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Kong GL, Nguyen TT, Rosales WK, Panikar AD, Cheney JHW, Lusardi TA, Yashar WM, Curtiss BM, Carratt SA, Braun TP, Maxson JE. CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny. BMC Bioinformatics 2024; 25:142. [PMID: 38566005 PMCID: PMC10988918 DOI: 10.1186/s12859-024-05762-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called "gating", and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data. RESULTS We applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations. CONCLUSIONS CITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.
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Affiliation(s)
- Garth L Kong
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA
| | - Thai T Nguyen
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA
| | - Wesley K Rosales
- Earle A. Chiles Research Institute, Providence, Portland, OR, 97213, USA
| | - Anjali D Panikar
- Knight Campus Graduate Internship Program - Bioinformatics, University of Oregon, Eugene, OR, 97403, USA
| | - John H W Cheney
- Knight Campus Graduate Internship Program - Bioinformatics, University of Oregon, Eugene, OR, 97403, USA
| | - Theresa A Lusardi
- Cancer Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, 97238, USA
| | - William M Yashar
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, USA
| | - Brittany M Curtiss
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA
| | - Sarah A Carratt
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA
| | - Theodore P Braun
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
- Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, USA.
| | - Julia E Maxson
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
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2
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Yashar WM, Curtiss BM, Coleman DJ, VanCampen J, Kong G, Macaraeg J, Estabrook J, Demir E, Long N, Bottomly D, McWeeney SK, Tyner JW, Druker BJ, Maxson JE, Braun TP. Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia. Mol Cancer Res 2023; 21:631-647. [PMID: 36976323 PMCID: PMC10330306 DOI: 10.1158/1541-7786.mcr-22-0745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Mutations in Fms-like tyrosine kinase 3 (FLT3) are common drivers in acute myeloid leukemia (AML) yet FLT3 inhibitors only provide modest clinical benefit. Prior work has shown that inhibitors of lysine-specific demethylase 1 (LSD1) enhance kinase inhibitor activity in AML. Here we show that combined LSD1 and FLT3 inhibition induces synergistic cell death in FLT3-mutant AML. Multi-omic profiling revealed that the drug combination disrupts STAT5, LSD1, and GFI1 binding at the MYC blood superenhancer, suppressing superenhancer accessibility as well as MYC expression and activity. The drug combination simultaneously results in the accumulation of repressive H3K9me1 methylation, an LSD1 substrate, at MYC target genes. We validated these findings in 72 primary AML samples with the nearly every sample demonstrating synergistic responses to the drug combination. Collectively, these studies reveal how epigenetic therapies augment the activity of kinase inhibitors in FLT3-ITD (internal tandem duplication) AML. IMPLICATIONS This work establishes the synergistic efficacy of combined FLT3 and LSD1 inhibition in FLT3-ITD AML by disrupting STAT5 and GFI1 binding at the MYC blood-specific superenhancer complex.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University; Portland, OR, 97239, USA
- These authors contributed equally to this work
| | - Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- These authors contributed equally to this work
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jake VanCampen
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Garth Kong
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Emek Demir
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd; Portland, OR 97239, USA
- Pacific Northwest National Laboratories; Richland, WA 99354, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Daniel Bottomly
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Shannon K. McWeeney
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Jeffrey W. Tyner
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University; Portland, OR, 97239, USA
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3
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Braun TP, Estabrook J, Schonrock Z, Curtiss BM, Darmusey L, Macaraeg J, Enright T, Coblentz C, Callahan R, Yashar W, Taherinasab A, Mohammed H, Coleman DJ, Druker BJ, Demir E, Lusardi TA, Maxson JE. Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors. Leukemia 2023; 37:478-487. [PMID: 36526735 PMCID: PMC9899319 DOI: 10.1038/s41375-022-01792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. However, the role of ASXL1 in myeloid lineage maturation is incompletely described. To define the role of ASXL1 in myelopoiesis, we employed single cell RNA sequencing and a murine model of hematopoietic-specific Asxl1 deletion. In granulocyte progenitors, Asxl1 deletion leads to hyperactivation of MYC and a quantitative decrease in neutrophil production. This loss of granulocyte production was not accompanied by significant changes in the landscape of covalent histone modifications. However, Asxl1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator in myeloid development.
