1
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Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu AC, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D’Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM. Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state. Res Sq 2024:rs.3.rs-3874821. [PMID: 38405837 PMCID: PMC10889081 DOI: 10.21203/rs.3.rs-3874821/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Clonal hematopoiesis (CH) arises when a hematopoietic stem cell (HSC) acquires a mutation that confers a competitive advantage over wild-type (WT) HSCs, resulting in its clonal expansion. Individuals with CH are at an increased risk of developing hematologic neoplasms and a range of age-related inflammatory illnesses1-3. Therapeutic interventions that suppress the expansion of mutant HSCs have the potential to prevent these CH-related illnesses; however, such interventions have not yet been identified. The most common CH driver mutations are in the DNA methyltransferase 3 alpha (DNMT3A) gene with arginine 882 (R882) being a mutation hotspot. Here we show that murine hematopoietic stem and progenitor cells (HSPCs) carrying the Dnmt3aR878H/+ mutation, which is equivalent to human DNMT3AR882H/+, have increased mitochondrial respiration compared with WT cells and are dependent on this metabolic reprogramming for their competitive advantage. Importantly, treatment with metformin, an oral anti-diabetic drug with inhibitory activity against complex I in the electron transport chain (ETC), reduced the fitness of Dnmt3aR878H/+ HSCs. Through a multi-omics approach, we discovered that metformin acts by enhancing the methylation potential in Dnmt3aR878H/+ HSPCs and reversing their aberrant DNA CpG methylation and histone H3K27 trimethylation (H3K27me3) profiles. Metformin also reduced the fitness of human DNMT3AR882H HSPCs generated by prime editing. Our findings provide preclinical rationale for investigating metformin as a preventive intervention against illnesses associated with DNMT3AR882 mutation-driven CH in humans.
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Affiliation(s)
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Ali Chegini
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Angelica Varesi
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Alex C.H. Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Yitong Yang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Vivian Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Abdula Maher
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Eric Grignano
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kira Young
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Yiyan Wu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Federico Gaiti
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shraddha Pai
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - John E. Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Steven M. Chan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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2
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Zeng AGX, Iacobucci I, Shah S, Mitchell A, Wong G, Bansal S, Gao Q, Kim H, Kennedy JA, Minden MD, Haferlach T, Mullighan CG, Dick JE. Precise single-cell transcriptomic mapping of normal and leukemic cell states reveals unconventional lineage priming in acute myeloid leukemia. bioRxiv 2023:2023.12.26.573390. [PMID: 38234771 PMCID: PMC10793439 DOI: 10.1101/2023.12.26.573390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic features. Yet, these traditional classification approaches lack precision, especially at the level of immature blasts. Single-cell RNA-sequencing (scRNA-seq) enables precise determination of cell state using thousands of markers, thus providing an opportunity to re-examine present-day classification schemes of acute leukemia. Here, we developed a detailed reference map of human bone marrow hematopoiesis from 263,519 single-cell transcriptomes spanning 55 cellular states. Cell state annotations were benchmarked against purified cell populations, and in-depth characterization of gene expression programs underlying hematopoietic differentiation was undertaken. Projection of single-cell transcriptomes from 175 samples spanning acute myeloid leukemia (AML), mixed phenotype acute leukemia (MPAL), and acute erythroid leukemia (AEL) revealed 11 subtypes involving distinct stages of hematopoietic differentiation. These included AML subtypes with notable lymphoid or erythroid lineage priming, challenging traditional diagnostic boundaries between AML, MPAL, and AEL. Quantification of lineage priming in bulk patient cohorts revealed specific genetic alterations associated with this unconventional lineage priming. Integration of transcriptional and genetic information at the single-cell level revealed how genetic subclones can induce lineage restriction, differentiation blocks, or expansion of mature myeloid cells. Furthermore, we demonstrate that distinct cellular hierarchies can co-exist within individual patients, providing insight into AML evolution in response to varying selection pressures. Together, precise mapping of hematopoietic cell states can serve as a foundation for refining disease classification in acute leukemia and understanding response or resistance to emerging therapies.
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Affiliation(s)
- Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Ilaria Iacobucci
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Gordon Wong
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Suraj Bansal
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Qingsong Gao
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hyerin Kim
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - James A Kennedy
- Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | | | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
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3
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Iacobucci I, Zeng AGX, Gao Q, Garcia-Prat L, Baviskar P, Shah S, Murison A, Voisin V, Chan-Seng-Yue M, Cheng C, Qu C, Bailey C, Lear M, Witkowski MT, Zhou X, Peraza AZ, Gangwani K, Advani AS, Luger SM, Litzow MR, Rowe JM, Paietta EM, Stock W, Dick JE, Mullighan CG. SINGLE CELL DISSECTION OF DEVELOPMENTAL ORIGINS AND TRANSCRIPTIONAL HETEROGENEITY IN B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA. bioRxiv 2023:2023.12.04.569954. [PMID: 38106088 PMCID: PMC10723356 DOI: 10.1101/2023.12.04.569954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations. However, ZNF384- r and DUX4- r B-ALL showed composition enrichment of hematopoietic stem cells, BCR::ABL1 and KMT2A -r ALL of Early Lymphoid progenitors, MEF2D -r and TCF3::PBX1 of Pre-B cells. Enrichment of Early Lymphoid progenitors correlated with high-risk clinical features. Understanding variation in transcriptional programs and developmental states of B-ALL by scRNA-seq refines existing clinical and genomic classifications and improves prediction of treatment outcome.
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4
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O'Brien C, Ling T, Berman JM, Culp-Hill R, Reisz JA, Rondeau V, Jahangiri S, St-Germain J, Macwan V, Astori A, Zeng A, Hong JY, Li M, Yang M, Jana S, Gamboni F, Tsao E, Liu W, Dick JE, Lin H, Melnick A, Tikhonova A, Arruda A, Minden MD, Raught B, D'Alessandro A, Jones CL. Simultaneous inhibition of Sirtuin 3 and cholesterol homeostasis targets acute myeloid leukemia stem cells by perturbing fatty acid β-oxidation and inducing lipotoxicity. Haematologica 2023; 108:2343-2357. [PMID: 37021547 PMCID: PMC10483359 DOI: 10.3324/haematol.2022.281894] [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: 08/05/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Outcomes for patients with acute myeloid leukemia (AML) remain poor due to the inability of current therapeutic regimens to fully eradicate disease-initiating leukemia stem cells (LSC). Previous studies have demonstrated that oxidative phosphorylation (OXPHOS) is an essential process that is targetable in LSC. Sirtuin 3 (SIRT3), a mitochondrial deacetylase with a multi-faceted role in metabolic regulation, has been shown to regulate OXPHOS in cancer models; however, it has not yet been studied in the context of LSC. Thus, we sought to identify if SIRT3 is important for LSC function. Using RNAi and a SIRT3 inhibitor (YC8-02), we demonstrate that SIRT3 is a critical target for the survival of primary human LSC but is not essential for normal human hematopoietic stem and progenitor cell function. In order to elucidate the molecular mechanisms by which SIRT3 is essential in LSC we combined transcriptomic, proteomic, and lipidomic approaches, showing that SIRT3 is important for LSC function through the regulation of fatty acid oxidation (FAO) which is required to support OXPHOS and ATP production in human LSC. Further, we discovered two approaches to further sensitize LSC to SIRT3 inhibition. First, we found that LSC tolerate the toxic effects of fatty acid accumulation induced by SIRT3 inhibition by upregulating cholesterol esterification. Disruption of cholesterol homeostasis sensitizes LSC to YC8-02 and potentiates LSC death. Second, SIRT3 inhibition sensitizes LSC to the BCL-2 inhibitor venetoclax. Together, these findings establish SIRT3 as a regulator of lipid metabolism and potential therapeutic target in primitive AML cells.
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Affiliation(s)
- Cristiana O'Brien
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tianyi Ling
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jacob M Berman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Rachel Culp-Hill
- Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julie A Reisz
- Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Vincent Rondeau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Soheil Jahangiri
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Vinitha Macwan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Andy Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jun Young Hong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Meng Li
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Min Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sadhan Jana
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Fabia Gamboni
- Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Weiyi Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Anastasia Tikhonova
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Andrea Arruda
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Angelo D'Alessandro
- Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Courtney L Jones
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
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5
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Kim JC, Chan-Seng-Yue M, Ge S, Zeng AGX, Ng K, Gan OI, Garcia-Prat L, Flores-Figueroa E, Woo T, Zhang AXW, Arruda A, Chithambaram S, Dobson SM, Khoo A, Khan S, Ibrahimova N, George A, Tierens A, Hitzler J, Kislinger T, Dick JE, McPherson JD, Minden MD, Notta F. Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia. Nat Genet 2023:10.1038/s41588-023-01429-4. [PMID: 37337105 DOI: 10.1038/s41588-023-01429-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
In BCR-ABL1 lymphoblastic leukemia, treatment heterogeneity to tyrosine kinase inhibitors (TKIs), especially in the absence of kinase domain mutations in BCR-ABL1, is poorly understood. Through deep molecular profiling, we uncovered three transcriptomic subtypes of BCR-ABL1 lymphoblastic leukemia, each representing a maturation arrest at a stage of B-cell progenitor differentiation. An earlier arrest was associated with lineage promiscuity, treatment refractoriness and poor patient outcomes. A later arrest was associated with lineage fidelity, durable leukemia remissions and improved patient outcomes. Each maturation arrest was marked by specific genomic events that control different transition points in B-cell development. Interestingly, these events were absent in BCR-ABL1+ preleukemic stem cells isolated from patients regardless of subtype, which supports that transcriptomic phenotypes are determined downstream of the leukemia-initialing event. Overall, our data indicate that treatment response and TKI efficacy are unexpected outcomes of the differentiation stage at which this leukemia transforms.
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Affiliation(s)
- Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sabrina Ge
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Tristan Woo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Shivapriya Chithambaram
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Amanda Khoo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Ann George
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Anne Tierens
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Johann Hitzler
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John D McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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6
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Kan WL, Dhagat U, Kaufmann KB, Hercus TR, Nero TL, Zeng AG, Toubia J, Barry EF, Broughton SE, Gomez GA, Benard BA, Dottore M, Cheung Tung Shing KS, Boutzen H, Samaraweera SE, Simpson KJ, Jin L, Goodall GJ, Begley CG, Thomas D, Ekert PG, Tvorogov D, D'Andrea RJ, Dick JE, Parker MW, Lopez AF. Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia. Cancer Discov 2023:726397. [PMID: 37191437 PMCID: PMC10401075 DOI: 10.1158/2159-8290.cd-22-1396] [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: 12/13/2022] [Revised: 04/06/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
Leukemia stem cells (LSC) possess distinct self-renewal and arrested differentiation properties that are responsible for disease emergence, therapy failure and recurrence in acute myeloid leukemia (AML). Despite AML displaying extensive biological and clinical heterogeneity, LSC with high interleukin-3 receptor (IL-3R) levels are a constant yet puzzling feature as this receptor lacks tyrosine kinase activity. Here we show that the heterodimeric IL3Ra/Bc receptor assembles into hexamers and dodecamers through a unique interface in the 3D structure, where high IL3Ra/Bc ratios bias hexamer formation. Importantly, receptor stoichiometry is clinically relevant as it varies across the individual cells in the AML hierarchy, where high IL3Ra/Bc ratios in LSCs drive hexamer-mediated stemness programs and poor patient survival, whilst low ratios mediate differentiation. Our study establishes a new paradigm where alternative cytokine receptor stoichiometries differentially regulate cell fate; a signaling mechanism that may be generalizable to other transformed cellular hierarchies and of potential therapeutic significance.
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Affiliation(s)
- Winnie L Kan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Urmi Dhagat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Timothy R Hercus
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Tracy L Nero
- University of Melbourne, Parkville, Victoria, Australia
| | - Andy Gx Zeng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - John Toubia
- University of South Australia, Adelaide, SA, Australia
| | - Emma F Barry
- University of South Australia, Adelaide, South Australia, Australia
| | - Sophie E Broughton
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | | | - Mara Dottore
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | | | | | | | | | - Liqing Jin
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - C Glenn Begley
- Begley Biotech Consulting Pty Ltd, Wallington, Victoria, Australia
| | - Daniel Thomas
- University of Adelaide, Adelaide, South Australia, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Randwick, NSW, Australia
| | - Denis Tvorogov
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | | | - John E Dick
- University Health Network, Toronto, Ontario, Canada
| | - Michael W Parker
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
| | - Angel F Lopez
- Centre for Cancer Biology, Adelaide, South Austrazlia, Australia
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7
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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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8
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Itkin T, Houghton S, Schreiner R, Lin Y, Badwe CR, Voisin V, Murison A, Seyedhassantehrani N, Kaufmann KB, Garcia-Prat L, Booth GT, Geng F, Liu Y, Gomez-Salinero JM, Shieh JH, Redmond D, Xiang JZ, Josefowicz SZ, Trapnell C, Spencer JA, Zangi L, Hadland B, Dick JE, Xie SZ, Rafii S. Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing. bioRxiv 2023:2023.03.27.534417. [PMID: 37034724 PMCID: PMC10081204 DOI: 10.1101/2023.03.27.534417] [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: 06/19/2023]
Abstract
Transition between activation and quiescence programs in hematopoietic stem and progenitor cells (HSC/HSPCs) is perceived to be governed intrinsically and by microenvironmental co-adaptation. However, HSC programs dictating both transition and adaptability, remain poorly defined. Single cell multiome analysis divulging differential transcriptional activity between distinct HSPC states, indicated for the exclusive absence of Fli-1 motif from quiescent HSCs. We reveal that Fli-1 activity is essential for HSCs during regenerative hematopoiesis. Fli-1 directs activation programs while manipulating cellular sensory and output machineries, enabling HSPCs co-adoptability with a stimulated vascular niche. During regenerative conditions, Fli-1 presets and enables propagation of niche-derived Notch1 signaling. Constitutively induced Notch1 signaling is sufficient to recuperate functional HSC impairments in the absence of Fli-1. Applying FLI-1 modified-mRNA transduction into lethargic adult human mobilized HSPCs, enables their vigorous niche-mediated expansion along with superior engraftment capacities. Thus, decryption of stem cell activation programs offers valuable insights for immune regenerative medicine.
