Genomic characterisation of hormone receptor-positive breast cancer arising in very young women

Abstract

Background: Very young premenopausal women diagnosed with hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+HER2-) early breast cancer (EBC) have higher rates of recurrence and death for reasons that remain largely unexplained.

Patients and methods: Genomic sequencing was applied to HR+HER2- tumours from patients enrolled in the Suppression of Ovarian Function Trial (SOFT) to determine genomic drivers that are enriched in young premenopausal women. Genomic alterations were characterised using next-generation sequencing from a subset of 1276 patients (deep targeted sequencing, n = 1258; whole-exome sequencing in a young-age, case-control subsample, n = 82). We defined copy number (CN) subgroups and assessed for features suggestive of homologous recombination deficiency (HRD). Genomic alteration frequencies were compared between young premenopausal women (<40 years) and older premenopausal women (≥40 years), and assessed for associations with distant recurrence-free interval (DRFI) and overall survival (OS).

Results: Younger women (<40 years, n = 359) compared with older women (≥40 years, n = 917) had significantly higher frequencies of mutations in GATA3 (19% versus 16%) and CN amplifications (CNAs) (47% versus 26%), but significantly lower frequencies of mutations in PIK3CA (32% versus 47%), CDH1 (3% versus 9%), and MAP3K1 (7% versus 12%). Additionally, they had significantly higher frequencies of features suggestive of HRD (27% versus 21%) and a higher proportion of PIK3CA mutations with concurrent CNAs (23% versus 11%). Genomic features suggestive of HRD, PIK3CA mutations with CNAs, and CNAs were associated with significantly worse DRFI and OS compared with those without these features. These poor prognostic features were enriched in younger patients: present in 72% of patients aged <35 years, 54% aged 35-39 years, and 40% aged ≥40 years. Poor prognostic features [n = 584 (46%)] versus none [n = 692 (54%)] had an 8-year DRFI of 84% versus 94% and OS of 88% versus 96%. Younger women (<40 years) had the poorest outcomes: 8-year DRFI 74% versus 85% and OS 80% versus 93%, respectively.

Conclusion: These results provide insights into genomic alterations that are enriched in young women with HR+HER2- EBC, provide rationale for genomic subgrouping, and highlight priority molecular targets for future clinical trials.

Keywords: breast cancer; genomics; hormone receptor positive; prognosis; young women.

Figure 1.. The genomic landscape of premenopausal HRDHER2−L breast cancer in SOFT.

(A) Summary of the sequencing cohorts derived from the SOFT clinical trial, including overlapping cases. Further details on patient selection are shown in Supplementary Figure S1, available at https://doi.org/10.1016/j.annonc.2023.01.009. (B) Plot demonstrating the frequencies and co-existence of clinicopathological variables (top panel), genomic driver alterations (middle panel), and poor prognostic genomic features (bottom panel) in the SOFT combined sequencing cohort (n = 1276). (C) Hazard ratio estimates (boxes) and 95% confidence intervals (lines) derived from Cox proportional hazards regression models comparing patients with tumours that harbour the driver alteration with patients with tumours that do not harbour the driver alteration for the endpoint of distant recurrence-free interval in the SOFT combined sequencing cohort (n = 1276). Only driver alterations with ≥5 events are included. (D) Kaplan–Meier plot estimating the rate of freedom from distant recurrence based on the copy number-amplified subgrouping in the SOFT combined sequencing cohort (n = 1276). CI, confidence interval; ER, estrogen receptor; HER2−, human epidermal growth factor receptor 2-negative; HR+, hormone receptor-positive; PR, progesterone receptor; SOFT, Suppression of Ovarian Function Trial.

Figure 2.. Genomic drivers of poor prognosis breast cancer in the very young.

(A) Kaplan–Meier plot estimating the rate of freedom from distant recurrence according to age at randomisation in the SOFT combined sequencing cohort (n = 1276). (B) A comparison of genomic driver alteration frequencies of patients in the SOFT combined sequencing cohort (n = 1276) aged <40 years at randomisation with those of patients aged ≥40 years at randomisation. The dotted line provides demonstration of the plot points that represent equal frequencies between the groups. Points in burgundy demonstrated significantly different frequencies after adjustment for multiple testing using the false discovery method. (C) A comparison of the frequencies of copy number-altered subgroups according to patients’ age at randomisation in the SOFT combined sequencing cohort (n = 1276). CI, confidence interval; HR, hazard ratio; SOFT, Suppression of Ovarian Function Trial.

