{"doi":"10.1101/2020.03.10.981001","title":"Non-canonical open reading frames encode functional proteins essential for cancer cell survival","abstract":"A key question in genome research is whether biologically active proteins are restricted to the ∼20,000 canonical, well-annotated genes, or rather extend to the many non-canonical open reading frames (ORFs) predicted by genomic analyses. To address this, we experimentally interrogated 553 ORFs nominated in ribosome profiling datasets. Of these 553 ORFs, 57 (10%) induced a viability defect when the endogenous ORF was knocked out using CRISPR/Cas9 in 8 human cancer cell lines, 257 (46%) showed evidence of protein translation when ectopically expressed in HEK293T cells, and 401 (73%) induced gene expression changes measured by transcriptional profiling following ectopic expression across 4 cell types. CRISPR tiling and start codon mutagenesis indicated that the biological effects of these non-canonical ORFs required their translation as opposed to RNA-mediated effects. We selected one of these ORFs, G029442 --renamed GREP1 (Glycine-Rich Extracellular Protein-1) -- for further characterization. We found that GREP1 encodes a secreted protein highly expressed in breast cancer, and its knock-out in 263 cancer cell lines showed preferential essentiality in breast cancer derived lines. Analysis of the secretome of GREP1-expressing cells showed increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth inhibitory effect of GREP1 knock-out. Taken together, these experiments suggest that the non-canonical ORFeome is surprisingly rich in biologically active proteins and potential cancer therapeutic targets deserving of further study.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":120104,"datarank":0.685705237980101,"base_score":2.5649493574615367,"endowment":2.5649493574615367,"self_citation_contribution":0.38474240361923057,"citation_network_contribution":0.3009628343608704,"self_endowment_contribution":0.38474240361923057,"citer_contribution":0.3009628343608704,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":10,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8937,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":556977,"name":"Oana M. Enache","orcid":"0000-0002-9541-0058","position":1,"is_corresponding":false},{"id":350424,"name":"Victor Luria","orcid":"0000-0003-0558-0983","position":2,"is_corresponding":false},{"id":2205,"name":"Karsten Krug","orcid":"0000-0001-7248-3783","position":3,"is_corresponding":false},{"id":2216,"name":"Karl R. Clauser","orcid":"0000-0002-1052-9456","position":4,"is_corresponding":false},{"id":556978,"name":"Joshua M. Dempster","orcid":"0000-0002-3634-9576","position":5,"is_corresponding":false},{"id":350428,"name":"Amir Karger","orcid":"0000-0002-4561-3850","position":6,"is_corresponding":false},{"id":16800,"name":"Li Wang","orcid":"0000-0002-4460-8670","position":7,"is_corresponding":false},{"id":558023,"name":"Karolina Stumbraite","orcid":null,"position":8,"is_corresponding":false},{"id":107857,"name":"Vickie M. Wang","orcid":null,"position":9,"is_corresponding":false},{"id":203642,"name":"Ginevra Botta","orcid":null,"position":10,"is_corresponding":false},{"id":107865,"name":"Nicholas Lyons","orcid":"0000-0003-3921-106X","position":11,"is_corresponding":false},{"id":556979,"name":"Amy Goodale","orcid":"0000-0003-4294-5777","position":12,"is_corresponding":false},{"id":556980,"name":"Zohra Kalani","orcid":"0000-0003-2707-8097","position":13,"is_corresponding":false},{"id":558024,"name":"Briana Fritchman","orcid":null,"position":14,"is_corresponding":false},{"id":556981,"name":"Adam D. Brown","orcid":"0000-0003-2191-6061","position":15,"is_corresponding":false},{"id":558025,"name":"Douglas Alan","orcid":null,"position":16,"is_corresponding":false},{"id":558026,"name":"Thomas Green","orcid":null,"position":17,"is_corresponding":false},{"id":54725,"name":"Xiaoping Yang","orcid":"0000-0002-6811-4915","position":18,"is_corresponding":false},{"id":28650,"name":"Jacob D. Jaffe","orcid":"0000-0001-9845-1210","position":19,"is_corresponding":false},{"id":58616,"name":"Jennifer A. Roth","orcid":"0000-0002-5117-5586","position":20,"is_corresponding":false},{"id":3750,"name":"Federica Piccioni","orcid":"0000-0003-1210-3210","position":21,"is_corresponding":false},{"id":63534,"name":"Marc W. Kirschner","orcid":"0000-0001-6540-6130","position":22,"is_corresponding":false},{"id":11007,"name":"Zhe Ji","orcid":"0000-0002-1809-8099","position":23,"is_corresponding":false},{"id":3751,"name":"David E. Root","orcid":"0000-0001-5122-861X","position":24,"is_corresponding":false},{"id":16671,"name":"Todd R. Golub","orcid":"0000-0003-0113-2403","position":25,"is_corresponding":false},{"id":35299,"name":"John R. Prensner","orcid":"0000-0002-7024-636X","position":0,"is_corresponding":true}],"reference_count":95,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:14:33.640077Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}