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Samant C, Kale R, Pai KSR, Nandakumar K, Bhonde M. Role of Wnt/β-catenin pathway in cancer drug resistance: Insights into molecular aspects of major solid tumors. Biochem Biophys Res Commun 2024; 729:150348. [PMID: 38986260 DOI: 10.1016/j.bbrc.2024.150348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/23/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Adaptive resistance to conventional and targeted therapies remains one of the major obstacles in the effective management of cancer. Aberrant activation of key signaling mechanisms plays a pivotal role in modulating resistance to drugs. An evolutionarily conserved Wnt/β-catenin pathway is one of the signaling cascades which regulate resistance to drugs. Elevated Wnt signaling confers resistance to anticancer therapies, either through direct activation of its target genes or via indirect mechanisms and crosstalk over other signaling pathways. Involvement of the Wnt/β-catenin pathway in cancer hallmarks like inhibition of apoptosis, promotion of invasion and metastasis and cancer stem cell maintenance makes this pathway a potential target to exploit for addressing drug resistance. Accumulating evidences suggest a critical role of Wnt/β-catenin pathway in imparting resistance across multiple cancers including PDAC, NSCLC, TNBC, etc. Here we present a comprehensive assessment of how Wnt/β-catenin pathway mediates cancer drug resistance in majority of the solid tumors. We take a deep dive into the Wnt/β-catenin signaling-mediated modulation of cellular and downstream molecular mechanisms and their impact on cancer resistance.
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Affiliation(s)
- Charudatt Samant
- Department of Pharmacology, Novel Drug Discovery and Development (NDDD), Lupin Limited, Survey No. 46A/47A, Village Nande, Taluka Mulshi, Pune, 412115, Maharashtra, India.
| | - Ramesh Kale
- Department of Pharmacology, Novel Drug Discovery and Development (NDDD), Lupin Limited, Survey No. 46A/47A, Village Nande, Taluka Mulshi, Pune, 412115, Maharashtra, India
| | - K Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Krishnadas Nandakumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Mandar Bhonde
- Department of Pharmacology, Novel Drug Discovery and Development (NDDD), Lupin Limited, Survey No. 46A/47A, Village Nande, Taluka Mulshi, Pune, 412115, Maharashtra, India
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Altinok Gunes B, Ozkan T, Karadag Gurel A, Dalkilic S, Belder N, Ozkeserli Z, Ozdag H, Beksac M, Sayinalp N, Yagci AM, Sunguroglu A. Transcriptome Analysis of Beta-Catenin-Related Genes in CD34+ Haematopoietic Stem and Progenitor Cells from Patients with AML. Mediterr J Hematol Infect Dis 2024; 16:e2024058. [PMID: 38984092 PMCID: PMC11232677 DOI: 10.4084/mjhid.2024.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Background Acute myeloid leukaemia (AML) is a disease of the haematopoietic stem cells(HSCs) that is characterised by the uncontrolled proliferation and impaired differentiation of normal haematopoietic stem/progenitor cells. Several pathways that control the proliferation and differentiation of HSCs are impaired in AML. Activation of the Wnt/beta-catenin signalling pathway has been shown in AML and beta-catenin, which is thought to be the key element of this pathway, has been frequently highlighted. The present study was designed to determine beta-catenin expression levels and beta-catenin-related genes in AML. Methods In this study, beta-catenin gene expression levels were determined in 19 AML patients and 3 controls by qRT-PCR. Transcriptome analysis was performed on AML grouped according to beta-catenin expression levels. Differentially expressed genes(DEGs) were investigated in detail using the Database for Annotation Visualisation and Integrated Discovery(DAVID), Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG), STRING online tools. Results The transcriptome profiles of our AML samples showed different molecular signature profiles according to their beta-catenin levels(high-low). A total of 20 genes have been identified as hub genes. Among these, TTK, HJURP, KIF14, BTF3, RPL17 and RSL1D1 were found to be associated with beta-catenin and poor survival in AML. Furthermore, for the first time in our study, the ELOV6 gene, which is the most highly up-regulated gene in human AML samples, was correlated with a poor prognosis via high beta-catenin levels. Conclusion It is suggested that the identification of beta-catenin-related gene profiles in AML may help to select new therapeutic targets for the treatment of AML.
