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Lindström HJG, de Wijn AS, Friedman R. Interplay of mutations, alternate mechanisms, and treatment breaks in leukaemia: Understanding and implications studied with stochastic models. Comput Biol Med 2024; 169:107826. [PMID: 38101118 DOI: 10.1016/j.compbiomed.2023.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Bcr-Abl1 kinase domain mutations are the most prevalent cause of treatment resistance in chronic myeloid leukaemia (CML). Alternate resistance pathways nevertheless exist, and cell line experiments show certain patterns in the gain, and loss, of some of these alternate adaptations. These adaptations have clinical consequences when the tumour develops mechanisms that are beneficial to its growth under treatment, but slow down its growth when not treated. The results of temporarily halting treatment in CML have not been widely discussed in the clinic and there is no robust theoretical model that could suggest when such a pause in therapy can be tolerated. We constructed a dynamic model of how mechanisms such as Bcr-Abl1 overexpression and drug transporter upregulation evolve to produce resistance in cell lines, and investigate its behaviour subject to different treatment schedules, in particular when the treatment is paused ('drug holiday'). Our study results suggest that the presence of additional resistance mechanisms creates an environment which favours mutations that are either preexisting or occur late during treatment. Importantly, the results suggest the existence of tumour drug addiction, where cancer cells become dependent on the drug for (optimal) survival, which could be exploited through a treatment holiday. All simulation code is available at https://github.com/Sandalmoth/dual-adaptation.
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MESH Headings
- Humans
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/therapeutic use
- Protein Kinase Inhibitors/pharmacology
- Drug Resistance, Neoplasm
- Mutation
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
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Affiliation(s)
- H Jonathan G Lindström
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Astrid S de Wijn
- Department of Mechanical and Industrial Engineering, , Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, SE-39182, Sweden.
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Friedman R. The molecular mechanisms behind activation of FLT3 in acute myeloid leukemia and resistance to therapy by selective inhibitors. Biochim Biophys Acta Rev Cancer 2021; 1877:188666. [PMID: 34896257 DOI: 10.1016/j.bbcan.2021.188666] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
Acute myeloid leukemia is an aggressive cancer, which, in spite of increasingly better understanding of its genetic background remains difficult to treat. Mutations in the FLT3 gene are observed in ≈30% of the patients. Most of these mutations are internal tandem duplications (ITDs) of a sequence within the protein coding region, an activation mechanism that is almost non-existent with other genes and cancers. As patients each carry their own unique set of mutations, it is challenging to understand how ITDs activate the protein, and ascertain the risk for each individual patient. Available treatment options are limited due to development of drug resistance. Here, recent studies are reviewed that help to better understand the molecular mechanism behind activation of the FLT3 protein due to mutations. It is argued that difference in mutation sequences and especially location might be coupled to prognosis. When it comes to FLT3 inhibitors, key differences between them can be attributed to the mode of inhibition (type-1 and type-2 inhibitors), effective inhibitory coefficient in the blood plasma and off-target binding. Accounting for the position and length of insertions may in the future be used to predict prognosis and rationalise treatment. Development of new inhibitors must take into account the potential for resistance mutations. Inhibitors aimed at multiple specific targets are currently being developed. These, and as well as combination therapies will hopefully lead to longer periods during which targeted FLT3 therapy will remain effective.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnæus University, 391 82 Kalmar, Sweden.
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Della Bella E, Buetti-Dinh A, Licandro G, Ahmad P, Basoli V, Alini M, Stoddart MJ. Dexamethasone Induces Changes in Osteogenic Differentiation of Human Mesenchymal Stromal Cells via SOX9 and PPARG, but Not RUNX2. Int J Mol Sci 2021; 22:4785. [PMID: 33946412 PMCID: PMC8124248 DOI: 10.3390/ijms22094785] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 01/10/2023] Open
Abstract
Despite the huge body of research on osteogenic differentiation and bone tissue engineering, the translation potential of in vitro results still does not match the effort employed. One reason might be that the protocols used for in vitro research have inherent pitfalls. The synthetic glucocorticoid dexamethasone is commonly used in protocols for trilineage differentiation of human bone marrow mesenchymal stromal cells (hBMSCs). However, in the case of osteogenic commitment, dexamethasone has the main pitfall of inhibiting terminal osteoblast differentiation, and its pro-adipogenic effect is well known. In this work, we aimed to clarify the role of dexamethasone in the osteogenesis of hBMSCs, with a particular focus on off-target differentiation. The results showed that dexamethasone does induce osteogenic differentiation by inhibiting SOX9 expression, but not directly through RUNX2 upregulation as it is commonly thought. Rather, PPARG is concomitantly and strongly upregulated, leading to the formation of adipocyte-like cells within osteogenic cultures. Limiting the exposure to dexamethasone to the first week of differentiation did not affect the mineralization potential. Gene expression levels of RUNX2, SOX9, and PPARG were simulated using approximate Bayesian computation based on a simplified theoretical model, which was able to reproduce the observed experimental trends but with a different range of responses, indicating that other factors should be integrated to fully understand how dexamethasone influences cell fate. In summary, this work provides evidence that current in vitro differentiation protocols based on dexamethasone do not represent a good model, and further research is warranted in this field.
