1
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Rames M, Kenison JP, Heineck D, Civitci F, Szczepaniak M, Zheng T, Shangguan J, Zhang Y, Tao K, Esener S, Nan X. Multiplexed and Millimeter-Scale Fluorescence Nanoscopy of Cells and Tissue Sections via Prism-Illumination and Microfluidics-Enhanced DNA-PAINT. Chem Biomed Imaging 2023; 1:817-830. [PMID: 38155726 PMCID: PMC10751790 DOI: 10.1021/cbmi.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 12/30/2023]
Abstract
Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) of around 50 μm × 50 μm at once and more recently up to ∼200 μm × 200 μm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints to the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ∼520 μm × 520 μm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm2 sample areas can be completed in as little as 40 min per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality, particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ∼106 caveolae structures in ∼1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems.
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Affiliation(s)
- Matthew
J. Rames
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - John P. Kenison
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Daniel Heineck
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Fehmi Civitci
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Malwina Szczepaniak
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Ting Zheng
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Julia Shangguan
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Yujia Zhang
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Kai Tao
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Sadik Esener
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Xiaolin Nan
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
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2
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Biswas S, Mandal G, Anadon CM, Chaurio RA, Lopez-Bailon LU, Nagy MZ, Mine JA, Hänggi K, Sprenger KB, Innamarato P, Harro CM, Powers JJ, Johnson J, Fang B, Eysha M, Nan X, Li R, Perez BA, Curiel TJ, Yu X, Rodriguez PC, Conejo-Garcia JR. Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers. Immunity 2023; 56:2570-2583.e6. [PMID: 37909039 DOI: 10.1016/j.immuni.2023.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/05/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023]
Abstract
Dimeric IgA (dIgA) can move through cells via the IgA/IgM polymeric immunoglobulin receptor (PIGR), which is expressed mainly on mucosal epithelia. Here, we studied the ability of dIgA to target commonly mutated cytoplasmic oncodrivers. Mutation-specific dIgA, but not IgG, neutralized KRASG12D within ovarian carcinoma cells and expelled this oncodriver from tumor cells. dIgA binding changed endosomal trafficking of KRASG12D from accumulation in recycling endosomes to aggregation in the early/late endosomes through which dIgA transcytoses. dIgA targeting of KRASG12D abrogated tumor cell proliferation in cell culture assays. In vivo, KRASG12D-specific dIgA1 limited the growth of KRASG12D-mutated ovarian and lung carcinomas in a manner dependent on CD8+ T cells. dIgA specific for IDH1R132H reduced colon cancer growth, demonstrating effective targeting of a cytoplasmic oncodriver not associated with surface receptors. dIgA targeting of KRASG12D restricted tumor growth more effectively than small-molecule KRASG12D inhibitors, supporting the potential of this approach for the treatment of human cancers.
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Affiliation(s)
- Subir Biswas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Tumor Immunology and Immunotherapy, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Division of Cancer Biology, DBT-Institute of Life Sciences, Bhubaneswar 751023, India
| | - Carmen M Anadon
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Ricardo A Chaurio
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Luis U Lopez-Bailon
- Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Mate Z Nagy
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jessica A Mine
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Kay Hänggi
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kimberly B Sprenger
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Carly M Harro
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John J Powers
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Joseph Johnson
- Analytic Microscopy Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Mostafa Eysha
- Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR 97239, USA
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bradford A Perez
- Department of Radiation Therapy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Tyler J Curiel
- Departments of Medicine and Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH 03755, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Paulo C Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA.
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3
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Liu DA, Tao K, Wu B, Yu Z, Szczepaniak M, Rames M, Yang C, Svitkina T, Zhu Y, Xu F, Nan X, Guo W. A phosphoinositide switch mediates exocyst recruitment to multivesicular endosomes for exosome secretion. Nat Commun 2023; 14:6883. [PMID: 37898620 PMCID: PMC10613218 DOI: 10.1038/s41467-023-42661-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
Exosomes are secreted to the extracellular milieu when multivesicular endosomes (MVEs) dock and fuse with the plasma membrane. However, MVEs are also known to fuse with lysosomes for degradation. How MVEs are directed to the plasma membrane for exosome secretion rather than to lysosomes is unclear. Here we report that a conversion of phosphatidylinositol-3-phosphate (PI(3)P) to phosphatidylinositol-4-phosphate (PI(4)P) catalyzed sequentially by Myotubularin 1 (MTM1) and phosphatidylinositol 4-kinase type IIα (PI4KIIα) on the surface of MVEs mediates the recruitment of the exocyst complex. The exocyst then targets the MVEs to the plasma membrane for exosome secretion. We further demonstrate that disrupting PI(4)P generation or exocyst function blocked exosomal secretion of Programmed death-ligand 1 (PD-L1), a key immune checkpoint protein in tumor cells, and led to its accumulation in lysosomes. Together, our study suggests that the PI(3)P to PI(4)P conversion on MVEs and the recruitment of the exocyst direct the exocytic trafficking of MVEs for exosome secretion.
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Affiliation(s)
- Di-Ao Liu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Tao
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
| | - Bin Wu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ziyan Yu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Malwina Szczepaniak
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
| | - Matthew Rames
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Changsong Yang
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tatyana Svitkina
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yueyao Zhu
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, 19104, USA
| | - Fengyuan Xu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaolin Nan
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Ave, Portland, OR, 97201, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Yu W, Nan X, Schroyen M, Wang Y, Xiong B. Inulin-induced differences on serum extracellular vesicles derived miRNAs in dairy cows suffering from subclinical mastitis. Animal 2023; 17:100954. [PMID: 37690274 DOI: 10.1016/j.animal.2023.100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023] Open
Abstract
MicroRNA (miRNA) profiles vary with the nutritional and pathological conditions of cattle. In this study, we aimed to investigate the effects of inulin supplement on miRNA profiles derived from serum extracellular vesicles (EVs). Our goal was to determine the differences in miRNA expressions and analyse the pathways in which they are involved. Based on the results of California mastitis test and milk somatic cell counts, ten lactating cows with subclinical mastitis were randomly divided into two groups: an inulin group and a control group (n = 5 in each group). The inulin group received a daily supplement of 300 g of inulin while the control group did not receive any supplementation. After a 5-week treatment period, serum-derived EV-miRNAs from each cow were isolated. High-throughput sequencing was conducted to identify differentially expressed miRNAs. GO and KEGG bioinformatics analysis was performed to examine the target genes of these differentially expressed miRNAs. The EV-RNA concentration and small RNA content were not affected by the inulin treatment. A total of 162 known miRNAs and 180 novel miRNAs were identified from 10 samples in the two groups. Among the known miRNAs, 23 miRNAs were found to be differentially expressed between the two groups, with 18 upregulated and five downregulated in the inulin group compared to the control group. Pathway analysis revealed the involvement of these differentially expressed miRNAs in the regulation of cell structure and function, lipid oxidation and metabolism, immunity and inflammation, as well as digestion and absorption of nutrients. Overall, our study provides a molecular-level explanation for the reported beneficial health effects of inulin supplementation in cows with subclinical mastitis.