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Affiliation(s)
- B Altinok Gunes
- Vocational School of Health Services, Ankara University, Ankara, Turkey
| | - T Ozkan
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - A Karadag Gurel
- Department of Medical Biology, Faculty of Medicine, Usak University, Usak, Turkey
| | - S Dalkilic
- Department of Molecular Biology, Faculty of Science, Firat University, Elazig, Turkey
| | - N Belder
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - Z Ozkeserli
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - H Ozdag
- Ankara University Biotechnology Institute, Ankara, Turkey
| | - M Beksac
- Department of Hematology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - N Sayinalp
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - A M Yagci
- Department of Internal Medicine, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - A Sunguroglu
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
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Nasimian A, Younus S, Tatli Ö, Hammarlund EU, Pienta KJ, Rönnstrand L, Kazi JU. AlphaML: A clear, legible, explainable, transparent, and elucidative binary classification platform for tabular data. PATTERNS (NEW YORK, N.Y.) 2024; 5:100897. [PMID: 38264719 PMCID: PMC10801203 DOI: 10.1016/j.patter.2023.100897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/07/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
Leveraging the potential of machine learning and recognizing the broad applications of binary classification, it becomes essential to develop platforms that are not only powerful but also transparent, interpretable, and user friendly. We introduce alphaML, a user-friendly platform that provides clear, legible, explainable, transparent, and elucidative (CLETE) binary classification models with comprehensive customization options. AlphaML offers feature selection, hyperparameter search, sampling, and normalization methods, along with 15 machine learning algorithms with global and local interpretation. We have integrated a custom metric for hyperparameter search that considers both training and validation scores, safeguarding against under- or overfitting. Additionally, we employ the NegLog2RMSL scoring method, which uses both training and test scores for a thorough model evaluation. The platform has been tested using datasets from multiple domains and offers a graphical interface, removing the need for programming expertise. Consequently, alphaML exhibits versatility, demonstrating promising applicability across a broad spectrum of tabular data configurations.
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Affiliation(s)
- Ahmad Nasimian
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
| | - Saleena Younus
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
| | - Özge Tatli
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
| | - Emma U. Hammarlund
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
- Tissue Development and Evolution (TiDE), Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Kenneth J. Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund University Cancer Centre (LUCC), Lund University, Lund, Sweden
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Nasimian A, Al Ashiri L, Ahmed M, Duan H, Zhang X, Rönnstrand L, Kazi JU. A Receptor Tyrosine Kinase Inhibitor Sensitivity Prediction Model Identifies AXL Dependency in Leukemia. Int J Mol Sci 2023; 24:ijms24043830. [PMID: 36835239 PMCID: PMC9959897 DOI: 10.3390/ijms24043830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
Despite incredible progress in cancer treatment, therapy resistance remains the leading limiting factor for long-term survival. During drug treatment, several genes are transcriptionally upregulated to mediate drug tolerance. Using highly variable genes and pharmacogenomic data for acute myeloid leukemia (AML), we developed a drug sensitivity prediction model for the receptor tyrosine kinase inhibitor sorafenib and achieved more than 80% prediction accuracy. Furthermore, by using Shapley additive explanations for determining leading features, we identified AXL as an important feature for drug resistance. Drug-resistant patient samples displayed enrichment of protein kinase C (PKC) signaling, which was also identified in sorafenib-treated FLT3-ITD-dependent AML cell lines by a peptide-based kinase profiling assay. Finally, we show that pharmacological inhibition of tyrosine kinase activity enhances AXL expression, phosphorylation of the PKC-substrate cyclic AMP response element binding (CREB) protein, and displays synergy with AXL and PKC inhibitors. Collectively, our data suggest an involvement of AXL in tyrosine kinase inhibitor resistance and link PKC activation as a possible signaling mediator.
