1
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Suske T, Sorger H, Manhart G, Ruge F, Prutsch N, Zimmerman MW, Eder T, Abdallah DI, Maurer B, Wagner C, Schönefeldt S, Spirk K, Pichler A, Pemovska T, Schweicker C, Pölöske D, Hubanic E, Jungherz D, Müller TA, Aung MMK, Orlova A, Pham HTT, Zimmel K, Krausgruber T, Bock C, Müller M, Dahlhoff M, Boersma A, Rülicke T, Fleck R, de Araujo ED, Gunning PT, Aittokallio T, Mustjoki S, Sanda T, Hartmann S, Grebien F, Hoermann G, Haferlach T, Staber PB, Neubauer HA, Look AT, Herling M, Moriggl R. Hyperactive STAT5 hijacks T cell receptor signaling and drives immature T cell acute lymphoblastic leukemia. J Clin Invest 2024; 134:e168536. [PMID: 38618957 PMCID: PMC11014662 DOI: 10.1172/jci168536] [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: 01/04/2023] [Accepted: 02/27/2024] [Indexed: 04/16/2024] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T cell cancer. Mutations in IL7R have been analyzed genetically, but downstream effector functions such as STAT5A and STAT5B hyperactivation are poorly understood. Here, we studied the most frequent and clinically challenging STAT5BN642H driver in T cell development and immature T cell cancer onset and compared it with STAT5A hyperactive variants in transgenic mice. Enhanced STAT5 activity caused disrupted T cell development and promoted an early T cell progenitor-ALL phenotype, with upregulation of genes involved in T cell receptor (TCR) signaling, even in absence of surface TCR. Importantly, TCR pathway genes were overexpressed in human T-ALL and mature T cell cancers and activation of TCR pathway kinases was STAT5 dependent. We confirmed STAT5 binding to these genes using ChIP-Seq analysis in human T-ALL cells, which were sensitive to pharmacologic inhibition by dual STAT3/5 degraders or ZAP70 tyrosine kinase blockers in vitro and in vivo. We provide genetic and biochemical proof that STAT5A and STAT5B hyperactivation can initiate T-ALL through TCR pathway hijacking and suggest similar mechanisms for other T cell cancers. Thus, STAT5 or TCR component blockade are targeted therapy options, particularly in patients with chemoresistant clones carrying STAT5BN642H.
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Affiliation(s)
| | | | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Frank Ruge
- Institute of Animal Breeding and Genetics and
| | - Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Diaaeldin I. Abdallah
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | - Alexander Pichler
- Department of Medicine I, Clinical Division of Hematology, Medical University of Vienna, Vienna, Austria
| | - Tea Pemovska
- Department of Medicine I, Clinical Division of Hematology, Medical University of Vienna, Vienna, Austria
| | - Carmen Schweicker
- Department of Medicine I, Clinical Division of Hematology, Medical University of Vienna, Vienna, Austria
| | | | | | - Dennis Jungherz
- Department I of Internal Medicine, Center for Integrated Oncology, Aachen-Bonn-Cologne-Duesseldorf, University of Cologne, Cologne, Germany
| | - Tony Andreas Müller
- Department I of Internal Medicine, Center for Integrated Oncology, Aachen-Bonn-Cologne-Duesseldorf, University of Cologne, Cologne, Germany
| | | | - Anna Orlova
- Institute of Animal Breeding and Genetics and
| | | | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Vienna, Austria
| | | | - Maik Dahlhoff
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Auke Boersma
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rülicke
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | | | - Elvin Dominic de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Thomas Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Janpix, London, United Kingdom
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Satu Mustjoki
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Takaomi Sanda
- Cancer Science Institute of Singapore and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute, Vienna, Austria
| | | | | | - Philipp Bernhard Staber
- Department of Medicine I, Clinical Division of Hematology, Medical University of Vienna, Vienna, Austria
| | | | - Alfred Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marco Herling
- Department I of Internal Medicine, Center for Integrated Oncology, Aachen-Bonn-Cologne-Duesseldorf, University of Cologne, Cologne, Germany
- Department of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, Leipzig, Germany
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics and
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg, Austria
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2
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Müller H, Dicker F, Bär C, Walter W, Hutter S, Nadarajah N, Meggendorfer M, Gao Q, Iacobucci I, Mullighan CG, Kern W, Haferlach T, Haferlach C. Proximally biased V(D)J recombination in the clonal evolution of IGH alleles in KMT2A::AFF1 BCP-ALL of all age classes. Hemasphere 2024; 8:e71. [PMID: 38650597 PMCID: PMC11033919 DOI: 10.1002/hem3.71] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Affiliation(s)
| | | | | | | | | | | | | | - Qingsong Gao
- Department of PathologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Ilaria Iacobucci
- Department of PathologySt. Jude Children's Research HospitalMemphisTennesseeUSA
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3
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Baumgartner F, Baer C, Bamopoulos S, Ayoub E, Truger M, Meggendorfer M, Lenk M, Hoermann G, Hutter S, Müller H, Walter W, Müller ML, Nadarajah N, Blombery P, Keller U, Kern W, Haferlach C, Haferlach T. Comparing malignant monocytosis across the updated WHO and ICC classifications of 2022. Blood 2024; 143:1139-1156. [PMID: 38064663 DOI: 10.1182/blood.2023021199] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/16/2023] [Indexed: 03/22/2024] Open
Abstract
ABSTRACT The World Health Organization (WHO) classification of hematolymphoid tumors and the International Consensus Classification (ICC) of 2022 introduced major changes to the definition of chronic myelomonocytic leukemia (CMML). To assess its qualitative and quantitative implications for patient care, we started with 3311 established CMML cases (according to WHO 2017 criteria) and included 2130 oligomonocytosis cases fulfilling the new CMML diagnostic criteria. Applying both 2022 classification systems, 356 and 241 of oligomonocytosis cases were newly classified as myelodysplastic (MD)-CMML (WHO and ICC 2022, respectively), most of which were diagnosed as myelodysplastic syndrome (MDS) according to the WHO 2017 classification. Importantly, 1.5 times more oligomonocytosis cases were classified as CMML according to WHO 2022 than based on ICC, because of different diagnostic criteria. Genetic analyses of the newly classified CMML cases showed a distinct mutational profile with strong enrichment of MDS-typical alterations, resulting in a transcriptional subgroup separated from established MD and myeloproliferative CMML. Despite a different cytogenetic, molecular, immunophenotypic, and transcriptional landscape, no differences in overall survival were found between newly classified and established MD-CMML cases. To the best of our knowledge, this study represents the most comprehensive analysis of routine CMML cases to date, both in terms of clinical characterization and transcriptomic analysis, placing newly classified CMML cases on a disease continuum between MDS and previously established CMML.
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Affiliation(s)
- Francis Baumgartner
- Munich Leukemia Laboratory, Munich, Germany
- Department of Hematology, Oncology, and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | | | - Stefanos Bamopoulos
- Department of Hematology, Oncology, and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Edward Ayoub
- Munich Leukemia Laboratory, Munich, Germany
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | - Piers Blombery
- Munich Leukemia Laboratory, Munich, Germany
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ulrich Keller
- Department of Hematology, Oncology, and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center, Berlin, Germany
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4
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Greiner G, Witzeneder N, Klein K, Tangermann S, Kodajova P, Jaeger E, Ratzinger F, Gerner MC, Jawhar M, Baumgartner S, Fruehwirth K, Schmetterer KG, Zuber J, Gleixner KV, Mayerhofer M, Schwarzinger I, Simonitsch-Klupp I, Esterbauer H, Baer C, Walter W, Meggendorfer M, Strassl R, Haferlach T, Hartmann K, Kenner L, Sperr WR, Reiter A, Sexl V, Arock M, Valent P, Hoermann G. Tumor necrosis factor α promotes clonal dominance of KIT D816V+ cells in mastocytosis: role of survivin and impact on prognosis. Blood 2024; 143:1006-1017. [PMID: 38142424 DOI: 10.1182/blood.2023020515] [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: 03/20/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023] Open
Abstract
ABSTRACT Systemic mastocytosis (SM) is defined by the expansion and accumulation of neoplastic mast cells (MCs) in the bone marrow (BM) and extracutaneous organs. Most patients harbor a somatic KIT D816V mutation, which leads to growth factor-independent KIT activation and accumulation of MC. Tumor necrosis factor α (TNF) is a proapoptotic and inflammatory cytokine that has been implicated in the clonal selection of neoplastic cells. We found that KIT D816V increases the expression and secretion of TNF. TNF expression in neoplastic MCs is reduced by KIT-targeting drugs. Similarly, knockdown of KIT or targeting the downstream signaling cascade of MAPK and NF-κB signaling reduced TNF expression levels. TNF reduces colony formation in human BM cells, whereas KIT D816V+ cells are less susceptible to the cytokine, potentially contributing to clonal selection. In line, knockout of TNF in neoplastic MC prolonged survival and reduced myelosuppression in a murine xenotransplantation model. Mechanistic studies revealed that the relative resistance of KIT D816V+ cells to TNF is mediated by the apoptosis-regulator BIRC5 (survivin). Expression of BIRC5 in neoplastic MC was confirmed by immunohistochemistry of samples from patients with SM. TNF serum levels are significantly elevated in patients with SM and high TNF levels were identified as a biomarker associated with inferior survival. We here characterized TNF as a KIT D816V-dependent cytokine that promotes clonal dominance. We propose TNF and apoptosis-associated proteins as potential therapeutic targets in SM.
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Affiliation(s)
- Georg Greiner
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Ihr Labor, Medical Diagnostic Laboratories, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Nadine Witzeneder
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Klara Klein
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Simone Tangermann
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Petra Kodajova
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Eva Jaeger
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Marlene C Gerner
- Division of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Mohamad Jawhar
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany
- Department of Hematology and Oncology, Helios Pforzheim, Pforzheim, Germany
| | - Sigrid Baumgartner
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University of Vienna, Vienna, Austria
| | - Karin Fruehwirth
- Medical Central Laboratory, State Hospital Feldkirch, Feldkirch, Austria
| | - Klaus G Schmetterer
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Karoline V Gleixner
- 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
| | | | - Ilse Schwarzinger
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | | | | | - Robert Strassl
- Division of Clinical Virology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Karin Hartmann
- Division of Allergy, Department of Dermatology, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Lukas Kenner
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Vienna, Austria
- Center for Biomarker Research in Medicine, Graz, Austria
| | - Wolfgang R Sperr
- 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
| | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany
| | | | - Michel Arock
- Department of Hematological Biology and French National Reference Center for Mastocytosis (CEREMAST), Pitié-Salpêtrière Hospital, Paris Sorbonne University, Paris, France
| | - 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
| | - Gregor Hoermann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Munich Leukemia Laboratory, Munich, Germany
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5
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Piehler AP, Truger M, Kozik JH, Weissmann S, Schwonzen M, Meggendorfer M, Kern W, Haferlach T, Hoermann G, Haferlach C. Classical meets malignant hematology: a case of acquired εγδβ-thalassemia in clonal hematopoiesis. Haematologica 2024. [PMID: 38497167 DOI: 10.3324/haematol.2024.285083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 03/19/2024] Open
Abstract
Hemoglobinopathies including thalassemias are among the most frequent genetic disorders worldwide. Primarily, these entities result from germline variants in the globin gene clusters and their cis-acting regulatory elements, and thus the WHO classifies thalassemias as inherited diseases. Non-inherited disorders of globin chain synthesis mimicking the phenotype of thalassemias have also been described and are referred to as acquired thalassemias. These forms mainly affect the alpha-globin genes and are observed at much lower frequencies...
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6
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Kubota Y, Gu X, Terkawi L, Bodo J, Przychodzen BP, Awada H, Williams N, Gurnari C, Kawashima N, Aly M, Durmaz A, Mori M, Ponvilawan B, Kewan T, Bahaj W, Meggendorfer M, Jha BK, Visconte V, Rogers HJ, Haferlach T, Maciejewski JP. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting. Nat Commun 2024; 15:1832. [PMID: 38418452 PMCID: PMC10901781 DOI: 10.1038/s41467-024-46134-w] [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: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Here we show three main findings in our comprehensive genomic and proteomic study. Firstly, we show a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 are co-mutated with PHF6. In contrast, female cases reveal co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis reveals a direct interaction between PHF6 and RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrate a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival are additive as PHF6MT cases with RUNX1 mutations have worse outcomes when compared to cases carrying single mutation or wild-type.
