Project description:Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. Here, we used Illumina RNAseq to profile the transcriptomes of a ccRCC cell line RCC4 treated with pro-inflammatory cytokines. Our results here validates the existence of novel isoforms and genes that were discovered in the archival tumour samples by long-read sequencing. In addition, results here revealed potential tumour origin of these novel isoforms and genes.
Project description:Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. Following primary tumour resection approximately 30% of patients experience disease recurrence associated with metastasis. To date, long-read RNA sequencing has not been applied to kidney cancer. Here, we used ONT long-read Direct RNA sequencing to profile the transcriptomes of ccRCC archival tumours, 6 of which were from patients who went on to relapse. Our results revealed a loss of immune infiltrate in tumours of patients who relapse. Moreover, thousands of novel isoforms were discovered, including a novel PD-L1 transcript encoding for the soluble version of the protein but having a longer 3'UTR than the currently annotated transcript. Finally, we have identified a novel non-coding gene that was over-expressed in patients who experience recurrence. Our data shows that DRS can be used in archival tumour samples to comprehensively characterise tumour transcriptomes, and to reveal novel features that would have been missed by short-read RNAseq.
Project description:We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC) patients to investigate intra-tumour heterogeneity.
Project description:We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC) patients to investigate intra-tumour heterogeneity. We selected 56 tumour samples and 6 normal samples from the 9 patients for expression analysis using microarray data. All samples were fresh frozen upon extraction.