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9
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Boila LD, Ghosh S, Bandyopadhyay SK, Jin L, Murison A, Zeng AGX, Shaikh W, Bhowmik S, Muddineni SSNA, Biswas M, Sinha S, Chatterjee SS, Mbong N, Gan OI, Bose A, Chakraborty S, Arruda A, Kennedy JA, Mitchell A, Lechman ER, Banerjee D, Milyavsky M, Minden MD, Dick JE, Sengupta A. KDM6 demethylases integrate DNA repair gene regulation and loss of KDM6A sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition. Leukemia 2023; 37:751-764. [PMID: 36720973 DOI: 10.1038/s41375-023-01833-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/01/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous, aggressive malignancy with dismal prognosis and with limited availability of targeted therapies. Epigenetic deregulation contributes to AML pathogenesis. KDM6 proteins are histone-3-lysine-27-demethylases that play context-dependent roles in AML. We inform that KDM6-demethylase function critically regulates DNA-damage-repair-(DDR) gene expression in AML. Mechanistically, KDM6 expression is regulated by genotoxic stress, with deficiency of KDM6A-(UTX) and KDM6B-(JMJD3) impairing DDR transcriptional activation and compromising repair potential. Acquired KDM6A loss-of-function mutations are implicated in chemoresistance, although a significant percentage of relapsed-AML has upregulated KDM6A. Olaparib treatment reduced engraftment of KDM6A-mutant-AML-patient-derived xenografts, highlighting synthetic lethality using Poly-(ADP-ribose)-polymerase-(PARP)-inhibition. Crucially, a higher KDM6A expression is correlated with venetoclax tolerance. Loss of KDM6A increased mitochondrial activity, BCL2 expression, and sensitized AML cells to venetoclax. Additionally, BCL2A1 associates with venetoclax resistance, and KDM6A loss was accompanied with a downregulated BCL2A1. Corroborating these results, dual targeting of PARP and BCL2 was superior to PARP or BCL2 inhibitor monotherapy in inducing AML apoptosis, and primary AML cells carrying KDM6A-domain mutations were even more sensitive to the combination. Together, our study illustrates a mechanistic rationale in support of a novel combination therapy for AML based on subtype-heterogeneity, and establishes KDM6A as a molecular regulator for determining therapeutic efficacy.
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Affiliation(s)
- Liberalis Debraj Boila
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Subhadeep Ghosh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Subham K Bandyopadhyay
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Wasim Shaikh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Satyaki Bhowmik
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | | | - Mayukh Biswas
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Irving Cancer Research Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sayantani Sinha
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shankha Subhra Chatterjee
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Anwesha Bose
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Sayan Chakraborty
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Debasis Banerjee
- Park Clinic, Gorky Terrace and Ramakrishna Mission Seva Pratisthan, Kolkata, 700017, West Bengal, India
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Amitava Sengupta
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India. .,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India. .,CSIR-IICB-Cancer Biology & Inflammatory Disorder Division, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India.
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10
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Lackraj T, Ben Barouch S, Medeiros JJF, Pedersen S, Danesh A, Bakhtiari M, Hong M, Tong K, Joynt J, Arruda A, Minden MD, Kuruvilla J, Bhella S, Kukreti V, Crump M, Prica A, Chen C, Deng Y, Xu W, Pugh TJ, Keating A, Dick JE, Abelson S, Kridel R. Clinical significance of clonal hematopoiesis in the setting of autologous stem cell transplantation for lymphoma. Am J Hematol 2022; 97:1538-1547. [PMID: 36087071 DOI: 10.1002/ajh.26726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/09/2022] [Accepted: 09/01/2022] [Indexed: 01/31/2023]
Abstract
Autologous stem cell transplantation (ASCT) remains a key therapeutic strategy for treating patients with relapsed or refractory non-Hodgkin and Hodgkin lymphoma. Clonal hematopoiesis (CH) has been proposed as a major contributor not only to the development of therapy-related myeloid neoplasms but also to inferior overall survival (OS) in patients who had undergone ASCT. Herein, we aimed to investigate the prognostic implications of CH after ASCT in a cohort of 420 lymphoma patients using ultra-deep, highly sensitive error-correction sequencing. CH was identified in the stem cell product samples of 181 patients (43.1%) and was most common in those with T-cell lymphoma (72.2%). The presence of CH was associated with a longer time to neutrophil and platelet recovery. Moreover, patients with evidence of CH had inferior 5-year OS from the time of first relapse (39.4% vs. 45.8%, p = .043) and from the time of ASCT (51.8% vs. 59.3%, p = .018). The adverse prognostic impact of CH was not due to therapy-related myeloid neoplasms, the incidence of which was low in our cohort (10-year cumulative incidence of 3.3% vs. 3.0% in those with and without CH, p = .445). In terms of specific-gene mutations, adverse OS was mostly associated with PPM1D mutations (hazard ratio (HR) 1.74, 95% confidence interval (CI) 1.13-2.67, p = .011). In summary, we found that CH is associated with an increased risk of non-lymphoma-related death after ASCT, which suggests that lymphoma survivors with CH may need intensified surveillance strategies to prevent and treat late complications.
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Affiliation(s)
- Tracy Lackraj
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sharon Ben Barouch
- Institute of Hematology, Assuta Ashdod Medical Center, Ashdod, Israel.,Faculty of Medicine, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mehran Bakhtiari
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Hong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kit Tong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jesse Joynt
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - John Kuruvilla
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sita Bhella
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vishal Kukreti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Crump
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anca Prica
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Christine Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yangqing Deng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Armand Keating
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sagi Abelson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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11
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Scolari FL, Brahmbhatt DH, Abelson S, Medeiros JJF, Anker MS, Fung NL, Otsuki M, Calvillo-Argüelles O, Lawler PR, Ross HJ, Luk AC, Anker S, Dick JE, Billia F. Clonal hematopoiesis confers an increased mortality risk in orthotopic heart transplant recipients. Am J Transplant 2022; 22:3078-3086. [PMID: 35971851 DOI: 10.1111/ajt.17172] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
Novel risk stratification and non-invasive surveillance methods are needed in orthotopic heart transplant (OHT) to reduce morbidity and mortality post-transplant. Clonal hematopoiesis (CH) refers to the acquisition of specific gene mutations in hematopoietic stem cells linked to enhanced inflammation and worse cardiovascular outcomes. The purpose of this study was to investigate the association between CH and OHT. Blood samples were collected from 127 OHT recipients. Error-corrected sequencing was used to detect CH-associated mutations. We evaluated the association between CH and acute cellular rejection, CMV infection, cardiac allograft vasculopathy (CAV), malignancies, and survival. CH mutations were detected in 26 (20.5%) patients, mostly in DNMT3A, ASXL1, and TET2. Patients with CH showed a higher frequency of CAV grade 2 or 3 (0% vs. 18%, p < .001). Moreover, a higher mortality rate was observed in patients with CH (11 [42%] vs. 15 [15%], p = .008) with an adjusted hazard ratio of 2.9 (95% CI, 1.4-6.3; p = .003). CH was not associated with acute cellular rejection, CMV infection or malignancies. The prevalence of CH in OHT recipients is higher than previously reported for the general population of the same age group, with an associated higher prevalence of CAV and mortality.
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Affiliation(s)
- Fernando L Scolari
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Darshan H Brahmbhatt
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,National Heart & Lung Institute, Imperial College London, London, UK
| | - Sagi Abelson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jessie J F Medeiros
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Markus S Anker
- Department of Cardiology and Berlin Institute of Health Center for Regenerative Therapies, German Center for Cardiovascular Research (DZHK) partner site Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nicole L Fung
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Madison Otsuki
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Oscar Calvillo-Argüelles
- Department of Cardiology, Department of Medical Oncology, Health Sciences North (HSN), Sudbury, Ontario, Canada.,Ted Rogers Program in Cardiotoxicity Prevention, Peter Munk Cardiac Centre, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada.,Division of Clinical Sciences, NOSM University, Sudbury, Ontario, Canada
| | - Patrick R Lawler
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Heather J Ross
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adriana C Luk
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stefan Anker
- Department of Cardiology and Berlin Institute of Health Center for Regenerative Therapies, German Center for Cardiovascular Research (DZHK) partner site Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Filio Billia
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada
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12
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Che JLC, Bode D, Kucinski I, Cull AH, Bain F, Becker HJ, Jassinskaja M, Barile M, Boyd G, Belmonte M, Zeng AGX, Igarashi KJ, Rubio‐Lara J, Shepherd MS, Clay A, Dick JE, Wilkinson AC, Nakauchi H, Yamazaki S, Göttgens B, Kent DG. Identification and characterization of in vitro expanded hematopoietic stem cells. EMBO Rep 2022; 23:e55502. [PMID: 35971894 PMCID: PMC9535767 DOI: 10.15252/embr.202255502] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved > 200-fold expansion of functional HSCs, but their molecular characterization has not been possible since the majority of cells are non-HSCs and single cell-initiated cultures have substantial clone-to-clone variability. Using the Fgd5 reporter mouse in combination with the EPCR surface marker, we report exclusive identification of HSCs from non-HSCs in expansion cultures. By directly linking single-clone functional transplantation data with single-clone gene expression profiling, we show that the molecular profile of expanded HSCs is similar to proliferating fetal HSCs and reveals a gene expression signature, including Esam, Prdm16, Fstl1, and Palld, that can identify functional HSCs from multiple cellular states. This "repopulation signature" (RepopSig) also enriches for HSCs in human datasets. Together, these findings demonstrate the power of integrating functional and molecular datasets to better derive meaningful gene signatures and opens the opportunity for a wide range of functional screening and molecular experiments previously not possible due to limited HSC numbers.