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Affiliation(s)
- Ahmad Nasimian
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Lina Al Ashiri
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Mehreen Ahmed
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Hongzhi Duan
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Xiaoyue Zhang
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, 22185 Lund, Sweden
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden
- Correspondence: ; Tel.: +46-462226407
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Ferrero Restelli F, Federicci F, Ledda F, Paratcha G. Sprouty4 at the crossroads of Trk neurotrophin receptor signaling suppression by glucocorticoids. Front Mol Neurosci 2023; 16:1090824. [PMID: 36818650 PMCID: PMC9932978 DOI: 10.3389/fnmol.2023.1090824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Glucocorticoids (GC) affect neuronal plasticity, development and function of the nervous system by inhibiting neurotrophin-induced Trk signaling. It has been established that pretreatment with dexamethasone (DEX) restricts Neurotrophin-induced neurite outgrowth by inhibiting Trk-dependent activation of Ras-Erk1/2 signaling pathways. However, the precise molecular mechanism through which DEX interferes with neurotrophin signaling and Trk-mediated neurite outgrowth has not been clearly defined yet. Here, we observed that in PC12 cells DEX treatment promotes the transcription of Sprouty4, a regulatory molecule that is part of a negative feedback module that specifically abrogates Ras to Erk1/2 signaling in response to NGF. In line with this, either knockdown of Sprouty4 or overexpression of a dominant negative form of Sprouty4 (Y53A), rescue the inhibition of NGF/TrkA-promoted neurite outgrowth and Erk1/2 phosphorylation induced by DEX. Likewise, treatment of hippocampal neurons with DEX induces the expression of Sprouty4 and its knockdown abrogates the inhibitory effect of DEX on primary neurite formation, dendrite branching and Erk1/2 activation induced by BDNF. Thus, these results suggest that the induction of Sprouty4 mRNA by DEX translates into a significant inhibition of Trk to Erk1/2 signaling pathway. Together, these findings bring new insights into the crosstalk between DEX and neurotrophin signaling and demonstrate that Sprouty4 mediates the inhibitory effects of DEX on neurotrophin function.
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Affiliation(s)
- Facundo Ferrero Restelli
- Division de Neurociencia Molecular y Celular, Instituto de Biología Celular y Neurociencias Prof. E. De Robertis (IBCN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernando Federicci
- Division de Neurociencia Molecular y Celular, Instituto de Biología Celular y Neurociencias Prof. E. De Robertis (IBCN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina,Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Fernanda Ledda
- Division de Neurociencia Molecular y Celular, Instituto de Biología Celular y Neurociencias Prof. E. De Robertis (IBCN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina,Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Gustavo Paratcha
- Division de Neurociencia Molecular y Celular, Instituto de Biología Celular y Neurociencias Prof. E. De Robertis (IBCN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Gustavo Paratcha, ✉
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Nasimian A, Ahmed M, Hedenfalk I, Kazi JU. A deep tabular data learning model predicting cisplatin sensitivity identifies BCL2L1 dependency in cancer. Comput Struct Biotechnol J 2023; 21:956-964. [PMID: 36733702 PMCID: PMC9876747 DOI: 10.1016/j.csbj.2023.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Cisplatin, a platinum-based chemotherapeutic agent, is widely used as a front-line treatment for several malignancies. However, treatment outcomes vary widely due to intrinsic and acquired resistance. In this study, cisplatin-perturbed gene expression and pathway enrichment were used to define a gene signature, which was further utilized to develop a cisplatin sensitivity prediction model using the TabNet algorithm. The TabNet model performed better (>80 % accuracy) than all other machine learning models when compared to a wide range of machine learning algorithms. Moreover, by using feature importance and comparing predicted ovarian cancer patient samples, BCL2L1 was identified as an important gene contributing to cisplatin resistance. Furthermore, the pharmacological inhibition of BCL2L1 was found to synergistically increase cisplatin efficacy. Collectively, this study developed a tool to predict cisplatin sensitivity using cisplatin-perturbed gene expression and pathway enrichment knowledge and identified BCL2L1 as an important gene in this setting.
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Affiliation(s)
- Ahmad Nasimian
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden,Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Mehreen Ahmed
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden,Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, 223 81 Lund, Sweden
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden,Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden,Correspondence to: Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon village Building 404:C3, Scheelevägen 8, 22363 Lund, Sweden.