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Affiliation(s)
- Elena Della Bella
- AO Research Institute Davos, 7270 Davos Platz, Switzerland; (E.D.B.); (P.A.); (V.B.); (M.A.)
| | - Antoine Buetti-Dinh
- Laboratory of applied microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), 6500 Bellinzona, Switzerland;
- Swiss Institute of Bioinformatics, Quartier Sorge—Batiment Genopode, 1015 Lausanne, Switzerland
| | - Ginevra Licandro
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), 6928 Manno, Switzerland;
- University of Applied Science and Art of Southern Switzerland (SUPSI), 6928 Manno, Switzerland
| | - Paras Ahmad
- AO Research Institute Davos, 7270 Davos Platz, Switzerland; (E.D.B.); (P.A.); (V.B.); (M.A.)
| | - Valentina Basoli
- AO Research Institute Davos, 7270 Davos Platz, Switzerland; (E.D.B.); (P.A.); (V.B.); (M.A.)
| | - Mauro Alini
- AO Research Institute Davos, 7270 Davos Platz, Switzerland; (E.D.B.); (P.A.); (V.B.); (M.A.)
| | - Martin J. Stoddart
- AO Research Institute Davos, 7270 Davos Platz, Switzerland; (E.D.B.); (P.A.); (V.B.); (M.A.)
- Department of Orthopedics and Trauma Surgery, Medical Center—Albert-Ludwigs-University of Freiburg, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79106 Freiburg, Germany
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Yang J, Lindström HJG, Friedman R. Combating drug resistance in acute myeloid leukaemia by drug rotations: the effects of quizartinib and pexidartinib. Cancer Cell Int 2021; 21:198. [PMID: 33832508 PMCID: PMC8033742 DOI: 10.1186/s12935-021-01856-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is an aggressive blood cancer. In approximately 30% of the cases, driver mutations in the FLT3 gene are identified. FLT3 inhibitors are used in treatment of such patients together with cytotoxic drugs or (in refractory AML) as single agents. Unfortunately, resistance to FLT3 inhibitors limits their efficacy. Resistance is often due to secondary mutations in the gene encoding the molecular target. The gatekeeper mutation F691L confers resistance to specific FLT3 inhibitors such as quizartinib, but pexidartinib is much less resistance to this mutation. Pexidartinib alone is however sensitive to many other resistance mutations. In chronic myeloid leukaemia (CML), it has been suggested that rotation between drugs with a different landscape of resistance mutations might postpone the emergence of resistance. METHODS We studied the effect of quizartinib and pexidartinib in AML cell lines that express FLT3 (MOLM-14 and MV4-11). Using a rotation protocol, we further examined whether the emergence of resistance could be postponed. Computational modelling was used to analyse the onset of resistance and suggest which mutations are most likely to occur in a quantitative fashion. RESULTS The cells were sensitive to both inhibitors but quickly developed resistance that could be inherited, suggesting a genetic origin. Rotation protocols were not useful to postpone the emergence of resistance, which implies that such protocols, or changing from pexidartinib to quizartinib (or vice-versa) should not be used in patients. The computational modelling led to similar conclusions and suggested that F691L is the most common mutation to occur with quizartinib, and also when both drugs are used in rotation. CONCLUSIONS AML patients are not likely to benefit from a quizartinib/pexidartinib rotation protocol. A combination of tyrosine kinase inhibitors (with different molecular targets) might be more useful in the future. Development of specific FLT3 inhibitors that are less sensitive to resistance mutations might also lead to a better outcome.
