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Vujovic A, de Rooij L, Chahi AK, Chen HT, Yee BA, Loganathan SK, Liu L, Chan DC, Tajik A, Tsao E, Moreira S, Joshi P, Xu J, Wong N, Balde Z, Jahangiri S, Zandi S, Aigner S, Dick JE, Minden MD, Schramek D, Yeo GW, Hope KJ. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. Blood Cancer Discov 2023; 4:180-207. [PMID: 36763002 PMCID: PMC10150294 DOI: 10.1158/2643-3230.bcd-22-0086] [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: 05/17/2022] [Revised: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) selectively enriched in human AML LSCs. Using an in vivo two-step CRISPR-Cas9 screen to assay stem cell functionality, we found 32 RBPs essential for LSCs in MLL-AF9;NrasG12D AML. Loss-of-function approaches targeting key hit RBP ELAVL1 compromised LSC-driven in vivo leukemic reconstitution, and selectively depleted primitive malignant versus healthy cells. Integrative multiomics revealed differentiation, splicing, and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with mitochondrial import protein, TOMM34, being a direct ELAVL1-stabilized target whose repression impairs AML propagation. Altogether, using a stem cell-adapted in vivo CRISPR screen, this work demonstrates pervasive reliance on RBPs as regulators of LSCs and highlights their potential as therapeutic targets in AML. SIGNIFICANCE LSC-targeted therapies remain a significant unmet need in AML. We developed a stem-cell-adapted in vivo CRISPR screen to identify key LSC drivers. We uncover widespread RNA-binding protein dependencies in LSCs, including ELAVL1, which we identify as a novel therapeutic vulnerability through its regulation of mitochondrial metabolism. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Ana Vujovic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Laura de Rooij
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ava Keyvani Chahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - He Tian Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Lina Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Derek C.H. Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Amanda Tajik
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Emily Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Steven Moreira
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Pratik Joshi
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Nicholas Wong
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Soheil Jahangiri
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sasan Zandi
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - John E. Dick
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D. Minden
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Kristin J. Hope
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
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Kanwar N, Balde Z, Nair R, Dawe M, Chen S, Maganti M, Atenafu EG, Manolescu S, Wei C, Mao A, Fu F, Wang D, Cheung A, Yerofeyeva Y, Peters R, Liu K, Desmedt C, Sotiriou C, Szekely B, Kulka J, McKee TD, Hirano N, Bartlett JM, Yaffe MJ, Bedard PL, McCready D, Done SJ. Heterogeneity of Circulating Tumor Cell-Associated Genomic Gains in Breast Cancer and Its Association with the Host Immune Response. Cancer Res 2021; 81:6196-6206. [PMID: 34711609 PMCID: PMC9397625 DOI: 10.1158/0008-5472.can-21-1079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 10/25/2021] [Indexed: 01/07/2023]
Abstract
Tumor cells that preferentially enter circulation include the precursors of metastatic cancer. Previously, we characterized circulating tumor cells (CTC) from patients with breast cancer and identified a signature of genomic regions with recurrent copy-number gains. Through FISH, we now show that these CTC-associated regions are detected within the matched untreated primary tumors of these patients (21% to 69%, median 55.5%, n = 19). Furthermore, they are more prevalent in the metastases of patients who died from breast cancer after multiple rounds of treatment (70% to 100%, median 93%, samples n = 41). Diversity indices revealed that higher spatial heterogeneity for these regions within primary tumors is associated with increased dissemination and metastasis. An identified subclone with multiple regions gained (MRG clone) was enriched in a posttreatment primary breast carcinoma as well as multiple metastatic tumors and local breast recurrences obtained at autopsy, indicative of a distinct early subclone with the capability to resist multiple lines of treatment and eventually cause death. In addition, multiplex immunofluorescence revealed that tumor heterogeneity is significantly associated with the degree of infiltration of B lymphocytes in triple-negative breast cancer, a subtype with a large immune component. Collectively, these data reveal the functional potential of genetic subclones that comprise heterogeneous primary breast carcinomas and are selected for in CTCs and posttreatment breast cancer metastases. In addition, they uncover a relationship between tumor heterogeneity and host immune response in the tumor microenvironment. SIGNIFICANCE: As breast cancers progress, they become more heterogeneous for multiple regions amplified in circulating tumor cells, and intratumoral spatial heterogeneity is associated with the immune landscape.
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Affiliation(s)
- Nisha Kanwar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ranju Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Melanie Dawe
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shiyi Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Manjula Maganti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Eshetu G. Atenafu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sabrina Manolescu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Carrie Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Amanda Mao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Fred Fu
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | - Dan Wang
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Alison Cheung
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Yulia Yerofeyeva
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Rachel Peters
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Kela Liu
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Christos Sotiriou
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Borbala Szekely
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Janina Kulka
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Trevor D. McKee
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Immunology, University of Toronto, Toronto, Canada
| | - John M.S. Bartlett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - Martin J. Yaffe
- Biomarker Imaging Research Laboratory, Sunnybrook Research Institute, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - Philippe L. Bedard
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - David McCready
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Susan J. Done
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Canada.,Corresponding Author: Susan J. Done, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada. Phone: 416-340-4800, ext. 5573; E-mail:
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