1
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Jacoby MA, Duncavage ED, Khanna A, Chang GS, Nonavinkere Srivatsan S, Miller CA, Gao F, Robinson J, Shao J, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Brendel K, Chavez M, DiPersio JF, Abboud CN, Stockerl-Goldstein K, Westervelt P, Cashen A, Pusic I, Oh ST, Welch JS, Wells DA, Loken MR, Uy GL, Walter MJ. Monitoring clonal burden as an alternative to blast count for myelodysplastic neoplasm treatment response. Leukemia 2024:10.1038/s41375-024-02426-0. [PMID: 39367170 DOI: 10.1038/s41375-024-02426-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 09/13/2024] [Accepted: 09/23/2024] [Indexed: 10/06/2024]
Abstract
Accurate assessment of therapy response in myelodysplastic neoplasm (MDS) has been challenging. Directly monitoring mutational disease burden may be useful, but is not currently included in MDS response criteria, and the correlation of mutational burden and traditional response endpoints is not completely understood. Here, we used genome-wide and targeted next-generation sequencing (NGS) to monitor clonal and subclonal molecular disease burden in 452 samples from 32 patients prospectively treated in a clinical trial. Molecular responses were compared with International Working Group (IWG) 2006-defined response assessments. We found that myeloblast percentage consistently underestimates MDS molecular disease burden and that mutational clearance patterns for marrow complete remission (mCR), which depends on myeloblast assessment, was not different than stable disease or bone marrow aplasia, underscoring a major limitation of using mCR. In contrast, achieving a complete remission (CR) was associated with the highest level of mutation clearance and lowest residual mutational burden in higher-risk MDS patients. A targeted gene panel approach was inferior to genome-wide sequencing in defining subclones and their molecular responses but may be adequate for monitoring molecular disease burden when a targeted gene is present in the founding clone. Our work supports incorporating serial NGS-based monitoring into prospective MDS clinical trials.
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Affiliation(s)
- Meagan A Jacoby
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Eric D Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Ajay Khanna
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Gue Su Chang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | | | - Christopher A Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Feng Gao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Josh Robinson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jin Shao
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Michelle O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Sharon E Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberly Brendel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Monique Chavez
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - John F DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Camille N Abboud
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Keith Stockerl-Goldstein
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- MaineHealth Cancer Center, Scarborough, ME, USA
| | - Amanda Cashen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Iskra Pusic
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - John S Welch
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- A2 Biotherapeutics Inc., Agoura Hills, CA, USA
| | | | | | - Geoffrey L Uy
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
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2
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Mazzeo P, Ganster C, Wiedenhöft J, Shirneshan K, Rittscher K, Brzuszkiewicz EB, Steinemann D, Schieck M, Müller‐Thomas C, Treiber H, Braulke F, Germing U, Sockel K, Balaian E, Schanz J, Platzbecker U, Götze KS, Haase D. Comprehensive sequential genetic analysis delineating frequency, patterns, and prognostic impact of genomic dynamics in a real-world cohort of patients with lower-risk MDS. Hemasphere 2024; 8:e70014. [PMID: 39315323 PMCID: PMC11417473 DOI: 10.1002/hem3.70014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/13/2024] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
The acquisition of subsequent genetic lesions (clonal evolution, CE) and/or the expansion of existing clones (CEXP) contributes to clonal dynamics (CD) in myelodysplastic syndromes (MDS). Although CD plays an important role in high-risk patients in disease progression and transformation into acute myeloid leukemia (AML), knowledge about CD in lower-risk MDS (LR-MDS) patients is limited due to lack of robust longitudinal data considering the long clinically stable courses of the disease. In this retrospective analysis, we delineate the frequency and the prognostic impact of CD in an unselected real-world cohort of LR-MDS patients. We screened 68 patients with a median follow-up of 40.5 months and a median of 7.5 (range: 2-22) timepoints for CE and CEXP detected by chromosomal banding analysis, fluorescence in situ hybridization, sequencing, and molecular karyotyping. In 30/68 patients, 47 CE events and a CD rate of 1 event per 4 years were documented. Of note, patients with at least 1 CE event had an increased probability for subsequent treatment. Unexpectedly, CE did not correlate with inferior outcomes, which could be reasonably explained by CD detection triggering the subsequent start of a disease-modifying therapy.
