PreprintCited by 277RNA Research and SplicingCancer-related molecular mechanisms researchCancer Genomics and Diagnostics

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Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

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Sebestyén, Endre, Singh, Babita, Miñana, Belén, Pagès, Amadís, Mateo, Francesca, Pujana, Miguel Angel, Valcárcel, Juan, Eyras, Eduardo·2016·Genome Research

DOI 10.1101/gr.199935.115PMC PMC4889968

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Abstract

Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. We systematically analyzed mutation, copy number, and gene expression patterns of 1348 RNA-binding protein (RBP) genes in 11 solid tumor types, together with alternative splicing changes in these tumors and the enrichment of binding motifs in the alternatively spliced sequences. Our comprehensive study reveals widespread alterations in the expression of RBP genes, as well as novel mutations and copy number variations in association with multiple alternative splicing changes in cancer drivers and oncogenic pathways. Remarkably, the altered splicing patterns in several tumor types recapitulate those of undifferentiated cells. These patterns are predicted to be mainly controlled by MBNL1 and involve multiple cancer drivers, including the mitotic gene NUMA1 . We show that NUMA1 alternative splicing induces enhanced cell proliferation and centrosome amplification in nontumorigenic mammary epithelial cells. Our study uncovers novel splicing networks that potentially contribute to cancer development and progression.

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Authors: Sebestyén, E., Singh, B., Miñana, B., Pagès, A., Mateo, F., Pujana, M. A., Valcárcel, J., & Eyras, E.
Affiliations: Universitat Pompeu Fabra (ES)
Institut d'Investigació Biomédica de Bellvitge (ES)
Institució Catalana de Recerca i Estudis Avançats (ES)
ORCID: Sebestyén, Endre
Singh, Babita
Miñana, Belén
Mateo, Francesca
Valcárcel, Juan
Eyras, Eduardo
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2016-04-13
Volume: 26
Issue: 6
Pages: 732-744
ISSN: 1088-9051 (ISSN-L)
1549-5469
DOI: 10.1101/gr.199935.115
PMC: PMC4889968
OpenAlex: W2338046461
Cited by: 276
References: 61
Citations by year: 2026: 12 · 2025: 18 · 2024: 25 · 2023: 21 · 2022: 38 · 2021: 45 · 2020: 43 · 2019: 27 · 2018: 22 · 2017: 22 · 2016: 3
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by-nc)
HighWire Press Open Archive (submittedVersion)
RECERCAT (Consorci de Serveis Universitaris de Catalunya) (submittedVersion, cc-by-nc)
Funders: Ministerio de Economía y Competitividad
European Commission
FEDER (BIO2014-52566-R, PIE13/00022-ONCOPROFILE, PI15/00854, RD12/0036/0008)
Consolider RNAREG (CSD2009-00080)
Agència de Gestió d'Ajuts Universitaris i de Recerca (SGR2014-1121)
Sandra Ibarra Foundation for Cancer (FSI2013)
Fundación Botín
Santander Universities Global Division
MINECO
AGAUR (SGR2014-364)
AECC
Instituto de Salud Carlos III
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Keywords: alternative splicing, RNA-binding proteins, cancer, solid tumors, MBNL1, NUMA1, copy number variation, gene expression changes, binding motifs, centrosome amplification, cell proliferation, mammary epithelial cells, undifferentiated cells
MeSH terms: RNA Splicing Factors, Binding Sites, Humans, Mutation, Neoplasms, Genome, Human, Gene Expression Regulation, Neoplastic, Alternative Splicing, Amino Acid Motifs, Gene Expression Profiling, Cell Proliferation, Transcriptome

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Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

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