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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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2
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Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [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: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
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Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
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3
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Dudkina E, Ulyanova V, Asmandiyarova V, Vershinina V, Ilinskaya O. Two Main Cancer Biomarkers as Molecular Targets of Binase Antitumor Activity. BIOMED RESEARCH INTERNATIONAL 2024; 2024:8159893. [PMID: 38374954 PMCID: PMC10876309 DOI: 10.1155/2024/8159893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/15/2023] [Accepted: 01/27/2024] [Indexed: 02/21/2024]
Abstract
Cancer is frequently coupled with the disturbance of key signaling pathways. Aberrant activation of the mitogen-activated protein kinase (MAPK) signaling cascade, occurring in over 85% of cancers, is mainly caused by the genetic alterations of its main components-oncogenes EGFR and RAS, and plays a crucial role in cell fate. The importance of EGFR and RAS proteins in a variety of tumors suggests that they would be good therapeutic targets, but at present, no effective targeted therapy against these two oncogenes has been proven. Here, we show that ribonuclease from Bacillus pumilus (binase) inhibits MAPK signaling through direct interaction with EGFR and RAS proteins. This effect contributes to the antitumor potential of binase along with its enzymatic activity. Multitargeticity of binase prevents the development of drug resistance, which is considered a major obstacle to effective anticancer treatment.
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Affiliation(s)
- Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Vera Ulyanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Violetta Asmandiyarova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Valentina Vershinina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
| | - Olga Ilinskaya
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia
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4
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [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: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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5
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Phadnis VV, Snider J, Varadharajan V, Ramachandiran I, Deik AA, Lai ZW, Kunchok T, Eaton EN, Sebastiany C, Lyakisheva A, Vaccaro KD, Allen J, Yao Z, Wong V, Geng B, Weiskopf K, Clish CB, Brown JM, Stagljar I, Weinberg RA, Henry WS. MMD collaborates with ACSL4 and MBOAT7 to promote polyunsaturated phosphatidylinositol remodeling and susceptibility to ferroptosis. Cell Rep 2023; 42:113023. [PMID: 37691145 PMCID: PMC10591818 DOI: 10.1016/j.celrep.2023.113023] [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: 09/16/2022] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Ferroptosis is a form of regulated cell death with roles in degenerative diseases and cancer. Excessive iron-catalyzed peroxidation of membrane phospholipids, especially those containing the polyunsaturated fatty acid arachidonic acid (AA), is central in driving ferroptosis. Here, we reveal that an understudied Golgi-resident scaffold protein, MMD, promotes susceptibility to ferroptosis in ovarian and renal carcinoma cells in an ACSL4- and MBOAT7-dependent manner. Mechanistically, MMD physically interacts with both ACSL4 and MBOAT7, two enzymes that catalyze sequential steps to incorporate AA in phosphatidylinositol (PI) lipids. Thus, MMD increases the flux of AA into PI, resulting in heightened cellular levels of AA-PI and other AA-containing phospholipid species. This molecular mechanism points to a pro-ferroptotic role for MBOAT7 and AA-PI, with potential therapeutic implications, and reveals that MMD is an important regulator of cellular lipid metabolism.
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Affiliation(s)
- Vaishnavi V Phadnis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zon Weng Lai
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Elinor Ng Eaton
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kyle D Vaccaro
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Juliet Allen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Betty Geng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kipp Weiskopf
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Mediterranean Institute for Life Sciences, 21000 Split, Croatia
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Whitney S Henry
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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6
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Pathmanathan S, Yao Z, Coelho P, Valla R, Drecun L, Benz C, Snider J, Saraon P, Grozavu I, Kotlyar M, Jurisica I, Park M, Stagljar I. B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer. iScience 2022; 25:105419. [DOI: 10.1016/j.isci.2022.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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7
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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8
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Kong Q, Weng Y, Zheng Z, Chen W, Li P, Cai Z, Tian R. Integrated and High-Throughput Approach for Sensitive Analysis of Tyrosine Phosphoproteome. Anal Chem 2022; 94:13728-13736. [PMID: 36179360 DOI: 10.1021/acs.analchem.2c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation (pTyr) regulates various signaling pathways under normal and cancerous states. Due to their low abundance and transient and dynamic natures, systematic profiling of pTyr sites is challenging. Antibody and engineered binding domain-based approaches have been well applied to pTyr peptide enrichment. However, traditional methods have the disadvantage of a long sample preparation process, which makes them unsuitable for processing limited amount of samples, especially in a high-throughput manner. In this study we developed a 96-well microplate-based approach to integrate all the sample preparation steps starting from cell culture to MS-compatible pTyr peptide enrichment in three consecutive 96-well microplates. By assembling an engineered SH2 domain onto a microplate, nonspecific adsorption of phosphopeptides is greatly reduced, which allows us to remove the Ti-IMAC purification and three C18 desalting steps (after digestion, pTyr enrichment, and Ti-IMAC purification) and, therefore, greatly simplifies the entire pTyr peptide enrichment workflow, especially when processing a large number of samples. Starting with 96-well microplate-cultured, pervanadate-stimulated cells, our approach could enrich 21% more pTyr sites than the traditional serial pTyr enrichment approach and showed good sensitivity and reproducibility in the range of 200 ng to 200 μg peptides. Importantly, we applied this approach to profile tyrosine kinase inhibitor-mediated EGFR signaling pathway and could well differentiate the distinct response of different pTyr sites. Collectively, the integrated 96-well microplate-based approach is valuable for profiling pTyr sites from limited biological samples and in a high-throughput manner.
