U2AF1 mutations confer resistance to chemotherapy in AML
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ABSTRACT:
PROVIDER: PRJNA1078301 | ENA |
REPOSITORIES: ENA
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Project description:Patients with primary refractory acute myeloid leukemia (AML) have a dismal long-term prognosis. Elucidating the resistance mechanisms to induction chemotherapy could help identify strategies to improve AML patient outcomes. Herein, we retrospectively analyzed the multi-omics data of more than 1,500 AML cases and found that patients with spliceosome mutations had a higher risk of developing refractory disease. RNA splicing analysis revealed that the mis-spliced genes in refractory patients converged on translation-associated pathways, promoted mainly by U2AF1 mutations. Integrative analyses of binding and splicing in AML cell lines substantiated that the splicing perturbations of mRNA translation genes originated from both the loss and gain of mutant U2AF1 binding. In particular, the U2AF1-S34F and U2AF1-Q157R mutants orchestrated the inclusion of exon 11 (encoding a premature termination codon) in the eukaryotic translation initiation factor 4A2 (EIF4A2). This aberrant inclusion led to reduced eIF4A2 protein expression via nonsense-mediated mRNA decay. Consequently, U2AF1 mutations caused a net decrease in global mRNA translation that induced the integrated stress response (ISR) in AML cells, which was confirmed by single-cell RNA-seq. The induction of ISR enhanced the ability of AML cells to respond and adapt to stress, contributing to chemoresistance. A pharmacologic inhibitor of ISR, ISRIB, sensitized U2AF1 mutant cells to chemotherapy. These findings highlight a resistance mechanism by which U2AF1 mutations drive chemoresistance and provide a therapeutic approach for AML through targeting the ISR pathway.
2024-02-20 | GSE256127 | GEO
Project description:Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways implicated in myeloid disease such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show that U2AF1 mutations alter the preferred 3' splice site motif in vivo, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1’s zinc finger domains. mRNA profiles of K562 cells expressing U2AF1 WT, mutants and knockdown of U2AF1 generated by deep sequencing.
2014-09-23 | E-GEOD-58871 | biostudies-arrayexpress
Project description:The mechanisms by which mutations of the splicing factor gene U2AF1 contribute to lung adenocarcinoma pathogenesis are not well understood. Here, we used prime editing to modify the endogenous U2AF1 gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. One specific KRAS mutation, G12S, leads to skipping of KRAS exon 2 and generation of a non-functional KRAS transcript. However, expression of the U2AF1 S34F mutant reverts this exon skipping and restores KRAS function, leading to an enrichment of U2AF1 S34F mutations in KRAS G12S-mutant lung adenocarcinomas. A comprehensive analysis of splicing factor/oncogene mutation co-occurrence in cancer genomes also revealed significant co-enrichment of KRAS Q61R and U2AF1 I24T mutations. Experimentally, KRAS Q61R mutation leads to KRAS exon 3 skipping, which in turn can be rescued by the expression of U2AF1 I24T. Our findings provide evidence that splicing factor mutations can rescue splicing defects caused by oncogenic mutations in a dynamic process of cascading selection.
2026-04-29 | GSE328804 | GEO
Project description:The mechanisms by which mutations of the splicing factor gene U2AF1 contribute to lung adenocarcinoma pathogenesis are not well understood. Here, we used prime editing to modify the endogenous U2AF1 gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. One specific KRAS mutation, G12S, leads to skipping of KRAS exon 2 and generation of a non-functional KRAS transcript. However, expression of the U2AF1 S34F mutant reverts this exon skipping and restores KRAS function, leading to an enrichment of U2AF1 S34F mutations in KRAS G12S-mutant lung adenocarcinomas. A comprehensive analysis of splicing factor/oncogene mutation co-occurrence in cancer genomes also revealed significant co-enrichment of KRAS Q61R and U2AF1 I24T mutations. Experimentally, KRAS Q61R mutation leads to KRAS exon 3 skipping, which in turn can be rescued by the expression of U2AF1 I24T. Our findings provide evidence that splicing factor mutations can rescue splicing defects caused by oncogenic mutations in a dynamic process of cascading selection.
2026-04-29 | GSE328821 | GEO
Project description:Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. We find that U2AF1 mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure. U2AF1 mutations cause differential splicing of hundreds of genes, affecting biological pathways implicated in myeloid disease such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show that U2AF1 mutations alter the preferred 3' splice site motif in vivo, in cell culture, and in vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1’s zinc finger domains.
