Expression profiles of SOX11-positive and SOX11-negative Mantle Cell Lymphoma (MCL) primary samples from lymph node and reactive lymph nodes (RLN).

Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Immune Profiling Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain the differential immune gene expression comparing the lymph node microenvironment of SOX11-positive and SOX11-negative MCL primary samples and non-neoplastic nodal samples (RLN). In this study, 11 SOX11-positive nodal MCL primary samples, 3 SOX11-negative nodal MCL primary samples and 6 reactive lymph nodes were screened for gene expression of immune response-related genes (770 genes including 40 housekeeping genes). Nucleic acids were extracted from 10-µm sections of FFPE biopsies from lymph nodes using the QIAGEN AllPrep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) after deparaffinization according to the manufacturer´s instructions. The quality and concentration were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Isolated RNA (400 ng) was processed through the NanoString nCounter Prep Station. Subsequently, samples were processed according to the manufacturer’s instructions and signals of reporter probes were counted and tabulated using the nCounter Digital Analyzer (NanoString Technologies). Gene expression analysis was performed using the human nCounter® PanCancer Immune Profiling Panel (NanoString Technologies). Finally, housekeeping gene (geometric mean of 40 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 4.0 (NanoString Technologies, Hamburg, Germany) and standard settings.