Lack of Genomic Heterogeneity at High-Resolution aCGH between Primary Breast Cancers and Their Paired Lymph Node Metastases

<div><p>Lymph-node metastasis (LNM) predict high recurrence rates in breast cancer patients. Systemic treatment aims to eliminate (micro)metastatic cells. However decisions regarding systemic treatment depend largely on clinical and molecular characteristics of primary tumours. It remains, however, unclear to what extent metastases resemble the cognate primary breast tumours, especially on a genomic level, and as such will be eradicated by the systemic therapy chosen. In this study we used high-resolution aCGH to investigate DNA copy number differences between primary breast cancers and their paired LNMs. To date, no recurrent LNM-specific genomic aberrations have been identified using array comparative genomic hybridization (aCGH) analysis. In our study we employ a high-resolution platform and we stratify on different breast cancer subtypes, both aspects that might have underpowered previously performed studies.To test the possibility that genomic instability in triple-negative breast cancers (TNBCs) might cause increased random and potentially also recurrent copy number aberrations (CNAs) in their LNMs, we studied 10 primary TNBC–LNM pairs and 10 ER-positive (ER+) pairs and verified our findings adding additionally 5 TNBC-LNM and 22 ER+-LNM pairs. We found that all LNMs clustered nearest to their matched tumour except for two cases, of which one was due to the presence of two distinct histological components in one tumour. We found no significantly altered CNAs between tumour and their LNMs in the entire group or in the subgroups. Within the TNBC subgroup, no absolute increase in CNAs was found in the LNMs compared to their primary tumours, suggesting that increased genomic instability does not lead to more CNAs in LNMs. Our findings suggest a high clonal relationship between primary breast tumours and its LNMs, at least prior to treatment, and support the use of primary tumour characteristics to guide adjuvant systemic chemotherapy in breast cancer patients.</p></div

Investigation into discordant samples.

<p>Two samples that did not cluster together based on correlation were investigated for their discordance. A and B) Primary tumour and metastasis of patient 456 showed visually similar profiles, but the metastasis was a highly noisy hybridization. C and D) Primary tumour and metastasis profiles for patient 592 showed two highly different profiles. E) Two different histological phases were detected in the primary tumour, of which DNA was isolated separately and hybridized again.</p

Quantification of copy number differences between the tumour and lymph node metastasis.

<p>For each sample pair (Tumour-Lymph Node) we constructed a delta profile, which contains only the copy number differences between the two. For each delta profile we counted the unique segments that showed a difference above .2 log2 or below -.2 log2 and we subsequently counted the segments that contained 10 or more probes only. We split the tumours into the TNBC and ER+ subgroups.</p

Group-wise comparison of primary tumour copy number profiles with lymph node metastasis copy number profiles.

<p>Overall profiles were generated using the comparative module of the <i>KC-smart</i> package on either (A) the whole group, (B) just the ER+ tumours and (C) the triple negative tumours.</p