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Oku Y, Madia F, Lau P, Paparella M, McGovern T, Luijten M, Jacobs MN. Analyses of Transcriptomics Cell Signalling for Pre-Screening Applications in the Integrated Approach for Testing and Assessment of Non-Genotoxic Carcinogens. Int J Mol Sci 2022; 23:ijms232112718. [PMID: 36361516 PMCID: PMC9659232 DOI: 10.3390/ijms232112718] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022] Open
Abstract
With recent rapid advancement of methodological tools, mechanistic understanding of biological processes leading to carcinogenesis is expanding. New approach methodologies such as transcriptomics can inform on non-genotoxic mechanisms of chemical carcinogens and can be developed for regulatory applications. The Organisation for the Economic Cooperation and Development (OECD) expert group developing an Integrated Approach to the Testing and Assessment (IATA) of Non-Genotoxic Carcinogens (NGTxC) is reviewing the possible assays to be integrated therein. In this context, we review the application of transcriptomics approaches suitable for pre-screening gene expression changes associated with phenotypic alterations that underlie the carcinogenic processes for subsequent prioritisation of downstream test methods appropriate to specific key events of non-genotoxic carcinogenesis. Using case studies, we evaluate the potential of gene expression analyses especially in relation to breast cancer, to identify the most relevant approaches that could be utilised as (pre-) screening tools, for example Gene Set Enrichment Analysis (GSEA). We also consider how to address the challenges to integrate gene panels and transcriptomic assays into the IATA, highlighting the pivotal omics markers identified for assay measurement in the IATA key events of inflammation, immune response, mitogenic signalling and cell injury.
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Affiliation(s)
- Yusuke Oku
- The Organisation for Economic Cooperation and Development (OECD), 2 Rue Andre Pascal, 75016 Paris, France
- Correspondence: (Y.O.); (M.N.J.)
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi, 2749, 21027 Ispra, Italy
| | - Pierre Lau
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Martin Paparella
- Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innbruck, Austria
| | - Timothy McGovern
- US Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20901, USA
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, 3721 MA Utrecht, The Netherlands
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazard (CRCE), Public Health England (PHE), Chilton OX11 0RQ, Oxfordshire, UK
- Correspondence: (Y.O.); (M.N.J.)
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Salvucci M, Crawford N, Stott K, Bullman S, Longley DB, Prehn JHM. Patients with mesenchymal tumours and high Fusobacteriales prevalence have worse prognosis in colorectal cancer (CRC). Gut 2022; 71:1600-1612. [PMID: 34497144 PMCID: PMC9279747 DOI: 10.1136/gutjnl-2021-325193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Transcriptomic-based subtyping, consensus molecular subtyping (CMS) and colorectal cancer intrinsic subtyping (CRIS) identify a patient subpopulation with mesenchymal traits (CMS4/CRIS-B) and poorer outcome. Here, we investigated the relationship between prevalence of Fusobacterium nucleatum (Fn) and Fusobacteriales, CMS/CRIS subtyping, cell type composition, immune infiltrates and host contexture to refine patient stratification and to identify druggable context-specific vulnerabilities. DESIGN We coupled cell culture experiments with characterisation of Fn/Fusobacteriales prevalence and host biology/microenviroment in tumours from two independent colorectal cancer patient cohorts (Taxonomy: n=140, colon and rectal cases of The Cancer Genome Atlas (TCGA-COAD-READ) cohort: n=605). RESULTS In vitro, Fn infection induced inflammation via nuclear factor kappa-light-chain-enhancer of activated B cells/tumour necrosis factor alpha in HCT116 and HT29 cancer cell lines. In patients, high Fn/Fusobacteriales were found in CMS1, microsatellite unstable () tumours, with infiltration of M1 macrophages, reduced M2 macrophages, and high interleukin (IL)-6/IL-8/IL-1β signalling. Analysis of the Taxonomy cohort suggested that Fn was prognostic for CMS4/CRIS-B patients, despite having lower Fn load than CMS1 patients. In the TCGA-COAD-READ cohort, we likewise identified a differential association between Fusobacteriales relative abundance and outcome when stratifying patients in mesenchymal (either CMS4 and/or CRIS-B) versus non-mesenchymal (neither CMS4 nor CRIS-B). Patients with mesenchymal tumours and high Fusobacteriales had approximately twofold higher risk of worse outcome. These associations were null in non-mesenchymal patients. Modelling the three-way association between Fusobacteriales prevalence, molecular subtyping and host contexture with logistic models with an interaction term disentangled the pathogen-host signalling relationship and identified aberrations (including NOTCH, CSF1-3 and IL-6/IL-8) as candidate targets. CONCLUSION This study identifies CMS4/CRIS-B patients with high Fn/Fusobacteriales prevalence as a high-risk subpopulation that may benefit from therapeutics targeting mesenchymal biology.
