Background: Intratumoral heterogeneity may help drive resistance to targeted
therapies in cancer. In breast cancer, the presence of nodal metastases is a key
indicator of poorer overall survival. The aim of this study was to identify somatic
genetic alterations in early dissemination of breast cancer by whole genome next
generation sequencing (NGS) of a primary breast tumor, a matched locally-involved
axillary lymph node and healthy normal DNA from blood.
Methods: Whole genome NGS was performed on 12 mg (range 11.1–13.3 mg) of
DNA isolated from fresh-frozen primary breast tumor, axillary lymph node and
peripheral blood following the DNA nanoball sequencing protocol. Single nucleotide
variants, insertions, deletions, and substitutions were identified through a
bioinformatic pipeline and compared to CIN25, a key set of genes associated with
tumor metastasis.
Results: Whole genome sequencing revealed overlapping variants between the
tumor and node, but also variants that were unique to each. Novel mutations unique
to the node included those found in two CIN25 targets, TGIF2 and CCNB2, which
are related to transcription cyclin activity and chromosomal stability, respectively,
and a unique frameshift in PDS5B, which is required for accurate sister chromatid
segregation during cell division. We also identified dominant clonal variants that
progressed from tumor to node, including SNVs in TP53 and ARAP3, which
mediates rearrangements to the cytoskeleton and cell shape, and an insertion in TOP2A, the expression of which is significantly associated with tumor proliferation
and can segregate breast cancers by outcome.
Conclusion: This case study provides preliminary evidence that primary tumor and
early nodal metastasis have largely overlapping somatic genetic alterations. There
were very few mutations unique to the involved node. However, significant
conclusions regarding early dissemination needs analysis of a larger number of
patient samples.