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Silver AJ, Brown DJ, Olmstead SD, Watke JM, Gorska AE, Tanner L, Ramsey HE, Savona MR. Repair of leukemia-associated single nucleotide variants via interallelic gene conversion. bioRxiv 2024:2024.04.16.587991. [PMID: 38659776 PMCID: PMC11042315 DOI: 10.1101/2024.04.16.587991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
CRISPR-Cas9 is a useful tool for inserting precise genetic alterations through homology-directed repair (HDR), although current methods rely on provision of an exogenous repair template. Here, we tested the possibility of repairing heterozygous single nucleotide variants (SNVs) using the cell's own wild-type allele rather than an exogenous template. Using high-fidelity Cas9 to perform allele-specific CRISPR across multiple human leukemia cell lines as well as in primary hematopoietic cells from patients with leukemia, we find high levels of reversion to wild-type in the absence of exogenous template. Moreover, we demonstrate that bulk treatment to revert a truncating mutation in ASXL1 using CRISPR-mediated interallelic gene conversion (IGC) is sufficient to prolong survival in a human cell line-derived xenograft model (median survival 33 days vs 27.5 days; p = 0.0040). These results indicate that IGC can be applied to numerous types of leukemia and can meaningfully alter cellular phenotypes at scale. Because our method targets single-base mutations, rather than larger variants targeted by IGC in prior studies, it greatly expands the pool of risk-increasing genetic lesions which could potentially be targeted by IGC. This technique may reduce cost and complexity for experiments modeling phenotypic consequences of SNVs. The principles of SNV-specific IGC demonstrated in this proof-of-concept study could be applied to investigate the phenotypic effects of targeted clonal reduction of leukemogenic SNV driver mutations.
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Monteith AJ, Ramsey HE, Silver AJ, Brown D, Greenwood D, Smith BN, Wise AD, Liu J, Olmstead SD, Watke J, Arrate MP, Gorska AE, Fuller L, Locasale JW, Stubbs MC, Rathmell JC, Savona MR. Lactate Utilization Enables Metabolic Escape to Confer Resistance to BET Inhibition in Acute Myeloid Leukemia. Cancer Res 2024; 84:1101-1114. [PMID: 38285895 PMCID: PMC10984779 DOI: 10.1158/0008-5472.can-23-0291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/08/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Impairing the BET family coactivator BRD4 with small-molecule inhibitors (BETi) showed encouraging preclinical activity in treating acute myeloid leukemia (AML). However, dose-limiting toxicities and limited clinical activity dampened the enthusiasm for BETi as a single agent. BETi resistance in AML myeloblasts was found to correlate with maintaining mitochondrial respiration, suggesting that identifying the metabolic pathway sustaining mitochondrial integrity could help develop approaches to improve BETi efficacy. Herein, we demonstrated that mitochondria-associated lactate dehydrogenase allows AML myeloblasts to utilize lactate as a metabolic bypass to fuel mitochondrial respiration and maintain cellular viability. Pharmacologically and genetically impairing lactate utilization rendered resistant myeloblasts susceptible to BET inhibition. Low-dose combinations of BETi and oxamate, a lactate dehydrogenase inhibitor, reduced in vivo expansion of BETi-resistant AML in cell line and patient-derived murine models. These results elucidate how AML myeloblasts metabolically adapt to BETi by consuming lactate and demonstrate that combining BETi with inhibitors of lactate utilization may be useful in AML treatment. SIGNIFICANCE Lactate utilization allows AML myeloblasts to maintain metabolic integrity and circumvent antileukemic therapy, which supports testing of lactate utilization inhibitors in clinical settings to overcome BET inhibitor resistance in AML. See related commentary by Boët and Sarry, p. 950.
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Affiliation(s)
- Andrew J. Monteith
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Haley E. Ramsey
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander J. Silver
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Donovan Brown
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dalton Greenwood
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brianna N. Smith
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ashley D. Wise
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Sarah D. Olmstead
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jackson Watke
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Maria P. Arrate
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Agnieszka E. Gorska
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Londa Fuller
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | | | - Jeffrey C. Rathmell
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael R. Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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