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Affiliation(s)
- Manuela Salvucci
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nyree Crawford
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Katie Stott
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Susan Bullman
- Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, UK
| | - Jochen H M Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Zheng S, Wang W, Aldahdooh J, Malyutina A, Shadbahr T, Tanoli Z, Pessia A, Tang J. SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:587-596. [PMID: 35085776 PMCID: PMC9801064 DOI: 10.1016/j.gpb.2022.01.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 01/26/2023]
Abstract
Combinatorial therapies have been recently proposed to improve the efficacy of anticancer treatment. The SynergyFinder R package is a software used to analyze pre-clinical drug combination datasets. Here, we report the major updates to the SynergyFinder R package for improved interpretation and annotation of drug combination screening results. Unlike the existing implementations, the updated SynergyFinder R package includes five main innovations. 1) We extend the mathematical models to higher-order drug combination data analysis and implement dimension reduction techniques for visualizing the synergy landscape. 2) We provide a statistical analysis of drug combination synergy and sensitivity with confidence intervals and P values. 3) We incorporate a synergy barometer to harmonize multiple synergy scoring methods to provide a consensus metric for synergy. 4) We evaluate drug combination synergy and sensitivity to provide an unbiased interpretation of the clinical potential. 5) We enable fast annotation of drugs and cell lines, including their chemical and target information. These annotations will improve the interpretation of the mechanisms of action of drug combinations. To facilitate the use of the R package within the drug discovery community, we also provide a web server at www.synergyfinderplus.org as a user-friendly interface to enable a more flexible and versatile analysis of drug combination data.
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Shah K, Kazi JU. Phosphorylation-Dependent Regulation of WNT/Beta-Catenin Signaling. Front Oncol 2022; 12:858782. [PMID: 35359365 PMCID: PMC8964056 DOI: 10.3389/fonc.2022.858782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/16/2022] [Indexed: 01/11/2023] Open
Abstract
WNT/β-catenin signaling is a highly complex pathway that plays diverse roles in various cellular processes. While WNT ligands usually signal through their dedicated Frizzled receptors, the decision to signal in a β-catenin-dependent or -independent manner rests upon the type of co-receptors used. Canonical WNT signaling is β-catenin-dependent, whereas non-canonical WNT signaling is β-catenin-independent according to the classical definition. This still holds true, albeit with some added complexity, as both the pathways seem to cross-talk with intertwined networks that involve the use of different ligands, receptors, and co-receptors. β-catenin can be directly phosphorylated by various kinases governing its participation in either canonical or non-canonical pathways. Moreover, the co-activators that associate with β-catenin determine the output of the pathway in terms of induction of genes promoting proliferation or differentiation. In this review, we provide an overview of how protein phosphorylation controls WNT/β-catenin signaling, particularly in human cancer.
