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Pedersen RK, Andersen M, Skov V, Kjær L, Hasselbalch HC, Ottesen JT, Stiehl T. HSC Niche Dynamics in Regeneration, Pre-malignancy, and Cancer: Insights From Mathematical Modeling. Stem Cells 2023; 41:260-270. [PMID: 36371719 PMCID: PMC10020982 DOI: 10.1093/stmcls/sxac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/28/2022] [Indexed: 11/15/2022]
Abstract
The hematopoietic stem cell (HSC) niche is a crucial driver of regeneration and malignancy. Its interaction with hematopoietic and malignant stem cells is highly complex and direct experimental observations are challenging. We here develop a mathematical model which helps relate processes in the niche to measurable changes of stem and non-stem cell counts. HSC attached to the niche are assumed to be quiescent. After detachment HSC become activated and divide or differentiate. To maintain their stemness, the progeny originating from division must reattach to the niche. We use mouse data from literature to parametrize the model. By combining mathematical analysis and computer simulations, we systematically investigate the impact of stem cell proliferation, differentiation, niche attachment, and detachment on clinically relevant scenarios. These include bone marrow transplantation, clonal competition, and eradication of malignant cells. According to our model, sampling of blood or bulk marrow provides only limited information about cellular interactions in the niche and the clonal composition of the stem cell population. Furthermore, we investigate how interference with processes in the stem cell niche could help to increase the effect of low-dose chemotherapy or to improve the homing of genetically engineered cells.
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Affiliation(s)
- Rasmus Kristoffer Pedersen
- IMFUFA, Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Centre for Mathematical Modeling - Human Health and Disease, Roskilde University, Roskilde, Denmark
| | - Morten Andersen
- IMFUFA, Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Centre for Mathematical Modeling - Human Health and Disease, Roskilde University, Roskilde, Denmark
| | - Vibe Skov
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Lasse Kjær
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Hans C Hasselbalch
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Johnny T Ottesen
- IMFUFA, Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Centre for Mathematical Modeling - Human Health and Disease, Roskilde University, Roskilde, Denmark
| | - Thomas Stiehl
- Corresponding author: Dr. rer. nat. Thomas Stiehl, Aachen University, Pauwelsstr. 19, 52074 Aachen, Germany. E-mail:
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An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia. PLoS Comput Biol 2022; 18:e1010439. [PMID: 36099249 PMCID: PMC9469948 DOI: 10.1371/journal.pcbi.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
The over-expression of the Bcl-2 protein is a common feature of many solid cancers and hematological malignancies, and it is typically associated with poor prognosis and resistance to chemotherapy. Bcl-2-specific inhibitors, such as venetoclax, have recently been approved for the treatment of chronic lymphocytic leukemia and small lymphocytic lymphoma, and they are showing promise in clinical trials as a targeted therapy for patients with relapsed or refractory acute myeloid leukemia (AML). However, successful treatment of AML with Bcl-2-specific inhibitors is often followed by the rapid development of drug resistance. An emerging paradigm for overcoming drug resistance in cancer treatment is through the targeting of mitochondrial energetics and metabolism. In AML in particular, it was recently observed that inhibition of mitochondrial translation via administration of the antibiotic tedizolid significantly affects mitochondrial bioenergetics, activating the integrated stress response (ISR) and subsequently sensitizing drug-resistant AML cells to venetoclax. Here we develop an integrative systems biology approach to acquire a deeper understanding of the molecular mechanisms behind this process, and in particular, of the specific role of the ISR in the commitment of cells to apoptosis. Our multi-scale mathematical model couples the ISR to the intrinsic apoptosis pathway in venetoclax-resistant AML cells, includes the metabolic effects of treatment, and integrates RNA, protein level, and cellular viability data. Using the mathematical model, we identify the dominant mechanisms by which ISR activation helps to overcome venetoclax resistance, and we study the temporal sequencing of combination treatment to determine the most efficient and robust combination treatment protocol. In this work, we develop a multi-scale systems biology approach to study the mechanisms by which the integrated stress response (ISR) activation helps to overcome venetoclax resistance in acute myeloid leukemia (AML). The multi-scale model enables the integration of RNA-level, protein-level, and cellular viability and proliferation data. The model developed in this work can predict several important features of the resistant AML cell lines that are consistent with experimental data. Further, our integrative systems biology approach led to the determination of the optimal combination treatment protocol.
