Extracellular DNA circles surrounded by X-shaped chromosomes in an electron micrograph. Image courtesy of Paul Mischel.
New computational toolkit helps researchers identify and study cancer-driving DNA alterations, with a public repository of more than 15,000 samples
Extrachromosomal DNA (ecDNA) consists of circular, double-stranded DNA molecules that have separated from chromosomes. They frequently carry multiple copies of cancer-driving oncogenes that are then highly expressed. Thus, ecDNA is increasingly recognized as a particularly worrisome driver of cancers and treatment resistance.
Now, a multi-institutional research team co-led by Jill Mesirov, PhD, Distinguished Professor in the Cancer Genome and Epigenetics Program at Sanford Burnham Prebys, has released AmpliconSuite, a computational toolkit for identifying and characterizing ecDNA and other focal DNA amplifications in cancer genomes, along with Amplicon Repository for hosting and sharing the community’s samples and ecDNA analyses. The repository currently provides public access to results for more than 15,000 samples.
“The combination of these two resources democratizes both the complicated bioinformatic approaches required for identifying ecDNA and elucidating their structure, along with openly communicating the results of employing them,” said Mesirov.
The work is described in the October 16, 2026 online issue of Nature Methods.
Mesirov and colleagues, including co-senior study authors Vineet Bafna, PhD, a professor of computer science and engineering at UC San Diego, and Paul S. Mischel, MD, a professor of pathology at Stanford University, developed computational methods to identify ecDNA and distinguish it from other forms of DNA amplification, and the informatics workflow and platform to share them.
The researchers validated the toolkit using 175 genes examined through fluorescence in situ hybridization across 72 cancer cell lines. The latest classifier achieved 91 percent precision and 95 percent recall in the study’s ecDNA validation analysis. An analysis of 6,506 cancer samples from patients also revealed patterns in which cancer-promoting genes tend to be amplified together on ecDNA.
AmpliconSuite is only the latest of Mesirov’s contributions to advancing biomedical research tools and capabilities. Mesirov has also played a leading role in developing widely used computational biology resources, including Gene Set Enrichment Analysis, the Molecular Signatures Database, and the Integrative Genomics Viewer. Together, these tools help researchers analyze, interpret, and visualize complex genomic data. These resources are used by researchers worldwide in cancer biology and other areas of biomedical science.
False-colored image of dying superficial epithelial cells during osmotic stress, which results in water passing in and out of the cells. These cells act as shields, covering the body’s external and internal surfaces.
Image courtesy of Yue Rong Tan.
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Women in Science Lecture series features cancer research fundraising leader and entrepreneur
From left to right: Sherine Sun, Robin Toft, Susanne Heynen-Genel and Jessica Proulx. Image credit: Sanford Burnham Prebys.
The series highlights the groundbreaking work and unique perspectives of women leaders in the biomedical sciences
Sanford Burnham Prebys Medical Discovery Institute hosted another inspirational installment of the Women in Science Lecture Series on October 14, 2026. The featured guest speaker was Robin Toft, CEO of Curebound, a community-powered cancer research accelerator in San Diego that has invested more than $50 million in 170 scientific projects.
Toft shared the trajectory of her career in health care and research. Early in her professional journey as a clinical laboratory scientist, she found that she excelled at educating physicians about new technologies. That led her into molecular diagnostic sales and later into the San Francisco biotech industry. After being diagnosed with colon cancer on a business trip, she was determined to move her life and career in a different direction.
Toft built an executive search firm in San Diego focused on serving oncology companies. Her goal was to put the right people in the right places to succeed. After she grew her search firm and it was acquired, Toft focused even more intently on providing service to institutional boards.
“Having served on more than 15 boards in and around this area, I was pulled toward nonprofit service,” said Toft. “Curebound was by far my favorite, so when Anne Marbarger stepped down as CEO, I raised my hand and said, ‘choose me, I really, really need to do this job.’”
Toft then discussed enhancements to Curebound’s leadership team and fundraising strategies aimed at increasing the organization’s ability to invest in the region.
