ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/004/ERR3218684/ERR3218684_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/009/ERR3218679/ERR3218679_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/009/ERR3218669/ERR3218669_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/001/ERR3218681/ERR3218681_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/000/ERR3218680/ERR3218680_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/008/ERR3218668/ERR3218668_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/005/ERR3218675/ERR3218675_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/007/ERR3218677/ERR3218677_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/003/ERR3218673/ERR3218673_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/008/ERR3218678/ERR3218678_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/004/ERR3218674/ERR3218674_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/000/ERR3218680/ERR3218680_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/003/ERR3218683/ERR3218683_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/001/ERR3218681/ERR3218681_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/006/ERR3218676/ERR3218676_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/002/ERR3218682/ERR3218682_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/008/ERR3218678/ERR3218678_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/000/ERR3218670/ERR3218670_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/005/ERR3218675/ERR3218675_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/009/ERR3218679/ERR3218679_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/001/ERR3218671/ERR3218671_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/006/ERR3218676/ERR3218676_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/002/ERR3218672/ERR3218672_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/007/ERR3218677/ERR3218677_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/003/ERR3218683/ERR3218683_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/002/ERR3218682/ERR3218682_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/008/ERR3218668/ERR3218668_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/000/ERR3218670/ERR3218670_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/002/ERR3218672/ERR3218672_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/009/ERR3218669/ERR3218669_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/001/ERR3218671/ERR3218671_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/004/ERR3218674/ERR3218674_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/004/ERR3218684/ERR3218684_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR321/003/ERR3218673/ERR3218673_2.fastq.gzprimary200OKGenomicsEuropean Bioinformatics InstituteLaboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana , Salerno, Italyhttps://www.ebi.ac.uk/ena/browser/view/PRJEB31672ArrayExpressPurpose: Celiac disease (CD) is a risk factor for developing Small Bowel Carcinoma (SBC) with a 14 folds higher risk than that of the general population. As SBCs associated with CD (CD-SBCs) are extremely rare, very few molecular data are currently available about their pathogenesis and information about CD-SBC transcriptomic profiling is completely lacking. Patients and Methods: We generated RNA-seq data on 13 CD-SBCs selected from the largest and well-characterized series of CD-SBCs published so far that was collected by the Small Bowel Cancer Italian Consortium. In all cases we compared the CD-SBC transcriptional signatures with the four consensus molecular subtypes (CMS) of colorectal carcinoma (CRC) applying the ‘CMS classifier’. CpG Island Methylator Phenotype (CIMP+) was evaluated in all cases using methylation-sensitive multiple ligation-dependent probe amplification. Results: RNA-based signatures of CD-SBCs exhibited strong similarities with CRCs. Twelve of 13 CD-SBCs (92%) fell within the two main subtypes exhibiting high immune and inflammatory signatures, i.e. CMS1 and CMS4. CMS1 CD-SBCs (62% of cases) were commonly MSI/CIMP+ tumors and showed increased expression of genes associated with a diffuse TH1 and cytotoxic T immune infiltrate, up-regulation of apoptosis, cell cycle progression and proteasome pathways. CMS4 CD-SBCs (31% of cases) showed prominent TGF-β activation and were characterized by complement-associated inflammation, matrix remodeling, stromal invasion and angiogenesis Conclusions: RNA-based signatures of CD-SBCs strongly recapitulate CMS classification of CRC, give a promising tool to improve our knowledge of this rare entity and provide clinically useful information using the wealth of data available for CRC.ENAfalseSmall bowel carcinomas in celiac disease: transcriptomic profiling and comparison with the consensus molecular subtypes of colorectal cancersSmall bowel carcinomas in celiac disease: transcriptomic profiling and comparison with the consensus molecular subtypes of colorectal cancers2019-03-122020-03-01PRJEB31672