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Dall’Olio D, Sträng E, Turki AT, Tettero JM, Barbus M, Schulze-Rath R, Elicegui JM, Matteuzzi T, Merlotti A, Carota L, Sala C, Della Porta MG, Giampieri E, Hernández-Rivas JM, Bullinger L, Castellani G. Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. PLoS Comput Biol 2024; 20:e1011299. [PMID: 38306404 PMCID: PMC10880984 DOI: 10.1371/journal.pcbi.1011299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/21/2024] [Accepted: 01/02/2024] [Indexed: 02/04/2024] Open
Abstract
Onco-hematological studies are increasingly adopting statistical mixture models to support the advancement of the genomically-driven classification systems for blood cancer. Targeting enhanced patients stratification based on the sole role of molecular biology attracted much interest and contributes to bring personalized medicine closer to reality. In onco-hematology, Hierarchical Dirichlet Mixture Models (HDMM) have become one of the preferred method to cluster the genomics data, that include the presence or absence of gene mutations and cytogenetics anomalies, into components. This work unfolds the standard workflow used in onco-hematology to improve patient stratification and proposes alternative approaches to characterize the components and to assign patient to them, as they are crucial tasks usually supported by a priori clinical knowledge. We propose (a) to compute the parameters of the multinomial components of the HDMM or (b) to estimate the parameters of the HDMM components as if they were Multivariate Fisher's Non-Central Hypergeometric (MFNCH) distributions. Then, our approach to perform patients assignments to the HDMM components is designed to essentially determine for each patient its most likely component. We show on simulated data that the patients assignment using the MFNCH-based approach can be superior, if not comparable, to using the multinomial-based approach. Lastly, we illustrate on real Acute Myeloid Leukemia data how the utilization of MFNCH-based approach emerges as a good trade-off between the rigorous multinomial-based characterization of the HDMM components and the common refinement of them based on a priori clinical knowledge.
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Affiliation(s)
- Daniele Dall’Olio
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Eric Sträng
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Amin T. Turki
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Essen, Germany
- Department of Hematology and Oncology, Marienhospital University Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Jesse M. Tettero
- Department of Hematology, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | | | | | - Javier Martinez Elicegui
- Molecular Genetics in Oncohematology, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Tommaso Matteuzzi
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Alessandra Merlotti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
- Physics and Astronomy Department, University of Bologna, Bologna, Italy
| | - Luciana Carota
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, Bologna, Italy
| | - Matteo G. Della Porta
- Comprehensive Cancer Center, IRCCS Humanitas Clinical and Research Center and Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Enrico Giampieri
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, Bologna, Italy
| | - Jesús María Hernández-Rivas
- Molecular Genetics in Oncohematology, Institute of Biomedical Research of Salamanca, Salamanca, Spain
- Hematology Department, University Hospital of Salamanca, Salamanca, Spain
- Cancer Research Center of Salamanca, Salamanca, Spain
| | - Lars Bullinger
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gastone Castellani
- Department of Medical and Surgical Sciences—DIMEC, University of Bologna, Bologna, Italy
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Klever MK, Sträng E, Hetzel S, Jungnitsch J, Dolnik A, Schöpflin R, Schrezenmeier JF, Schick F, Blau O, Westermann J, Rücker FG, Xia Z, Döhner K, Schrezenmeier H, Spielmann M, Meissner A, Melo US, Mundlos S, Bullinger L. AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology. Blood Adv 2023; 7:6520-6531. [PMID: 37582288 PMCID: PMC10632680 DOI: 10.1182/bloodadvances.2023010887] [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: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/17/2023] Open
Abstract
Acute myeloid leukemia with complex karyotype (CK-AML) is associated with poor prognosis, which is only in part explained by underlying TP53 mutations. Especially in the presence of complex chromosomal rearrangements, such as chromothripsis, the outcome of CK-AML is dismal. However, this degree of complexity of genomic rearrangements contributes to the leukemogenic phenotype and treatment resistance of CK-AML remains largely unknown. Applying an integrative workflow for the detection of structural variants (SVs) based on Oxford Nanopore (ONT) genomic DNA long-read sequencing (gDNA-LRS) and high-throughput chromosome confirmation capture (Hi-C) in a well-defined cohort of CK-AML identified regions with an extreme density of SVs. These rearrangements consisted to a large degree of focal amplifications enriched in the proximity of mammalian-wide interspersed repeat elements, which often result in oncogenic fusion transcripts, such as USP7::MVD, or the deregulation of oncogenic driver genes as confirmed by RNA-seq and ONT direct complementary DNA sequencing. We termed this novel phenomenon chromocataclysm. Thus, our integrative SV detection workflow combing gDNA-LRS and Hi-C enables to unravel complex genomic rearrangements at a very high resolution in regions hard to analyze by conventional sequencing technology, thereby providing an important tool to identify novel important drivers underlying cancer with complex karyotypic changes.
