High-throughput gene expression profilng of SMARCA4-mutated extra-cranial rhabdoid tumours (ECRT-SMARCA4), SMARCB1-mutated ECRT, ATRT and SCCOHT tumours by RNA sequencing

Purpose: Molecular characterization of ECRT-SMARCA4 tumours and their place within the constellation of ECRT-SMARCB1, ATRT and SCCOHT Methods: Total RNA was obtained from 72 fresh-frozen tumour samples using the Qiagen RNAeasy kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s procedure. Barcode Illumina compatible libraries were generated from 750 ng of total RNA for each sample using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced using the Illumina HiSeq 2500 platform. RNA-seq data pre-processing was performed using an in-house pipeline developed at the Curie Institute Bioinformatics Core Facility. Read mapping and counting were performed using STAR, version 2.5.3) and the hg19 version of the human reference genome. Results: Dimensionality reduction and hierarchical clustering algorithms applied to the transcriptomics dataset show that ECRT-SMARCA4 display molecular features intermediate between SCCOHT and ECRTS-MARCB1. Seventy two tumour samples were analysed by RNA sequencing including 38 ATRTs (29 re-analyzed samples from Leruste et al., 2019), 19 ECRT_SMARCB1 (all re-analyzed from Leruste et al., 2019), 4 ECRT_SMARCA4 and 11 SCCOHT (10 re-analyzed from Loarer et al., 2015 which 3 are deposited in SRA SRP052896: SRX857513, SRX857516, SRX857514). All previously published and re-analyzed data included in our study (as detailed in the published_re-analyzed_data.xlsx) have been directly provided by the authors as fastq files. For those already published in Leruste et al. (2019), the data are now under submission in the dbGAP database (phs001915.v1.p1) as mentioned in the Leruste et al. (2019) publication. Therefore, the accession numbers for each sample are not yet available. For the data from Loarer et al. (2015), only 3 are publicly available in SRA database under the accession number SRP052896.