New biomarkers are discovered by mapping mutation 'hotspots' in cancer.

Researchers led by bioengineers at the University of California, San Diego, have discovered and characterised a previously unknown crucial candidate in cancer evolution: clusters of mutations in specific locations of the genome. These mutation clusters contribute to the progression of around 10% of human tumours, and can be used to predict patient survival.

The findings were published in the journal Nature on February 9th.

The study offers insight on a type of mutation known as clustered somatic mutations. Clustered somatic mutations are induced by internal and external stimuli such as age or UV radiation, and they are not inherited.

Clustered somatic mutations have been a little-studied aspect of cancer development (cancer sign and symptoms) thus far. However, researchers in the lab of Ludmil Alexandrov, a UC San Diego professor of bioengineering and cellular and molecular medicine, saw something peculiar about these mutations that needed additional investigation.

"Somatic mutations often occur at random across the genome. However, deeper examination of some of these mutations revealed that they were occurring in these hotspots. It's like throwing balls on the floor and then seeing them all clump together in one spot "Alexandrov stated. "As a result, we couldn't help but wonder: What's going on here? Why are there hotspots in the first place? Is there any clinical significance to them? Do they provide any insight into how cancer has progressed?"

"Clustered mutations have been generally overlooked since they account for such a small percentage of all mutations," said Erik Bergstrom, a bioengineering PhD student in Alexandrov's group and the study's first author. "However, as we dug deeper, we discovered that they play a key role in the aetiology of human cancer."

The researchers were able to make these discoveries thanks to the creation of the most comprehensive and detailed atlas of known clustered somatic mutations. They began by mapping all mutations (clustered and non-clustered) in the genomes of over 2500 cancer patients, a task that included 30 distinct cancer types in all. The researchers used next-generation artificial intelligence technologies developed in the Alexandrov group to construct their map. The researchers utilised these algorithms to find clustered mutations in specific individuals and learn more about the mutational processes that cause them. As a result, they discovered that clustered somatic mutations have a role in cancer evolution in about 10% of human malignancies.

The researchers went a step further and discovered that some cancer-driving clusters, notably those identified in known cancer driver genes, can be utilised to predict a patient's overall survival. When clustered mutations in the BRAF gene — the most commonly detected driver gene in melanoma — are present, patients have a greater overall survival rate than those with non-clustered mutations. Meanwhile, clustered mutations in the EGFR gene, which is the most commonly found driver gene in lung cancer, reduce patient survival.

"What's noteworthy is that we show differential survival just by having clustered mutations found inside these genes, and this can be diagnosed using existing platforms that are widely utilised in the clinic. As a result, this serves as a very straightforward and exact indicator for patient survival "Bergstrom stated.

"This elegant work highlights the importance of developing AI approaches to elucidate tumour biology, as well as biomarker discovery and rapid development on standard platforms with direct line of sight translation to the clinic," said Scott Lippman, director of Moores Cancer Center and associate vice chancellor for cancer research and care at UC San Diego. "This demonstrates UC San Diego's strength in merging engineering and artificial intelligence approaches to solve current cancer therapy concerns."

A new cancer evolution mode has emerged.

The researchers also discovered several factors that produce clustered somatic mutations in this study. UV exposure, alcohol intake, tobacco smoking, and most importantly, the activation of a group of antiviral enzymes known as APOBEC3 are among these factors.

In most cases, APOBEC3 enzymes are present inside cells as part of the cell's own immune response. They are primarily responsible for chopping up any viruses that enter the cell. However, the researchers believe that the APOBEC3 enzymes may be doing more harm than good in cancer cells.

The researchers discovered that cancer cells have clusters of mutations occurring across individual ecDNA molecules, which are often replete with circular rings of extrachromosomal DNA (ecDNA) that harbour known cancer driver genes. These alterations are attributed to the activity of APOBEC3 enzymes, according to the researchers. They believe that APOBEC3 enzymes mistake ecDNA's circular rings for invading viruses and try to limit and chop them up.

Individual ecDNA molecules form clusters of mutations as a result of the APOBEC3 enzymes' actions. This, in turn, hastens the progression of cancer and is likely to lead to medication resistance. These clustered mutation rings were given the term kyklonas, which is the Greek word for cyclones.

"This is an entirely new mode of oncogenesis," Alexandrov stated. "This establishes the framework for future therapeutic approaches, where clinicians can investigate reducing the activity of APOBEC3 enzymes and/or targeting extrachromosomal DNA for cancer treatment," he said, citing the team's other discoveries.

Journal Reference:

Erik N. Bergstrom, Jens Luebeck, Mia Petljak, Azhar Khandekar, Mark Barnes, Tongwu Zhang, Christopher D. Steele, Nischalan Pillay, Maria Teresa Landi, Vineet Bafna, Paul S. Mischel, Reuben S. Harris, Ludmil B. Alexandrov. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature, 2022; DOI: 10.1038/s41586-022-04398-6