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Affiliation(s)
- Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Yicheng Weng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zhendong Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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9
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Lei X, Zhang Y, Mao L, Jiang P, Huang Y, Gu J, Tai N. Prognostic value of receptor tyrosine kinases in malignant melanoma patients: A systematic review and meta-analysis of immunohistochemistry. Front Oncol 2022; 12:819051. [PMID: 36212475 PMCID: PMC9538722 DOI: 10.3389/fonc.2022.819051] [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: 11/20/2021] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
Background Substantial evidence suggests that receptor tyrosine kinases (RTKs) are overexpressed in tumors; however, few studies have focused on the prognostic value of RTKs in melanoma. Objectives The objective of this study is to evaluate the association between overexpression of RTKs and survival in melanoma patients based on immunohistochemistry (IHC) analysis. Methods Our review is registered on PROSPERO (http://www.crd.york.ac.uk/PROSPERO), registration number CRD42021261460. Seven databases were searched, and data were extracted. We used IHC to measure the association between overexpression of RTKs and overall survival (OS), disease-free survival (DFS), progression-free survival (PFS), and clinicopathology in melanoma patients. Pooled analysis was conducted to assess the differences between Hazard Ratios along with 95% confidence intervals. Results Of 5,508 publications examined following the database search, 23 publications were included in this study, which included data from a total of 2,072 patients. Vascular endothelial growth factor receptor 2 (VEGF-R2) overexpression was associated with worse OS and DFS in melanoma. Furthermore, there was an association between OS and the expression of several RTKs, including epidermal growth factor receptor (EGFR), mesenchymal-epithelial transition factor (MET), vascular endothelial growth factor receptor 1 (VEGF-R1), and insulin-like growth factor 1 receptor (IGF-1R). There were no significant correlations between EGFR overexpression and worse DFS or PFS. EGFR overexpression was associated with worse OS cutaneous and nasal melanoma, but not uveal melanoma. However, MET overexpression was related to worse OS in both cutaneous and uveal melanoma. Furthermore, EGFR overexpression was associated with a worse OS in Europe compared to other geographic areas. Moreover, EGFR and MET overexpression showed significant prognostic value in patients with the cut-off “≥10% staining”. Conclusions Our findings build concrete evidence that overexpression of RTKs is associated with poor prognosis and clinicopathology in melanoma, highlighting RTK expression has the potential to inform individualized combination therapies and accurate prognostic evaluation.
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Affiliation(s)
- Xuan Lei
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yiming Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lianghao Mao
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Pan Jiang
- Department of Orthopedics, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yumeng Huang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jia Gu
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ningzheng Tai
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Ningzheng Tai,
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10
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Stagljar I. The first 90 years of Ernesto Carafoli. Biochem Biophys Res Commun 2022; 633:3-5. [DOI: 10.1016/j.bbrc.2022.09.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
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11
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Polyakov VR, Alexandrov V, Maderna A, Bajjuri K, Li X, Zhou S. Indexing Ultrafast Shape-Based Descriptors in MongoDB to Identify TLR4 Pathway Agonists. J Chem Inf Model 2022; 62:2446-2455. [PMID: 35522137 DOI: 10.1021/acs.jcim.2c00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A method is presented for an ultrafast shape-based search workflow for the screening of large compound collections, i.e., those of vendors. The three-dimensional shape of a molecule dictates its biological activity by enabling the molecule to fit into binding pockets of proteins. Quite often, distinctly different chemical compounds that have similar shapes can bind in a similar way. OpenEye pioneered an algorithm for comparing shapes of molecules by overlaying them in a computer and measuring differences between a query molecule and a target molecule. Overlaying shapes is a computationally intensive process and represents a bottleneck in searching for similar molecules. More recent publications describe alternative methods of overlaying molecules, which are accomplished by comparing shape-based descriptors. These methods were implemented in the Open Drug Discovery Toolkit (ODDT) package. We utilized a combination of open-source software packages like ODDT and RDkit to implement a workflow for ultrafast conformer generation and matching that does not require storing precomputed conformers on the file system or in memory. Moreover, the generated descriptors could be optionally stored in MongoDB for performing searches in the future. To speed up the search, we created a set of indexes from the transformed shape-based descriptors. We are in the process of calculating descriptors for multiple vendors, including Enamine's "REAL" collection of 1.2 billion compounds. Currently, the shape similarity search on more than 70 million compounds takes less than 8 s! We exemplified our methodology with the screen of compounds that can act as putative TLR4 agonists. The search was based on a literature-known small-molecule TLR4 agonist series. In due course, we identified compounds with novel structural motifs that were active in mouse and human TLR4 reporter cell lines.