“We love to invest over $10 million annually, and I want that to go up to 15, 20 and 25 in the coming years,” she said.
Toft concluded by providing advice on career advancement for women in academic and industry science based on her experience placing high-level executives.
“It always comes down to three elements: confidence, competence and connections,” said Toft.
Demonstrating confidence starts with candidates applying to jobs even when they don’t meet every single qualification. Competence includes creating and demonstrating value, then leveraging it to ask for additional opportunities. On the topic of connections, Toft discussed mentors who provide direct guidance and sponsors who go to bat for you when you’re not in the room.
“I challenge each of you to create a board of directors for yourself that includes both mentors and sponsors, and you’ll have a network to push you forward.”
Curebound CEO Robin Toft shared the trajectory of her career in health care and research. She also provided advice on career advancement for women in academic science and industry based on her experience running an oncology-focused executive search firm. Image credit: Sanford Burnham Prebys.
Following Toft’s remarks, Jessica Proulx, PhD, postdoctoral associate in the lab of Peter Adams, PhD, moderated a fireside chat and audience question-and-answer session with Toft, Susanne Heynen-Genel, PhD, director of high content imaging platforms in the Center for Therapeutics Discovery, and Xueqin (Sherine) Sun, PhD, assistant professor in the Cancer Genome and Epigenetics Program at the Sanford Burnham Prebys NCI-designated Cancer Center. Heynen-Genel and Sun have active research projects supported by grants from Curebound.
Topics during the fireside chat included: the importance of funding for high-risk, high-reward research and pilot studies to generate preliminary data; how grantmakers and principal investigators manage risk and balance their professional portfolios; plans for investing in personalized therapy research; and how principal investigators can better serve as mentors and sponsors for female scientists.
The Women in Science Lecture Series features events that are free and open to the public. The series is part of broader efforts at Sanford Burnham Prebys to foster an environment that nurtures the success of individuals from all backgrounds. The events are hosted by the Office of Workforce Engagement & Belonging and highlight the groundbreaking work and unique perspectives of women leaders in the biomedical sciences, while fostering mentorship and collaboration across the Torrey Pines Mesa.
Stay tuned for more information about the next event in the series scheduled for spring 2027.
The only way is up. What appears to be manmade is actually a scanning electron micrograph of a growing calcite crystal. The apparent arrows on the surface are formed by the crystal’s natural growth and the way proteins bind.
What appears to be some sort of horrific deep-sea creature is, in fact, the microscopic image of Taenia solium, a species of pig tapeworm that can cause human infections if it or its eggs are consumed in undercooked pork. What appear to be eyes and mouth are actually suckers and a hook-lined rostellum used to grip and anchor to the wall of the human small intestine.
Image courtesy of Teresa A. Zgoda.
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For Nobel laureates, the new Wertheim Prize is an opportunity to expand knowledge and benefit
The Dr. Herbert Wertheim Trust for Humanity has announced the Wertheim Laureate Prize, which invites eligible recipients of the Nobel Prize in Physiology or Medicine each year to individually direct $1 million to causes they believe will do the most good.
In its inaugural year, three 2026 recipients—Karl Deisseroth, Peter Hegemann, and George Nagel—were honored for their work developing optogenetics, a technique that uses light to control individual nerve cells in the brain. The trio, announced October 5, will share a Nobel prize of 12 million Swedish crowns ($1.2 million).
The Wertheim Laureate Prize rests on a simple idea, according to the Trust: “The scientists the world has just honored for transforming medicine and physiology are among the best judges of where philanthropy can make the greatest difference.”
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Sanford Burnham Prebys scientists support national aging research network
Recent Nature showcase features many discoveries made by Cellular Senescence Network program participants
Zombie-like entities lurk within each of us. They are known as senescent cells that no longer grow and divide. They tend to accumulate with age as our immune systems have more difficulty detecting and removing them.
These cells produce a complex mix of inflammatory molecules that can damage tissues. Senescence is involved in a range of human diseases of aging, such as Alzheimer’s disease, type 2 diabetes and cancer.