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Affiliation(s)
- Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Lucie Darmusey
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Trevor Enright
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Rowan Callahan
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - William Yashar
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Akram Taherinasab
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
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4
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Carratt SA, Braun TP, Coblentz C, Schonrock Z, Callahan R, Curtiss BM, Maloney L, Foley AC, Maxson JE. Correction to: Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia. Leukemia 2022:10.1038/s41375-022-01710-1. [PMID: 36195644 DOI: 10.1038/s41375-022-01710-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Cody Coblentz
- Oregon Health & Science University, Portland, OR, USA
| | | | | | | | | | - Amy C Foley
- Oregon Health & Science University, Portland, OR, USA
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5
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Carratt SA, Kong GL, Curtiss BM, Schonrock Z, Maloney L, Maniaci BN, Blaylock HZ, Baris A, Druker BJ, Braun TP, Maxson JE. Mutated SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood 2022; 140:644-658. [PMID: 35482940 PMCID: PMC9373012 DOI: 10.1182/blood.2021014777] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 11/24/2021] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
Colony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of patients with CNL also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutated leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutated hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs, most strongly upregulating Myc and Myc target genes. This upregulation of Myc can be reversed by LSD1 inhibitors. In summary, we found that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutated CSF3R through the upregulation of Myc-associated gene expression programs.
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Affiliation(s)
- Sarah A Carratt
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Garth L Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brittany M Curtiss
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Lauren Maloney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Breanna N Maniaci
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Hunter Z Blaylock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Adrian Baris
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Theodore P Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
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6
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Carratt SA, Braun TP, Coblentz C, Schonrock Z, Callahan R, Curtiss BM, Maloney L, Foley AC, Maxson JE. Correction: Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia. Leukemia 2022; 36:2149. [PMID: 35794242 DOI: 10.1038/s41375-022-01646-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Cody Coblentz
- Oregon Health & Science University, Portland, OR, USA
| | | | | | | | | | - Amy C Foley
- Oregon Health & Science University, Portland, OR, USA
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7
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Yashar WM, Kong G, VanCampen J, Curtiss BM, Coleman DJ, Carbone L, Yardimci GG, Maxson JE, Braun TP. GoPeaks: histone modification peak calling for CUT&Tag. Genome Biol 2022; 23:144. [PMID: 35788238 PMCID: PMC9252088 DOI: 10.1186/s13059-022-02707-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/15/2022] [Indexed: 12/27/2022] Open
Abstract
Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms.
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Affiliation(s)
- William M. Yashar
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Garth Kong
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Jake VanCampen
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Brittany M. Curtiss
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Daniel J. Coleman
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Lucia Carbone
- grid.5288.70000 0000 9758 5690Knight Cardiovascular Institute, Oregon Health & Science University, Portland, USA
| | - Galip Gürkan Yardimci
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA ,grid.5288.70000 0000 9758 5690Center for Early Cancer Detection, Oregon Health & Science University, Portland, USA
| | - Julia E. Maxson
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA ,grid.5288.70000 0000 9758 5690Division of Oncologic Sciences, Oregon Health & Science University, Portland, USA
| | - Theodore P. Braun
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, USA ,grid.5288.70000 0000 9758 5690Division of Oncologic Sciences, Oregon Health & Science University, Portland, USA ,grid.5288.70000 0000 9758 5690Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, USA
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8
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Curtiss BM, VanCampen J, Macaraeg J, Kong GL, Taherinasab A, Tsuchiya M, Yashar WM, Tsang YH, Horton W, Coleman DJ, Estabrook J, Lusardi TA, Mills GB, Druker BJ, Maxson JE, Braun TP. PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia. Leukemia 2022; 36:1781-1793. [PMID: 35590033 PMCID: PMC9256806 DOI: 10.1038/s41375-022-01594-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 01/03/2023]
Abstract
Responses to kinase-inhibitor therapy in AML are frequently short-lived due to the rapid development of resistance, limiting the clinical efficacy. Combination therapy may improve initial therapeutic responses by targeting pathways used by leukemia cells to escape monotherapy. Here we report that combined inhibition of KIT and lysine-specific demethylase 1 (LSD1) produces synergistic cell death in KIT-mutant AML cell lines and primary patient samples. This drug combination evicts both MYC and PU.1 from chromatin driving cell cycle exit. Using a live cell biosensor for AKT activity, we identify early adaptive changes in kinase signaling following KIT inhibition that are reversed with the addition of LSD1 inhibitor via modulation of the GSK3a/b axis. Multi-omic analyses, including scRNA-seq, ATAC-seq and CUT&Tag, confirm these mechanisms in primary KIT-mutant AML. Collectively, this work provides rational for a clinical trial to assess the efficacy of KIT and LSD1 inhibition in patients with KIT-mutant AML.
