Single-gene diagnostic assay for rapid subclassification of basal like breast cancer with mRNA targeted antisense oligonucleotide capped molecular probe

Basal-like breast cancers (BLBCs) represent a subset of ∼70% of triple negative breast cancers (TNBCs) and is significantly more aggressive than tumors of other molecular subtypes. The primary hurdle to develop an effective therapeutic possibility for BLBC lies in the failure to accurately classify this molecular subtype using typical histopathological practices. A clear clinical unmet need is therefore to develop a simple robust diagnostic assay for BLBC that can be made widely available to every pathology laboratory. Elevated expression of transcription factor Forkhead box C1 (FOXC1) has recently been reported as an important prognostic biomarker and functional regulator of BLBC. We herein developed a new nanotechnology-enabled molecular diagnostic assay that will target FOXC1 to directly classify BLBC types from tissue extracts. The molecular assay is comprised of unique antisense oligonucleotide (ASO) guided nanoprobe designed for specific targeting of FOXC1 mRNA. The developed assay has been optimized and validated analytically and demonstrated for its clinical applicability in a small cohort of breast cancer tissues. The significance of the results was further established and corroborated using FOXC1 protein-based ELISA, RT-PCR and fluorescence in-situ hybridization (FISH) assay by detecting the endogenous mRNAs at the ultrastructural level. The results reported herein could greatly improve accessibility of single gene based oncologic assay and help accelerate the accurate identification of this aggressive disease.