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Mistry JJ, Young KA, Colom Díaz PA, Maestre IF, Levine RL, Trowbridge JJ. Mesenchymal Stromal Cell Senescence Induced by Dnmt3a -Mutant Hematopoietic Cells is a Targetable Mechanism Driving Clonal Hematopoiesis and Initiation of Hematologic Malignancy. bioRxiv 2024:2024.03.28.587254. [PMID: 38585779 PMCID: PMC10996614 DOI: 10.1101/2024.03.28.587254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Clonal hematopoiesis (CH) can predispose to blood cancers due to enhanced fitness of mutant hematopoietic stem and progenitor cells (HSPCs), but the mechanisms driving this progression are not understood. We hypothesized that malignant progression is related to microenvironment-remodelling properties of CH-mutant HSPCs. Single-cell transcriptomic profiling of the bone marrow microenvironment in Dnmt3a R878H/+ mice revealed signatures of cellular senescence in mesenchymal stromal cells (MSCs). Dnmt3a R878H/+ HSPCs caused MSCs to upregulate the senescence markers SA-β-gal, BCL-2, BCL-xL, Cdkn1a (p21) and Cdkn2a (p16), ex vivo and in vivo . This effect was cell contact-independent and can be replicated by IL-6 or TNFα, which are produced by Dnmt3a R878H/+ HSPCs. Depletion of senescent MSCs in vivo reduced the fitness of Dnmt3a R878H/+ hematopoietic cells and the progression of CH to myeloid neoplasms using a sequentially inducible Dnmt3a ; Npm1 -mutant model. Thus, Dnmt3a -mutant HSPCs reprogram their microenvironment via senescence induction, creating a self-reinforcing niche favoring fitness and malignant progression. Statement of Significance Mesenchymal stromal cell senescence induced by Dnmt3a -mutant hematopoietic stem and progenitor cells drives clonal hematopoiesis and initiation of hematologic malignancy.
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Longhini ALF, Fernández-Maestre I, Kennedy MC, Wereski MG, Mowla S, Xiao W, Lowe SW, Levine RL, Gardner R. Development of a customizable mouse backbone spectral flow cytometry panel to delineate immune cell populations in normal and tumor tissues. Front Immunol 2024; 15:1374943. [PMID: 38605953 PMCID: PMC11008467 DOI: 10.3389/fimmu.2024.1374943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction In vivo studies of cancer biology and assessment of therapeutic efficacy are critical to advancing cancer research and ultimately improving patient outcomes. Murine cancer models have proven to be an invaluable tool in pre-clinical studies. In this context, multi-parameter flow cytometry is a powerful method for elucidating the profile of immune cells within the tumor microenvironment and/or play a role in hematological diseases. However, designing an appropriate multi-parameter panel to comprehensively profile the increasing diversity of immune cells across different murine tissues can be extremely challenging. Methods To address this issue, we designed a panel with 13 fixed markers that define the major immune populations -referred to as the backbone panel- that can be profiled in different tissues but with the option to incorporate up to seven additional fluorochromes, including any marker specific to the study in question. Results This backbone panel maintains its resolution across different spectral flow cytometers and organs, both hematopoietic and non-hematopoietic, as well as tumors with complex immune microenvironments. Discussion Having a robust backbone that can be easily customized with pre-validated drop-in fluorochromes saves time and resources and brings consistency and standardization, making it a versatile solution for immuno-oncology researchers. In addition, the approach presented here can serve as a guide to develop similar types of customizable backbone panels for different research questions requiring high-parameter flow cytometry panels.
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Affiliation(s)
- Ana Leda F. Longhini
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
| | - Inés Fernández-Maestre
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Margaret C. Kennedy
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Shoron Mowla
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Wenbin Xiao
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ross L. Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, United States
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3
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Paudel BB, Tan SF, Fox TE, Ung J, Golla U, Shaw JJP, Dunton W, Lee I, Fares WA, Patel S, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Feith DJ, Claxton D, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as 2 clinically relevant sphingolipidomic subtypes. Blood Adv 2024; 8:1137-1142. [PMID: 38170742 PMCID: PMC10909712 DOI: 10.1182/bloodadvances.2023010535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology/Immunology/Cancer Biology, University of Virginia, Charlottesville, VA
| | - Upendarrao Golla
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Jeremy J. P. Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX
| | - Wisam A. Fares
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Satyam Patel
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Department of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Herbert Irving Comprehensive Cancer Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK
| | - Martin S. Tallman
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
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4
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Amor C, Fernández-Maestre I, Chowdhury S, Ho YJ, Nadella S, Graham C, Carrasco SE, Nnuji-John E, Feucht J, Hinterleitner C, Barthet VJA, Boyer JA, Mezzadra R, Wereski MG, Tuveson DA, Levine RL, Jones LW, Sadelain M, Lowe SW. Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Nat Aging 2024; 4:336-349. [PMID: 38267706 PMCID: PMC10950785 DOI: 10.1038/s43587-023-00560-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024]
Abstract
Senescent cells, which accumulate in organisms over time, contribute to age-related tissue decline. Genetic ablation of senescent cells can ameliorate various age-related pathologies, including metabolic dysfunction and decreased physical fitness. While small-molecule drugs that eliminate senescent cells ('senolytics') partially replicate these phenotypes, they require continuous administration. We have developed a senolytic therapy based on chimeric antigen receptor (CAR) T cells targeting the senescence-associated protein urokinase plasminogen activator receptor (uPAR), and we previously showed these can safely eliminate senescent cells in young animals. We now show that uPAR-positive senescent cells accumulate during aging and that they can be safely targeted with senolytic CAR T cells. Treatment with anti-uPAR CAR T cells improves exercise capacity in physiological aging, and it ameliorates metabolic dysfunction (for example, improving glucose tolerance) in aged mice and in mice on a high-fat diet. Importantly, a single administration of these senolytic CAR T cells is sufficient to achieve long-term therapeutic and preventive effects.
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Grants
- R01 CA188134 NCI NIH HHS
- R01 CA190092 NCI NIH HHS
- DP5 OD033055 NIH HHS
- U01 CA224013 NCI NIH HHS
- R35 CA197594 NCI NIH HHS
- P30 CA045508 NCI NIH HHS
- R01 AG065396 NIA NIH HHS
- R01 CA229699 NCI NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 AG082800 NIA NIH HHS
- U01 AG077925 NIA NIH HHS
- S10 OD028632 NIH HHS
- U01 CA210240 NCI NIH HHS
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- NIH-NIA: 1R01 AG082800-01 NIH-Common Fund: 1DP5OD033055-01 Longevity Impetus Grant
- European Research Council (ERC-StG-949667).
- JLM Benevolent Fund. Cancer Research Institute.
- Netherlands Organization for Scientific Research Cancer Research Institute
- Lustgarten Foundation, Thompson Foundation, the Pershing Square Foundation, the Cold Spring Harbor Laboratory and Northwell Health Affiliation, the Northwell Health Tissue Donation Program, the Cold Spring Harbor Laboratory Association, the Simons Foundation (552716), and the National Institutes of Health (5P30CA45508, U01CA210240, R01CA229699, U01CA224013, 1R01CA188134, and 1R01CA190092).
- NIH-NCI (R35CA197594) NIH-NIA (U01AG077925)
- NIH: S10OD028632-01 and P30 CA008748 NIH-NIA: AG065396 Pasteur-Weizmann/Servier Award Leopold Griffuel Award Stephen and Barbara Friedman Chair at MSKCC
- NIH: S10OD028632-01 and P30 CA008748 NIH-NIA: AG065396 Technology Development Fund project grant from MSKCC Geoffrey Beene Chair of Cancer Biology at MSKCC Howard Hughes Medical Institute
- La Caixa Foundation.Mark Foundation.
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Affiliation(s)
- Corina Amor
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Inés Fernández-Maestre
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Jui Ho
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Courtenay Graham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian E Carrasco
- Laboratory of Comparative Pathology. Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center, and Rockefeller University, New York, NY, USA
| | - Emmanuella Nnuji-John
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor School of Biological Sciences, Cold Spring Harbor, NY, USA
| | - Judith Feucht
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cluster of Excellence iFIT, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - Clemens Hinterleitner
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valentin J A Barthet
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob A Boyer
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | - Riccardo Mezzadra
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew G Wereski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Lee W Jones
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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5
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Stonestrom AJ, Menghrajani KN, Devlin SM, Franch-Expósito S, Ptashkin RN, Patel SY, Spitzer B, Wu X, Jee J, Sánchez Vela P, Milbank JH, Shah RH, Mohanty AS, Brannon AR, Xiao W, Berger MF, Mantha S, Levine RL. High-risk and silent clonal hematopoietic genotypes in patients with nonhematologic cancer. Blood Adv 2024; 8:846-856. [PMID: 38147626 PMCID: PMC10875331 DOI: 10.1182/bloodadvances.2023011262] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) identified by somatic gene variants with variant allele fraction (VAF) ≥ 2% is associated with an increased risk of hematologic malignancy. However, CH defined by a broader set of genotypes and lower VAFs is ubiquitous in older individuals. To improve our understanding of the relationship between CH genotype and risk of hematologic malignancy, we analyzed data from 42 714 patients who underwent blood sequencing as a normal comparator for nonhematologic tumor testing using a large cancer-related gene panel. We cataloged hematologic malignancies in this cohort using natural language processing and manual curation of medical records. We found that some CH genotypes including JAK2, RUNX1, and XPO1 variants were associated with high hematologic malignancy risk. Chronic disease was predicted better than acute disease suggesting the influence of length bias. To better understand the implications of hematopoietic clonality independent of mutational function, we evaluated a set of silent synonymous and noncoding mutations. We found that silent CH, particularly when multiple variants were present or VAF was high, was associated with increased risk of hematologic malignancy. We tracked expansion of CH mutations in 26 hematologic malignancies sequenced with the same platform. JAK2 and TP53 VAF consistently expanded at disease onset, whereas DNMT3A and silent CH VAFs mostly decreased. These data inform the clinical and biological interpretation of CH in the context of nonhematologic cancer.
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Affiliation(s)
- Aaron J. Stonestrom
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal N. Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sebastià Franch-Expósito
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaodi Wu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Jee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer H. Milbank
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronak H. Shah
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S. Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Mantha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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6
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Codilupi T, Szybinski J, Arunasalam S, Jungius S, Dunbar AC, Stivala S, Brkic S, Albrecht C, Vokalova L, Yang JL, Buczak K, Ghosh N, Passweg JR, Rovo A, Angelillo-Scherrer A, Pankov D, Dirnhofer S, Levine RL, Koche R, Meyer SC. Development of Resistance to Type II JAK2 Inhibitors in MPN Depends on AXL Kinase and Is Targetable. Clin Cancer Res 2024; 30:586-599. [PMID: 37992313 PMCID: PMC10831334 DOI: 10.1158/1078-0432.ccr-23-0163] [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: 03/20/2023] [Revised: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023]
Abstract
PURPOSE Myeloproliferative neoplasms (MPN) dysregulate JAK2 signaling. Because clinical JAK2 inhibitors have limited disease-modifying effects, type II JAK2 inhibitors such as CHZ868 stabilizing inactive JAK2 and reducing MPN clones, gain interest. We studied whether MPN cells escape from type ll inhibition. EXPERIMENTAL DESIGN MPN cells were continuously exposed to CHZ868. We used phosphoproteomic analyses and ATAC/RNA sequencing to characterize acquired resistance to type II JAK2 inhibition, and targeted candidate mediators in MPN cells and mice. RESULTS MPN cells showed increased IC50 and reduced apoptosis upon CHZ868 reflecting acquired resistance to JAK2 inhibition. Among >2,500 differential phospho-sites, MAPK pathway activation was most prominent, while JAK2-STAT3/5 remained suppressed. Altered histone occupancy promoting AP-1/GATA binding motif exposure associated with upregulated AXL kinase and enriched RAS target gene profiles. AXL knockdown resensitized MPN cells and combined JAK2/AXL inhibition using bemcentinib or gilteritinib reduced IC50 to levels of sensitive cells. While resistant cells induced tumor growth in NOD/SCID gamma mice despite JAK2 inhibition, JAK2/AXL inhibition largely prevented tumor progression. Because inhibitors of MAPK pathway kinases such as MEK are clinically used in other malignancies, we evaluated JAK2/MAPK inhibition with trametinib to interfere with AXL/MAPK-induced resistance. Tumor growth was halted similarly to JAK2/AXL inhibition and in a systemic cell line-derived mouse model, marrow infiltration was decreased supporting dependency on AXL/MAPK. CONCLUSIONS We report on a novel mechanism of AXL/MAPK-driven escape from type II JAK2 inhibition, which is targetable at different nodes. This highlights AXL as mediator of acquired resistance warranting inhibition to enhance sustainability of JAK2 inhibition in MPN.
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Affiliation(s)
- Tamara Codilupi
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jakub Szybinski
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Stefanie Arunasalam
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sarah Jungius
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrew C. Dunbar
- Human Oncology and Pathogenesis Program and Leukemia service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Simona Stivala
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Sime Brkic
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Camille Albrecht
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Lenka Vokalova
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Julie L. Yang
- Human Oncology and Pathogenesis Program and Leukemia service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katarzyna Buczak
- Proteomics Core Facility Biozentrum, University of Basel, Basel, Switzerland
| | - Nilabh Ghosh
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jakob R. Passweg
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Alicia Rovo
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anne Angelillo-Scherrer
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dmitry Pankov
- Immunology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Stefan Dirnhofer
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Koche
- Human Oncology and Pathogenesis Program and Leukemia service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sara C. Meyer
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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7
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Sung PJ, Selvam M, Riedel SS, Xie HM, Bryant K, Manning B, Wertheim GB, Kulej K, Pham L, Bowman RL, Peresie J, Nemeth MJ, Levine RL, Garcia BA, Meyer SE, Sidoli S, Bernt KM, Carroll M. FLT3 tyrosine kinase inhibition modulates PRC2 and promotes differentiation in acute myeloid leukemia. Leukemia 2024; 38:291-301. [PMID: 38182819 DOI: 10.1038/s41375-023-02131-4] [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: 04/10/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
Internal tandem duplication mutations in fms-like tyrosine kinase 3 (FLT3-ITD) are recurrent in acute myeloid leukemia (AML) and increase the risk of relapse. Clinical responses to FLT3 inhibitors (FLT3i) include myeloid differentiation of the FLT3-ITD clone in nearly half of patients through an unknown mechanism. We identified enhancer of zeste homolog 2 (EZH2), a component of polycomb repressive complex 2 (PRC2), as a mediator of this effect using a proteomic-based screen. FLT3i downregulated EZH2 protein expression and PRC2 activity on H3K27me3. FLT3-ITD and loss-of-function mutations in EZH2 are mutually exclusive in human AML. We demonstrated that FLT3i increase myeloid maturation with reduced stem/progenitor cell populations in murine Flt3-ITD AML. Combining EZH1/2 inhibitors with FLT3i increased terminal maturation of leukemic cells and reduced leukemic burden. Our data suggest that reduced EZH2 activity following FLT3 inhibition promotes myeloid differentiation of FLT3-ITD leukemic cells, providing a mechanistic explanation for the clinical observations. These results demonstrate that in addition to its known cell survival and proliferation signaling, FLT3-ITD has a second, previously undefined function to maintain a myeloid stem/progenitor cell state through modulation of PRC2 activity. Our findings support exploring EZH1/2 inhibitors as therapy for FLT3-ITD AML.