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Affiliation(s)
- Jingmei Yang
- Department of Chemistry and Biomedical Science, Linnaeus University, Kalmar Campus, Kalmar, 391 82, Sweden
| | - H Jonathan G Lindström
- Department of Chemistry and Biomedical Science, Linnaeus University, Kalmar Campus, Kalmar, 391 82, Sweden
- Faeth Therapeutics Inc., 237 Kearny Street, #9245, San Francisco, CA, 94108, US
| | - Ran Friedman
- Department of Chemistry and Biomedical Science, Linnaeus University, Kalmar Campus, Kalmar, 391 82, Sweden.
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Takenaga K, Ochiya T, Endo H. Inhibition of the invasion and metastasis of mammary carcinoma cells by NBD peptide targeting S100A4 via the suppression of the Sp1/MMP‑14 axis. Int J Oncol 2021; 58:397-408. [PMID: 33650647 PMCID: PMC7864152 DOI: 10.3892/ijo.2021.5173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/12/2020] [Indexed: 12/30/2022] Open
Abstract
A synthetic peptide that blocks the interaction between the metastasis‑enhancing calcium‑binding protein, S100A4, and its effector protein, methionine aminopeptidase 2 (MetAP2) (the NBD peptide), was previously demonstrated to inhibit the angiogenesis of endothelial cells, leading to the regression of human prostate cancer in a xenograft model. However, the effects of the NBD peptide on the malignant properties of cancer cells that express S100A4 remain to be elucidated. The present study demonstrates that the NBD peptide inhibits the invasiveness and metastasis of highly metastatic human mammary carcinoma cells. The introduction of the peptide into MDA‑MB‑231 variant cells resulted in the suppression of matrix degradation in a gelatin invadopodia assay and invasiveness in a Matrigel invasion assay. In line with these results, the peptide significantly downregulated the expression of matrix metalloproteinase (MMP)‑14 (MT1‑MMP). Mechanistic analysis of the downregulation of MMP‑14 revealed the suppression of the expression of the transcription factor, specificity protein 1 (Sp1), but not that of nuclear factor (NF)‑κB, early growth response 1 (EGR1) or ELK3, all of which were reported to be involved in transcriptional regulation of the MMP‑14 gene. At the same time, evidence suggested that the NBD peptide also suppressed Sp1 and MMP‑14 expression levels in MDA‑MB‑468 cells. Importantly, the intravenous administration of the NBD peptide encapsulated in liposomes inhibited pulmonary metastasis from mammary gland tumors in mice with xenograft tumors. These results indicate that the NBD peptide can suppress malignant tumor growth through the suppression of the Sp1/MMP‑14 axis. Taken together, these results reveal that the NBD peptide acts on not only endothelial cells, but also on tumor cells in an integrated manner, suggesting that the peptide may prove to be a promising cancer therapeutic peptide drug.
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Affiliation(s)
- Keizo Takenaga
- Department of Life Science, Faculty of Medicine, Shimane University, Shimane 690-0823
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo 104-0045
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023
| | - Hideya Endo
- Division of Cellular and Molecular Biology, Department of Cancer Biology
- Division of Molecular Pathology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
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A new horizon for the steroidal alkaloid cyclovirobuxine D (huangyangning) and analogues: Anticancer activities and mechanism of action. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2020. [DOI: 10.1016/j.jtcms.2020.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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7
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Friedman R, Bjelic S. Simulations Studies of Protein Kinases that are Molecular Targets in Cancer. Isr J Chem 2020. [DOI: 10.1002/ijch.202000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ran Friedman
- Computational Chemistry and Biochemistry GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
| | - Sinisa Bjelic
- Protein Engineering GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
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G. Lindström HJ, Friedman R. The effects of combination treatments on drug resistance in chronic myeloid leukaemia: an evaluation of the tyrosine kinase inhibitors axitinib and asciminib. BMC Cancer 2020; 20:397. [PMID: 32380976 PMCID: PMC7204252 DOI: 10.1186/s12885-020-06782-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 03/23/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Chronic myeloid leukaemia is in principle a treatable malignancy but drug resistance is lowering survival. Recent drug discoveries have opened up new options for drug combinations, which is a concept used in other areas for preventing drug resistance. Two of these are (I) Axitinib, which inhibits the T315I mutation of BCR-ABL1, a main source of drug resistance, and (II) Asciminib, which has been developed as an allosteric BCR-ABL1 inhibitor, targeting an entirely different binding site, and as such does not compete for binding with other drugs. These drugs offer new treatment options. METHODS We measured the proliferation of KCL-22 cells exposed to imatinib-dasatinib, imatinib-asciminib and dasatinib-asciminib combinations and calculated combination index graphs for each case. Moreover, using the median-effect equation we calculated how much axitinib can