Coexisting genomic aberrations associated with lymph node metastasis in breast cancer
Li Bao, … , Jun Wang, Henrik J. Ditzel
Li Bao, … , Jun Wang, Henrik J. Ditzel
Published June 1, 2018; First published March 15, 2018
Citation Information: J Clin Invest. 2018;128(6):2310-2324. https://doi.org/10.1172/JCI97449.
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Categories: Research Article Genetics Oncology

Coexisting genomic aberrations associated with lymph node metastasis in breast cancer

Abstract

Single cancer cell–sequencing studies currently use randomly selected cells, limiting correlations among genomic aberrations, morphology, and spatial localization. We laser-captured microdissected single cells from morphologically distinct areas of primary breast cancer and corresponding lymph node metastasis and performed whole-exome or deep-target sequencing of more than 100 such cells. Two major subclones coexisted in different areas of the primary tumor, and the lymph node metastasis originated from a minor subclone in the invasive front of the primary tumor, with additional copy number changes, including chr8q gain, but no additional point mutations in driver genes. Lack of metastasis-specific driver events led us to assess whether other clonal and subclonal genomic aberrations preexisting in primary tumors contribute to lymph node metastasis. Gene mutations and copy number variations analyzed in 5 breast cancer tissue sample sets revealed that copy number variations in several genomic regions, including areas within chr1p, chr8q, chr9p, chr12q, and chr20q, harboring several metastasis-associated genes, were consistently associated with lymph node metastasis. Moreover, clonal expansion was observed in an area of morphologically normal breast epithelia, likely driven by a driver mutation and a subsequent amplification in chr1q. Our study illuminates the molecular evolution of breast cancer and genomic aberrations contributing to metastases.

Authors

Li Bao, Zhaoyang Qian, Maria B. Lyng, Ling Wang, Yuan Yu, Ting Wang, Xiuqing Zhang, Huanming Yang, Nils Brünner, Jun Wang, Henrik J. Ditzel

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Figure 3

Mutations and CNV of chr1q in normal breast epithelial single cells and cell pools.

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Mutations and CNV of chr1q in normal breast epithelial single cells and ...
(A) Heatmap depicting BN-T–specific SNVs identified by sequencing of 11 normal single breast epithelial cells and 3 normal cell pools (brown, mutated; pink, WT; white, WT and sequencing depth of less than 8×). (B) Two distinct haplotypes of chr1q in 4 samples, including Ly-T, lymph node metastasis tissue, BN-T, and a population of macroscopically dissected normal breast epithelial cells (BNM-3). The left panels show the distribution of SNP allele frequencies of haplotypes 1 (red) and 2 (blue) in the amplified genome region chr1q, while the horizontal axis shows VAF and the vertical axis the number of SNPs within the corresponding VAF. The right panels plot SNP allele frequencies of haplotypes 1 (red) and 2 (blue) across chr1q, while the horizontal axis shows coordinate of SNPs in chr1q and the vertical axis shows the AF. Haplotype 1 was amplified in MT, while haplotype 2 was amplified in BN-T and BNM. (C) LOH of chr1q in BN single cells. Variant allele frequencies of SNPs in 2 haplotypes of chr1q are shown as blue and red points (the same color code for each haplotype as in B). P values of LOH in each cell were calculated using Wilcoxon’s rank sum test. Error bars represent the values of median, upper, and lower quartiles and maximum and minimum.