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Affiliation(s)
- Pamela J Sung
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
| | - Murugan Selvam
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Simone S Riedel
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katie Bryant
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bryan Manning
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Lucie Pham
- Department of Medicine - Leukemia, Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Robert L Bowman
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jennifer Peresie
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Sara E Meyer
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Kathrin M Bernt
- Department of Pediatrics, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine and Abramson Cancer Center, Philadelphia, PA, USA
| | - Martin Carroll
- Department of Medicine, Division of Hematology/Oncology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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8
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Cai SF, Huang Y, Lance JR, Mao HC, Dunbar AJ, McNulty SN, Druley T, Li Y, Baer MR, Stock W, Kovacsovics T, Blum WG, Schiller GJ, Olin RL, Foran JM, Litzow M, Lin T, Patel P, Foster MC, Boyiadzis M, Collins RH, Chervin J, Shoben A, Vergilio JA, Heerema NA, Rosenberg L, Chen TL, Yocum AO, Druggan F, Marcus S, Stefanos M, Druker BJ, Mims AS, Borate U, Burd A, Byrd JC, Levine RL, Stein EM. A study to assess the efficacy of enasidenib and risk-adapted addition of azacitidine in newly diagnosed IDH2-mutant AML. Blood Adv 2024; 8:429-440. [PMID: 37871309 PMCID: PMC10827405 DOI: 10.1182/bloodadvances.2023010563] [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: 04/26/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 10/25/2023] Open
Abstract
ABSTRACT Enasidenib (ENA) is an inhibitor of isocitrate dehydrogenase 2 (IDH2) approved for the treatment of patients with IDH2-mutant relapsed/refractory acute myeloid leukemia (AML). In this phase 2/1b Beat AML substudy, we applied a risk-adapted approach to assess the efficacy of ENA monotherapy for patients aged ≥60 years with newly diagnosed IDH2-mutant AML in whom genomic profiling demonstrated that mutant IDH2 was in the dominant leukemic clone. Patients for whom ENA monotherapy did not induce a complete remission (CR) or CR with incomplete blood count recovery (CRi) enrolled in a phase 1b cohort with the addition of azacitidine. The phase 2 portion assessing the overall response to ENA alone demonstrated efficacy, with a composite complete response (cCR) rate (CR/CRi) of 46% in 60 evaluable patients. Seventeen patients subsequently transitioned to phase 1b combination therapy, with a cCR rate of 41% and 1 dose-limiting toxicity. Correlative studies highlight mechanisms of clonal elimination with differentiation therapy as well as therapeutic resistance. This study demonstrates both efficacy of ENA monotherapy in the upfront setting and feasibility and applicability of a risk-adapted approach to the upfront treatment of IDH2-mutant AML. This trial is registered at www.clinicaltrials.gov as #NCT03013998.
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Affiliation(s)
- Sheng F. Cai
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Huang
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Jennie R. Lance
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Hsiaoyin Charlene Mao
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Andrew J. Dunbar
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Yan Li
- Bristol Myers Squibb, New York, NY
| | - Maria R. Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Wendy Stock
- Department of Hematology and Oncology, University of Chicago Medical Center, Chicago, IL
| | | | - William G. Blum
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - Gary J. Schiller
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Rebecca L. Olin
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Mark Litzow
- Department of Hematology, Mayo Clinic, Rochester, MN
| | - Tara Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, University of Kansas, Kansas City, KS
| | - Prapti Patel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Michael Boyiadzis
- Division of Hematolog/Oncology, Department of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Robert H. Collins
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jordan Chervin
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abigail Shoben
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Nyla A. Heerema
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Timothy L. Chen
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Franchesca Druggan
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Mona Stefanos
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Alice S. Mims
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Uma Borate
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Amy Burd
- Leukemia and Lymphoma Society, Rye Brook, NY
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Ross L. Levine
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M. Stein
- Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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9
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Pritchard JE, Pearce JE, Snoeren IAM, Fuchs SNR, Götz K, Peisker F, Wagner S, Benabid A, Lutterbach N, Klöker V, Nagai JS, Hannani MT, Galyga AK, Sistemich E, Banjanin B, Flosdorf N, Bindels E, Olschok K, Biaesch K, Chatain N, Bhagwat N, Dunbar A, Sarkis R, Naveiras O, Berres ML, Koschmieder S, Levine RL, Costa IG, Gleitz HFE, Kramann R, Schneider RK. Non-canonical Hedgehog signaling mediates profibrotic hematopoiesis-stroma crosstalk in myeloproliferative neoplasms. Cell Rep 2024; 43:113608. [PMID: 38117649 PMCID: PMC10828549 DOI: 10.1016/j.celrep.2023.113608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
The role of hematopoietic Hedgehog signaling in myeloproliferative neoplasms (MPNs) remains incompletely understood despite data suggesting that Hedgehog (Hh) pathway inhibitors have therapeutic activity in patients. We aim to systematically interrogate the role of canonical vs. non-canonical Hh signaling in MPNs. We show that Gli1 protein levels in patient peripheral blood mononuclear cells (PBMCs) mark fibrotic progression and that, in murine MPN models, absence of hematopoietic Gli1, but not Gli2 or Smo, significantly reduces MPN phenotype and fibrosis, indicating that GLI1 in the MPN clone can be activated in a non-canonical fashion. Additionally, we establish that hematopoietic Gli1 has a significant effect on stromal cells, mediated through a druggable MIF-CD74 axis. These data highlight the complex interplay between alterations in the MPN clone and activation of stromal cells and indicate that Gli1 represents a promising therapeutic target in MPNs, particularly that Hh signaling is dispensable for normal hematopoiesis.
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Affiliation(s)
- Jessica E Pritchard
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany; Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Juliette E Pearce
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Inge A M Snoeren
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stijn N R Fuchs
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Katrin Götz
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Fabian Peisker
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Silke Wagner
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Adam Benabid
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Niklas Lutterbach
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Vanessa Klöker
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
| | - James S Nagai
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
| | - Monica T Hannani
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Hospital, Aachen, Germany; Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna K Galyga
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Ellen Sistemich
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Bella Banjanin
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Niclas Flosdorf
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany
| | - Eric Bindels
- Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kathrin Olschok
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University Hospital, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Katharina Biaesch
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University Hospital, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University Hospital, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | | | - Andrew Dunbar
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rita Sarkis
- Laboratory of Regenerative Hematopoiesis, Department of Biomedical Sciences (DSB), Université de Lausanne (UNIL), Lausanne, Switzerland
| | - Olaia Naveiras
- Laboratory of Regenerative Hematopoiesis, Department of Biomedical Sciences (DSB), Université de Lausanne (UNIL), Lausanne, Switzerland
| | - Marie-Luise Berres
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany; Medical Department III, RWTH University Hospital Aachen, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University Hospital, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
| | - Hélène F E Gleitz
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Hospital, Aachen, Germany; Department of Internal Medicine, Nephrology and Transplantation, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Rebekka K Schneider
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen, Germany; Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands; Oncode Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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10
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Suehnholz SP, Nissan MH, Zhang H, Kundra R, Nandakumar S, Lu C, Carrero S, Dhaneshwar A, Fernandez N, Xu BW, Arcila ME, Zehir A, Syed A, Brannon AR, Rudolph JE, Paraiso E, Sabbatini PJ, Levine RL, Dogan A, Gao J, Ladanyi M, Drilon A, Berger MF, Solit DB, Schultz N, Chakravarty D. Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer. Cancer Discov 2024; 14:49-65. [PMID: 37849038 PMCID: PMC10784742 DOI: 10.1158/2159-8290.cd-23-0467] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 05/11/2023] [Revised: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023]
Abstract
There is a continuing debate about the proportion of cancer patients that benefit from precision oncology, attributable in part to conflicting views as to which molecular alterations are clinically actionable. To quantify the expansion of clinical actionability since 2017, we annotated 47,271 solid tumors sequenced with the MSK-IMPACT clinical assay using two temporally distinct versions of the OncoKB knowledge base deployed 5 years apart. Between 2017 and 2022, we observed an increase from 8.9% to 31.6% in the fraction of tumors harboring a standard care (level 1 or 2) predictive biomarker of therapy response and an almost halving of tumors carrying nonactionable drivers (44.2% to 22.8%). In tumors with limited or no clinical actionability, TP53 (43.2%), KRAS (19.2%), and CDKN2A (12.2%) were the most frequently altered genes. SIGNIFICANCE Although clear progress has been made in expanding the availability of precision oncology-based treatment paradigms, our results suggest a continued unmet need for innovative therapeutic strategies, particularly for cancers with currently undruggable oncogenic drivers. See related commentary by Horak and Fröhling, p. 18. This article is featured in Selected Articles from This Issue, p. 5.
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Affiliation(s)
- Sarah P. Suehnholz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Moriah H. Nissan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Calvin Lu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephanie Carrero
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amanda Dhaneshwar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicole Fernandez
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin W. Xu
- Department of Computer Science, Yale University, New Haven, Connecticut
| | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aijazuddin Syed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julia E. Rudolph
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eder Paraiso
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul J. Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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11
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Dunbar AJ, Bowman RL, Park YC, O'Connor K, Izzo F, Myers RM, Karzai A, Zaroogian Z, Kim WJ, Fernandez-Maestre I, Waarts MR, Nazir A, Xiao W, Codilupi T, Brodsky M, Farina M, Cai L, Cai SF, Wang B, An W, Yang JL, Mowla S, Eisman SE, Hanasoge Somasundara AV, Glass JL, Mishra T, Houston R, Guzzardi E, Martinez Benitez AR, Viny AD, Koche RP, Meyer SC, Landau DA, Levine RL. Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. Cancer Discov 2024:733210. [PMID: 38230747 DOI: 10.1158/2159-8290.cd-22-0952] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 01/18/2024]
Abstract
Gain-of-function mutations activating JAK/STAT signaling are seen in the majority of patients with myeloproliferative neoplasms (MPNs), most commonly JAK2V617F. While clinically-approved JAK inhibitors improve symptoms and outcomes in MPNs, remissions are rare, and mutant allele burden does not substantively change with chronic therapy. We hypothesized this is due to limitations of current JAK inhibitors to potently and specifically abrogate mutant JAK2 signaling. We therefore developed a conditionally inducible mouse model allowing for sequential activation, and then inactivation, of Jak2V617F from its endogenous locus using a combined, Dre-rox/Cre-lox dual recombinase system. Jak2V617F deletion abrogates MPN features, induces depletion of mutant-specific hematopoietic stem/progenitor cells, and extends overall survival to an extent not observed with pharmacologic JAK inhibition, including when co-occurring with somatic Tet2 loss. Our data suggest JAK2V617F represents the best therapeutic target in MPNs and demonstrate the therapeutic relevance of a dual-recombinase system to assess mutant-specific oncogenic dependencies in vivo.
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Affiliation(s)
- Andrew J Dunbar
- Memorial Sloan Kettering Cancer Center, New York, United States
| | - Robert L Bowman
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Young C Park
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Franco Izzo
- Weill Cornell Medicine, New York, NY, United States
| | | | - Abdul Karzai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Zach Zaroogian
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Won Jun Kim
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Abbas Nazir
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Wenbin Xiao
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Max Brodsky
- Johns Hopkins University School of Medicine, Baltimore, United States
| | - Mirko Farina
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Louise Cai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sheng F Cai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Benjamin Wang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Wenbin An
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Julie L Yang
- Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shoron Mowla
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Shira E Eisman
- Columbia University Medical Center, New York, United States
| | | | - Jacob L Glass
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Tanmay Mishra
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Remie Houston
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Emily Guzzardi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Aaron D Viny
- Columbia University Medical Center, New York, NY, United States
| | - Richard P Koche
- Memorial Sloan Kettering Cancer Center, New York, United States
| | | | | | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
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12
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Sánchez Vela P, Trowbridge JJ, Levine RL. Author Correction: Clonal hematopoiesis, aging and Alzheimer's disease. Nat Med 2024; 30:305. [PMID: 37985693 DOI: 10.1038/s41591-023-02718-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Affiliation(s)
- Pablo Sánchez Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Doctoral Programme in Biomedicine, University of Barcelona, Barcelona, Spain
| | | | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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13
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Nazaret A, Fan JL, Lavallée VP, Cornish AE, Kiseliovas V, Masilionis I, Chun J, Bowman RL, Eisman SE, Wang J, Shi L, Levine RL, Mazutis L, Blei D, Pe'er D, Azizi E. Deep generative model deciphers derailed trajectories in acute myeloid leukemia. bioRxiv 2023:2023.11.11.566719. [PMID: 38014231 PMCID: PMC10680623 DOI: 10.1101/2023.11.11.566719] [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: 11/29/2023]
Abstract
Single-cell genomics has the potential to map cell states and their dynamics in an unbiased way in response to perturbations like disease. However, elucidating the cell-state transitions from healthy to disease requires analyzing data from perturbed samples jointly with unperturbed reference samples. Existing methods for integrating and jointly visualizing single-cell datasets from distinct contexts tend to remove key biological differences or do not correctly harmonize shared mechanisms. We present Decipher, a model that combines variational autoencoders with deep exponential families to reconstruct derailed trajectories ( https://github.com/azizilab/decipher ). Decipher jointly represents normal and perturbed single-cell RNA-seq datasets, revealing shared and disrupted dynamics. It further introduces a novel approach to visualize data, without the need for methods such as UMAP or TSNE. We demonstrate Decipher on data from acute myeloid leukemia patient bone marrow specimens, showing that it successfully characterizes the divergence from normal hematopoiesis and identifies transcriptional programs that become disrupted in each patient when they acquire NPM1 driver mutations.
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14
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Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA. Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. J Exp Med 2023; 220:e20230011. [PMID: 37615936 PMCID: PMC10450614 DOI: 10.1084/jem.20230011] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/12/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.
