Abstract LB-051: Tumor heterogeneity and dissemination in breast cancer: Deep sequencing of single disseminated cells from bone marrow compared to primary tumor and lymph node metastases
Authors: Møller Elen , Kumar Parveen , Nord Silje , Wedge David , van Loo Peter , Peterson April , Mathiesen Randi R. , Fjelldal Renathe , Esteki Masoud Z. , Grundstad Jason A. , Borgen Elin , Baumbusch Lars O. , Børresen-Dale Anne-Lise , White Kevin P. , Voet Thierry , Naume Bjørn , Kristensen Vessela N. 
Published: August 2015

Metastasis is the main cause of death amongst breast cancer patients. Our knowledge of the metastatic cascade and how to inhibit it is limited. Here we dissect the genetic profile of multiple single disseminated tumor cells (DTCs) taken at various time points after diagnosis, and compare them to their matched primary tumors and lymph node metastasis. We have previously published a method for studying CNAs in single DTCs by whole genome sequencing, where we compared two primary breast carcinomas to two corresponding DTCs. Copy number profiles from whole genome sequencing (WGS) from 40 DTCs were analyzed. The single cell whole genome amplified (WGA) DNA was used to generate WGS libraries, and the DTCs were subsequently sequenced on the Illumina HiSeq 2000. The WGS reads were trimmed for WGA adapters and aligned to GRCh37 human reference using Burrows-Wheeler Aligner (BWA). LogR values were calculated for genomic bins and corrected for% GC-bias and segmented using the piecewise constant fitting (PCF) algorithm (the penalty parameter, γ, was set to 25). Copy number was estimated per segment as 2logR × Ψ, where Ψ is the average ploidy. B allele frequency (BAF) was calculated for each known SNP position from dbSNP (dbSNP build 135) and somatic mutations read-outs generated. In this study we compared the mutation spectre and CNAs in six primary tumors, one with corresponding lymph node metastasis and single DTCs. In total, CN profile from 40 DTCs showed evidence of dissemination at both early and late stage of disease progression. At large, the copy number profile of the examined DTCs exhibited either a limited number of alterations, or a pattern similar to the primary tumor and lymph node metastasis suggesting continuous dissemination of single tumor cells throughout the tumor evolution. By demonstrating sub-clonality in the lymph node metastasis we provide novel insight into the metastatic process. Further, the correlation in aberration pattern between the lymph node metastasis and multiple DTCs, implies that cells found in the bone marrow may have originated from the lymph node metastasis. The DTCs exhibited common aberrations typically found in breast carcinomas, and several DTCs had deletion of 16q and17p, and gain of 1q, 8q. Certain DTCs exhibited CNAs not visible in the primary tumor or lymph node including gain of 9q, 14q, 19q and Xq, and loss of 2p, 6p, 8p, 18p and 19p. Two DTCs from time of diagnosis exhibited gain of the whole chromosome 5 that was not observed in the primary tumor or the lymph node. These results reveal the importance of assessing the sub-clonal genetic alterations in the primary tumor, as well as in the lymph node metastasis and DTCs, in order to evaluate patient treatment and prognosis.

Citation Format: Elen Møller, Parveen Kumar, Silje Nord, David Wedge, Peter van Loo, April Peterson, Randi R. Mathiesen, Renathe Fjelldal, Masoud Z. Esteki, Jason A. Grundstad, Elin Borgen, Lars O. Baumbusch, Anne-Lise Børresen-Dale, Kevin P. White, Thierry Voet, Bjørn Naume, Vessela N. Kristensen. Tumor heterogeneity and dissemination in breast cancer: Deep sequencing of single disseminated cells from bone marrow compared to primary tumor and lymph node metastases. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-051. doi:10.1158/1538-7445.AM2015-LB-051