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Affiliation(s)
- Valery R Polyakov
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Vadim Alexandrov
- Liquid Algo LLC, 85 Thistle Ln, Hopewell Junction, New York 12533, United States
| | - Andreas Maderna
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Krishna Bajjuri
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Xiaofan Li
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Sihong Zhou
- Sutro Biopharma, 111 Oyster Point Blvd, South San Francisco, California 94080, United States
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12
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Lim SH, Snider J, Birimberg‐Schwartz L, Ip W, Serralha JC, Botelho HM, Lopes‐Pacheco M, Pinto MC, Moutaoufik MT, Zilocchi M, Laselva O, Esmaeili M, Kotlyar M, Lyakisheva A, Tang P, López Vázquez L, Akula I, Aboualizadeh F, Wong V, Grozavu I, Opacak‐Bernardi T, Yao Z, Mendoza M, Babu M, Jurisica I, Gonska T, Bear CE, Amaral MD, Stagljar I. CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system. Mol Syst Biol 2022; 18:e10629. [PMID: 35156780 PMCID: PMC8842165 DOI: 10.15252/msb.202110629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel in secretory epithelia with a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. While remarkable treatment advances have been made recently in the form of modulator drugs directly rescuing CFTR dysfunction, there is still considerable scope for improvement of therapeutic effectiveness. Here, we report the application of a high‐throughput screening variant of the Mammalian Membrane Two‐Hybrid (MaMTH‐HTS) to map the protein–protein interactions of wild‐type (wt) and mutant CFTR (F508del), in an effort to better understand CF cellular effects and identify new drug targets for patient‐specific treatments. Combined with functional validation in multiple disease models, we have uncovered candidate proteins with potential roles in CFTR function/CF pathophysiology, including Fibrinogen Like 2 (FGL2), which we demonstrate in patient‐derived intestinal organoids has a significant effect on CFTR functional expression.
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Affiliation(s)
- Sang Hyun Lim
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | - Jamie Snider
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Liron Birimberg‐Schwartz
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Wan Ip
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
| | - Joana C Serralha
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
- Faculty of Life Sciences and Medicine School of Bioscience Education King’s College London London UK
| | - Hugo M Botelho
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Miquéias Lopes‐Pacheco
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Madalena C Pinto
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Onofrio Laselva
- Department of Physiology University of Toronto Toronto ON Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto ON Canada
| | - Max Kotlyar
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
| | | | | | | | - Indira Akula
- Donnelly Centre University of Toronto Toronto ON Canada
| | | | - Victoria Wong
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Ingrid Grozavu
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | | | - Zhong Yao
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Meg Mendoza
- Department of Molecular Genetics University of Toronto Toronto ON Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Igor Jurisica
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
- Departments of Medical Biophysics and Computer Science University of Toronto Toronto ON Canada
- Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia
| | - Tanja Gonska
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Christine E Bear
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Physiology University of Toronto Toronto ON Canada
| | - Margarida D Amaral
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Igor Stagljar
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Molecular Genetics University of Toronto Toronto ON Canada
- Mediterranean Institute for Life Sciences Split Croatia
- School of Medicine University of Split Split Croatia
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13
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Shi Y, Xu Y, Xu Z, Wang H, Zhang J, Wu Y, Tang B, Zheng S, Wang K. TKI resistant-based prognostic immune related gene signature in LUAD, in which FSCN1 contributes to tumor progression. Cancer Lett 2022; 532:215583. [PMID: 35149175 DOI: 10.1016/j.canlet.2022.215583] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/21/2022]
Abstract
Drug resistance reflects the evolution of tumors, which is the main cause of recurrence and death. Currently, EGFR-TKI treatment is the first-line therapy for lung adenocarcinoma (LUAD) patients. Although EGFR-TKI achieved good effects at the beginning, most of the LUAD patients eventually acquired resistance. Therefore, it's urgently need to develop a strong criterion for identifying these patients who may benefit from additional therapy. In this study, we established a three TKI resistant-related gene signature (DDIT4, OAS3, FSCN1), and determined that's an accuracy, independent and specific prognostic model for LUAD patients. Patients categorized as high-risk by this signature showed more sensitive to chemotherapy, and exhibited higher expression of common immune checkpoints such as PD-L1/B3H7/PD-L2/IDO1. Moreover, these patients were characterized by increased infiltration of M0 macrophage and activated memory CD4+ T cells. The expression and prognostic values of DDIT4, FSCN1 and OAS3 were further confirmed in clinical data. In addition, experimental data showed that FSCN1 promoted LUAD development via PI3K/AKT signaling. In conclusion, this signature is highly predictive of prognostic in LUAD patients, and may serve as a powerful prediction tool for LUAD patients to further choose chemo- and immunotherapies.