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Affiliation(s)
- Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Jake VanCampen
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Garth L. Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Akram Taherinasab
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Mitsuhiro Tsuchiya
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Yiu H. Tsang
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Wesley Horton
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Theresa A. Lusardi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon, 97239, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Oncological Sciences, Oregon Health & Science University, Portland, Oregon, 97239, USA,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon, 97239, USA
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9
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Carratt SA, Braun TP, Coblentz C, Schonrock Z, Callahan R, Curtiss BM, Maloney L, Foley AC, Maxson JE. Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia. Leukemia 2021; 35:3594-3599. [PMID: 34002029 PMCID: PMC8595361 DOI: 10.1038/s41375-021-01278-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/12/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023]
Abstract
Mutations in SET-binding protein 1 (SETBP1) are associated with poor outcomes in myeloid leukemias. In the Ras-driven leukemia, juvenile myelomonocytic leukemia, SETBP1 mutations are enriched in relapsed disease. While some mechanisms for SETBP1-driven oncogenesis have been established, it remains unclear how SETBP1 specifically modulates the biology of Ras-driven leukemias. In this study, we found that when co-expressed with Ras pathway mutations, SETBP1 promoted oncogenic transformation of murine bone marrow in vitro and aggressive myeloid leukemia in vivo. We demonstrate that SETBP1 enhances the NRAS gene expression signature, driving upregulation of mitogen-activated protein kinase (MAPK) signaling and downregulation of differentiation pathways. SETBP1 also enhances NRAS-driven phosphorylation of MAPK proteins. Cells expressing NRAS and SETBP1 are sensitive to inhibitors of the MAPK pathway, and treatment with the MEK inhibitor trametinib conferred a survival benefit in a mouse model of NRAS/SETBP1-mutant disease. Our data demonstrate that despite driving enhanced MAPK signaling, SETBP1-mutant cells remain susceptible to trametinib in vitro and in vivo, providing encouraging preclinical data for the use of trametinib in SETBP1-mutant disease.
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Affiliation(s)
| | | | | | | | | | | | | | - Amy C. Foley
- Oregon Health & Science University, Portland, OR
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10
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Braun TP, Okhovat M, Coblentz C, Carratt SA, Foley A, Schonrock Z, Curtiss BM, Nevonen K, Davis B, Garcia B, LaTocha D, Weeder BR, Grzadkowski MR, Estabrook JC, Manning HG, Watanabe-Smith K, Jeng S, Smith JL, Leonti AR, Ries RE, McWeeney S, Di Genua C, Drissen R, Nerlov C, Meshinchi S, Carbone L, Druker BJ, Maxson JE. Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nat Commun 2019; 10:5455. [PMID: 31784538 PMCID: PMC6884457 DOI: 10.1038/s41467-019-13364-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022] Open
Abstract
Acute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. The interaction between these distinct classes of mutations occurs at the level of myeloid lineage enhancers where mutant CEBPA prevents activation of a subset of differentiation associated enhancers. To confirm this enhancer-dependent mechanism, we demonstrate that CEBPA mutations must occur as the initial event in AML initiation. This improved mechanistic understanding will facilitate therapeutic development targeting the intersection of oncogene cooperativity.
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Affiliation(s)
- Theodore P. Braun
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Mariam Okhovat
- 0000 0000 9758 5690grid.5288.7Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239 USA
| | - Cody Coblentz
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Sarah A. Carratt
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Amy Foley
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Zachary Schonrock
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Brittany M. Curtiss
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Kimberly Nevonen
- 0000 0000 9758 5690grid.5288.7Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239 USA
| | - Brett Davis
- 0000 0000 9758 5690grid.5288.7Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239 USA
| | - Brianna Garcia
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Dorian LaTocha
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Benjamin R. Weeder
- 0000 0000 9758 5690grid.5288.7Program in Molecular and Cellular Biology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Michal R. Grzadkowski
- 0000 0000 9758 5690grid.5288.7Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Joey C. Estabrook
- 0000 0000 9758 5690grid.5288.7Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Hannah G. Manning
- 0000 0000 9758 5690grid.5288.7Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Kevin Watanabe-Smith
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Sophia Jeng
- 0000 0000 9758 5690grid.5288.7Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jenny L. Smith
- 0000 0001 2180 1622grid.270240.3Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
| | - Amanda R. Leonti
- 0000 0001 2180 1622grid.270240.3Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
| | - Rhonda E. Ries
- 0000 0001 2180 1622grid.270240.3Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
| | - Shannon McWeeney
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Cristina Di Genua
- 0000 0001 2306 7492grid.8348.7MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS UK
| | - Roy Drissen
- 0000 0001 2306 7492grid.8348.7MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS UK
| | - Claus Nerlov
- 0000 0001 2306 7492grid.8348.7MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS UK
| | - Soheil Meshinchi
- 0000 0001 2180 1622grid.270240.3Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA ,0000000122986657grid.34477.33Division of Pediatric Hematology/Oncology, University of Washington, Seattle, WA 98195 USA
| | - Lucia Carbone
- 0000 0000 9758 5690grid.5288.7Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Brian J. Druker
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Portland, OR USA
| | - Julia E. Maxson
- 0000 0000 9758 5690grid.5288.7Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR 97239 USA
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