Scientists at Sanford Burnham Prebys Medical Discovery Institute are contributing to a nationwide effort known as the Cellular Senescence Network (SenNet) program, which aims to create a comprehensive atlas of how and where aging cells accumulate in our tissues and open new avenues for treating age-related diseases.
SenNet brings together a large network of U.S. labs and research institutions supported by the National Institutes of Health’s Common Fund. The NIH awarded $125 million in SenNet grants in 2021 with plans to provide more than $190 million in total funding.
Peter Adams, PhD, is the Jeanne and Gary Herberger Leadership Chair in Cancer Research at Sanford Burnham Prebys. Image credit: Sanford Burnham Prebys.
Peter Adams, PhD, the Jeanne and Gary Herberger Leadership Chair in Cancer Research at Sanford Burnham Prebys, is the contact principal investigator for SenNet’s San Diego Tissue Mapping Center and is co-chair of the SenNet Steering Committee.
Adams and his colleagues at the San Diego Tissue Mapping Center map senescent cells in five different tissues in mice: the liver, the brain, mammary glands, the intestines and bone marrow. The research team uses state-of-the-art, single-cell technologies applied to intact tissues to analyze specific changes in gene expression and chromatin structures within aging cells across tissues, life stages and organ systems. The center’s data analysis core is co-directed by Yuk-Lap (Kevin) Yip, PhD, the Andrew and Erna Viterbi Distinguished Chair and director of the Center for Data Science and Artificial Intelligence at Sanford Burnham Prebys.
The Nature family of journals recently launched an immersive webpage called “The SenNet Collection” that highlights studies from SenNet participants, including many led by or featuring Sanford Burnham Prebys authors.
Yuk-Lap (Kevin) Yip, PhD, the Andrew and Erna Viterbi Distinguished Chair and director of the Center for Data Science and Artificial Intelligence at Sanford Burnham Prebys. Image credit: Sanford Burnham Prebys.
The secret identity of a cell cycle regulator in cells that don’t cycle
Cell proliferation protein cyclin D1 paradoxically promotes inflammation in non-proliferating senescent cells
In a tale of identities as divergent as “The Prince and the Pauper,” a well-known cancer-causing gene also influences cells in a senescent state meant to prevent cancer.
The Adams lab and an international team of collaborators published findings August 20, 2026, in Nature Aging unpacking this biological paradox, finding that this cell proliferation gene played a distinct role in cells that no longer proliferate. It served as a driver of chronic inflammation linked to age-related disease, marking it as a promising target for future therapies to reduce sustained inflammation and promote healthier aging.
Altered metabolism in senescent cells helps promote destructive inflammation as we age
Study finds new mitochondrial pathway in senescent cells that changes how DNA is stored to expose inflammatory genes
The immune system’s rapid response to danger—called inflammation—is critical for our health, but it should only last as long as needed to stop infections and heal our wounds. As we grow older, however, we accumulate senescent cells that promote chronic inflammation—and which have been linked to many age-related diseases.
Scientists at Sanford Burnham Prebys Medical Discovery Institute, Mayo Clinic and their international collaborators published findings July 29, 2026, in Nature revealing a new connection between energy-producing mitochondria and this sustained inflammation. They also found that blocking a related gene reduced inflammation and promoted healthier aging in mice.
Single-cell sequencing analysis allows seeing the forest and trees
Study demonstrates a new method that makes massive, multidimensional datasets more manageable while preserving rare signals lost by other techniques
Sequencing technologies now routinely capture the RNA transcripts linked to thousands of genes in each cell of a sample. The immensity of these observations presents data scientists with the challenge of structuring and analyzing an output that is like a Rubik’s Cube but with thousands of faces, rows and columns.
To cut this problem down to size, researchers have developed methods to reduce the number of dimensions while preserving as much of the original data as possible. This can, however, lead to the loss of rare but biologically interesting signals, a bit like conservationists protecting a forest while inadvertently losing some unusual trees that may be important to the ecosystem.