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Affiliation(s)
- Yueli Shi
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Yun Xu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Zhiyong Xu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Huan Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Jingnan Zhang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Yuan Wu
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China
| | - Bufu Tang
- School of Medicine, Zhejiang University, Hangzhou, 323000, China
| | - Shenfei Zheng
- School of Medicine, Zhejiang University, Hangzhou, 323000, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, 322000, China.
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14
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Grozavu I, Stuart S, Lyakisheva A, Yao Z, Pathmanathan S, Ohh M, Stagljar I. D154Q Mutation does not Alter KRAS Dimerization. J Mol Biol 2021; 434:167392. [PMID: 34896362 DOI: 10.1016/j.jmb.2021.167392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 10/19/2022]
Abstract
KRAS is one of the most frequently mutated oncogenes in human cancers. Despite nearly 40 years of research, KRAS remains largely undruggable, in part due to an incomplete understanding of its biology. Recently, KRAS dimerization was discovered to play an important role in its signalling function. The KRAS D154Q mutant was described as a dimer-deficient variant that can be used to study the effect of dimerization in KRAS oncogenicity. However, we show here that KRAS D154Q homo- and heterodimerized with KRAS WT using three separate protein-protein interaction assays, and that oncogenic KRAS dimerization was not negatively impacted by the presence of a secondary D154Q mutation. In conclusion, we advise caution in using this variant to study the purpose of dimerization in KRAS oncogenic behaviour.
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Affiliation(s)
- Ingrid Grozavu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Sarah Stuart
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Shivanthy Pathmanathan
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Ohh
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Mediterranean Institute for Life Sciences (MedILS), Split, Croatia; School of Medicine, University of Split, Croatia.
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15
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Saraon P, Snider J, Schormann W, Rai A, Radulovich N, Sánchez-Osuna M, Coulombe-Huntington J, Huard C, Mohammed M, Lima-Fernandes E, Thériault B, Halabelian L, Chan M, Joshi D, Drecun L, Yao Z, Pathmanathan S, Wong V, Lyakisheva A, Aboualizadeh F, Niu L, Li F, Kiyota T, Subramanian R, Joseph B, Aman A, Prakesch M, Isaac M, Mamai A, Poda G, Vedadi M, Marcellus R, Uehling D, Leighl N, Sacher A, Samaržija M, Jakopović M, Arrowsmith C, Tyers M, Tsao MS, Andrews D, Al-Awar R, Stagljar I. Chemical Genetics Screen Identifies COPB2 Tool Compounds That Alters ER Stress Response and Induces RTK Dysregulation in Lung Cancer Cells. J Mol Biol 2021; 433:167294. [PMID: 34662547 DOI: 10.1016/j.jmb.2021.167294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
Activating mutations in the epidermal growth factor receptor (EGFR) are common driver mutations in non-small cell lung cancer (NSCLC). First, second and third generation EGFR tyrosine kinase inhibitors (TKIs) are effective at inhibiting mutant EGFR NSCLC, however, acquired resistance is a major issue, leading to disease relapse. Here, we characterize a small molecule, EMI66, an analog of a small molecule which we previously identified to inhibit mutant EGFR signalling via a novel mechanism of action. We show that EMI66 attenuates receptor tyrosine kinase (RTK) expression and signalling and alters the electrophoretic mobility of Coatomer Protein Complex Beta 2 (COPB2) protein in mutant EGFR NSCLC cells. Moreover, we demonstrate that EMI66 can alter the subcellular localization of EGFR and COPB2 within the early secretory pathway. Furthermore, we find that COPB2 knockdown reduces the growth of mutant EGFR lung cancer cells, alters the post-translational processing of RTKs, and alters the endoplasmic reticulum (ER) stress response pathway. Lastly, we show that EMI66 treatment also alters the ER stress response pathway and inhibits the growth of mutant EGFR lung cancer cells and organoids. Our results demonstrate that targeting of COPB2 with EMI66 presents a viable approach to attenuate mutant EGFR signalling and growth in NSCLC.