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Affiliation(s)
- James L C Che
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Daniel Bode
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Iwo Kucinski
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
| | - Alyssa H Cull
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Fiona Bain
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Hans J Becker
- Division of Stem Cell Biology, Distinguished Professor Unit, The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Institute for Stem Cell Biology and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
| | - Maria Jassinskaja
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Melania Barile
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
| | - Grace Boyd
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
| | - Andy G X Zeng
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Kyomi J Igarashi
- Department of GeneticsStanford University School of MedicineStanfordCAUSA
| | - Juan Rubio‐Lara
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Mairi S Shepherd
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
| | - Anna Clay
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - John E Dick
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Adam C Wilkinson
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Hiromitsu Nakauchi
- Division of Stem Cell Biology, Distinguished Professor Unit, The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Institute for Stem Cell Biology and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
- Department of GeneticsStanford University School of MedicineStanfordCAUSA
| | - Satoshi Yamazaki
- Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Laboratory of Stem Cell Therapy, Faculty of MedicineUniversity of TsukubaIbarakiJapan
| | - Berthold Göttgens
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
| | - David G Kent
- Wellcome MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of HaematologyUniversity of CambridgeCambridgeUK
- Department of Biology, York Biomedical Research InstituteUniversity of YorkYorkUK
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13
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Scolari FL, Abelson S, Brahmbhatt DH, Medeiros JJF, Fan CPS, Fung NL, Mihajlovic V, Anker MS, Otsuki M, Lawler PR, Ross HJ, Luk AC, Anker S, Dick JE, Billia F. Clonal haematopoiesis is associated with higher mortality in patients with cardiogenic shock. Eur J Heart Fail 2022; 24:1573-1582. [PMID: 35729851 DOI: 10.1002/ejhf.2588] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 06/19/2022] [Indexed: 11/05/2022] Open
Abstract
AIMS Cardiogenic shock (CS) with variable systemic inflammation may be responsible for the patient heterogeneity and the exceedingly high mortality rate. Cardiovascular events have been associated with clonal haematopoiesis (CH) where specific gene mutations in hematopoietic stem cells lead to clonal expansion and the development of inflammation. This study aims to assess the prevalence of CH and its association with survival in a population of CS patients in a quaternary center. METHODS We compared the frequency of CH mutations among 341 CS patients and 345 ambulatory heart failure (HF) matched for age, sex, ejection fraction, and HF aetiology. The association of CH with survival and levels of circulating inflammatory cytokines was analysed. RESULTS We detected 266 CH mutations in 149 of 686 (22%) patients. CS patients had a higher prevalence of CH-related mutations than HF patients (OR 1.5; 95% CI 1.0-2.1, P=0.02) and was associated with decreased survival (30-days: HR 2.7; 95% CI 1.3-5.7, P=0.006; 90-days: HR 2.2; 95% CI 1.3-3.9, P=0.003; and 3-years: HR 1.7; 95% CI 1.1-2.8, P=0.01). TET2 or ASXL1 mutations were associated with lower survival in CS patients at all-time points (P≤0.03). CS patients with TET2 mutations had higher circulating levels of SCD40L, IFNγ, IL-4, and TNFα (P≤0.04), while those with ASXL1 mutations had decreased levels of CCL7 (P=0.03). CONCLUSIONS CS patients have high frequency of CH, notably mutations in TET2 and ASXL1. This was associated with reduced survival and dysregulation of circulating inflammatory cytokines in those CS patients with CH. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fernando L Scolari
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada
| | - Sagi Abelson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Darshan H Brahmbhatt
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Jessie J F Medeiros
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Chun-Po S Fan
- Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nicole L Fung
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Vesna Mihajlovic
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Markus S Anker
- Department of Cardiology (CBF), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Madison Otsuki
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Patrick R Lawler
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Heather J Ross
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adriana C Luk
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Stefan Anker
- Department of Cardiology (CBF), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Filio Billia
- Ted Rogers Centre for Heart Research, Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada.,Division of Cardiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, Toronto, Ontario, Canada
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14
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Thomas GE, Egan G, García-Prat L, Botham A, Voisin V, Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, MacLean N, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, Bader GD, Hakem R, Kornblau S, Dick JE, Schimmer AD. The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness. Nat Cell Biol 2022; 24:872-884. [PMID: 35668135 PMCID: PMC9203277 DOI: 10.1038/s41556-022-00925-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 05/11/2021] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
Abstract
Mitochondrial metabolites regulate leukaemic and normal stem cells by affecting epigenetic marks. How mitochondrial enzymes localize to the nucleus to control stem cell function is less understood. We discovered that the mitochondrial metabolic enzyme hexokinase 2 (HK2) localizes to the nucleus in leukaemic and normal haematopoietic stem cells. Overexpression of nuclear HK2 increases leukaemic stem cell properties and decreases differentiation, whereas selective nuclear HK2 knockdown promotes differentiation and decreases stem cell function. Nuclear HK2 localization is phosphorylation-dependent, requires active import and export, and regulates differentiation independently of its enzymatic activity. HK2 interacts with nuclear proteins regulating chromatin openness, increasing chromatin accessibilities at leukaemic stem cell-positive signature and DNA-repair sites. Nuclear HK2 overexpression decreases double-strand breaks and confers chemoresistance, which may contribute to the mechanism by which leukaemic stem cells resist DNA-damaging agents. Thus, we describe a non-canonical mechanism by which mitochondrial enzymes influence stem cell function independently of their metabolic function. Thomas, Egan et al. report that hexokinase 2 localizes to the nucleus of leukaemic and normal haematopoietic cells to maintain stemness by interacting with nuclear proteins and modulating chromatin accessibility independently of its kinase activity.
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Affiliation(s)
- Geethu Emily Thomas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Laura García-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron Botham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Veronique Voisin
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fieke W Hoff
- Department of Pediatric Hematology/Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Jordan Chin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Boaz Nachmias
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dilshad H Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cristiana O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rashim P Singh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Courtney L Jones
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shane M Harding
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Razq Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Steve Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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15
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Zeng AGX, Bansal S, Jin L, Mitchell A, Chen WC, Abbas HA, Chan-Seng-Yue M, Voisin V, van Galen P, Tierens A, Cheok M, Preudhomme C, Dombret H, Daver N, Futreal PA, Minden MD, Kennedy JA, Wang JCY, Dick JE. A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia. Nat Med 2022; 28:1212-1223. [PMID: 35618837 DOI: 10.1038/s41591-022-01819-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising therapies entering clinical translation, yet patient responses remain heterogeneous, and biomarkers for tailoring treatment are lacking. To understand how disease heterogeneity links with therapy response, we determined the leukemia cell hierarchy makeup from bulk transcriptomes of more than 1,000 patients through deconvolution using single-cell reference profiles of leukemia stem, progenitor and mature cell types. Leukemia hierarchy composition was associated with functional, genomic and clinical properties and converged into four overall classes, spanning Primitive, Mature, GMP and Intermediate. Critically, variation in hierarchy composition along the Primitive versus GMP or Primitive versus Mature axes were associated with response to chemotherapy or drug sensitivity profiles of targeted therapies, respectively. A seven-gene biomarker derived from the Primitive versus Mature axis was associated with response to 105 investigational drugs. Cellular hierarchy composition constitutes a novel framework for understanding disease biology and advancing precision medicine in AML.
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Affiliation(s)
- Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Suraj Bansal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Weihsu Claire Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Biologics Discovery, Amgen British Columbia, Burnaby, BC, Canada
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Anne Tierens
- Laboratory Medicine Program, Hematopathology, University Health Network, Toronto, ON, Canada
| | - Meyling Cheok
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | - Claude Preudhomme
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | - Hervé Dombret
- Department of Hematology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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16
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Wintersinger JA, Dobson SM, Kulman E, Stein LD, Dick JE, Morris Q. Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree. Blood Cancer Discov 2022; 3:208-219. [PMID: 35247876 PMCID: PMC9780082 DOI: 10.1158/2643-3230.bcd-21-0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/03/2021] [Revised: 11/23/2021] [Accepted: 02/28/2022] [Indexed: 01/25/2023] Open
Abstract
Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions. SIGNIFICANCE Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible. See related commentary by Miller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Jeff A. Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Stephanie M. Dobson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ethan Kulman
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John E. Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Quaid Morris
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Memorial Sloan Kettering Cancer Center, New York, New York.,Corresponding Author: Quaid Morris, Sloan Kettering Institute, 417 East 68th Street, New York, NY 10021. Phone: 646-888-2201; E-mail:
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17
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Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. Cell Rep 2022; 38:110481. [PMID: 35263585 DOI: 10.1016/j.celrep.2022.110481] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 02/11/2022] [Indexed: 11/18/2022] Open
Abstract
Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSCs) point to shared core stemness properties. However, discordance between mRNA and protein signatures highlights an important role for post-transcriptional regulation by microRNAs (miRNAs) in governing this critical nexus. Here, we identify miR-130a as a regulator of HSC self-renewal and differentiation. Enforced expression of miR-130a impairs B lymphoid differentiation and expands long-term HSCs. Integration of protein mass spectrometry and chimeric AGO2 crosslinking and immunoprecipitation (CLIP) identifies TBL1XR1 as a primary miR-130a target, whose loss of function phenocopies miR-130a overexpression. Moreover, we report that miR-130a is highly expressed in t(8;21) acute myeloid leukemia (AML), where it is critical for maintaining the oncogenic molecular program mediated by the AML1-ETO complex. Our study establishes that identification of the comprehensive miRNA targetome within primary cells enables discovery of genes and molecular networks underpinning stemness properties of normal and leukemic cells.
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Affiliation(s)
- Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Erwin M Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Martino M Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexander A Shishkin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Karin G Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Program of Developmental & Stem Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada
| | - Aaron C Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON M4N3M5, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leonardo Salmena
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Gary D Bader
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A5, Canada.
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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18
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Medeiros JJF, Capo-Chichi JM, Shlush LI, Dick JE, Arruda A, Minden MD, Abelson S. SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data. Bioinformatics 2022; 38:2088-2095. [PMID: 35150236 PMCID: PMC9004652 DOI: 10.1093/bioinformatics/btac081] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging. RESULTS We introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated. AVAILABILITY AND IMPLEMENTATION The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Ontario Institute for Cancer Research, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Genome Diagnostics, Department of Clinical Laboratory Genetics, University Health Network, Toronto, ON, Canada
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Hematology and Medical Oncology, University Health Network, Toronto, ON, Canada
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19
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Arruda LCM, Stikvoort A, Lambert M, Jin L, Rivera LS, Alves RMP, De Moura TR, Mim C, Lehmann S, Axelsson-Robertson R, Dick JE, Mattsson J, Önfelt B, Carlsten M, Uhlin M. A novel CD34-specific T-cell engager efficiently depletes acute myeloid leukemia and leukemic stem cells in vitro and in vivo. Haematologica 2022; 107:1786-1795. [PMID: 35142149 PMCID: PMC9335119 DOI: 10.3324/haematol.2021.279486] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/02/2022] Open
Abstract
Less than a third of patients with acute myeloid leukemia (AML) are cured by chemotherapy and/or hematopoietic stem cell transplantation, highlighting the need to develop more efficient drugs. The low efficacy of standard treatments is associated with inadequate depletion of CD34+ blasts and leukemic stem cells, the latter a drug-resistant subpopulation of leukemia cells characterized by the CD34+CD38- phenotype. To target these drug-resistant primitive leukemic cells better, we have designed a CD34/CD3 bi-specific T-cell engager (BTE) and characterized its anti-leukemia potential in vitro, ex vivo and in vivo. Our results show that this CD34-specific BTE induces CD34-dependent T-cell activation and subsequent leukemia cell killing in a dose-dependent manner, further corroborated by enhanced T-cell-mediated killing at the singlecell level. Additionally, the BTE triggered efficient T-cell-mediated depletion of CD34+ hematopoietic stem cells from peripheral blood stem cell grafts and CD34+ blasts from AML patients. Using a humanized AML xenograft model, we confirmed that the CD34-specific BTE had in vivo efficacy by depleting CD34+ blasts and leukemic stem cells without side effects. Taken together, these data demonstrate that the CD34-specific BTE has robust antitumor effects, supporting development of a novel treatment modality with the aim of improving outcomes of patients with AML and myelodysplastic syndromes.
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Affiliation(s)
- Lucas C M Arruda
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm.