reduce the growth advantage of T315I mutant clones in combination with available drugs. In addition, we calculated how much the total drug burden could be reduced by combinations using asciminib and other drugs, and evaluated which mutations such combinations might be sensitive to. RESULTS Asciminib had synergistic interactions with imatinib or dasatinib in KCL-22 cells at high degrees of inhibition. Interestingly, some antagonism between asciminib and the other drugs was present at lower degrees on inhibition. Simulations revealed that asciminib may allow for dose reductions, and its complementary resistance profile could reduce the risk of mutation based resistance. Axitinib, however, had only a minor effect on T315I growth advantage. CONCLUSIONS Given how asciminib combinations were synergistic in vitro, our modelling suggests that drug combinations involving asciminib should allow for lower total drug doses, and may result in a reduced spectrum of observed resistance mutations. On the other hand, a combination involving axitinib was not shown to be useful in countering drug resistance.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Axitinib/administration & dosage
- Cell Line, Tumor
- Computer Simulation
- Dasatinib/administration & dosage
- Drug Discovery/methods
- Drug Resistance, Neoplasm/genetics
- Drug Synergism
- Humans
- Imatinib Mesylate/administration & dosage
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mutation
- Niacinamide/administration & dosage
- Niacinamide/analogs & derivatives
- Pyrazoles/administration & dosage
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Affiliation(s)
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, 391 82 Sweden
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Buetti-Dinh A, Herold M, Christel S, El Hajjami M, Delogu F, Ilie O, Bellenberg S, Wilmes P, Poetsch A, Sand W, Vera M, Pivkin IV, Friedman R, Dopson M. Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics 2020; 21:23. [PMID: 31964336 PMCID: PMC6975020 DOI: 10.1186/s12859-019-3337-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. METHODS We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. RESULTS The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. CONCLUSIONS The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.
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Affiliation(s)
- Antoine Buetti-Dinh
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | | | - Francesco Delogu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Oslo, Norway
| | - Olga Ilie
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Sören Bellenberg
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- Center for Marine and Molecular Biotechnology, QNLM, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wolfgang Sand
- Faculty of Chemistry, Essen, Germany
- College of Environmental Science and Engineering, Donghua University, Shanghai, People’s Republic of China
- Mining Academy and Technical University Freiberg, Freiberg, Germany
| | - Mario Vera
- Institute for Biological and Medical Engineering. Schools of Engineering, Medicine & Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Hydraulic & Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Igor V. Pivkin
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
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Lindström HJG, de Wijn AS, Friedman R. Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia. BMC Cancer 2019; 19:508. [PMID: 31138173 PMCID: PMC6540367 DOI: 10.1186/s12885-019-5690-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/08/2019] [Indexed: 01/05/2023] Open
Abstract
Background Resistance towards targeted cancer treatments caused by single nucleotide variations is a major issue in many malignancies. Currently, there are a number of available drugs for chronic myeloid leukaemia (CML), which are overcome by different sets of mutations. The main aim of this study was to explore if it can be possible to exploit this and create a treatment protocol that outperforms each drug on its own. Methods We present a computer program to test different treatment protocols against CML, based on available resistance mutation growth data. The evolution of a relatively stable pool of cancer stem cells is modelled as a stochastic process, with the growth of cells expressing a tumourigenic protein (here, Abl1) and any emerging mutants determined principally by the drugs used in the therapy. Results There can be some benefit to Bosutinib-Ponatinib rotation therapy even if the mutation status is unknown, whereas Imatinib-Nilotinib rotation is unlikely to improve the outcomes. Furthermore, an interplay between growth inhibition and selection effects generates a non-linear relationship between drug doses and the risk of developing resistance. Conclusions Drug rotation therapy might be able to delay the onset of resistance in CML patients without costly ongoing observation of mutation status. Moreover, the simulations give credence to the suggestion that lower drug concentrations may achieve better results following major molecular response in CML. Electronic supplementary material The online version of this article (10.1186/s12885-019-5690-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H Jonathan G Lindström
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, 391 82, Sweden
| | - Astrid S de Wijn
- Department of Mechanical and Industrial Engineering, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, 391 82, Sweden.