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Affiliation(s)
- Paolo Mazzeo
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Christina Ganster
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - John Wiedenhöft
- Department of Human GeneticsUniversity of Leipzig Medical CenterLeipzigGermany
| | - Katayoon Shirneshan
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Katharina Rittscher
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Elzbieta B. Brzuszkiewicz
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | | | - Catharina Müller‐Thomas
- Department of Medicine IIITechnical University of Munich School of Medicine and HealthMunichGermany
| | - Hannes Treiber
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Friederike Braulke
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
- Comprehensive Cancer CenterUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical ImmunologyHeinrich‐Heine‐UniversitätDüsseldorfGermany
| | - Katja Sockel
- Medical Clinic and Policlinic IUniversity Hospital Carl Gustav Carus DresdenDresdenGermany
| | - Ekaterina Balaian
- Medical Clinic and Policlinic IUniversity Hospital Carl Gustav Carus DresdenDresdenGermany
| | - Julie Schanz
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular TherapyLeipzig University HospitalLeipzigGermany
| | - Katharina S. Götze
- Department of Medicine IIITechnical University of Munich School of Medicine and HealthMunichGermany
| | - Detlef Haase
- Department of Hematology and Medical Oncology, INDIGHO laboratoryUniversity Medical Center Göttingen (UMG)GöttingenGermany
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3
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Duployez N, Preudhomme C. Monitoring molecular changes in the management of myelodysplastic syndromes. Br J Haematol 2024. [PMID: 38934371 DOI: 10.1111/bjh.19614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
The ongoing or anticipated therapeutic advances as well as previous experience in other malignancies, including acute myeloid leukaemia, have made molecular monitoring a potential interesting tool for predicting outcomes and demonstrating treatment efficacy in patients with myelodysplastic syndromes (MDS). The important genetic heterogeneity in MDS has made challenging the establishment of recommendations. In this context, high-throughput/next-generation sequencing (NGS) has emerged as an attractive tool, especially in patients with high-risk diseases. However, its implementation in clinical practice still suffers from a lack of standardization in terms of sensitivity, bioinformatics and result interpretation. Data from literature, mostly gleaned from retrospective cohorts, show NGS monitoring when used appropriately could help clinicians to guide therapy, detect early relapse and predict disease evolution. Translating these observations into personalized patient management requires a prospective evaluation in clinical research and remains a major challenge for the next years.
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Affiliation(s)
- Nicolas Duployez
- Laboratory of Haematology, CHU Lille, Lille, France
- U1277 CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), University of Lille, INSERM, Lille, France
| | - Claude Preudhomme
- Laboratory of Haematology, CHU Lille, Lille, France
- U1277 CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), University of Lille, INSERM, Lille, France
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4
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Abdulbaki R, Pullarkat ST. A Brief Overview of the Molecular Landscape of Myelodysplastic Neoplasms. Curr Oncol 2024; 31:2353-2363. [PMID: 38785456 PMCID: PMC11119831 DOI: 10.3390/curroncol31050175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Myelodysplastic neoplasm (MDS) is a heterogeneous group of clonal hematological disorders that originate from the hematopoietic and progenitor cells and present with cytopenias and morphologic dysplasia with a propensity to progress to bone marrow failure or acute myeloid leukemia (AML). Genetic evolution plays a critical role in the pathogenesis, progression, and clinical outcomes of MDS. This process involves the acquisition of genetic mutations in stem cells that confer a selective growth advantage, leading to clonal expansion and the eventual development of MDS. With the advent of next-generation sequencing (NGS) assays, an increasing number of molecular aberrations have been discovered in recent years. The knowledge of molecular events in MDS has led to an improved understanding of the disease process, including the evolution of the disease and prognosis, and has paved the way for targeted therapy. The 2022 World Health Organization (WHO) Classification and the International Consensus Classification (ICC) have incorporated the molecular signature into the classification system for MDS. In addition, specific germline mutations are associated with MDS development, especially in pediatrics and young adults. This article reviews the genetic abnormalities of MDS in adults with a brief review of germline predisposition syndromes.
