequently developed cancer in people in their 20s and 30s.

M.H.: I agree that lifestyle is probably a big factor in the increase in cases. Everything from tanning beds to taking a vacation to lie on the beach is going to give UV rays more opportunity to cause damage that could lead to melanoma. Sunlight feels good to everyone, but unprotected exposure is harmful. People get addicted to damaging UV because our skin secretes endorphins when exposed to UV, and that’s more reason to be cautious.

It’s true that people with less melanin in their skin are more at risk — which is why, for example, more leisure travel from countries in the Global North to equatorial regions that get more sun probably causes more melanoma overall — but everyone has skin, which means anyone can get melanoma. And that’s why awareness of exposure risk is so important.

Wistar’s Women and Science Program Talks Melanoma Research

After a day of virtual scientific talks that concluded Wistar’s 4th annual Noreen O’Neill Melanoma Research Symposium, a lay-friendly examination of melanoma with a group of interdisciplinary scientists continued into the evening during the Women & Science event Advances in Melanoma and Skin Cancer Research.

Distinguished epidemiologist Dr. Marianne Berwick, from the University of New Mexico, and Wistar Drs. Chengyu Liang, Jessie Villanueva, and Noam Auslander met for a roundtable discussion on melanoma research, prevention, diagnosis, and treatment advances. Dr. Maureen Murphy moderated a lively exchange that touched on the history of melanoma up to the latest solutions to treat and prevent this dangerous skin cancer.

Dr. Berwick kicked off the conversation by addressing why melanoma seems much more prevalent than in the past.

“We wear less clothing, we test for skin cancer with more biopsies, and people spend more time indoors,” says Berwick. “Melanoma incidence increased because we are not covered by our clothes like we were during Victorian times. Also, we have more sensitive detection tools and folks that spend a lot of time indoors then get intermittent but intense sun exposure, increasing the risk of sunburns and developing melanoma.”

Berwick went on to remind the audience of the ABCDs of melanoma and how important it is to know our bodies as any changes in Asymmetry, Border, Color, and Diameter (no wider than a pencil eraser) can be a sign of melanoma.

Cancer researcher Dr. Chengyu Liang spoke of melanoma treatment and why it’s so stubborn to treat.

“For some patients with melanoma, we have different treatments to stimulate their immune system. We can use immunotherapy—finding the wolf (or cancer) in sheep’s clothing, or we can use targeted therapy—finding a way to stop or put on the brakes of an out-of-control car,” says Liang. “Wistar is a front runner in melanoma-targeted therapies and Wistar’s cell bank is vital in the research and treatments that have been accomplished thanks to Dr. Meenhard Herlyn’s lab.”

Dr. Liang joined Wistar less than a year ago and is recognized for her study of melanoma development and progression, with a particular focus on autophagy, or “self-eating”— a process in which cells digest and recycle waste.

“We now can have many patients survive and have their disease controlled through targeted or immunotherapy or a hybrid combo therapy,” said Liang. “But we want 100% survival, and we want to know the right therapy for the right patient at the right time.”

Dr. Jessie Villanueva is a research leader in how tumor cells become resistant. She discussed the challenges of therapy resistance in melanoma—when tumors become indifferent to drugs and escape therapy.

“Some tumors rewire and bypass the effect of the drugs,” says Villanueva. “Sometimes treatment works great for a period, but then tumors become resistant. The genetic make-up of the cancer cells is highly variable within tumors, and even from one another, so drugs can work on some cells but not others. Cancer cells that ‘escape’ treatment can remain asleep and then can be triggered to reawaken, which leads to tumor relapse.”

Dr. Villanueva is developing ways to target NRAS mutations in melanoma.

“The tumors that I work on harbor mutations in NRAS and account for 25-30% of all melanomas,” says Villanueva. “These tumors are highly aggressive and can spread to other organs. NRAS acts as a molecular switch controlling (molecular) signals that instruct the cell to grow or proliferate. A mutation in NRAS breaks the molecular switch, causing cells to proliferate indefinitely and accumulate additional mutations.”

Villanueva continued, “At Wistar, we have the tools and sophisticated models to mimic what happens in a patient’s tumor and we have faculty with diverse skills and backgrounds—from cancer biology, proteomics, and structural biology—to develop novel drugs to combat drug resistant melanoma.”

Dr. Noam Auslander is a computer scientist and uses artificial intelligence to interpret biomedical research data and extract and identify new information. She joined Wistar in June and focuses on the question of who responds to which cancer treatments.

“I do computational work and analyze data sets to generate research questions,” says Auslander. “I build predictors for treatment responses to predict who will respond and who will be resistant. Using these predictors and evaluating large scale data sets for the next drug targets, I hope to find new solutions to drug resistance.”

Before the event ended, the scientists shared challenges or helpful advice they considered key to their success and reminded the attendees to check and protect their skin.