Rare subclonal sequencing of breast cancers indicates putative metastatic driver mutations are predominately acquired after dissemination

• Published in: Genome medicine 2024-02, Vol.16 (1), p.26-19, Article 26
• Main Authors: Lawrence-Paul, Matthew R, Pan, Tien-Chi, Pant, Dhruv K, Shih, Natalie N C, Chen, Yan, Belka, George K, Feldman, Michael, DeMichele, Angela, Chodosh, Lewis A
• Format: Article
• Language: English
• Subjects: AKT1 protein; Analysis; Breast cancer; Breast Neoplasms - genetics; Cancer therapies; Cell cycle; Development and progression; DNA glycosylase; ESR1 protein; Estrogens; Exome Sequencing; Female; Genes; Genetic aspects; Genetic testing; Genomics; Humans; LRP5 protein; Metastases; Metastasis; Metastatic driver mutation; Metastatic seeding; Mutation; Pyrimidines; Rare subclonal sequencing; Tumor cells; Tumorigenesis; Tumors; Ultra-deep sequencing; Uracil; Uracil-DNA glycosidase
• ISSN: 1756-994X; 1756-994X
• DOI: 10.1186/s13073-024-01293-9

Evolutionary models of breast cancer progression differ on the extent to which metastatic potential is pre-encoded within primary tumors. Although metastatic recurrences often harbor putative driver mutations that are not detected in their antecedent primary tumor using standard sequencing technologies, whether these mutations were acquired before or after dissemination remains unclear. To ascertain whether putative metastatic driver mutations initially deemed specific to the metastasis by whole exome sequencing were, in actuality, present within rare ancestral subclones of the primary tumors from which they arose, we employed error-controlled ultra-deep sequencing (UDS-UMI) coupled with FFPE artifact mitigation by uracil-DNA glycosylase (UDG) to assess the presence of 132 "metastasis-specific" mutations within antecedent primary tumors from 21 patients. Maximum mutation detection sensitivity was ~1% of primary tumor cells. A conceptual framework was developed to estimate relative likelihoods of alternative models of mutation acquisition. The ancestral primary tumor subclone responsible for seeding the metastasis was identified in 29% of patients, implicating several putative drivers in metastatic seeding including LRP5 A65V and PEAK1 K140Q. Despite this, 93% of metastasis-specific mutations in putative metastatic driver genes remained undetected within primary tumors, as did 96% of metastasis-specific mutations in known breast cancer drivers, including ERRB2 V777L, ESR1 D538G, and AKT1 D323H. Strikingly, even in those cases in which the rare ancestral subclone was identified, 87% of metastasis-specific putative driver mutations remained undetected. Modeling indicated that the sequential acquisition of multiple metastasis-specific driver or passenger mutations within the same rare subclonal lineage of the primary tumor was highly improbable. Our results strongly suggest that metastatic driver mutations are sequentially acquired and selected within the same clonal lineage both before, but more commonly after, dissemination from the primary tumor, and that these mutations are biologically consequential. Despite inherent limitations in sampling archival primary tumors, our findings indicate that tumor cells in most patients continue to undergo clinically relevant genomic evolution after their dissemination from the primary tumor. This provides further evidence that metastatic recurrence is a multi-step, mutation-driven process that extends beyond primary tumo