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Affiliation(s)
- W Yu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - X Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - M Schroyen
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - Y Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - B Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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5
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Palani S, Kenison JP, Sabuncu S, Huang T, Civitci F, Esener S, Nan X. Multispectral Localized Surface Plasmon Resonance (msLSPR) Reveals and Overcomes Spectral and Sensing Heterogeneities of Single Gold Nanoparticles. ACS Nano 2023; 17:2266-2278. [PMID: 36660770 PMCID: PMC9933608 DOI: 10.1021/acsnano.2c08702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Metal nanoparticles can be sensitive molecular sensors due to enhanced absorption and scattering of light near a localized surface plasmon resonance (LSPR). Variations in both intrinsic properties such as the geometry and extrinsic properties such as the environment can cause heterogeneity in nanoparticle LSPR and impact the overall sensing responses. To date, however, few studies have examined LSPR and sensing heterogeneities, due to technical challenges in obtaining the full LSPR spectra of individual nanoparticles in dynamic assays. Here, we report multispectral LSPR (msLSPR), a wide-field imaging technique for real-time spectral monitoring of light scattering from individual nanoparticles across the whole field of view (FOV) at ∼0.5 nm spectral and ∼100 ms temporal resolutions. Using msLSPR, we studied the spectral and sensing properties of gold nanoparticles commonly used in LSPR assays, including spheres, rods, and bipyramids. Complemented with electron microscopy imaging, msLSPR analysis revealed that all classes of gold nanoparticles exhibited variations in LSPR peak wavelengths that largely paralleled variations in morphology. Compared with the rods and spheres, gold nanobipyramids exhibited both more uniform and stronger sensing responses as long as the bipyramids are structurally intact. Simulations incorporating the experimental LSPR properties demonstrate the negative impact of spectral heterogeneity on the overall performance of conventional, intensity-based LSPR assays and the ability of msLSPR in overcoming both particle heterogeneity and measurement noise. These results highlight the importance of spectral heterogeneity in LSPR-based sensors and the potential advantage of performing LSPR assays in the spectral domain.
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Affiliation(s)
- Stephen Palani
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
- Department
of Biomedical Engineering, Oregon Health
& Science University, 2730 S Moody Ave., Portland, Oregon 97201, United States
| | - John P. Kenison
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
| | - Sinan Sabuncu
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
| | - Tao Huang
- Department
of Biomedical Engineering, Oregon Health
& Science University, 2730 S Moody Ave., Portland, Oregon 97201, United States
| | - Fehmi Civitci
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
| | - Sadik Esener
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
- Department
of Biomedical Engineering, Oregon Health
& Science University, 2730 S Moody Ave., Portland, Oregon 97201, United States
| | - Xiaolin Nan
- Knight
Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 2720 S. Moody Ave., Portland, Oregon 97201, United States
- Department
of Biomedical Engineering, Oregon Health
& Science University, 2730 S Moody Ave., Portland, Oregon 97201, United States
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6
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Kim S, Palani S, Civitci F, Nan X, Ibsen S. A Versatile Synthetic Pathway for Producing Mesostructured Plasmonic Nanostructures. Small 2022; 18:e2203940. [PMID: 36269871 DOI: 10.1002/smll.202203940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Highly branched gold (Au) nanostructures with sharp tips are considered excellent substrates for surface-enhanced Raman scattering (SERS)-based sensing technologies. Here, a simple synthetic route for producing Au or Au-Ag bimetallic mesostructures with multiple sharpened tips in the presence of carbon quantum dots (CQDs) is presented. The morphologies of these mesostructured plasmonic nanoparticles (MSPNs) can be controlled by adjusting the concentration of CQDs, reaction temperatures, and seed particles. The optimal molar ratio for [HAuCl4 ]/[CQDs] is found to be ≈25. At this molar ratio, the diameters of MSPNs can be tuned from 80 to 200 nm by changing the reaction temperature from 25 to 80 °C. In addition, it is found that hierarchical MSPNs consisting of multiple Au nanocrystals can be formed over the entire seed particle surface. Finally, the SERS activity of these MSPNs is examined through the detection of rhodamine 6G and methylene blue. Of the different mesostructures, the bimetallic MSPNs have the highest sensitivity with the ability to detect 10-7 m of rhodamine 6G and 10-6 m of methylene blue. The properties of these MSPN particles, made using a novel synthetic process, make them excellent candidates for SERS-based chemical sensing applications.
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Affiliation(s)
- Sejung Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
- School of Chemical Engineering, School of Semiconductor and Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekjedae-ro, Jeonju-si, Jeollabuk-do, 54896, South Korea
| | - Stephen Palani
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Fehmi Civitci
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Stuart Ibsen
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
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7
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Abstract
Recent advances in super resolution microscopy have enabled imaging at the 10-20 nm scale on a light microscope, providing unprecedented details of native biological structures and processes in intact and hydrated samples. Of the existing strategies, DNA points accumulation in imaging nanoscale topography (DNA-PAINT) affords convenient multiplexing, an important feature in interrogating complex biological systems. A practical limitation of DNA-PAINT, however, has been the slow imaging speed. In its original form, DNA-PAINT imaging of each target takes tens of minutes to hours to complete. To address this challenge, several improved implementations have been introduced. These include DNA-PAINT-ERS (where E = ethylene carbonate; R = repeat sequence; S = spacer), a set of strategies that leads to both accelerated DNA-PAINT imaging speed and improved image quality. With DNA-PAINT-ERS, imaging of typical cellular targets such as microtubules takes only 5-10 min. Importantly, DNA-PAINT-ERS also facilitates multiplexing and can be easily integrated into current workflows for fluorescence staining of biological samples. Here, we provide a detailed, step-by-step guide for fast and multiplexed DNA-PAINT-ERS imaging of fixed and immunostained cells grown on glass substrates as adherent monolayers. The protocol should be readily extended to biological samples of a different format (for example tissue sections) or staining mechanisms (for example using nanobodies). © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of probes for DNA-PAINT-ERS Basic Protocol 2: Sample preparation for imaging membrane targets with DNA-PAINT-ERS in fixed cells Alternate Protocol: Immunostaining of extracted U2OS cells Basic Protocol 3: Super resolution image acquisition and analysis.