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Affiliation(s)
- Rami Abdulbaki
- Department of Pathology, Laboratory Medicine, UCLA, David Geffen School of Medicine, Los Angeles, CA 90095, USA;
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5
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Campillo-Marcos I, Casado-Pelaez M, Davalos V, Ferrer G, Mata C, Mereu E, Roué G, Valcárcel D, Molero A, Zamora L, Xicoy B, Palomo L, Acha P, Manzanares A, Tobiasson M, Hellström-Lindberg E, Solé F, Esteller M. Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy. CANCER RESEARCH COMMUNICATIONS 2024; 4:365-377. [PMID: 38300528 PMCID: PMC10860538 DOI: 10.1158/2767-9764.crc-23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Alterations in epigenetic marks, such as DNA methylation, represent a hallmark of cancer that has been successfully exploited for therapy in myeloid malignancies. Hypomethylating agents (HMA), such as azacitidine, have become standard-of-care therapy to treat myelodysplastic syndromes (MDS), myeloid neoplasms that can evolve into acute myeloid leukemia. However, our capacity to identify who will respond to HMAs, and the duration of response, remains limited. To shed light on this question, we have leveraged the unprecedented analytic power of single-cell technologies to simultaneously map the genome and immunoproteome of MDS samples throughout clinical evolution. We were able to chart the architecture and evolution of molecular clones in precious paired bone marrow MDS samples at diagnosis and posttreatment to show that a combined imbalance of specific cell lineages with diverse mutational profiles is associated with the clinical response of patients with MDS to hypomethylating therapy. SIGNIFICANCE MDS are myeloid clonal hemopathies with a low 5-year survival rate, and approximately half of the cases do not respond to standard HMA therapy. Our innovative single-cell multiomics approach offers valuable biological insights and potential biomarkers associated with the demethylating agent efficacy. It also identifies vulnerabilities that can be targeted using personalized combinations of small drugs and antibodies.
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Affiliation(s)
- Ignacio Campillo-Marcos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Marta Casado-Pelaez
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Gerardo Ferrer
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Caterina Mata
- Single Cell Unit, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Elisabetta Mereu
- Cellular Systems Genomics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - David Valcárcel
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Antonieta Molero
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Lurdes Zamora
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Blanca Xicoy
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Laura Palomo
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Pamela Acha
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Ana Manzanares
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Magnus Tobiasson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Francesc Solé
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
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6
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Biernacki MA, Lok J, Black RG, Foster KA, Cummings C, Woodward KB, Monahan T, Oehler VG, Stirewalt DL, Wu D, Rongvaux A, Deeg HJ, Bleakley M. Discovery of U2AF1 neoantigens in myeloid neoplasms. J Immunother Cancer 2023; 11:e007490. [PMID: 38164756 PMCID: PMC10729103 DOI: 10.1136/jitc-2023-007490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) arise from somatic mutations acquired in hematopoietic stem and progenitor cells, causing cytopenias and predisposing to transformation into secondary acute myeloid leukemia (sAML). Recurrent mutations in spliceosome genes, including U2AF1, are attractive therapeutic targets as they are prevalent in MDS and sAML, arise early in neoplastic cells, and are generally absent from normal cells, including normal hematopoietic cells. MDS and sAML are susceptible to T cell-mediated killing, and thus engineered T-cell immunotherapies hold promise for their treatment. We hypothesized that targeting spliceosome mutation-derived neoantigens with transgenic T-cell receptor (TCR) T cells would selectively eradicate malignant cells in MDS and sAML. METHODS We identified candidate neoantigen epitopes from recurrent protein-coding mutations in the spliceosome genes SRSF2 and U2AF1 using a multistep in silico process. Candidate epitopes predicted to bind human leukocyte antigen (HLA) class I, be processed and presented from the parent protein, and not to be subject to tolerance then underwent in vitro immunogenicity screening. CD8+ T cells recognizing immunogenic neoantigen epitopes were evaluated in in vitro assays to assess functional avidity, confirm the predicted HLA restriction, the potential for recognition of similar peptides, and the ability to kill neoplastic cells in an antigen-specific manner. Neoantigen-specific TCR were sequenced, cloned into lentiviral vectors, and transduced into third-party T cells after knock-out of endogenous TCR, then tested in vitro for specificity and ability to kill neoplastic myeloid cells presenting the neoantigen. The efficacy of neoantigen-specific T cells was evaluated in vivo in a murine cell line-derived xenograft model. RESULTS We identified two neoantigens created from a recurrent mutation in U2AF1, isolated CD8+ T cells specific for the neoantigens, and demonstrated that transferring their TCR to third-party CD8+ T cells is feasible and confers specificity for the U2AF1 neoantigens. Finally, we showed that these neoantigen-specific TCR-T cells do not recognize normal hematopoietic cells but efficiently kill malignant myeloid cells bearing the specific U2AF1 mutation, including primary cells, in vitro and in vivo. CONCLUSIONS These data serve as proof-of-concept for developing precision medicine approaches that use neoantigen-directed T-cell receptor-transduced T cells to treat MDS and sAML.