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Affiliation(s)
- Yang Feng
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Qingchen Yuan
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Rachel C. Newsome
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley N. Zuniga
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kendra N. Hall
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Cassandra M. Bernsten
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Daniil E. Shabashvili
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kathryn I. Krajcik
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Zachary J. Zaroogian
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Heidi L. Casellas Roman
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Christian Jobin
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
- Immunology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
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15
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Galera P, Dilip D, Derkach A, Chan A, Zhang Y, Persuad S, Mishera T, Liu Y, Famulare C, Gao Q, Mata DA, Arcila M, Geyer MB, Stein E, Dogan A, Levine RL, Roshal M, Glass J, Xiao W. Acute myeloid leukemia with mixed phenotype is characterized by stemness transcriptomic signatures and limited lineage plasticity. medRxiv 2023:2023.11.01.23297696. [PMID: 37961275 PMCID: PMC10635245 DOI: 10.1101/2023.11.01.23297696] [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: 11/15/2023]
Abstract
Mixed phenotype (MP) in acute leukemias poses unique classification and management dilemmas and can be seen in entities other than de novo mixed phenotype acute leukemia (MPAL). Although WHO classification empirically recommends excluding AML with myelodysplasia related changes (AML-MRC) and therapy related AML (t-AML) with mixed phenotype (AML-MP) from MPAL, there is lack of studies investigating the clinical, genetic, and biologic features of AML-MP. We report the first cohort of AML-MRC and t-AML with MP integrating their clinical, immunophenotypic, genomic and transcriptomic features with comparison to MPAL and AML-MRC/t-AML without MP. Both AML cohorts with and without MP shared similar clinical features including adverse outcomes but were different from MPAL. The genomic landscape of AML-MP overlaps with AML without MP but differs from MPAL. AML-MP harbors more frequent RUNX1 mutations than AML without MP and MPAL. RUNX1 mutations did not impact the survival of patients with MPAL. Unsupervised hierarchal clustering based on immunophenotype identified biologically distinct clusters with phenotype/genotype correlation and outcome differences. Furthermore, transcriptomic analysis showed an enrichment for stemness signature in AML-MP and AML without MP as compared to MPAL. Lastly, MPAL but not AML-MP often switched to lymphoid only immunophenotype after treatment. Expression of transcription factors critical for lymphoid differentiation were upregulated only in MPAL, but not in AML-MP. Our study for the first time demonstrates that AML-MP clinically and biologically resembles its AML counterpart without MP and differs from MPAL, supporting the recommendation to exclude these patients from the diagnosis of MPAL. Future studies are needed to elucidate the molecular mechanism of mixed phenotype in AML. Key points AML-MP clinically and biologically resembles AML but differs from MPAL. AML-MP shows RUNX1 mutations, stemness signatures and limited lymphoid lineage plasticity.
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16
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Cai SF, Levine RL. 15 years after a giant leap for cancer genomics. Nature 2023; 623:920-921. [PMID: 38012374 DOI: 10.1038/d41586-023-03626-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
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17
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Ptashkin RN, Ewalt MD, Jayakumaran G, Kiecka I, Bowman AS, Yao J, Casanova J, Lin YTD, Petrova-Drus K, Mohanty AS, Bacares R, Benhamida J, Rana S, Razumova A, Vanderbilt C, Balakrishnan Rema A, Rijo I, Son-Garcia J, de Bruijn I, Zhu M, Lachhander S, Wang W, Haque MS, Seshan VE, Wang J, Liu Y, Nafa K, Borsu L, Zhang Y, Aypar U, Suehnholz SP, Chakravarty D, Park JH, Abdel-Wahab O, Mato AR, Xiao W, Roshal M, Yabe M, Batlevi CL, Giralt S, Salles G, Rampal R, Tallman M, Stein EM, Younes A, Levine RL, Perales MA, van den Brink MRM, Dogan A, Ladanyi M, Berger MF, Brannon AR, Benayed R, Zehir A, Arcila ME. Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing. Nat Commun 2023; 14:6895. [PMID: 37898613 PMCID: PMC10613284 DOI: 10.1038/s41467-023-42585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Genomic profiling of hematologic malignancies has augmented our understanding of variants that contribute to disease pathogenesis and supported development of prognostic models that inform disease management in the clinic. Tumor only sequencing assays are limited in their ability to identify definitive somatic variants, which can lead to ambiguity in clinical reporting and patient management. Here, we describe the MSK-IMPACT Heme cohort, a comprehensive data set of somatic alterations from paired tumor and normal DNA using a hybridization capture-based next generation sequencing platform. We highlight patterns of mutations, copy number alterations, and mutation signatures in a broad set of myeloid and lymphoid neoplasms. We also demonstrate the power of appropriate matching to make definitive somatic calls, including in patients who have undergone allogeneic stem cell transplant. We expect that this resource will further spur research into the pathobiology and clinical utility of clinical sequencing for patients with hematologic neoplasms.
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Affiliation(s)
- Ryan N Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- C2i Genomics, New York, NY, USA
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Gowtham Jayakumaran
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guardant Health, Palo Alto, CA, USA
| | - Iwona Kiecka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Te David Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruben Bacares
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Razumova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anoop Balakrishnan Rema
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie Son-Garcia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohammad S Haque
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiajing Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah P Suehnholz
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jae H Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony R Mato
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Connie Lee Batlevi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raajit Rampal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Tallman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anas Younes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Oncology R&D, AstraZeneca, New York, NY, USA.
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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18
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Borate U, Yang F, Press R, Ruppert AS, Jones D, Caruthers S, Zhao W, Vergilio JA, Pavlick DC, Juckett L, Norris B, Bucy T, Burd A, Stein EM, Patel P, Baer MR, Stock W, Schiller G, Blum W, Kovacsovics T, Litzow M, Foran J, Heerema NA, Rosenberg L, Marcus S, Yocum A, Stefanos M, Druker B, Byrd JC, Levine RL, Mims A. Samples from patients with AML show high concordance in detection of mutations by NGS at local institutions vs central laboratories. Blood Adv 2023; 7:6048-6054. [PMID: 37459200 PMCID: PMC10582272 DOI: 10.1182/bloodadvances.2022009008] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/20/2023] [Indexed: 10/12/2023] Open
Abstract
Next-generation sequencing (NGS) to identify pathogenic mutations is an integral part of acute myeloid leukemia (AML) therapeutic decision-making. The concordance in identifying pathogenic mutations among different NGS platforms at different diagnostic laboratories has been studied in solid tumors but not in myeloid malignancies to date. To determine this interlaboratory concordance, we collected a total of 194 AML bone marrow or peripheral blood samples from newly diagnosed patients with AML enrolled in the Beat AML Master Trial (BAMT) at 2 academic institutions. We analyzed the diagnostic samples from patients with AML for the detection of pathogenic myeloid mutations in 8 genes (DNMT3A, FLT3, IDH1, IDH2, NPM1, TET2, TP53, and WT1) locally using the Hematologic Neoplasm Mutation Panel (50-gene myeloid indication filter) (site 1) or the GeneTrails Comprehensive Heme Panel (site 2) at the 2 institutions and compared them with the central results from the diagnostic laboratory for the BAMT, Foundation Medicine, Inc. The overall percent agreement was over 95% each in all 8 genes, with almost perfect agreement (κ > 0.906) in all but WT1, which had substantial agreement (κ = 0.848) when controlling for site. The minimal discrepancies were due to reporting variants of unknown significance (VUS) for the WT1 and TP53 genes. These results indicate that the various NGS methods used to analyze samples from patients with AML enrolled in the BAMT show high concordance, a reassuring finding given the wide use of NGS for therapeutic decision-making in AML.
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Affiliation(s)
- Uma Borate
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Fei Yang
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Richard Press
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Amy S. Ruppert
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Dan Jones
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Sean Caruthers
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Weiqiang Zhao
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | | | - Brianna Norris
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Taylor Bucy
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Amy Burd
- Leukemia and Lymphoma Society, Rye Brook, NY
| | | | - Prapti Patel
- The University of Texas Southwestern Medical Center, Dallas, TX
| | - Maria R. Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Wendy Stock
- Division of Hematology-Oncology, Department of Internal Medicine, University of Chicago, Chicago, IL
| | - Gary Schiller
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - William Blum
- Winship Cancer Institute of Emory University, Atlanta, GA
| | - Tibor Kovacsovics
- Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN
| | - James Foran
- Division of Hematology, Mayo Clinic Florida, Jacksonville, FL
| | - Nyla A. Heerema
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | | | - Mona Stefanos
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Brian Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - John C. Byrd
- Division of Hematology-Oncology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | | | - Alice Mims
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
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19
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Amor C, Fernández-Maestre I, Chowdhury S, Ho YJ, Nadella S, Graham C, Carrasco SE, Nnuji-John E, Feucht J, Hinterleitner C, Barthet VJ, Boyer JA, Mezzadra R, Wereski MG, Tuveson DA, Levine RL, Jones LW, Sadelain M, Lowe SW. Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction. Res Sq 2023:rs.3.rs-3385749. [PMID: 37841853 PMCID: PMC10571605 DOI: 10.21203/rs.3.rs-3385749/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: 10/17/2023]
Abstract
Senescent cells accumulate in organisms over time because of tissue damage and impaired immune surveillance and contribute to age-related tissue decline1,2. In agreement, genetic ablation studies reveal that elimination of senescent cells from aged tissues can ameliorate various age-related pathologies, including metabolic dysfunction and decreased physical fitness3-7. While small-molecule drugs capable of eliminating senescent cells (known as 'senolytics') partially replicate these phenotypes, many have undefined mechanisms of action and all require continuous administration to be effective. As an alternative approach, we have developed a cell-based senolytic therapy based on chimeric antigen receptor (CAR) T cells targeting uPAR, a cell-surface protein upregulated on senescent cells, and previously showed these can safely and efficiently eliminate senescent cells in young animals and reverse liver fibrosis8. We now show that uPAR-positive senescent cells accumulate during physiological aging and that they can be safely targeted with senolytic CAR T cells. Treatment with anti uPAR CAR T cells ameliorates metabolic dysfunction by improving glucose tolerance and exercise capacity in physiological aging as well as in a model of metabolic syndrome. Importantly, a single administration of a low dose of these senolytic CAR T cells is sufficient to achieve long-term therapeutic and preventive effects.
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Affiliation(s)
- Corina Amor
- Cold Spring Harbor Laboratory. Cold Spring Harbor, NY, USA
| | - Inés Fernández-Maestre
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yu-Jui Ho
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Courtenay Graham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian E. Carrasco
- Laboratory of Comparative Pathology. Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center, and Rockefeller University, New York, NY, USA
| | - Emmanuella Nnuji-John
- Cold Spring Harbor Laboratory. Cold Spring Harbor, NY, USA
- Cold Spring Harbor School of Biological Sciences, Cold Spring Harbor, NY, USA
| | - Judith Feucht
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cluster of Excellence iFIT, University Children’s Hospital Tuebingen, Tuebingen, Germany
| | - Clemens Hinterleitner
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valentin J.A. Barthet
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob A. Boyer
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Riccardo Mezzadra
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew G Wereski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Lee W Jones
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics. Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, USA
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20
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Robinson TM, Bowman RL, Persaud S, Liu Y, Neigenfind R, Gao Q, Zhang J, Sun X, Miles LA, Cai SF, Sciambi A, Llanso A, Famulare C, Goldberg A, Dogan A, Roshal M, Levine RL, Xiao W. Single-cell genotypic and phenotypic analysis of measurable residual disease in acute myeloid leukemia. Sci Adv 2023; 9:eadg0488. [PMID: 37729414 PMCID: PMC10881057 DOI: 10.1126/sciadv.adg0488] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/21/2023] [Indexed: 09/22/2023]
Abstract
Measurable residual disease (MRD), defined as the population of cancer cells that persist following therapy, serves as the critical reservoir for disease relapse in acute myeloid leukemia and other malignancies. Understanding the biology enabling MRD clones to resist therapy is necessary to guide the development of more effective curative treatments. Discriminating between residual leukemic clones, preleukemic clones, and normal precursors remains a challenge with current MRD tools. Here, we developed a single-cell MRD (scMRD) assay by combining flow cytometric enrichment of the targeted precursor/blast population with integrated single-cell DNA sequencing and immunophenotyping. Our scMRD assay shows high sensitivity of approximately 0.01%, deconvolutes clonal architecture, and provides clone-specific immunophenotypic data. In summary, our scMRD assay enhances MRD detection and simultaneously illuminates the clonal architecture of clonal hematopoiesis/preleukemic and leukemic cells surviving acute myeloid leukemia therapy.
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Affiliation(s)
- Troy M. Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonali Persaud
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rosemary Neigenfind
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jingping Zhang
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaotian Sun
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sheng F. Cai
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron Goldberg
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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21
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McCarter JGW, Nemirovsky D, Famulare CA, Farnoud N, Mohanty AS, Stone-Molloy ZS, Chervin J, Ball BJ, Epstein-Peterson ZD, Arcila ME, Stonestrom AJ, Dunbar A, Cai SF, Glass JL, Geyer MB, Rampal RK, Berman E, Abdel-Wahab OI, Stein EM, Tallman MS, Levine RL, Goldberg AD, Papaemmanuil E, Zhang Y, Roshal M, Derkach A, Xiao W. Interaction between myelodysplasia-related gene mutations and ontogeny in acute myeloid leukemia. Blood Adv 2023; 7:5000-5013. [PMID: 37142255 PMCID: PMC10471939 DOI: 10.1182/bloodadvances.2023009675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/01/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
Accurate classification and risk stratification are critical for clinical decision making in patients with acute myeloid leukemia (AML). In the newly proposed World Health Organization and International Consensus classifications of hematolymphoid neoplasms, the presence of myelodysplasia-related (MR) gene mutations is included as 1 of the diagnostic criteria for AML, AML-MR, based largely on the assumption that these mutations are specific for AML with an antecedent myelodysplastic syndrome. ICC also prioritizes MR gene mutations over ontogeny (as defined in the clinical history). Furthermore, European LeukemiaNet (ELN) 2022 stratifies these MR gene mutations into the adverse-risk group. By thoroughly annotating a cohort of 344 newly diagnosed patients with AML treated at the Memorial Sloan Kettering Cancer Center, we show that ontogeny assignments based on the database registry lack accuracy. MR gene mutations are frequently observed in de novo AML. Among the MR gene mutations, only EZH2 and SF3B1 were associated with an inferior outcome in the univariate analysis. In a multivariate analysis, AML ontogeny had independent prognostic values even after adjusting for age, treatment, allo-transplant and genomic classes or ELN risks. Ontogeny also helped stratify the outcome of AML with MR gene mutations. Finally, de novo AML with MR gene mutations did not show an adverse outcome. In summary, our study emphasizes the importance of accurate ontogeny designation in clinical studies, demonstrates the independent prognostic value of AML ontogeny, and questions the current classification and risk stratification of AML with MR gene mutations.
