Microenvironment-related genes expression profile from lymph nodes of breast cancer patients using OSNA samples

The One Step Nucleic Acid Amplification (OSNA) assay is used to identify occult metastases in the axillary Sentinel Lymph Nodes (SLNs) of early stage breast cancer patients by quantification of the expression of cytokeratin19 (CK19) gene. The discarded samples of OSNA assay were explored as a source of information of SLN microenvironment response in patients with early stage Luminal A breast cancer using an RNAseq panel. Funding: project “GenomePT—National Laboratory for Genome Sequencing and Analysis” (POCI-01-0145-FEDER-022184), and project “Central Region Training Project for Personalized/Precision Medicine, with a genomic basis”, financed by the program CENTRO2020 [CENTRO-08-5864-FSE-000039 (PEP IN1194) 07-2021]. Discarded samples of OSNA assay from 32 patients with Luminal A early stage breast cancer (cT1-T2 N0) (8th Ed Edition of the AJCC Cancer Staging Manual; 2019 World Health Organization classification of tumours of the breast) were analysed. OSNA assay was performed accoring to Sysmex Corporation protocol. Based on the calculated number of CK19 mRNA copies/ul, in accordance with the previous cut off level determined by Tsujimoto et al.: > 5000 copies/uL correspond to macrometastasis (pN1), 250 to 5000 copies/uL to micrometastasis (pN1mi), and values < 250 copies/uL are classified as negative (pN0) SLN. For RNA sequencing, a NGS panel of 395 genes involved in tumor-immune interactions and inflammatory signalling was used. No replicates were included.