NEW YORK (GenomeWeb) – By sequencing multiple metastatic tumors that arose within the same patients, researchers led by Steven Bova from the University of Tampere in Finland traced how prostate cancer spreads from a primary tumor to multiple other sites and, finally, becomes resistant to treatment.
Bova and his colleagues sequenced more than four dozen tumors from 10 men to find that tumor cells sharing common genetic glitches typically spread from one site to the next and, under selective pressure, develop multiple, convergent mutations bestowing resistance to androgen-deprivation therapy, as they reported today in Nature.
"The common faults we found in each man could potentially offer new targets for treatment," co-author Ros Eeles from the Institute of Cancer Research in London said in a statement. "But we found that, once cancer cells have spread, they continue to evolve genetically, so choosing the most effective treatments will remain a key challenge."
Bova, Eeles, and their colleagues performed whole-genome sequencing to an average depth of 55x on 51 tumors collected from 10 men, representing metastases from various body sites as well as five primary tumors.
After identifying high-confidence indels, copy-number variations, and other mutations, the researchers grouped the tumor cell populations within each patient into clonal and subclonal groups. They calculated the fraction of tumor cells carrying each mutation from the mutant allele fraction. By plotting the cancer cell fractions of mutations from sample pairs, the researchers could examine relationships between the subclones.
These plots indicated that multiple clones could seed metastases. For instance, one patient, called A22, had a cluster of mutations that were present in the most common ancestor of both metastases, but also additional mutational clusters that were present in subclonal populations at varying percentages.
In about half of the patients, the researchers found such clusters of mutations present at subclonal levels across metastatic prostate cancer, suggesting to them that polyclonal seeding at various organ sites is common.
In those five patients with polyclonal seeding, the researchers found that the subclones that reseeded multiple sites carried alterations to the androgen receptor (AR) gene or other genes involved in AR signaling, or alternative mechanisms of castration resistance such as MYC amplification or CTNNB1 mutations. This, they noted, indicated that tumor subpopulations with a survival advantage can spread to seed other sites.
To trace how such seeding occurred, the researchers examined the patients for whom primary tumor samples were also analyzed, to find that patients' metastases more closely resembled one another than the original tumor.
By developing phylogenetic trees, the researchers also established the order in which the mutations arose, and then by overlaying those on a body map, they visualized how clones emerged and moved throughout the patients. That, they reported, followed either a linear or a branching pattern.
Patient A22, they said, exhibited both patterns, while A24 showed sequential metastasis-to-metastasis spread followed by parallel polyclonal spread of subclones between metastases.
Overall, the researchers observed one metastasis seeding others in eight of the 10 patients.
Tumor cells in each patient shared a common clonal origin that usually represented the largest cluster of mutation and had the highest number of driver mutations.
Mutations that disrupted AR signaling, the researchers noted, were rarely among the early mutations, though all the patients had at least one mutation affecting AR or another gene in the AR signaling pathway. However, those cropped up after metastatic spread in most cases.
"A picture emerges of a diaspora of tumor cells, sharing a common heritage, spreading from one site to another, while retaining the genetic imprint of their ancestors," the researchers said in their paper.
Still, that each tumor shared a certain set of alterations could be their "Achilles' heel," the Wellcome Trust Sanger Institute's Ultan McDermott said in a statement.
"Many of these shared mutations are in tumor suppressor genes and our approach to therapeutically targeting these needs to be prioritized," he said.