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Affiliation(s)
- Punit Saraon
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada.
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Wiebke Schormann
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3548CH Utrecht, the Netherlands
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Maria Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montreal, QC H3C 3J7, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montreal, QC H3C 3J7, Canada
| | - Caroline Huard
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montreal, QC H3C 3J7, Canada
| | - Mohammed Mohammed
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | | | - Brigitte Thériault
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Manuel Chan
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Dhananjay Joshi
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Shivanthy Pathmanathan
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Ontario, Canada
| | | | | | - Li Niu
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | | | - Babu Joseph
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Methvin Isaac
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Ahmed Mamai
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada; University of Toronto, Leslie Dan Faculty of Pharmacy, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Ontario, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Miroslav Samaržija
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montreal, QC H3C 3J7, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David Andrews
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Ontario, Canada.
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Ontario, Canada; Mediterranean Institute for Life Sciences, Split, Croatia; School of Medicine, University of Split, Split, Croatia.
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16
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Aboualizadeh F, Yao Z, Guan J, Drecun L, Pathmanathan S, Snider J, Umapathy G, Kotlyar M, Jurisica I, Palmer R, Stagljar I. Mapping the Phospho-dependent ALK Interactome to Identify Novel Components in ALK Signaling. J Mol Biol 2021; 433:167283. [PMID: 34606829 DOI: 10.1016/j.jmb.2021.167283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 10/25/2022]
Abstract
Protein-protein interactions (PPIs) play essential roles in Anaplastic Lymphoma Kinase (ALK) signaling. Systematic characterization of ALK interactors helps elucidate novel ALK signaling mechanisms and may aid in the identification of novel therapeutics targeting related diseases. In this study, we used the Mammalian Membrane Two-Hybrid (MaMTH) system to map the phospho-dependent ALK interactome. By screening a library of 86 SH2 domain-containing full length proteins, 30 novel ALK interactors were identified. Many of their interactions are correlated to ALK phosphorylation activity: oncogenic ALK mutations potentiate the interactions and ALK inhibitors attenuate the interactions. Among the novel interactors, NCK2 was further verified in neuroblastoma cells using co-immunoprecipitation. Modulation of ALK activity by addition of inhibitors lead to concomitant changes in the tyrosine phosphorylation status of NCK2 in neuroblastoma cells, strongly supporting the functionality of the ALK/NCK2 interaction. Our study provides a resource list of potential novel ALK signaling components for further study.
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Affiliation(s)
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Ontario, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Ontario, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Ontario, Canada; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Ruth Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada; Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, Split, Croatia; School of Medicine, University of Split, Split, Croatia. https://twitter.com/stagljar
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17
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Herholt A, Sahoo VK, Popovic L, Wehr MC, Rossner MJ. Dissecting intercellular and intracellular signaling networks with barcoded genetic tools. Curr Opin Chem Biol 2021; 66:102091. [PMID: 34644670 DOI: 10.1016/j.cbpa.2021.09.002] [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: 06/08/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022]
Abstract
The power of next-generation sequencing has stimulated the development of many analysis techniques for transcriptomics and genomics. More recently, the concept of 'molecular barcoding' has broadened the spectrum of sequencing-based applications to dissect different aspects of intracellular and intercellular signaling. In these assay formats, barcode reporters replace standard reporter genes. The virtually infinitive number of expressed barcode sequences allows high levels of multiplexing, hence accelerating experimental progress. Furthermore, reporter barcodes are used to quantitatively monitor a variety of biological events in living cells which has already provided much insight into complex cellular signaling and will further increase our knowledge in the future.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Luksa Popovic
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany.