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Affiliation(s)
- Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaorong Gu
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Juraj Bodo
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej P Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nakisha Williams
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Naomi Kawashima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mai Aly
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Babal K Jha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Heesun J Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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7
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Fuchs SNR, Stalmann USA, Snoeren IAM, Bindels E, Schmitz S, Banjanin B, Hoogenboezem RM, van Herk S, Saad M, Walter W, Haferlach T, Seillier L, Saez-Rodriguez J, Dugourd AJF, Lehmann KV, Ben-Neriah Y, Gleitz HFE, Schneider RK. Collaborative effect of Csnk1a1 haploinsufficiency and mutant p53 in Myc induction can promote leukemic transformation. Blood Adv 2024; 8:766-779. [PMID: 38147624 PMCID: PMC10847877 DOI: 10.1182/bloodadvances.2022008926] [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: 09/12/2022] [Revised: 11/21/2023] [Accepted: 12/09/2023] [Indexed: 12/28/2023] Open
Abstract
ABSTRACT It is still not fully understood how genetic haploinsufficiency in del(5q) myelodysplastic syndrome (MDS) contributes to malignant transformation of hematopoietic stem cells. We asked how compound haploinsufficiency for Csnk1a1 and Egr1 in the common deleted region on chromosome 5 affects hematopoietic stem cells. Additionally, Trp53 was disrupted as the most frequently comutated gene in del(5q) MDS using CRISPR/Cas9 editing in hematopoietic progenitors of wild-type (WT), Csnk1a1-/+, Egr1-/+, Csnk1a1/Egr1-/+ mice. A transplantable acute leukemia only developed in the Csnk1a1-/+Trp53-edited recipient. Isolated blasts were indefinitely cultured ex vivo and gave rise to leukemia after transplantation, providing a tool to study disease mechanisms or perform drug screenings. In a small-scale drug screening, the collaborative effect of Csnk1a1 haploinsufficiency and Trp53 sensitized blasts to the CSNK1 inhibitor A51 relative to WT or Csnk1a1 haploinsufficient cells. In vivo, A51 treatment significantly reduced blast counts in Csnk1a1 haploinsufficient/Trp53 acute leukemias and restored hematopoiesis in the bone marrow. Transcriptomics on blasts and their normal counterparts showed that the derived leukemia was driven by MAPK and Myc upregulation downstream of Csnk1a1 haploinsufficiency cooperating with a downregulated p53 axis. A collaborative effect of Csnk1a1 haploinsufficiency and p53 loss on MAPK and Myc upregulation was confirmed on the protein level. Downregulation of Myc protein expression correlated with efficient elimination of blasts in A51 treatment. The "Myc signature" closely resembled the transcriptional profile of patients with del(5q) MDS with TP53 mutation.
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Affiliation(s)
- Stijn N. R. Fuchs
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Ursula S. A. Stalmann
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Inge A. M. Snoeren
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Stephani Schmitz
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Bella Banjanin
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Remco M. Hoogenboezem
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Mohamed Saad
- Department of Cell and Tumor Biology, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | | | | | - Lancelot Seillier
- Cancer Research Center Cologne Essen, University Hospital Cologne, Cologne, Germany
- Joint Research Center for Computational Biomedicine, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Aurélien J. F. Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Kjong-Van Lehmann
- Cancer Research Center Cologne Essen, University Hospital Cologne, Cologne, Germany
- Joint Research Center for Computational Biomedicine, University Hospital Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Hélène F. E. Gleitz
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - Rebekka K. Schneider
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
- Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
- Department of Cell and Tumor Biology, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
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8
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Kewan T, Durmaz A, Bahaj W, Gurnari C, Terkawi L, Awada H, Ogbue OD, Ahmed R, Pagliuca S, Awada H, Kubota Y, Mori M, Ponvilawan B, Al-Share B, Patel BJ, Carraway HE, Scott J, Balasubramanian SK, Bat T, Madanat Y, Sekeres MA, Haferlach T, Visconte V, Maciejewski JP. Author Correction: Molecular patterns identify distinct subclasses of myeloid neoplasia. Nat Commun 2024; 15:1184. [PMID: 38332139 PMCID: PMC10853187 DOI: 10.1038/s41467-024-45644-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Affiliation(s)
- Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Hematology and Medical Oncology, Yale University, New Haven, CT, USA.
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Olisaemeka D Ogbue
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ramsha Ahmed
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bayan Al-Share
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Bhumika J Patel
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Suresh K Balasubramanian
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Taha Bat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yazan Madanat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | | | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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9
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Georgi JA, Stasik S, Kramer M, Meggendorfer M, Röllig C, Haferlach T, Valk P, Linch D, Herold T, Duployez N, Taube F, Middeke JM, Platzbecker U, Serve H, Baldus CD, Muller-Tidow C, Haferlach C, Koch S, Berdel WE, Woermann BJ, Krug U, Braess J, Hiddemann W, Spiekermann K, Boertjes EL, Hills RK, Burnett A, Ehninger G, Metzeler K, Rothenberg-Thurley M, Dufour A, Dombret H, Pautas C, Preudhomme C, Fenwarth L, Bornhäuser M, Gale R, Thiede C. Prognostic impact of CEBPA mutational subgroups in adult AML. Leukemia 2024; 38:281-290. [PMID: 38228680 PMCID: PMC10844079 DOI: 10.1038/s41375-024-02140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Despite recent refinements in the diagnostic and prognostic assessment of CEBPA mutations in AML, several questions remain open, i.e. implications of different types of basic region leucin zipper (bZIP) mutations, the role of co-mutations and the allelic state. Using pooled primary data analysis on 1010 CEBPA-mutant adult AML patients, a comparison was performed taking into account the type of mutation (bZIP: either typical in-frame insertion/deletion (InDel) mutations (bZIPInDel), frameshift InDel or nonsense mutations inducing translational stop (bZIPSTOP) or single base-pair missense alterations (bZIPms), and transcription activation domain (TAD) mutations) and the allelic state (single (smCEBPA) vs. double mutant (dmCEBPA)). Only bZIPInDel patients had significantly higher rates of complete remission and longer relapse free and overall survival (OS) compared with all other CEBPA-mutant subgroups. Moreover, co-mutations in bZIPInDel patients (e.g. GATA2, FLT3, WT1 as well as ELN2022 adverse risk aberrations) had no independent impact on OS, whereas in non-bZIPInDel patients, grouping according to ELN2022 recommendations added significant prognostic information. In conclusion, these results demonstrate bZIPInDel mutations to be the major independent determinant of outcome in CEBPA-mutant AML, thereby refining current classifications according to WHO (including all dmCEBPA and smCEBPA bZIP) as well as ELN2022 and ICC recommendations (including CEBPA bZIPms).
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Affiliation(s)
- Julia-Annabell Georgi
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sebastian Stasik
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | | | - Christoph Röllig
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Peter Valk
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Linch
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Nicolas Duployez
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Franziska Taube
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jan Moritz Middeke
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Uwe Platzbecker
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Hubert Serve
- Medizinische Klinik 2, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Claudia D Baldus
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Carsten Muller-Tidow
- Klinik für Hämatologie, Onkologie und Rheumatologie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Sarah Koch
- MLL Münchner Leukämielabor GmbH, Munich, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | | | - Utz Krug
- Department of Medicine 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | | | | | - Robert K Hills
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Alan Burnett
- Department of Haematology, Cardiff University, University Hospital of Wales, Cardiff, UK
| | | | - Klaus Metzeler
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | | | - Annika Dufour
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | - Hervé Dombret
- Hôpital Saint-Louis (AP-HP), EA 3518, Université de Paris, Paris, France
| | - Cecile Pautas
- Service d'Hématologie et de thérapie cellulaire, Hôpital Henri Mondor, Créteil, France
| | - Claude Preudhomme
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Laurene Fenwarth
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Nationales Zentrum für Tumorerkrankungen (NCT), Dresden, Germany
| | - Rosemary Gale
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Christian Thiede
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- AgenDix GmbH, Dresden, Germany.
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10
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Eisenach S, Zinke J, Brämer D, Hartinger S, Haferlach T, Kreipe HH, Hammersen J, Hamadanchi A, Otto S, Schulze PC, Bürckenmeyer F, Teichgräber U, Hochhaus A, Witte OW, Günther A, Schrenk KG. Detection of a rare JAK2 exon13InDel-mutation in chronic eosinophilic leukemia with bilateral cerebral infarctions and Löffler endocarditis. Ann Hematol 2024; 103:363-365. [PMID: 37843619 PMCID: PMC10761506 DOI: 10.1007/s00277-023-05490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/30/2023] [Indexed: 10/17/2023]
Affiliation(s)
- Sven Eisenach
- Klinik für Neurologie, Universitätsklinikum Jena, Jena, Germany
| | - Jan Zinke
- Klinik für Neurologie, Universitätsklinikum Jena, Jena, Germany
- Klinik für Neurologie, Klinikum St. Georg, Leipzig, Germany
| | - Dirk Brämer
- Klinik für Neurologie, Universitätsklinikum Jena, Jena, Germany
| | | | | | | | - Jakob Hammersen
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Am Klinikum 1, 07747, Jena, Germany
- Mitteldeutsches Krebszentrum, Standort Jena, Jena, Germany
| | - Ali Hamadanchi
- Kardiologie, Angiologie und, Internistische Intensivmedizin, Klinik für Innere Medizin I, Universitätsklinikum Jena, Jena, Germany
| | - Sylvia Otto
- Kardiologie, Angiologie und, Internistische Intensivmedizin, Klinik für Innere Medizin I, Universitätsklinikum Jena, Jena, Germany
| | - Paul Christian Schulze
- Kardiologie, Angiologie und, Internistische Intensivmedizin, Klinik für Innere Medizin I, Universitätsklinikum Jena, Jena, Germany
| | - Florian Bürckenmeyer
- Institut für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Jena, Jena, Germany
| | - Ulf Teichgräber
- Institut für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Jena, Jena, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Am Klinikum 1, 07747, Jena, Germany
- Mitteldeutsches Krebszentrum, Standort Jena, Jena, Germany
| | - Otto W Witte
- Klinik für Neurologie, Universitätsklinikum Jena, Jena, Germany
| | | | - Karin G Schrenk
- Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Am Klinikum 1, 07747, Jena, Germany.
- Mitteldeutsches Krebszentrum, Standort Jena, Jena, Germany.
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11
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Zeng AGX, Iacobucci I, Shah S, Mitchell A, Wong G, Bansal S, Gao Q, Kim H, Kennedy JA, Minden MD, Haferlach T, Mullighan CG, Dick JE. Precise single-cell transcriptomic mapping of normal and leukemic cell states reveals unconventional lineage priming in acute myeloid leukemia. bioRxiv 2023:2023.12.26.573390. [PMID: 38234771 PMCID: PMC10793439 DOI: 10.1101/2023.12.26.573390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic features. Yet, these traditional classification approaches lack precision, especially at the level of immature blasts. Single-cell RNA-sequencing (scRNA-seq) enables precise determination of cell state using thousands of markers, thus providing an opportunity to re-examine present-day classification schemes of acute leukemia. Here, we developed a detailed reference map of human bone marrow hematopoiesis from 263,519 single-cell transcriptomes spanning 55 cellular states. Cell state annotations were benchmarked against purified cell populations, and in-depth characterization of gene expression programs underlying hematopoietic differentiation was undertaken. Projection of single-cell transcriptomes from 175 samples spanning acute myeloid leukemia (AML), mixed phenotype acute leukemia (MPAL), and acute erythroid leukemia (AEL) revealed 11 subtypes involving distinct stages of hematopoietic differentiation. These included AML subtypes with notable lymphoid or erythroid lineage priming, challenging traditional diagnostic boundaries between AML, MPAL, and AEL. Quantification of lineage priming in bulk patient cohorts revealed specific genetic alterations associated with this unconventional lineage priming. Integration of transcriptional and genetic information at the single-cell level revealed how genetic subclones can induce lineage restriction, differentiation blocks, or expansion of mature myeloid cells. Furthermore, we demonstrate that distinct cellular hierarchies can co-exist within individual patients, providing insight into AML evolution in response to varying selection pressures. Together, precise mapping of hematopoietic cell states can serve as a foundation for refining disease classification in acute leukemia and understanding response or resistance to emerging therapies.
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Affiliation(s)
- Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Ilaria Iacobucci
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Gordon Wong
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Suraj Bansal
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Qingsong Gao
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hyerin Kim
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - James A Kennedy
- Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | | | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
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12
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Maierhofer A, Mehta N, Chisholm RA, Hutter S, Baer C, Nadarajah N, Pohlkamp C, Thompson ER, James PA, Kern W, Haferlach C, Meggendorfer M, Haferlach T, Blombery P. The clinical and genomic landscape of patients with DDX41 variants identified during diagnostic sequencing. Blood Adv 2023; 7:7346-7357. [PMID: 37874914 PMCID: PMC10701587 DOI: 10.1182/bloodadvances.2023011389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
Deleterious germ line variants in DDX41 are a common cause of genetic predisposition to hematologic malignancies, particularly myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML). Targeted next-generation sequencing was performed in a large cohort of sequentially recruited patients with myeloid malignancy, covering DDX41 as well as 30 other genes frequently mutated in myeloid malignancy. Whole genome transcriptome sequencing data was analyzed on a separate cohort of patients with a range of hematologic malignancies to investigate the spectrum of cancer predisposition. Altogether, 5737 patients with myeloid malignancies were studied, with 152 different DDX41 variants detected. Multiple novel variants were detected, including synonymous variants affecting splicing as demonstrated by RNA-sequencing. The presence of a somatic DDX41 variant was highly associated with DDX41 germ line variants in patients with MDS and AML, and we developed a statistical approach to incorporate the co-occurrence of a somatic DDX41 variant into germ line variant classification at a very strong level (as per the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines). Using this approach, the MDS cohort contained 108 of 2865 (3.8%) patients with germ line likely pathogenic/pathogenic (LP/P) variants, and the AML cohort 106 of 2157 (4.9%). DDX41 LP/P variants were markedly enriched in patients with AML and MDS compared with those in patients with myeloproliferative neoplasms, B-cell neoplasm, and T- or B-cell acute lymphoblastic leukemia. In summary, we have developed a framework to enhance DDX41 variant curation as well as highlighted the importance of assessment of all types of genomic variants (including synonymous and multiexon deletions) to fully detect the landscape of possible clinically relevant DDX41 variants.