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MESH Headings
- Humans
- Mice
- Animals
- CD8-Positive T-Lymphocytes
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Antigens, Neoplasm
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/metabolism
- Epitopes/metabolism
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Affiliation(s)
- Melinda Ann Biernacki
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Lok
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ralph Graeme Black
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kimberly A Foster
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Carrie Cummings
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kyle B Woodward
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tim Monahan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Vivian G Oehler
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Derek L Stirewalt
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Anthony Rongvaux
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hans Joachim Deeg
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Marie Bleakley
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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7
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Vallelonga V, Gandolfi F, Ficara F, Della Porta MG, Ghisletti S. Emerging Insights into Molecular Mechanisms of Inflammation in Myelodysplastic Syndromes. Biomedicines 2023; 11:2613. [PMID: 37892987 PMCID: PMC10603842 DOI: 10.3390/biomedicines11102613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Inflammation impacts human hematopoiesis across physiologic and pathologic conditions, as signals derived from the bone marrow microenvironment, such as pro-inflammatory cytokines and chemokines, have been shown to alter hematopoietic stem cell (HSCs) homeostasis. Dysregulated inflammation can skew HSC fate-related decisions, leading to aberrant hematopoiesis and potentially contributing to the pathogenesis of hematological disorders such as myelodysplastic syndromes (MDS). Recently, emerging studies have used single-cell sequencing and muti-omic approaches to investigate HSC cellular heterogeneity and gene expression in normal hematopoiesis as well as in myeloid malignancies. This review summarizes recent reports mechanistically dissecting the role of inflammatory signaling and innate immune response activation due to MDS progression. Furthermore, we highlight the growing importance of using multi-omic techniques, such as single-cell profiling and deconvolution methods, to unravel MDSs' heterogeneity. These approaches have provided valuable insights into the patterns of clonal evolution that drive MDS progression and have elucidated the impact of inflammation on the composition of the bone marrow immune microenvironment in MDS.
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Affiliation(s)
- Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesco Gandolfi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesca Ficara
- Milan Unit, CNR-IRGB, 20090 Milan, Italy
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
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8
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Schulz E, Aplan PD, Freeman SD, Pavletic SZ. Moving toward a conceptualization of measurable residual disease in myelodysplastic syndromes. Blood Adv 2023; 7:4381-4394. [PMID: 37267435 PMCID: PMC10432617 DOI: 10.1182/bloodadvances.2023010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
Approximately 90% of patients with myelodysplastic syndromes (MDSs) have somatic mutations that are known or suspected to be oncogenic in the malignant cells. The genetic risk stratification of MDSs has evolved substantially with the introduction of the clinical molecular international prognostic scoring system, which establishes next-generation sequencing at diagnosis as a standard of care. Furthermore, the International Consensus Classification of myeloid neoplasms and acute leukemias has refined the MDS diagnostic criteria with the introduction of a new MDS/acute myeloid leukemia category. Monitoring measurable residual disease (MRD) has historically been used to define remission status, improve relapse prediction, and determine the efficacy of antileukemic drugs in patients with acute and chronic leukemias. However, in contrast to leukemias, assessment of MRD, including tracking of patient-specific mutations, has not yet been formally defined as a biomarker for MDS. This article summarizes current evidence and challenges and provides a conceptual framework for incorporating MRD into the treatment of MDS and future clinical trials.
