Abstract
Original language | English |
---|---|
Pages (from-to) | 261-276.e18 |
Journal | Molecular Cell |
Volume | 84 |
Issue number | 2 |
DOIs | |
Publication status | Published - 18 Jan 2024 |
Keywords
- CRISPR
- Ribo-seq
- cancer
- gene dependency
- lncRNAs
- medulloblastoma
- non-canonical ORFs
- translational regulation
- uORF
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In: Molecular Cell, Vol. 84, No. 2, 18.01.2024, p. 261-276.e18.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma
AU - Hofman, Damon A.
AU - Ruiz-Orera, Jorge
AU - Yannuzzi, Ian
AU - Murugesan, Rakesh
AU - Brown, Adam
AU - Clauser, Karl R.
AU - Condurat, Alexandra L.
AU - van Dinter, Jip T.
AU - Engels, Sem A. G.
AU - Goodale, Amy
AU - van der Lugt, Jasper
AU - Abid, Tanaz
AU - Wang, Li
AU - Zhou, Kevin N.
AU - Vogelzang, Jayne
AU - Ligon, Keith L.
AU - Phoenix, Timothy N.
AU - Roth, Jennifer A.
AU - Root, David E.
AU - Hubner, Norbert
AU - Golub, Todd R.
AU - Bandopadhayay, Pratiti
AU - van Heesch, Sebastiaan
AU - Prensner, John R.
N1 - Funding Information: We thank Greg Newby and David Liu from the Broad Institute for their gracious insights with base editing experiments and providing the ABE8e-NRCH base editor. We thank Edmond Chan (Columbia University) for insights into chromatin immunoprecipitation experiments. We thank Ross Tomiano at the Taplin Mass Spectrometry Facility and Julian Mintseris at the Thermo-Fisher Center for Multiplexed Proteomics at the Harvard Medical School for assistance with mass spectrometry experiments. We thank Maura Berkeley and Zachary Herbert at the Dana-Farber Cancer Institute Molecular Biology Core Facility for assistance with next-generation sequencing. We thank the Dana-Farber Cancer Institute Center for Patient Derived Models for cell line support. We thank the Boston Children’s Hospital biobank and the DFHCC Neurooncology Program Tissue and Data Bank for biobanking support. We thank the PRISM team at the Broad Institute for assistance with PRISM cell line screening and PRISM cell library sample preparation. We thank Joelle Straehla for sharing Med2112-mCherry-Luc and Med411-GFP-Luc cells. We thank Quang-De Nguyen, Amy Cameron, and Murry Morrow at the Lurie Family Animal Imaging Center at the Dana-Farber Cancer Institute . J.R.P. acknowledges funding from the National Institutes of Health – National Cancer Institute ( K08-CA263552-01A1 ), the Alex’s Lemonade Stand Foundation Young Investigator Award (# 21-23983 ), the St. Baldrick’s Foundation Scholar Award (# 931638 ), the DIPG/DMG Research Funding Alliance , the Cure ATRT Now Fund , the Musella Foundation for Brain Tumor Research , and a Collaborative Pediatric Cancer Research Awards Program/Kids Join the Fight award (# 22FN23 ). T.R.G. acknowledges funding from the National Cancer Institute (1 R35 CA242457–01 ). K.L.L. and J.V. acknowledge support from the Pediatric Brain Tumor Foundation , the National Brain Tumor Society , and 3000 Miles to the Cure . S.v.H. acknowledges funding from Fonds Cancers ( FOCA, Belgium ), Stichting Reggeborgh (the Netherlands), and Bergh in het Zadel (the Netherlands). N.H. acknowledges funding from the European Union Horizon 2020 Research and Innovation Program ( AdG788970 ), the Deutsche Forschungsgemeinschaft ( SFB-1470 – B03 ), the Chan Zuckerberg Foundation ( 2019-202666 ), the Leducq Foundation ( 16CVD03 ), the British Heart Foundation , and the Deutsches Zentrum für Herz-Kreislauf-Forschung ( BHF/DZHK: SP/19/1/34461 ). P.B. acknowledges funding from the Isabel V. Marxuach Fund for Medulloblastoma Research and the Jared Branfman Sunflowers for Life Fund for Pediatric Brain and Spinal Cancer Research . Funding Information: K.L.L. reports the following interests: equity in Travera; research funds from Bristol Myers Squibb, SEngine Precision Medicine, Multiple Myeloma Research Foundation, and Eli Lilly and Company; and being a consultant or on the scientific advisory board for Bristol Myers Squibb, Travera, and IntegraGen. P.B. receives grant funding from Novartis Institute of Biomedical Research, and has received grant funding from Deerfield Therapeutics, both for unrelated projects. P.B. has also served on a paid advisory board for qed Therapeutics, unrelated to this work. D.E.R. receives research funding from members of the Functional Genomics Consortium (AbbVie, BMS, Jannsen, Merck, and Vir) and is a director of Addgene, Inc. Publisher Copyright: © 2023 The Author(s)
PY - 2024/1/18
Y1 - 2024/1/18
N2 - A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
AB - A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
KW - CRISPR
KW - Ribo-seq
KW - cancer
KW - gene dependency
KW - lncRNAs
KW - medulloblastoma
KW - non-canonical ORFs
KW - translational regulation
KW - uORF
UR - http://www.scopus.com/inward/record.url?scp=85182357581&partnerID=8YFLogxK
U2 - https://doi.org/10.1016/j.molcel.2023.12.003
DO - https://doi.org/10.1016/j.molcel.2023.12.003
M3 - Article
C2 - 38176414
SN - 1097-2765
VL - 84
SP - 261-276.e18
JO - Molecular Cell
JF - Molecular Cell
IS - 2
ER -