Figure 3.. Genomic features of the very young, high-risk subsample.

Combined plot demonstrating the number of somatic mutations, mutational signature proportions, clinicopathological variables, and genomic driver alterations in the SOFT matched case-control subsample that had paired tumour-normal whole-exome sequencing (n = 73). Mutational signature 1 is associated with spontaneous deamination of 5-methylcytosine, signature 3 is associated with HRD, and signatures 2 and 13 are associated with APOBEC mutagenesis. ER, estrogen receptor; HRD, homologous recombination deficiency; PR, progesterone receptor; SOFT, Suppression of Ovarian Function Trial.

Figure 4.. Genomic features of HRD and high-risk PIK3CA mutations in young patients.

(A) Plot demonstrating eHRDetect probability score (top panel) in 68 assessable patients in the case-control subsample who underwent paired tumour-normal whole-exome sequencing. Green bars indicate eHRDetect score above the 0.7 probability score threshold, termed eHRDetect positive. Genomic alterations in HRD-related genes (bottom panel) are also shown. (B) Plots demonstrating the associations between eHRDetect-positive score with age at randomisation, Ki-67 expression level, and number of somatic mutations in the case-control subsample who were assessable for eHRDetect (n = 68). (C) Bar plot demonstrating the frequency of patients with genomic features of HRD according to age at randomisation in the SOFT combined sequencing cohort (n = 1276). Genomic features of HRD included eHRDetect positivity and/or genetic alterations in HRD-related genes. (D) Pairwise analysis of HRD-related genes in the SOFT combined sequencing cohort (n = 1276). Only genes with ≥10 patients with genetic alterations were included. Fisher’s exact test was applied to each genetic alteration pair. Multiple testing correction using false discovery rate was applied. Only log-odds with a false discovery rate of <0.2 are displayed. Burgundy colour indicates an association with mutual exclusivity. (E) Bar plot demonstrating the proportion of tumours with genomic features of HRD according to age at randomisation in the SOFT combined sequencing cohort (n = 1276). Genomic features of HRD included eHRDetect positivity and/ or genetic alterations in HRD-related genes. (F) Boxplot demonstrating the association between concurrent copy number amplification status with PIK3CA mutations and Ki-67 expression levels in the SOFT combined sequencing cohort (n = 1276). (G) Bar plot demonstrating the frequency of patients with a PIK3CA mutation and concurrent copy number amplification according to age at randomisation in the SOFT combined sequencing cohort (n = 1276). (H) Kaplan–Meier plots and forest plots estimating the rate of freedom from distant recurrence according to PIK3CA mutation status and copy number amplification status in the SOFT combined sequencing cohort (n = 1276). HRD, homologous recombination deficiency; SOFT, Suppression of Ovarian Function Trial.

Figure 5.. Framework for genomic subgrouping of premenopausal HRDHER2− breast cancer.

(A) Proposed framework for genomic subgrouping for premenopausal patients with HR+HER2− early breast cancers, and number of patients with each feature in the SOFT combined sequencing cohort (n = 1276). (B) Venn diagram demonstrating the number and proportion of tumours assigned to each poor prognosis genomic subgroup in the SOFT combined sequencing cohort (n = 1276) using the proposed framework. (C) Pie charts demonstrating the frequencies of the proposed genomic subgroups according to age at randomisation in the SOFT combined sequencing cohort (n = 1276). (D) Kaplan–Meier plot estimating the rate of freedom from distant recurrence according to the proposed genomic subgroups in the SOFT combined sequencing cohort (n = 1276). (E) Kaplan–Meier plot estimating the overall survival according to the proposed genomic subgroups in the SOFT combined sequencing cohort (n = 1276). CI, confidence interval; CNA, copy number amplification; ER, estrogen receptor; HER2−, human epidermal growth factor receptor 2-negative; HR, hazard ratio; HR+, hormone receptor-positive; HRD, homologous recombination deficiency; SOFT, Suppression of Ovarian Function Trial.