Somatic mutations in leukocytes infiltrating primary breast cancers

Abstract

Background: Malignant transformation requires the interaction of cancer cells with their microenvironment, including infiltrating leukocytes. However, somatic mutational studies have focused on alterations in cancer cells, assuming that the microenvironment is genetically normal. Because we hypothesized that this might not be a valid assumption, we performed exome sequencing and targeted sequencing to investigate for the presence of pathogenic mutations in tumor-associated leukocytes in breast cancers.

Methods: We used targeted sequencing and exome sequencing to evaluate the presence of mutations in sorted tumor-infiltrating CD45-positive cells from primary untreated breast cancers. We used high-depth sequencing to determine the presence/absence of the mutations we identified in breast cancer-infiltrating leukocytes in purified tumor cells and in circulating blood cells.

Results: Capture-based sequencing of 15 paired tumor-infiltrating leukocytes and matched germline DNA identified variants in known cancer genes in all 15 primary breast cancer patients in our cohort. We validated the presence of mutations identified by targeted sequencing in infiltrating leukocytes through orthogonal exome sequencing. Ten patients harbored alterations previously reported as somatically acquired variants, including in known leukemia genes (DNTM3A, TET2, and BCOR). One of the mutations observed in the tumor-infiltrating leukocytes was also detected in the circulating leukocytes of the same patients at a lower allele frequency than observed in the tumor-infiltrating cells.

Conclusions: Here we show that somatic mutations, including mutations in known cancer genes, are present in the leukocytes infiltrating a subset of primary breast cancers. This observation allows for the possibility that the cancer cells interact with mutant infiltrating leukocytes, which has many potential clinical implications.

Figure 1

Sequencing analysis of 15 primary breast cancers identified somatically acquired mutations in tumor-infiltrating leukocytes. (a) Gating scheme for fluorescent-activated cell sorting of CD45-positive hematopoietic cells. DAPI was included as live-dead stain. Cell doublets were excluded prior to gating on APC-Cy7 (not shown). DNA extracted from the CD45-positive fraction was analyzed using three independent sequencing platforms. (b) Representative integrated genomics viewer image showing the presence of acquired mutations. Reads that do not match the reference nucleotide are colored. Gray bar chart on top displays the read depth. Reference nucleotide and protein sequence are depicted for each mutation. Variant allele frequency (VAF) and the number of altered and total reads are shown (alt|total, VAF). DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein.