Mar 11, 2020

Non-canonical open reading frames encode functional proteins essential for cancer cell survival

bioRxiv
John R PrensnerTodd R Golub

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 sh...Continue Reading

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Mentioned in this Paper

Profile (Lab Procedure)
Genome
Malignant Neoplasm of Breast
CRISPR-Cas Systems
Cancer Treatment
Open Reading Frames
Extracellular
LSM4
Ectopic Expression
Ectopic (Qualifier Value)

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