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Affiliation(s)
| | - Nikita Mehta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan A. Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | | | | | - Ella R. Thompson
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Australia
| | - Paul A. James
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | | | | | - Piers Blombery
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Australia
- Torsten Haferlach Leukaemiediagnostik Stiftung, Munich, Germany
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13
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Lorenzi L, Haferlach T, Mori L, Simbeni M, Walter W, Balzarini P, Meggendorfer M, Döring C, Lonardi S, Bugatti M, Agostinelli C, Mehta J, Borges A, Agaimy A, Simonitsch-Klupp I, Cabeçadas J, Campo E, Pileri SA, Facchetti F, Leo Hansmann M, Hartmann S. Massive parallel sequencing unveils homologous recombination deficiency in follicular dendritic cell sarcoma. Haematologica 2023. [PMID: 37994105 DOI: 10.3324/haematol.2023.283669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Indexed: 11/24/2023] Open
Abstract
Standardized treatment options are lacking for patients with unresectable or multifocal follicular dendritic cell sarcoma (FDCS) and disease-related mortality is as high as 20%. Applying whole genome sequencing (WGS) in one case and whole exome sequencing (WES) in additional twelve, this study adds information on the molecular landscape of FDCS, expanding knowledge on pathobiological mechanisms and identifying novel markers of potential theragnostic significance. Massive parallel sequencing showed high frequency of mutations on oncosuppressor genes, particularly in RB1, CARS and BRCA2 and unveiled alterations on homologous recombination DNA damage repair related genes in 70% (9/13) of cases. This indicates that patients with high stage FDCS may be eligible for poly ADP ribose polymerase inhibition protocols. Low tumor mutational burden was confirmed in this study despite common PDL1 expression in FDCS arguing on the efficacy of immune checkpoint inhibitors. CDKN2A deletion, detected by WGS and confirmed by FISH in 41% of cases (9/22) indicates that impairment of cell cycle regulation may sustain oncogenesis in FDCS. Absence of mutations in the RAS/RAF/MAPK pathway and lack of clonal hematopoiesis related mutations in FDCS sanction its differences from dendritic cell-derived neoplasms of haematopoietic derivation. WGS and WES in FDCS provides additional information on the molecular landscape of this rare tumor, proposing novel candidate genes for innovative therapeutical approaches to improve survival of patients with multifocal disease.
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Affiliation(s)
- Luisa Lorenzi
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia.
| | | | - Luigi Mori
- Laboratory of Molecular Medicine, Department of Clinical and Experimental Science, University of Brescia, Brescia
| | - Matteo Simbeni
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia
| | | | - Piera Balzarini
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia
| | | | - Claudia Döring
- Dr Senckenberg Institute of Pathology, Goethe University, Frankfurt
| | - Silvia Lonardi
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia
| | - Mattia Bugatti
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia
| | - Claudio Agostinelli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy"
| | | | | | - Abbas Agaimy
- Institute of Pathology, University Hospital, Erlangen
| | | | - José Cabeçadas
- Department of Pathology, Portuguese Institute of Oncology, Lisbon, Portugal
| | - Elias Campo
- Hematopathology Section, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Stefano Aldo Pileri
- Division of Haematopathology, European Institute of Oncology (IEO) IRCCS, Milan
| | - Fabio Facchetti
- Pathology Unit, ASST Spedali Civili di Brescia, Department of Molecular and Translational Medicine, University of Brescia, Brescia
| | - Martin Leo Hansmann
- Institute for General Pharmacology and Toxicology, Goethe University, Frankfurt
| | - Sylvia Hartmann
- Dr Senckenberg Institute of Pathology, Goethe University, Frankfurt
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14
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Delamare M, Le Roy A, Pacault M, Schmitt L, Garrec C, Maaziz N, Myllykoski M, Rimbert A, Karaghiannis V, Aral B, Catherwood M, Airaud F, Mansour-Hendili L, Hoogewijs D, Peroni E, Idriss S, Lesieur V, Caillaud A, Si-Tayeb K, Chariau C, Gaignerie A, Rab M, Haferlach T, Meggendorfer M, Bézieau S, Benetti A, Casadevall N, Hirsch P, Rose C, Wemeau M, Galacteros F, Cassinat B, Bellosillo B, Bento C, Van Wijk R, Petrides PE, Randi ML, McMullin MF, Koivunen P, Girodon F, Gardie B. Characterization of genetic variants in the EGLN1/PHD2 gene identified in a European collection of patients with erythrocytosis. Haematologica 2023; 108:3068-3085. [PMID: 37317877 PMCID: PMC10620589 DOI: 10.3324/haematol.2023.282913] [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: 02/10/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Hereditary erythrocytosis is a rare hematologic disorder characterized by an excess of red blood cell production. Here we describe a European collaborative study involving a collection of 2,160 patients with erythrocytosis sequenced in ten different laboratories. We focused our study on the EGLN1 gene and identified 39 germline missense variants including one gene deletion in 47 probands. EGLN1 encodes the PHD2 prolyl 4-hydroxylase, a major inhibitor of hypoxia-inducible factor. We performed a comprehensive study to evaluate the causal role of the identified PHD2 variants: (i) in silico studies of localization, conservation, and deleterious effects; (ii) analysis of hematologic parameters of carriers identified in the UK Biobank; (iii) functional studies of the protein activity and stability; and (iv) a comprehensive study of PHD2 splicing. Altogether, these studies allowed the classification of 16 pathogenic or likely pathogenic mutants in a total of 48 patients and relatives. The in silico studies extended to the variants described in the literature showed that a minority of PHD2 variants can be classified as pathogenic (36/96), without any differences from the variants of unknown significance regarding the severity of the developed disease (hematologic parameters and complications). Here, we demonstrated the great value of federating laboratories working on such rare disorders in order to implement the criteria required for genetic classification, a strategy that should be extended to all hereditary hematologic diseases.
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Affiliation(s)
- Marine Delamare
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Amandine Le Roy
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Mathilde Pacault
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France; Service de Génétique Médicale, CHU de Nantes, Nantes
| | - Loïc Schmitt
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Céline Garrec
- Service de Génétique Médicale, CHU de Nantes, Nantes
| | - Nada Maaziz
- Service d'Hématologie Biologique, Pôle Biologie, CHU de Dijon, Dijon
| | - Matti Myllykoski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, 90014 Oulu, Finland. 90014 Oulu
| | - Antoine Rimbert
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Valéna Karaghiannis
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Bernard Aral
- Service d'Hématologie Biologique, Pôle Biologie, CHU de Dijon, Dijon
| | | | | | - Lamisse Mansour-Hendili
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale AP-HP, Hôpitaux Universitaires Henri Mondor, Créteil, France; Université Paris-Est Créteil, IMRB Equipe Pirenne, Laboratoire d'excellence LABEX GRex, Créteil
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, CH-1700 Fribourg, Switzerland; National Center of Competence in Research "Kidney.CH"
| | - Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro
| | - Salam Idriss
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Valentine Lesieur
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Amandine Caillaud
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Karim Si-Tayeb
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes
| | - Caroline Chariau
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, FR-44000, Nantes
| | - Anne Gaignerie
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, FR-44000, Nantes
| | - Minke Rab
- Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Department of Hematology, University Medical Center Utrecht, Utrecht University, Utrecht
| | | | | | - Stéphane Bézieau
- Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France; Service de Génétique Médicale, CHU de Nantes, Nantes
| | - Andrea Benetti
- Department of Medicine-DIMED, University of Padua, Via Giustiniani 2, 35128, Padua
| | - Nicole Casadevall
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, 75012, Paris
| | - Pierre Hirsch
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, 75012, Paris
| | - Christian Rose
- Service d'onco-hématologie, Saint-Vincent de Paul Hospital, Boulevard de Belfort, Université Catholique de Lille, Univ. Nord de France, F-59000 Lille
| | - Mathieu Wemeau
- Hematology Department, Claude Huriez Hospital, Lille Hospital, 59000 Lille
| | - Frédéric Galacteros
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale AP-HP, Hôpitaux Universitaires Henri Mondor, Créteil, France; Red Cell Disease Referral Center-UMGGR, AP-HP, Hôpitaux Universitaires Henri Mondor, Créteil
| | - Bruno Cassinat
- Université Paris Cité, APHP, Hôpital Saint-Louis, Laboratoire de Biologie Cellulaire, Paris
| | | | - Celeste Bento
- Hematology Department, Centro Hospitalar e Universitário de Coimbra; CIAS, University of Coimbra
| | - Richard Van Wijk
- Central Diagnostic Laboratory - Research, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Department of Hematology, University Medical Center Utrecht, Utrecht University, Utrecht
| | - Petro E Petrides
- Hematology Oncology Center and Ludwig-Maximilians-University Munich Medical School, Munich
| | - Maria Luigia Randi
- Department of Medicine-DIMED, University of Padua, Via Giustiniani 2, 35128, Padua
| | - Mary Frances McMullin
- Belfast Health and Social Care Trust, Belfast N.Ireland; Queen's University, Belfast, N. Ireland
| | - Peppi Koivunen
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, 90014 Oulu, Finland. 90014 Oulu
| | - François Girodon
- Service d'Hématologie Biologique, Pôle Biologie, CHU de Dijon, Dijon, France; Inserm U1231, Université de Bourgogne, Dijon, France; Laboratoire d'Excellence GR-Ex
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France; Laboratoire d'Excellence GR-Ex
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15
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Heyes E, Wilhelmson AS, Wenzel A, Manhart G, Eder T, Schuster MB, Rzepa E, Pundhir S, D'Altri T, Frank AK, Gentil C, Woessmann J, Schoof EM, Meggendorfer M, Schwaller J, Haferlach T, Grebien F, Porse BT. TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression. Nat Commun 2023; 14:6185. [PMID: 37794021 PMCID: PMC10550934 DOI: 10.1038/s41467-023-41927-x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML) with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. The most frequently co-mutated genes in CEBPADM AML are GATA2 and TET2, however the molecular mechanisms underlying this co-mutational spectrum are incomplete. By combining transcriptomic and epigenomic analyses of CEBPA-TET2 co-mutated patients with models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Elevated CEBPA levels, driven by CEBPANT, mediate recruitment of TET2 to the Gata2 distal hematopoietic enhancer thereby increasing Gata2 expression. Concurrent loss of TET2 in CEBPADM AML induces a competitive advantage by increasing Gata2 promoter methylation, thereby rebalancing GATA2 levels. Of clinical relevance, demethylating treatment of Cebpa-Tet2 co-mutated AML restores Gata2 levels and prolongs disease latency.
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Affiliation(s)
- Elizabeth Heyes
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Anna S Wilhelmson
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Manhart
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Thomas Eder
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Mikkel B Schuster
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edwin Rzepa
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria
| | - Sachin Pundhir
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Teresa D'Altri
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital Basel, Basel, Switzerland
| | | | - Florian Grebien
- University of Veterinary Medicine, Institute of Medical Biochemistry, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
| | - Bo T Porse
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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16
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Mori M, Kubota Y, Durmaz A, Gurnari C, Goodings C, Adema V, Ponvilawan B, Bahaj WS, Kewan T, LaFramboise T, Meggendorfer M, Haferlach C, Barnard J, Wlodarski M, Visconte V, Haferlach T, Maciejewski JP. Genomics of deletion 7 and 7q in myeloid neoplasm: from pathogenic culprits to potential synthetic lethal therapeutic targets. Leukemia 2023; 37:2082-2093. [PMID: 37634012 PMCID: PMC10539177 DOI: 10.1038/s41375-023-02003-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/28/2023]
Abstract
Complete or partial deletions of chromosome 7 (-7/del7q) belong to the most frequent chromosomal abnormalities in myeloid neoplasm (MN) and are associated with a poor prognosis. The disease biology of -7/del7q and the genes responsible for the leukemogenic properties have not been completely elucidated. Chromosomal deletions may create clonal vulnerabilities due to haploinsufficient (HI) genes contained in the deleted regions. Therefore, HI genes are potential targets of synthetic lethal strategies. Through the most comprehensive multimodal analysis of more than 600 -7/del7q MN samples, we elucidated the disease biology and qualified a list of most consistently deleted and HI genes. Among them, 27 potentially synthetic lethal target genes were identified with the following properties: (i) unaffected genes by hemizygous/homozygous LOF mutations; (ii) prenatal lethality in knockout mice; and (iii) vulnerability of leukemia cells by CRISPR and shRNA knockout screens. In -7/del7q cells, we also identified 26 up or down-regulated genes mapping on other chromosomes as downstream pathways or compensation mechanisms. Our findings shed light on the pathogenesis of -7/del7q MNs, while 27 potential synthetic lethal target genes and 26 differential expressed genes allow for a therapeutic window of -7/del7q.
