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TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL

The brain is the foremost non-gonadal tissue for expression of non-coding RNAs of unclear function. Yet, whether such transcripts are truly non-coding or rather the source of non-canonical protein translation is unknown. Here, we used functional genomic screens to establish the cellular bioactivity...

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Autores principales: Prensner, John, Enache, Oana, Luria, Victor, Krug, Karsten, Clauser, Karl, Dempster, Joshua, Karger, Amir, Wang, Li, Stumbraite, Karolina, Wang, Vickie, Botta, Ginevra, Lyons, Nicholas, Goodale, Amy, Kalani, Zohra, Fritchman, Briana, Brown, Adam, Alan, Douglas, Green, Thomas, Yang, Xiaoping, Jaffe, Jacob, Roth, Jennifer, Piccioni, Federica, Kirschner, Marc, Ji, Zhe, Root, David, Golub, Todd
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715501/
http://dx.doi.org/10.1093/neuonc/noaa222.849
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author Prensner, John
Enache, Oana
Luria, Victor
Krug, Karsten
Clauser, Karl
Dempster, Joshua
Karger, Amir
Wang, Li
Stumbraite, Karolina
Wang, Vickie
Botta, Ginevra
Lyons, Nicholas
Goodale, Amy
Kalani, Zohra
Fritchman, Briana
Brown, Adam
Alan, Douglas
Green, Thomas
Yang, Xiaoping
Jaffe, Jacob
Roth, Jennifer
Piccioni, Federica
Kirschner, Marc
Ji, Zhe
Root, David
Golub, Todd
author_facet Prensner, John
Enache, Oana
Luria, Victor
Krug, Karsten
Clauser, Karl
Dempster, Joshua
Karger, Amir
Wang, Li
Stumbraite, Karolina
Wang, Vickie
Botta, Ginevra
Lyons, Nicholas
Goodale, Amy
Kalani, Zohra
Fritchman, Briana
Brown, Adam
Alan, Douglas
Green, Thomas
Yang, Xiaoping
Jaffe, Jacob
Roth, Jennifer
Piccioni, Federica
Kirschner, Marc
Ji, Zhe
Root, David
Golub, Todd
author_sort Prensner, John
collection PubMed
description The brain is the foremost non-gonadal tissue for expression of non-coding RNAs of unclear function. Yet, whether such transcripts are truly non-coding or rather the source of non-canonical protein translation is unknown. Here, we used functional genomic screens to establish the cellular bioactivity of non-canonical proteins located in putative non-coding RNAs or untranslated regions of protein-coding genes. We experimentally interrogated 553 open reading frames (ORFs) identified by ribosome profiling for three major phenotypes: 257 (46%) demonstrated protein translation when ectopically expressed in HEK293T cells, 401 (73%) induced gene expression changes following ectopic expression across 4 cancer cell types, and 57 (10%) induced a viability defect when the endogenous ORF was knocked out using CRISPR/Cas9 in 8 human cancer cell lines. CRISPR tiling and start codon mutagenesis indicated that the biological impact of these non-canonical ORFs required their translation as opposed to RNA-mediated effects. We functionally characterized one of these ORFs, G029442—renamed GREP1 (Glycine-Rich Extracellular Protein-1)—as a cancer-implicated gene with high expression in multiple cancer types, such as gliomas. GREP1 knockout in >200 cancer cell lines reduced cell viability in multiple cancer types, including glioblastoma, in a cell-autonomous manner and produced cell cycle arrest via single-cell RNA sequencing. 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.
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spelling pubmed-77155012020-12-09 TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL Prensner, John Enache, Oana Luria, Victor Krug, Karsten Clauser, Karl Dempster, Joshua Karger, Amir Wang, Li Stumbraite, Karolina Wang, Vickie Botta, Ginevra Lyons, Nicholas Goodale, Amy Kalani, Zohra Fritchman, Briana Brown, Adam Alan, Douglas Green, Thomas Yang, Xiaoping Jaffe, Jacob Roth, Jennifer Piccioni, Federica Kirschner, Marc Ji, Zhe Root, David Golub, Todd Neuro Oncol Tumor Biology (not fitting a specific disease category) The brain is the foremost non-gonadal tissue for expression of non-coding RNAs of unclear function. Yet, whether such transcripts are truly non-coding or rather the source of non-canonical protein translation is unknown. Here, we used functional genomic screens to establish the cellular bioactivity of non-canonical proteins located in putative non-coding RNAs or untranslated regions of protein-coding genes. We experimentally interrogated 553 open reading frames (ORFs) identified by ribosome profiling for three major phenotypes: 257 (46%) demonstrated protein translation when ectopically expressed in HEK293T cells, 401 (73%) induced gene expression changes following ectopic expression across 4 cancer cell types, and 57 (10%) induced a viability defect when the endogenous ORF was knocked out using CRISPR/Cas9 in 8 human cancer cell lines. CRISPR tiling and start codon mutagenesis indicated that the biological impact of these non-canonical ORFs required their translation as opposed to RNA-mediated effects. We functionally characterized one of these ORFs, G029442—renamed GREP1 (Glycine-Rich Extracellular Protein-1)—as a cancer-implicated gene with high expression in multiple cancer types, such as gliomas. GREP1 knockout in >200 cancer cell lines reduced cell viability in multiple cancer types, including glioblastoma, in a cell-autonomous manner and produced cell cycle arrest via single-cell RNA sequencing. 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. Oxford University Press 2020-12-04 /pmc/articles/PMC7715501/ http://dx.doi.org/10.1093/neuonc/noaa222.849 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Tumor Biology (not fitting a specific disease category)
Prensner, John
Enache, Oana
Luria, Victor
Krug, Karsten
Clauser, Karl
Dempster, Joshua
Karger, Amir
Wang, Li
Stumbraite, Karolina
Wang, Vickie
Botta, Ginevra
Lyons, Nicholas
Goodale, Amy
Kalani, Zohra
Fritchman, Briana
Brown, Adam
Alan, Douglas
Green, Thomas
Yang, Xiaoping
Jaffe, Jacob
Roth, Jennifer
Piccioni, Federica
Kirschner, Marc
Ji, Zhe
Root, David
Golub, Todd
TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title_full TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title_fullStr TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title_full_unstemmed TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title_short TBIO-26. NON-CANONICAL OPEN READING FRAMES ENCODE FUNCTIONAL PROTEINS ESSENTIAL FOR CANCER CELL SURVIVAL
title_sort tbio-26. non-canonical open reading frames encode functional proteins essential for cancer cell survival
topic Tumor Biology (not fitting a specific disease category)
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7715501/
http://dx.doi.org/10.1093/neuonc/noaa222.849
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