UCLA Jonsson Comprehensive Cancer Center study details changes in chromosomes that allow melanomas to develop drug resistance
Newswise – Precision therapies targeting melanoma and other cancers have improved patient survival, but tumors often stop responding to drugs, and recent studies indicate DNA changes – both to the inside and outside of chromosomes – are a determining factor in the genesis of tumors as well as in resistance to treatment. .
To study mutations in a key cancer-promoting genetic pathway, researchers at UCLA Jonsson Comprehensive Cancer Center led the development of a model of drug resistance melanoma, allowing them to study the structures and dynamics resulting in intrachromosomal and extrachromosomal changes that support resistance in cancer cells. The model also allowed them to experimentally manipulate drug regimens and observe resistance-related responses, eventually leading to therapeutic approaches that will extend efficacy.
“Tumor genomes, especially those of aggressive cancers, have the ability to change quickly and unpredictably. With the many advancements in genome sequencing, mapping, and data analysis technologies, we are beginning to understand the conditions, structures, and interactions at the chromosome level that influence oncogenesis and drug resistance. In this study, we describe the mechanisms involved in the focal amplification of BRAF and other genes in the MAPK signaling pathway, which is a driver of many types of cancer, ”said Thomas Graeber, PhD, researcher at UCLA Jonsson Comprehensive Cancer Center and director of UCLA Metabolomics Center, senior author of a article published online December 20 to Discovery of cancer (DOI: 10.1158 / 2159-8290.CD-20-0936).
BRAF mutations, relatively common in thyroid cancer and melanoma, have been targeted with drugs such as vemurafenib and dabrafenib and other inhibitors of the MAPK pathway. Resistance often occurs, however, by reactivation of this pathway, activation of a different pathway, or both. A mechanism of reactivation of the MAPK pathway often observed in melanoma is the acquisition of BRAF amplifications.
A segment of chromosomal DNA that undergoes amplification, known as an amplicon, can lead to overexpression of genes that promote cancer and those that interfere with targeted therapies. However, unlike the DNA of normal human cells, this DNA can be separated from chromosomes and thus float more freely in the nucleus. This type of amplicon is known as extrachromosomal DNA (ecDNA), originally called double minutes (DM) because of the way they appear under a microscope.
Over time, these amplicons can reintegrate into a different chromosome, and these integration sites are known as regions of homogeneous staining (HSR) because they contain long stretches of copies of amplicons aligned in a row. Both of these forms of focal amplification are known contributors to cancer development and drug resistance, and switching between DM and HSR modes is an example of how cancer cells can grow or exhibit “plasticity.” Although they were first observed over 60 years ago, it is only in recent years that technological advancements have started to fully reveal their structure, organization and role in the evolution of tumors.
“This study was designed to provide details on the structure, dynamics, and vulnerabilities of MAPK-related focal amplifications with respect to drug resistance in melanoma,” said Kai Song, Graeber Lab graduate student and premier author of the article. “A comprehensive knowledge of these structures and interactions is essential to our understanding of tumor evolution and plasticity and to the development of therapeutic approaches that overcome resistance. “
Researchers treated a human melanoma cell line with kinase inhibitors that target the MAPK signaling pathway to develop a model of drug resistance. Initially, strong amplification of the BRAF gene was observed in the extrachromosomal DNA form, but over months of culture at a stable drug dose, the mechanism shifted to the intrachromosomal HSR form. According to the authors, the observation of a mode change in melanoma adds to several related reports in the literature of similar events in focal amplified oncogenes from different types of cancer, including leukemia and neuroblastoma.
The study found that each form of DNA provided different “fitness” benefits to tumor cells, for example in response to changing therapeutic conditions. For example, when cells are exposed to constant and stable drug therapy, intrachromosomal HSRs appear to be “more adept” than their extrachromosomal counterparts at promoting cancer growth – supporting a fitness-driven evolution from DMs to HSRs in these. conditions. However, an unstable or oscillating drug dose challenge creates an advantage in not having the amplicon copy number bound to chromosomes, and thus DM harboring cells are conserved.
Even though cells harboring DM are traditionally thought to be more plastic than HSR cells, research has found that HSR cells also possess amplicon copy number plasticity. The duration of HSR may shorten when the dose of the drug is reduced, allowing cancer cells to escape the “addiction” that occurs when they develop resistance to drugs. The mechanism by which the shortening of HSR occurs, the removal of amplicons without further modification of HSR, was revealed by a structural DNA analysis conducted in collaboration with a team from the Department of Computer Science at the University of California. in San Diego, edited by Vineet Bafna. , PhD.
The findings were supported by reports in the literature and clinical studies from a team led by collaborator Dr. Roger Lo, a member of the UCLA Jonsson Comprehensive Cancer Center. They find evidence for the plasticity of focal amplifications of MAPK genes in patient tumors and in xenograft model tumors derived from patients who have become resistant to MAPK inhibitory treatments.
Among other important findings, the research team documented that although melanoma cells can become resistant to drugs that inhibit the signaling pathway, treatment with these drugs appears to make them vulnerable to another form of treatment. With the inhibition of MAPK, melanoma cells shift their primary energy generation program from glycolysis, or glucose metabolism, to the mitochondrial pathways where respiration and energy production occur in cells. This leads to a high production of reactive oxidative stress in the treated cells. This cascade has been observed in previous studies, and the UCLA-led research team extended the results in the context of focal amplification to identify the involvement of the oxidation of fat molecules in the cell. This discovery revealed that cells under oxidative stress are vulnerable to a new class of drugs, called pro-ferroptotic drugs, which trigger programmed cell death mediated by oxidized lipids.
“An important value of this model system is that it allows us to search for new vulnerabilities in cancer cells that use these resistance methods based on focal amplification. Therapeutic targeting of these vulnerabilities is our end goal, ”said Graeber.