Journal Article

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

Wang, Li, Karger, Amir, Root, David E., Golub, Todd R., Clauser, Karl R., Ji, Zhe, Kalani, Zohra, Kirschner, Marc W., Prensner, John R., Botta, Ginevra, Alan, Douglas, Brown, Adam, Enache, Oana M., Roth, Jennifer A., Fritchman, Briana, Stumbraite, Karolina, Jaffe, Jacob D., Dempster, Joshua M., Piccioni, Federica, Luria, Victor, Goodale, Amy, Green, Thomas, Yang, Xiaoping, Krug, Karsten, Wang, Vickie M., Lyons, Nicholas J.

2021

Overview

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 g lycine-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. Noncanonical open reading frames are shown to be essential for cancer cell function.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/337/574 / 631/67/69 / Agriculture / Bioinformatics / Biological activity / Biological effects / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Breast cancer / Cancer cells / Cell Line, Tumor / Cell survival / Cell Survival - physiology / Clustered Regularly Interspaced Short Palindromic Repeats / CRISPR / Cytokines / Ectopic expression / Frames / Gene expression / Genetic aspects / Genomic analysis / Glycine / Health aspects / HEK293 Cells / Human genome / Humans / Letter / Life Sciences / Mutagenesis / Neoplasm Proteins - genetics / Neoplasm Proteins - physiology / Neoplasms - genetics / Neoplasms - pathology / Open Reading Frames / Physiological aspects / Proteins / Secretome / Supplements / Therapeutic targets / Tiling / Tumor cell lines