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Nat Biotechnol DOI:10.1038/s41587-020-00806-2

Noncanonical open reading frames encode functional proteins essential for cancer cell survival.

Publication TypeJournal Article
Year of Publication2021
AuthorsPrensner, JR, Enache, OM, Luria, V, Krug, K, Clauser, KR, Dempster, JM, Karger, A, Wang, L, Stumbraite, K, Wang, VM, Botta, G, Lyons, NJ, Goodale, A, Kalani, Z, Fritchman, B, Brown, A, Alan, D, Green, T, Yang, X, Jaffe, JD, Roth, JA, Piccioni, F, Kirschner, MW, Ji, Z, Root, DE, Golub, TR
JournalNat Biotechnol
Date Published2021 Jan 28
ISSN1546-1696
Abstract

Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth-inhibitory effect of GREP1 knockout. Our experiments suggest that noncanonical ORFs can express biologically active proteins that are potential therapeutic targets.

DOI10.1038/s41587-020-00806-2
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/33510483?dopt=Abstract

Alternate JournalNat Biotechnol
PubMed ID33510483
Grant ListR35 GM138192 / GM / NIGMS NIH HHS / United States
R00 CA207865 / CA / NCI NIH HHS / United States
R01 HD091846 / HD / NICHD NIH HHS / United States
5K12 CA 90354-18 / / U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) /
R01 HD073104 / HD / NICHD NIH HHS / United States