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Published on: December 9, 2016
Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias
Meenakshi Venkatasubramanian1,2, Leya Schwartz3, Nandini Ramachandra3
1Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Abstract:
The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations remains poorly understood. Prompted by the finding that splicing uniquely resolved genetic subtypes of cancer, we developed an unsupervised computational workflow called OncoSplice to comprehensively define tumor molecular landscapes. In adult and pediatric acute myeloid leukemia (AML), OncoSplice identified the spectrum of driver genetics from splicing profiles alone, defined more than a dozen previously unreported molecular subtypes recurrent across AML cohorts, and discovered a dominant splicing subtype that partially phenocopies U2AF1-mutant splicing. Although pediatric leukemias lack splicing factor mutations, this U2AF1-like subtype similarly spanned pediatric and adult AML genetics and consistently predicted poor prognosis. Using long-read single-cell RNA sequencing, we confirmed that discovered U2AF1-like splicing was shared across cell states, co-opted a healthy circadian gene program, was stable through relapse, and induced a leukemic stem cell program. Pharmacological inhibition of an implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia missplicing and inhibited leukemic cell growth. Finally, genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treatment, blocked leukemia development in xenograft models and induced differentiation. This work suggests that broad splicing dysregulation, in the absence of select mutations, is a therapeutic target in heterogeneous leukemias.
Insights
Splicing dysregulation, even without mutations, drives leukemia subtypes. Targeting splicing regulators like PRMT5 and IRAK4 offers a new therapeutic avenue for acute myeloid leukemia (AML).
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Splicing dysregulation is implicated in cancer, but its role without specific mutations is unclear.
- Splicing patterns can uniquely define cancer genetic subtypes.
- Acute myeloid leukemia (AML) presents a complex genetic landscape.
Purpose of the Study:
- To develop a computational method (OncoSplice) to analyze tumor molecular landscapes based on splicing.
- To identify novel molecular subtypes and driver genetics in AML using splicing profiles.
- To investigate the therapeutic potential of targeting splicing dysregulation in AML.
Main Methods:
- Developed OncoSplice, an unsupervised computational workflow for splicing analysis.
- Applied OncoSplice to adult and pediatric AML cohorts.
- Utilized long-read single-cell RNA sequencing for detailed splicing analysis.
- Investigated pharmacological inhibition of PRMT5 and genetic deletion of IRAK4.
Main Results:
- OncoSplice identified driver genetics and over a dozen new AML molecular subtypes from splicing data alone.
- A novel "U2AF1-like" splicing subtype was discovered, present in both pediatric and adult AML, predicting poor prognosis.
- This subtype was stable, co-opted gene programs, and was targeted effectively by PRMT5 inhibition and IRAK4 deletion.
- PRMT5 inhibition rescued splicing defects and reduced leukemia cell growth; IRAK4 deletion blocked leukemia development.
Conclusions:
- Broad splicing dysregulation, independent of specific mutations, is a significant driver in heterogeneous leukemias.
- OncoSplice is a powerful tool for defining molecular subtypes and identifying therapeutic targets in cancer.
- Targeting splicing regulators like PRMT5 and IRAK4 shows promise as a therapeutic strategy for AML.
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