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Di Cara G, Marabeti MR, Musso R, Riili I, Cancemi P, Pucci Minafra I. New Insights into the Occurrence of Matrix Metalloproteases -2 and -9 in a Cohort of Breast Cancer Patients and Proteomic Correlations. Cells 2018; 7:cells7080089. [PMID: 30060564 PMCID: PMC6115737 DOI: 10.3390/cells7080089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 01/01/2023] Open
Abstract
Matrix metalloproteases (MMPs) are a family of well-known enzymes which operate prevalently in the extracellular domain, where they fulfil the function of remodeling the extracellular matrix (ECM). Within the 26 family members, encoded by 24 genes in humans, MMP-2 and MMP-9 have been regarded as primarily responsible for the basement membrane and peri-cellular ECM rearrangement. In cases of infiltrating carcinomas, which arise from the epithelial tissues of a gland or of an internal organ, a marked alteration of the expression and the activity levels of both MMPs is known to occur. The present investigation represents the continuation and upgrading of our previous studies, now focusing on the occurrence and intensity levels of MMP-2 and -9 and their proteomic correlations in a cohort of 80 breast cancer surgical tissues.
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Affiliation(s)
- Gianluca Di Cara
- Centro di Oncobiologia Sperimentale, Università di Palermo, 90146 Palermo, Italy.
| | - Maria Rita Marabeti
- Centro di Oncobiologia Sperimentale, Università di Palermo, 90146 Palermo, Italy.
| | - Rosa Musso
- Centro di Oncobiologia Sperimentale, Università di Palermo, 90146 Palermo, Italy.
| | | | - Patrizia Cancemi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, 90100 Palermo, Italy.
| | - Ida Pucci Minafra
- Centro di Oncobiologia Sperimentale, Università di Palermo, 90146 Palermo, Italy.
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12
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Buetti-Dinh A, Jensen R, Friedman R. A computational study of hedgehog signalling involved in basal cell carcinoma reveals the potential and limitation of combination therapy. BMC Cancer 2018; 18:569. [PMID: 29776351 PMCID: PMC5960207 DOI: 10.1186/s12885-018-4451-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/30/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The smoothened (SMO) receptor is an essential component of the Sonic hedgehog (SHH) signalling, which is associated with the development of skin basal cell carcinoma (BCC). SMO inhibitors are indicated for BCC patients when surgical treatment or radiation therapy are not possible. Unfortunately, SMO inhibitors are not always well tolerated due to severe side effects, and their therapeutical success is limited by resistance mutations. METHODS We investigated how common are resistance-causing mutations in two genomic databases which are not linked to BCC or other cancers, namely 1000 Genomes and ExAC. To examine the potential for combination therapy or other treatments, we further performed knowledge-based simulations of SHH signalling, in the presence or absence of SMO and PI3K/Akt inhibitors. RESULTS The database analysis revealed that of 18 known mutations associated with Vismodegib-resistance, three were identified in the databases. Treatment of individuals carrying such mutations is thus liable to fail a priori. Analysis of the simulations suggested that a combined inhibition of SMO and the PI3K/Akt signalling pathway may provide an effective reduction in tumour proliferation. However, the inhibition dosage of SMO and PI3K/Akt depended on the activity of phosphodiesterases (PDEs). Under high PDEs activities, SMO became the most important control node of the network. By applying PDEs inhibition, the control potential of SMO decreased and PI3K appeared as a significant factor in controlling tumour proliferation. CONCLUSIONS Our systems biology approach employs knowledge-based computer simulations to help interpret the large amount of data available in public databases, and provides application-oriented solutions for improved cancer resistance treatments.
