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Early Spatial Mutation Patterns May Affect Colorectal Cancer Invasiveness

NEW YORK (GenomeWeb) – The spatial distribution of mutations in early stage colorectal cancers (CRC) may provide clues to their ultimate aggressiveness and invasiveness, new research suggests.

"Because treating a patient aggressively can cause them harm and side-effects, it is important to understand which of the small screen-detected [CRC] tumors are relatively benign and slowly growing, and which ones are born to be bad," senior author Darryl Shibata, a pathology researcher at the University of Southern California's Keck School of Medicine, said in a statement.

Shibata and his colleagues did exome sequencing, multi-region targeted sequencing, and/or array-based copy number profiling on tumor samples from 19 individuals with CRC, using mutations identified in the tumors as well as tumor expansion and evolution modeling to identify spatial mutation signatures in early-stage CRCs that were linked to the tumors' ultimate invasiveness. The findings appear online this week in the Proceedings of the National Academy of Sciences.

"We found evidence that benign and malignant tumors start differently, and that cell movement — an important feature of malignancy — manifests itself very early on during tumor growth," first author Marc Ryser, a postdoctoral researcher in the surgery and mathematics departments at Duke University, noted in the statement. "By testing screen-detected, small tumors for early cell movement as a sign of malignancy, it might be possible to identify which patients are likely to benefit from aggressive treatment."

The team reasoned that it should be possible to reconstruct early tumor evolution events by comparing samples from the opposite sides of the tumor, using these samples to start untangling some of the early driver mutation and cell migration events.

"[I]n the absence of early cell movement, we expect private mutations in the final tumor to cluster spatially, in alignment with the respective branches of the early tree," the authors wrote. "On the other hand, if early cell movement is present, we expect private mutations to be side-variegated in the final tumor and present on branches that cross sides of the early tree."

After using Illumina TruSeq or Nextera kits to capture protein-coding portions of the genome in matched tumor and normal samples from 15 individuals with colorectal adenocarcinoma and four with colorectal adenoma, the researchers sequenced the exomes on Illumina HiSeq2000 or NextSeq500 instruments. To that, they added multi-region deep AmpliSeq panel sequencing on the IonTorrent instrument and Illumina SNP array-based chromosome copy number profiling, examining up to five gland regions per tumor.

Together with the team's computational modeling of stochastic multiscale tumor expansions, done in the context of the glandular structures previously described for CRC tumors, the mutations and copy number patterns detected in the samples supported the notion that mutation profiles at opposite tumor points could offer a look back at events in the tumor.

Moreover, the researchers saw apparent differences in the types of early cell movement predicted from their data in the more invasive cases. In particular, nine of the 15 invasive CRCs had mutation patterns pointing to "abnormal" early cell movement — a pattern not detected in the four benign colorectal adenoma cases.

While they cautioned that additional analyses on larger tumor sets are needed to verify the current findings, the investigators proposed a model in which the potential for invasiveness and metastasis is present early on in CRC in the form of altered cell movements that might be traceable using tumor sub-clone mutation profiles to offer insights into everything from disease biology to patient prognoses. 

"[S]ome malignant tumors start with more invasive potential ('born to be bad')," they wrote, "and this early abnormal cell mobility can potentially be used to identify patients more likely to benefit from aggressive treatment."

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