| | - Arwen Stikvoort
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm
| | - Melanie Lambert
- Center for Hematology and Regenerative Medicine, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto
| | - Laura Sanchez Rivera
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm
| | - Renato M P Alves
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm
| | - Tales Rocha De Moura
- Department for Biomedical Engineering and Health Systems, KTH Royal Institute of Technology Stockholm
| | - Carsten Mim
- Department for Biomedical Engineering and Health Systems, KTH Royal Institute of Technology Stockholm
| | - Sören Lehmann
- Center for Hematology and Regenerative Medicine, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm
| | - Rebecca Axelsson-Robertson
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden; Department of Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Molecular Genetics, University of Toronto
| | - Jonas Mattsson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Gloria and Seymour Epstein Chair in Cell Therapy and Transplantation, Princess Margaret Cancer Centre, University Health Network, Toronto
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm
| | - Mattias Carlsten
- Center for Hematology and Regenerative Medicine, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden; Center for Cell Therapy and Allogeneic Stem Cell Transplantation, Karolinska University Hospital, Stockholm
| | - Michael Uhlin
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden; Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm
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20
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Vanner RJ, Dobson SM, Gan OI, McLeod J, Schoof EM, Grandal I, Wintersinger JA, Garcia-Prat L, Hosseini M, Xie SZ, Jin L, Mbong N, Voisin V, Chan-Seng-Yue M, Kennedy JA, Waanders E, Morris Q, Porse B, Chan SM, Guidos CJ, Danska JS, Minden MD, Mullighan CG, Dick JE. Multiomic Profiling of Central Nervous System Leukemia Identifies mRNA Translation as a Therapeutic Target. Blood Cancer Discov 2022; 3:16-31. [PMID: 35019858 PMCID: PMC9783958 DOI: 10.1158/2643-3230.bcd-20-0216] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Central nervous system (CNS) dissemination of B-precursor acute lymphoblastic leukemia (B-ALL) has poor prognosis and remains a therapeutic challenge. Here we performed targeted DNA sequencing as well as transcriptional and proteomic profiling of paired leukemia-infiltrating cells in the bone marrow (BM) and CNS of xenografts. Genes governing mRNA translation were upregulated in CNS leukemia, and subclonal genetic profiling confirmed this in both BM-concordant and BM-discordant CNS mutational populations. CNS leukemia cells were exquisitely sensitive to the translation inhibitor omacetaxine mepesuccinate, which reduced xenograft leptomeningeal disease burden. Proteomics demonstrated greater abundance of secreted proteins in CNS-infiltrating cells, including complement component 3 (C3), and drug targeting of C3 influenced CNS disease in xenografts. CNS-infiltrating cells also exhibited selection for stemness traits and metabolic reprogramming. Overall, our study identifies targeting of mRNA translation as a potential therapeutic approach for B-ALL leptomeningeal disease. SIGNIFICANCE: Cancer metastases are often driven by distinct subclones with unique biological properties. Here we show that in B-ALL CNS disease, the leptomeningeal environment selects for cells with unique functional dependencies. Pharmacologic inhibition of mRNA translation signaling treats CNS disease and offers a new therapeutic approach for this condition.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Robert J Vanner
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Ildiko Grandal
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jeff A Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Veronique Voisin
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, University Medical Center, Utrecht, the Netherlands
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quaid Morris
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cynthia J Guidos
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jayne S Danska
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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21
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Montefiori LE, Bendig S, Gu Z, Chen X, Pölönen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, Xu B, Cheng Z, Chang TC, Westover T, Ma J, Stengel A, Kimura S, Qu C, Valentine MB, Rashkovan M, Luger S, Litzow MR, Rowe JM, den Boer ML, Wang V, Yin J, Kornblau SM, Hunger SP, Loh ML, Pui CH, Yang W, Crews KR, Roberts KG, Yang JJ, Relling MV, Evans WE, Stock W, Paietta EM, Ferrando AA, Zhang J, Kern W, Haferlach T, Wu G, Dick JE, Klco JM, Haferlach C, Mullighan CG. Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. Cancer Discov 2021; 11:2846-2867. [PMID: 34103329 PMCID: PMC8563395 DOI: 10.1158/2159-8290.cd-21-0145] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [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: 02/02/2021] [Revised: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Lineage-ambiguous leukemias are high-risk malignancies of poorly understood genetic basis. Here, we describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification. Mechanistically, this deregulation was driven by chromosomal rearrangements that juxtapose BCL11B to superenhancers active in hematopoietic progenitors, or focal amplifications that generate a superenhancer from a noncoding element distal to BCL11B. Chromatin conformation analyses demonstrated long-range interactions of rearranged enhancers with the expressed BCL11B allele and association of BCL11B with activated hematopoietic progenitor cell cis-regulatory elements, suggesting BCL11B is aberrantly co-opted into a gene regulatory network that drives transformation by maintaining a progenitor state. These data support a role for ectopic BCL11B expression in primitive hematopoietic cells mediated by enhancer hijacking as an oncogenic driver of human lineage-ambiguous leukemia. SIGNIFICANCE: Lineage-ambiguous leukemias pose significant diagnostic and therapeutic challenges due to a poorly understood molecular and cellular basis. We identify oncogenic deregulation of BCL11B driven by diverse structural alterations, including de novo superenhancer generation, as the driving feature of a subset of lineage-ambiguous leukemias that transcend current diagnostic boundaries.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alex Murison
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Andy Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Laura Garcia-Prat
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Paul E Mead
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cyrus M Mehr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marcus B Valentine
- Cytogenetics Core Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jacob M Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jun Yin
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York
- Department of Pediatrics, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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22
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Subedi A, Liu Q, Ayyathan DM, Sharon D, Cathelin S, Hosseini M, Xu C, Voisin V, Bader GD, D'Alessandro A, Lechman ER, Dick JE, Minden MD, Wang JCY, Chan SM. Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis. Cell Stem Cell 2021; 28:1851-1867.e8. [PMID: 34293334 DOI: 10.1016/j.stem.2021.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 09/28/2020] [Revised: 05/05/2021] [Accepted: 06/22/2021] [Indexed: 12/29/2022]
Abstract
Current treatments for acute myeloid leukemia (AML) are often ineffective in eliminating leukemic stem cells (LSCs), which perpetuate the disease. Here, we performed a metabolic drug screen to identify LSC-specific vulnerabilities and found that nicotinamide phosphoribosyltransferase (NAMPT) inhibitors selectively killed LSCs, while sparing normal hematopoietic stem and progenitor cells. Treatment with KPT-9274, a NAMPT inhibitor, suppressed the conversion of saturated fatty acids to monounsaturated fatty acids, a reaction catalyzed by the stearoyl-CoA desaturase (SCD) enzyme, resulting in apoptosis of AML cells. Transcriptomic analysis of LSCs treated with KPT-9274 revealed an upregulation of sterol regulatory-element binding protein (SREBP)-regulated genes, including SCD, which conferred partial protection against NAMPT inhibitors. Inhibition of SREBP signaling with dipyridamole enhanced the cytotoxicity of KPT-9274 on LSCs in vivo. Our work demonstrates that altered lipid homeostasis plays a key role in NAMPT inhibitor-induced apoptosis and identifies NAMPT inhibition as a therapeutic strategy for targeting LSCs in AML.
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Affiliation(s)
- Amit Subedi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Qiang Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Dhanoop M Ayyathan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - David Sharon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Severine Cathelin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Changjiang Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Veronique Voisin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Gary D Bader
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, ON, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada.
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23
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Wagenblast E, Araújo J, Gan OI, Cutting SK, Murison A, Krivdova G, Azkanaz M, McLeod JL, Smith SA, Gratton BA, Marhon SA, Gabra M, Medeiros JJF, Manteghi S, Chen J, Chan-Seng-Yue M, Garcia-Prat L, Salmena L, De Carvalho DD, Abelson S, Abdelhaleem M, Chong K, Roifman M, Shannon P, Wang JCY, Hitzler JK, Chitayat D, Dick JE, Lechman ER. Mapping the cellular origin and early evolution of leukemia in Down syndrome. Science 2021; 373:eabf6202. [PMID: 34244384 DOI: 10.1126/science.abf6202] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/09/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022]
Abstract
Children with Down syndrome have a 150-fold increased risk of developing myeloid leukemia, but the mechanism of predisposition is unclear. Because Down syndrome leukemogenesis initiates during fetal development, we characterized the cellular and developmental context of preleukemic initiation and leukemic progression using gene editing in human disomic and trisomic fetal hematopoietic cells and xenotransplantation. GATA binding protein 1 (GATA1) mutations caused transient preleukemia when introduced into trisomy 21 long-term hematopoietic stem cells, where a subset of chromosome 21 microRNAs affected predisposition to preleukemia. By contrast, progression to leukemia was independent of trisomy 21 and originated in various stem and progenitor cells through additional mutations in cohesin genes. CD117+/KIT proto-oncogene (KIT) cells mediated the propagation of preleukemia and leukemia, and KIT inhibition targeted preleukemic stem cells.
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MESH Headings
- Animals
- Antigens, CD34/analysis
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Lineage
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Disease Models, Animal
- Disease Progression
- Down Syndrome/complications
- Down Syndrome/genetics
- Female
- GATA1 Transcription Factor/genetics
- GATA1 Transcription Factor/metabolism
- Hematopoiesis
- Hematopoietic Stem Cell Transplantation
- Hematopoietic Stem Cells/physiology
- Heterografts
- Humans
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Leukemia, Myeloid/pathology
- Liver/embryology
- Male
- Megakaryocytes/physiology
- Mice
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Mutation
- Preleukemia/genetics
- Preleukemia/metabolism
- Preleukemia/pathology
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Mas
- Proto-Oncogene Proteins c-kit/analysis
- Proto-Oncogene Proteins c-kit/antagonists & inhibitors
- Cohesins
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Affiliation(s)
- Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Joana Araújo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Hematology, Centro Hospitalar Universitário de São João, Porto, 4200-319, Portugal
- Faculty of Medicine, University of Porto, Porto, 4200-319, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, 4200-135, Portugal
- Instituto Nacional de Investigação Biomédica, University of Porto, Porto, 4200-135, Portugal
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sarah K Cutting
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maria Azkanaz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sabrina A Smith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Blaise A Gratton
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Martino Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Sanaz Manteghi
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
| | - Jian Chen
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Leonardo Salmena
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sagi Abelson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Mohamed Abdelhaleem
- Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maian Roifman
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Johann K Hitzler
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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24
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Meza-León B, Gratzinger D, Aguilar-Navarro AG, Juárez-Aguilar FG, Rebel VI, Torlakovic E, Purton LE, Dorantes-Acosta EM, Escobar-Sánchez A, Dick JE, Flores-Figueroa E. Human, mouse, and dog bone marrow show similar mesenchymal stromal cells within a distinctive microenvironment. Exp Hematol 2021; 100:41-51. [PMID: 34228982 DOI: 10.1016/j.exphem.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/02/2021] [Revised: 06/22/2021] [Accepted: 06/26/2021] [Indexed: 12/22/2022]
Abstract
Bone marrow stromal cells (BMSCs) are a key part of the hematopoietic niche. Mouse and human BMSCs are recognized by different markers (LepR and NGFR/CD271, respectively). However, there has not been a detailed in situ comparison of both populations within the hematopoietic microenvironment. Moreover, dog BMSCs have not been characterized in situ by any of those markers. We conducted a systematic histopathological comparison of mouse, human, and dog BMSCs within their bone marrow architecture and microenvironment. Human and dog CD271+ BMSCs had a morphology, frequency, and distribution within trabecular bone marrow similar to those of mouse LepR+ BMSCs. However, mouse bone marrow had higher cellularity and megakaryocyte content. In conclusion, highly comparable bone marrow mesenchymal stromal cell distribution among the three species establishes the validity of using mouse and dog as a surrogate experimental model of hematopoietic stem cell-BMSC interactions. However, the distinct differences in adipocyte and megakaryocyte microenvironment content of mouse bone marrow and how they might influence hematopoietic stem cell interactions as compared with humans require further study.
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Affiliation(s)
- Berenice Meza-León
- Unidad de Investigación Médica en Enfermedades Oncológicas. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Alicia G Aguilar-Navarro
- Unidad de Investigación Médica en Enfermedades Oncológicas. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Fany G Juárez-Aguilar
- Departamento de Patología, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | - Vivienne I Rebel
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Emina Torlakovic
- Saskatchewan Health Authority (SHA), Saskatoon, Saskatchewan, Canada; University of Saskatchewan, Saskatchewan, Canada
| | - Louise E Purton
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Elisa M Dorantes-Acosta
- Biobanco de Investigación en Células Leucémicas, Hospital Infantil de México Federico Gómez, Mexico City, México
| | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eugenia Flores-Figueroa
- Unidad de Investigación Médica en Enfermedades Oncológicas. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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25
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Schoof EM, Furtwängler B, Üresin N, Rapin N, Savickas S, Gentil C, Lechman E, Keller UAD, Dick JE, Porse BT. Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun 2021; 12:3341. [PMID: 34099695 PMCID: PMC8185083 DOI: 10.1038/s41467-021-23667-y] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses. By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying ~1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we develop a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a foundation for implementing global single-cell proteomics studies across the world.
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Affiliation(s)
- Erwin M Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Benjamin Furtwängler
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nil Üresin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simonas Savickas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Eric Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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26
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Surka C, Jin L, Mbong N, Lu CC, Jang IS, Rychak E, Mendy D, Clayton T, Tindall E, Hsu C, Fontanillo C, Tran E, Contreras A, Ng SWK, Matyskiela M, Wang K, Chamberlain P, Cathers B, Carmichael J, Hansen J, Wang JCY, Minden MD, Fan J, Pierce DW, Pourdehnad M, Rolfe M, Lopez-Girona A, Dick JE, Lu G. CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Blood 2021; 137:661-677. [PMID: 33197925 PMCID: PMC8215192 DOI: 10.1182/blood.2020008676] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [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: 08/17/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
A number of clinically validated drugs have been developed by repurposing the CUL4-DDB1-CRBN-RBX1 (CRL4CRBN) E3 ubiquitin ligase complex with molecular glue degraders to eliminate disease-driving proteins. Here, we present the identification of a first-in-class GSPT1-selective cereblon E3 ligase modulator, CC-90009. Biochemical, structural, and molecular characterization demonstrates that CC-90009 coopts the CRL4CRBN to selectively target GSPT1 for ubiquitination and proteasomal degradation. Depletion of GSPT1 by CC-90009 rapidly induces acute myeloid leukemia (AML) apoptosis, reducing leukemia engraftment and leukemia stem cells (LSCs) in large-scale primary patient xenografting of 35 independent AML samples, including those with adverse risk features. Using a genome-wide CRISPR-Cas9 screen for effectors of CC-90009 response, we uncovered the ILF2 and ILF3 heterodimeric complex as a novel regulator of cereblon expression. Knockout of ILF2/ILF3 decreases the production of full-length cereblon protein via modulating CRBN messenger RNA alternative splicing, leading to diminished response to CC-90009. The screen also revealed that the mTOR signaling and the integrated stress response specifically regulate the response to CC-90009 in contrast to other cereblon modulators. Hyperactivation of the mTOR pathway by inactivation of TSC1 and TSC2 protected against the growth inhibitory effect of CC-90009 by reducing CC-90009-induced binding of GSPT1 to cereblon and subsequent GSPT1 degradation. On the other hand, GSPT1 degradation promoted the activation of the GCN1/GCN2/ATF4 pathway and subsequent apoptosis in AML cells. Collectively, CC-90009 activity is mediated by multiple layers of signaling networks and pathways within AML blasts and LSCs, whose elucidation gives insight into further assessment of CC-90009s clinical utility. These trials were registered at www.clinicaltrials.gov as #NCT02848001 and #NCT04336982).