In a study led by the Yip lab published in Genome Biology on February 4, 2026, SenNet researchers detailed a new dimensionality reduction method called Single-cell data Analysis with Knowledge inputs from User using Regularized Autoencoders (SAKURA). The research team showed that it helped cluster rare cells and demonstrated its effectiveness in identifying endocrine cell subtypes in the pancreatic islet, highly similar hematopoietic subpopulations and rare senescent cells.
Cellular circuit controls how DNA damage is repaired, affecting risk of disease as we age
Study reveals new information about how to prevent chronic inflammation from zombie-like cells that accumulate with age
In addition to no longer growing and proliferating, the other hallmark of senescent cells is that they have an inflammatory program causing them to secrete inflammatory molecules. Cells “running” this inflammatory program are considered to exhibit the senescence-associated secretory phenotype (SASP). Too many cells with SASP secreting inflammatory molecules can contribute to chronic inflammation in the body. This pervasive inflammation — called “inflammaging” — has been linked to many age-related diseases.
Scientists at Sanford Burnham Prebys and collaborators across the country published findings March 5, 2025, in Nature Communications showing that the mitochondria powering our cells also control the ability of a DNA repair protein to suppress SASP, which may reduce or delay inflammaging.
An artistic rendition of an Ishihara pattern comprised of more than 500 photographs of people’s retinas. An Ishihara pattern is a circular design made of randomized colored dots that hides a number or shape. It is used in eye tests to check for red-green color blindness.
A colorized scanning electron micrograph cardiovascular calcification, showing a calcium phosphate spherical particle (orange) within the extracellular matrix. Abnormal calcium and phosphate levels in the blood promote hardening and narrowing of blood vessels.
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Erik Hultenius awarded Melvin and Phyllis McCardle Clause Scholarship
The scholarship program for graduate students was created by the Clause family’s generous donation to Sanford Burnham Prebys
Erik Hultenius, a third-year doctoral student in the Sanford Burnham Prebys Medical Discovery Institute’s Graduate School of Biomedical Sciences, was selected as the 2026 recipient of the Melvin and Phyllis McCardle Clause Scholarship.
The scholarship was established in honor of Phyllis McCardle Clause after her long struggle with Alzheimer’s disease. The award supports graduate student education in age-related neurodegeneration within the Institute’s graduate school.
“Receiving this honor is very reassuring for the direction of my project,” said Hultenius. “Receiving positive feedback from the selection committee is encouraging, as is having my research project singled out from a competitive field of proposals.”
Hultenius became passionate about understanding the biology of aging during his undergraduate coursework. He remembers a particular class where he and his peers discussed a manuscript about epigenetic reprogramming to reverse features of aging in mice.
“It was fascinating to me that there are people working on interventions that targeted aging almost as if it was a disease,” said Hultenius. “At that point, I knew I wanted to develop ways to intervene in the biological aging process to prevent age-related neurodegeneration and other diseases before they become too difficult to treat.”
After graduating in 2023, Hultenius conducted an internship with Altos Labs, a biotechnology company focused on restoring cell health and resilience through cell rejuvenation. He then joined Sanford Burnham Prebys and experienced a “full circle” moment with his PhD program mentor, Xiao Tian, PhD, assistant professor in the Center for Neurologic Diseases.
“I realized that Xiao was one of the lead authors on the paper I read in class that introduced me to this field,” said Hultenius. “He is partly responsible for sparking my research interest to begin with, so it was serendipitous to end up joining his lab.”
Hultenius investigates the brain’s immune cells, which are called microglial cells. He wants to understand how they change with aging and how those age-related changes might contribute to how Alzheimer’s disease progresses.
“Microglia are intimately involved in the processes that help to prevent disease from spreading in the brain,” said Hultenius. “They also mediate inflammation, and we know that increased levels of inflammation correlate with poor outcomes in patients with Alzheimer’s disease.”
Hultenius sees the potential to make a meaningful difference in this ever more prevalent age-related disease.
“There is a tremendous gap in patient care right now as treatment options are limited and lacking in effectiveness for most individuals. I want to make an impact on Alzheimer’s disease for all those affected, and the support from the Clause scholarship will help me advance my research and move closer to my goal.”