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Affiliation(s)
- Joseph G. W. McCarter
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Memorial Sloan Kettering Kids, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Nemirovsky
- Department of Epidemiology & Biostatistics, Biostatistics Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Noushin Farnoud
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S. Mohanty
- Department of Pathology and Laboratory Medicine, Diagnostic Molecular Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zoe S. Stone-Molloy
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jordan Chervin
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian J. Ball
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Diagnostic Molecular Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron J. Stonestrom
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew Dunbar
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sheng F. Cai
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob L. Glass
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark B. Geyer
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raajit K. Rampal
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ellin Berman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Omar I. Abdel-Wahab
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Molecular Cancer Medicine Service, Human Oncogenesis & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M. Stein
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Molecular Cancer Medicine Service, Human Oncogenesis & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron D. Goldberg
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elli Papaemmanuil
- Department of Epidemiology & Biostatistics, Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andriy Derkach
- Department of Epidemiology & Biostatistics, Biostatistics Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY
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22
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Foran JM, Sun Z, Lai C, Fernandez HF, Cripe LD, Ketterling RP, Racevskis J, Luger SM, Paietta E, Lazarus HM, Zhang Y, Bennett JM, Levine RL, Rowe JM, Litzow MR, Tallman MS. Obesity in adult acute myeloid leukemia is not associated with inferior response or survival even when dose capping anthracyclines: An ECOG-ACRIN analysis. Cancer 2023; 129:2479-2490. [PMID: 37185873 PMCID: PMC10932613 DOI: 10.1002/cncr.34807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/04/2023] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Obesity (body mass index [BMI] ≥30 kg/m2 ) is an important epidemiological risk factor for developing acute myeloid leukemia (AML). Therefore, the authors studied the association of obesity with clinical and genetic phenotype and its impact on outcome in adults with AML. METHODS The authors analyzed BMI in 1088 adults who were receiving intensive remission induction and consolidation therapy in two prospective, randomized therapeutic clinical trials of the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network: E1900 (ClinicalTrials.gov identifier NCT00049517; patients younger than 60 years) and E3999 (ClinicalTrials.gov identifier NCT00046930; patients aged 60 years or older). RESULTS Obesity was prevalent at diagnosis (33%) and, compared with nonobesity, was associated with intermediate-risk cytogenetics group (p = .008), poorer performance status (p = .01), and a trend toward older age (p = .06). Obesity was not associated with somatic mutations among a selected 18-gene panel that was tested in a subset of younger patients. Obesity was not associated with clinical outcome (including complete remission, early death, or overall survival), and the authors did not identify any patient subgroup that had inferior outcomes based on BMI. Obese patients were significantly more likely to receive <90% of the intended daunorubicin dose despite protocol specification, particularly in the E1900 high-dose (90 mg/m2 ) daunorubicin arm (p = .002); however, this did not correlate with inferior overall survival on multivariate analysis (hazard ratio, 1.39; 95% confidence interval, 0.90-2.13; p = .14). CONCLUSIONS Obesity is associated with unique clinical and disease-related phenotypic features in AML and may influence physician treatment decisions regarding daunorubicin dosing. However, the current study demonstrates that obesity is not a factor in survival, and strict adherence to body surface area-based dosing is not necessary because dose adjustments do not affect outcomes.
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Affiliation(s)
- James M. Foran
- Division of Hematology and Medical Oncology and Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, Florida
| | - Zhuoxin Sun
- ECOG-ACRIN Biostatistics Center, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Catherine Lai
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hugo F. Fernandez
- Blood & Marrow Transplantation, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Larry D. Cripe
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Rhett P. Ketterling
- Department of Laboratory Medicine and Pathology and Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | | | - Selina M. Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Yanming Zhang
- Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John M. Bennett
- Hematopathology Division, Department of Pathology, James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | - Ross L. Levine
- Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Mark R. Litzow
- Department of Laboratory Medicine and Pathology and Division of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Martin S. Tallman
- Northwestern University Feinberg School of Medicine, Robert H.Lurie Comprehensive Cancer Center, Chicago, Illinois
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23
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Novetsky Friedman D, Chan ICC, Moskowitz CS, Li S, Turner K, Liu J, Bouvier N, Walsh MF, Spitzer B, Kung AL, Berger M, Cooper MA, Pusic I, Uy G, Link D, Druley TE, Diaz LA, Levine RL, Shukla N, Bolton KL. Clonal hematopoiesis in survivors of childhood cancer. Blood Adv 2023; 7:4102-4106. [PMID: 37235557 PMCID: PMC10388722 DOI: 10.1182/bloodadvances.2023009817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/29/2023] [Indexed: 05/28/2023] Open
Affiliation(s)
| | - Irenaeus C. C. Chan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Chaya S. Moskowitz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shanita Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kimberly Turner
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jie Liu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Megan A. Cooper
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Iskra Pusic
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Geoffrey Uy
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel Link
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
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24
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Boucai L, Ptashkin RN, Levine RL, Fagin JA. Effects of radioactive iodine on clonal hematopoiesis in patients with thyroid cancer: A prospective study. Clin Endocrinol (Oxf) 2023; 99:122-129. [PMID: 37088956 PMCID: PMC10644358 DOI: 10.1111/cen.14925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
OBJECTIVE Exposure to therapeutic radioactive iodine (RAI) is associated with an increased relative risk of myeloid malignancies. Clonal hematopoiesis (CH) is a precursor state that can be detected in blood of healthy individuals decades before overt development of leukemia. We prospective studied the effects of RAI on CH. DESIGN Prospective cohort study. PATIENTS AND MEASUREMENTS We examined the effect of RAI on CH in 20 patients exposed to RAI for thyroid carcinoma and 20 age-matched unexposed controls. CH status was determined at baseline, 6, 12, 18 and 24 months. We also examined the effect of CH on structural progression of disease. RESULTS No CH mutations were observed in the patient population that were not present at baseline. Using a variant allelic fraction (VAF) of 2% to define CH, 6/20 older patients (55-80 years old) had CH compared to 2/20 younger patients (20-40 years old) (p = 0.11). Six patients exposed to RAI had CH compared to two patients not exposed to RAI (30% vs. 10%, p = 0.11). There was no significant difference in CH VAF increase in patients treated with RAI compared to untreated age-matched controls (3.8% vs. 1.2%, p = 0.2). CH was significantly associated with somatic BRAFV600E mutations and with worse progression-free survival in the overall cohort as well as among BRAFV600E-mutant tumors. CONCLUSIONS There was no increase in CH in patients treated with RAI over a 2-year follow-up period. Larger studies with longer follow-up periods are needed to investigate the association between RAI and clonal dynamics. The presence of CH is associated with worse structural progression in both BRAFV600E-mutant and wild-type thyroid cancers.
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Affiliation(s)
- Laura Boucai
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan N. Ptashkin
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ross L. Levine
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James A. Fagin
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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25
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Sánchez Vela P, Trowbridge JJ, Levine RL. Clonal hematopoiesis, aging and Alzheimer's disease. Nat Med 2023; 29:1605-1606. [PMID: 37402877 DOI: 10.1038/s41591-023-02406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Affiliation(s)
- Pablo Sánchez Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Doctoral Programme in Biomedicine, University of Barcelona, Barcelona, Spain
| | | | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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26
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Saliba AN, Kaufmann SH, Stein EM, Patel PA, Baer MR, Stock W, Deininger M, Blum W, Schiller GJ, Olin RL, Litzow MR, Lin TL, Ball BJ, Boyiadzis MM, Traer E, Odenike O, Arellano ML, Walker A, Duong VH, Kovacsovics T, Collins RH, Shoben AB, Heerema NA, Foster MC, Peterson KL, Schneider PA, Martycz M, Gana TJ, Rosenberg L, Marcus S, Yocum AO, Chen T, Stefanos M, Mims AS, Borate U, Burd A, Druker BJ, Levine RL, Byrd JC, Foran JM. Pevonedistat with azacitidine in older patients with TP53-mutated AML: a phase 2 study with laboratory correlates. Blood Adv 2023; 7:2360-2363. [PMID: 36315007 PMCID: PMC10230164 DOI: 10.1182/bloodadvances.2022008625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Antoine N. Saliba
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Scott H. Kaufmann
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN
| | - Eytan M. Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prapti A. Patel
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Maria R. Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Wendy Stock
- Department of Medicine, Section of Hematology Oncology, University of Chicago, Chicago, IL
| | - Michael Deininger
- Division of Hematology and Oncology, Department of Medicine, University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - William Blum
- Winship Cancer Institute of Emory University, Atlanta, GA
| | - Gary J. Schiller
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA
| | | | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
| | - Tara L. Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, University of Kansas Medical Center, Kansas City, KS
| | - Brian J. Ball
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA
| | | | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Olatoyosi Odenike
- Department of Medicine, Section of Hematology Oncology, University of Chicago, Chicago, IL
| | | | | | - Vu H. Duong
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Tibor Kovacsovics
- Division of Hematology and Oncology, Department of Medicine, University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - Robert H. Collins
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | | | | | - Matthew C. Foster
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC
| | - Kevin L. Peterson
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN
| | - Paula A. Schneider
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | | | | | | | - Amy Burd
- Leukemia and Lymphoma Society, White Plains, NY
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Ross L. Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John C. Byrd
- Department of Medicine, University of Cincinnati, Cincinnati, OH
| | - James M. Foran
- Division of Hematology-Oncology, Department of Medicine, Mayo Clinic, Jacksonville, FL
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27
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Dunbar AJ, Kim D, Lu M, Farina M, Bowman RL, Yang JL, Park Y, Karzai A, Xiao W, Zaroogian Z, O’Connor K, Mowla S, Gobbo F, Verachi P, Martelli F, Sarli G, Xia L, Elmansy N, Kleppe M, Chen Z, Xiao Y, McGovern E, Snyder J, Krishnan A, Hill C, Cordner K, Zouak A, Salama ME, Yohai J, Tucker E, Chen J, Zhou J, McConnell T, Migliaccio AR, Koche R, Rampal R, Fan R, Levine RL, Hoffman R. CXCL8/CXCR2 signaling mediates bone marrow fibrosis and is a therapeutic target in myelofibrosis. Blood 2023; 141:2508-2519. [PMID: 36800567 PMCID: PMC10273167 DOI: 10.1182/blood.2022015418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 02/19/2023] Open
Abstract
Proinflammatory signaling is a hallmark feature of human cancer, including in myeloproliferative neoplasms (MPNs), most notably myelofibrosis (MF). Dysregulated inflammatory signaling contributes to fibrotic progression in MF; however, the individual cytokine mediators elicited by malignant MPN cells to promote collagen-producing fibrosis and disease evolution are yet to be fully elucidated. Previously, we identified a critical role for combined constitutive JAK/STAT and aberrant NF-κB proinflammatory signaling in MF development. Using single-cell transcriptional and cytokine-secretion studies of primary cells from patients with MF and the human MPLW515L (hMPLW515L) murine model of MF, we extend our previous work and delineate the role of CXCL8/CXCR2 signaling in MF pathogenesis and bone marrow fibrosis progression. Hematopoietic stem/progenitor cells from patients with MF are enriched for a CXCL8/CXCR2 gene signature and display enhanced proliferation and fitness in response to an exogenous CXCL8 ligand in vitro. Genetic deletion of Cxcr2 in the hMPLW515L-adoptive transfer model abrogates fibrosis and extends overall survival, and pharmacologic inhibition of the CXCR1/2 pathway improves hematologic parameters, attenuates bone marrow fibrosis, and synergizes with JAK inhibitor therapy. Our mechanistic insights provide a rationale for therapeutic targeting of the CXCL8/CXCR2 pathway among patients with MF.
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Affiliation(s)
- Andrew J. Dunbar
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Min Lu
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Hematology/Oncology, Tisch Cancer Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Mirko Farina
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Blood Diseases and Bone Marrow Transplantation Unit, Cell Therapies and Hematology Research Program, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Julie L. Yang
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Young Park
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abdul Karzai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zach Zaroogian
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kavi O’Connor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shoron Mowla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francesca Gobbo
- Department of Veterinary Medical Sciences, University of Bologna, Italy
| | - Paola Verachi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Fabrizio Martelli
- Department of Technology and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Sarli
- Department of Veterinary Medical Sciences, University of Bologna, Italy
| | - Lijuan Xia
- Division of Hematology/Oncology, Tisch Cancer Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nada Elmansy
- Division of Hematology/Oncology, Tisch Cancer Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Maria Kleppe
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Erin McGovern
- Leukemia Service, Department of Medicine and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jenna Snyder
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aishwarya Krishnan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Corrine Hill
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Keith Cordner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anouar Zouak
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mohamed E. Salama
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pathology, Mayo Clinic School of Medicine, Rochester, MN
| | - Jayden Yohai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Anna R. Migliaccio
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
- Altius Institute for Biomedical Sciences, Seattle, WA
- Unit of Microscopic and Ultrastructural Anatomy, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Richard Koche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raajit Rampal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald Hoffman
- Myeloproliferative Neoplasm-Research Consortium, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Hematology/Oncology, Tisch Cancer Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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28
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Vekariya U, Toma M, Nieborowska-Skorska M, Le BV, Caron MC, Kukuyan AM, Sullivan-Reed K, Podszywalow-Bartnicka P, Chitrala KN, Atkins J, Drzewiecka M, Feng W, Chan J, Chatla S, Golovine K, Jelinek J, Sliwinski T, Ghosh J, Matlawska-Wasowska K, Chandramouly G, Nejati R, Wasik M, Sykes SM, Piwocka K, Hadzijusufovic E, Valent P, Pomerantz RT, Morton G, Childers W, Zhao H, Paietta EM, Levine RL, Tallman MS, Fernandez HF, Litzow MR, Gupta GP, Masson JY, Skorski T. DNA polymerase θ protects leukemia cells from metabolically induced DNA damage. Blood 2023; 141:2372-2389. [PMID: 36580665 PMCID: PMC10273171 DOI: 10.1182/blood.2022018428] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK-dependent nonhomologous end-joining, was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.