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Affiliation(s)
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | | | | | | | | | | | | | | | | | | | - Stanley W K Ng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Kai Wang
- Bristol-Myers Squibb, San Diego, CA
| | | | | | | | | | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Jinhong Fan
- Bristol-Myers Squibb, San Francisco, CA; and
| | | | | | | | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gang Lu
- Bristol-Myers Squibb, San Diego, CA
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27
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Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, McLeod J, Wagenblast E, Mitchell A, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE. Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation. Blood Cancer Discov 2021; 2:32-53. [PMID: 33458693 PMCID: PMC7116590 DOI: 10.1158/2643-3230.bcd-20-0155] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 09/01/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is a caricature of normal hematopoiesis, driven from leukemia stem cells (LSC) that share some hematopoietic stem cell (HSC) programs including responsiveness to inflammatory signaling. Although inflammation dysregulates mature myeloid cells and influences stemness programs and lineage determination in HSC by activating stress myelopoiesis, such roles in LSC are poorly understood. Here, we show that S1PR3, a receptor for the bioactive lipid sphingosine-1-phosphate, is a central regulator which drives myeloid differentiation and activates inflammatory programs in both HSC and LSC. S1PR3-mediated inflammatory signatures varied in a continuum from primitive to mature myeloid states across AML patient cohorts, each with distinct phenotypic and clinical properties. S1PR3 was high in LSC and blasts of mature myeloid samples with linkages to chemosensitivity, while S1PR3 activation in primitive samples promoted LSC differentiation leading to eradication. Our studies open new avenues for therapeutic target identification specific for each AML subset.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Weijia Wang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa, Japan
| | - Stanley W K Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - ChangJiang Xu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Qiang Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Melissa Kleinau
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yang Zhang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yusuf A Hannun
- Stony Brook Cancer Center and Departments of Medicine, Biochemistry, and Pathology, Stony Brook University, Stony Brook, New York
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook School of Medicine, Stony Brook, New York
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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28
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Abelson S, Zeng AGX, Nofech-Mozes I, Wang TT, Ng SWK, Minden MD, Pugh TJ, Awadalla P, Shlush LI, Murphy T, Chan SM, Dick JE, Bratman SV. Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing. Sci Adv 2020; 6:6/50/eabe3722. [PMID: 33298453 PMCID: PMC7725472 DOI: 10.1126/sciadv.abe3722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
Sensitive mutation detection by next-generation sequencing is critical for early cancer detection, monitoring minimal/measurable residual disease (MRD), and guiding precision oncology. Nevertheless, because of artifacts introduced during library preparation and sequencing, the detection of low-frequency variants at high specificity is problematic. Here, we present Espresso, an error suppression method that considers local sequence features to accurately detect single-nucleotide variants (SNVs). Compared to other advanced error suppression techniques, Espresso consistently demonstrated lower numbers of false-positive mutation calls and greater sensitivity. We demonstrated Espresso's superior performance in detecting MRD in the peripheral blood of patients with acute myeloid leukemia (AML) throughout their treatment course. Furthermore, we showed that accurate mutation calling in a small number of informative genomic loci might provide a cost-efficient strategy for pragmatic risk prediction of AML development in healthy individuals. More broadly, we aim for Espresso to aid with accurate mutation detection in many other research and clinical settings.
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Affiliation(s)
- Sagi Abelson
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andy G X Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ido Nofech-Mozes
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Stanley W K Ng
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Liran I Shlush
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tracy Murphy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
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29
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Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell 2020; 28:488-501.e10. [PMID: 33242413 DOI: 10.1016/j.stem.2020.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 05/22/2020] [Revised: 09/17/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Abstract
Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.
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Affiliation(s)
- Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa 236-0004, Japan
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erwin Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ken Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael D Taylor
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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30
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Dick JE. Abstract IA21: Stem cells play a role in human leukemia from origin to relapse. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-ia21] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Individual cancer cells exhibit functional heterogeneity of many cancer hallmarks including the capacity for sustaining long-term clonal maintenance, a stemness property involving self-renewal. Our studies established that only rare AML cells possessed such leukemia stem cell (LSC) properties and that AML is a cellular hierarchy. LSC were found to be highly relevant to human disease as gene signatures specific to LSC were much more predictive of patient response to therapy and overall survival compared to the bulk non-LSC AML cells. We have now provided insights into how LSC develop during leukemogenesis. Through sequencing of purified populations of normal blood cells, AML cells, and xenografts from paired diagnosis/relapse AML samples, we tracked the full arc of leukemia development in humans: from the cell of origin (an HSC) that acquires the first genetic mutation; to pre-leukemic clonal expansion of HSC; the generation of genetically diverse LSC; and finally to the cellular origin of relapse (rare LSC subclones) within the diagnosis sample. Similar studies have been undertaken in B-ALL where relapse-fated subclones were found within the diagnosis sample before exposure to chemotherapy. These clones possess distinct epigenetic and metabolic properties that underlie their partially resistance to chemotherapy and they possess stemness signatures that drive their ability to regenerate relapse disease. These studies resulted in identification of novel therapeutic targets of relapse-fated subclones to begin envisioning approaches to eradicate relapse before it develops. Finally, the identification of clonally expanded pre-leukemic HSPC in the diagnosis blood sample of many AML samples predicted that it should be possible to identify individuals who are at risk for progressing to AML long before AML develops. We genotyped individuals from the general population who were enrolled in the large cohort (EPIC) who eventually developed AML and compared them to the enrollment sample of others who never progressed to AML. We have found a clear signature that is able to predict with high accuracy those individuals who have age related clonal hematopoiesis who progress to AML, almost 10 years prior to AML development. This is distinct from individuals who have benign clonal hematopoiesis who never progress. These new findings offer the potential for future intervention to permit AML prevention trials.
Citation Format: John E. Dick. Stem cells play a role in human leukemia from origin to relapse [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA21.
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Affiliation(s)
- John E. Dick
- Princess Margaret Cancer Centre, Toronto, ON, Canada
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31
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Bao EL, Nandakumar SK, Liao X, Bick AG, Karjalainen J, Tabaka M, Gan OI, Havulinna AS, Kiiskinen TTJ, Lareau CA, de Lapuente Portilla AL, Li B, Emdin C, Codd V, Nelson CP, Walker CJ, Churchhouse C, de la Chapelle A, Klein DE, Nilsson B, Wilson PWF, Cho K, Pyarajan S, Gaziano JM, Samani NJ, Regev A, Palotie A, Neale BM, Dick JE, Natarajan P, O'Donnell CJ, Daly MJ, Milyavsky M, Kathiresan S, Sankaran VG. Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Nature 2020; 586:769-775. [PMID: 33057200 PMCID: PMC7606745 DOI: 10.1038/s41586-020-2786-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Myeloproliferative neoplasms (MPNs) are blood cancers that are characterized by the excessive production of mature myeloid cells and arise from the acquisition of somatic driver mutations in haematopoietic stem cells (HSCs). Epidemiological studies indicate a substantial heritable component of MPNs that is among the highest known for cancers1. However, only a limited number of genetic risk loci have been identified, and the underlying biological mechanisms that lead to the acquisition of MPNs remain unclear. Here, by conducting a large-scale genome-wide association study (3,797 cases and 1,152,977 controls), we identify 17 MPN risk loci (P < 5.0 × 10-8), 7 of which have not been previously reported. We find that there is a shared genetic architecture between MPN risk and several haematopoietic traits from distinct lineages; that there is an enrichment for MPN risk variants within accessible chromatin of HSCs; and that increased MPN risk is associated with longer telomere length in leukocytes and other clonal haematopoietic states-collectively suggesting that MPN risk is associated with the function and self-renewal of HSCs. We use gene mapping to identify modulators of HSC biology linked to MPN risk, and show through targeted variant-to-function assays that CHEK2 and GFI1B have roles in altering the function of HSCs to confer disease risk. Overall, our results reveal a previously unappreciated mechanism for inherited MPN risk through the modulation of HSC function.
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Affiliation(s)
- Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaotian Liao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander G Bick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marcin Tabaka
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tuomo T J Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Bo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Connor Emdin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Christopher J Walker
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Albert de la Chapelle
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Daryl E Klein
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, USA
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Peter W F Wilson
- Atlanta VA Medical Center, Atlanta, GA, USA
- Emory Clinical Cardiovascular Research Institute, Atlanta, GA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Centre, Glenfield Hospital, Leicester, UK
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biology, Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare, Section of Cardiology, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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32
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Aguilar-Navarro AG, Meza-León B, Gratzinger D, Juárez-Aguilar FG, Chang Q, Ornatsky O, Tsui H, Esquivel-Gómez R, Hernández-Ramírez A, Xie SZ, Dick JE, Flores-Figueroa E. Human Aging Alters the Spatial Organization between CD34+ Hematopoietic Cells and Adipocytes in Bone Marrow. Stem Cell Reports 2020; 15:317-325. [PMID: 32649902 PMCID: PMC7419665 DOI: 10.1016/j.stemcr.2020.06.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 02/29/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 02/08/2023] Open
Abstract
Age-related clonal hematopoiesis is a major risk factor for myeloid malignancy and myeloid skewing is a hallmark of aging. However, while it is known that non-cell-autonomous components of the microenvironment can also influence this risk, there have been few studies of how the spatial architecture of human bone marrow (BM) changes with aging. Here, we show that BM adiposity increases with age, which correlates with increased density of maturing myeloid cells and CD34+ hematopoietic stem/progenitor cells (HSPCs) and an increased proportion of HSPCs adjacent to adipocytes. However, NGFR+ bone marrow stromal cell (NGFR+ BMSC) density and distance to HSPCs and vessels remained stable. Interestingly, we found that, upon aging, maturing myeloid cell density increases in hematopoietic areas surrounding adipocytes. We propose that increased adjacency to adipocytes in the BM microenvironment may influence myeloid skewing of aging HSPCs, contributing to age-related risk of myeloid malignancies. Aging increases adipose, myeloid, and CD34+ HSPC density in the human bone marrow Human CD34+ HSPC niche is reticular, perivascular, and periadipocytic in aging Aging increases maturing myeloid cell density surrounding adipocytes
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Affiliation(s)
- Alicia G Aguilar-Navarro
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Berenice Meza-León
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fany G Juárez-Aguilar
- Departamento de Patología, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Qing Chang
- Fluidigm Canada Inc., Markham, ON, Canada
| | | | - Hubert Tsui
- Division of Hematopathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Ricardo Esquivel-Gómez
- División de Ortopedia, Hospital de Traumatología y Ortopedia Lomas Verdes, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Antonio Hernández-Ramírez
- Unidad de Reemplazo Articular, Hospital de Traumatología y Ortopedia Lomas Verdes, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Eugenia Flores-Figueroa
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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33
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Dobson SM, García-Prat L, Vanner RJ, Wintersinger J, Waanders E, Gu Z, McLeod J, Gan OI, Grandal I, Payne-Turner D, Edmonson MN, Ma X, Fan Y, Voisin V, Chan-Seng-Yue M, Xie SZ, Hosseini M, Abelson S, Gupta P, Rusch M, Shao Y, Olsen SR, Neale G, Chan SM, Bader G, Easton J, Guidos CJ, Danska JS, Zhang J, Minden MD, Morris Q, Mullighan CG, Dick JE. Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs. Cancer Discov 2020; 10:568-587. [PMID: 32086311 PMCID: PMC7122013 DOI: 10.1158/2159-8290.cd-19-1059] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [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: 09/11/2019] [Revised: 12/21/2019] [Accepted: 02/18/2020] [Indexed: 12/26/2022]
Abstract
Disease recurrence causes significant mortality in B-progenitor acute lymphoblastic leukemia (B-ALL). Genomic analysis of matched diagnosis and relapse samples shows relapse often arising from minor diagnosis subclones. However, why therapy eradicates some subclones while others survive and progress to relapse remains obscure. Elucidation of mechanisms underlying these differing fates requires functional analysis of isolated subclones. Here, large-scale limiting dilution xenografting of diagnosis and relapse samples, combined with targeted sequencing, identified and isolated minor diagnosis subclones that initiate an evolutionary trajectory toward relapse [termed diagnosis Relapse Initiating clones (dRI)]. Compared with other diagnosis subclones, dRIs were drug-tolerant with distinct engraftment and metabolic properties. Transcriptionally, dRIs displayed enrichment for chromatin remodeling, mitochondrial metabolism, proteostasis programs, and an increase in stemness pathways. The isolation and characterization of dRI subclones reveals new avenues for eradicating dRI cells by targeting their distinct metabolic and transcriptional pathways before further evolution renders them fully therapy-resistant. SIGNIFICANCE: Isolation and characterization of subclones from diagnosis samples of patients with B-ALL who relapsed showed that relapse-fated subclones had increased drug tolerance and distinct metabolic and survival transcriptional programs compared with other diagnosis subclones. This study provides strategies to identify and target clinically relevant subclones before further evolution toward relapse.
