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CORDIS

Pinpointing novel molecular and cellular functions generated by retroelement onco-exaptation

Project description

Retroelements and cancer evolution

Nearly 50 % of the human genome consists of mobile genetic elements that are thought to have emerged from the integration of retroelement genomes. Although these are believed to confer novel functions and a host fitness advantage, they may also have an oncogenic role. The EU-funded RETROFIT project aims to detect and quantify the transcription of endogenous retroelements and decipher their participation in the cancer transcriptome. Researchers will identify retroelements that have a potential impact on overall cancer survival rates or that respond to immunotherapy. RETROFIT is expected to unveil novel targets for the design of cancer treatments.

Objective

Exaptation, the co-option of endogenous retroelements (EREs) for new molecular and cellular functions that confer a host fitness advantage, is a major force in evolution, but may also be exploited, through onco-exaptation, by tumour cells to promote the oncogenic process. There are over 4 million well-recognised and annotated individual ERE integrations in the human genome. However, their participation at the level of the more complex transcriptome is far less well understood and, therefore, the number of onco-exaptation events is likely vastly underestimated. To allow detection and quantitation of ERE transcription, we have recently de novo assembled the cancer transcriptome. This resulted in a doubling of the known transcriptome, particularly of unannotated or partially annotated transcripts derived from or overlapping with EREs. Here, we propose to utilise this extended view of ERE transcription as the framework for:
•building a genome-wide map of functionally validated ERE onco-exaptation events and
•pinpointing novel, targetable functions of EREs in immunity, cancer and their intersection
Although we identified thousands of novel ERE-overlapping transcripts in cancer, the majority are likely the consequence of transcriptional activation of normally silent EREs, with little or no impact on host cell function. Impactful and inconsequential ERE integrations will be distinguished based on a number of features, including association with cancer overall survival or response to immunotherapy, impact on adjacent gene function, evolutionary conservation and functional domain and folding predictions. Postulated function will ultimately be tested extensively in in vitro cancer cell lines, ex vivo cancer patient material and in vivo mouse cancer models, tailored to the relevant onco-exaptation event. The modification of existing gene function or the creation of new function by ERE onco-exaptation will undoubtedly uncover new targets and opportunities for cancer treatment.

Host institution

THE FRANCIS CRICK INSTITUTE LIMITED
Net EU contribution
€ 2 483 691,00
Address
1 MIDLAND ROAD
NW1 1AT London
United Kingdom

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Region
London Inner London — West Camden and City of London
Activity type
Research Organisations
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Total cost
€ 2 483 691,00

Beneficiaries (1)