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Affiliation(s)
- Umeshkumar Vekariya
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Monika Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Marie-Christine Caron
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Anna-Mariya Kukuyan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Kumaraswamy N. Chitrala
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Jessica Atkins
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Malgorzata Drzewiecka
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joe Chan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Stephen M. Sykes
- Division of Hematology/Oncology, Department of Pediatrics, Washington University at St. Louis, St. Louis, MO
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Emir Hadzijusufovic
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
- Department for Companion Animals & Horses, Clinic for Internal Medicine and Infectious Diseases, University of Veterinary Medicine Vienna, Austria
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - George Morton
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Wayne Childers
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Huaqing Zhao
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Elisabeth M. Paietta
- Department of Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hugo F. Fernandez
- Moffitt Malignant Hematology & Cellular Therapy at Memorial Healthcare System, Pembroke Pines, FL
| | - Mark R. Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jean-Yves Masson
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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29
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Duong VH, Ruppert AS, Mims AS, Borate U, Stein EM, Baer MR, Stock W, Kovacsovics T, Blum W, Arellano ML, Schiller GJ, Olin RL, Foran JM, Litzow MR, Lin TL, Patel PA, Foster MC, Redner RL, Al-Mansour Z, Cogle CR, Swords RT, Collins RH, Vergilio JA, Heerema NA, Rosenberg L, Yocum AO, Marcus S, Chen T, Druggan F, Stefanos M, Gana TJ, Shoben AB, Druker BJ, Burd A, Byrd JC, Levine RL, Boyiadzis MM. Entospletinib with decitabine in acute myeloid leukemia with mutant TP53 or complex karyotype: A phase 2 substudy of the Beat AML Master Trial. Cancer 2023. [PMID: 37078412 DOI: 10.1002/cncr.34780] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/24/2022] [Accepted: 01/13/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND Patients with acute myeloid leukemia (AML) who have tumor protein p53 (TP53) mutations or a complex karyotype have a poor prognosis, and hypomethylating agents are often used. The authors evaluated the efficacy of entospletinib, an oral inhibitor of spleen tyrosine kinase, combined with decitabine in this patient population. METHODS This was a multicenter, open-label, phase 2 substudy of the Beat AML Master Trial (ClinicalTrials.gov identifier NCT03013998) using a Simon two-stage design. Eligible patients aged 60 years or older who had newly diagnosed AML with mutations in TP53 with or without a complex karyotype (cohort A; n = 45) or had a complex karyotype without TP53 mutation (cohort B; n = 13) received entospletinib 400 mg twice daily with decitabine 20 mg/m2 on days 1-10 every 28 days for up to three induction cycles, followed by up to 11 consolidation cycles, in which decitabine was reduced to days 1-5. Entospletinib maintenance was given for up to 2 years. The primary end point was complete remission (CR) and CR with hematologic improvement by up to six cycles of therapy. RESULTS The composite CR rates for cohorts A and B were 13.3% (95% confidence interval, 5.1%-26.8%) and 30.8% (95% confidence interval, 9.1%-61.4%), respectively. The median duration of response was 7.6 and 8.2 months, respectively, and the median overall survival was 6.5 and 11.5 months, respectively. The study was stopped because the futility boundary was crossed in both cohorts. CONCLUSIONS The combination of entospletinib and decitabine demonstrated activity and was acceptably tolerated in this patient population; however, the CR rates were low, and overall survival was short. Novel treatment strategies for older patients with TP53 mutations and complex karyotype remain an urgent need.
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Affiliation(s)
- Vu H Duong
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Amy S Ruppert
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Alice S Mims
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Uma Borate
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Eytan M Stein
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria R Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Wendy Stock
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, USA
| | - Tibor Kovacsovics
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah, USA
| | - William Blum
- Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | | | - Gary J Schiller
- David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA
| | - Rebecca L Olin
- Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, California, USA
| | - James M Foran
- Hematology and Oncology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mark R Litzow
- Departments of Medical Oncology, Hematology, and Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Tara L Lin
- Division of Hematologic Malignancies and Cellular Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Prapti A Patel
- University of Texas Southwestern Medical Center Medical School, Dallas, Texas, USA
| | - Matthew C Foster
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Robert L Redner
- Hillman Cancer Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Zeina Al-Mansour
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Ronan T Swords
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Robert H Collins
- University of Texas Southwestern Medical Center Medical School, Dallas, Texas, USA
| | | | - Nyla A Heerema
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Ashley O Yocum
- The Leukemia & Lymphoma Society, Rye Brook, New York, USA
| | - Sonja Marcus
- The Leukemia & Lymphoma Society, Rye Brook, New York, USA
| | - Timothy Chen
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Franchesca Druggan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mona Stefanos
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Abigail B Shoben
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Amy Burd
- The Leukemia & Lymphoma Society, Rye Brook, New York, USA
| | - John C Byrd
- Internal Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael M Boyiadzis
- Hillman Cancer Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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30
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Paudel BB, Tan SF, Fox TE, Ung J, Shaw J, Dunton W, Lee I, Sharma A, Viny AD, Barth BM, Tallman MS, Cabot M, Garrett-Bakelman FE, Levine RL, Kester M, Claxton D, Feith DJ, Janes KA, Loughran TP. Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes. bioRxiv 2023:2023.04.13.536805. [PMID: 37131653 PMCID: PMC10153188 DOI: 10.1101/2023.04.13.536805] [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: 05/04/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive disease with complex and heterogeneous biology. Although several genomic classifications have been proposed, there is a growing interest in going beyond genomics to stratify AML. In this study, we profile the sphingolipid family of bioactive molecules in 213 primary AML samples and 30 common human AML cell lines. Using an integrative approach, we identify two distinct sphingolipid subtypes in AML characterized by a reciprocal abundance of hexosylceramide (Hex) and sphingomyelin (SM) species. The two Hex-SM clusters organize diverse samples more robustly than known AML driver mutations and are coupled to latent transcriptional states. Using transcriptomic data, we develop a machine-learning classifier to infer the Hex-SM status of AML cases in TCGA and BeatAML clinical repositories. The analyses show that the sphingolipid subtype with deficient Hex and abundant SM is enriched for leukemic stemness transcriptional programs and comprises an unappreciated high-risk subgroup with poor clinical outcomes. Our sphingolipid-focused examination of AML identifies patients least likely to benefit from standard of care and raises the possibility that sphingolipidomic interventions could switch the subtype of AML patients who otherwise lack targetable alternatives.
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Affiliation(s)
- B. Bishal Paudel
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Todd E. Fox
- Department of Pharmacology, University of Virginia, Charlottesville, VA
| | - Johnson Ung
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA
| | - Jeremy Shaw
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Wendy Dunton
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Irene Lee
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
| | - Arati Sharma
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA
- Penn State Cancer Institute, Hershey, PA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
| | - Brian M. Barth
- Department of Chemistry, Biology, and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD
| | - Martin S. Tallman
- Northwestern University Feinberg School of Medicine Robert H. Lurie Comprehensive Cancer Center Chicago, IL
| | - Myles Cabot
- Department of Biochemistry & Molecular Biology, Brody School of Medicine, and the East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - David Claxton
- Penn State Cancer Institute, Hershey, PA
- Department of Medicine, Division of Hematology and Oncology, Pennsylvania State University College of Medicine, Hershey, PA
| | - David J. Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
| | - Thomas P. Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA
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31
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Perner F, Cai SF, Wenge DV, Kim J, Cutler J, Nowak RP, Cassel J, Singh S, Bijpuria S, Miller WH, Stein EM, Levine RL, Fischer ES, McGeehan GM, Armstrong SA. Abstract 3457: Characterization of acquired resistance mutations to menin inhibitors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3457] [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: 04/07/2023]
Abstract
Abstract
The menin-MLL1 interaction is critical for development of acute leukemias driven by MLL1 rearrangements (MLLr) or mutations in the Nucleophosmin 1 gene (NPM1c). Inhibition of the menin-MLL1 interaction by SNDX-5613 (revumenib) has demonstrated robust clinical responses in the current AUGMENT clinical trial (NCT04065399). During the trial, some responders relapsed during treatment due to acquired resistance in MEN1. Somatic MEN1 mutations were found at residues M327, G331 or T349 which diminished SDNX-5613 binding affinity and mediated therapeutic resistance. The presence of acquired resistance validates MEN1 as a therapeutic target in MLLr and NPM1c AML patients.
Here we characterize the effects of these mutations on the activity of 6 menin inhibitor chemotypes currently in clinical trials (NCT04065399/Syndax, NCT04067336/Kura, NCT04811560/JNJ, NCT04988555/Sumitomo, NCT04752163/Daiichi, NCT05153330/Biomea). In vitro activity and binding modes for these compounds were evaluated in wild-type (WT) and mutant menins using (i) competition binding assays, (ii) cell-based proliferation assays and (iii) X-ray co-crystallography.
For binding, His6-tagged MEN1 mutant proteins (G331R, M327I, M327V, T349M) were expressed and purified. Binding affinities were measured in competition binding format. The menin-MLL interaction was monitored by HTRF using Terbium labeled anti-His6 antibody and FITC labeled MLL peptide (4-43). Acquired mutations affected binding affinities (Ki) to varying degrees. Notably, M327I/V mutations reduced binding for all menin-MLL inhibitors ranging from ~30-300, indicating a class effect for this mutation. An irreversible Biomea chemotype did not inhibit menin-MLL binding in our assays.
The decreased binding affinity to M327I was reflected in cell-based proliferation assays. Menin mutations were introduced into MV4;11 cells using CRISPR-Cas9 in conjunction with a homology directed repair template to edit the endogenous MEN1 coding sequence. Clonal lines were established harboring homozygous (homo) and heterozygous (het) M327I mutations. The M327I (het) MV4;11 cells experienced 15-50-fold shifts in IC50 vs WT cells, consistent with the reduced binding affinities.
The molecular basis for sensitivity to M327 acquired resistance was examined by X-ray co-crystallography of inhibitors bound to M327I and WT menin. Both KO-539 and SNDX-5613 show notable changes in binding in M327I vs WT menin. The isoleucine creates a steric clash, displacing their position in the pocket as previously noted. The Janssen chemotype shows a novel binding mode. Although it has 30-fold lower affinity for M327I, it shows little change in its bound position to M327I menin.
Given the clinical validation of menin inhibition in AML, the design of next generation compounds that block MLL1 binding while avoiding acquired MEN1 mutations may be a strategy to overcome acquired resistance to first generation menin inhibitors.
Citation Format: Florian Perner, Sheng F. Cai, Daniela V. Wenge, Jeonghyeon Kim, Jevon Cutler, Radosław P. Nowak, Joel Cassel, Shivendra Singh, Shipra Bijpuria, William H. Miller, Eytan M. Stein, Ross L. Levine, Eric S. Fischer, Gerard M. McGeehan, Scott A. Armstrong. Characterization of acquired resistance mutations to menin inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3457.
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Affiliation(s)
| | - Sheng F. Cai
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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Gurska LM, Okabe R, Schurer A, Tong MM, Soto M, Choi D, Ames K, Glushakow-Smith S, Montoya A, Tein E, Miles LA, Cheng H, Hankey-Giblin P, Levine RL, Goel S, Halmos B, Gritsman K. Crizotinib Has Preclinical Efficacy in Philadelphia-Negative Myeloproliferative Neoplasms. Clin Cancer Res 2023; 29:943-956. [PMID: 36537918 PMCID: PMC9992133 DOI: 10.1158/1078-0432.ccr-22-1763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE The Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) polycythemia vera, essential thrombocythemia, and primary myelofibrosis are characterized by JAK/STAT pathway activation. JAK inhibitors are approved for MPN treatment, but persistence has been observed, due to JAK/STAT reactivation. EXPERIMENTAL DESIGN Using MPN patient samples, JAK2-mutated cell lines, and MPN mouse models, we examined both the efficacy and mechanism by which crizotinib, the ALK/MET/RON/ROS1 inhibitor approved for the treatment of non-small cell lung cancer, alters MPN cell proliferation and JAK/STAT activation. RESULTS We found that crizotinib suppresses proliferation and activation of JAK/STAT signaling, and decreases the disease burden in the JAK2V617F mouse model of MPN. Furthermore, we found that crizotinib could overcome JAK inhibitor persistence to ruxolitinib. Interestingly, phosphorylation of the crizotinib target RON kinase was enhanced in ruxolitinib-persistent cells. We show that phospho-JAK2 and phospho-RON can physically interact to sustain JAK/STAT signaling, and that the combination of crizotinib and ruxolitinib disrupts this interaction. Furthermore, RON knockdown suppresses proliferation and activation of JAK/STAT signaling in JAK2-mutated cells, and RON deletion in a JAK2V617F mouse MPN model decreases the disease burden. We also observed RON hyperactivation in MPN patient cells, suggesting that RON may be an important target of crizotinib in MPN. CONCLUSIONS In summary, we demonstrate that crizotinib has preclinical efficacy in MPN patient cells, JAK2-mutated cell lines, and a JAK2-mutated mouse model, and that the combination of crizotinib with JAK inhibitors suppresses JAK inhibitor persistence. Our work suggests that crizotinib should be investigated for the treatment of patients with MPN.
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Affiliation(s)
- Lindsay M. Gurska
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Rachel Okabe
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Alexandra Schurer
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Meng Maxine Tong
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Mark Soto
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Daniel Choi
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Kristina Ames
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Shira Glushakow-Smith
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Allison Montoya
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Ellen Tein
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Haiying Cheng
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Pamela Hankey-Giblin
- Department of Immunology and Infectious Diseases, Penn State Cancer Institute, University Park, PA, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Swati Goel
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Balazs Halmos
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine; Bronx, New York, USA
| | - Kira Gritsman
- Department of Cell Biology, Albert Einstein College of Medicine; Bronx, New York, USA
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine; Bronx, New York, USA
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Perner F, Stein EM, Wenge DV, Singh S, Kim J, Apazidis A, Rahnamoun H, Anand D, Marinaccio C, Hatton C, Wen Y, Stone RM, Schaller D, Mowla S, Xiao W, Gamlen HA, Stonestrom AJ, Persaud S, Ener E, Cutler JA, Doench JG, McGeehan GM, Volkamer A, Chodera JD, Nowak RP, Fischer ES, Levine RL, Armstrong SA, Cai SF. MEN1 mutations mediate clinical resistance to menin inhibition. Nature 2023; 615:913-919. [PMID: 36922589 PMCID: PMC10157896 DOI: 10.1038/s41586-023-05755-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [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: 03/07/2022] [Accepted: 01/24/2023] [Indexed: 03/17/2023]
Abstract
Chromatin-binding proteins are critical regulators of cell state in haematopoiesis1,2. Acute leukaemias driven by rearrangement of the mixed lineage leukaemia 1 gene (KMT2Ar) or mutation of the nucleophosmin gene (NPM1) require the chromatin adapter protein menin, encoded by the MEN1 gene, to sustain aberrant leukaemogenic gene expression programs3-5. In a phase 1 first-in-human clinical trial, the menin inhibitor revumenib, which is designed to disrupt the menin-MLL1 interaction, induced clinical responses in patients with leukaemia with KMT2Ar or mutated NPM1 (ref. 6). Here we identified somatic mutations in MEN1 at the revumenib-menin interface in patients with acquired resistance to menin inhibition. Consistent with the genetic data in patients, inhibitor-menin interface mutations represent a conserved mechanism of therapeutic resistance in xenograft models and in an unbiased base-editor screen. These mutants attenuate drug-target binding by generating structural perturbations that impact small-molecule binding but not the interaction with the natural ligand MLL1, and prevent inhibitor-induced eviction of menin and MLL1 from chromatin. To our knowledge, this study is the first to demonstrate that a chromatin-targeting therapeutic drug exerts sufficient selection pressure in patients to drive the evolution of escape mutants that lead to sustained chromatin occupancy, suggesting a common mechanism of therapeutic resistance.