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Affiliation(s)
- Stephanie M Dobson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura García-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert J Vanner
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ildiko Grandal
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael N Edmonson
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yiping Fan
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Veronique Voisin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sagi Abelson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Pankaj Gupta
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Rusch
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ying Shao
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gary Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - John Easton
- Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cynthia J Guidos
- Developmental & Stem Cell Biology Program, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jayne S Danska
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jinghui Zhang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto. Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Vector Institute, Toronto, Canada
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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34
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Heidemann S, Bursic B, Zandi S, Li H, Abelson S, Klaassen RJ, Abish S, Rayar M, Breakey VR, Moshiri H, Dhanraj S, de Borja R, Shlien A, Dick JE, Dror Y. Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure. JCI Insight 2020; 5:131018. [PMID: 31990679 DOI: 10.1172/jci.insight.131018] [Citation(s) in RCA: 6] [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: 06/18/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Inherited bone marrow failure syndromes, such as Fanconi anemia (FA) and Shwachman-Diamond syndrome (SDS), feature progressive cytopenia and a risk of acute myeloid leukemia (AML). Using deep phenotypic analysis of early progenitors in FA/SDS bone marrow samples, we revealed selective survival of progenitors that phenotypically resembled granulocyte-monocyte progenitors (GMP). Whole-exome and targeted sequencing of GMP-like cells in leukemia-free patients revealed a higher mutation load than in healthy controls and molecular changes that are characteristic of AML: increased G>A/C>T variants, decreased A>G/T>C variants, increased trinucleotide mutations at Xp(C>T)pT, and decreased mutation rates at Xp(C>T)pG sites compared with other Xp(C>T)pX sites and enrichment for Cancer Signature 1 (X indicates any nucleotide). Potential preleukemic targets in the GMP-like cells from patients with FA/SDS included SYNE1, DST, HUWE1, LRP2, NOTCH2, and TP53. Serial analysis of GMPs from an SDS patient who progressed to leukemia revealed a gradual increase in mutational burden, enrichment of G>A/C>T signature, and emergence of new clones. Interestingly, the molecular signature of marrow cells from 2 FA/SDS patients with leukemia was similar to that of FA/SDS patients without transformation. The predicted founding clones in SDS-derived AML harbored mutations in several genes, including TP53, while in FA-derived AML the mutated genes included ARID1B and SFPQ. We describe an architectural change in the hematopoietic hierarchy of FA/SDS with remarkable preservation of GMP-like populations harboring unique mutation signatures. GMP-like cells might represent a cellular reservoir for clonal evolution.
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Affiliation(s)
- Stephanie Heidemann
- Genetics & Genome Biology Program and.,Marrow Failure and Myelodysplasia (Pre-leukemia) Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Sagi Abelson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Robert J Klaassen
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sharon Abish
- Hematology-Oncology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Meera Rayar
- Division of Hematology, Oncology & Bone Marrow Transplant, University of British Columbia and British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Vicky R Breakey
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Santhosh Dhanraj
- Genetics & Genome Biology Program and.,Institute of Medical Science and
| | | | | | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yigal Dror
- Genetics & Genome Biology Program and.,Marrow Failure and Myelodysplasia (Pre-leukemia) Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science and
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35
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Waanders E, Gu Z, Dobson SM, Antić Ž, Crawford JC, Ma X, Edmonson MN, Payne-Turner D, van der Vorst M, Jongmans MCJ, McGuire I, Zhou X, Wang J, Shi L, Pounds S, Pei D, Cheng C, Song G, Fan Y, Shao Y, Rusch M, McCastlain K, Yu J, van Boxtel R, Blokzijl F, Iacobucci I, Roberts KG, Wen J, Wu G, Ma J, Easton J, Neale G, Olsen SR, Nichols KE, Pui CH, Zhang J, Evans WE, Relling MV, Yang JJ, Thomas PG, Dick JE, Kuiper RP, Mullighan CG. Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:96-111. [PMID: 32793890 PMCID: PMC7418874 DOI: 10.1158/0008-5472.bcd-19-0041] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Relapse of acute lymphoblastic leukemia (ALL) remains a leading cause of childhood death. Prior studies have shown clonal mutations at relapse often arise from relapse-fated subclones that exist at diagnosis. However, the genomic landscape, evolutionary trajectories and mutational mechanisms driving relapse are incompletely understood. In an analysis of 92 cases of relapsed childhood ALL, incorporating multimodal DNA and RNA sequencing, deep digital mutational tracking and xenografting to formally define clonal structure, we identify 50 significant targets of mutation with distinct patterns of mutational acquisition or enrichment. CREBBP, NOTCH1, and Ras signaling mutations rose from diagnosis subclones, whereas variants in NCOR2, USH2A and NT5C2 were exclusively observed at relapse. Evolutionary modeling and xenografting demonstrated that relapse-fated clones were minor (50%), major (27%) or multiclonal (18%) at diagnosis. Putative second leukemias, including those with lineage shift, were shown to most commonly represent relapse from an ancestral clone rather than a truly independent second primary leukemia. A subset of leukemias prone to repeated relapse exhibited hypermutation driven by at least three distinct mutational processes, resulting in heightened neoepitope burden and potential vulnerability to immunotherapy. Finally, relapse-driving sequence mutations were detected prior to relapse using deep digital PCR at levels comparable to orthogonal approaches to monitor levels of measurable residual disease. These results provide a genomic framework to anticipate and circumvent relapse by earlier detection and targeting of relapse-fated clones.
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Affiliation(s)
- Esmé Waanders
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Željko Antić
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maartje van der Vorst
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Irina McGuire
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly McCastlain
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jiangyan Yu
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Francis Blokzijl
- Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geoffrey Neale
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Scott R Olsen
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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36
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van Galen P, Mbong N, Kreso A, Schoof EM, Wagenblast E, Ng SWK, Krivdova G, Jin L, Nakauchi H, Dick JE. Integrated Stress Response Activity Marks Stem Cells in Normal Hematopoiesis and Leukemia. Cell Rep 2019; 25:1109-1117.e5. [PMID: 30380403 DOI: 10.1016/j.celrep.2018.10.021] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 04/05/2018] [Revised: 07/25/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022] Open
Abstract
Lifelong maintenance of the blood system requires equilibrium between clearance of damaged hematopoietic stem cells (HSCs) and long-term survival of the HSC pool. Severe perturbations of cellular homeostasis result in rapid HSC loss to maintain clonal purity. However, normal homeostatic processes can also generate lower-level stress; how HSCs survive these conditions remains unknown. Here we show that the integrated stress response (ISR) is uniquely active in HSCs and facilitates their persistence. Activating transcription factor 4 (ATF4) mediates the ISR and is highly expressed in HSCs due to scarcity of the eIF2 translation initiation complex. Amino acid deprivation results in eIF2α phosphorylation-dependent upregulation of ATF4, promoting HSC survival. Primitive acute myeloid leukemia (AML) cells also display eIF2 scarcity and ISR activity marks leukemia stem cells (LSCs) in primary AML samples. These findings identify a link between the ISR and stem cell survival in the normal and leukemic contexts.
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Affiliation(s)
- Peter van Galen
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Antonia Kreso
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Erwin M Schoof
- The Finsen Laboratory, Rigshospitalet/Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stanley W K Ng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5G 1A1, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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37
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Wang TT, Abelson S, Zou J, Li T, Zhao Z, Dick JE, Shlush LI, Pugh TJ, Bratman SV. High efficiency error suppression for accurate detection of low-frequency variants. Nucleic Acids Res 2019; 47:e87. [PMID: 31127310 PMCID: PMC6735726 DOI: 10.1093/nar/gkz474] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 05/23/2018] [Revised: 04/28/2019] [Accepted: 05/16/2019] [Indexed: 12/30/2022] Open
Abstract
Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to technical artefacts that can limit the accuracy for calling low-allele-frequency mutations. State-of-the-art methods to improve detection of low-frequency mutations often employ unique molecular identifiers (UMIs) for error suppression; however, these methods are highly inefficient as they depend on redundant sequencing to assemble consensus sequences. Here, we present a novel strategy to enhance the efficiency of UMI-based error suppression by retaining single reads (singletons) that can participate in consensus assembly. This 'Singleton Correction' methodology outperformed other UMI-based strategies in efficiency, leading to greater sensitivity with high specificity in a cell line dilution series. Significant benefits were seen with Singleton Correction at sequencing depths ≤16 000×. We validated the utility and generalizability of this approach in a cohort of >300 individuals whose peripheral blood DNA was subjected to hybrid capture sequencing at ∼5000× depth. Singleton Correction can be incorporated into existing UMI-based error suppression workflows to boost mutation detection accuracy, thus improving the cost-effectiveness and clinical impact of NGS.
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Affiliation(s)
- Ting Ting Wang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sagi Abelson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Liran I Shlush
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
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38
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Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE. Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal. Cell Stem Cell 2019; 25:639-653.e7. [PMID: 31631013 PMCID: PMC6838675 DOI: 10.1016/j.stem.2019.09.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
Cellular stress responses serve as crucial decision points balancing persistence or culling of hematopoietic stem cells (HSCs) for lifelong blood production. Although strong stressors cull HSCs, the linkage between stress programs and self-renewal properties that underlie human HSC maintenance remains unknown, particularly at quiescence exit when HSCs must also dynamically shift metabolic state. Here, we demonstrate distinct wiring of the sphingolipidome across the human hematopoietic hierarchy and find that genetic or pharmacologic modulation of the sphingolipid enzyme DEGS1 regulates lineage differentiation. Inhibition of DEGS1 in hematopoietic stem and progenitor cells during the transition from quiescence to cellular activation with N-(4-hydroxyphenyl) retinamide activates coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs to maintain immunophenotypic and functional HSCs. Thus, our work identifies a linkage between sphingolipid metabolism, proteostatic quality control systems, and HSC self-renewal and provides therapeutic targets for improving HSC-based cellular therapeutics.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada.
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Robin Ferrari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; R&D Division, Kyowa Kirin Co., Ltd., Tokyo 194-8533, Japan
| | - Ishita Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Esther K Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Guy Romm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kristele Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Michelle Shoong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Aditi Vedi
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Elisa Laurenti
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada.
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39
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Aqaqe N, Yassin M, Yassin AA, Ershaid N, Katz-Even C, Zipin-Roitman A, Kugler E, Lechman ER, Gan OI, Mitchell A, Dick JE, Izraeli S, Milyavsky M. An ERG Enhancer-Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation. Cancer Res 2019; 79:3862-3876. [PMID: 31175119 DOI: 10.1158/0008-5472.can-18-3215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/21/2019] [Accepted: 06/04/2019] [Indexed: 11/16/2022]
Abstract
Acute leukemia is a rapidly progressing blood cancer with low survival rates. Unfavorable prognosis is attributed to insufficiently characterized subpopulations of leukemia stem cells (LSC) that drive chemoresistance and leukemia relapse. Here we utilized a genetic reporter that assesses stemness to enrich and functionally characterize LSCs. We observed heterogeneous activity of the ERG+85 enhancer-based fluorescent reporter in human leukemias. Cells with high reporter activity (tagBFPHigh) exhibited elevated expression of stemness and chemoresistance genes and demonstrated increased clonogenicity and resistance to chemo- and radiotherapy as compared with their tagBFPNeg counterparts. The tagBFPHigh fraction was capable of regenerating the original cellular heterogeneity and demonstrated increased invasive ability. Moreover, the tagBFPHigh fraction was enriched for leukemia-initiating cells in a xenograft assay. We identified the ubiquitin hydrolase USP9X as a novel ERG transcriptional target that sustains ERG+85-positive cells by controlling ERG ubiquitination. Therapeutic targeting of USP9X led to preferential inhibition of the ERG-dependent leukemias. Collectively, these results characterize human leukemia cell functional heterogeneity and suggest that targeting ERG via USP9X inhibition may be a potential treatment strategy in patients with leukemia. SIGNIFICANCE: This study couples a novel experimental tool with state-of-the-art approaches to delineate molecular mechanisms underlying stem cell-related characteristics in leukemia cells.
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Affiliation(s)
- Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abed Alkader Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nour Ershaid
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Katz-Even
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Zipin-Roitman
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eitan Kugler
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center Petah-Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shai Izraeli
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center Petah-Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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40
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Yassin M, Aqaqe N, Yassin AA, van Galen P, Kugler E, Bernstein BE, Koren-Michowitz M, Canaani J, Nagler A, Lechman ER, Dick JE, Wienholds E, Izraeli S, Milyavsky M. A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity. Leukemia 2019; 33:2061-2077. [PMID: 30705411 DOI: 10.1038/s41375-019-0386-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/02/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023]
Abstract
Acute leukemia is an aggressive blood malignancy with low survival rates. A high expression of stem-like programs in leukemias predicts poor prognosis and is assumed to act in an aberrant fashion in the phenotypically heterogeneous leukemia stem cell (LSC) population. A lack of suitable genome engineering tools that can isolate LSCs based on their stemness precludes their comprehensive examination and full characterization. We hypothesized that tagging endogenous stemness-regulatory regions could generate a genome reporter for the putative leukemia stemness-state. Our analysis revealed that the ERG + 85 enhancer region can serve as a marker for stemness-state and a fluorescent lentiviral reporter was developed that can accurately recapitulate the endogenous activity. Using our novel reporter, we revealed cellular heterogeneity in several leukemia cell lines and patient-derived samples. Alterations in reporter activity were associated with transcriptomic and functional changes that were closely related to the hematopoietic stem cell (HSC) identity. Notably, the differentiation potential was skewed towards the erythro-megakaryocytic lineage. Moreover, an ERG + 85High fraction of AML cells could regenerate the original cellular heterogeneity and was enriched for LSCs. RNA-seq analysis coupled with in silico drug-screen analysis identified 4HPR as an effective inhibitor of ERG + 85High leukemia growth. We propose that further utilization of our novel molecular tool will identify crucial determinants of LSCs, thus providing a rationale for their therapeutic targeting.