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Affiliation(s)
- Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Hematology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Charnise Goodings
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vera Adema
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Waled S Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - John Barnard
- Department of Quantitative Health Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
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17
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Huber S, Baer C, Hutter S, Dicker F, Fuhrmann I, Meggendorfer M, Pohlkamp C, Kern W, Haferlach T, Haferlach C, Hoermann G. Risk assessment according to IPSS-M is superior to AML ELN risk classification in MDS/AML overlap patients defined by ICC. Leukemia 2023; 37:2138-2141. [PMID: 37573403 PMCID: PMC10539168 DOI: 10.1038/s41375-023-02004-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023]
Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Frank Dicker
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Irene Fuhrmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Christian Pohlkamp
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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18
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Stengel A, Meggendorfer M, Walter W, Baer C, Nadarajah N, Hutter S, Kern W, Haferlach T, Haferlach C. Interplay of TP53 allelic state, blast count, and complex karyotype on survival of patients with AML and MDS. Blood Adv 2023; 7:5540-5548. [PMID: 37505914 PMCID: PMC10515307 DOI: 10.1182/bloodadvances.2023010312] [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: 03/27/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Several clinical and genetic factors impact overall survival (OS) in myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML), including complex karyotype (CK), TP53 allelic state, and blast count. We analyzed the interplay of these factors by performing Cox regression analysis and by determining the frequency of TP53 single-hit (sh) and double-hit (dh) events and OS in MDS (n = 747) with <5% blasts, with ≥5% but <10% blasts, and ≥10% but <20% blasts and AML (n = 772). MDS with <5% blasts showed the best outcome, followed by with ≥5% but <10% blasts, and ≥10% but <20% blasts, and AML (median OS: 75, 54, 27, and 18 months, respectively). The same hierarchy was observed when each subgroup was divided into TP53sh, TP53dh, and without TP53 alterations (alt), revealing a dismal outcome of TP53dh in all subgroups (17, 10, 8, and 1 month[s], respectively). MDS with <5% blasts differed from the other subgroups by showing predominantly TP53sh (76% of TP53alt cases), and by an independent adverse impact of CK on OS (hazard ratio, 5.2; P < .001). The remaining subgroups displayed many similarities, with TP53dh found at high frequencies (67%, 91%, and 71%, respectively) and only TP53alt but not CK independently influencing OS, and TP53dh showing the strongest influence. When the total cohort was split based on TP53 state, only the blast count and not CK had an independent adverse impact on OS in all subgroups. Thus, TP53dh is the strongest prognostic factor, further supporting its integration into risk stratification guidelines and classification as a separate entity. However, the blast count also influences OS independent of TP53 state, whereas CK plays a minor prognostic role.
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19
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Lee H, Ahn S, Maity R, Leblay N, Ziccheddu B, Truger M, Chojnacka M, Cirrincione A, Durante M, Tilmont R, Barakat E, Poorebrahim M, Sinha S, McIntyre J, M Y Chan A, Wilson H, Kyman S, Krishnan A, Landgren O, Walter W, Meggendorfer M, Haferlach C, Haferlach T, Einsele H, Kortüm MK, Knop S, Alberge JB, Rosenwald A, Keats JJ, Rasche L, Maura F, Neri P, Bahlis NJ. Mechanisms of antigen escape from BCMA- or GPRC5D-targeted immunotherapies in multiple myeloma. Nat Med 2023; 29:2295-2306. [PMID: 37653344 PMCID: PMC10504087 DOI: 10.1038/s41591-023-02491-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [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: 03/05/2023] [Accepted: 07/05/2023] [Indexed: 09/02/2023]
Abstract
B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates multiple myeloma (MM) resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or bispecific T cell engager (TCE) therapies. Emerging data report that downregulation of G-protein-coupled receptor family C group 5 member D (GPRC5D) protein often occurs at relapse after anti-GPRC5D CAR T therapy. To examine the tumor-intrinsic factors that promote MM antigen escape, we performed combined bulk and single-cell whole-genome sequencing and copy number variation analysis of 30 patients treated with anti-BCMA and/or anti-GPRC5D CAR T/TCE therapy. In two cases, MM relapse post-TCE/CAR T therapy was driven by BCMA-negative clones harboring focal biallelic deletions at the TNFRSF17 locus at relapse or by selective expansion of pre-existing subclones with biallelic TNFRSF17 loss. In another five cases of relapse, newly detected, nontruncating, missense mutations or in-frame deletions in the extracellular domain of BCMA negated the efficacies of anti-BCMA TCE therapies, despite detectable surface BCMA protein expression. In the present study, we also report four cases of MM relapse with biallelic mutations of GPRC5D after anti-GPRC5D TCE therapy, including two cases with convergent evolution where multiple subclones lost GPRC5D through somatic events. Immunoselection of BCMA- or GPRC5D-negative or mutant clones is an important tumor-intrinsic driver of relapse post-targeted therapies. Mutational events on BCMA confer distinct sensitivities toward different anti-BCMA therapies, underscoring the importance of considering the tumor antigen landscape for optimal design and selection of targeted immunotherapies in MM.
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Grants
- P30 CA033572 NCI NIH HHS
- P30 CA240139 NCI NIH HHS
- Terry Fox Foundation
- Terry Fox Foundation, and Leukemia Lymphoma Society of Canada
- International Myeloma Society, Myeloma Canada, and Leukemia Lymphoma Society of Canada
- Terry Fox Foundation, International Myeloma Society, Myeloma Canada, and Leukemia Lymphoma Society of Canada
- Judy and Bernard Briskin Center for Multiple Myeloma Research at City of Hope, the MMRF, and the City of Hope Comprehensive Cancer Center NCI Core Grant (P30 CA 033572).
- Paula and Rodger Riney Multiple Myeloma Research Program Fund, the Multiple Myeloma Research Foundation (MMRF), the Perelman Family Foundation, and by a Sylvester Comprehensive Cancer Center NCI Core Grant (P30 CA 240139).
- German Cancer Aid and The Paula and Rodger Riney Foundation.
- Terry Fox Foundation, International Myeloma Society, Myeloma Canada, and Leukemia Lymphoma Society of Canada.
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Affiliation(s)
- Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sungwoo Ahn
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Noemie Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | | | | | | | | | | | - Remi Tilmont
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Elie Barakat
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Mansour Poorebrahim
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John McIntyre
- Precision Oncology Hub Laboratory, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Angela M Y Chan
- Precision Oncology Hub Laboratory, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Holly Wilson
- Precision Oncology Hub Laboratory, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Shari Kyman
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Ola Landgren
- Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | | | | | | | | | - Hermann Einsele
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Martin K Kortüm
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Stefan Knop
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Department of Internal Medicine 5, Paracelsus Medical School, Nuremberg General Hospital, Nuremberg, Germany
| | | | | | - Jonathan J Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Leo Rasche
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany.
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany.
| | | | - Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada.
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20
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Metzgeroth G, Steiner L, Naumann N, Lübke J, Kreil S, Fabarius A, Haferlach C, Haferlach T, Hofmann WK, Cross NCP, Schwaab J, Reiter A. Myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions: reevaluation of the defining characteristics in a registry-based cohort. Leukemia 2023; 37:1860-1867. [PMID: 37454239 PMCID: PMC10457188 DOI: 10.1038/s41375-023-01958-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/12/2022] [Revised: 05/18/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In a registry-based analysis of 135 patients with "myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions" (MLN-TK; FIP1L1::PDGFRA, n = 78; PDGFRB, diverse fusions, n = 26; FGFR1, diverse, n = 9; JAK2, diverse, n = 11; ETV6::ABL1, n = 11), we sought to evaluate the disease-defining characteristics. In 81/135 (60%) evaluable patients, hypereosinophilia (>1.5 × 109/l) was observed in 40/44 (91%) FIP1L1::PDGFRA and 7/7 (100%) ETV6::ABL1 positive patients but only in 13/30 (43%) patients with PDGFRB, FGFR1, and JAK2 fusion genes while 9/30 (30%) patients had no eosinophilia. Monocytosis >1 × 109/l was identified in 27/81 (33%) patients, most frequently in association with hypereosinophilia (23/27, 85%). Overall, a blast phase (BP) was diagnosed in 38/135 (28%) patients (myeloid, 61%; lymphoid, 39%), which was at extramedullary sites in 18 (47%) patients. The comparison between patients with PDGFRA/PDGFRB vs. FGFR1, JAK2, and ETV6::ABL1 fusion genes revealed a similar occurrence of primary BP (17/104, 16% vs. 8/31 26%, p = 0.32), a lower frequency (5/87, 6% vs. 8/23, 35%, p = 0.003) of and a later progression (median 87 vs. 19 months, p = 0.053) into secondary BP, and a better overall survival from diagnosis of BP (17.1 vs. 1.7 years, p < 0.0008). We conclude that hypereosinophilia with or without monocytosis and various phenotypes of BP occur at variable frequencies in MLN-TK.
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Affiliation(s)
- Georgia Metzgeroth
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Laurenz Steiner
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Nicole Naumann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Lübke
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Sebastian Kreil
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Alice Fabarius
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Nicholas C P Cross
- Wessex Regional Genetics Laboratory, Salisbury, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Juliana Schwaab
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany.
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21
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Nazha A, Elemento O, McWeeney S, Miles M, Haferlach T. How I read an article that uses machine learning methods. Blood Adv 2023; 7:4550-4554. [PMID: 37276509 PMCID: PMC10425665 DOI: 10.1182/bloodadvances.2023010140] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/07/2023] Open
Affiliation(s)
- Aziz Nazha
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York City, NY
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR
| | - Moses Miles
- American Thrombosis and Hemostasis Network, Rochester, NY
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22
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. bioRxiv 2023:2023.08.03.551876. [PMID: 37577681 PMCID: PMC10418284 DOI: 10.1101/2023.08.03.551876] [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: 08/15/2023]
Abstract
Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.
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23
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Bahaj W, Kewan T, Gurnari C, Durmaz A, Ponvilawan B, Pandit I, Kubota Y, Ogbue OD, Zawit M, Madanat Y, Bat T, Balasubramanian SK, Awada H, Ahmed R, Mori M, Meggendorfer M, Haferlach T, Visconte V, Maciejewski JP. Novel scheme for defining the clinical implications of TP53 mutations in myeloid neoplasia. J Hematol Oncol 2023; 16:91. [PMID: 37537667 PMCID: PMC10401750 DOI: 10.1186/s13045-023-01480-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/14/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND TP53 mutations (TP53MT) occur in diverse genomic configurations. Particularly, biallelic inactivation is associated with poor overall survival in cancer. Lesions affecting only one allele might not be directly leukemogenic, questioning the presence of cryptic biallelic subclones in cases with dismal prognosis. METHODS We have collected clinical and molecular data of 7400 patients with myeloid neoplasms and applied a novel model by identifying an optimal VAF cutoff using a statistically robust strategy of sampling-based regression on survival data to accurately classify the TP53 allelic configuration and assess prognosis more precisely. RESULTS Overall, TP53MT were found in 1010 patients. Following the traditional criteria, 36% of the cases were classified as single hits, while 64% exhibited double hits genomic configuration. Using a newly developed molecular algorithm, we found that 579 (57%) patients had unequivocally biallelic, 239 (24%) likely contained biallelic, and 192 (19%) had most likely monoallelic TP53MT. Interestingly, our method was able to upstage 192 out of 352 (54.5%) traditionally single hit lesions into a probable biallelic category. Such classification was further substantiated by a survival-based model built after re-categorization. Among cases traditionally considered monoallelic, the overall survival of those with probable monoallelic mutations was similar to the one of wild-type patients and was better than that of patients with a biallelic configuration. As a result, patients with certain biallelic hits, regardless of the disease subtype (AML or MDS), had a similar prognosis. Similar results were observed when the model was applied to an external cohort. In addition, single-cell DNA studies unveiled the biallelic nature of previously considered monoallelic cases. CONCLUSION Our novel approach more accurately resolves TP53 genomic configuration and uncovers genetic mosaicism for the use in the clinical setting to improve prognostic evaluation.
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Affiliation(s)
- Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
- Division of Medical Oncology & Hematology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
- Division of Hematology & Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Ishani Pandit
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Olisaemeka D Ogbue
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Misam Zawit
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Yazan Madanat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taha Bat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Ramsha Ahmed
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA
| | | | | | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA.
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 9620 Carnegie Ave N Building, Building NE6-250, Cleveland, OH, 44106, USA.
