NEW YORK (GenomeWeb) – By digging into the mutational signatures of nearly 1,600 human cancer cell lines and patient-derived xenografts (PDX), a team from the UK, US, Korea, and Spain has started distinguishing between mutagenic processes that persist and those that go away or happen in bursts in cultured cancer cell lines.
Researchers from the Wellcome Sanger Institute; the University of California, San Diego; and elsewhere analyzed the exomes of more than 1,000 human cancer cell lines and almost 600 PDX samples before following serially cultivated cancer cell clones from 28 cancer cell lines with exome, genome, or single-cell sequencing. Their results, appearing online today in Cell, revealed differences in the arrival of new mutations in cell lines depending on the mutagenesis process involved.
"The cancer lines and PDX models analyzed here now provide a substantial resource for exploring mechanistic questions relating to the mutational processes underlying the majority of mutational signatures," senior and corresponding author Michael Stratton, director of the Sanger Institute, and his colleagues wrote.
Prior studies have highlighted dozens of distinct mutational signatures made up of base substitutions and rearrangements, providing clues to the mutagenic events behind a tumor's formation — from DNA repair defects to ultraviolet light or tobacco smoke exposure. Even so, the team noted that additional research is needed to tease out all of the mutational processes behind the signatures, and to determine whether they continue after a tumor is sampled.
"Comparisons of mutations generated during different phases of the evolution of individual human cancer in vivo suggest that some mutational processes show varying degrees of activity over time," the authors wrote.
To dig into such questions, the researchers looked at the mutational signatures present in 1,001 cancer cell lines from the Sanger Institute's "Catalogue of Somatic Mutations in Cancer" (COSMIC) Cell Line Project and 577 patient-derived xenograft samples, which span more than 40 cancer types, using available exome sequence data. They also considered sequences for 2,709 primary human cancers that were previously profiled for the International Cancer Genome Consortium.
To gauge mutational activity in these cancer cell lines in vitro and to distinguish between new and historical mutation events, the team developed serial clones from 28 of the human cancer cell line stocks, representing B cell lymphoma, leukemia, breast, lung, skin, and other solid tumor types, containing a range of mutational signatures.
There, the researchers systematically selected individual cells to propagate new clonal cultures. Each of those cultures was grown for up to 161 days before further sub-cloning steps, they explained, and samples were assessed by bulk whole-genome sequencing, exome sequencing, or single-cell sequencing along the way.
The team noted that mutational signatures associated with exposure to tobacco smoke or ultraviolet light did not to endure in vitro. On the other hand, the cancer cell lines did display steady, ongoing rates of mutagenesis from DNA repair or replication.
In contrast to both of those external and internal mutation sources, the researchers noted that the human cell lines were marked by intermittent eruptions of mutagenesis involving the cytidine deaminase DNA editing enzyme APOBEC — a source of APOBEC-related mutational signatures such as SBS2 and SBS13 that turned up in the current analyses of breast, lung, bladder, head and neck, cervical, esophageal, and non-melanoma skin cancer types.
"Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro," the authors wrote, while the results "indicate that SBS2 and SBS13 mutations can be generated in short, intense bursts of activity with long intervening periods of silence, a pattern that we have termed 'episodic mutagenesis.'"
Based on these and other findings, the authors suggested that "initiators of APOBEC mutagenesis in vitro are cell intrinsic and have intermittent and irregular activity."