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Affiliation(s)
- Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Malwina Szczepaniak
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Xiaolin Nan
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA
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8
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Abstract
Förster resonance energy transfer (FRET) is a powerful tool for studying molecular interactions. Its use for studying interactions involving more than two molecules, however, has been limited by spectral crosstalk among the fluorophores. Here, we report multispectral FRET (msFRET) for imaging multiple pairs of interactions in parallel by spectrally resolving single fluorescent molecules. By using a dual (positional and spectral) channel and wide-field imaging configuration, fluorophores with emission maxima as close as 6-10 nm could be reliably distinguished. We demonstrate msFRET by continuously monitoring the hybridization dynamics among 2 × 2 pairs of DNA oligos in parallel using Cy3 and Cy3.5 as donors and Cy5 and Cy5.5 as acceptors. Aside from studying molecular interactions, msFRET may also find applications in probing fluorophore photophysics during FRET and in multiplexed superresolution imaging.
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Affiliation(s)
- Carey Phelps
- †Department
of Biomedical Engineering, and ‡Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Tao Huang
- †Department
of Biomedical Engineering, and ‡Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Jing Wang
- †Department
of Biomedical Engineering, and ‡Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Xiaolin Nan
- †Department
of Biomedical Engineering, and ‡Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States,
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9
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Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med 2022; 3:100525. [PMID: 35243422 PMCID: PMC8861971 DOI: 10.1016/j.xcrm.2022.100525] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/15/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms in individual people, here we present an omic and multidimensional spatial (OMS) atlas generated from four serial biopsies of an individual with metastatic breast cancer during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata that includes treatment times and doses, anatomic imaging, and blood-based response measurements to clinical and exploratory analyses, which includes comprehensive DNA, RNA, and protein profiles; images of multiplexed immunostaining; and 2- and 3-dimensional scanning electron micrographs. These data report aspects of heterogeneity and evolution of the cancer genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples of how integrative analyses of these data reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.
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Affiliation(s)
- Brett E. Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Allison L. Creason
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jayne M. Stommel
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jamie M. Keck
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Swapnil Parmar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Courtney B. Betts
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Boniface
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erik Burlingame
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Todd Camp
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Koei Chin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer Eng
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Heidi S. Feiler
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael B. Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zhi Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ben L. Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jinho Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Souraya Mitri
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Janice Patterson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica L. Riesterer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR 97239, USA
| | - Shamilene Sivagnanam
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Guillaume Thibault
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin R. Weeder
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina Zheng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F. Thompson
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR 97239, USA
| | - Laura M. Heiser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T. Spellman
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lisa M. Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexander R. Guimaraes
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Corless
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jeremy Goecks
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Raymond Bergan
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zahi Mitri
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W. Gray
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
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10
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:genes13020219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the ‘old’ field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
- Correspondence:
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11
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Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu S, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. Interpretation of cancer mutations using a multiscale map of protein systems. Science 2021; 374:eabf3067. [PMID: 34591613 PMCID: PMC9126298 DOI: 10.1126/science.abf3067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A major goal of cancer research is to understand how mutations distributed across diverse genes affect common cellular systems, including multiprotein complexes and assemblies. Two challenges—how to comprehensively map such systems and how to identify which are under mutational selection—have hindered this understanding. Accordingly, we created a comprehensive map of cancer protein systems integrating both new and published multi-omic interaction data at multiple scales of analysis. We then developed a unified statistical model that pinpoints 395 specific systems under mutational selection across 13 cancer types. This map, called NeST (Nested Systems in Tumors), incorporates canonical processes and notable discoveries, including a PIK3CA-actomyosin complex that inhibits phosphatidylinositol 3-kinase signaling and recurrent mutations in collagen complexes that promote tumor proliferation. These systems can be used as clinical biomarkers and implicate a total of 548 genes in cancer evolution and progression. This work shows how disparate tumor mutations converge on protein assemblies at different scales.
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Affiliation(s)
- Fan Zheng
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Marcus R. Kelly
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Dana J. Ramms
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Marissa L. Heintschel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Beril Tutuncuoglu
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - John J. Lee
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Keiichiro Ono
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Helene Foussard
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael Chen
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kari A. Herrington
- Department of Biochemistry and Biophysics Center for Advanced Light Microscopy at UCSF, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Erica Silva
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sophie Liu
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jing Chen
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Churas
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wilson
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anton Kratz
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Rudolf T. Pillich
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Devin N. Patel
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Jisoo Park
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Brent Kuenzi
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Michael K. Yu
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Dexter Pratt
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jason F. Kreisberg
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Minkyu Kim
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Danielle L. Swaney
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, 97201, USA
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - J. Silvio Gutkind
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nevan J. Krogan
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
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12
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Lovell TC, Bolton SG, Kenison JP, Shangguan J, Otteson CE, Civitci F, Nan X, Pluth MD, Jasti R. Subcellular Targeted Nanohoop for One- and Two-Photon Live Cell Imaging. ACS Nano 2021; 15:15285-15293. [PMID: 34472331 PMCID: PMC8764753 DOI: 10.1021/acsnano.1c06070] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fluorophores are powerful tools for interrogating biological systems. Carbon nanotubes (CNTs) have long been attractive materials for biological imaging due to their near-infrared excitation and bright, tunable optical properties. The difficulty in synthesizing and functionalizing these materials with precision, however, has hampered progress in this area. Carbon nanohoops, which are macrocyclic CNT substructures, are carbon nanostructures that possess ideal photophysical characteristics of nanomaterials, while maintaining the precise synthesis of small molecules. However, much work remains to advance the nanohoop class of fluorophores as biological imaging agents. Herein, we report an intracellular targeted nanohoop. This fluorescent nanostructure is noncytotoxic at concentrations up to 50 μM, and cellular uptake investigations indicate internalization through endocytic pathways. Additionally, we employ this nanohoop for two-photon fluorescence imaging, demonstrating a high two-photon absorption cross-section (65 GM) and photostability comparable to a commercial probe. This work further motivates continued investigations into carbon nanohoop photophysics and their biological imaging applications.