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Kelesoglu N, Kori M, Turanli B, Arga KY, Yilmaz BK, Duru OA. Acute Myeloid Leukemia: New Multiomics Molecular Signatures and Implications for Systems Medicine Diagnostics and Therapeutics Innovation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:392-403. [PMID: 35763314 DOI: 10.1089/omi.2022.0051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acute myeloid leukemia (AML) is a common, complex, and multifactorial malignancy of the hematopoietic system. AML diagnosis and treatment outcomes display marked heterogeneity and patient-to-patient variations. To date, AML-related biomarker discovery research has employed single omics inquiries. Multiomics analyses that reconcile and integrate the data streams from multiple levels of the cellular hierarchy, from genes to proteins to metabolites, offer much promise for innovation in AML diagnostics and therapeutics. We report, in this study, a systems medicine and multiomics approach to integrate the AML transcriptome data and reporter biomolecules at the RNA, protein, and metabolite levels using genome-scale biological networks. We utilized two independent transcriptome datasets (GSE5122, GSE8970) in the Gene Expression Omnibus database. We identified new multiomics molecular signatures of relevance to AML: miRNAs (e.g., mir-484 and miR-519d-3p), receptors (ACVR1 and PTPRG), transcription factors (PRDM14 and GATA3), and metabolites (in particular, amino acid derivatives). The differential expression profiles of all reporter biomolecules were crossvalidated in independent RNA-Seq and miRNA-Seq datasets. Notably, we found that PTPRG holds important prognostication potential as evaluated by Kaplan-Meier survival analyses. The multiomics relationships unraveled in this analysis point toward the genomic pathogenesis of AML. These multiomics molecular leads warrant further research and development as potential diagnostic and therapeutic targets.
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Affiliation(s)
- Nurdan Kelesoglu
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Medi Kori
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Betul Karademir Yilmaz
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
- Department of Biochemistry, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Ozlem Ates Duru
- Department of Nutrition and Dietetics, School of Health Sciences, Nişantaşı University, Istanbul, Turkey
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Hoffmann H, Baldow C, Zerjatke T, Gottschalk A, Wagner S, Karg E, Niehaus S, Roeder I, Glauche I, Scherf N. How to predict relapse in leukemia using time series data: A comparative in silico study. PLoS One 2021; 16:e0256585. [PMID: 34780493 PMCID: PMC8592437 DOI: 10.1371/journal.pone.0256585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Risk stratification and treatment decisions for leukemia patients are regularly based on clinical markers determined at diagnosis, while measurements on system dynamics are often neglected. However, there is increasing evidence that linking quantitative time-course information to disease outcomes can improve the predictions for patient-specific treatment responses. We designed a synthetic experiment simulating response kinetics of 5,000 patients to compare different computational methods with respect to their ability to accurately predict relapse for chronic and acute myeloid leukemia treatment. Technically, we used clinical reference data to first fit a model and then generate de novo model simulations of individual patients' time courses for which we can systematically tune data quality (i.e. measurement error) and quantity (i.e. number of measurements). Based hereon, we compared the prediction accuracy of three different computational methods, namely mechanistic models, generalized linear models, and deep neural networks that have been fitted to the reference data. Reaching prediction accuracies between 60 and close to 100%, our results indicate that data quality has a higher impact on prediction accuracy than the specific choice of the particular method. We further show that adapted treatment and measurement schemes can considerably improve the prediction accuracy by 10 to 20%. Our proof-of-principle study highlights how computational methods and optimized data acquisition strategies can improve risk assessment and treatment of leukemia patients.
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Affiliation(s)
- Helene Hoffmann
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Christoph Baldow
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Sebastian Wagner
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Elena Karg
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Sebastian Niehaus
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- AICURA Medical GmbH, Berlin, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- National Center of Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
| | - Nico Scherf
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, School of Medicine, TU Dresden, Dresden, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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Roeder I, Glauche I. Overlooking the obvious? On the potential of treatment alterations to predict patient-specific therapy response. Exp Hematol 2020; 94:26-30. [PMID: 33246016 DOI: 10.1016/j.exphem.2020.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/08/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Prognostic or therapeutic classification of diseases is often based on clinical or genetic characteristics at diagnosis or response landmarks determined at a certain time point of treatment. On the other hand, there are more and more means, such as molecular markers and sensor data, that allow for quantification of disease or therapeutic parameters over time. Although a general value of time-resolved disease monitoring is widely accepted, the full potential of using the available information on disease and treatment dynamics in the context of outcome prediction or individualized treatment optimization still seems to be, at least partially, overlooked. Within this Perspective, we summarize the conceptual idea of using dynamic information to obtain a better understanding of complex pathophysiological processes within their particular "host environment," which also allows us to intrinsically map patient-specific heterogeneity. Specifically, we discuss to which extent treatment alterations can provide additional information to understand a patient's individual condition and use this information to further adapt the therapeutic strategy. This conceptual discussion is illustrated by using examples from myeloid leukemias to which we recently applied this concept using statistical and mathematical modeling.
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Affiliation(s)
- Ingo Roeder
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Institute for Medical Informatics and Biometry, Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Core Unit: Data Management and Analytics, Dresden, Germany.
| | - Ingmar Glauche
- Technische Universität Dresden, Carl Gustav Carus Faculty of Medicine, Institute for Medical Informatics and Biometry, Dresden, Germany
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