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Affiliation(s)
- Kinjal Shah
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
- *Correspondence: Julhash U. Kazi,
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Feizi N, Nair SK, Smirnov P, Beri G, Eeles C, Esfahani PN, Nakano M, Tkachuk D, Mammoliti A, Gorobets E, Mer AS, Lin E, Yu Y, Martin S, Hafner M, Haibe-Kains B. PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. Nucleic Acids Res 2022; 50:D1348-D1357. [PMID: 34850112 PMCID: PMC8728279 DOI: 10.1093/nar/gkab1084] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/14/2022] Open
Abstract
Cancer pharmacogenomics studies provide valuable insights into disease progression and associations between genomic features and drug response. PharmacoDB integrates multiple cancer pharmacogenomics datasets profiling approved and investigational drugs across cell lines from diverse tissue types. The web-application enables users to efficiently navigate across datasets, view and compare drug dose-response data for a specific drug-cell line pair. In the new version of PharmacoDB (version 2.0, https://pharmacodb.ca/), we present (i) new datasets such as NCI-60, the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) dataset, as well as updated data from the Genomics of Drug Sensitivity in Cancer (GDSC) and the Genentech Cell Line Screening Initiative (gCSI); (ii) implementation of FAIR data pipelines using ORCESTRA and PharmacoDI; (iii) enhancements to drug-response analysis such as tissue distribution of dose-response metrics and biomarker analysis; and (iv) improved connectivity to drug and cell line databases in the community. The web interface has been rewritten using a modern technology stack to ensure scalability and standardization to accommodate growing pharmacogenomics datasets. PharmacoDB 2.0 is a valuable tool for mining pharmacogenomics datasets, comparing and assessing drug-response phenotypes of cancer models.
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Affiliation(s)
- Nikta Feizi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Sisira Kadambat Nair
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Parinaz Nasr Esfahani
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Minoru Nakano
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Anthony Mammoliti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Evgeniya Gorobets
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eva Lin
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Yihong Yu
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Scott Martin
- Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA
| | - Marc Hafner
- Department of Oncology Bioinformatics, Genentech Inc, South San Francisco, CA 94080, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
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12
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Rafique R, Islam SR, Kazi JU. Machine learning in the prediction of cancer therapy. Comput Struct Biotechnol J 2021; 19:4003-4017. [PMID: 34377366 PMCID: PMC8321893 DOI: 10.1016/j.csbj.2021.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Resistance to therapy remains a major cause of cancer treatment failures, resulting in many cancer-related deaths. Resistance can occur at any time during the treatment, even at the beginning. The current treatment plan is dependent mainly on cancer subtypes and the presence of genetic mutations. Evidently, the presence of a genetic mutation does not always predict the therapeutic response and can vary for different cancer subtypes. Therefore, there is an unmet need for predictive models to match a cancer patient with a specific drug or drug combination. Recent advancements in predictive models using artificial intelligence have shown great promise in preclinical settings. However, despite massive improvements in computational power, building clinically useable models remains challenging due to a lack of clinically meaningful pharmacogenomic data. In this review, we provide an overview of recent advancements in therapeutic response prediction using machine learning, which is the most widely used branch of artificial intelligence. We describe the basics of machine learning algorithms, illustrate their use, and highlight the current challenges in therapy response prediction for clinical practice.
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Affiliation(s)
| | - S.M. Riazul Islam
- Department of Computer Science and Engineering, Sejong University, Seoul, South Korea
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Corresponding author at: Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon village Building 404:C3, Scheelevägen 8, 22363 Lund, Sweden.
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13
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Zheng S, Aldahdooh J, Shadbahr T, Wang Y, Aldahdooh D, Bao J, Wang W, Tang J. DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. Nucleic Acids Res 2021; 49:W174-W184. [PMID: 34060634 PMCID: PMC8218202 DOI: 10.1093/nar/gkab438] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/18/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Combinatorial therapies that target multiple pathways have shown great promises for treating complex diseases. DrugComb (https://drugcomb.org/) is a web-based portal for the deposition and analysis of drug combination screening datasets. Since its first release, DrugComb has received continuous updates on the coverage of data resources, as well as on the functionality of the web server to improve the analysis, visualization and interpretation of drug combination screens. Here, we report significant updates of DrugComb, including: (i) manual curation and harmonization of more comprehensive drug combination and monotherapy screening data, not only for cancers but also for other diseases such as malaria and COVID-19; (ii) enhanced algorithms for assessing the sensitivity and synergy of drug combinations; (iii) network modelling tools to visualize the mechanisms of action of drugs or drug combinations for a given cancer sample and (iv) state-of-the-art machine learning models to predict drug combination sensitivity and synergy. These improvements have been provided with more user-friendly graphical interface and faster database infrastructure, which make DrugComb the most comprehensive web-based resources for the study of drug sensitivities for multiple diseases.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Tolou Shadbahr
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Dalal Aldahdooh
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Jie Bao
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki FI-00290, Finland
| | - Wenyu Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki FI-00290, Finland
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