ArticleeLife2017
Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.
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Article in eLife, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50citing papers in PubMed
5.4field-weighted citation impact, top 3% of its field
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Who cites it
50 citing papers in PubMed, 83 citations in OpenAlex.
- Impact of Chromosomal Instability and Aneuploidy in Cancer Development.Annual review of cancer biology · 2026Article
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- SF3A3 Drives Tumorigenesis in Endometrial Cancer by Enhancing c-FOS Expression and Represents a Potential Therapeutic Target.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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- Bio-primed machine learning to enhance discovery of relevant biomarkers.NPJ precision oncology · 2025Article
- SF3B1K700E mutation in human embryonic stem cells causes aberrant expression of immune-related genes.PloS one · 2025Article
- Aneuploidy as a driver of human cancer.Nature genetics · 2024Review
- Expression of GNAQ, BAP1, SF3B1, and EIF1AX Proteins in the Aqueous Humor of Eyes Affected by Uveal Melanoma.Investigative ophthalmology & visual science · 2024Article
- Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity.NAR cancer · 2023Article
- Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal.Genome biology · 2023Article
- Alternative mRNA Splicing and Promising Therapies in Cancer.Biomolecules · 2023Review
- Predicting gene knockout effects from expression data.BMC medical genomics · 2023Article
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- Systematic illumination of druggable genes in cancer genomes.Cell reports · 2022Article
- Co-occurrence of BAP1 and SF3B1 mutations in uveal melanoma induces cellular senescence.Molecular oncology · 2022Article
- A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.Cell chemical biology · 2021Article
- Targeting the transcription cycle and RNA processing in cancer treatment.Current opinion in pharmacology · 2021Review
- Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies.Frontiers in molecular biosciences · 2021Review
- Determination of Genetic and Epigenetic Modifications-Related Prognostic Biomarkers of Breast Cancer: Genome High-Throughput Data Analysis.Journal of oncology · 2021Article
- Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.Scientific reports · 2020Article
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Authors and funding
27 authors at 4 institutions in 1 country.
Brenton R PaolellaDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.ORCID 0000-0003-3394-828X
William J GibsonDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Laura M UrbanskiDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
John A AlbertaDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Travis I ZackDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Pratiti BandopadhayayDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Caitlin A NicholsDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Pankaj K AgarwallaDepartment of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States.
Meredith S BrownDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Rebecca LamotheDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Yong YuDepartment of Cell Biology, Harvard Medical School, Boston, United States.
Peter S ChoiBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Esther A ObengBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Dirk HecklDivision of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.
Guo WeiBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Belinda WangBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Aviad TsherniakBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.ORCID 0000-0002-3797-1877
Francisca VazquezBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Barbara A WeirBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
David E RootBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Glenn S CowleyBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
Sara J BuhrlageDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Charles D StilesDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Benjamin L EbertBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.
William C HahnBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.ORCID 0000-0003-2840-9791
Robin ReedDepartment of Cell Biology, Harvard Medical School, Boston, United States.
Rameen BeroukhimDepartment of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.
Broad Institute · USHarvard University · USBoston University · USBrigham and Women's Hospital · US
Funding
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0MTargeting the Vasular SystemP50CA165962 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI KEITH LLOYD LIGON · 2013 to 2026
$33.5MMECHANISMS OF PREMRNA SPLICING IN HIGHER EUKARYOTESR01GM043375 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI REED, ROBIN E. · 1990 to 2015
$12.6MThe Dana-Farber Cancer Institute Cancer Target Discovery and Development CenterU01CA176058 · NCI · DANA-FARBER CANCER INST · PI HAHN, WILLIAM C. · 2013 to 2021
$7.8MGenetic evolution of glioblastomas during radiation and temozolomide therapyR01CA188228 · NCI · DANA-FARBER CANCER INST · PI BEROUKHIM, RAMEEN, CHAKRAVARTI, ARNAB · 2015 to 2025
$6.9MRNA Processing Machines in Biology and DiseaseR35GM122524 · NIGMS · HARVARD MEDICAL SCHOOL · PI MOAZED, DANESH · 2017 to 2023
$4.1MCharacterizing the resistance mechanisms to BET-bromodomain inhibition in MYC-amplified medulloblastomaK99CA201592 · NCI · DANA-FARBER CANCER INST · PI BANDOPADHAYAY, PRATITI · 2016 to 2017
$302kCancer Specific Sensitivity to Suppression of Spliceosome ComponentsF32CA180653 · NCI · DANA-FARBER CANCER INST · PI PAOLELLA, BRENTON ROBERT · 2014 to 2017
$148kHemizygous deletion of esential genes enables a novel therqpeutic vulnerability in cancerF30CA192725 · NCI · HARVARD MEDICAL SCHOOL · PI GIBSON, WILLIAM J · 2015 to 2017
$121kNCI NIH HHS F30 CA192725NCI NIH HHS F32 CA180653NCI NIH HHS K99 CA201592NCI NIH HHS P50 CA165962NCI NIH HHS R01 CA188228NCI NIH HHS U01 CA176058NIGMS NIH HHS R01 GM043375NIGMS NIH HHS R35 GM122524NIGMS NIH HHS T32 GM007753
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor
Indexed as
Gene DosageCell Line, TumorHumansNeoplasmsPhosphoproteinsRNA Splicing FactorsPhosphoproteinsRNA Splicing FactorsSF3B1 protein, humancancer biologyCancer therapeuticsCopy number alterationsCYCLOPS geneshumanhuman biologymedicinemouseSF3B1SpliceosomeTarget identification and validation
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