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Affiliation(s)
- Antoine Buetti-Dinh
- Department of Chemistry and Biomedical Sciences, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Landgången 3, Kalmar, SE-391 82 Sweden
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Rebecca Jensen
- Department of Chemistry and Biomedical Sciences, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Norra vägen 49, Kalmar, SE-391 82 Sweden
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Buetti-Dinh A, Friedman R. Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6. BMC Bioinformatics 2018; 19:155. [PMID: 29699481 PMCID: PMC5921566 DOI: 10.1186/s12859-018-2145-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Mutations in the FMS-like tyrosine kinase 3 (FLT3) are associated with uncontrolled cellular functions that contribute to the development of acute myeloid leukaemia (AML). We performed computer simulations of the FLT3-dependent signalling network in order to study the pathways that are involved in AML development and resistance to targeted therapies. Results Analysis of the simulations revealed the presence of alternative pathways through phosphoinositide 3 kinase (PI3K) and SH2-containing sequence proteins (SHC), that could overcome inhibition of FLT3. Inhibition of cyclin dependent kinase 6 (CDK6), a related molecular target, was also tested in the simulation but was not found to yield sufficient benefits alone. Conclusions The PI3K pathway provided a basis for resistance to treatments. Alternative signalling pathways could not, however, restore cancer growth signals (proliferation and loss of apoptosis) to the same levels as prior to treatment, which may explain why FLT3 resistance mutations are the most common resistance mechanism. Finally, sensitivity analysis suggested the existence of optimal doses of FLT3 and CDK6 inhibitors in terms of efficacy and toxicity. Electronic supplementary material The online version of this article (10.1186/s12859-018-2145-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Buetti-Dinh
- Department of Chemistry and Biomedical Sciences, Linnæus University, Norra vägen 49, Kalmar, SE-391 82, Sweden.,Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Norra vägen 49, Kalmar, SE-391 82, Sweden.,Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Landgången 3, Kalmar, SE-391 82, Sweden.,Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, Lausanne, CH-1015, Switzerland
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Norra vägen 49, Kalmar, SE-391 82, Sweden. .,Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Norra vägen 49, Kalmar, SE-391 82, Sweden.
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Increased S100A15 expression and decreased DNA methylation of its gene promoter are involved in high metastasis potential and poor outcome of lung adenocarcinoma. Oncotarget 2018; 8:45710-45724. [PMID: 28498804 PMCID: PMC5542220 DOI: 10.18632/oncotarget.17391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/10/2017] [Indexed: 01/02/2023] Open
Abstract
Purpose This study aims to determine the functional role of S100A15 and its promoter DNA methylation patterns in lung cancer progression. Experimental Design We analyzed 178 formalin-fixed paraffin embedded specimens from lung cancer patients, including 24 early stage and 91 advanced stage adenocarcinoma. S100A15 protein expression was evaluated by immunohistochemistry stain, and its DNA methylation levels were measured by pyrosequencing. Results S100A15 nuclear staining was increased in lung adenocarcinoma patients with distant metastasis versus those without distant metastasis. There was reduced one/three-year overall survival in adenocarcinoma patients receiving first line target therapy and harboring high nuclear expressions of S100A15. Both DNA methylation levels over -423 and -248 CpG sites of the S100A15 gene promoter were decreased in adenocarcinoma patients with distant metastasis, and the former was associated with lower one-year overall survival. The highly invasive CL1-5 cell lines display decreased DNA methylation over −412/−248/−56 CpG sites of the S100A15 gene promoter and increased S100A15 gene/protein expressions as compared with the less invasive CL1-0 cell lines. Knockdown of S100A15 in CL1-5 cell line inhibited cell proliferation, migration, and invasion, while over-expression of S100A15 in CL1-0 cell line promoted cell proliferation, migration, and invasion. RNA sequencing analysis revealed potential biological effects of S100A15 over-expression and knock-down with CTNNB1, ZEB1, CDC42, HSP90AA1, BST2, and PCNA being the pivotal down-stream mediators. Conclusions Increased S100A15 expression and decreased DNA methylation of its gene promoter region were associated with high metastasis potential and poor outcome in lung adenocarcinoma, probably through triggering CTNNB1 -centered pathways.
