Micro-Scale Genomic DNA Copy Number Aberrations as Another Means of Mutagenesis in Breast Cancer

Abstract

IntroductionIn breast cancer, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations, as shown by a previously described micro-deletion event in the PTEN gene in the Basal-like SUM149 breast cancer cell line.MethodsWe sought to identify if small regions of genomic DNA copy number changes exist by using a high density, gene-centric Comparative Genomic Hybridizations (CGH) array on cell lines and primary tumors. A custom tiling array for CGH (244,000 probes, 200 bp tiling resolution) was created to identify small regions of genomic change, which was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments were called micro-aberrations (<64 contiguous probes, ∼ 15 kb).ResultsOur data showed that primary tumor breast cancer genomes frequently contained many small-scale copy number gains and losses, termed micro-aberrations, most of which are undetectable using typical-density genome-wide aCGH arrays. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene. We confirmed the presence of the PTEN micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5′ regions of the affected genes, including the promoter region, and high frequency of micro-aberrations was associated with poor survival.ConclusionUsing a high-probe-density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that can contribute to gene inactivation. These events may contribute to tumor formation through mechanisms not detected using conventional DNA copy number analyses.

Whole-exome sequencing reveals the mutational spectrum of testicular germ cell tumours

“…FSIP2 amplifications were all 8–9 kb in length spanning a sub-region of the gene coding sequence, encompassing exons 16–17. Recent functional evidence has demonstrated that part-gene amplifications do affect gene expression levels, with an effect size comparable to that of full-gene amplification 37 . Our finding of recurrent FSIP2 amplification is corroborated by recent high resolution SNP array data on an independent series of seminomas 38 , which documented FSIP2 amplification in 22% of tumours.…”

Loss of PTEN promotes formation of signaling-capable clathrin-coated pits

“…Importantly, we find that both EGFR and PTEN are localized to short-lived CCPs. We examined the role of PTEN more closely by reconstituting PTEN in triple-negative inflammatory breast cancer SUM149 cells, which do not express functional PTEN due to a genetic micro-amplification within the PTEN gene (Saal et al, 2008;Chao et al, 2012), and by deleting PTEN in MCF10A and MDA231 cells. By analyzing CCP dynamics, we demonstrate a role for PTEN in regulating the proportion of short-lived CCPs and initiation density.…”

Loss of PTEN promotes formation of signaling-capable clathrin-coated pits

“…Importantly, we find that both EGFR and PTEN are localized to short-lived CCPs. We examined the role of PTEN more closely by reconstituting PTEN in triple negative inflammatory breast cancer SUM149 cells, which do not express functional PTEN due to a genetic micro-amplification within the PTEN gene 35,36 , and by deleting PTEN in MCF10A and MDA231 cells. By analyzing CCP dynamics, we demonstrate a role for PTEN in regulating the proportion of short-lived CCPs and initiation density.…”