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18
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Drugging the undruggable proteins in cancer: A systems biology approach. Curr Opin Chem Biol 2021; 66:102079. [PMID: 34426091 DOI: 10.1016/j.cbpa.2021.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
In recent years, the research community has, with comprehensive systems biology approaches and related technologies, gained insight into the vast complexity of numerous cancers. These approaches allow an in-depth exploration that cannot be achieved solely using conventional low-throughput methods, which do not closely mimic the natural cellular environment. In this review, we discuss recent integrative multiple omics approaches for understanding and modulating previously identified 'undruggable' targets such as members of the RAS family, MYC, TP53, and various E3 ligases and deubiquitinases. We describe how these technologies have revolutionized drug discovery by overcoming an array of biological and technological challenges and how, in the future, they will be pivotal in assessing cancer states in individual patients, allowing for the prediction and application of personalized disease treatments.
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19
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Beitz AM, Oakes CG, Galloway KE. Synthetic gene circuits as tools for drug discovery. Trends Biotechnol 2021; 40:210-225. [PMID: 34364685 DOI: 10.1016/j.tibtech.2021.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Within mammalian systems, there exists enormous opportunity to use synthetic gene circuits to enhance phenotype-based drug discovery, to map the molecular origins of disease, and to validate therapeutics in complex cellular systems. While drug discovery has relied on marker staining and high-content imaging in cell-based assays, synthetic gene circuits expand the potential for precision and speed. Here we present a vision of how circuits can improve the speed and accuracy of drug discovery by enhancing the efficiency of hit triage, capturing disease-relevant dynamics in cell-based assays, and simplifying validation and readouts from organoids and microphysiological systems (MPS). By tracking events and cellular states across multiple length and time scales, circuits will transform how we decipher the causal link between molecular events and phenotypes to improve the selectivity and sensitivity of cell-based assays.
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Affiliation(s)
- Adam M Beitz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Conrad G Oakes
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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20
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Receptor tyrosine kinases and cancer: oncogenic mechanisms and therapeutic approaches. Oncogene 2021; 40:4079-4093. [PMID: 34079087 DOI: 10.1038/s41388-021-01841-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/29/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease, notably cancer. Since their discovery, several mechanisms of RTK dysregulation have been identified, resulting in multiple cancer types displaying 'oncogenic addiction' to RTKs. As a result, RTKs have represented a major class for targeted therapeutics over the past two decades, with numerous small molecule-based tyrosine kinase inhibitor (TKI) therapeutics having been developed and clinically approved for several cancers. However, many of the current RTK inhibitor treatments eventually result in the rapid development of acquired resistance and subsequent tumor relapse. Recent technological advances and tools are being generated for the identification of novel RTK small molecule therapeutics. These newer technologies will be important for the identification of diverse types of RTK inhibitors, targeting both the receptors themselves as well as key cellular factors that play important roles in the RTK signaling cascade.
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21
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Yao Z, Drecun L, Aboualizadeh F, Kim SJ, Li Z, Wood H, Valcourt EJ, Manguiat K, Plenderleith S, Yip L, Li X, Zhong Z, Yue FY, Closas T, Snider J, Tomic J, Drews SJ, Drebot MA, McGeer A, Ostrowski M, Mubareka S, Rini JM, Owen S, Stagljar I. A homogeneous split-luciferase assay for rapid and sensitive detection of anti-SARS CoV-2 antibodies. Nat Commun 2021; 12:1806. [PMID: 33753733 PMCID: PMC7985487 DOI: 10.1038/s41467-021-22102-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/23/2021] [Indexed: 01/05/2023] Open
Abstract
Better diagnostic tools are needed to combat the ongoing COVID-19 pandemic. Here, to meet this urgent demand, we report a homogeneous immunoassay to detect IgG antibodies against SARS-CoV-2. This serological assay, called SATiN, is based on a tri-part Nanoluciferase (tNLuc) approach, in which the spike protein of SARS-CoV-2 and protein G, fused respectively to two different tNLuc tags, are used as antibody probes. Target engagement of the probes allows reconstitution of a functional luciferase in the presence of the third tNLuc component. The assay is performed directly in the liquid phase of patient sera and enables rapid, quantitative and low-cost detection. We show that SATiN has a similar sensitivity to ELISA, and its readouts are consistent with various neutralizing antibody assays. This proof-of-principle study suggests potential applications in diagnostics, as well as disease and vaccination management.
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Affiliation(s)
- Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Farzaneh Aboualizadeh
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Sun Jin Kim
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Heidi Wood
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Emelissa J Valcourt
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Kathy Manguiat
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Lily Yip
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Xinliu Li
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Zoe Zhong
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Feng Yun Yue
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Jelena Tomic
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Steven J Drews
- Canadian Blood Services, Edmonton, AB, Canada
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Allison McGeer
- Department of Microbiology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Mario Ostrowski
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Samira Mubareka
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - James M Rini
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shawn Owen
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA.