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Affiliation(s)
- Eduard Schulz
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Peter D. Aplan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Sylvie D. Freeman
- Department of Clinical Immunology, Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Steven Z. Pavletic
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
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9
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Kotini AG, Carcamo S, Cruz-Rodriguez N, Olszewska M, Wang T, Demircioglu D, Chang CJ, Bernard E, Chao MP, Majeti R, Luo H, Kharas MG, Hasson D, Papapetrou EP. Patient-Derived iPSCs Faithfully Represent the Genetic Diversity and Cellular Architecture of Human Acute Myeloid Leukemia. Blood Cancer Discov 2023; 4:318-335. [PMID: 37067914 PMCID: PMC10320625 DOI: 10.1158/2643-3230.bcd-22-0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/18/2023] Open
Abstract
The reprogramming of human acute myeloid leukemia (AML) cells into induced pluripotent stem cell (iPSC) lines could provide new faithful genetic models of AML, but is currently hindered by low success rates and uncertainty about whether iPSC-derived cells resemble their primary counterparts. Here we developed a reprogramming method tailored to cancer cells, with which we generated iPSCs from 15 patients representing all major genetic groups of AML. These AML-iPSCs retain genetic fidelity and produce transplantable hematopoietic cells with hallmark phenotypic leukemic features. Critically, single-cell transcriptomics reveal that, upon xenotransplantation, iPSC-derived leukemias faithfully mimic the primary patient-matched xenografts. Transplantation of iPSC-derived leukemias capturing a clone and subclone from the same patient allowed us to isolate the contribution of a FLT3-ITD mutation to the AML phenotype. The results and resources reported here can transform basic and preclinical cancer research of AML and other human cancers. SIGNIFICANCE We report the generation of patient-derived iPSC models of all major genetic groups of human AML. These exhibit phenotypic hallmarks of AML in vitro and in vivo, inform the clonal hierarchy and clonal dynamics of human AML, and exhibit striking similarity to patient-matched primary leukemias upon xenotransplantation. See related commentary by Doulatov, p. 252. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Andriana G. Kotini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nataly Cruz-Rodriguez
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Malgorzata Olszewska
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tiansu Wang
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chan-Jung Chang
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark P. Chao
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
- Cancer Institute, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
- Cancer Institute, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael G. Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Bioinformatics for Next-Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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10
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Hasserjian RP, Orazi A, Orfao A, Rozman M, Wang SA. The International Consensus Classification of myelodysplastic syndromes and related entities. Virchows Arch 2023; 482:39-51. [PMID: 36287260 DOI: 10.1007/s00428-022-03417-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The International Consensus Classification (ICC) of myeloid neoplasms and acute leukemia has updated the classification of myelodysplastic syndromes (MDSs) and placed MDS in a broader group of clonal cytopenias that includes clonal cytopenia of undetermined significance (CCUS) and related entities. Although subject to some interobserver variability and lack of specificity, morphologic dysplasia remains the main feature that distinguishes MDS from other clonal cytopenias and defines MDS as a hematologic malignancy. The ICC has introduced some changes in the definition of MDS whereby some cases categorized as MDS based on cytogenetic abnormalities are now classified as CCUS, while SF3B1 and multi-hit TP53 mutations are now considered to be MDS-defining in a cytopenic patient. The ICC has also recognized several cytogenetic and molecular abnormalities that reclassify some cases of MDS with excess blasts as acute myeloid leukemia (AML) and has introduced a new MDS/AML entity that encompasses cases with 10-19% blasts that lie on the continuum between MDS and AML. Two new genetically defined categories of MDS have been introduced: MDS with mutated SF3B1 and MDS with mutated TP53, the latter requiring bi-allelic aberrations in the TP53 gene. The entity MDS, unclassifiable has been eliminated. These changes have resulted in an overall simplification of the MDS classification scheme from 8 separate entities (including 1 that was genetically defined) in the revised 4th edition WHO classification to 7 separate entities (including 3 that are genetically defined) in the ICC.
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Affiliation(s)
- Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit St, Warren 244, Boston, MA, 02114, USA.