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Liu Y, Men C, Xu Y, Zhao K, Luo L, Dong D, Yu Q. Clusterin promotes growth and invasion of clear cell renal carcinoma cell by upregulation of S100A4 expression. Cancer Biomark 2018; 21:915-923. [PMID: 29400663 DOI: 10.3233/cbm-171018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yuan Liu
- Department of Urology, The Central Hospital of Linyi, Yishui, Shandong, China
- Department of Urology, The Central Hospital of Linyi, Yishui, Shandong, China
| | - Changping Men
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong, China
- Department of Urology, The Central Hospital of Linyi, Yishui, Shandong, China
| | - Yingmin Xu
- Department of Urology, The Central Hospital of Linyi, Yishui, Shandong, China
| | - Kai Zhao
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lei Luo
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Dahai Dong
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Qinchao Yu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Friedman R. Drug resistance in cancer: molecular evolution and compensatory proliferation. Oncotarget 2017; 7:11746-55. [PMID: 26909596 PMCID: PMC4914245 DOI: 10.18632/oncotarget.7459] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/08/2016] [Indexed: 01/31/2023] Open
Abstract
Targeted therapies have revolutionized cancer treatment. Unfortunately, their success is limited due to the development of drug resistance within the tumor, which is an evolutionary process. Understanding how drug resistance evolves is a prerequisite to a better success of targeted therapies. Resistance is usually explained as a response to evolutionary pressure imposed by treatment. Thus, evolutionary understanding can and should be used in the design and treatment of cancer. In this article, drug-resistance to targeted therapies is reviewed from an evolutionary standpoint. The concept of apoptosis-induced compensatory proliferation (AICP) is developed. It is shown that AICP helps to explain some of the phenomena that are observed experimentally in cancers. Finally, potential drug targets are suggested in light of AICP.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, Sweden
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Li N, Yi L, He Z, Zhang W, Li H, Lin JM. A DNA-directed covalent conjugation fluorescence probe for in vitro detection of functional matrix metalloproteinases. Analyst 2017; 142:634-640. [PMID: 28112295 DOI: 10.1039/c6an02339h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Matrix metalloproteinases (MMPs) have been considered to contribute to the progression of tumorigenesis and tumor invasion; MMP-9 in particular, has been regarded as a priority target in cancer treatment due to its massive up-regulation in malignant tissues and its ability to degrade type IV collagen. In this work, we employed a DNA-directed covalent conjugation method to design a fluorescence probe for in vitro detection of functional matrix metalloproteinases, by which a nitrilotriacetic acid (NTA)-modified DNA probe can combine with the Zn2+ in the active site of MMPs, and then a molecule beacon (MB) modified FITC and BHQ1 can open to bond with their complementary base, NTA-modified DNA. We can evaluate the amount of MMPs in the medium according to the fluorescence intensity. The detection procedure can be finished in 30 min with good selectivity, cheap reagents and easy preparation. All the results and the amount of secreted MMPs under three different cell culture conditions are in accordance with previous reports. Satisfactory results are obtained. Furthermore, owing to the importance of MMP-9, we designed an approach to achieve the desired selectivity and specificity of our work, using dual amplification for improving fluorescence intensity based on RCA to detect the amount of MMP-9.
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Affiliation(s)
- Nan Li
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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Buetti-Dinh A, O’Hare T, Friedman R. Sensitivity Analysis of the NPM-ALK Signalling Network Reveals Important Pathways for Anaplastic Large Cell Lymphoma Combination Therapy. PLoS One 2016; 11:e0163011. [PMID: 27669408 PMCID: PMC5036789 DOI: 10.1371/journal.pone.0163011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
A large subset of anaplastic large cell lymphoma (ALCL) patients harbour a somatic aberration in which anaplastic lymphoma kinase (ALK) is fused to nucleophosmin (NPM) resulting in a constitutively active signalling fusion protein, NPM-ALK. We computationally simulated the signalling network which mediates pathological cell survival and proliferation through NPM-ALK to identify therapeutically targetable nodes through which it may be possible to regain control of the tumourigenic process. The simulations reveal the predominant role of the VAV1-CDC42 (cell division control protein 42) pathway in NPM-ALK-driven cellular proliferation and of the Ras / mitogen-activated ERK kinase (MEK) / extracellular signal-regulated kinase (ERK) cascade in controlling cell survival. Our results also highlight the importance of a group of interleukins together with the Janus kinase 3 (JAK3) / signal transducer and activator of transcription 3 (STAT3) signalling in the development of NPM-ALK derived ALCL. Depending on the activity of JAK3 and STAT3, the system may also be sensitive to activation of protein tyrosine phosphatase-1 (SHP1), which has an inhibitory effect on cell survival and proliferation. The identification of signalling pathways active in tumourigenic processes is of fundamental importance for effective therapies. The prediction of alternative pathways that circumvent classical therapeutic targets opens the way to preventive approaches for countering the emergence of cancer resistance.
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Affiliation(s)
- Antoine Buetti-Dinh
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Kalmar, Sweden
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Lugano, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (ABD); (RF)
| | - Thomas O’Hare
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, United States of America
- Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, United States of America
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Kalmar, Sweden
- * E-mail: (ABD); (RF)
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