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Affiliation(s)
- Marius-Konstantin Klever
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, Berlin, Germany
| | - Eric Sträng
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Julius Jungnitsch
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, Berlin, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna Dolnik
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Schöpflin
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jens-Florian Schrezenmeier
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix Schick
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Olga Blau
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Jörg Westermann
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Frank G. Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Zuyao Xia
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Uirá Souto Melo
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité University Medicine Berlin, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Lars Bullinger
- Division of Hematology, Oncology, and Cancer Immunology, Medical Department, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Cocciardi S, Dolnik A, Kapp-Schwoerer S, Rücker FG, Lux S, Blätte TJ, Skambraks S, Krönke J, Heidel FH, Schnöder TM, Corbacioglu A, Gaidzik VI, Paschka P, Teleanu V, Göhring G, Thol F, Heuser M, Ganser A, Weber D, Sträng E, Kestler HA, Döhner H, Bullinger L, Döhner K. Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation. Nat Commun 2019; 10:2031. [PMID: 31048683 PMCID: PMC6497712 DOI: 10.1038/s41467-019-09745-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Mutations in the nucleophosmin 1 (NPM1) gene are considered founder mutations in the pathogenesis of acute myeloid leukemia (AML). To characterize the genetic composition of NPM1 mutated (NPM1mut) AML, we assess mutation status of five recurrently mutated oncogenes in 129 paired NPM1mut samples obtained at diagnosis and relapse. We find a substantial shift in the genetic pattern from diagnosis to relapse including NPM1mut loss (n = 11). To better understand these NPM1mut loss cases, we perform whole exome sequencing (WES) and RNA-Seq. At the time of relapse, NPM1mut loss patients (pts) feature distinct mutational patterns that share almost no somatic mutation with the corresponding diagnosis sample and impact different signaling pathways. In contrast, profiles of pts with persistent NPM1mut are reflected by a high overlap of mutations between diagnosis and relapse. Our findings confirm that relapse often originates from persistent leukemic clones, though NPM1mut loss cases suggest a second "de novo" or treatment-associated AML (tAML) as alternative cause of relapse.
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Affiliation(s)
- Sibylle Cocciardi
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Anna Dolnik
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Silke Kapp-Schwoerer
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Susanne Lux
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Tamara J Blätte
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Sabrina Skambraks
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Jan Krönke
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Florian H Heidel
- Department of Internal Medicine II, Hematology and Oncology, Friedrich-Schiller-University Medical Center, Jena, 07743, Germany.,Leibniz-Institute on Aging, Fritz-Lipmann-Institute, Jena, 07745, Germany
| | - Tina M Schnöder
- Department of Internal Medicine II, Hematology and Oncology, Friedrich-Schiller-University Medical Center, Jena, 07743, Germany.,Leibniz-Institute on Aging, Fritz-Lipmann-Institute, Jena, 07745, Germany
| | - Andrea Corbacioglu
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Verena I Gaidzik
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Peter Paschka
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Veronica Teleanu
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Gudrun Göhring
- Institute of Cell & Molecular Pathology, Hannover Medical School, Hannover, 30625, Germany
| | - Felicitas Thol
- Department of Haematology, Haemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, 30625, Germany
| | - Michael Heuser
- Department of Haematology, Haemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, 30625, Germany
| | - Arnold Ganser
- Department of Haematology, Haemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, 30625, Germany
| | - Daniela Weber
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Eric Sträng
- Institute of Medical Systems Biology, Ulm University, Ulm, 30625, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, 30625, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany. .,Department of Hematology, Oncology and Tumorimmunology, Charité University Medicine, Berlin, 13353, Germany.
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, 89081, Germany.
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