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Long read transcriptome sequencing of ccRCC tumour cell line RCC4

ABSTRACT: Long read transcriptome sequencing of ccRCC tumour cell line RCC4

PROVIDER: PRJNA1011308 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25844591_1.fastq.gz	Fastqsanger.gz
	SRR25844592_1.fastq.gz	Fastqsanger.gz
	SRR25844593_1.fastq.gz	Fastqsanger.gz
	SRR25844594_1.fastq.gz	Fastqsanger.gz
	SRR25844595_1.fastq.gz	Fastqsanger.gz

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Long read transcriptome sequencing of ccRCC tumour cell line RCC4

Project description:Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. 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 cell line RCC4, with and without exposure to pro-inflammatory cytokines. Our results revealed differentially expressed genes induced by the pro-inflammatory cytokines. Moreover, results here revealed potential tumour origin of novel isoforms and genes that were discovered in the archival tumour samples by long-read sequencing.

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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 PCR-cDNAseq 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 ONT long-read PCR-cDNAseq 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.

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