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24
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de Almeida JG, Gudgin E, Besser M, Dunn WG, Cooper J, Haferlach T, Vassiliou GS, Gerstung M. Computational analysis of peripheral blood smears detects disease-associated cytomorphologies. Nat Commun 2023; 14:4378. [PMID: 37474506 PMCID: PMC10359268 DOI: 10.1038/s41467-023-39676-y] [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: 04/27/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Many hematological diseases are characterized by altered abundance and morphology of blood cells and their progenitors. Myelodysplastic syndromes (MDS), for example, are a group of blood cancers characterised by cytopenias, dysplasia of hematopoietic cells and blast expansion. Examination of peripheral blood slides (PBS) in MDS often reveals changes such as abnormal granulocyte lobulation or granularity and altered red blood cell (RBC) morphology; however, some of these features are shared with conditions such as haematinic deficiency anemias. Definitive diagnosis of MDS requires expert cytomorphology analysis of bone marrow smears and complementary information such as blood counts, karyotype and molecular genetics testing. Here, we present Haemorasis, a computational method that detects and characterizes white blood cells (WBC) and RBC in PBS. Applied to over 300 individuals with different conditions (SF3B1-mutant and SF3B1-wildtype MDS, megaloblastic anemia, and iron deficiency anemia), Haemorasis detected over half a million WBC and millions of RBC and characterized their morphology. These large sets of cell morphologies can be used in diagnosis and disease subtyping, while identifying novel associations between computational morphotypes and disease. We find that hypolobulated neutrophils and large RBC are characteristic of SF3B1-mutant MDS. Additionally, while prevalent in both iron deficiency and megaloblastic anemia, hyperlobulated neutrophils are larger in the latter. By integrating cytomorphological features using machine learning, Haemorasis was able to distinguish SF3B1-mutant MDS from other MDS using cytomorphology and blood counts alone, with high predictive performance. We validate our findings externally, showing that they generalize to other centers and scanners. Collectively, our work reveals the potential for the large-scale incorporation of automated cytomorphology into routine diagnostic workflows.
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Affiliation(s)
- José Guilherme de Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Champalimaud Foundation-Centre for the Unknown, Lisbon, Portugal
| | - Emma Gudgin
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Besser
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - William G Dunn
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jonathan Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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25
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D'Amico S, Dall’Olio D, Sala C, Dall’Olio L, Sauta E, Zampini M, Asti G, Lanino L, Maggioni G, Campagna A, Ubezio M, Russo A, Bicchieri ME, Riva E, Tentori CA, Travaglino E, Morandini P, Savevski V, Santoro A, Prada-Luengo I, Krogh A, Santini V, Kordasti S, Platzbecker U, Diez-Campelo M, Fenaux P, Haferlach T, Castellani G, Della Porta MG. Synthetic Data Generation by Artificial Intelligence to Accelerate Research and Precision Medicine in Hematology. JCO Clin Cancer Inform 2023; 7:e2300021. [PMID: 37390377 PMCID: PMC10569771 DOI: 10.1200/cci.23.00021] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/16/2023] [Accepted: 04/05/2023] [Indexed: 07/02/2023] Open
Abstract
PURPOSE Synthetic data are artificial data generated without including any real patient information by an algorithm trained to learn the characteristics of a real source data set and became widely used to accelerate research in life sciences. We aimed to (1) apply generative artificial intelligence to build synthetic data in different hematologic neoplasms; (2) develop a synthetic validation framework to assess data fidelity and privacy preservability; and (3) test the capability of synthetic data to accelerate clinical/translational research in hematology. METHODS A conditional generative adversarial network architecture was implemented to generate synthetic data. Use cases were myelodysplastic syndromes (MDS) and AML: 7,133 patients were included. A fully explainable validation framework was created to assess fidelity and privacy preservability of synthetic data. RESULTS We generated MDS/AML synthetic cohorts (including information on clinical features, genomics, treatment, and outcomes) with high fidelity and privacy performances. This technology allowed resolution of lack/incomplete information and data augmentation. We then assessed the potential value of synthetic data on accelerating research in hematology. Starting from 944 patients with MDS available since 2014, we generated a 300% augmented synthetic cohort and anticipated the development of molecular classification and molecular scoring system obtained many years later from 2,043 to 2,957 real patients, respectively. Moreover, starting from 187 MDS treated with luspatercept into a clinical trial, we generated a synthetic cohort that recapitulated all the clinical end points of the study. Finally, we developed a website to enable clinicians generating high-quality synthetic data from an existing biobank of real patients. CONCLUSION Synthetic data mimic real clinical-genomic features and outcomes, and anonymize patient information. The implementation of this technology allows to increase the scientific use and value of real data, thus accelerating precision medicine in hematology and the conduction of clinical trials.
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Affiliation(s)
| | | | - Claudia Sala
- Experimental, Diagnostic and Specialty Medicine—DIMES, Bologna, Italy
| | | | | | | | | | - Luca Lanino
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Giulia Maggioni
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | | | | | | | - Elena Riva
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Cristina A. Tentori
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Erica Travaglino
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | | | - Armando Santoro
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Iñigo Prada-Luengo
- Department of Computer Science & Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Anders Krogh
- Department of Computer Science & Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Valeria Santini
- Hematology, Azienda Ospedaliero-Universitaria Careggi & University of Florence, Florence, Italy
| | - Shahram Kordasti
- Hematology, Guy's Hospital & Comprehensive Cancer Centre, King's College, London, United Kingdom
- Hematology Department & Stem Cell Transplant Unit, DISCLIMO-Università Politecnica delle Marche, Ancona, Italy
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University Hospital Leipzig, Leipzig, Germany
| | - Maria Diez-Campelo
- Hematology Department, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Pierre Fenaux
- Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis/University Paris 7, Paris, France
| | | | - Gastone Castellani
- Department of Physics and Astronomy (DIFA), Bologna, Italy
- Experimental, Diagnostic and Specialty Medicine—DIMES, Bologna, Italy
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
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26
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Kewan T, Durmaz A, Bahaj W, Gurnari C, Terkawi L, Awada H, Ogbue OD, Ahmed R, Pagliuca S, Awada H, Kubota Y, Mori M, Ponvilawan B, Al-Share B, Patel BJ, Carraway HE, Scott J, Balasubramanian SK, Bat T, Madanat Y, Sekeres MA, Haferlach T, Visconte V, Maciejewski JP. Molecular patterns identify distinct subclasses of myeloid neoplasia. Nat Commun 2023; 14:3136. [PMID: 37253784 PMCID: PMC10229666 DOI: 10.1038/s41467-023-38515-4] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
Genomic mutations drive the pathogenesis of myelodysplastic syndromes and acute myeloid leukemia. While morphological and clinical features have dominated the classical criteria for diagnosis and classification, incorporation of molecular data can illuminate functional pathobiology. Here we show that unsupervised machine learning can identify functional objective molecular clusters, irrespective of anamnestic clinico-morphological features, despite the complexity of the molecular alterations in myeloid neoplasia. Our approach reflects disease evolution, informed classification, prognostication, and molecular interactions. We apply machine learning methods on 3588 patients with myelodysplastic syndromes and secondary acute myeloid leukemia to identify 14 molecularly distinct clusters. Remarkably, our model shows clinical implications in terms of overall survival and response to treatment even after adjusting to the molecular international prognostic scoring system (IPSS-M). In addition, the model is validated on an external cohort of 412 patients. Our subclassification model is available via a web-based open-access resource ( https://drmz.shinyapps.io/mds_latent ).
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Affiliation(s)
- Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Hematology and Medical Oncology, Yale University, New Haven, CT, USA.
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, Ph.D. in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Laila Terkawi
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Olisaemeka D Ogbue
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ramsha Ahmed
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bayan Al-Share
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Bhumika J Patel
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hetty E Carraway
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Suresh K Balasubramanian
- Department of Hematology and Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Taha Bat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yazan Madanat
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Cancer Center, University of Miami, Miami, FL, USA
| | | | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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27
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Sauta E, Robin M, Bersanelli M, Travaglino E, Meggendorfer M, Zhao LP, Caballero Berrocal JC, Sala C, Maggioni G, Bernardi M, Di Grazia C, Vago L, Rivoli G, Borin L, D'Amico S, Tentori CA, Ubezio M, Campagna A, Russo A, Mannina D, Lanino L, Chiusolo P, Giaccone L, Voso MT, Riva M, Oliva EN, Zampini M, Riva E, Nibourel O, Bicchieri M, Bolli N, Rambaldi A, Passamonti F, Savevski V, Santoro A, Germing U, Kordasti S, Santini V, Diez-Campelo M, Sanz G, Sole F, Kern W, Platzbecker U, Ades L, Fenaux P, Haferlach T, Castellani G, Della Porta MG. Real-World Validation of Molecular International Prognostic Scoring System for Myelodysplastic Syndromes. J Clin Oncol 2023; 41:2827-2842. [PMID: 36930857 PMCID: PMC10414702 DOI: 10.1200/jco.22.01784] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [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: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 03/19/2023] Open
Abstract
PURPOSE Myelodysplastic syndromes (MDS) are heterogeneous myeloid neoplasms in which a risk-adapted treatment strategy is needed. Recently, a new clinical-molecular prognostic model, the Molecular International Prognostic Scoring System (IPSS-M) was proposed to improve the prediction of clinical outcome of the currently available tool (Revised International Prognostic Scoring System [IPSS-R]). We aimed to provide an extensive validation of IPSS-M. METHODS A total of 2,876 patients with primary MDS from the GenoMed4All consortium were retrospectively analyzed. RESULTS IPSS-M improved prognostic discrimination across all clinical end points with respect to IPSS-R (concordance was 0.81 v 0.74 for overall survival and 0.89 v 0.76 for leukemia-free survival, respectively). This was true even in those patients without detectable gene mutations. Compared with the IPSS-R based stratification, the IPSS-M risk group changed in 46% of patients (23.6% and 22.4% of subjects were upstaged and downstaged, respectively).In patients treated with hematopoietic stem cell transplantation (HSCT), IPSS-M significantly improved the prediction of the risk of disease relapse and the probability of post-transplantation survival versus IPSS-R (concordance was 0.76 v 0.60 for overall survival and 0.89 v 0.70 for probability of relapse, respectively). In high-risk patients treated with hypomethylating agents (HMA), IPSS-M failed to stratify individual probability of response; response duration and probability of survival were inversely related to IPSS-M risk.Finally, we tested the accuracy in predicting IPSS-M when molecular information was missed and we defined a minimum set of 15 relevant genes associated with high performance of the score. CONCLUSION IPSS-M improves MDS prognostication and might result in a more effective selection of candidates to HSCT. Additional factors other than gene mutations can be involved in determining HMA sensitivity. The definition of a minimum set of relevant genes may facilitate the clinical implementation of the score.
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Affiliation(s)
- Elisabetta Sauta
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Marie Robin
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis/Assistance Publique-Hôpitaux de Paris (AP-HP)/University Paris 7, Paris, France
| | - Matteo Bersanelli
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Erica Travaglino
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | - Lin-Pierre Zhao
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis/Assistance Publique-Hôpitaux de Paris (AP-HP)/University Paris 7, Paris, France
| | | | - Claudia Sala
- Experimental, Diagnostic and Specialty Medicine, DIMES, Bologna, Italy
| | - Giulia Maggioni
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Massimo Bernardi
- Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, University Vita-Salute San Raffaele, Milan, Italy
| | - Carmen Di Grazia
- Hematology and Transplant Center, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Luca Vago
- Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, University Vita-Salute San Raffaele, Milan, Italy
| | - Giulia Rivoli
- Hematology and Transplant Center, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Saverio D'Amico
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | - Marta Ubezio
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Alessia Campagna
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Antonio Russo
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Daniele Mannina
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Luca Lanino
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Patrizia Chiusolo
- Hematology, IRCCS Fondazione Policlinico Universitario Gemelli & Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luisa Giaccone
- Stem Cell Transplant Program, Department of Oncology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Maria Teresa Voso
- Hematology, Policlinico Tor Vergata & Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Marta Riva
- Hematology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Esther Natalie Oliva
- Hematology, Grande Ospedale Metropolitano Bianchi Melacrino Morelli, Reggio Calabria, Italy
| | - Matteo Zampini
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Elena Riva
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | | | - Niccolo’ Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Italy
| | - Alessandro Rambaldi
- Hematology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Italy
| | - Francesco Passamonti
- Hematology, ASST Sette Laghi, Ospedale di Circolo of Varese, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Victor Savevski
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Armando Santoro
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Ulrich Germing
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University, University Clinic, Düsseldorf, Germany
| | - Shahram Kordasti
- Haematology, Guy's Hospital and Comprehensive Cancer Centre, King's College, London, United Kingdom
- Hematology Department and Stem Cell Transplant Unit, DISCLIMO-Università Politecnica delle Marche, Ancona, Italy
| | - Valeria Santini
- Hematology, Azienda Ospedaliero-Universitaria Careggi & University of Florence, Florence, Italy
| | - Maria Diez-Campelo
- Hematology Department, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Guillermo Sanz
- Hematology, Hospital Universitario La Fe, Valencia, Spain
| | - Francesc Sole
- Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | | | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University Hospital Leipzig, Leipzig, Germany
| | - Lionel Ades
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis/Assistance Publique-Hôpitaux de Paris (AP-HP)/University Paris 7, Paris, France
| | - Pierre Fenaux
- Department of Hematology and Bone Marrow Transplantation, Hôpital Saint-Louis/Assistance Publique-Hôpitaux de Paris (AP-HP)/University Paris 7, Paris, France
| | | | | | - Matteo Giovanni Della Porta
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
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Carter BZ, Mak PY, Tao W, Ayoub E, Ostermann LB, Huang X, Loghavi S, Boettcher S, Nishida Y, Ruvolo V, Hughes PE, Morrow PK, Haferlach T, Kornblau S, Muftuoglu M, Andreeff M. Correction: Combined inhibition of BCL-2 and MCL-1 overcomes BAX deficiency-mediated resistance of TP53-mutant acute myeloid leukemia to individual BH3 mimetics. Blood Cancer J 2023; 13:80. [PMID: 37193700 DOI: 10.1038/s41408-023-00857-z] [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: 05/18/2023] Open
Affiliation(s)
- Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenjing Tao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren B Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steffen Boettcher
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul E Hughes
- Oncology Research, Amgen Inc, Thousand Oaks, CA, USA
| | | | | | - Steven Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muharrem Muftuoglu
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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29
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Huber S, Baer C, Hutter S, Dicker F, Meggendorfer M, Pohlkamp C, Kern W, Haferlach T, Haferlach C, Hoermann G. AML classification in the year 2023: How to avoid a Babylonian confusion of languages. Leukemia 2023:10.1038/s41375-023-01909-w. [PMID: 37120689 DOI: 10.1038/s41375-023-01909-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
In parallel to the 5th edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO 2022), an alternative International Consensus Classification (ICC) has been proposed. To evaluate the impact of the new classifications on AML diagnoses and ELN-based risk classification, we analyzed 717 MDS and 734 AML non-therapy-related patients diagnosed according to the revised 4th WHO edition (WHO 2017) by whole genome and transcriptome sequencing. In both new classifications, the purely morphologically defined AML entities decreased from 13% to 5%. Myelodysplasia-related (MR) AML increased from 22% to 28% (WHO 2022) and 26% (ICC). Other genetically-defined AML remained the largest group, and the abandoned AML-RUNX1 was mainly reclassified as AML-MR (WHO 2022: 77%; ICC: 96%). Different inclusion criteria of AML-CEBPA and AML-MR (i.a. exclusion of TP53 mutated cases according to ICC) were associated with differences in overall survival. In conclusion, both classifications focus on more genetics-based definitions with similar basic concepts and a large degree of agreement. The remaining non-comparability (e.g., TP53 mutated AML) needs additional studies to definitely answer open questions on disease categorization in an unbiased way.
