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Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

ABSTRACT: Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

PROVIDER: PRJNA859788 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20283800_1.fastq.gz	Fastqsanger.gz
	SRR20283800_2.fastq.gz	Fastqsanger.gz
	SRR20283801.fastq.gz	Fastqsanger.gz
	SRR20283801_1.fastq.gz	Fastqsanger.gz
	SRR20283801_2.fastq.gz	Fastqsanger.gz

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Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

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Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

Project description:To study the expression of junctions between exons and transposable elements (TEs), we generated paired-end RNAseq from various mouse tumor cell lines, with several biological replicates (cultures from different days). To analyse regulation of JET expression, we generated Setdb1-deficient B16F10 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to generate paired-end RNAseq, with several biological replicates (cultures on different days). We generated paired-end RNAseq from healthy female mouse tissues, to compare JET expression in healthy and tumor cells.

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Non-canonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in cancer patients

Project description:ost characterized tumor antigens are ‘genomic’, i.e. encoded by canonical, non-canonical or somatically mutated genomic sequences. We investigate here the presentation and immunogenicity of tumor antigens derived from non-canonical mRNA splicing events between coding exons and transposable elements (TEs). Comparing non-small cell lung cancer (NSCLC), an immunogenic tumor type, and diverse non-tumor tissues, we identify several thousand splicing junctions between exons and diverse TE classes. A subset of these junctions is both tumor-specific and shared across patients. HLA-I peptidomic identifies peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides are immunogenic in vitro and CD8+ T cells specific for junction-encoded epitopes are present in tumors and tumor-draining lymph nodes from NSCLC patients. We conclude that non-canonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in NSCLC cancer patients.

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Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

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Back-splice junctions of KSHV circular RNAs

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