Program Archives - Sanford Burnham Prebys

San Diego Nathan Shock Center

San Diego Nathan Shock Center

Established in 2020 with funding from the National Institute of Aging, part of the National Institutes of Health, the San Diego Nathan Shock Center of Excellence in the Basic Biology of Aging is a consortium of Sanford Burnham Prebys, Salk Institute for Biological Studies and the University of California San Diego. 

The center focuses on the heterogeneity of aging, the fact that cells, organs and people age at different rates and that this “biological age” is a better indicator of an individual’s susceptibility to age-related declines and diseases.

The center provides resources to scientist-members to develop new human cell models of aging, enabling deeper analyses of molecular, cellular and tissue heterogeneity and support of basic biology of aging research through development, training and mentoring activities.

Recent Publications

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.

Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB, ENCODE Imputation Challenge Participants

Genome Biol 2025 Feb 13 ;26(1):31

ArfGAP2 promotes STING proton channel activity, cytokine transit, and autoinflammation.

Poddar S, Chauvin SD, Archer CH, Qian W, Castillo-Badillo JA, Yin X, Disbennett WM, Miner CA, Holley JA, Naismith TV, Stinson WA, Wei X, Ning Y, Fu J, Ochoa TA, Surve N, Zaver SA, Wodzanowski KA, Balka KR, Venkatraman R, Liu C, Rome K, Bailis W, Shiba Y, Cherry S, Shin S, Semenkovich CF, De Nardo D, Yoh S, Roberson EDO, Chanda SK, Kast DJ, Miner JJ

Cell 2025 Feb 5 ;():

Metabolic and Liver Diseases Program

liver cell

Mastering Metabolism

Metabolism is the sum of the chemical reactions that take place within each cell of a living organism. It is the fundamental process of converting food into energy, creating the building blocks of life—proteins, lipids, nucleic acids and more—and ensuring that the organism thrives.

Metabolic dysfunction disrupts this universal commonality of life and can lead to a broad spectrum of devastating, chronic diseases. At the center of metabolic functioning is the liver, which makes it at particular risk. Dysfunction in the body’s largest internal organ can create a cascade of harm.


Recent Publications

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Immunity and Pathogenesis Program

t cell-sem-niaid

Disease and the Immune Response

Pathogenesis—literally how disease (pathos) begins (genesis) or develops—is a broad and important area of research.

Many diseases can arise from pathogens, but the immune system protects us through various lines of defense. If the immune system fails to function properly and becomes too weak or too strong, it can lead to disease states that include immunodeficiencies that lead to enhanced susceptibly to infections disease, autoimmune conditions, such as lupus and arthritis, and even cancer. 


Director’s Statement

“Our focus is on understanding the regulation and interplay of host immune responses and microbial pathogenesis. We study pathogen-host interactions, innate and humoral immunity, inflammation and T cell checkpoint regulation. A better understanding of these aspects of the immune system will provide novel therapeutic opportunities to address many unmet medical needs, including the treatment of endemic and pandemic infectious diseases, autoimmune disorders, cancer and inflammatory diseases.”

Portrait of Jamey Marth, PhD
Jamey Marth, PhD Program Director

Recent Publications

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Human Genetics Program

A child and mother and toured through a lab with Duc Dong, PhD

Harrows of Heredity

Most genetic disorders are present from birth. Fortunately, they are also exceedingly rare, perhaps affecting only one person in every several thousand or million.

Some are well known, such as sickle cell anemia and cystic fibrosis, but others are so infrequently seen or documented by clinicians that there may only be a handful of known cases in the world or in history. 

Whether a genetic disease afflicts thousands or a single person, it poses distinct and daunting  challenges for patients, their families and caregivers, not least that the average time it takes for most patients with a rare disease to get a correct diagnosis is nine years. We strive to shorten that diagnostic journey and point toward potential treatments.


Director’s Statement

“We want to better understand some of the many rare diseases we already know (approximately 7,000) and identify for the first time new genetic disorders that lack names but not victims. Using a variety of animal models, stem cell technologies and patient samples, we peer into the pathological mechanisms of genetic disorders for answers that will lead to clinically useful diagnostic tests and novel therapies. Strong relationships with and advocacy for patients and their families is a foundation of our work, and every year we bring together scientists, patients, families and advocates to share news of the latest discoveries, clinical advances and listen to their concerns. With their help, we build momentum and progress for those whose conditions are unknown to most people. ”

Portrait of Hudson Freeze, PhD
Hudson Freeze, PhD Program Director

Recent Publications

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Cancer Molecular Therapeutics Program

People working in a lab

Drug Discovery

Our mission is to expand and expedite the discovery and development of new cancer therapeutic agents based on novel insights into cancer biology.

We focus on the early stages of the drug discovery process, from target validation through “proof-of concept” studies, which seek to demonstrate that a newly discovered drug candidate can successfully alter the course of cancer disease progression. 

We combine the strengths and resources of faculty with complementary expertise in assay development, high-throughput screening, downstream medicinal chemistry and pharmacology through our partnership with the Conrad Prebys Center for Chemical Genomics.


Director’s Statement

“Through cross-program, early translational efforts, we leverage novel findings to identify and validate new targets for cancer, develop small molecule compounds that modify or control  identified targets and test potential drug candidates in state-of-the-art animal, computational and in vitro models of cancer.”