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Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Frank Dicker
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Christian Pohlkamp
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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30
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Carter BZ, Mak PY, Tao W, Ayoub E, Ostermann LB, Huang X, Loghavi S, Boettcher S, Nishida Y, Ruvolo V, Hughes PE, Morrow PK, Haferlach T, Kornblau S, Muftuoglu M, Andreeff M. Combined inhibition of BCL-2 and MCL-1 overcomes BAX deficiency-mediated resistance of TP53-mutant acute myeloid leukemia to individual BH3 mimetics. Blood Cancer J 2023; 13:57. [PMID: 37088806 PMCID: PMC10123065 DOI: 10.1038/s41408-023-00830-w] [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: 12/13/2022] [Revised: 03/07/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
TP53-mutant acute myeloid leukemia (AML) respond poorly to currently available treatments, including venetoclax-based drug combinations and pose a major therapeutic challenge. Analyses of RNA sequencing and reverse phase protein array datasets revealed significantly lower BAX RNA and protein levels in TP53-mutant compared to TP53-wild-type (WT) AML, a finding confirmed in isogenic CRISPR-generated TP53-knockout and -mutant AML. The response to either BCL-2 (venetoclax) or MCL-1 (AMG176) inhibition was BAX-dependent and much reduced in TP53-mutant compared to TP53-WT cells, while the combination of two BH3 mimetics effectively activated BAX, circumventing survival mechanisms in cells treated with either BH3 mimetic, and synergistically induced cell death in TP53-mutant AML and stem/progenitor cells. The BH3 mimetic-driven stress response and cell death patterns after dual inhibition were largely independent of TP53 status and affected by apoptosis induction. Co-targeting, but not individual targeting of BCL-2 and MCL-1 in mice xenografted with TP53-WT and TP53-R248W Molm13 cells suppressed both TP53-WT and TP53-mutant cell growth and significantly prolonged survival. Our results demonstrate that co-targeting BCL-2 and MCL-1 overcomes BAX deficiency-mediated resistance to individual BH3 mimetics in TP53-mutant cells, thus shifting cell fate from survival to death in TP53-deficient and -mutant AML. This concept warrants clinical evaluation.
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Affiliation(s)
- Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenjing Tao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren B Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steffen Boettcher
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul E Hughes
- Oncology Research, Amgen Inc, Thousand Oaks, CA, USA
| | | | | | - Steven Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muharrem Muftuoglu
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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31
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Choi IY, Ling J, Zhang J, Helmenstine E, Walter W, Bergman R, Philippe C, Manley J, Rouault-Pierre K, Li B, Wiseman D, Ouseph M, Bernard E, Li X, Haferlach T, Fazal S, Jain T, Gocke C, DeZern A, Dalton WB. The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts. Res Sq 2023:rs.3.rs-2802265. [PMID: 37090662 PMCID: PMC10120771 DOI: 10.21203/rs.3.rs-2802265/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Among the most common genetic alterations in the myelodysplastic syndromes (MDS) are mutations in the spliceosome gene SF3B1. Such mutations induce specific RNA missplicing events, directly promote ring sideroblast (RS) formation, generally associate with more favorable prognosis, and serve as a predictive biomarker of response to luspatercept. However, not all SF3B1 mutations are the same, and here we report that the E592K variant of SF3B1 associates with high-risk disease features in MDS, including a lack of RS, increased myeloblasts, a distinct co-mutation pattern, and decreased survival. Moreover, in contrast to canonical SF3B1 mutations, E592K induces a unique RNA missplicing pattern, retains an interaction with the splicing factor SUGP1, and preserves normal RNA splicing of the sideroblastic anemia genes TMEM14C and ABCB7. These data expand our knowledge of the functional diversity of spliceosome mutations, and they suggest that patients with E592K should be approached differently from low-risk, luspatercept-responsive MDS patients with ring sideroblasts and canonical SF3B1 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bing Li
- Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College
| | | | | | | | - Xiao Li
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital
| | | | | | - Tania Jain
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University
| | | | - Amy DeZern
- Johns Hopkins University School of Medicine
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32
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Haferlach T, Walter W. Challenging gold standard hematology diagnostics through the introduction of whole genome sequencing and artificial intelligence. Int J Lab Hematol 2023; 45:156-162. [PMID: 36737231 DOI: 10.1111/ijlh.14033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The diagnosis of hematological malignancies is rather complex and requires the application of a plethora of different assays, techniques and methodologies. Some of the methods, like cytomorphology, have been in use for decades, while other methods, such as next-generation sequencing or even whole genome sequencing (WGS), are relatively new. The application of the methods and the evaluation of the results require distinct skills and knowledge and place different demands on the practitioner. However, even with experienced hematologists, diagnostic ambiguity remains a regular occurrence and the comprehensive analysis of high-dimensional WGS data soon exceeds any human's capacity. Hence, in order to reduce inter-observer variability and to improve the timeliness and accuracy of diagnoses, machine learning based approaches have been developed to assist in the decision making process. Moreover, to achieve the goal of precision oncology, comprehensive genomic profiling is increasingly being incorporated into routine standard of care.
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33
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Mayerhofer E, Strecker C, Becker H, Georgakis MK, Uddin MM, Hoffmann MM, Nadarajah N, Meggendorfer M, Haferlach T, Rosand J, Natarajan P, Anderson CD, Harloff A, Hoermann G. Prevalence and Therapeutic Implications of Clonal Hematopoiesis of Indeterminate Potential in Young Patients With Stroke. Stroke 2023; 54:938-946. [PMID: 36789775 PMCID: PMC10050122 DOI: 10.1161/strokeaha.122.041416] [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: 09/23/2022] [Accepted: 01/19/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Undetermined stroke etiology hampers optimal secondary prevention in a large proportion of young patients. We explored whether genetic screening for clonal hematopoiesis of indetermined potential (CHIP), a novel risk factor for stroke, could identify patients with myeloid precursor lesions or covert myeloid neoplasm requiring specific treatment. METHODS We performed targeted sequencing on 56 genes recurrently mutated in hematologic neoplasms in a prospective cohort of patients with acute brain ischemia between 18 and 60 years. CHIP prevalence was compared with age-matched healthy controls from the Nijmegen Biomedical Study (n=1604) and the UK Biobank (n=101 678). Patients with suspicion of high-risk CHIP or myeloid neoplasm were invited for further hematologic evaluation. RESULTS We included 248 consecutive patients (39% women) of whom 176 (71%) had cryptogenic stroke etiology. Fifty-one (21%) patients had CHIP, 3-fold more than in the general population (7.7% versus 2.6% for the Nijmegen Biomedical Study and 11.9% versus 4.1% for UK Biobank; P<0.001 for both). Patients with CHIP were older (median [interquartile range], 53 [50-59] versus 51 [41-56] years; P<0.001), had higher carotid intima-media thickness (0.68 [0.58-0.80] versus 0.59 [0.51-0.73] mm; P=0.009), and had higher burden of atherosclerosis (29.4% versus 16.7%; P=0.04). We invited 11 patients (4.4%) for further hematologic assessment, which in 7 led to the diagnosis of high-risk CHIP and in 2 to the new diagnosis of a myeloproliferative neoplasm with indication for cytoreductive therapy. CONCLUSIONS Using genetic screening for myeloid disorders in patients with stroke of predominantly undetermined etiology, we found a 3-fold higher CHIP prevalence than in the general population. We identified high-risk CHIP and previously covert myeloproliferative neoplasms as potential stroke etiologies in 4.4% and 1% of patients, respectively. Our findings demonstrate the diagnostic and therapeutic yield of genetic screening in young patients with stroke. Future studies should investigate the role of CHIP for stroke recurrence and optimal secondary prevention.
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Affiliation(s)
- Ernst Mayerhofer
- Department of Neurology and Neurophysiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Neurology, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Boston, USA
| | - Christoph Strecker
- Department of Neurology and Neurophysiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Heiko Becker
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Marios K Georgakis
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Neurology, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Boston, USA
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU) Munich, Germany
| | - Md Mesbah Uddin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Boston, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, USA
| | - Michael M Hoffmann
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | | | | | | | - Jonathan Rosand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Neurology, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Boston, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Boston, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, USA
| | | | - Andreas Harloff
- Department of Neurology and Neurophysiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
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34
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Durmaz A, Gurnari C, Hershberger CE, Pagliuca S, Daniels N, Awada H, Awada H, Adema V, Mori M, Ponvilawan B, Kubota Y, Kewan T, Bahaj WS, Barnard J, Scott J, Padgett RA, Haferlach T, Maciejewski JP, Visconte V. A multimodal analysis of genomic and RNA splicing features in myeloid malignancies. iScience 2023; 26:106238. [PMID: 36926651 PMCID: PMC10011742 DOI: 10.1016/j.isci.2023.106238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
RNA splicing dysfunctions are more widespread than what is believed by only estimating the effects resulting by splicing factor mutations (SFMT) in myeloid neoplasia (MN). The genetic complexity of MN is amenable to machine learning (ML) strategies. We applied an integrative ML approach to identify co-varying features by combining genomic lesions (mutations, deletions, and copy number), exon-inclusion ratio as measure of RNA splicing (percent spliced in, PSI), and gene expression (GE) of 1,258 MN and 63 normal controls. We identified 15 clusters based on mutations, GE, and PSI. Different PSI levels were present at various extents regardless of SFMT suggesting that changes in RNA splicing were not strictly related to SFMT. Combination of PSI and GE further distinguished the features and identified PSI similarities and differences, common pathways, and expression signatures across clusters. Thus, multimodal features can resolve the complex architecture of MN and help identifying convergent molecular and transcriptomic pathways amenable to therapies.