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Affiliation(s)
- Florian Perner
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniela V Wenge
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sukrit Singh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Athina Apazidis
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Homa Rahnamoun
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Disha Anand
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Christian Marinaccio
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yanhe Wen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Schaller
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Shoron Mowla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Holly A Gamlen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron J Stonestrom
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonali Persaud
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Ener
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jevon A Cutler
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute, Cambridge, MA, USA
| | | | - Andrea Volkamer
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Sheng F Cai
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Robinson TM, Levine RL. Oncogenic IDH1 Mutation Imparts Therapeutically Targetable Metabolic Dysfunction in Multiple Tumor Types. Cancer Discov 2023; 13:266-268. [PMID: 36744320 DOI: 10.1158/2159-8290.cd-22-1325] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUMMARY In this issue of Cancer Discovery, Thomas and colleagues leverage mass spectrometry metabolomics, stable isotope labeling, and functional studies to explore metabolic vulnerabilities in cancers harboring mutations in isocitrate dehydrogenase (IDH). The authors present compelling data to support the claim that dysregulated lipid synthesis underpins a synthetic lethal target in cancers with IDH1, but not IDH2, mutations. See related article by Thomas et al., p. 496 (9).
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Affiliation(s)
- Troy M Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Fortin J, Chiang MF, Meydan C, Foox J, Ramachandran P, Leca J, Lemonnier F, Li WY, Gams MS, Sakamoto T, Chu M, Tobin C, Laugesen E, Robinson TM, You-Ten A, Butler DJ, Berger T, Minden MD, Levine RL, Guidos CJ, Melnick AM, Mason CE, Mak TW. Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells. Proc Natl Acad Sci U S A 2023; 120:e2208176120. [PMID: 36652477 PMCID: PMC9942850 DOI: 10.1073/pnas.2208176120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional deregulation in Idh2R172K cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of IDH1/2 and TET2 mutations, providing support for the optimization of genotype-specific therapies.
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Affiliation(s)
- Jerome Fortin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- 2To whom correspondence may be addressed. , , or
| | - Ming-Feng Chiang
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Cem Meydan
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Jonathan Foox
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
| | | | - Julie Leca
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - François Lemonnier
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- eInstitut Mondor de Recherche Biomédicale, INSERMU955, Université Paris Est Créteil, Créteil94010, France
| | - Wanda Y. Li
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Miki S. Gams
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Takashi Sakamoto
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- hDepartment of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Mandy Chu
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Chantal Tobin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Eric Laugesen
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Troy M. Robinson
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- jLouis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Annick You-Ten
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Daniel J. Butler
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
| | - Thorsten Berger
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Mark D. Minden
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Ross L. Levine
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- kCenter for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY10065
- lCenter for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Cynthia J. Guidos
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Ari M. Melnick
- mDepartment of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY10021
| | - Christopher E. Mason
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Tak W. Mak
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- nDepartment of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- 2To whom correspondence may be addressed. , , or
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Vela PS, Benitez AM, Krishnan A, Kleppe M, Cai SF, Levine RL. Abstract P073: Targeting JAK1 signaling for molecular prevention in clonal hematopoiesis. Cancer Prev Res (Phila) 2023. [DOI: 10.1158/1940-6215.precprev22-p073] [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: 01/05/2023]
Abstract
Abstract
Myeloid malignancies are characterized by the stepwise acquisition of different somatic mutations in hematopoietic stem and progenitor cells (HSPCs) that promote subsequent leukemic transformation. When these mutations, including in the epigenetic regulator TET2, are found in the blood cells of individuals without any signs of hematologic malignancy, this condition is termed clonal hematopoiesis (CH). The incidence of CH increases with age and has been recognized as a risk factor for the development of secondary heme malignancies and cardiovascular disease. Nonetheless, currently no therapies exist to alter the natural course of CH. Accumulating evidence indicates that inflammatory signals can enhance myeloproliferation of CH HSPCs suggesting a key role of inflammatory stressors in the promotion of the clonal advantage of Tet2-mutant stem cells. However, whether hijacking this inflammatory signaling will prevent clonal expansion and leukemogenesis is currently unknown. The members of the Janus family of nonreceptor tyrosine kinases (JAK) transmit a diversity of ligand-mediated signals and act as a signaling-hub for inflammation. Our central hypothesis is that CH and progression to acute myeloid leukemia (AML) occurs in the setting of inflammatory stress and that mutant clonal expansion is mediated by JAK/STAT inflammatory signaling, primarily through JAK1, a non-essential gene in adult hematopoiesis. We previously showed that Jak1 is critical for stress hematopoiesis in HSPCs. To assess whether Tet2-mediated clonal expansion requires Jak1, signaling, we established a conditional Scl driven Cre-inducible deletion model of Tet2-/- and Jak1-/-. We have adapted a bone marrow derived endothelial cell organoid system that allows to maintain and expand HSPCs during longer periods of time. In this setting Tet2-/- HSPCs show increased sensitivity to IL3, a Jak1-dependent cytokine that mediates exit of quiescence in HSPCs. The loss of competitive advantage of Tet2-/- Jak1-/- cells persists even in the context of co-culture with Jak1-/- Tet2-wildtype cells, and to a lesser extent in the presence of the Jak1 inhibitor Itacitinib, suggesting a denser requirement for Jak1 in CH mutant clones compared to wild-type HSPCs. Ex-vivo colony forming assays and in vivo competitive transplants demonstrate that the self-renewal abilities of Tet2-mutant HSPCs require Jak1 signaling. Furthermore, the extramedullary hematopoiesis observed in a primary model of Tet2-/- pre-leukemic myeloproliferation, was also dependent on Jak1. Moreover, studies in Tet2-/-/Flt3ITD and Mll-AF9 AML models showed that pharmacologic Jak1 inhibition abrogated ex vivo colony formation in both AMLs. This study is significant because targeting JAK/STAT mediated inflammatory signaling in CH-mutant HSPCs has the ability to translate into a precision interception strategy aimed at preventing clonal expansion and leukemic transformation.
Citation Format: Pablo Sánchez Vela, Anthony Martinez Benitez, Aishwarya Krishnan, Maria Kleppe, Sheng F. Cai, Ross L. Levine. Targeting JAK1 signaling for molecular prevention in clonal hematopoiesis. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P073.
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Affiliation(s)
| | | | | | | | - Sheng F. Cai
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
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Stopsack KH, Chan IC, Schmidt E, Panchot A, McNulty S, Schreiber NA, Zhang Y, Penney KL, Berger MF, Diaz LA, Levine RL, Bolton KL, Mucci LA, Kantoff PW. Abstract P011: Clonal hematopoiesis and risk of lethal prostate cancer: a prospective cohort study with long-term follow-up. Cancer Prev Res (Phila) 2023. [DOI: 10.1158/1940-6215.precprev22-p011] [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: 01/05/2023]
Abstract
Abstract
Background: Clonal hematopoiesis (CH), the presence of acquired mutations in leukemia driver genes, promotes systemic inflammation and is common among aging men. Prostate cancer, a subset of which is lethal, also develops in aging men. We hypothesized that CH contributes to development of lethal prostate cancer. Methods: We conducted nested case-cohort studies for metastatic prostate cancer and prostate cancer-specific death (lethal prostate cancer) within the prospective Health Professionals Follow-up Study. First, we followed 1155 men free of prostate cancer and cardiovascular disease at blood draw (1993-1995) for development of lethal prostate cancer over up to 26 years. Second, we followed 532 men with incident non-metastatic prostate cancer for development of lethal prostate cancer. We sequenced blood DNA from 1488 participants for putative CH driver mutations in the 9 most common CH-defining genes with a custom targeted panel (VariantPlex, Invitae, Inc.) at ultra-high depth (mean, 18,000x), employing unique molecular identifiers for error correction. CH variant calling used a novel ensemble calling approach, ArCCH, validated with in-silico tumor dilutions and blinded technical replicates, which had high accuracy for variant allele frequencies (VAFs) as low as 0.1%. We estimated hazard ratios (HRs) with 95% confidence intervals (CIs) in proportional hazards regression with Prentice case-cohort weights. Results: In a random sample of 968 men initially free of prostate cancer and cardiovascular disease (median age at blood draw 60 years, interquartile range 52 to 67), 80% of men had CH at a variant allele frequency (VAF) of >0.1%, 15% had VAFs >2%, and 3% had VAFs >10%; 75% of men had variants in epigenetic modifier genes (DNMT3A, TET2, ASXL1), and 21% had variants in DNA repair genes (PPM1D, TP53, CHEK2). CH burden was strongly age-associated, with approximately one additional CH variant per decade of age at blood draw (mean difference 1.07 variants, 95% CI 0.93 to 1.21). Among men initially free from prostate cancer, after adjusting for age at blood draw, CH clones between 0.1% and 10% VAF were not related to lethal prostate cancer (206 events total; HR 0.93, 95% CI 0.49-1.76 for VAFs 2-10% vs. no variants detected at >0.1% VAF). Results for epigenetic modifiers and DNA repair genes were similar. While inconclusive, data were compatible with positive associations among younger men (< 65 years) or for VAFs >10%. Among men initially diagnosed with non-metastatic prostate cancer, results were similarly null for progression to lethal prostate cancer (164 events). Conclusions: This large prospective study with long-term follow-up suggests that low-level CH is unlikely a major contributor to and not well suited for early detection of lethal prostate cancer.
Citation Format: Konrad H. Stopsack, Irenaeus C. Chan, Evelyn Schmidt, Alex Panchot, Samantha McNulty, Nicole A. Schreiber, Yiwen Zhang, Kathryn L. Penney, Michael F. Berger, Luis A. Diaz, Ross L. Levine, Kelly L. Bolton, Lorelei A. Mucci, Philip W. Kantoff. Clonal hematopoiesis and risk of lethal prostate cancer: a prospective cohort study with long-term follow-up. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P011.
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Affiliation(s)
| | | | | | - Alex Panchot
- 2Washington University St. Louis, St. Louis, MO,
| | | | | | - Yiwen Zhang
- 1Harvard T.H. Chan School of Public Health, Boston, MA,
| | | | | | - Luis A. Diaz
- 4Memorial Sloan Kettering Cancer Center, New York, NY
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38
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Stahl M, Derkach A, Farnoud N, Bewersdorf JP, Robinson T, Famulare C, Cho C, Devlin S, Menghrajani K, Patel MA, Cai SF, Miles LA, Bowman RL, Geyer MB, Dunbar A, Epstein-Peterson ZD, McGovern E, Schulman J, Glass JL, Taylor J, Viny AD, Stein EM, Getta B, Arcila ME, Gao Q, Barker J, Shaffer BC, Papadopoulos EB, Gyurkocza B, Perales MA, Abdel-Wahab O, Levine RL, Giralt SA, Zhang Y, Xiao W, Pai N, Papaemmanuil E, Tallman MS, Roshal M, Goldberg AD. Molecular predictors of immunophenotypic measurable residual disease clearance in acute myeloid leukemia. Am J Hematol 2023; 98:79-89. [PMID: 36251406 PMCID: PMC10080561 DOI: 10.1002/ajh.26757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 02/04/2023]
Abstract
Measurable residual disease (MRD) is a powerful prognostic factor in acute myeloid leukemia (AML). However, pre-treatment molecular predictors of immunophenotypic MRD clearance remain unclear. We analyzed a dataset of 211 patients with pre-treatment next-generation sequencing who received induction chemotherapy and had MRD assessed by serial immunophenotypic monitoring after induction, subsequent therapy, and allogeneic stem cell transplant (allo-SCT). Induction chemotherapy led to MRD- remission, MRD+ remission, and persistent disease in 35%, 27%, and 38% of patients, respectively. With subsequent therapy, 34% of patients with MRD+ and 26% of patients with persistent disease converted to MRD-. Mutations in CEBPA, NRAS, KRAS, and NPM1 predicted high rates of MRD- remission, while mutations in TP53, SF3B1, ASXL1, and RUNX1 and karyotypic abnormalities including inv (3), monosomy 5 or 7 predicted low rates of MRD- remission. Patients with fewer individual clones were more likely to achieve MRD- remission. Among 132 patients who underwent allo-SCT, outcomes were favorable whether patients achieved early MRD- after induction or later MRD- after subsequent therapy prior to allo-SCT. As MRD conversion with chemotherapy prior to allo-SCT is rarely achieved in patients with specific baseline mutational patterns and high clone numbers, upfront inclusion of these patients into clinical trials should be considered.
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Affiliation(s)
- Maximilian Stahl
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medical Oncology, Division of Leukemia, Dana-Farber Cancer Institute, Boston, MA
| | - Andriy Derkach
- Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Noushin Farnoud
- Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jan Philipp Bewersdorf
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY
| | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christina Cho
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Sean Devlin
- Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Minal A Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sheng F Cai
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark B. Geyer
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrew Dunbar
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zachary D. Epstein-Peterson
- Weill Cornell Medical College, New York, NY
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin McGovern
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica Schulman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob L Glass
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center at the University of Miami, Miami, FL
| | - Aaron D Viny
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M. Stein
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Bartlomiej Getta
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Maria E. Arcila
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Gao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juliet Barker
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Brian C. Shaffer
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Esperanza B. Papadopoulos
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Boglarka Gyurkocza
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Miguel-Angel Perales
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Omar Abdel-Wahab
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio A. Giralt
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nidhi Pai
- Georgia Institute of Technology, Atlanta, GA
| | - Elli Papaemmanuil
- Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Martin S. Tallman
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron D Goldberg
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
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39
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Ganzel C, Sun Z, Baslan T, Zhang Y, Gönen M, Abdel-Wahab OI, Racevskis J, Garrett-Bakelman F, Lowe SW, Fernandez HF, Ketterling R, Luger SM, Litzow M, Lazarus HM, Rowe JM, Tallman MS, Levine RL, Paietta E. Measurable residual disease by flow cytometry in acute myeloid leukemia is prognostic, independent of genomic profiling. Leuk Res 2022; 123:106971. [PMID: 36332294 PMCID: PMC9789386 DOI: 10.1016/j.leukres.2022.106971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/04/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
Abstract
Measurable residual disease (MRD) assessment provides a potent indicator of the efficacy of anti-leukemic therapy. It is unknown, however, whether integrating MRD with molecular profiling better identifies patients at risk of relapse. To investigate the clinical relevance of MRD in relation to a molecular-based prognostic schema, we measured MRD by flow cytometry in 189 AML patients enrolled in ECOG-ACRIN E1900 trial (NCT00049517) in morphologic complete remission (CR) (28.8 % of the original cohort) representing 44.4 % of CR patients. MRD positivity was defined as ≥ 0.1 % of leukemic bone marrow cells. Risk classification was based on standard cytogenetics, fluorescence-in-situ-hybridization, somatic gene analysis, and sparse whole genome sequencing for copy number ascertainment. At 84.6 months median follow-up of patients still alive at the time of analysis (range 47.0-120 months), multivariate analysis demonstrated that MRD status at CR (p = 0.001) and integrated molecular risk (p = 0.0004) independently predicted overall survival (OS). Among risk classes, MRD status significantly affected OS only in the favorable risk group (p = 0.002). Expression of CD25 (α-chain of the interleukin-2 receptor) by leukemic myeloblasts at diagnosis negatively affected OS independent of post-treatment MRD levels. These data suggest that integrating MRD with genetic profiling and pre-treatment CD25 expression may improve prognostication in AML.