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA.
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Mediterranean Institute for Life Sciences, Split, Croatia.
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22
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Pacini L, Jenks AD, Vyse S, Wilding CP, Arthur A, Huang PH. Tackling Drug Resistance in EGFR Exon 20 Insertion Mutant Lung Cancer. Pharmgenomics Pers Med 2021; 14:301-317. [PMID: 33727854 PMCID: PMC7955704 DOI: 10.2147/pgpm.s242045] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/22/2021] [Indexed: 12/25/2022] Open
Abstract
Insertion mutations in exon 20 (Ex20ins) of the epidermal growth factor receptor (EGFR) gene are the largest class of EGFR mutations in non-small cell lung cancer (NSCLC) for which there are currently no approved targeted therapies. NSCLC patients with these mutations do not respond to clinically approved EGFR tyrosine kinase inhibitors (TKIs) and have poor outcomes. A number of early phase clinical trials are currently underway to evaluate the efficacy of a new generation of TKIs that are capable of binding to and blocking Ex20ins. Although these agents have shown some clinical activity, patient responses have been restricted by dose-limiting toxicity or rapid acquisition of resistance after a short response. Here we review the current understanding of the mechanisms of resistance to these compounds, which include on-target EGFR secondary mutations, compensatory bypass pathway activation and acquisition of an EMT phenotype. Taking lessons from conventional EGFR inhibitor therapy in NSCLC, we also consider other potential sources of resistance including the presence of drug-tolerant persister cells. We will discuss therapeutic strategies which have the potential to overcome different forms of drug resistance. We conclude by evaluating recent technological developments in drug discovery such as PROTACs as a means to better tackle TKI resistance in NSCLC harbouring Ex20ins mutations.
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Affiliation(s)
- Laura Pacini
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Andrew D Jenks
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Simon Vyse
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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23
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Abstract
There are up to 650,000 'undruggable' protein-protein interactions (PPIs) in the human interactome that can be potentially considered as novel therapeutic targets. How does the 'undruggable' become 'druggable'?
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24
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Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. Comput Struct Biotechnol J 2020; 18:2535-2546. [PMID: 33033576 PMCID: PMC7522539 DOI: 10.1016/j.csbj.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/30/2022] Open
Abstract
Neuropsychiatric disorders (NPDs) such as bipolar disorder (BD), schizophrenia (SZ) and mood disorder (MD) are hard to manage due to overlapping symptoms and lack of biomarkers. Risk alleles of BD/SZ/MD are emerging, with evidence suggesting mitochondrial (mt) dysfunction as a critical factor for disease onset and progression. Mood stabilizing treatments for these disorders are scarce, revealing the need for biomarker discovery and artificial intelligence approaches to design synthetically accessible novel therapeutics. Here, we show mt involvement in NPDs by associating 245 mt proteins to BD/SZ/MD, with 7 common players in these disease categories. Analysis of over 650 publications suggests that 245 NPD-linked mt proteins are associated with 800 other mt proteins, with mt impairment likely to rewire these interactions. High dosage of mood stabilizers is known to alleviate manic episodes, but which compounds target mt pathways is another gap in the field that we address through mood stabilizer-gene interaction analysis of 37 prescriptions and over-the-counter psychotropic treatments, which we have refined to 15 mood-stabilizing agents. We show 26 of the 245 NPD-linked mt proteins are uniquely or commonly targeted by one or more of these mood stabilizers. Further, induced pluripotent stem cell-derived patient neurons and three-dimensional human brain organoids as reliable BD/SZ/MD models are outlined, along with multiomics methods and machine learning-based decision making tools for biomarker discovery, which remains a bottleneck for precision psychiatry medicine.
