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Acute myeloid leukemia

Data mining for mutation-specific targets in acute myeloid leukemia

Leukemia volume 33, pages 826–843 (2019)Cite this article

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Abstract

Three mutation-specific targeted therapies have recently been approved by the FDA for the treatment of acute myeloid leukemia (AML): midostaurin for FLT3 mutations, enasidenib for relapsed or refractory cases with IDH2 mutations, and ivosidenib for cases with an IDH1 mutation. Together, these agents offer a mutation-directed treatment approach for up to 45% of de novo adult AML cases, a welcome deluge after a prolonged drought. At the same time, a number of computational tools have recently been developed that promise to further accelerate progress in mutation-specific therapy for AML and other cancers. Technical advances together with comprehensively annotated AML tissue banks have resulted in the availability of large and complex data sets for exploration by the end-user, including (i) microarray gene expression, (ii) exome sequencing, (iii) deep sequencing data of sub-clone heterogeneity, (iv) RNA sequencing of gene expression (bulk and single cell), (v) DNA methylation and chromatin, (vi) and germline quantitative trait loci. Yet few clinicians or experimental hematologists have the time or the training to access or analyze these repositories. This review summarizes the data sets and bioinformatic tools currently available to further the discovery of mutation-specific targets with an emphasis on web-based applications that are open, accessible, user-friendly, and do not require coding experience to navigate. We show examples of how available data can be mined to identify potential targets using synthetic lethality, drug repurposing, epigenetic sub-grouping, and proteomic networks while also highlighting strengths and limitations and the need for superior models for validation.

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Acknowledgements

The authors thank Amy Fan for her critical review of this manuscript. BB is supported by NIH training grant 5T32CA9302-40. DT was funded by a Pathway-to-Independence K99 National Institutes of Health, National Cancer Institute Grant Number 5K99CA207731-02. Supported by NIH R01-CA188055 (to RM) and the Ludwig Institute for Cancer Research (to RM). RM is a Leukemia & Lymphoma Society Scholar. Due to citation limits, we apologize for not referencing all notable studies.

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  1. Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA

    Brooks Benard, Thomas Köhnke, Ravindra Majeti & Daniel Thomas

  2. Departments of Medicine (Biomedical Informatics), and Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA

    Andrew J. Gentles

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  1. Brooks Benard
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Benard, B., Gentles, A.J., Köhnke, T. et al. Data mining for mutation-specific targets in acute myeloid leukemia. Leukemia 33, 826–843 (2019). https://doi.org/10.1038/s41375-019-0387-y

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