High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing

Abstract

The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10−2– 5.2 × 10−1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10−2–10−4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.

Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer—Insights from Histologically Normal Urothelium

“…The novelty of our approach lies in the experimental design based on profiling the landscape of chromosomal alterations across several tissues, including multiple non-cancerous margin samples (2–8 per patient) located at different distances from the tumor (PMs and DMs). Furthermore, our current BLCA data are well aligned with our previous studies of histologically normal margins of breast tissue from breast cancer patients [ 42 , 43 , 44 , 45 ].…”

“…Yet another advantage of our approach is allowing us to reliably distinguish between the inherited via germline and true acquired post-zygotic (PZ) alterations. Generally speaking, the normal urothelium cells can acquire a considerable number of genetic aberrations before their abnormal histology will be seen under the microscope, which is reminiscent of results previously shown for breast cancer patients [ 42 , 43 , 44 , 45 ].…”

“…Our study follows the concept of age-related clonal expansions of normal cells in tissue that give rise to solid tumors of the breast [ 42 , 43 , 44 , 45 ] and the model of field cancerization [ 46 , 47 , 48 , 49 ], which was the main rationale behind collecting multiple samples from normal margin of bladder urothelium as well as primary tumors and blood. The blood-derived DNA allows genotypic comparisons with the tissue that is not primarily involved in the initiation of tumor formation.…”

“…Although we present the genetic architecture of CPCs in normal urothelium from patients with BLCA, 55% of patients are free of large post-zygotic alterations in normal urothelium detectable via MoChA and this category should be investigated for the presence of other types of mutations, such as point mutations and epigenetic modifications of DNA/chromatin. Indeed, similar studies utilizing targeted sequencing and more sensitive duplex sequencing, reveal frequent mutations in cancer-driver genes, which could be primers of tumorigenesis [ 44 , 69 , 70 ]. Moreover, the above-mentioned changes are likely going to affect the global portrait of transcriptome and this should also be considered in future studies, as it may lead to description of gene expression signature related to a higher risk of BLCA.…”

Role of T-box transcription factor 3 in gastric cancers

“…These studies demonstrated that TBX3 is one of the key players in breast cancers. Recently, Kostecka et al [ 39 ] reported that sequencing of cancer-associated genes, including TBX3, in normal mammary glands of 52 patients with reportedly sporadic breast cancer revealed that subclonal somatic pathogenic variants of these genes were identified at considerable allelic frequencies. This suggests that TBX3 plays an important role in the initiation of breast cancers.…”