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Affiliation(s)
- Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | | | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Clinical Hematology, CHRU de Nancy, Nancy, France
| | - Noah Daniels
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Hassan Awada
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Hussein Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Vera Adema
- MD Anderson Cancer Center, Houston, TX, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Waled S. Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard A. Padgett
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | | | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Corresponding author
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Bahaj W, Kewan T, Gurnari C, Durmaz A, Ponvilawan B, Pandit I, Kubota Y, Ogbue OD, Zawit M, Madanat Y, Bat T, Balasubramanian SK, Awada H, Ahmed R, Mori M, Meggendorfer M, Haferlach T, Visconte V, Maciejewski JP. Novel Scheme for Defining the Clinical Implications of TP53 Mutations in Myeloid Neoplasia. Res Sq 2023:rs.3.rs-2656206. [PMID: 36945617 PMCID: PMC10029089 DOI: 10.21203/rs.3.rs-2656206/v1] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Background: TP53 mutations ( TP53 MT ) occur in diverse genomic configurations. Particularly, biallelic inactivation is associated with poor overall survival in cancer. Lesions affecting only one allele might not be directly leukemogenic, questioning the presence of cryptic biallelic subclones in cases with dismal prognosis. Methods: We have collected clinical and molecular data of 7400 patients with myeloid neoplasms and applied a novel model to properly resolve the allelic configuration of TP53 MT and assess prognosis more precisely. Results: Overall, TP53 MT were found in 1010 patients. Following the traditional criteria, 36% of cases were classified as single hits while 64% exhibited double hits genomic configuration. Using a newly developed molecular algorithm, we found that 579 (57%) patients had unequivocally biallelic, 239 (24%) likely contained biallelic, and 192 (19%) had most likely monoallelic TP53 MT . Such classification was further substantiated by a survival-based model built after re-categorization. Among cases traditionally considered monoallelic, the overall survival of those with probable monoallelic mutations was similar to the one of wild-type patients and was better than that of patients with a biallelic configuration. As a result, patients with certain biallelic hits, regardless of the disease subtype (AML or MDS), had a similar prognosis. Similar results were observed when the model was applied to an external cohort. These results were recapitulated by single-cell DNA studies, which unveiled the biallelic nature of previously considered monoallelic cases. Conclusion: Our novel approach more accurately resolves TP53 genomic configuration and uncovers genetic mosaicism for the use in the clinical setting to improve prognostic evaluation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Taha Bat
- University of Texas Southwestern Medical Center
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Hehr M, Sadafi A, Matek C, Lienemann P, Pohlkamp C, Haferlach T, Spiekermann K, Marr C. Explainable AI identifies diagnostic cells of genetic AML subtypes. PLOS Digit Health 2023; 2:e0000187. [PMID: 36921004 PMCID: PMC10016704 DOI: 10.1371/journal.pdig.0000187] [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] [Received: 05/26/2022] [Accepted: 12/19/2022] [Indexed: 03/16/2023]
Abstract
Explainable AI is deemed essential for clinical applications as it allows rationalizing model predictions, helping to build trust between clinicians and automated decision support tools. We developed an inherently explainable AI model for the classification of acute myeloid leukemia subtypes from blood smears and found that high-attention cells identified by the model coincide with those labeled as diagnostically relevant by human experts. Based on over 80,000 single white blood cell images from digitized blood smears of 129 patients diagnosed with one of four WHO-defined genetic AML subtypes and 60 healthy controls, we trained SCEMILA, a single-cell based explainable multiple instance learning algorithm. SCEMILA could perfectly discriminate between AML patients and healthy controls and detected the APL subtype with an F1 score of 0.86±0.05 (mean±s.d., 5-fold cross-validation). Analyzing a novel multi-attention module, we confirmed that our algorithm focused with high concordance on the same AML-specific cells as human experts do. Applied to classify single cells, it is able to highlight subtype specific cells and deconvolve the composition of a patient's blood smear without the need of single-cell annotation of the training data. Our large AML genetic subtype dataset is publicly available, and an interactive online tool facilitates the exploration of data and predictions. SCEMILA enables a comparison of algorithmic and expert decision criteria and can present a detailed analysis of individual patient data, paving the way to deploy AI in the routine diagnostics for identifying hematopoietic neoplasms.
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Affiliation(s)
- Matthias Hehr
- Institute of AI for Health, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Laboratory of Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Ario Sadafi
- Institute of AI for Health, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Computer Aided Medical Procedures, Technical University of Munich, Munich, Germany
| | - Christian Matek
- Institute of AI for Health, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Laboratory of Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Peter Lienemann
- Institute of AI for Health, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Laboratory of Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | | | | | - Karsten Spiekermann
- Laboratory of Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- * E-mail:
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Walter W, Pohlkamp C, Meggendorfer M, Nadarajah N, Kern W, Haferlach C, Haferlach T. Artificial intelligence in hematological diagnostics: Game changer or gadget? Blood Rev 2023; 58:101019. [PMID: 36241586 DOI: 10.1016/j.blre.2022.101019] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022]
Abstract
The future of clinical diagnosis and treatment of hematologic diseases will inevitably involve the integration of artificial intelligence (AI)-based systems into routine practice to support the hematologists' decision making. Several studies have shown that AI-based models can already be used to automatically differentiate cells, reliably detect malignant cell populations, support chromosome banding analysis, and interpret clinical variants, contributing to early disease detection and prognosis. However, even the best tool can become useless if it is misapplied or the results are misinterpreted. Therefore, in order to comprehensively judge and correctly apply newly developed AI-based systems, the hematologist must have a basic understanding of the general concepts of machine learning. In this review, we provide the hematologist with a comprehensive overview of various machine learning techniques, their current implementations and approaches in different diagnostic subfields (e.g., cytogenetics, molecular genetics), and the limitations and unresolved challenges of the systems.
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Affiliation(s)
- Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Christian Pohlkamp
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 München, Germany.
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Weiß E, Walter W, Meggendorfer M, Baer C, Haferlach C, Haferlach T, Kern W. Identification of a specific immunophenotype associated with a consistent pattern of genetic mutations including SRFS2 and gene expression profile in MDS. Cytometry B Clin Cytom 2023; 104:173-182. [PMID: 35088567 DOI: 10.1002/cyto.b.22057] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) comprise a heterogeneous group of diseases classified by comprehensive diagnostics. Identification of homogeneous subgroups is desirable to understand differences in clinical course and to develop targeted treatment approaches. We identified a specific CD11b/CD16 expression pattern in granulocytes associated with reduced CD45 expression in myeloid progenitor cells (MPC) in MDS cases and assessed its genetic background by whole genome (WGS) and whole transcriptome sequencing (WTS). METHODS The cohort consisted of 32 MDS cases with the specific aberrant immunophenotype. Since all these 32 cases were found to be SRSF2 mutated additional 51 SRSF2 mutated MDS cases without this specific immunophenotype were selected as controls. For all cases WGS and WTS were performed. RESULTS The immunophenotype newly identified in SRSF2 mutated MDS patients is characterized (1) by a specific maturation pattern, i.e. an increase of CD11b expression without CD16 expression followed by an increase in CD16 expression without further CD11b expression and (2) by only dim CD45 expression of MPC. STAG2 mutations were exclusively found in MDS cases with the specific immunophenotype (17/32, 53% vs. 0%, p < 0.001). Hence, >50% of cases with the specific immunophenotype were characterized by co-mutations in SRSF2 and STAG2. In addition, cluster analysis revealed a specific gene expression profile of such cases. CONCLUSION We here for the first time describe a specific immunophenotype which defines MDS cases with SRSF2 mutations and a consistent and specific mutational and gene expression profile. This comprehensive data warrants analysis of further such cases to assess the feasibility of defining a new sub-entity of MDS.
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Sakuma M, Blombery P, Meggendorfer M, Haferlach C, Lindauer M, Martens UM, Kern W, Haferlach T, Walter W. Novel causative variants of VEXAS in UBA1 detected through whole genome transcriptome sequencing in a large cohort of hematological malignancies. Leukemia 2023; 37:1080-1091. [PMID: 36823397 PMCID: PMC10169658 DOI: 10.1038/s41375-023-01857-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
UBA1 is an X-linked gene and encodes an ubiquitin-activating enzyme. Three somatic mutations altering the alternative start codon (M41) in UBA1 in hematopoietic precursor cells have recently been described, resulting in a syndrome of severe inflammation, cytopenias, and the presence of intracellular vacuoles in hematopoietic precursors - termed VEXAS syndrome, a predominantly male disease. Here we present a patient with clinical features of VEXAS who harbored two novel somatic variants in UBA1 (I894S and N606I). To better understand the clinical relevance and biological consequences of non-M41 (UBA1non-M41) variants, we analyzed the whole genome and transcriptome data of 4168 patients with hematological malignancies and detected an additional 16 UBA1non-M41 putative somatic variants with a clear sex-bias in patients with myeloid malignancies. Patients diagnosed with myeloid malignancies carrying UBA1non-M41 putative somatic variants either had vacuoles or immunodysregulatory symptoms. Analysis of the transcriptome confirmed neutrophil activation in VEXAS patients compared to healthy controls but did not result in a specific transcriptomic signature of UBA1M41 patients in comparison with MDS patients. In summary, we have described multiple putative novel UBA1non-M41 variants in patients with various hematological malignancies expanding the genomic spectrum of VEXAS syndrome.
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Affiliation(s)
- Maki Sakuma
- MLL Munich Leukemia Laboratory, Munich, Germany.,Medical Graduate Center, Technical University Munich, Munich, Germany
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | | | - Markus Lindauer
- Department for Hematology and Oncology, SLK-Clinics Heilbronn, Heilbronn, Germany
| | - Uwe M Martens
- Department for Hematology and Oncology, SLK-Clinics Heilbronn, Heilbronn, Germany
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Huber S, Haferlach T, Müller H, Meggendorfer M, Hutter S, Hoermann G, Baer C, Kern W, Haferlach C. MDS subclassification-do we still have to count blasts? Leukemia 2023; 37:942-945. [PMID: 36813994 PMCID: PMC10079547 DOI: 10.1038/s41375-023-01855-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Heiko Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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Makishima H, Saiki R, Nannya Y, Korotev S, Gurnari C, Takeda J, Momozawa Y, Best S, Krishnamurthy P, Yoshizato T, Atsuta Y, Shiozawa Y, Iijima-Yamashita Y, Yoshida K, Shiraishi Y, Nagata Y, Kakiuchi N, Onizuka M, Chiba K, Tanaka H, Kon A, Ochi Y, Nakagawa MM, Okuda R, Mori T, Yoda A, Itonaga H, Miyazaki Y, Sanada M, Ishikawa T, Chiba S, Tsurumi H, Kasahara S, Müller-Tidow C, Takaori-Kondo A, Ohyashiki K, Kiguchi T, Matsuda F, Jansen JH, Polprasert C, Blombery P, Kamatani Y, Miyano S, Malcovati L, Haferlach T, Kubo M, Cazzola M, Kulasekararaj AG, Godley LA, Maciejewski JP, Ogawa S. Germ line DDX41 mutations define a unique subtype of myeloid neoplasms. Blood 2023; 141:534-549. [PMID: 36322930 PMCID: PMC10935555 DOI: 10.1182/blood.2022018221] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [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: 08/23/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Germ line DDX41 variants have been implicated in late-onset myeloid neoplasms (MNs). Despite an increasing number of publications, many important features of DDX41-mutated MNs remain to be elucidated. Here we performed a comprehensive characterization of DDX41-mutated MNs, enrolling a total of 346 patients with DDX41 pathogenic/likely-pathogenic (P/LP) germ line variants and/or somatic mutations from 9082 MN patients, together with 525 first-degree relatives of DDX41-mutated and wild-type (WT) patients. P/LP DDX41 germ line variants explained ∼80% of known germ line predisposition to MNs in adults. These risk variants were 10-fold more enriched in Japanese MN cases (n = 4461) compared with the general population of Japan (n = 20 238). This enrichment of DDX41 risk alleles was much more prominent in male than female (20.7 vs 5.0). P/LP DDX41 variants conferred a large risk of developing MNs, which was negligible until 40 years of age but rapidly increased to 49% by 90 years of age. Patients with myelodysplastic syndromes (MDS) along with a DDX41-mutation rapidly progressed to acute myeloid leukemia (AML), which was however, confined to those having truncating variants. Comutation patterns at diagnosis and at progression to AML were substantially different between DDX41-mutated and WT cases, in which none of the comutations affected clinical outcomes. Even TP53 mutations made no exceptions and their dismal effect, including multihit allelic status, on survival was almost completely mitigated by the presence of DDX41 mutations. Finally, outcomes were not affected by the conventional risk stratifications including the revised/molecular International Prognostic Scoring System. Our findings establish that MDS with DDX41-mutation defines a unique subtype of MNs that is distinct from other MNs.
