SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO

Cancer genome alterations often lead to vulnerabilities that can be used to selectively target cancer cells. Various inhibitors of such synthetic lethal targets have been approved by the FDA or are in clinical trials, highlighting the potential of this approach<sup>1-3</sup>. Here we analysed large-scale CRISPR knockout screening data from the Cancer Dependency Map and identified a new synthetic lethal target, PELO, for two independent molecular subtypes of cancer: biallelic deletion of chromosomal region 9p21.3 or microsatellite instability-high (MSI-H). In 9p21.3-deleted cancers, PELO dependency emerges from biallelic deletion of the 9p21.3 gene FOCAD, a stabilizer of the superkiller complex (SKIc). In MSI-H cancers, PELO is required owing to MSI-H-associated mutations in TTC37 (also known as SKIC3), a critical component of the SKIc. We show that both cancer subtypes converge to destabilize the SKIc, which extracts mRNA from stalled ribosomes. In SKIc-deficient cells, PELO depletion induces the unfolded protein response, a stress response to accumulation of misfolded or unfolded nascent polypeptides. Together, our findings indicate PELO as a promising therapeutic target for a large patient population with cancers characterized as MSI-H with deleterious TTC37 mutations or with biallelic 9p21.3 deletions involving FOCAD.

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Journal
Nature
Published
2025-02-05
DOI
https://doi.org/10.1038/s41586-024-08509-3
Citations
18
Primary Topic
RNA modifications and cancer
Type
article
Field-Weighted Citation Impact
13.70
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article

SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO

Todd R. Golub, Edmond M. Chan, Kyla Foster, Joshua M. Dempster et al.
18 citations
Nature
RNA modifications and cancer
13.70
article

SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO

Todd R. Golub, Edmond M. Chan, Kyla Foster, Joshua M. Dempster, Kristina Janković, Srivatsan Raghavan, Patrícia Cristine Borck, Nolan Bick, Elisa Aquilanti, Francisca Vázquez, Tianxia Li, John M. Krill-Burger, Ashir A. Borah, Sohani Das Sharma, Isabella Boyle, Timothy A. Chan, Anthony C. Lau, Catarina D. Campbell, John R. Prensner, Lucy Parker-Burns, Anisah Adeagbo, Nicholas J. Lofaso, Riya V. Kishen, Daniel A. Lubicki
article en
18 citations

Abstract

Cancer genome alterations often lead to vulnerabilities that can be used to selectively target cancer cells. Various inhibitors of such synthetic lethal targets have been approved by the FDA or are in clinical trials, highlighting the potential of this approach<sup>1-3</sup>. Here we analysed large-scale CRISPR knockout screening data from the Cancer Dependency Map and identified a new synthetic lethal target, PELO, for two independent molecular subtypes of cancer: biallelic deletion of chromosomal region 9p21.3 or microsatellite instability-high (MSI-H). In 9p21.3-deleted cancers, PELO dependency emerges from biallelic deletion of the 9p21.3 gene FOCAD, a stabilizer of the superkiller complex (SKIc). In MSI-H cancers, PELO is required owing to MSI-H-associated mutations in TTC37 (also known as SKIC3), a critical component of the SKIc. We show that both cancer subtypes converge to destabilize the SKIc, which extracts mRNA from stalled ribosomes. In SKIc-deficient cells, PELO depletion induces the unfolded protein response, a stress response to accumulation of misfolded or unfolded nascent polypeptides. Together, our findings indicate PELO as a promising therapeutic target for a large patient population with cancers characterized as MSI-H with deleterious TTC37 mutations or with biallelic 9p21.3 deletions involving FOCAD.

NatureVol. 638(8052)
Broad Institute (US), Harvard University (US), University of Michigan (US), Columbia University Irving Medical Center (US), Michigan Medicine (US), Dana-Farber Cancer Institute (US), New York Genome Center (US), Columbia University (US)
Good health and well-being
Openalex Percentile: Top 1%
RNA modifications and cancer
13.70
DOIOpen Access PDFOpenAlex
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