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Affiliation(s)
- Terri C Lovell
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Sarah G Bolton
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - John P Kenison
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Avenue, Portland, Oregon 97201, United States
| | - Julia Shangguan
- Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Avenue, Portland, Oregon 97201, United States
| | - Claire E Otteson
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Fehmi Civitci
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Avenue, Portland, Oregon 97201, United States
| | - Xiaolin Nan
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Avenue, Portland, Oregon 97201, United States
- Department of Biomedical Engineering, Oregon Health and Science University, 2730 S. Moody Avenue, Portland, Oregon 97201, United States
| | - Michael D Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Ramesh Jasti
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
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13
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Hua D, Zhao Y, Nan X, Xue F, Wang Y, Jiang L, Xiong B. Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro. J Appl Microbiol 2020; 130:1868-1882. [PMID: 32998176 PMCID: PMC8247007 DOI: 10.1111/jam.14873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022]
Abstract
Aims This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities. Methods and Results Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others. Conclusions When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio. Significance and Impact of the Study The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.
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Affiliation(s)
- D Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, The Netherlands
| | - Y Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - F Xue
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Jiang
- Beijing Key Laboratory for Dairy Cattle Nutrition, Beijing Agricultural College, Beijing, China
| | - B Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Yan X, Gong L, Chen X, Ye P, Zhou H, Cai L, Nan X. Survivin promotes piperlongumine resistance in ovarian cancer. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Yan X, Chen X, Cai L, Nan X, Chen J, Chen X, Zhou H. Erastin enhances docetaxel efficacy in ovarian cancer by targeting ABCB1 transporter. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Yan X, Chen X, Zhao N, Ye P, Chen J, Nan X, Zhou H, Zhou K, Zhang Y, Xue J, Zhao H. Comparison of laparoscopic and open radical hysterectomy in cervical cancer patients with tumor size ≤2cm. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Song P, Song B, Liu J, Wang X, Nan X, Wang J. Blockage of PAK1 alleviates the proliferation and invasion of NSCLC cells via inhibiting ERK and AKT signaling activity. Clin Transl Oncol 2020; 23:892-901. [PMID: 32974862 DOI: 10.1007/s12094-020-02486-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/31/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE P21-activated kinase 1 (PAK1), a serine/threonine protein kinase which functions downstream of RAC and CDC42 GTPase, is activated by a variety of stimuli, including RAS and other growth signaling factors. The extracellular signal kinase (ERK) and protein kinase B (AKT) signal pathways have been implicated in the pathogenesis of cancers. Whether PAK1 is sensitive to KRAS mutation signals and plays a role through ERK and AKT signaling pathways in NSCLC needs to be studied. METHODS The expression of PAK1, ERK and AKT was detected in both lung cancer cell lines and clinical samples. PAK1 RNA interference and specific inhibitor of PAK1(IPA-3) were applied to lung cancer cell lines and mouse xenograft tumors. Cell growth was measured by MTT and colony formation assays. Cell migration and invasion were detected by wound healing and transwell assays. RAS mutation was detected by Taqman probe method. Correlation between KRAS, PAK1, ERK and AKT activities was analyzed in lung cancer patients. RESULTS PAK1 was highly expressed not only in RAS mutant but also in RAS wild-type lung cancer cells. Using specific inhibitor of PAK1, IPA-3 and PAK1 RNA interference, cell proliferation, migration and invasion of lung cancer cells were reduced significantly, accompanied by decreased activities of ERK and AKT. Dual inhibition of ERK and AKT suppressed these cellular processes to levels comparable to those achieved by reduction in PAK1 expression. In NSCLC patients, PAK1 was not correlated with KRAS mutation but was significantly positively correlated with pERK and pAKT. CONCLUSION PAK1 played roles in NSCLC proliferation and invasion via ERK and AKT signaling and suggested a therapeutic target for NSCLC.
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Affiliation(s)
- P Song
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - B Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jiyan Road 440, Jjinan, China.
| | - J Liu
- Department of Respiratory Internal, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - X Wang
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jiyan Road 440, Jjinan, China
| | - X Nan
- Department of Respiratory Internal, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - J Wang
- Department of Respiratory Internal, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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18
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Civitci F, Shangguan J, Zheng T, Tao K, Rames M, Kenison J, Zhang Y, Wu L, Phelps C, Esener S, Nan X. Author Correction: Fast and multiplexed superresolution imaging with DNA-PAINT-ERS. Nat Commun 2020; 11:4846. [PMID: 32958801 PMCID: PMC7505831 DOI: 10.1038/s41467-020-18724-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Fehmi Civitci
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Julia Shangguan
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Ting Zheng
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Kai Tao
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Matthew Rames
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - John Kenison
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Ying Zhang
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Lei Wu
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Rd., Wuhan, 430079, Hubei, China
| | - Carey Phelps
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Sadik Esener
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA.,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Xiaolin Nan
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA. .,Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA. .,Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA.
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19
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Iizuka S, Leon RP, Gribbin KP, Zhang Y, Navarro J, Smith R, Devlin K, Wang LG, Gibbs SL, Korkola J, Nan X, Courtneidge SA. Crosstalk between invadopodia and the extracellular matrix. Eur J Cell Biol 2020; 99:151122. [PMID: 33070041 DOI: 10.1016/j.ejcb.2020.151122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/24/2020] [Accepted: 08/12/2020] [Indexed: 12/27/2022] Open
Abstract
The scaffold protein Tks5α is required for invadopodia-mediated cancer invasion both in vitro and in vivo. We have previously also revealed a role for Tks5 in tumor cell growth using three-dimensional (3D) culture model systems and mouse transplantation experiments. Here we use both 3D and high-density fibrillar collagen (HDFC) culture to demonstrate that native collagen-I, but not a form lacking the telopeptides, stimulated Tks5-dependent growth, which was dependent on the DDR collagen receptors. We used microenvironmental microarray (MEMA) technology to determine that laminin, fibronectin and tropoelastin also stimulated invadopodia formation. A Tks5α-specific monoclonal antibody revealed its expression both on microtubules and at invadopodia. High- and super-resolution microscopy of cells in and on collagen was then used to place Tks5α at the base of invadopodia, separated from much of the actin and cortactin, but coincident with both matrix metalloprotease and cathepsin proteolytic activity. Inhibition of the Src family kinases, cathepsins or metalloproteases all reduced invadopodia length but each had distinct effects on Tks5α localization. These studies highlight the crosstalk between invadopodia and extracellular matrix components, and reveal the invadopodium to be a spatially complex structure.