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Affiliation(s)
- Chezi Ganzel
- Hematology Department, Shaare Zedek Medical Center, and Faculty of Medicine, Hebrew University of Jerusalem, Israel.
| | - Zhuoxin Sun
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar I Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janis Racevskis
- Department of Oncology, Montefiore Medical Center, Bronx, NY, USA
| | - Francine Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Departments of Medicine and Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; University of Virginia Cancer Center, Charlottesville, VA, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Hugo F Fernandez
- Malignant Hematology and Cellular Therapy, Moffitt Cancer Center, Tampa, FL, USA
| | - Rhett Ketterling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Selina M Luger
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Litzow
- Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jacob M Rowe
- Hematology Department, Shaare Zedek Medical Center, and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Martin S Tallman
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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40
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Jee J, Lebow ES, Yeh R, Das JP, Namakydoust A, Paik PK, Chaft JE, Jayakumaran G, Rose Brannon A, Benayed R, Zehir A, Donoghue M, Schultz N, Chakravarty D, Kundra R, Madupuri R, Murciano-Goroff YR, Tu HY, Xu CR, Martinez A, Wilhelm C, Galle J, Daly B, Yu HA, Offin M, Hellmann MD, Lito P, Arbour KC, Zauderer MG, Kris MG, Ng KK, Eng J, Preeshagul I, Victoria Lai W, Fiore JJ, Iqbal A, Molena D, Rocco G, Park BJ, Lim LP, Li M, Tong-Li C, De Silva M, Chan DL, Diakos CI, Itchins M, Clarke S, Pavlakis N, Lee A, Rekhtman N, Chang J, Travis WD, Riely GJ, Solit DB, Gonen M, Rusch VW, Rimner A, Gomez D, Drilon A, Scher HI, Shah SP, Berger MF, Arcila ME, Ladanyi M, Levine RL, Shen R, Razavi P, Reis-Filho JS, Jones DR, Rudin CM, Isbell JM, Li BT. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer. Nat Med 2022; 28:2353-2363. [PMID: 36357680 PMCID: PMC10338177 DOI: 10.1038/s41591-022-02047-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [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: 02/15/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing guides therapy decisions but has been studied mostly in small cohorts without sufficient follow-up to determine its influence on overall survival. We prospectively followed an international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy. ctDNA detection was associated with shorter survival (hazard ratio (HR), 2.05; 95% confidence interval (CI), 1.74-2.42; P < 0.001) independently of clinicopathologic features and metabolic tumor volume. Among the 722 (64%) patients with detectable ctDNA, 255 (23%) matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy (HR, 0.63; 95% CI, 0.52-0.76; P < 0.001). Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance, including RICTOR and PIK3CA alterations, and were associated with short survival. Minimally invasive ctDNA profiling can identify heterogeneous drivers not captured in tissue sequencing and expand community access to life-prolonging therapy.
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Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Randy Yeh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeeban P Das
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - A Rose Brannon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hai-Yan Tu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chong-Rui Xu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | | | - Clare Wilhelm
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bobby Daly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Michael Offin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kathryn C Arbour
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marjorie G Zauderer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kenneth K Ng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Juliana Eng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Isabel Preeshagul
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - W Victoria Lai
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John J Fiore
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Afsheen Iqbal
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniela Molena
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gaetano Rocco
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bernard J Park
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Lee P Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Candace Tong-Li
- GenesisCare, University of Sydney, Sydney, Australia
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - David L Chan
- GenesisCare, University of Sydney, Sydney, Australia
| | | | | | | | - Nick Pavlakis
- GenesisCare, University of Sydney, Sydney, Australia
| | - Adrian Lee
- GenesisCare, University of Sydney, Sydney, Australia
| | - Natasha Rekhtman
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Travis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory J Riely
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mithat Gonen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie W Rusch
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Andreas Rimner
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniel Gomez
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sohrab P Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jorge S Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - James M Isbell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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41
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Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 2022; 611:387-398. [PMID: 36289338 PMCID: PMC10060167 DOI: 10.1038/s41586-022-05365-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [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: 07/10/2020] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
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Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Fan Song
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mikoto Kobayashi
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Baozhen Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ziyu Zhao
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bei Jia
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Lena Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Josiah Hiu-Yuen Wong
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yihao Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Sinisa Dovat
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yue Yang
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tomoko Yamada
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Aaron D Viny
- Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Hong Zheng
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Aivalioti MM, Bartholdy BA, Pradhan K, Bhagat TD, Zintiridou A, Jeong JJ, Thiruthuvanathan VJ, Pujato M, Paranjpe A, Zhang C, Levine RL, Viny AD, Wickrema A, Verma A, Will B. PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation. Blood Cancer Discov 2022; 3:444-467. [PMID: 35820129 PMCID: PMC9894728 DOI: 10.1158/2643-3230.bcd-21-0226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 12/12/2021] [Revised: 04/05/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022] Open
Abstract
Cytosine hypermethylation in and around DNA-binding sites of master transcription factors, including PU.1, occurs in aging hematopoietic stem cells following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase ten-eleven translocation-2 (TET2), albeit functional relevance has been unclear. We show that Tet2-deficient mouse hematopoietic stem and progenitor cells undergo malignant transformation upon compromised gene regulation through heterozygous deletion of an upstream regulatory region (UREΔ/WT) of the PU.1 gene. Although compatible with multilineage blood formation at young age, Tet2-deficient PU.1 UREΔ/WT mice develop highly penetrant, transplantable acute myeloid leukemia (AML) during aging. Leukemic stem and progenitor cells show hypermethylation at putative PU.1-binding sites, fail to activate myeloid enhancers, and are hallmarked by a signature of genes with impaired expression shared with human AML. Our study demonstrates that Tet2 and PU.1 jointly suppress leukemogenesis and uncovers a methylation-sensitive PU.1-dependent gene network as a unifying molecular vulnerability associated with AML. SIGNIFICANCE We identify moderately impaired PU.1 mRNA expression as a biological modality predisposing Tet2-deficient hematopoietic stem and progenitor cells to malignant transformation. Our study furthermore uncovers a methylation-sensitive PU.1 gene network as a common feature of myeloid leukemia potentially allowing for the identification of patients at risk for malignant transformation. See related commentary by Schleicher and Pietras, p. 378. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Maria M. Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Graduate Programs in the Biomedical Sciences, Albert Einstein College of Medicine, Bronx, New York
| | - Boris A. Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Tushar D. Bhagat
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Victor J. Thiruthuvanathan
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chi Zhang
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron D. Viny
- Department of Genetics and Development, Columbia University, New York, New York
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Amit Verma
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Department of Medicine (Oncology), Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
- Corresponding Author: Britta Will, Albert Einstein College of Medicine, 1300 Morris Park Ave, Chanin 401A, Bronx, NY 10461. Phone: 718-430-3786; E-mail:
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Ung J, Tan SF, Fox TE, Shaw JJP, Vass LR, Costa-Pinheiro P, Garrett-Bakelman FE, Keng MK, Sharma A, Claxton DF, Levine RL, Tallman MS, Cabot MC, Kester M, Feith DJ, Loughran TP. Harnessing the power of sphingolipids: Prospects for acute myeloid leukemia. Blood Rev 2022; 55:100950. [PMID: 35487785 PMCID: PMC9475810 DOI: 10.1016/j.blre.2022.100950] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive, heterogenous malignancy characterized by clonal expansion of bone marrow-derived myeloid progenitor cells. While our current understanding of the molecular and genomic landscape of AML has evolved dramatically and opened avenues for molecularly targeted therapeutics to improve upon standard intensive induction chemotherapy, curative treatments are elusive, particularly in older patients. Responses to current AML treatments are transient and incomplete, necessitating the development of novel treatment strategies to improve outcomes. To this end, harnessing the power of bioactive sphingolipids to treat cancer shows great promise. Sphingolipids are involved in many hallmarks of cancer of paramount importance in AML. Leukemic blast survival is influenced by cellular levels of ceramide, a bona fide pro-death molecule, and its conversion to signaling molecules such as sphingosine-1-phosphate and glycosphingolipids. Preclinical studies demonstrate the efficacy of therapeutics that target dysregulated sphingolipid metabolism as well as their combinatorial synergy with clinically-relevant therapeutics. Thus, increased understanding of sphingolipid dysregulation may be exploited to improve AML patient care and outcomes. This review summarizes the current knowledge of dysregulated sphingolipid metabolism in AML, evaluates how pro-survival sphingolipids promote AML pathogenesis, and discusses the therapeutic potential of targeting these dysregulated sphingolipid pathways.
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Affiliation(s)
- Johnson Ung
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Su-Fern Tan
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Todd E Fox
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Jeremy J P Shaw
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Experimental Pathology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Luke R Vass
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Experimental Pathology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Pedro Costa-Pinheiro
- Cancer Biology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Francine E Garrett-Bakelman
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Michael K Keng
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Arati Sharma
- Penn State Cancer Institute, Hershey, PA, United States of America
| | - David F Claxton
- Penn State Cancer Institute, Hershey, PA, United States of America
| | - Ross L Levine
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Martin S Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Myles C Cabot
- Department of Biochemistry and Molecular Biology, East Carolina University, Brody School of Medicine, Greenville, NC, United States of America; East Carolina Diabetes and Obesity Institute, East Carolina University, Brody School of Medicine, Greenville, NC, United States of America
| | - Mark Kester
- University of Virginia Cancer Center, Charlottesville, VA, United States of America; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - David J Feith
- Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America
| | - Thomas P Loughran
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, United States of America; University of Virginia Cancer Center, Charlottesville, VA, United States of America.
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44
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Davidson NE, Gilbertson RJ, Letai A, Levine RL, McAllister F, Siu LL. Challenges and opportunities for physician-scientists in advancing cancer research. Trends Cancer 2022; 8:615-619. [PMID: 35717535 DOI: 10.1016/j.trecan.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/22/2022]
Affiliation(s)
| | - Richard J Gilbertson
- University of Cambridge, CRUK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | | | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | | | - Lillian L Siu
- Princess Margaret Cancer Centre, Toronto, ON, Canada.
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45
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Zhang Y, Truong B, Fahl SP, Martinez E, Cai KQ, Al-Saleem ED, Gong Y, Liebermann DA, Soboloff J, Dunbrack R, Levine RL, Fletcher S, Kappes D, Sykes SM, Shapiro P, Wiest DL. The ERK2-DBP domain opposes pathogenesis of a mouse JAK2V617F-driven myeloproliferative neoplasm. Blood 2022; 140:359-373. [PMID: 35436326 PMCID: PMC9335498 DOI: 10.1182/blood.2021013068] [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: 06/23/2021] [Accepted: 03/30/2022] [Indexed: 01/18/2023] Open
Abstract
Although Ras/mitogen-activated protein kinase (MAPK) signaling is activated in most human cancers, attempts to target this pathway using kinase-active site inhibitors have not typically led to durable clinical benefit. To address this shortcoming, we sought to test the feasibility of an alternative targeting strategy, focused on the ERK2 substrate binding domains, D and DEF binding pocket (DBP). Disabling the ERK2-DBP domain in mice caused baseline erythrocytosis. Consequently, we investigated the role of the ERK2-D and -DBP domains in disease, using a JAK2-dependent model of polycythemia vera (PV). Of note, inactivation of the ERK2-DBP domain promoted the progression of disease from PV to myelofibrosis, suggesting that the ERK2-DBP domain normally opposes progression. ERK2-DBP inactivation also prevented oncogenic JAK2 kinase (JAK2V617F) from promoting oncogene-induced senescence in vitro. The ERK2-DBP mutation attenuated JAK2-mediated oncogene-induced senescence by preventing the physical interaction of ERK2 with the transcription factor Egr1. Because inactivation of the ERK2-DBP created a functional ERK2 kinase limited to binding substrates through its D domain, these data suggested that the D domain substrates were responsible for promoting oncogene-induced progenitor growth and tumor progression and that pharmacologic targeting of the ERK2-D domain may attenuate cancer cell growth. Indeed, pharmacologic agents targeting the ERK2-D domain were effective in attenuating the growth of JAK2-dependent myeloproliferative neoplasm cell lines. Taken together, these data indicate that the ERK-D and -DBP domains can play distinct roles in the progression of neoplasms and that the D domain has the potential to be a potent therapeutic target in Ras/MAPK-dependent cancers.
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Affiliation(s)
- Yong Zhang
- Blood Cell Development and Function Program
| | | | | | | | | | | | - Yulan Gong
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Dan A Liebermann
- Fels Institute for Personalized Medicine and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Jonathan Soboloff
- Fels Institute for Personalized Medicine and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Roland Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Ross L Levine
- Department of Medicine, Leukemia Service, Center for Hematologic Malignancies, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
| | | | | | - Paul Shapiro
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD
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Suehnholz SP, Nissan M, Zhang H, Kundra R, Lu C, Xu B, Arcila ME, Ladanyi M, Berger MF, Zehir A, Syed A, Rudolph JE, Levine RL, Dogan A, Gao J, Solit DB, Schultz N, Chakravarty D. Abstract 1189: OncoKB, MSK’s precision oncology knowledge base. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1189] [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
OncoKB, Memorial Sloan Kettering Cancer Center’s (MSK) precision oncology knowledge base (www.oncokb.org), is a comprehensive database that annotates the oncogenic effects and clinical actionability of somatic alterations in cancer. OncoKB supports variant interpretation by the cBioPortal for Cancer Genomics and is used to annotate >12,000 MSK patient sequencing reports annually. Since its introduction in 2016, OncoKB has expanded to include 5685 alterations in 682 genes, and in October 2021, it became the first somatic knowledge base to be partially recognized by the FDA. The scope of the OncoKB FDA recognition includes clinically actionable variants that map to an FDA level of evidence, the processes of variant curation, and policies regarding database oversight, personnel training and transparency of data sources and operations. This recognition credentials OncoKB as providing accurate, reliable and clinically meaningful information to the medical and scientific communities.
