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Whole transcriptome splicing analysis in isogenic lung epithelial and adenocarcinoma cell lines with or without a recurrent splicing factor mutation, U2AF1 (S34F)

ABSTRACT: The splicing factor gene, U2AF1, is recurrently mutated in a variety of human cancers, including lung adenocarcinomas. The most frequent U2AF1 mutant, U2AF1 p.Ser34Phe (S34F), induces specific changes in pre-mRNA splicing, but it is unclear how these splicing changes are regulated. We have used genomic editing methods to modify the U2AF1 gene locus in an immortalized human bronchial epithelial cell line (HBEC3kt) and in human lung adenocarcinoma cells with pre-existing U2AF1 alleles, creating a U2AF1 S34F allele in the endogenous locus of HBEC3kts and inactivating U2AF1 S34F alleles in two lung adenocarcinoma cell lines (H441 and HCC78). By comparing global splicing alterations in these isogenic pairs of cell lines, we have identified many splicing alterations that are associated with the U2AF1 S34F mutation. Further, by decreasing the levels of wild-type U2AF1 in the isogenic HBEC3kt cells, we show that the magnitude of mutant-associated splicing is proportional to the ratio of S34F:WT gene products. This observation suggest that wild-type U2AF1 is a negative regulator of splicing alterations induced by U2AF1 S34F.

ORGANISM(S): Homo sapiens

PROVIDER: GSE80136 | GEO | 2016/09/30

SECONDARY ACCESSION(S): PRJNA318018

REPOSITORIES: GEO

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Nanopore sequencing reveals isoform-specific alterations in human bronchial epithelial cells with U2AF1 S34F mutations

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