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Affiliation(s)
- Shinji Iizuka
- Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, USA.
| | - Ronald P Leon
- Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Kyle P Gribbin
- Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Ying Zhang
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - Jose Navarro
- Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Rebecca Smith
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - Kaylyn Devlin
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Lei G Wang
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - Summer L Gibbs
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA; Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - James Korkola
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA; Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Xiaolin Nan
- Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA; Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Sara A Courtneidge
- Departments of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon, USA; Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA; Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA.
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20
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Civitci F, Shangguan J, Zheng T, Tao K, Rames M, Kenison J, Zhang Y, Wu L, Phelps C, Esener S, Nan X. Fast and multiplexed superresolution imaging with DNA-PAINT-ERS. Nat Commun 2020; 11:4339. [PMID: 32859909 PMCID: PMC7455722 DOI: 10.1038/s41467-020-18181-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.
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Affiliation(s)
- Fehmi Civitci
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Julia Shangguan
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Ting Zheng
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Kai Tao
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Matthew Rames
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - John Kenison
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Ying Zhang
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Lei Wu
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Rd., Wuhan, 430079, Hubei, China
| | - Carey Phelps
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Sadik Esener
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Xiaolin Nan
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA.
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA.
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21
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Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas G12D diffusion and trafficking. eLife 2019; 8:46393. [PMID: 31674905 PMCID: PMC7060040 DOI: 10.7554/elife.46393] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Membrane nanodomains have been implicated in Ras signaling, but what these domains are and how they interact with Ras remain obscure. Here, using single particle tracking with photoactivated localization microscopy (spt-PALM) and detailed trajectory analysis, we show that distinct membrane domains dictate KRasG12D (an active KRas mutant) diffusion and trafficking in U2OS cells. KRasG12D exhibits an immobile state in ~70 nm domains, each embedded in a larger domain (~200 nm) that confers intermediate mobility, while the rest of the membrane supports fast diffusion. Moreover, KRasG12D is continuously removed from the membrane via the immobile state and replenished to the fast state, reminiscent of Ras internalization and recycling. Importantly, both the diffusion and trafficking properties of KRasG12D remain invariant over a broad range of protein expression levels. Our results reveal how membrane organization dictates membrane diffusion and trafficking of Ras and offer new insight into the spatial regulation of Ras signaling. The Ras family of proteins play an important role in relaying signals from the outside to the inside of the cell. Ras proteins are attached by a fatty tail to the inner surface of the cell membrane. When activated they transmit a burst of signal that controls critical behaviors like growth, survival and movement. It has been suggested that to prevent these signals from being accidently activated, Ras molecules must group together at specialized sites within the membrane before passing on their message. However, visualizing how Ras molecules cluster together at these domains has thus far been challenging. As a result, little is known about where these sites are located and how Ras molecules come to a stop at these domains. Now, Lee et al. have combined two microscopy techniques called ‘single-particle tracking’ and ‘photoactivated localization microscopy' to track how individual molecules of activated Ras move in human cells grown in the lab. This revealed that Ras molecules quickly diffuse along the inside of the membrane until they arrive at certain locations that cause them to halt. However, computer models consisting of just the ‘fast’ and ‘immobile’ state could not correctly re-capture the way Ras molecules moved along the membrane. Lee et al. found that for these models to mimic the movement of Ras, a third ‘intermediate’ state of Ras mobility needed to be included. To investigate this further, Lee et al. created a fluorescent map that overlaid all the individual paths taken by each Ras molecule. The map showed regions in the membrane where the Ras molecules had stopped and possibly clustered together. Each of these ‘immobilization domains’ were then surrounded by an ‘intermediate domain’ where Ras molecules had begun to slow down their movement. Although the intermediate domains did not last long, they seemed to guide Ras molecules into the immobilization domains where they could cluster together with other molecules. From there, the cell constantly removed Ras molecules from these membrane domains and returned them back to their ‘fast’ diffusing state. Mutations in Ras proteins occur in around a third of all cancers, so a better understanding of their dynamics could help with future drug discovery. The methods used here could also be used to investigate the movement of other signaling molecules.
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Affiliation(s)
- Yerim Lee
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Carey Phelps
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Barmak Mostofian
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Lei Wu
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Philip Js Stork
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Knight Cancer Early Detection Advanced Research (CEDAR) Center, Oregon Health and Science University, Portland, United States
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22
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Rames MJ, Civitci F, Zheng T, Wagner J, Link J, Nan X. Abstract 799: Aberrant mitochondrial protein involvement through early PDAC initiation and progression using multiplexed DNA-PAINT and correlative histology. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prior to pancreatic ductal adenocarcinoma (PDAC), pancreatic acini cells change their morphology through pancreatic intraepithelial neoplasia (PanIN) stages, becoming increasingly dysplastic as stroma and tissue hypoxia increase. This increasing hypoxia forms a cancer promoting microenvironment, wherein we propose metabolic changes trigger aberrant mitochondrial networks form healthy tissue. We developed tissue superresolution imaging to directly quantify structural mitochondrial response through patient histology, whereby DNA-PAINT can provide super-resolution detail decoupled from photo bleaching to visualize mitochondria through tissue layers. Expanding from preliminary data, target mitochondrial dynamics proteins’ organization will also be correlated to PanIN stages.
Introduction: Early oncogene involvement in PDAC progression links to metabolic and mitochondrial regulatory changes. Typically nutrient deprivation and hypoxia trigger cell death from increased reactive oxygen species production and organelle damage which trigger apoptosis, yet these prolonged effects can be cancer promoting when less severe. Mitochondrial dynamics and proteins related to mitochondrial fission and fusion can reduce apoptotic signaling, enhance aerobic glycolysis, and increase ROS to allow cancer progression.
Materials and Methods: Adapting from previous proof of concept, mitochondria (TOM20) within formalin-fixed paraffin embedded (FFPE) tissue sections were imaged with stochastic optical reconstruction microscopy (STORM). In brief: cadaver healthy pancreas FFPE tissue samples underwent deparafinization, antigen retrieval, indirect immuno-labeling with AlexaFluor647, TIRF illumination with a 60x objective was used for data collection, whereby data processing was conducted using the open-source FIJI and custom MATLAB software.
Results and Discussion: Preliminary data shows proof of principle that both STORM and DNA-PAINT can be correlated to histological staining of human pancreas.
