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Cho IS, Gupta P, Mostafazadeh N, Wong SW, Saichellappa S, Lenzini S, Peng Z, Shin J. Deterministic Single Cell Encapsulation in Asymmetric Microenvironments to Direct Cell Polarity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206014. [PMID: 36453581 PMCID: PMC9875620 DOI: 10.1002/advs.202206014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Indexed: 06/17/2023]
Abstract
Various signals in tissue microenvironments are often unevenly distributed around cells. Cellular responses to asymmetric cell-matrix adhesion in a 3D space remain generally unclear and are to be studied at the single-cell resolution. Here, the authors developed a droplet-based microfluidic approach to manufacture a pure population of single cells in a microscale layer of compartmentalized 3D hydrogel matrices with a tunable spatial presentation of ligands at the subcellular level. Cells elongate with an asymmetric presentation of the integrin adhesion ligand Arg-Gly-Asp (RGD), while cells expand isotropically with a symmetric presentation of RGD. Membrane tension is higher on the side of single cells interacting with RGD than on the side without RGD. Finite element analysis shows that a non-uniform isotropic cell volume expansion model is sufficient to recapitulate the experimental results. At a longer timescale, asymmetric ligand presentation commits mesenchymal stem cells to the osteogenic lineage. Cdc42 is an essential mediator of cell polarization and lineage specification in response to asymmetric cell-matrix adhesion. This study highlights the utility of precisely controlling 3D ligand presentation around single cells to direct cell polarity for regenerative engineering and medicine.
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Affiliation(s)
- Ik Sung Cho
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Prerak Gupta
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Nima Mostafazadeh
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Sing Wan Wong
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Saiumamaheswari Saichellappa
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Stephen Lenzini
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Zhangli Peng
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
| | - Jae‐Won Shin
- Department of Pharmacology and Regenerative MedicineUniversity of Illinois at Chicago College of MedicineChicagoIL60612USA
- Department of Biomedical EngineeringUniversity of Illinois at ChicagoChicagoIL60607USA
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Du H, Jiang D, Gao J, Zhang X, Jiang L, Zeng Y, Wu Z, Shen C, Xu L, Cao D, Hou T, Pan P. Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network. Research (Wash D C) 2022; 2022:9873564. [PMID: 35958111 PMCID: PMC9343084 DOI: 10.34133/2022/9873564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022] Open
Abstract
Covalent ligands have attracted increasing attention due to their unique advantages, such as long residence time, high selectivity, and strong binding affinity. They also show promise for targets where previous efforts to identify noncovalent small molecule inhibitors have failed. However, our limited knowledge of covalent binding sites has hindered the discovery of novel ligands. Therefore, developing in silico methods to identify covalent binding sites is highly desirable. Here, we propose DeepCoSI, the first structure-based deep graph learning model to identify ligandable covalent sites in the protein. By integrating the characterization of the binding pocket and the interactions between each cysteine and the surrounding environment, DeepCoSI achieves state-of-the-art predictive performances. The validation on two external test sets which mimic the real application scenarios shows that DeepCoSI has strong ability to distinguish ligandable sites from the others. Finally, we profiled the entire set of protein structures in the RCSB Protein Data Bank (PDB) with DeepCoSI to evaluate the ligandability of each cysteine for covalent ligand design, and made the predicted data publicly available on website.
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Affiliation(s)
- Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lingxiao Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Yundian Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410004 Hunan, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
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