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Affiliation(s)
- Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Abed Alkader Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Peter van Galen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Eitan Kugler
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center, Petah Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bradley E Bernstein
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Jonathan Canaani
- Hematology Division, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Arnon Nagler
- Hematology Division, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shai Izraeli
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center, Petah Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.
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41
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Luciani GM, Xie L, Dilworth D, Tierens A, Moskovitz Y, Murison A, Szewczyk MM, Mitchell A, Lupien M, Shlush L, Dick JE, Arrowsmith CH, Barsyte-Lovejoy D, Minden MD. Characterization of inv(3) cell line OCI-AML-20 with stroma-dependent CD34 expression. Exp Hematol 2018; 69:27-36. [PMID: 30352278 DOI: 10.1016/j.exphem.2018.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 11/26/2022]
Abstract
Acute myeloid leukemia (AML) is a complex, heterogeneous disease with variable outcomes following curative intent chemotherapy. AML with inv(3) is a genetic subgroup characterized by a very low response rate to current induction type chemotherapy and thus has among the worst long-term survivorship of the AMLs. Here, we describe OCI-AML-20, a new AML cell line with inv(3) and deletion of chromosome 7; the latter is a common co-occurrence in inv(3) AML. In OCI-AML-20, CD34 expression is maintained and required for repopulation in vitro and in vivo. CD34 expression in OCI-AML-20 shows dependence on the co-culture with stromal cells. Transcriptome analysis indicates that the OCI-AML-20 clusters with other AML patient data sets that have poor prognosis, as well as other AML cell lines, including another inv(3) line, MUTZ-3. OCI-AML-20 is a new cell line resource for studying the biology of inv(3) AML that can be used to identify potential therapies for this poor outcome disease.
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Affiliation(s)
- Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Lihua Xie
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Anne Tierens
- Toronto General Hospital, Laboratory Medicine Program, Toronto, Ontario, Canada
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alex Murison
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Liran Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | | | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada.
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42
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Golan K, Kumari A, Kollet O, Khatib-Massalha E, Subramaniam MD, Ferreira ZS, Avemaria F, Rzeszotek S, García-García A, Xie S, Flores-Figueroa E, Gur-Cohen S, Itkin T, Ludin-Tal A, Massalha H, Bernshtein B, Ciechanowicz AK, Brandis A, Mehlman T, Bhattacharya S, Bertagna M, Cheng H, Petrovich-Kopitman E, Janus T, Kaushansky N, Cheng T, Sagi I, Ratajczak MZ, Méndez-Ferrer S, Dick JE, Markus RP, Lapidot T. Daily Onset of Light and Darkness Differentially Controls Hematopoietic Stem Cell Differentiation and Maintenance. Cell Stem Cell 2018; 23:572-585.e7. [PMID: 30174297 DOI: 10.1016/j.stem.2018.08.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [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: 08/15/2017] [Revised: 04/10/2018] [Accepted: 08/06/2018] [Indexed: 12/31/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) tightly couple maintenance of the bone marrow (BM) reservoir, including undifferentiated long-term repopulating hematopoietic stem cells (LT-HSCs), with intensive daily production of mature leukocytes and blood replenishment. We found two daily peaks of BM HSPC activity that are initiated by onset of light and darkness providing this coupling. Both peaks follow transient elevation of BM norepinephrine and TNF secretion, which temporarily increase HSPC reactive oxygen species (ROS) levels. Light-induced norepinephrine and TNF secretion augments HSPC differentiation and increases vascular permeability to replenish the blood. In contrast, darkness-induced TNF increases melatonin secretion to drive renewal of HSPCs and LT-HSC potential through modulating surface CD150 and c-Kit expression, increasing COX-2/αSMA+ macrophages, diminishing vascular permeability, and reducing HSPC ROS levels. These findings reveal that light- and darkness-induced daily bursts of norepinephrine, TNF, and melatonin within the BM are essential for synchronized mature blood cell production and HSPC pool repopulation.
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Affiliation(s)
- Karin Golan
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Anju Kumari
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Orit Kollet
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Zulma S Ferreira
- Physiology Department, University of São Paulo, São Paulo, Brazil
| | | | - Sylwia Rzeszotek
- Physiology Department, Pomeranian Medical University, Szczecin, Poland
| | | | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Eugenia Flores-Figueroa
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Oncology Research Unit, Oncology Hospital, National Medical Center Century XXI, IMSS, Mexico City, Mexico
| | - Shiri Gur-Cohen
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Itkin
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Aya Ludin-Tal
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Hassan Massalha
- Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Biana Bernshtein
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alexander Brandis
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mayla Bertagna
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Hui Cheng
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel; State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | | | - Tomasz Janus
- Forensic Medicine Department, Pomeranian Medical University, Szczecin, Poland
| | | | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Irit Sagi
- Biological Regulation Department, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Regina P Markus
- Physiology Department, University of São Paulo, São Paulo, Brazil
| | - Tsvee Lapidot
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
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43
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Wang W, Fujii H, Kim HJ, Hermans K, Usenko T, Xie S, Luo ZJ, Ma J, Celso CL, Dick JE, Schroeder T, Krueger J, Wall D, Egeler RM, Zandstra PW. Enhanced human hematopoietic stem and progenitor cell engraftment by blocking donor T cell-mediated TNFα signaling. Sci Transl Med 2018; 9:9/421/eaag3214. [PMID: 29263228 DOI: 10.1126/scitranslmed.aag3214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/21/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative therapy, but the large number of HSCs required limits its widespread use. Host conditioning and donor cell composition are known to affect HSCT outcomes. However, the specific role that the posttransplantation signaling environment plays in donor HSC fate is poorly understood. To mimic clinical HSCT, we injected human umbilical cord blood (UCB) cells at different doses and compositions into immunodeficient NOD/SCID/IL-2Rgc-null (NSG) mice. Surprisingly, higher UCB cell doses inversely correlated with stem and progenitor cell engraftment. This observation was attributable to increased donor cell-derived inflammatory signals. Donor T cell-derived tumor necrosis factor-α (TNFα) was specifically found to directly impair the survival and division of transplanted HSCs and progenitor cells. Neutralizing donor T cell-derived TNFα in vivo increased short-term stem and progenitor cell engraftment, accelerated hematopoietic recovery, and altered donor immune cell compositions. This direct effect of TNFα on transplanted cells could be decoupled from the indirect effect of alleviating graft-versus-host disease (GVHD) by interleukin-6 (IL-6) blockade. Our study demonstrates that donor immune cell-derived inflammatory signals directly influence HSC fate, and provides new clinically relevant strategies to improve engraftment efficiency during HSCT.
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Affiliation(s)
- Weijia Wang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel 4058, Switzerland
| | - Hisaki Fujii
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Hye Jin Kim
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Karin Hermans
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Tatiana Usenko
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Zhi-Juan Luo
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jennifer Ma
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Cristina Lo Celso
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel 4058, Switzerland
| | - Joerg Krueger
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Donna Wall
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - R Maarten Egeler
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Medicine by Design-A Canada First Research Excellence Fund program, Toronto, Ontario M5G 1M1, Canada
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44
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Vanner RJ, Dobson SM, Grandal I, Gan O, McLeod J, Kennedy J, Voisin V, Daghrach A, Schoof EM, Guidos C, Danska J, Waanders E, Minden M, Mullighan CG, Dick JE. Abstract 5173: Genetic profiling of central nervous system dissemination of B-acute lymphoblastic leukemia reveals clonal selection and therapeutic vulnerability. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5173] [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] [Indexed: 11/16/2022]
Abstract
Abstract
B-cell acute lymphoblastic leukemia (B-ALL) readily disseminates to the leptomeninges of the central nervous system (CNS). CNS involvement is more frequent in certain poor prognosis subgroups including patients with MLL-AF4 translocations, and late CNS relapse is often lethal. The biology and clonal history of CNS leukemia are poorly defined and consequently therapies exploiting drivers of metastasis are lacking. To characterize leptomeningeal leukemia we performed targeted DNA sequencing, SNP copy number analysis, RNA sequencing, and functional analysis on cells isolated from the bone marrow (BM) and CNS of xenografts generated from a cohort of paired diagnosis and relapse samples from 14 B-ALL patients. The majority of patient samples disseminated to the CNS following intrafemoral injection into irradiated NSG mice, with greater CNS involvement in xenografts derived from relapse patient samples. Secondary transplantation of both BM- and CNS-purified cells demonstrated their capacity to re-engraft BM, CNS, and spleen. Targeted-sequencing results were analyzed using a Bayesian clustering method to determine the clonal composition of matched BM and CNS, demonstrating discordance in subclonal prevalence in nearly half the xenografts tested. Xenografts derived from two patient samples demonstrated recurrent enrichment of a particular subclone in the CNS versus BM. Similarly, copy number analysis identified frequent discordance between BM and CNS tissues within individual mice. All xenografts from one patient exhibited chromosome 6p and 17p hemi-deletions that were exclusive to CNS cells. While these data suggest that individual B-ALLs harbor subclones with CNS tropism, there were no recurrently enriched single nucleotide mutations or copy number alterations across all patients. RNA-sequencing of 45 BM and CNS pairs from primary xenografts demonstrated that CNS-isolated cells were consistently distinct from their matched BM. GSEA analysis of xenografts generated from patients with MLL-AF4 translocations (MLL) (n=2 patients, 26 mice), identified CNS cell enrichment of gene sets related to mRNA translation and nascent peptide elongation compared to BM. MLL-CNS cells exhibited altered rates of protein synthesis compared to BM cells from the same mouse. The clinically-approved translation inhibitor omacetaxine mepesuccinate effectively diminished protein translation rates of CNS isolated cells and reduced CNS engraftment by four fold in xenografts derived from two MLL-AF4 patients. These data demonstrate that the CNS microenvironment selects for the outgrowth of B-ALL cells with genetically and/or biologically distinct properties. Moreover, we demonstrate that in MLL-AF4 patients, altered protein synthesis occurs in CNS dissemination and that targeting this process may clinically benefit patients with CNS disease.
Citation Format: Robert J. Vanner, Stephanie M. Dobson, Ildiko Grandal, Olga Gan, Jessica McLeod, James Kennedy, Veroniqu Voisin, Abdellatif Daghrach, Erwin M. Schoof, Cynthia Guidos, Jayne Danska, Esme Waanders, Mark Minden, Charles G. Mullighan, John E. Dick. Genetic profiling of central nervous system dissemination of B-acute lymphoblastic leukemia reveals clonal selection and therapeutic vulnerability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5173.
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Affiliation(s)
| | | | | | - Olga Gan
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jessica McLeod
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - James Kennedy
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | | | | | - Jayne Danska
- 3Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Mark Minden
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - John E. Dick
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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45
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Abelson S, Collord G, Ng SWK, Weissbrod O, Mendelson Cohen N, Niemeyer E, Barda N, Zuzarte PC, Heisler L, Sundaravadanam Y, Luben R, Hayat S, Wang TT, Zhao Z, Cirlan I, Pugh TJ, Soave D, Ng K, Latimer C, Hardy C, Raine K, Jones D, Hoult D, Britten A, McPherson JD, Johansson M, Mbabaali F, Eagles J, Miller JK, Pasternack D, Timms L, Krzyzanowski P, Awadalla P, Costa R, Segal E, Bratman SV, Beer P, Behjati S, Martincorena I, Wang JCY, Bowles KM, Quirós JR, Karakatsani A, La Vecchia C, Trichopoulou A, Salamanca-Fernández E, Huerta JM, Barricarte A, Travis RC, Tumino R, Masala G, Boeing H, Panico S, Kaaks R, Krämer A, Sieri S, Riboli E, Vineis P, Foll M, McKay J, Polidoro S, Sala N, Khaw KT, Vermeulen R, Campbell PJ, Papaemmanuil E, Minden MD, Tanay A, Balicer RD, Wareham NJ, Gerstung M, Dick JE, Brennan P, Vassiliou GS, Shlush LI. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature 2018; 559:400-404. [PMID: 29988082 PMCID: PMC6485381 DOI: 10.1038/s41586-018-0317-6] [Citation(s) in RCA: 506] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 05/03/2018] [Indexed: 02/07/2023]
Abstract
The incidence of acute myeloid leukaemia (AML) increases with age and mortality exceeds 90% when diagnosed after age 65. Most cases arise without any detectable early symptoms and patients usually present with the acute complications of bone marrow failure1. The onset of such de novo AML cases is typically preceded by the accumulation of somatic mutations in preleukaemic haematopoietic stem and progenitor cells (HSPCs) that undergo clonal expansion2,3. However, recurrent AML mutations also accumulate in HSPCs during ageing of healthy individuals who do not develop AML, a phenomenon referred to as age-related clonal haematopoiesis (ARCH)4-8. Here we use deep sequencing to analyse genes that are recurrently mutated in AML to distinguish between individuals who have a high risk of developing AML and those with benign ARCH. We analysed peripheral blood cells from 95 individuals that were obtained on average 6.3 years before AML diagnosis (pre-AML group), together with 414 unselected age- and gender-matched individuals (control group). Pre-AML cases were distinct from controls and had more mutations per sample, higher variant allele frequencies, indicating greater clonal expansion, and showed enrichment of mutations in specific genes. Genetic parameters were used to derive a model that accurately predicted AML-free survival; this model was validated in an independent cohort of 29 pre-AML cases and 262 controls. Because AML is rare, we also developed an AML predictive model using a large electronic health record database that identified individuals at greater risk. Collectively our findings provide proof-of-concept that it is possible to discriminate ARCH from pre-AML many years before malignant transformation. This could in future enable earlier detection and monitoring, and may help to inform intervention.