Conclusions: Superresolution imaging reveals ultrastructural details of mitochondria in FFPE patient samples not resolved via conventional fluorescence imaging. Through quantitative feature analysis, we would be able to correlate aberrant mitochondria structure and abundance to PDAC progression.
Acknowledgements: Funding provided by the Cancer Early Detection Advanced Research (CEDAR) Center of OHSU Knight Cancer Institute.
Citation Format: Matthew J. Rames, Fehmi Civitci, Ting Zheng, Josiah Wagner, Jason Link, Xiaolin Nan. Aberrant mitochondrial protein involvement through early PDAC initiation and progression using multiplexed DNA-PAINT and correlative histology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 799.
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Affiliation(s)
| | | | - Ting Zheng
- Oregon Health & Science University, Portland, OR
| | | | - Jason Link
- Oregon Health & Science University, Portland, OR
| | - Xiaolin Nan
- Oregon Health & Science University, Portland, OR
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23
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Kim H, Civitci F, Wagner J, Anur P, Rames M, Nan X, Morgan T, Ngo T. Abstract 2286: Liquid biopsy for early cancer detection. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Early cancer detection remains as a critical challenge to improve patient’s survival and clinical outcome. A non-invasive liquid biopsy permits the analysis of multiple circulating biomarkers including cell free nucleic acids and extracellular vesicles that facilitate the discovery of disease. We hypothesize that cancer-derived circulating biomarkers contain heterogeneous surface membrane proteins and/or nucleic acids representing the original tumor, requiring tools which can identify multiple biomarkers to be detected simultaneously. However, challenges including a lack of established isolation standards and determining sufficiently sensitive detection platforms remain for clinical implementation. Our goal is to develop a multiplexed biomarker based assay which can be leveraged to capture the molecular heterogeneity of distinct subpopulations of tumor derived circulating biomarkers.
Materials and Methods: Materials and methods vary greatly by project, each project design will be briefly summarized: 1) Single molecule imaging of ctDNA was conducted using PEG-coated surface whereby biotin streptavidin linked DNA reference strands were exposed to fluorophore conjugated mutant DNA strands for FRET imaging of mutant specific sequences. 2) Extracellular vesicle imaging and profiling was conducted using antibody based surface capture and high-resolution flow cytometry for high throughput exosome characterization. 3) RNA-biomarkers were identified by converting RNA into cDNA using target gene panels selected from data bases at each cycle during a PCR.
Results and Discussion: RNA profiling of initial sample cohort distinguished cancer from healthy, while detecting early cancer patients with high sensitivity. Differentiating genes with biological relevance were identified which can classify pancreatic cancer patients from healthy donor. cfDNA imaging method had nonspecific signal < 0.1-1%, wherein 1-10% mutant fraction can be genotyped. High resolution flow cytometry identified distinct subpopulations of plasma exosomes and revealed their molecular heterogeneity and cancer specific marker candidates can be screened against purified exosomes.
Conclusions: Extracellular vesicle imaging and profiling co-validated by high resolution flow cytometry, exemplifying the utility of a multi-platform detection scheme to characterize plasma-derived extracellular vesicle populations. Cell free RNA biomarkers of cancer by cell-free RNA sequencing were analyzed that can improve early cancer detection outcome, this proof of concept was done on pancreatic patient plasma and is being expanded into other cancer cohorts.
Citation Format: Hyunji Kim, Fehmi Civitci, Josiah Wagner, Pavana Anur, Matthew Rames, Xiaolin Nan, Terry Morgan, Thuy Ngo. Liquid biopsy for early cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2286.
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Affiliation(s)
- Hyunji Kim
- Oregon Health & Science University, Portland, OR
| | | | | | - Pavana Anur
- Oregon Health & Science University, Portland, OR
| | | | - Xiaolin Nan
- Oregon Health & Science University, Portland, OR
| | - Terry Morgan
- Oregon Health & Science University, Portland, OR
| | - Thuy Ngo
- Oregon Health & Science University, Portland, OR
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24
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Yan X, Zhao N, Chen X, Ye P, Xu L, Nan X, Shang H, Zhao H. Long-term oncological outcomes after laparoscopic versus open radical hysterectomy in stage IB1 cervical cancer patients with tumor size ≤2cm and without lymph-node metastasis. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Huang T, Phelps C, Wang J, Lin LJ, Bittel A, Scott Z, Jacques S, Gibbs SL, Gray JW, Nan X. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J 2019; 114:301-310. [PMID: 29401428 DOI: 10.1016/j.bpj.2017.11.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
Single-molecule tracking (SMT) offers rich information on the dynamics of underlying biological processes, but multicolor SMT has been challenging due to spectral cross talk and a need for multiple laser excitations. Here, we describe a single-molecule spectral imaging approach for live-cell tracking of multiple fluorescent species at once using a single-laser excitation. Fluorescence signals from all the molecules in the field of view are collected using a single objective and split between positional and spectral channels. Images of the same molecule in the two channels are then combined to determine both the location and the identity of the molecule. The single-objective configuration of our approach allows for flexible sample geometry and the use of a live-cell incubation chamber required for live-cell SMT. Despite a lower photon yield, we achieve excellent spatial (20-40 nm) and spectral (10-15 nm) resolutions comparable to those obtained with dual-objective, spectrally resolved Stochastic Optical Reconstruction Microscopy. Furthermore, motions of the fluorescent molecules did not cause loss of spectral resolution owing to the dual-channel spectral calibration. We demonstrate SMT in three (and potentially more) colors using spectrally proximal fluorophores and single-laser excitation, and show that trajectories of each species can be reliably extracted with minimal cross talk.
