The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies

Abstract

The whole-genome sequencing of prospectively collected tissue biopsies from 442 patients with metastatic breast cancer reveals that, compared to primary breast cancer, tumor mutational burden doubles, the relative contributions of mutational signatures shift and the mutation frequency of six known driver genes increases in metastatic breast cancer. Significant associations with pretreatment are also observed. The contribution of mutational signature 17 is significantly enriched in patients pretreated with fluorouracil, taxanes, platinum and/or eribulin, whereas the de novo mutational signature I identified in this study is significantly associated with pretreatment containing platinum-based chemotherapy. Clinically relevant subgroups of tumors are identified, exhibiting either homologous recombination deficiency (13%), high tumor mutational burden (11%) or specific alterations (24%) linked to sensitivity to FDA-approved drugs. This study provides insights into the biology of metastatic breast cancer and identifies clinically useful genomic features for the future improvement of patient management.

Figure 1. Overview of study design and biopsy sites (n = 442)

(a) Flowchart of patient inclusion. From the CPCT-02 cohort, patients with mBC were selected. Patients were excluded if the only available biopsy was from the primary lesion. *Non-evaluable biopsies were defined as no biopsy taken at all, <30% tumour cells or too low DNA yield for WGS. (b) Overview of biopsy sites. Number of biopsies per metastatic site analysed with WGS.

Figure 2. De novo signature I is associated with prior platinum-based chemotherapy

(a) De novo signature calling revealed 10 mutational processes operative in mBC. These de novo mutational signatures have high cosine similarities with known Cosmic signatures. (b) The mutational spectrum of de novo signature I and Cosmic signatures 4 and 8. (c) The number of CC>AA or GG>TT mutations in patients with a low (<10%) or high (≥10%) relative contribution of de novo signature I. (d) Boxplot of the cosine similarity of the cisplatin signature defined by Boot et al. and samples of patients who did or did not receive prior treatment with platinum-based chemotherapy. (e) Boxplot of the contribution of mutational signature I and samples with a high (permutation p<0.05) or low (permutation p>0.05) similarity to the cisplatin signature of Boot et al.

Figure 3. Mutational signatures: mBC versus primary BC

Bean plots showing the relative contribution of 12 Cosmic signatures which are dominantly contributing to the total number of SNVs in the metastatic cohort. Relative contributions were compared between mBC and primary BC samples from the BASIS cohort and shown per breast cancer subtype: ER+/HER2- (a), TNBC (b), HER2+ (c). Per graph, left of centre (green) indicate the distribution of primary tumours from the BASIS cohort, right of centre (purple) metastatic biopsy. Mann-Whitney U: * P < 0.05, ** P < 0.01, *** P < 0.001.

Figure 4. Unsupervised clustering reveals distinct genomic phenotypes in mBC

(a) Dendrogram of unsupervised clustering. The top eight clusters are denoted A to H. The Y-axis displays clustering distance (Pearson; ward.D). (b) Number of genomic mutations per Mb (TMB) divided into mutational categories SNV, InDels and MNV. All genome-wide somatic mutations were taken in to consideration. (c) Relative contribution of Cosmic mutational signatures. (d) Relative contribution of rearrangement signatures. (e) Absolute number of unique structural variants per sample. (f) Relative frequency per structural variant category, tandem duplications, deletions and inversions are subdivided into <10kb and >10kb categories. (g) Breast cancer subtype subdivided in ER+/HER2-, HER2+ and triple negative and unknown at time of analysis. (h) Germline BRCA1/2 mutational status. (i) HR-deficient score as assessed by CHORD. Predicted phenotypes BRCA1 deficiency and BRCA2 deficiency are depicted.

Figure 5. Actionability

(a) Percentage of patients with and without an actionable target for treatment. (b) Actionable targets by type: HR deficiency (HRD), high TMB (≥10 mutations/Mb) and/or targetable alterations for which an FDA approved drug is available (OncoKB). (c) Genes indicated by OncoKB for which targeted drugs are FDA approved (ERBB2 for breast cancer, all other genes for other cancer types).