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Affiliation(s)
- Sagi Abelson
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Grace Collord
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Stanley W K Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Omer Weissbrod
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Mendelson Cohen
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisabeth Niemeyer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Barda
- Clalit Research Institute, Tel Aviv, Israel
| | | | | | | | - Robert Luben
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Shabina Hayat
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Karen Ng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Calli Latimer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Claire Hardy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - David Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Diana Hoult
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Abigail Britten
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Jenna Eagles
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Rui Costa
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Philip Beer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - Kristian M Bowles
- Department of Molecular Haematology, Norwich Medical School, The University of East Anglia, Norwich, UK
- Department of Haematology, Norfolk and Norwich University Hospitals NHS Trust, Norwich, UK
| | | | - Anna Karakatsani
- Hellenic Health Foundation, Athens, Greece
- 2nd Pulmonary Medicine Department, School of Medicine, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, Haidari, Athens, Greece
| | - Carlo La Vecchia
- Hellenic Health Foundation, Athens, Greece
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | | | - Elena Salamanca-Fernández
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - José M Huerta
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Aurelio Barricarte
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
- Navarra Public Health Institute, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, Civic-M. P. Arezzo Hospital, Azienda Sanitaria Provinciale, Ragusa, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute - ISPO, Florence, Italy
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Matthieu Foll
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program and Translational Research Laboratory, Catalan Institute of Oncology, ICO-IDIBELL, Barcelona, Spain
| | | | - Roel Vermeulen
- Division of Environmental Epidemiology and Veterinary Public Health, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Elli Papaemmanuil
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Center for Molecular Oncology and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France.
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Liran I Shlush
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel.
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46
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Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, Murison A, Langenfeld K, Petretich M, Scognamiglio R, Zeisberger P, Benk AS, Amit I, Zandstra PW, Lupien M, Dick JE, Trumpp A, Spitz F. Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018; 558:E4. [PMID: 29769714 DOI: 10.1038/s41586-018-0113-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the originally published version of this Letter, ref. 43 was erroneously provided twice. In the 'Estimation of relative cell-type-specific composition of AML samples' section in the Methods, the citation to ref. 43 after the GEO dataset GSE24759 is correct. However, in the 'Mice' section of the Methods, the citation to ref. 43 after 'TAMERE' should have been associated with a new reference1. The original Letter has been corrected online (with the new reference included as ref. 49).
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Affiliation(s)
- Carsten Bahr
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Lisa von Paleske
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Veli V Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stanley W Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Katja Langenfeld
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Massimo Petretich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roberta Scognamiglio
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Amelie S Benk
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Michael Smith Laboratories, School of Biomedical Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany. .,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,Nationales Zentrum für Tumorerkrankungen (NCT), Heidelberg, Germany.
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,CNRS, UMR3738, 25 Rue du Dr Roux, Paris, France.,(Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department, Institut Pasteur, Paris, France
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47
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Krivdova G, Lechman ER, Schoof EM, Voisin V, Gan OI, Trotman-Grant A, Hermans KG, Bader GD, Dick JE. Abstract PR07: MicroRNA-130a regulates hematopoietic stem cell self-renewal and erythroid differentiation. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.hemmal17-pr07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hematopoietic homeostasis is tightly regulated by controlling the balance between quiescence, self-renewal, and lineage-commitment of hematopoietic stem cells (HSCs). Deregulation of these processes and aberrant acquisition of stem cell-like properties is believed to be central to the pathogenesis of hematologic malignancies, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). However, little is known about the molecular networks maintaining the stem cell state and the epigenetic and post-transcriptional regulation of determinants that control these programs. MicroRNAs (miRNAs) represent a large class of post-transcriptional regulators that mediate repression of multiple target mRNAs. We have previously shown that miR-126 and miR-125a are differentially expressed across the human hematopoietic hierarchy and function to control self-renewal and cell fate decisions by reinforcing gene expression programs in a developmental stage-specific manner (Lechman et al. Cell Stem Cell, 2012; Wojtowitz et al. Cell Stem Cell, 2016).
To identify additional miRNA(s) that play a functional role in hematopoiesis, we performed an in vivo competitive repopulation screen in which candidate miRNAs were overexpressed (OE) in human CD34+CD38- umbilical cord blood (CB) cells and subsequently transplanted into immune-deficient mice for 24 weeks. miR-130a was shown to enhance long-term hematopoietic reconstitution and chosen for further investigation. At 12 and 24 weeks after transplantation, enforced miR-130a expression (including an mOrange-mO+ indicator) conferred a competitive advantage over untransduced CB cells demonstrated by increased CD45+ human chimerism in the injected femur (IF), bone marrow (BM), and spleen of recipient mice. miR-130 enforced expression (miR-130a OE) increased the proportion of mO+/hCD45+ cells by approximately 2- and 5-fold after 12 and 24 weeks of repopulation, respectively. miR-130a OE xenografts showed multilineage engraftment with increased myeloid lineage output and significantly enhanced erythroid development at the expense of B-lymphoid lineage output in BM and spleen of recipient mice. Detailed flow cytometry analysis of xenografts revealed accumulation of immature GlyA+/CD71+/CD36+ erythroid progenitors, suggesting a differentiation block at the polychromic erythroblast stage. Notably, miR-130a OE induced the expansion of CD34+CD38- Lin- compartment and increased proportion of CD34+CD38-CD90+CD45RA- immuno-phenotypic HSC. Secondary transplantation involving limiting dilution analysis revealed approximately a 10-fold increase in HSC frequency, consistent with a role of miR-130a in HSC self-renewal. The lineage potential of miR-130OE primitive cells was assessed in vitro using single-cell stromal-based myelo-erythroid differentiation assay. Enforced expression of miR-130a in human HSC and multipotent progenitors (MPP) resulted in the decreased frequency of unipotent myeloid output (M colonies) and increased multipotent output (M/E/Meg, E/Meg colonies), supporting a role of miR-130a in erythroid-megakaryocytic fate specification. Label-free semiquantitative proteomics and subsequent gene set enrichment pathway analysis (GSEA) were performed on miR-130a OE and control transduced CD34+ CB cells to elucidate molecular mechanism(s) of miR-130a function. We identified that miR-130a modulated pathways centered on translational regulation and chromatin modification. Together, our data suggest that miR-130a plays a role in the regulation of the HSC self-renewal and erythroid differentiation. Given that several studies showed aberrant expression of miR-130a in MDS and some AML subtypes, it is important to delineate the role of miR-130a in normal hematopoiesis to comprehend its potential contribution to the development of hematologic malignancies.
This abstract is also being presented as Poster 40.
Citation Format: Gabriela Krivdova, Eric R. Lechman, Erwin M. Schoof, Veronique Voisin, Olga I. Gan, Aaron Trotman-Grant, Karin G. Hermans, Gary D. Bader, John E. Dick. MicroRNA-130a regulates hematopoietic stem cell self-renewal and erythroid differentiation [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR07.
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Affiliation(s)
- Gabriela Krivdova
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Eric R. Lechman
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | - Erwin M. Schoof
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | | | - Olga I. Gan
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | | | - Karin G. Hermans
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
| | | | - John E. Dick
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada,
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48
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Lee J, Minden MD, Chen WC, Streck E, Chen B, Kang H, Arruda A, Ly D, Der SD, Kang S, Achita P, D'Souza C, Li Y, Childs RW, Dick JE, Zhang L. Allogeneic Human Double Negative T Cells as a Novel Immunotherapy for Acute Myeloid Leukemia and Its Underlying Mechanisms. Clin Cancer Res 2017; 24:370-382. [PMID: 29074605 DOI: 10.1158/1078-0432.ccr-17-2228] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 07/31/2017] [Revised: 09/26/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
Purpose: To explore the potential of ex vivo expanded healthy donor-derived allogeneic CD4 and CD8 double-negative cells (DNT) as a novel cellular immunotherapy for leukemia patients.Experimental Design: Clinical-grade DNTs from peripheral blood of healthy donors were expanded and their antileukemic activity and safety were examined using flow cytometry-based in vitro killing assays and xenograft models against AML patient blasts and healthy donor-derived hematopoietic cells. Mechanism of action was investigated using antibody-mediated blocking assays and recombinant protein treatment assays.Results: Expanded DNTs from healthy donors target a majority (36/46) of primary AML cells, including 9 chemotherapy-resistant patient samples in vitro, and significantly reduce the leukemia load in patient-derived xenograft models in a DNT donor-unrestricted manner. Importantly, allogeneic DNTs do not attack normal hematopoietic cells or affect hematopoietic stem/progenitor cell engraftment and differentiation, or cause xenogeneic GVHD in recipients. Mechanistically, DNTs express high levels of NKG2D and DNAM-1 that bind to cognate ligands preferentially expressed on AML cells. Upon recognition of AML cells, DNTs rapidly release IFNγ, which further increases NKG2D and DNAM-1 ligands' expression on AML cells. IFNγ pretreatment enhances the susceptibility of AML cells to DNT-mediated cytotoxicity, including primary AML samples that are otherwise resistant to DNTs, and the effect of IFNγ treatment is abrogated by NKG2D and DNAM-1-blocking antibodies.Conclusions: This study supports healthy donor-derived allogeneic DNTs as a therapy to treat patients with chemotherapy-resistant AML and also reveals interrelated roles of NKG2D, DNAM-1, and IFNγ in selective targeting of AML by DNTs. Clin Cancer Res; 24(2); 370-82. ©2017 AACR.
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MESH Headings
- Animals
- Antigens, Differentiation, T-Lymphocyte/metabolism
- Biomarkers
- Cytotoxicity, Immunologic
- Disease Models, Animal
- Drug Resistance, Neoplasm
- Graft vs Host Reaction/immunology
- Humans
- Immunophenotyping
- Immunotherapy, Adoptive/methods
- Interferon-gamma/biosynthesis
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice
- NK Cell Lectin-Like Receptor Subfamily K/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Transplantation, Homologous
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Affiliation(s)
- JongBok Lee
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Weihsu C Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Elena Streck
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Branson Chen
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hyeonjeong Kang
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dalam Ly
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sandy D Der
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sohyeong Kang
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Paulina Achita
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl D'Souza
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yueyang Li
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Richard W Childs
- National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Li Zhang
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada.
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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49
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Zipin-Roitman A, Aqaqe N, Yassin M, Biechonski S, Amar M, van Delft MF, Gan OI, McDermott SP, Buzina A, Ketela T, Shlush L, Xie S, Voisin V, Moffat J, Minden MD, Dick JE, Milyavsky M. SMYD2 lysine methyltransferase regulates leukemia cell growth and regeneration after genotoxic stress. Oncotarget 2017; 8:16712-16727. [PMID: 28187429 PMCID: PMC5369996 DOI: 10.18632/oncotarget.15147] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 11/23/2016] [Accepted: 01/24/2017] [Indexed: 12/12/2022] Open
Abstract
The molecular determinants governing escape of Acute Myeloid Leukemia (AML) cells from DNA damaging therapy remain poorly defined and account for therapy failures. To isolate genes responsible for leukemia cells regeneration following multiple challenges with irradiation we performed a genome-wide shRNA screen. Some of the isolated hits are known players in the DNA damage response (e.g. p53, CHK2), whereas other, e.g. SMYD2 lysine methyltransferase (KMT), remains uncharacterized in the AML context. Here we report that SMYD2 knockdown confers relative resistance to human AML cells against multiple classes of DNA damaging agents. Induction of the transient quiescence state upon SMYD2 downregulation correlated with the resistance. We revealed that diminished SMYD2 expression resulted in the upregulation of the related methyltransferase SET7/9, suggesting compensatory relationships. Indeed, pharmacological targeting of SET7/9 with (R)-PFI2 inhibitor preferentially inhibited the growth of cells expressing low levels of SMYD2. Finally, decreased expression of SMYD2 in AML patients correlated with the reduced sensitivity to therapy and lower probability to achieve complete remission. We propose that the interplay between SMYD2 and SET7/9 levels shifts leukemia cells from growth to quiescence state that is associated with the higher resistance to DNA damaging agents and rationalize SET7/9 pharmacological targeting in AML.
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Affiliation(s)
- Adi Zipin-Roitman
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Biechonski
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mariam Amar
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mark F van Delft
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sean P McDermott
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Leidos Biomedical Research, Washington D.C., USA
| | - Alla Buzina
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Troy Ketela
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Liran Shlush
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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50
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Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, Bader G, Voisin V, Xu C, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE. Tracing the origins of relapse in acute myeloid leukaemia to stem cells. Nature 2017; 547:104-108. [DOI: 10.1038/nature22993] [Citation(s) in RCA: 339] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/17/2017] [Indexed: 01/06/2023]
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