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Affiliation(s)
- Tao Huang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Carey Phelps
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Jing Wang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Li-Jung Lin
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Amy Bittel
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Zubenelgenubi Scott
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Steven Jacques
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
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26
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Mitrugno A, Tassi Yunga S, Sylman JL, Zilberman-Rudenko J, Shirai T, Hebert JF, Kayton R, Zhang Y, Nan X, Shatzel JJ, Esener S, Duvernay MT, Hamm HE, Gruber A, Williams CD, Takata Y, Armstrong R, Morgan TK, McCarty OJT. The role of coagulation and platelets in colon cancer-associated thrombosis. Am J Physiol Cell Physiol 2018; 316:C264-C273. [PMID: 30462538 DOI: 10.1152/ajpcell.00367.2018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer-associated thrombosis is a common first presenting sign of malignancy and is currently the second leading cause of death in cancer patients after their malignancy. However, the molecular mechanisms underlying cancer-associated thrombosis remain undefined. In this study, we aimed to develop a better understanding of how cancer cells affect the coagulation cascade and platelet activation to induce a prothrombotic phenotype. Our results show that colon cancer cells trigger platelet activation in a manner dependent on cancer cell tissue factor (TF) expression, thrombin generation, activation of the protease-activated receptor 4 (PAR4) on platelets and consequent release of ADP and thromboxane A2. Platelet-colon cancer cell interactions potentiated the release of platelet-derived extracellular vesicles (EVs) rather than cancer cell-derived EVs. Our data show that single colon cancer cells were capable of recruiting and activating platelets and generating fibrin in plasma under shear flow. Finally, in a retrospective analysis of colon cancer patients, we found that the number of venous thromboembolism events was 4.5 times higher in colon cancer patients than in a control population. In conclusion, our data suggest that platelet-cancer cell interactions and perhaps platelet procoagulant EVs may contribute to the prothrombotic phenotype of colon cancer patients. Our work may provide rationale for targeting platelet-cancer cell interactions with PAR4 antagonists together with aspirin and/or ADP receptor antagonists as a potential intervention to limit cancer-associated thrombosis, balancing safety with efficacy.
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Affiliation(s)
- Annachiara Mitrugno
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,Division of Hematology & Medical Oncology, Oregon Health & Science University , Portland, Oregon
| | - Samuel Tassi Yunga
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University , Portland, Oregon.,Cancer Early Detection & Advanced Research Center, Oregon Health & Science University , Portland, Oregon
| | - Joanna L Sylman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,VA Palo Alto Health Care System, Palo Alto, California.,Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine , Stanford, California
| | - Jevgenia Zilberman-Rudenko
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon
| | - Toshiaki Shirai
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon
| | - Jessica F Hebert
- Department of Pathology, Oregon Health & Science University , Portland, Oregon
| | - Robert Kayton
- Department of Pathology, Oregon Health & Science University , Portland, Oregon
| | - Ying Zhang
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon
| | - Joseph J Shatzel
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,Division of Hematology & Medical Oncology, Oregon Health & Science University , Portland, Oregon
| | - Sadik Esener
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University , Portland, Oregon.,Cancer Early Detection & Advanced Research Center, Oregon Health & Science University , Portland, Oregon
| | - Matthew T Duvernay
- Department of Pharmacology, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - András Gruber
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon
| | | | - Yumie Takata
- College of Public Health & Human Science, Oregon State University , Corvallis, Oregon
| | - Randall Armstrong
- Knight Cancer Institute, Oregon Health & Science University , Portland, Oregon.,Cancer Early Detection & Advanced Research Center, Oregon Health & Science University , Portland, Oregon
| | - Terry K Morgan
- Department of Pathology, Oregon Health & Science University , Portland, Oregon
| | - Owen J T McCarty
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University , Portland, Oregon.,Division of Hematology & Medical Oncology, Oregon Health & Science University , Portland, Oregon
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Abstract
Multicolor single-molecule localization microscopy (SMLM) expands our understanding of subcellular details and enables the study of biomolecular interactions through precise visualization of multiple molecules in a single sample with resolution of ~10–20 nm. Probe selection is vital to multicolor SMLM, as the fluorophores must not only exhibit minimal spectral crosstalk, but also be compatible with the same photochemical conditions that promote fluorophore photoswitching. While there are numerous commercially available photoswitchable fluorophores that are optimally excited in the standard Cy3 channel, they are restricted to short Stokes shifts (<30 nm), limiting the number of colors that can be resolved in a single sample. Furthermore, while imaging buffers have been thoroughly examined for commonly used fluorophore scaffolds including cyanine, rhodamine, and oxazine, optimal conditions have not been found for the BODIPY scaffold, precluding its routine use for multicolor SMLM. Herein, we screened common imaging buffer conditions including seven redox reagents with five additives, resulting in 35 overall imaging buffer conditions to identify compatible combinations for BODIPY-based fluorophores. We then demonstrated that novel, photoswitchable BODIPY-based fluorophores with varied length Stokes shifts provide additional color options for SMLM using a combination of BODIPY-based and commercially available photoswitchable fluorophores.
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Affiliation(s)
- Amy M. Bittel
- Biomedical Engineering Department, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Isaac S. Saldivar
- Biomedical Engineering Department, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Nick J. Dolman
- Thermo Fisher Scientific, Pittsburg, Pennsylvania, United States of America
| | - Xiaolin Nan
- Biomedical Engineering Department, Oregon Health & Science University, Portland, Oregon, United States of America
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, Oregon, United States of America
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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28
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Su Y, Pelz C, Huang T, Torkenczy K, Wang X, Cherry A, Daniel CJ, Liang J, Nan X, Dai MS, Adey A, Impey S, Sears RC. Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals. Genes Dev 2018; 32:1398-1419. [PMID: 30366908 PMCID: PMC6217735 DOI: 10.1101/gad.314377.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
In this study, Su et al. investigate how post-translational modifications of Myc that affect stability and oncogenic activity regulate its function. They show that Ser62 phosphorylation and PIN1-mediated isomerization of MYC dynamically regulate the spatial distribution of MYC in the nucleus, promoting its association with the inner basket of the nuclear pore in response to proliferative signals, where it recruits the histone acetyltransferase GCN5 to bind and regulate local gene acetylation and expression, thus providing new insights into how post-translational modification of MYC controls its spatial activity. The transcription factor MYC (also c-Myc) induces histone modification, chromatin remodeling, and the release of paused RNA polymerase to broadly regulate transcription. MYC is subject to a series of post-translational modifications that affect its stability and oncogenic activity, but how these control MYC's function on the genome is largely unknown. Recent work demonstrates an intimate connection between nuclear compartmentalization and gene regulation. Here, we report that Ser62 phosphorylation and PIN1-mediated isomerization of MYC dynamically regulate the spatial distribution of MYC in the nucleus, promoting its association with the inner basket of the nuclear pore in response to proliferative signals, where it recruits the histone acetyltransferase GCN5 to bind and regulate local gene acetylation and expression. We demonstrate that PIN1-mediated localization of MYC to the nuclear pore regulates MYC target genes responsive to mitogen stimulation that are involved in proliferation and migration pathways. These changes are also present at the chromatin level, with an increase in open regulatory elements in response to stimulation that is PIN1-dependent and associated with MYC chromatin binding. Taken together, our study indicates that post-translational modification of MYC controls its spatial activity to optimally regulate gene expression in response to extrinsic signals in normal and diseased states.
