City of Hope Developed a Foundational Map of Tumor Cells for Personalized Brain Cancer Treatments

Scientists developed a new framework to improve the ability of doctors to use precision medicine to identify therapeutic targets and potentially spotlight ways to prevent disease recurrence

City of Hope^®, one of the largest and most advanced cancer research and treatment organizations in the U.S. with its National Medical Center named top 5 in the nation for cancer by U.S. News & World Report, co-led the first study to demonstrate that characterizing genetic material near chromosomes forecasts how mutated, cancer-causing genes reengineer DNA and alter the tumor microenvironment. The leading-edge brain cancer research provides foundational knowledge that one day will improve the practice of precision medicine and allow oncologists to deliver more personalized therapies to cancer patients.

Tiny DNA molecules outside of chromosomes were once disregarded, but in the past decade research has revealed that these circles called extrachromosomal DNA, or ecDNA, fuel cancer by breaking the laws of biology.

“Our study offers new insights into the interplay between different ecDNA. Importantly, when there is a prevalence of ecDNA and cancer-causing ingredients like the EGFR protein or tumor protein p53, the tumor microenvironment becomes hypoxic. It falls into a state of reduced oxygen, which has been linked to cancer progression, resistance to therapy and poor clinical outcomes,” said David Craig, Ph.D., professor and chair of the Department of Integrative Translational Sciences at City of Hope and co-corresponding author of a study published today in Nature Communications.

Spatial transcriptomics (measuring and mapping of DNA activity) combined with genomic data can help identify groups of cells within a tumor that share a common ancestor but have acquired additional mutations. How they are distributed spatially informs the understanding of tumor evolution. The new translational science data underpins City of Hope’s precision medicine research, which applies innovation to create better outcomes with fewer side effects for more patients. City of Hope aspires to cure more cancer patients.

City of Hope researchers led a team that performed bulk RNA sequencing, tumor/normal DNA sequencing and spatial transcriptomics in a small sample of gliomas — tumors that develop in the brain or spinal cord. Through varied experiments and validation cohorts, they were able to identify common and distinct characteristics of the tumor microenvironment, developing an integrated analysis framework that can be leveraged by others.

“While our paper solely evaluated different types of brain cancers, the spatial transcriptomic principles and genome sequencing techniques we outlined will one day enable physicians to provide more personalized therapies for cancer patients,” said Gabriel Zada, M.D., a neurosurgeon with Keck Medicine of USC, professor of neurological surgery and physiology and neuroscience at the Keck School of Medicine of USC, co-director of the USC Brain Tumor Center and co-corresponding study author. “Cancer and its treatment is not one-size-fits-all. Understanding the molecular activity of ecDNA near inheritable and non-inheritable cells provides deep insights into potential therapeutic targets and risk of cancer recurrence.”

The researchers demonstrated that ecDNA drives rapid cancer cell (oncogene) proliferation outside of chromosomes, the thread-like structures inside the cell nucleus that houses DNA and RNA. EcDNA contributes to the development of gliomas, genetic instability and distinct tumor cell populations within a single tumor, making cancer more difficult to eliminate.

The dynamic nature of ecDNA may be what enables cancer cells to adapt and reprogram their genomes, driving tumor progression in response to changes in their microenvironment, including changes resulting from therapies.

“We have now demonstrated how cancer cells dynamically reprogram their own genome to control and respond to the tumor microenvironment. By uncovering these mechanisms, we are paving the way for more precise and effective treatments tailored to the unique biology of each patient,” Dr. Craig said.

The Nature Communications study entitled “Resolving Subclonal Genomic Heterogeneity in Gliomas by Integrating Spatial Transcriptomics with Loss of Heterozygosity and Extrachromosomal DNA Analysis” was supported by the National Center for Advancing Translational Science of the U.S. National Institutes of Health (KL2TR001854).

About City of Hope

City of Hope's mission is to make hope a reality for all touched by cancer and diabetes. Founded in 1913, City of Hope has grown into one of the largest and most advanced cancer research and treatment organizations in the U.S., and one of the leading research centers for diabetes and other life-threatening illnesses. City of Hope research has been the basis for numerous breakthrough cancer medicines, as well as human synthetic insulin and monoclonal antibodies. With an independent, National Cancer Institute-designated comprehensive cancer center that is ranked top 5 in the nation for cancer care by U.S. News & World Report at its core, City of Hope’s uniquely integrated model spans cancer care, research and development, academics and training, and a broad philanthropy program that powers its work. City of Hope’s growing national system includes its Los Angeles campus, a network of clinical care locations across Southern California, a new cancer center in Orange County, California, and cancer treatment centers and outpatient facilities in the Atlanta, Chicago and Phoenix areas. City of Hope’s affiliated group of organizations includes Translational Genomics Research Institute and AccessHope^TM. For more information about City of Hope, follow us on Facebook, X, YouTube, Instagram and LinkedIn.

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