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Xu L, Kan S, Yu X, Liu Y, Fu Y, Peng Y, Liang Y, Cen Y, Zhu C, Jiang W. Deep learning enables stochastic optical reconstruction microscopy-like superresolution image reconstruction from conventional microscopy. iScience 2023; 26:108145. [PMID: 37867953 PMCID: PMC10587619 DOI: 10.1016/j.isci.2023.108145] [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: 04/24/2023] [Revised: 08/05/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Abstract
Despite its remarkable potential for transforming low-resolution images, deep learning faces significant challenges in achieving high-quality superresolution microscopy imaging from wide-field (conventional) microscopy. Here, we present X-Microscopy, a computational tool comprising two deep learning subnets, UR-Net-8 and X-Net, which enables STORM-like superresolution microscopy image reconstruction from wide-field images with input-size flexibility. X-Microscopy was trained using samples of various subcellular structures, including cytoskeletal filaments, dot-like, beehive-like, and nanocluster-like structures, to generate prediction models capable of producing images of comparable quality to STORM-like images. In addition to enabling multicolour superresolution image reconstructions, X-Microscopy also facilitates superresolution image reconstruction from different conventional microscopic systems. The capabilities of X-Microscopy offer promising prospects for making superresolution microscopy accessible to a broader range of users, going beyond the confines of well-equipped laboratories.
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Affiliation(s)
- Lei Xu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Key Laboratory of Molecular and Cellular Systems Biology, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Shichao Kan
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Xiying Yu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ye Liu
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yuxia Fu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yiqiang Peng
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yanhui Liang
- HAMD (Ningbo) Intelligent Medical Technology Co., Ltd, Ningbo 315194, China
| | - Yigang Cen
- Institute of Information Science, Beijing Jiaotong University, Beijing 100044, China
| | - Changjun Zhu
- Key Laboratory of Molecular and Cellular Systems Biology, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Wei Jiang
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Park S, Lee J, Ahn KS, Shim HW, Yoon J, Hyun J, Lee JH, Jang S, Yoo KH, Jang Y, Kim T, Kim HK, Lee MR, Jang J, Shim H, Kim H. Cyclic Stretch Promotes Cellular Reprogramming Process through Cytoskeletal-Nuclear Mechano-Coupling and Epigenetic Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303395. [PMID: 37727069 PMCID: PMC10646259 DOI: 10.1002/advs.202303395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Indexed: 09/21/2023]
Abstract
Advancing the technologies for cellular reprogramming with high efficiency has significant impact on regenerative therapy, disease modeling, and drug discovery. Biophysical cues can tune the cell fate, yet the precise role of external physical forces during reprogramming remains elusive. Here the authors show that temporal cyclic-stretching of fibroblasts significantly enhances the efficiency of induced pluripotent stem cell (iPSC) production. Generated iPSCs are proven to express pluripotency markers and exhibit in vivo functionality. Bulk RNA-sequencing reveales that cyclic-stretching enhances biological characteristics required for pluripotency acquisition, including increased cell division and mesenchymal-epithelial transition. Of note, cyclic-stretching activates key mechanosensitive molecules (integrins, perinuclear actins, nesprin-2, and YAP), across the cytoskeletal-to-nuclear space. Furthermore, stretch-mediated cytoskeletal-nuclear mechano-coupling leads to altered epigenetic modifications, mainly downregulation in H3K9 methylation, and its global gene occupancy change, as revealed by genome-wide ChIP-sequencing and pharmacological inhibition tests. Single cell RNA-sequencing further identifies subcluster of mechano-responsive iPSCs and key epigenetic modifier in stretched cells. Collectively, cyclic-stretching activates iPSC reprogramming through mechanotransduction process and epigenetic changes accompanied by altered occupancy of mechanosensitive genes. This study highlights the strong link between external physical forces with subsequent mechanotransduction process and the epigenetic changes with expression of related genes in cellular reprogramming, holding substantial implications in the field of cell biology, tissue engineering, and regenerative medicine.
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Jacobs IV EJ, Graybill PM, Jana A, Agashe A, Nain AS, Davalos RV. Engineering high post-electroporation viabilities and transfection efficiencies for elongated cells on suspended nanofiber networks. Bioelectrochemistry 2023; 152:108415. [PMID: 37011476 DOI: 10.1016/j.bioelechem.2023.108415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/14/2023] [Accepted: 03/12/2023] [Indexed: 04/03/2023]
Abstract
The impact of cell shape on cell membrane permeabilization by pulsed electric fields is not fully understood. For certain applications, cell survival and recovery post-treatment is either desirable, as in gene transfection, electrofusion, and electrochemotherapy, or is undesirable, as in tumor and cardiac ablations. Understanding of how morphology affects cell viability post-electroporation may lead to improved electroporation methods. In this study, we use precisely aligned nanofiber networks within a microfluidic device to reproducibly generate elongated cells with controlled orientations to an applied electric field. We show that cell viability is significantly dependent on cell orientation, elongation, and spread. Further, these trends are dependent on the external buffer conductivity. Additionally, we see that cell survival for elongated cells is still supported by the standard pore model of electroporation. Lastly, we see that manipulating the cell orientation and shape can be leveraged for increased transfection efficiencies when compared to spherical cells. An improved understanding of cell shape and pulsation buffer conductivity may lead to improved methods for enhancing cell viability post-electroporation by engineering the cell morphology, cytoskeleton, and electroporation buffer conditions.
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Hsia CR, Melters DP, Dalal Y. The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology. J Mol Biol 2023; 435:168019. [PMID: 37330288 PMCID: PMC10567996 DOI: 10.1016/j.jmb.2023.168019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.
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Affiliation(s)
- Chieh-Ren Hsia
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/JeremiahHsia
| | - Daniël P Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/dpmelters
| | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/NCIYaminiDalal
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Alisafaei F, Moheimani H, Elson EL, Genin GM. A nuclear basis for mechanointelligence in cells. Proc Natl Acad Sci U S A 2023; 120:e2303569120. [PMID: 37126697 PMCID: PMC10175757 DOI: 10.1073/pnas.2303569120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Affiliation(s)
- Farid Alisafaei
- NSF Science and Technology Center for Engineering MechanoBiology and Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ07102
| | - Hamidreza Moheimani
- NSF Science and Technology Center for Engineering MechanoBiology, and Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO63130
| | - Elliot L. Elson
- NSF Science and Technology Center for Engineering MechanoBiology, and Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO63130
| | - Guy M. Genin
- NSF Science and Technology Center for Engineering MechanoBiology, and Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO63130
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Kaur H, Larson NG, Nain AS. Contractility and migration: New directions in cancer stem cell migration. Biophys J 2023; 122:1141-1142. [PMID: 36791721 PMCID: PMC10111253 DOI: 10.1016/j.bpj.2023.01.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Affiliation(s)
- Harsimran Kaur
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | | | - Amrinder S Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.
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