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Series GSE133460 Query DataSets for GSE133460
Status Public on Jun 28, 2019
Title Radiomic and gEnomic approaches for the enhanced DIagnosis of REnal Cancer (REDIRECt): A translational pilot study
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Introduction: The aim of this pilot study is to establish a radiogenomic characterisation of a clear-cell renal cell carcinoma (ccRCC) subpopulation, focusing on the transcriptomic underpinnings of radiomic features.
Materials & Methods: To establish the viability of conducting a combined analysis of both radiomic and genomic data, a pilot cohort of 6 patients with <5cm G2 unilateral non-metastatic T1a-b ccRCC, who underwent surgery, was evaluated. Transcriptomic analysis was conducted through RNA-seq on tumor samples, while radiomic data was extracted from pre-operative 4 phase contrast-enhanced multidetector CT scans. Genomic heterogeneity was assessed with principal component analysis run on unrestricted data, on a clear-cell renal cell carcinoma associated gene list with zero-centered Reads Per Kilobase of transcript, per million mapped reads values. The underlying pathways and gene ontologies were established with enrichment analysis. In addition, Pearson’s correlation between radiomic data and the transcription of significant genes was fitted, and dendrogram and heatmap plots were drawn.
Results: Even in a clinically homogeneous population, the employed analyses have demonstrated that RCC should be regarded as an intrinsically heterogeneous disease. The analysis of the radiomic features and gene expression correlation using heatmap and dendrogram showed four distinct radiogenomic correlation patterns: with one including 5 radiomic features, and the other three including 2 features each.
Conclusion: The current pilot study is the first investigation demonstrating an innovative radiogenomic characterisation of clear-cell RCC. Based on such observations, further investigation into the radiomic and genomic approaches for the enhanced diagnosis of RCC is warranted.
Overall design 6 ccRCC tumor samples collected from patients who underwent surgery for RCC were collected and analysed.
Contributor(s) Cianflone F, Lazarevic D, Morelli MJ, Scotti GM, Tonon G, Capitanio U
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Submission date Jun 27, 2019
Last update date Jun 30, 2019
Contact name Francesco Cianflone
Organization name IRCCS Ospedale San Raffaele
Department Department of Urology
Lab Urological Research Institute
Street address via Olgettina 60
City Milan
ZIP/Postal code 20100
Country Italy
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM3909676 s1
GSM3909677 s2
GSM3909678 s3
BioProject PRJNA551492
SRA SRP212217

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Supplementary file Size Download File type/resource
GSE133460_counts.txt.gz 392.2 Kb (ftp)(http) TXT
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Processed data are available on Series record

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