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25
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Wu C, Wu KJ, Liu JB, Wang W, Leung CH, Ma DL. Structure-guided discovery of a luminescent theranostic toolkit for living cancer cells and the imaging behavior effect. Chem Sci 2020; 11:11404-11412. [PMID: 34094382 PMCID: PMC8162881 DOI: 10.1039/d0sc04576d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023] Open
Abstract
Dual-functional theranostics are powerful tools that can allow for the in-field understanding of cancer pathology, yet their use is held back by the paucity of suitable theranostics for living systems. Moreover, typical in vitro screening conditions for probe molecules do not necessarily generate candidates that can function effectively in the natural in cellulo environment, limiting their follow-up use in living systems. We introduce herein a general strategy for the development of an iridium(iii) theranostic by grafting a well-known inhibitor as a "binding unit" onto an iridium(iii) complex precursor as a "signaling unit". To further optimize their emissive properties, we explored the effect of imaging behavior by incorporating different substituents onto the parental "signaling unit". This design concept was validated by a series of tailored iridium(iii) theranostics 2a-2h for the visualization and inhibition of EGFR in living cancer cells. By comprehensively assessing the theranostic potency of 2a-2h in both in vitro and in cellulo contexts, probe 2f containing electron-donating methoxy groups on the "signaling unit" was discovered to be the most promising candidate theranostic with desirable photophysical/chemical properties. Probe 2f selectively bound to EGFR in vitro and in cellulo, enabling it to selectively discriminate living EGFR-overexpressing cancer cells from normal cells that express low levels of EGFR with an "always-on" luminescence signal output. In particular, its long-lived lifetime enabled its luminescence signal to be readily distinguished from the interfering fluorescence of organic dyes by using time-resolved techniques. Complex 2f simultaneously visualized and inhibited EGFR in a dose-dependent manner, leading to a reduction in the phosphorylation of downstream proteins ERK and MEK, and inhibition of the activity of downstream transcription factor AP1. Notably, complex 2f is comparable to the parental EGFR inhibitor 1b, in terms of both inhibitory activity against EGFR and cytotoxicity against EGFR-overexpressing cancer cells. This tailored dual-functional iridium(iii) theranostic toolkit provides an alternative strategy for the personalized diagnosis and treatment of cancers.
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Affiliation(s)
- Chun Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR 999077
| | - Ke-Jia Wu
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau Taipa Macau SAR 999078
| | - Jin-Biao Liu
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR 999077
- School of Metallurgical and Chemical Engineering, Jiangxi University of Science and Technology Ganzhou China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR 999077
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau Taipa Macau SAR 999078
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong SAR 999077
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26
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Abdel-Basset M, Hawash H, Elhoseny M, Chakrabortty RK, Ryan M. DeepH-DTA: Deep Learning for Predicting Drug-Target Interactions: A Case Study of COVID-19 Drug Repurposing. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2020; 8:170433-170451. [PMID: 34786289 PMCID: PMC8545313 DOI: 10.1109/access.2020.3024238] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/11/2020] [Indexed: 05/04/2023]
Abstract
The rapid spread of novel coronavirus pneumonia (COVID-19) has led to a dramatically increased mortality rate worldwide. Despite many efforts, the rapid development of an effective vaccine for this novel virus will take considerable time and relies on the identification of drug-target (DT) interactions utilizing commercially available medication to identify potential inhibitors. Motivated by this, we propose a new framework, called DeepH-DTA, for predicting DT binding affinities for heterogeneous drugs. We propose a heterogeneous graph attention (HGAT) model to learn topological information of compound molecules and bidirectional ConvLSTM layers for modeling spatio-sequential information in simplified molecular-input line-entry system (SMILES) sequences of drug data. For protein sequences, we propose a squeezed-excited dense convolutional network for learning hidden representations within amino acid sequences; while utilizing advanced embedding techniques for encoding both kinds of input sequences. The performance of DeepH-DTA is evaluated through extensive experiments against cutting-edge approaches utilising two public datasets (Davis, and KIBA) which comprise eclectic samples of the kinase protein family and the pertinent inhibitors. DeepH-DTA attains the highest Concordance Index (CI) of 0.924 and 0.927 and also achieved a mean square error (MSE) of 0.195 and 0.111 on the Davis and KIBA datasets respectively. Moreover, a study using FDA-approved drugs from the Drug Bank database is performed using DeepH-DTA to predict the affinity scores of drugs against SARS-CoV-2 amino acid sequences, and the results show that that the model can predict some of the SARS-Cov-2 inhibitors that have been recently approved in many clinical studies.
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Affiliation(s)
| | - Hossam Hawash
- Faculty of Computers and InformaticsZagazig University Zagazig 44519 Egypt
| | - Mohamed Elhoseny
- Department of Computer ScienceCollege of Computer Information TechnologyAmerican University in the Emirates Dubai 503000 United Arab Emirates
- Faculty of Computers and InformationMansoura University Mansoura 35516 Egypt
| | - Ripon K Chakrabortty
- Capability Systems Centre, School of Engineering and ITUniversity of New South Wales Canberra Canberra ACT 2612 Australia
| | - Michael Ryan
- Capability Systems Centre, School of Engineering and ITUniversity of New South Wales Canberra Canberra ACT 2612 Australia
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