Open AccessNoncanonical open reading frames encode functional proteins essential for cancer cell survival
Author(s) -
John R. Prensner,
Oana Enache,
Victor Luria,
Karsten Krug,
Karl R. Clauser,
Joshua Dempster,
Amir Karger,
Li Wang,
Karolina Stumbraite,
Vickie M. Wang,
Ginevra Botta,
Nicholas Lyons,
Amy Goodale,
Zohra Kalani,
Briana Fritchman,
Adam D. Brown,
Douglas Alan,
Thomas Green,
Xiaoping Yang,
Jacob D. Jaffe,
Jennifer A. Roth,
Federica Piccioni,
Marc W. Kirschner,
Zhe Ji,
David E. Root,
Todd R. Golub
Publication year - 2021
Publication title -
nature biotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 15.358
H-Index - 445
eISSN - 1546-1696
pISSN - 1087-0156
DOI - 10.1038/s41587-020-00806-2
Subject(s) - orfs , open reading frame , biology , gene , genetics , ectopic expression , translation (biology) , encode , crispr , microbiology and biotechnology , messenger rna , peptide sequence
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.