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Affiliation(s)
- Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Sophia Korotev
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - June Takeda
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences (IMS), RIKEN, Yokohama, Japan
| | - Steve Best
- King’s College Hospital NHS Foundation Trust, and King’s College London, London, United Kingdom
| | - Pramila Krishnamurthy
- King’s College Hospital NHS Foundation Trust, and King’s College London, London, United Kingdom
| | | | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagakute, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Yuka Iijima-Yamashita
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- National Cancer Center Research Institute, Division of Genome Analysis Platform Development, Tokyo, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Makoto Onizuka
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Kenichi Chiba
- National Cancer Center Research Institute, Division of Genome Analysis Platform Development, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayana Kon
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Rurika Okuda
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Takuto Mori
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Akinori Yoda
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Hidehiro Itonaga
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | | | - Senji Kasahara
- Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
| | | | | | - Kazuma Ohyashiki
- Department of Hematology, Tokyo Medical University, Tokyo, Japan
| | | | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Joop H. Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chantana Polprasert
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoru Miyano
- National Cancer Center Research Institute, Division of Genome Analysis Platform Development, Tokyo, Japan
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Medical and Dental, Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Michiaki Kubo
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Austin G. Kulasekararaj
- King’s College Hospital NHS Foundation Trust, and King’s College London, London, United Kingdom
| | - Lucy A. Godley
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Korenkova I, Bitan M, Klymenko S, Lysytsia O, Zaucha J, Mytilineos J, Haferlach T, Hochaus A, Heyman M, Guilhot F, Bolanos N, Kuts R, Greinix HI, Koh MBC, Landgraf S, Hehlmann R, Aljurf M, Sureda A, Rondelli D, Niederwieser D. Help for Ukrainian Hematology Patients (HUP): A Global Initiative Supporting Hematopoietic Stem Cell Transplantation (HSCT) Programs in a Time of Conflict. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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43
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Baer C, Huber S, Hutter S, Meggendorfer M, Nadarajah N, Walter W, Platzbecker U, Götze KS, Kern W, Haferlach T, Hoermann G, Haferlach C. Risk prediction in MDS: independent validation of the IPSS-M-ready for routine? Leukemia 2023; 37:938-941. [PMID: 36725896 PMCID: PMC10079546 DOI: 10.1038/s41375-023-01831-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Affiliation(s)
- Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
| | - Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Niroshan Nadarajah
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
| | - Katharina S Götze
- Technical University of Munich (TUM), School of Medicine, Department of Internal Medicine III, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
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Stölzel F, Fordham SE, Nandana D, Lin WY, Blair H, Elstob C, Bell HL, Mohr B, Ruhnke L, Kunadt D, Dill C, Allsop D, Piddock R, Soura EN, Park C, Fadly M, Rahman T, Alharbi A, Wobus M, Altmann H, Röllig C, Wagenführ L, Jones GL, Menne T, Jackson GH, Marr HJ, Fitzgibbon J, Onel K, Meggendorfer M, Robinson A, Bziuk Z, Bowes E, Heidenreich O, Haferlach T, Villar S, Ariceta B, Diaz RA, Altschuler SJ, Wu LF, Prosper F, Montesinos P, Martinez-Lopez J, Bornhäuser M, Allan JM. Biallelic TET2 mutations confer sensitivity to 5'-azacitidine in acute myeloid leukemia. JCI Insight 2023; 8:e150368. [PMID: 36480300 PMCID: PMC9977313 DOI: 10.1172/jci.insight.150368] [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: 04/13/2021] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Precision medicine can significantly improve outcomes for patients with cancer, but implementation requires comprehensive characterization of tumor cells to identify therapeutically exploitable vulnerabilities. Here, we describe somatic biallelic TET2 mutations in an elderly patient with acute myeloid leukemia (AML) that was chemoresistant to anthracycline and cytarabine but acutely sensitive to 5'-azacitidine (5'-Aza) hypomethylating monotherapy, resulting in long-term morphological remission. Given the role of TET2 as a regulator of genomic methylation, we hypothesized that mutant TET2 allele dosage affects response to 5'-Aza. Using an isogenic cell model system and an orthotopic mouse xenograft, we demonstrate that biallelic TET2 mutations confer sensitivity to 5'-Aza compared with cells with monoallelic mutations. Our data argue in favor of using hypomethylating agents for chemoresistant disease or as first-line therapy in patients with biallelic TET2-mutated AML and demonstrate the importance of considering mutant allele dosage in the implementation of precision medicine for patients with cancer.
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Affiliation(s)
- Friedrich Stölzel
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Sarah E. Fordham
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Devi Nandana
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wei-Yu Lin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen Blair
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Claire Elstob
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hayden L. Bell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Brigitte Mohr
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Leo Ruhnke
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Desiree Kunadt
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Claudia Dill
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Daniel Allsop
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rachel Piddock
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Emmanouela-Niki Soura
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine Park
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mohd Fadly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thahira Rahman
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Abrar Alharbi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manja Wobus
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Heidi Altmann
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Christoph Röllig
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Lisa Wagenführ
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
| | - Gail L. Jones
- Department of Hematology, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - Tobias Menne
- Department of Hematology, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - Graham H. Jackson
- Department of Hematology, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - Helen J. Marr
- Department of Hematology, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - Jude Fitzgibbon
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Kenan Onel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Amber Robinson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Zuzanna Bziuk
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Emily Bowes
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Sara Villar
- Department of Hematology, Clínica Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Beñat Ariceta
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Navarra, Spain
- IdiSNA, Navarra, Spain
| | - Rosa Ayala Diaz
- Hematology Department, Hospital 12 de Octubre (i+12), Centro Nacional de Investigaciones Oncológicas (CNIO), Complutense University, Madrid, Spain
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, USA
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, USA
| | - Felipe Prosper
- Department of Hematology, Clínica Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Pau Montesinos
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12 de Octubre (i+12), Centro Nacional de Investigaciones Oncológicas (CNIO), Complutense University, Madrid, Spain
| | - Martin Bornhäuser
- Medical Clinic and Polyclinic I, University Hospital Dresden, Technical University of Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
| | - James M. Allan
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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45
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Müller J, Walter W, Haferlach C, Müller H, Fuhrmann I, Müller ML, Ruge H, Meggendorfer M, Kern W, Haferlach T, Stengel A. How T-lymphoblastic leukemia can be classified based on genetics using standard diagnostic techniques enhanced by whole genome sequencing. Leukemia 2023; 37:217-221. [PMID: 36335263 PMCID: PMC9883150 DOI: 10.1038/s41375-022-01743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Janine Müller
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Wencke Walter
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Claudia Haferlach
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Heiko Müller
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Irene Fuhrmann
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Martha-Lena Müller
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Henning Ruge
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Manja Meggendorfer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Wolfgang Kern
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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46
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Schmidts I, Haferlach T, Hoermann G. Precision Medicine in Therapy of Non-solid Cancer. Handb Exp Pharmacol 2023; 280:35-64. [PMID: 35989345 DOI: 10.1007/164_2022_608] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development and approval of the tyrosine kinase inhibitor imatinib in 2001 has heralded the advance of directed therapy options. Today, an armamentarium of targeted therapeutics is available and enables the use of precision medicine in non-solid cancer. Precision medicine is guided by the detection of tumor-specific and targetable characteristics. These include pathogenic fusions and/or mutations, dependency on specific signaling pathways, and the expression of certain cell surface markers. Within the first part, we review approved targeted therapies for the compound classes of small molecule inhibitors, antibody-based therapies and cellular therapies. Particular consideration is given to the underlying pathobiology and the respective mechanism of action. The second part emphasizes on how biomarkers, whether they are of diagnostic, prognostic, or predictive relevance, are indispensable tools to guide therapy choice and management in precision medicine. Finally, the examples of acute myeloid leukemia, chronic lymphocytic leukemia, and chronic myeloid leukemia illustrate how integration of these biomarkers helps to tailor therapy.
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47
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Huber S, Haferlach T, Meggendorfer M, Hutter S, Hoermann G, Summerer I, Fuhrmann I, Baer C, Kern W, Haferlach C. Mutations in spliceosome genes in myelodysplastic neoplasms and their association to ring sideroblasts. Leukemia 2023; 37:500-502. [PMID: 36463343 PMCID: PMC9898028 DOI: 10.1038/s41375-022-01783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022]
Affiliation(s)
- Sandra Huber
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Manja Meggendorfer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Stephan Hutter
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Gregor Hoermann
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Isolde Summerer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Irene Fuhrmann
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Constance Baer
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Wolfgang Kern
- grid.420057.40000 0004 7553 8497MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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48
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Valent P, Klion AD, Roufosse F, Simon D, Metzgeroth G, Leiferman KM, Schwaab J, Butterfield JH, Sperr WR, Sotlar K, Vandenberghe P, Hoermann G, Haferlach T, Moriggl R, George TI, Akin C, Bochner BS, Gotlib J, Reiter A, Horny HP, Arock M, Simon HU, Gleich GJ. Proposed refined diagnostic criteria and classification of eosinophil disorders and related syndromes. Allergy 2023; 78:47-59. [PMID: 36207764 PMCID: PMC9797433 DOI: 10.1111/all.15544] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/20/2022] [Accepted: 10/01/2022] [Indexed: 12/31/2022]
Abstract
Eosinophilia and eosinophil activation are recurrent features in various reactive states and certain hematologic malignancies. In patients with hypereosinophilia (HE), HE-induced organ damage is often encountered and may lead to the diagnosis of a hypereosinophilic syndrome (HES). A number of known mechanisms and etiologies contribute to the development of HE and HES. Based on these etiologies and the origin of eosinophils, HE and HES are divided into primary forms where eosinophils are clonal cells, reactive forms where an underlying reactive or neoplastic condition is detected and eosinophils are considered to be "non-clonal" cells, and idiopathic HE and HES in which neither a clonal nor a reactive underlying pathology is detected. Since 2012, this classification and the related criteria have been widely accepted and regarded as standard. However, during the past few years, new developments in the field and an increasing number of markers and targets have created a need to update these criteria and the classification of HE and HES. To address this challenge, a Working Conference on eosinophil disorders was organized in 2021. In this conference, a panel of experts representing the relevant fields, including allergy, dermatology, hematology, immunology, laboratory medicine, and pathology, met and discussed new markers and concepts as well as refinements in definitions, criteria and classifications of HE and HES. The outcomes of this conference are presented in this article and should assist in the diagnosis and management of patients with HE and HES in daily practice and in the preparation and conduct of clinical trials.
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Affiliation(s)
- Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria,Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria,Correspondence: Peter Valent, M.D. Department of Medicine I, Division of Hematology & Hemostaseology and Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Währinger Gürtel 18-20, A-1090 Vienna, Austria, Phone: 43 1 40400 4415; Fax: 43 1 40040 4030,
| | - Amy D. Klion
- Human Eosinophil Section, Laboratory of Parasitic Diseases, NIH/NIAID, Bethesda, MD, USA
| | - Florence Roufosse
- Department of Internal Medicine, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Dagmar Simon
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Georgia Metzgeroth
- Department of Hematology and Oncology, University Hospital Mannheim - Heidelberg University, Germany
| | | | - Juliana Schwaab
- Department of Hematology and Oncology, University Hospital Mannheim - Heidelberg University, Germany
| | | | - Wolfgang R. Sperr
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria,Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria
| | - Karl Sotlar
- Institute of Pathology, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Peter Vandenberghe
- Division of Hematology, University Hospital Leuven and Department of Human Genetics, KU Leuven, Belgium
| | | | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Tracy I. George
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Cem Akin
- Division of Allergy and Clinical Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Bruce S. Bochner
- Northwestern University Feinberg School of Medicine, Division of Allergy and Immunology, Chicago, IL, USA
| | - Jason Gotlib
- Stanford Cancer Institute/Stanford University School of Medicine, Stanford, CA, USA
| | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim - Heidelberg University, Germany
| | - Hans-Peter Horny
- Institute of Pathology, Ludwig Maximilian University Munich (LMU), Munich, Germany
| | - Michel Arock
- Department of Hematological Biology, Pitié-Salpêtrière Hospital, Pierre et Marie Curie University (UPMC), Paris, France
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland,Institute of Biochemistry, Brandenburg Medical School, Neuruppin, Germany
| | - Gerald J. Gleich
- Departments of Dermatology and Medicine, University of Utah Health, Salt Lake City, UT, USA
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49
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Huber S, Haferlach T, Meggendorfer M, Hutter S, Hoermann G, Baer C, Kern W, Haferlach C. SF3B1 mutations in AML are strongly associated with MECOM rearrangements and may be indicative of an MDS pre-phase. Leukemia 2022; 36:2927-2930. [PMID: 36271152 PMCID: PMC9712091 DOI: 10.1038/s41375-022-01734-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sandra Huber
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Gregor Hoermann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Constance Baer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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50
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Kubota Y, Zawit M, Durrani J, Shen W, Bahaj W, Kewan T, Ponvilawan B, Mori M, Meggendorfer M, Gurnari C, LaFramboise T, Feurstein S, Sekeres MA, Visconte V, Godley LA, Haferlach T, Maciejewski JP. Significance of hereditary gene alterations for the pathogenesis of adult bone marrow failure versus myeloid neoplasia. Leukemia 2022; 36:2827-2834. [PMID: 36266327 DOI: 10.1038/s41375-022-01729-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Broader genetic screening has led to the growing recognition of the role of germline variants associated with adult bone marrow failure (BMF) and myeloid neoplasia (MN) not exclusively in children and young adults. In this study, we applied a germline variant panel to 3008 adult BMF and MN cases to assess the importance of germline genetics and its impact on disease phenotype and prognosis. In our cohort, up to 9.7% of BMF and 5.3% of MN cases carried germline variants. Our cohort also included heterozygous carriers of recessive traits, suggesting they contribute to the risk of BMF and MN. By gene category, variants of Fanconi anemia gene family represented the highest-frequency category for both BMF and MN cases, found in 4.9% and 1.7% cases, respectively. In addition, about 1.4% of BMF and 0.19% of MN cases harbored multiple germline variants affecting often functionally related genes as compound heterozygous. The burden of germline variants in BMF and MN was clearly associated with acquisition of monosomy 7. While BMF cases carrying germline variants showed similar overall survival as compared to the wild-type (WT) cases, MN cases with germline variants experienced a significantly shorter overall survival as compared to WT cases.
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Affiliation(s)
- Yasuo Kubota
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Misam Zawit
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jibran Durrani
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Wenyi Shen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Waled Bahaj
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tariq Kewan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ben Ponvilawan
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Minako Mori
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Simone Feurstein
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
- Department of Internal Medicine, Section of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Mikkael A Sekeres
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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