The OncoKB Therapeutic (Tx) Levels of Evidence categorize variants based on their tumor type-specific predictive value of sensitivity or resistance to matched standard care or investigational targeted therapies. To date, OncoKB includes 43 Level 1 genes (included in the FDA drug label), 23 Level 2 genes (included in professional guidelines), 25 Level 3A genes (predictive of drug response in well-powered clinical studies), 23 Level 4 genes (predictive of drug response based on compelling biological evidence), and 11 R1 or R2 resistance genes. Initially focused on solid tumors, OncoKB was expanded to include hematologic disease annotation in 2019 and introduced Diagnostic (Dx) and Prognostic (Px) levels of evidence. All three level of evidence systems (Tx, Dx and Px) are consistent with the guidelines for evidence-based categorization of somatic variants published as a joint consensus recommendation by AMP/ASCO/CAP.
OncoKB is governed by a Clinical Genomics Annotation Committee, composed of MSK physicians and scientists who ensure that the information captured is accurate and current, and an external advisory board composed of leaders in the clinical oncology and genomics communities who oversee OncoKB updates and progress. OncoKB curation rules and processes are transparent and documented in the OncoKB Curation Standard Operating Procedure, which is publicly available via the website. User feedback to OncoKB content is encouraged via the website and through cBioPortal. Queries or suggestions by OncoKB users are addressed by the OncoKB team within 72 hours.
OncoKB offers licenses for academic, commercial and hospital use, with which users can programmatically access the web API. Future work includes coverage of additional cancer-associated genes, annotation of germline alterations that are predictive of drug response and/or associated with increased heritable cancer risk and the development of a clinical trial matching system.
Citation Format: Sarah P. Suehnholz, Moriah Nissan, Hongxin Zhang, Ritika Kundra, Calvin Lu, Benjamin Xu, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Ahmet Zehir, Aijaz Syed, Julia E. Rudolph, Ross L. Levine, Ahmet Dogan, Jianjiong Gao, David B. Solit, Nikolaus Schultz, Debyani Chakravarty. OncoKB, MSK’s precision oncology knowledge base [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1189.
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Affiliation(s)
| | | | | | | | - Calvin Lu
- 1Memorial Sloan Kettering, New York, NY
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Xu J, Song F, Zhang B, Lyu H, Kobayashi M, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wang Q, Jin Q, Jin Q, Fu Y, Hardison RC, Dovat S, Platanias LC, Yang Y, Yamada T, Viny AD, Levine RL, Claxton DF, Broach JR, Zheng H, Yue F. Abstract 2953: Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2953] [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
Acute myeloid leukemia (AML) represents a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors, and kinases that can cause epigenetic reshaping. It is unclear to what extent AML mutations drive chromatin 3D structure alteration and contribute to myeloid transformation. We first performed Hi-C and whole-genome sequencing in 25 AML patient samples and seven healthy donor samples, and identified recurrent alterations of A/B compartments, TADs, and chromatin loops that are unique to different subtypes. To investigate how altered chromatin organization contributes to transcriptional misregulation, we performed RNA-Seq, ATAC-Seq and CUT&ag for CTCF, H3K27ac, and H3K27me3 in the same AML samples. We identified extensive and recurrent AML-specific promoter-enhancer and promoter-repressor loops. We performed both CRISPR deletion and interference experiments and validated two repressor loops that downregulated cancer related genes IKZF2 and RTTN. Furthermore, by using our recently developed algorithm, we identified structural variation-induced enhancer-hijacking and repressor-hijacking events in AML samples. We further demonstrated the role of hijacked enhancers in AML cell growth by CRISPR screening, and the role of hijacked repressors by CRISPR de-repression. We performed whole-genome bisulfite sequencing in 20 AML and normal samples, and showed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Finally, by treating the AML cells with the DNA hypomethylating agent and performing triple knockdown of DNMT1/3A/3B, we demonstrated the impact of altered DNA methylation on gene expression and 3D genome organization. Overall this study provides an invaluable resource for leukemia studies and also highlighted the role of repressor-loops and hijacked cis-elements in gene regulation and human diseases.
Citation Format: Jie Xu, Fan Song, Baozhen Zhang, Huijue Lyu, Mikoto Kobayashi, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Ross C. Hardison, Sinisa Dovat, Leonidas C. Platanias, Yue Yang, Tomoko Yamada, Aaron D. Viny, Ross L. Levine, David F. Claxton, James R. Broach, Hong Zheng, Feng Yue. Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2953.
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Affiliation(s)
- Jie Xu
- 1Northwestern University, Chicago, IL
| | - Fan Song
- 1Northwestern University, Chicago, IL
| | | | | | | | - Ziyu Zhao
- 1Northwestern University, Chicago, IL
| | - Ye Hou
- 1Northwestern University, Chicago, IL
| | | | - Yu Luan
- 1Northwestern University, Chicago, IL
| | - Bei Jia
- 2Penn State University, Hershey, PA
| | | | | | - Qi Jin
- 1Northwestern University, Chicago, IL
| | | | - Yihao Fu
- 1Northwestern University, Chicago, IL
| | | | | | | | - Yue Yang
- 1Northwestern University, Chicago, IL
| | | | | | | | | | | | | | - Feng Yue
- 1Northwestern University, Chicago, IL
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Tao J, Setton J, Sanchez Vela P, Safonov AM, Comen EA, Braunstein LZ, Reis-Filho JS, Riaz N, Powell SN, Levine RL, Norton L, Khan AJ, Razavi P. Impact of clonal hematopoiesis on tumor control following radiation therapy. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3145] [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: 11/20/2022] Open
Abstract
3145 Background: Clonal hematopoiesis (CH) has well established associations with adverse clinical outcomes including all-cause mortality, cardiovascular disease, and progression to hematologic malignancy. The presence of CH has also been demonstrated to adversely impact survival from non-hematologic cancers, however whether CH may modulate response to radiation therapy (RT) in solid tumors is not known. Here we investigate the potential impact of CH mutations on radiation outcomes. Methods: We analyzed data from two previously well annotated cohorts of patients with tumors harboring somatic ATM mutations (n = 358) and FAT1 mutations (n = 365) who received RT and underwent prospective tumor and matched WBC sequencing utilizing the MSK-IMPACT assay. CH variants were detected in the blood samples utilizing a well-validated variant detection and filtration pipeline. Given that pathogenic mutations in ATM have been shown to be strongly associated with improved response to RT, these patients were excluded to avoid confounding. Additionally, patients with blood sampling for CH assessment that occurred more than 6 months after RT were excluded to address the possibility of therapy-related CH. We compared outcomes including irradiated tumor progression in patients with and without CH. Results: The final analysis consisted of 412 patients who underwent 811 total courses of radiation. A wide spectrum of solid tumor types were represented, most commonly non-small cell lung cancer (32.5%) and breast cancer (11.9%). A total of 161 patients (39.0%) had CH, with the most commonly mutated genes being DNMT3A (25.6%), PPM1D (6.2%), TET2 (5.8%), and TP53 (5.0%), consistent with prior studies of CH. Patients with CH were older at blood sample collection (67.6 vs 60.2 years, p < 0.001), reflecting an expected increase in CH burden with age. Fine Gray competing risks analysis, with death treated as a competing event and with clustering around patient identifier, showed no difference in irradiated tumor progression between patients with and without CH (HR 1.03, 95% CI 0.69 – 1.53, p = 0.896). Similarly, subanalyses by CH variant allele frequency and putative CH-driver mutations did not reveal an association between CH and response to RT. A hypothesis generating subgroup analysis by common cancer types, however, suggested that CH was associated with increased risk of progression post-radiation in prostate (HR 4.68, 1.14 – 19.1) and thyroid (HR 3.13, 1.55 – 6.34) cancer cohorts, warranting further investigation. Conclusions: We found no difference in irradiated tumor progression among patients who did and did not have CH. There may be an association between CH and poor radiation outcomes in certain cancer types, and further studies are needed to clarify the specific clinical and genomic factors that may influence radiation response.
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Affiliation(s)
- Jacqueline Tao
- Department of Medicine, New York-Presbyterian Weill Cornell, New York, NY
| | - Jeremy Setton
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Atif J. Khan
- NSABP/NRG Oncology, and Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
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49
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Epstein-Peterson ZD, Spitzer B, Derkach A, Arango JE, McCarter JG, Medina-Martínez JS, McGovern E, Farnoud NR, Levine RL, Tallman MS. De Novo myelodysplastic syndromes in patients 20-50 years old are enriched for adverse risk features. Leuk Res 2022; 117:106857. [PMID: 35598475 PMCID: PMC9875161 DOI: 10.1016/j.leukres.2022.106857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/01/2022] [Accepted: 05/07/2022] [Indexed: 01/27/2023]
Abstract
Data concerning the treatment approach and clinical outcomes in younger patients with myelodysplastic syndromes (MDS) are lacking. Furthermore, published results from genomic profiling in the young adult MDS population are few. We identified patients aged 20-50 at diagnosis evaluated for de novo MDS at our institution over a 32-year period. Clinical information and results from sequencing panels were extracted for analysis. 68 eligible patients were found, including 32% with multilineage dysplasia and 29% with excess blasts-2 WHO subtypes. Revised International Prognostic Scoring System for MDS (IPSS-R) categorization had 47% high/very high-risk, and this classification held prognostic significance. The median overall survival was 59 months, and most patients (75%) underwent allogeneic hematopoietic cell transplantation (alloHCT). Thirty-four patients had mutational profiling; the most commonly mutated gene was TP53 and most commonly altered gene category was epigenetic regulators. Younger patients with de novo MDS represented a unique subset with high-risk disease features (adverse cytogenetics, higher R-IPSS) frequently observed along with alterations in TP53 and genes related to epigenetic and transcription pathways.
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Affiliation(s)
| | - Barbara Spitzer
- Department of Pediatrics, Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriy Derkach
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E. Arango
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph G.W. McCarter
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan S. Medina-Martínez
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin McGovern
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ross L. Levine
- Division of Hematologic Malignancies, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center 1275 York Ave, New York, NY, 10065, USA,Department of Medicine, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA
| | - Martin S. Tallman
- Division of Hematologic Malignancies, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Weill Cornell Medical College, 1300 York Ave, New York, NY, 10065, USA
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Mims AS, Huang Y, Eisenmann E, Buelow D, Swords RT, Foster MC, Lin TL, Baer MR, Kovacsovics T, Al-Mansour Z, Stefanos M, Druggan F, Chen T, Yocum A, Borate U, Druker BJ, Burd A, Levine RL, Baker SD, Byrd JC. A phase 1b/2 study of TP-0903 and decitabine targeting mutant TP53 and/or complex karyotype in patients with untreated acute myeloid leukemia ≥ age 60 years: Phase 1b interim results. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.7027] [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: 11/20/2022] Open
Abstract
7027 Background: TP-0903 is a multi-kinase inhibitor designed to target AXL, a receptor tyrosine kinase, and also inhibits cell cycle regulators such as Chk1/2 and other AML associated kinases. TP-0903 has shown prior anti-tumor activity at a safe dose in solid tumors. In pre-clinical AML studies, TP-0903 shows potent cytotoxicity in TP53 mutant ( TP53m) AML cell lines, an adverse prognostic genomic sub-group of AML. TP-0903 also had synergistic activity with decitabine (dec) in TP53m AML and prolonged survival in xenograft and genetically engineered mouse models. We report here on the initial safety and clinical results from the Leukemia and Lymphoma Society’s ongoing Beat AML phase 1b/2 (Ph1b/2) trial of TP-0903 in combination with dec (ClinicalTrials.gov NCT03013998). Methods: Newly diagnosed AML pts ≥60 years with TP53m and/or complex karyotype (≥3 abnormalities) were selected for a Ph1b/2 dose escalation study of TP-0903 combined with dec. Seven Ph1b pts were given TP-0903 every 28-day cycle from days 1-21 (Dose level (DL) 1 = 37 mg/day) and dec IV days 1-10 (20 mg/m2). A standard 3+3 design was used to evaluate the safety and tolerability. Nine additional patients enrolled onto Ph2 at DL1, but further assessments of safety, pharmacokinetics (PK) and correlative data was used to update the final recommended Ph2 dose (RP2D) of TP-0903 to DL-1 (25 mg/day) with dec. Results: At data cutoff (10Jan2022), 16 total pts were accrued. Ph1b treated 7 pts at DL1, 6 were DLT evaluable, and no DLTs were observed. Ph2 enrolled and treated 9 pts at DL1 before concerns of delayed count recovery led to the reduction of the Ph2 dose of TP-0903 to DL-1 (25 mg/day). For all 16 pts treated at DL1, 1 pt achieved CR, 4 pts CRh, and 1 pt CRi, for a composite CR (CR/CRh/CRi) rate of 37.5% (95% CI, 15.2-64.6), with 4 pts achieving MRD negativity by central flow cytometry. For the remaining 10 pts, 1 pt achieved MLFS (6%), 6 pts had stable disease (37.5%), 1 pt had treatment failure (6%), and 2 pts were not evaluable (12.5%) due to withdrawal of consent and death from early disease progression. Two pts (1 CR and 1 CRh) proceeded to stem cell transplantation. The most common grade 3 and above treatment-related AEs include decreased neutrophil counts (37.5%), platelet counts (31.3%), and anemia (18.8%). Finally, PK and correlative data analysis looking at soluble Axl and Gas6 also supported reduction to DL-1. Conclusions: Initial results with DL1 suggest that TP-0903/dec shows preliminary clinical activity in the prognostically poor TP53m/complex karyotype AML sub-group, with 4 pts achieving MRD negative status out of 6 patients who achieved a CR/CRh/CRi (66%). After further patients were treated on DL1, the toxicity profile and correlative data supported the de-escalation to DL-1 as the RP2D. The Ph2 study is ongoing to determine the clinical activity of this new RP2D (DL-1). Clinical trial information: NCT03013998.
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Affiliation(s)
- Alice S. Mims
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Ying Huang
- Division of Hematology, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | - Tara L. Lin
- University of Kansas Medical Center, Kansas City, KS
| | - Maria R. Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | | | | | | | - Franchesca Druggan
- The Ohio State University Comprehensive Cancer Center & LLS, Columbus, OH
| | | | | | - Uma Borate
- Oregon Health & Science University, Portland, OR
| | | | - Amy Burd
- The Leukemia and Lymphoma Society, Rye Brook, NY
| | | | | | - John C. Byrd
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
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