Portrait of Michael Jackson
Michael Jackson, PhD Interim Program Director

Recent Publications

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Degenerative Diseases Program

mouse brain with alz plaque ncats

Perilous Proteins

Proteins are the workhorses of the cell. They are required for the structure, function and regulation of the body’s tissues and organs. What they do and how well they do it depends upon their three-dimensional shape, which determines whether a protein can interact with other molecules.

When proteins are misfolded or damaged, they cannot perform their duties. Faulty proteins must be eliminated before they can accumulate, clump or become toxic. Although there are intrinsic cell mechanisms that recognize defective proteins and attempt to remove them, these systems can go awry or fail as we age. Almost every age-related degenerative disease is linked to protein misfolding.


Director’s Statement

“We want to understand how cells discriminate between functional and nonfunctional proteins. We have already made important discoveries about the damaging impact of oxidative stress on protein structure and function in neurodegenerative diseases like Alzheimer’s and Parkinson’s, in metabolic diseases like diabetes and liver failure, and in inflammatory diseases and cancer. Our goal is to translate these findings into new therapies that improve or repair protein folding and preserve cell function in diseases that affect millions of people. ”

Portrait of Randal J. Kaufman, PhD
Randal J. Kaufman, PhD Program Director

Recent Publications

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Cancer Metabolism and Microenvironment Program

breast cancer cells

Malignant Machinery

Like any complex machine comprised of multifarious but highly synchronized parts, cancer is the creation of diverse but organized cells and molecules driven by disinformation and dysfunction to produce malignant tissues and tumors.

Our program focuses on determining how nutrients and the microenvironment surrounding tumors interact to direct the formation, growth and spread of cancer cells. From individual metabolites to stromal cells, such as fibroblasts and immune cells, our goal is to discern the basic workings of tumors that cause disease, revealing a more comprehensive view of cancer biology that can be a guide to new therapies.


Director’s Statement

“We live and work in the tumor ecosystem, probing its nooks, crannies and complexities for new insights into how tumors begin and grow—and how best to prevent or stop both. We study paramount processes in cancer, including metabolism, signal transduction, tumor-stroma crosstalk and molecular machines. We want to know what different parts of a tumor do, how they work alone or together and why so that we can, ultimately, fix the problems that result in cancer. ”

Portrait of Brooke Emerling, PhD
Brooke Emerling, PhD Program Director

Recent Publications

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Development, Aging and Regeneration Program

Scientists collaborate at a microscope

Biology of Becoming

Development, growth and aging are all directed or controlled by constant cues and signals from inside and outside the body, influenced by factors like injury, infection, stress and even what we eat. 

To adjust and adapt to these cues, cells send and receive signals through biological pathways. Our research investigates the codes, signals and cell changes associated with normal development and aging, seeking to distinguish them from those cues and signals linked to disease and disability. By translating this critical, constant chatter of life, we hope to create and speak a new vocabulary for improved health. 


Director’s Statement

“From fish, flies, worms and mice to human stem cells, we use model organisms to probe and  unravel gene functions linked to mutations and epigenetic factors, explore the development and regenerative capacity of different organs and tissues (brain, heart, muscles, pancreas, limbs, liver) and parse the biology of aging, including how organism’s preserve healthy functioning.  These insights provide the tools needed to uncover novel therapeutic targets for heart disease, neurodegeneration, muscle disorders, diabetes, cancer and other debilitating diseases.”

Pier Lorenzo Puri, MD and Alessandra Sacco, PhD Program Directors

Recent Publications

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Cancer Genome and Epigenetics Program

breast cancer cells

Controlling Cancer

All cancers depend upon dysregulation and dysfunction of normal cell processes. These processes are often controlled by the cell nucleus, specifically by DNA sequence (the genome) and its regulation (the epigenome).

Dysregulation of nuclear processes encoded within the genome and/or epigenome drive many of the detrimental properties of cancer cells, such as defective DNA repair and mutation accumulation, altered inflammatory signaling and immune regulation, unrestrained cell growth and survival, tissue invasion, metastasis and drug resistance. Understanding these processes, including their dysregulation in aging and differences between races and ethnicities, can lead to new approaches for patient- and population-specific risk assessment, early detection and diagnoses of cancer, as well as novel therapeutic interventions.


Director’s Statement

“We bring together experts in nuclear dysfunction in cancer. Analysis of the genome and epigenome is intensive, and so too is our program. Our faculty pursue diverse research interests, and share a fundamental focus on how nuclear dysregulation drives cancer growth—all intended to lead to breakthrough discoveries and treatments for cancer.”

Peter Adams, PhD Program Director

Recent Publications

Showing 3 of 3

Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.

Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB, ENCODE Imputation Challenge Participants

Genome Biol 2025 Feb 13 ;26(1):31

A forward genetic screen identifies potassium channel essentiality in SHH medulloblastoma maintenance.

Fan JJ, Erickson AW, Carrillo-Garcia J, Wang X, Skowron P, Wang X, Chen X, Shan G, Dou W, Bahrampour S, Xiong Y, Dong W, Abeysundara N, Francisco MA, Pusong RJ, Wang W, Li M, Ying E, Suárez RA, Farooq H, Holgado BL, Wu X, Daniels C, Dupuy AJ, Cadiñanos J, Bradley A, Bagchi A, Moriarity BS, Largaespada DA, Morrissy AS, Ramaswamy V, Mack SC, Garzia L, Dirks PB, Li X, Wanggou S, Egan S, Sun Y, Taylor MD, Huang X

Dev Cell 2025 Jan 20 ;():