Transposable Element Activation in Pre-invasive and Early Invasive Breast Cancer Development in High-Risk Women: Developing a Spatial Proteogenomic and Liquid Biopsy Platform for Molecular Characterization and Early Detection

Background Women carrying germline BRCA1/2 mutations (gBRCAm carriers) have a 75% lifetime risk of developing breast cancer (BC). There is a need for additional biomarkers to predict their risk of developing cancer.

Our Challenge is to get an in-depth understanding of the cancer initiation in normal breast tissue (NBT) to deliver better risk estimates for high-risk women.

While driver somatic mutations in NBT have been reported, the influence of the “dark genome” has not been explored and is a knowledge gap.

Here, we ask whether activation of retrotransposable elements (RTE) contributes to a precancerous milieu in NBT, whether RTEs might indicate early signs of BC, and how RTEs are associated with early BC progression.

Aims In this joint KCL-OICR initiative, we will map the RTE expression in the epithelium and stroma from NBT individuals with a spectrum of risk for developing BC, determine molecular features, and define cell identities, cell states and their neighbourhood patterns associated with cancer risk in NBT.

In parallel, we aim to evaluate RTE expression in patient-matched tissue and blood, for the development of an applicable reproducible RTE assay.

We will develop a novel assay to identify RTE signatures in blood leukocytes based on our published data that tumours secrete RTE-containing extracellular vesicles.

Methods Aim 1: Tissue sections from a sample and database of NBT patients at KCL derived from reduction surgery from non-gBRCAm carriers, risk-reducing mastectomy (RRM), contralateral and peri-tumoural NBT from gBRCAm carriers and women with breast cancer will be generated.

Sections will be analysed with NanoString GeoMX containing RTE RNA probes and antibodies for RTE ORFs (e.g., HERV-K, LINE-1), and analysed with our analytical pipelines.

Aim 2: Samples at OICR will be probed for RTE expression in buffy coats and plasma samples from early BC patients versus normal donors using Illumina-based short-read and Nanopore long-read sequencing. How the results of this research will be used.

Contemporary strategies, such as annual mammography and/or MRI, or chemoprevention, assume that all carriers are uniformly at high risk leading many to choose RRM. Identifying markers in NBT and the blood of gBRCAm carriers will provide new avenues for early cancer detection. Healthy gBRCAm carriers could opt for periodical innovative blood tests, avoiding unnecessary RRM.

If validated prospectively, our tools provide a new management option adoptable by the NHS clinical screening programme for gBRCAm carriers, with the intent to intervene if elevated risk features are observed.