Abstract P3-09-14: Whole exome sequencing of matched primary and metastatic triple-negative breast cancer samples
Authors: Kaur Jaspreet , Chandrashekar Darshan S. , Varga Zsuzsanna , Janssen Emiel , Gandhi Khanjan , Mittal Karuna , Kiraz Umay , Varambally Sooryanarayana , Aneja Ritu 
Published: March 2022

Abstract
Background: Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer subtype with distinct biological features and clinical behavior. TNBC is associated with an increased risk of metastasis and recurrence. In this whole exome study, we investigated the genetic profiles of primary TNBC tumors and paired metastases using next-generation sequencing (NGS). Methods: Genomic DNA extracted from 35 paraffin-embedded formalin-fixed (FFPE) tissues (15 primary tumors that did not metastasize, 11 primary tumors that metastasized, and nine paired metastatic tumors to the lymph nodes) was analyzed by whole exome sequencing (WES). Reads were trimmed using Trim-Galore and were aligned to the reference genome GRCh38 using Burrows-Wheeler Aligner (BWA). BAM files were preprocessed to optimize variant calling, and variant calling was carried out using the GATK pipeline. Variants were annotated using SnpEff. Tumors were analyzed for single nucleotide variants (SNV), point mutations, and insertions/deletions (indels). Results: Primary tumors that did not metastasize had a higher number of variants (~13,500) than primary tumors that metastasized (~12,900). However, the number of variants was similar between the primary tumors (~12,900 variants) and their matched metastases (~12,500 variants). MUC3A was the top mutated gene both in primary tumors that did not metastasize and in those that metastasized. MUC3A was also the top mutated gene in matched metastatic lesions. Moreover, we compared the mutational status of the most frequently mutated genes in TNBC samples from the TCGA and METABRIC datasets. We found that in our dataset, TP53, MAP3K1, and PTEN were mutated in 60%, 93%, and 7% of primary TNBC tumors without metastases and in 36%, 0%, and 36% of primary TNBC tumors that metastasized. Mutations in TP53 and PTEN were found in 2/9 and 1/9 of primary and metastases pairs, respectively. No mutations in PI3KCA were observed in any of the primary or matched metastatic tumors. Conclusions: We used WES to compare the genomic landscapes of primary TNBC tumors and matched metastatic tumors, as well as of primary TNBC tumors that metastasized and those that did not metastasize. We found very similar genomic alterations between the primary and paired metastatic tumors, indicating that genomic features may be retained during metastasis. Primary tumors that did not metastasize showed a greater extent of genomic alterations than primary tumors that metastasized.
Citation Format: Jaspreet Kaur, Darshan S. Chandrashekar, Zsuzsanna Varga, Emiel Janssen, Khanjan Gandhi, Karuna Mittal, Umay Kiraz, Sooryanarayana Varambally, Ritu Aneja. Whole exome sequencing of matched primary and metastatic triple-negative breast cancer samples [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-14.