2014-09-23 | GSE58871 | GEO
Project description:U2AF1 is a core component of spliceosome and controls cell-fate specific alternative splicing. U2AF1 mutations have been frequently identified in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) patients, and mutations in U2AF1 are associated with poor prognosis in hematopoietic malignant diseases. To investigate the effects of U2af1 S34F in hematopoietic cells, we performed global gene expression profiling by RNA sequencing on U2af1-WT and U2af1 S34F 32D cells. We find that U2AF1 S34F causes increased reactive oxygen species (ROS) production. In hematopoietic cell line, a defect in mitochondrial function and DNA damage response deficiency are found in U2AF1 S34F expressing 32D cells.
2025-12-01 | GSE282085 | GEO
Project description:U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations
| PRJNA1456563 | ENA
Project description:Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA binding motifs; yet how they affect splicing and promote cancer remains unclear. The U2AF1/U2AF2 heterodimer is critical for 3’ splice site (3’SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure detecting contacts between U2AF1 and the 3’SS AG at single-nucleotide resolution (fractionated eCLIP-seq or freCLIP-seq). Our data reveal that U2AF1 S34F and Q157R mutants establish new 3’SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding (eCLIP-seq and freCLIP-seq), splicing (RNA-seq) and turnover (TimeLapse-seq or TL-seq) data, we predicted that U2AF1 mutations directly affect stress granule components. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies. Keywords: splicing, RNA binding, U2AF1, U2AF2, S34F, Q157R, hotspot mutations, 3'SS, 3' splice site, myeloid malignancies, eCLIP, freCLIP, RNA-seq, RNA turnover, TimeLapse-seq, TL-seq, RNA granules, stress granules, stress response, biomolecular condensates, MDS, AML
2022-03-17 | GSE195620 | GEO
Project description:U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations [RNA-Seq]
| PRJNA1456598 | ENA
Project description:Recurrent somatic mutations in a subset of spliceosome genes (SF3B1, SRSF2, and U2AF1) are frequently identified in patients with myeloid malignancies such as myelodysplastic syndromes (MDS). These heterozygous and mutually exclusive mutations are enriched in hotspot codons in these 3’ splicing factor proteins resulting in aberrant alternative mRNA splicing in hematopoietic cells. However, each mutant protein predominantly affects a distinct set of alternatively spliced downstream target genes suggesting that global mRNA splicing alterations, rather than specific splicing targets, may be responsible for MDS phenotypes, including dysplasia, ineffective hematopoiesis, and cytopenias. U2AF1 provides a unique opportunity to address this question because it has two hotspot positions (serine 34 [S34] and glutamine 157 [Q157]) that are each commonly mutated in MDS and are associated with unique mRNA splicing consequences. In addition, U2AF1 S34 and Q157 codon mutations co-occur with mutations in different genes (e.g., BCOR and ASXL1, respectively) and patients with these mutations may have different hematopoietic phenotypes—highlighting that these mutations may induce distinct phenotypes. We asked if the splicing differences resulting from S34F and Q157R mutations were thus associated with different or similar effects on hematopoiesis. To do so, we engineered a new Cre/lox conditional mouse model with the Q157R mutation knocked-in to the endogenous U2af1 locus based on our established conditional S34F knock-in mouse model and utilized both models to directly study the hematopoietic phenotype, transcriptional, and mRNA splicing consequences of individual U2AF1 gene mutations in vivo. Our results indicate that the two mutations induce distinct hematopoietic phenotypes in mice, suggesting that the U2af1S34F and U2af1Q157R mutations should not be conflated as they may impact disease pathogenesis differently in patients. Mice expressing U2af1S34F have a more severe reduction in their PB and BM cell counts, and reduced HSPCs repopulating ability, compared to mice expressing U2af1Q157R. The expression and splicing of the majority of target genes are unique between the mutations, in both mouse and human samples, potentially driving the phenotypic differences induced by the two mutations. The two mutations co-occur with different gene mutations and are not equally represented in various myeloid neoplasms, suggesting that multiple mechanisms are likely to drive the pathogenesis of U2AF1 mutant myeloid diseases. Collectively, our results support that U2AF1S34F and U2AF1Q157R mutations induce distinct hematopoietic, gene expression, and RNA splicing phenotypes in vivo, suggesting that larger prospective studies are needed to understand if patients with these mutations should be classified differently.
2026-05-10 | GSE282060 | GEO