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Alberto Orfao
- Department of Medicine, Cytometry Service, Cancer Research Center (IBMCC-CSIC/USAL), Institute for Biomedical Research of Salamanca (IBSAL) and CIBERONC, University of Salamanca, Salamanca, Spain
| | - Maria Rozman
- Hematopathology Section, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Sa A Wang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA
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11
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Novel Molecular Insights into Leukemic Evolution of Myeloproliferative Neoplasms: A Single Cell Perspective. Int J Mol Sci 2022; 23:ijms232315256. [PMID: 36499582 PMCID: PMC9740017 DOI: 10.3390/ijms232315256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are clonal disorders originated by the serial acquisition of somatic mutations in hematopoietic stem/progenitor cells. The major clinical entities are represented by polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), that are caused by driver mutations affecting JAK2, MPL or CALR. Disease progression is related to molecular and clonal evolution. PV and ET can progress to secondary myelofibrosis (sMF) but can also evolve to secondary acute myeloid leukemia (sAML). PMF is associated with the highest frequency of leukemic transformation, which represents the main cause of death. sAML is associated with a dismal prognosis and clinical features that differ from those of de novo AML. The molecular landscape distinguishes sAML from de novo AML, since the most frequent hits involve TP53, epigenetic regulators, spliceosome modulators or signal transduction genes. Single cell genomic studies provide novel and accurate information about clonal architecture and mutation acquisition order, allowing the reconstruction of clonal dynamics and molecular events that accompany leukemic transformation. In this review, we examine our current understanding of the genomic heterogeneity in MPNs and how it affects disease progression and leukemic transformation. We focus on molecular events elicited by somatic mutations acquisition and discuss the emerging findings coming from single cell studies.
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12
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Romine KA, van Galen P. Rise of the Clones: Myelodysplastic Syndrome to Secondary Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:270-272. [PMID: 35709709 PMCID: PMC9338726 DOI: 10.1158/2643-3230.bcd-22-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Myelodysplastic syndrome (MDS) describes a family of blood disorders driven by the clonal expansion of mutated blood cells that can evolve into secondary acute myeloid leukemia (sAML). Two new studies use single-cell and deep sequencing to elucidate the progression of MDS to AML, revealing discrete clonal architectures and the driving role of signaling mutations.
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Affiliation(s)
- Kyle A. Romine
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts.,Corresponding Author: Peter van Galen, Harvard Medical School, 4 Blackfan Circle, Boston MA 02115. Phone: 857-399-5149; E-mail:
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13
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Guess T, Potts CR, Bhat P, Cartailler JA, Brooks A, Holt C, Yenamandra A, Wheeler FC, Savona MR, Cartailler JP, Ferrell PB. Distinct Patterns of Clonal Evolution Drive Myelodysplastic Syndrome Progression to Secondary Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:316-329. [PMID: 35522837 PMCID: PMC9610896 DOI: 10.1158/2643-3230.bcd-21-0128] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 02/22/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Clonal evolution in myelodysplastic syndrome (MDS) can result in clinical progression and secondary acute myeloid leukemia (sAML). To dissect changes in clonal architecture associated with this progression, we performed single-cell genotyping of paired MDS and sAML samples from 18 patients. Analysis of single-cell genotypes revealed patient-specific clonal evolution and enabled the assessment of single-cell mutational cooccurrence. We discovered that changes in clonal architecture proceed via distinct patterns, classified as static or dynamic, with dynamic clonal architectures having a more proliferative phenotype by blast count fold change. Proteogenomic analysis of a subset of patients confirmed that pathogenic mutations were primarily confined to primitive and mature myeloid cells, though we also identify rare but present mutations in lymphocyte subsets. Single-cell transcriptomic analysis of paired sample sets further identified gene sets and signaling pathways involved in two cases of progression. Together, these data define serial changes in the MDS clonal landscape with clinical and therapeutic implications. SIGNIFICANCE Precise clonal trajectories in MDS progression are made possible by single-cell genomic sequencing. Here we use this technology to uncover the patterns of clonal architecture and clonal evolution that drive the transformation to secondary AML. We further define the phenotypic and transcriptional changes of disease progression at the single-cell level. See related article by Menssen et al., p. 330 (31). See related commentary by Romine and van Galen, p. 270. This article is highlighted in the In This Issue feature, p. 265.
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Affiliation(s)
- Tiffany Guess
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Chad R. Potts
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Pawan Bhat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Justin A. Cartailler
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Austin Brooks
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Clinton Holt
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Ferrin C. Wheeler
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Michael R. Savona
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Jean-Philippe Cartailler
- Creative Data Solutions Shared Resource, Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee
| | - P. Brent Ferrell
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.,Corresponding Author: P. Brent Ferrell Jr, Vanderbilt University Medical Center, 777 Preston Research Building, 2220 Pierce Avenue, Nashville, TN 37232. Phone: 615-875-8619; E-mail:
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