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Affiliation(s)
- Yulong Su
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Carl Pelz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA.,Oregon Stem Cell Center, Oregon Health and Science University, Oregon 97239, USA
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University, Oregon 97239, USA
| | - Kristof Torkenczy
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Xiaoyan Wang
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Allison Cherry
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Colin J Daniel
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Juan Liang
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Oregon 97239, USA
| | - Mu-Shui Dai
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Andrew Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
| | - Soren Impey
- Oregon Stem Cell Center, Oregon Health and Science University, Oregon 97239, USA
| | - Rosalie C Sears
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Oregon 97239, USA
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29
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Abstract
BACKGROUND Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing. RESULTS In transfected cells, a total of 748 biotinylated proteins were identified from cells expressing biotin ligase-tagged K-Ras variants. Significant differences were observed between membrane-associated variants and a farnesylation-defective mutant. In pancreatic cancer cells, 56 K-Ras interaction partners were identified. Most of these were cytoskeletal or plasma membrane proteins, and many have been identified previously as potential cancer biomarkers. CONCLUSION Biotin ligase tagging offers a rapid and convenient approach to the characterization of K-Ras interaction networks.
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Affiliation(s)
- Christopher Ritchie
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Philip J S Stork
- Department of Vollum Institute, Oregon Health & Science University, Portland, OR, U.S.A
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, U.S.A
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A.
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30
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Yun J, Phelps C, Morales D, Nan X, Reich N. Light Controlled Intracellular Protein Release: Tracking Ras Interactions With Superresolution Fluorescence Microscopy. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.801.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jason Yun
- Chemistry & BiochemistryUCSBSanta BarbaraCA
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31
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Zhang J, Ma M, Nan X, Sheng B. Obesity inversely correlates with prostate-specific antigen levels in a population with normal screening results of prostate cancer in northwestern China. ACTA ACUST UNITED AC 2017; 49:S0100-879X2016000800704. [PMID: 27409334 PMCID: PMC4954736 DOI: 10.1590/1414-431x20165272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/13/2016] [Indexed: 01/21/2023]
Abstract
Serum prostate-specific antigen (PSA) is a diagnostic biomarker of prostate cancer and is possibly associated with obesity. This study aimed to explore the relationships between obesity indicators [body mass index (BMI) and waist circumference (WC)] with PSA in Chinese men. A cross-sectional study of men aged 30-85 years undergoing prostate cancer screening was conducted from August 2008 to July 2013 in Xi'an, China. Data were obtained from clinical reports, condition was recorded based on self-report including demographics, weight, height, and WC (>90 cm=obese). Fasting blood glucose (FBG) and prostate volume (PV) were assessed clinically. Patients were grouped by BMI (normal=22.9, overweight=23-27.4, obese≥27.5 kg/m2). PSA parameters of density (PSAD), PSA serum level, and PSA increasing rate per year (PSAR) were calculated per BMI and age groups (30-40, 41-59, 60-85 years). Obesity indicators (BMI and WC) and PSA parameter relationships were modeled by age-stratified linear regression. Of 35,632 Chinese men surveyed, 13,084 were analyzed, including 13.44% obese, 57.44% overweight, and 29.12% normal weight, according to BMI; 25.84% were centrally (abdominally) obese according to WC. BMI and WC were negatively associated with all PSA parameters, except PSAD and PSAR [P<0.05, BMI: β=-0.081 (95%CI=-0.055 to -0.036), WC: β=-0.101 (-0.021 to -0.015)], and independent of FBG and PV (P<0.05) in an age-adjusted model. In conclusion, obesity was associated with lower PSA in Chinese men. Therefore, an individual's BMI and WC should be considered when PSA is used to screen for prostate cancer.
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Affiliation(s)
- J Zhang
- Nutrition Department, The First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - M Ma
- Geriatric Surgery Department, The First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - X Nan
- Urology Institute, The First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
| | - B Sheng
- Geriatric Surgery Department, The First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China
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32
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Zhang Y, Huang T, Jorgens DM, Nickerson A, Lin LJ, Pelz J, Gray JW, López CS, Nan X. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy. PLoS One 2017; 12:e0176839. [PMID: 28562683 PMCID: PMC5451012 DOI: 10.1371/journal.pone.0176839] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/18/2017] [Indexed: 11/19/2022] Open
Abstract
Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.
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Affiliation(s)
- Ying Zhang
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Tao Huang
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Danielle M. Jorgens
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Andrew Nickerson
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Li-Jung Lin
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joshua Pelz
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joe W. Gray
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
| | - Claudia S. López
- Multiscale Microscopy Core, OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, Oregon, United States of America
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33
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Dai S, Nan X, Zhao H, Song Q, Zhang C. 489 Nagashima-type palmoplantar keratoderma: Mutation analysis of the SERPINB 7 gene. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Ngo AT, Thierheimer ML, Babur Ö, Rocheleau AD, Nan X, McCarty OJ, Aslan J. Abstract 524: Identification of Roles for the Rho-Specific Guanine Nucleotide Dissociation Inhibitor (RhoGDI) Ly-Gdi in Platelet Function. Arterioscler Thromb Vasc Biol 2017. [DOI: 10.1161/atvb.37.suppl_1.524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction:
Upon activation, platelets undergo specific morphological alterations critical to hemostatic plug and thrombus formation via actin cytoskeletal reorganizations driven by the Rho GTPases Rac1, Cdc42 and RhoA. Here we investigate roles for Rho-specific guanine nucleotide dissociation inhibitor proteins (RhoGDIs) in regulating platelet function.
Methods and Hypothesis:
Through an approach combining pharmacology, cell biology and systems biology methods we assessed the hypothesis that RhoGDI proteins regulate Rho GTPase-driven platelet functions downstream of platelet integrin and glycoprotein receptors.
Results:
We find that platelets express two RhoGDI family members, RhoGDI and Ly-GDI. Antibody interference and platelet spreading experiments suggest a specific role for Ly-GDI in platelet function. Intracellular staining and super resolution microscopy assays find that Ly-GDI displays an asymmetric, polarized localization that largely overlaps with Rac1 and Cdc42 as well as microtubules and protein kinase C (PKC) in platelets adherent to fibrinogen. Signaling studies based on interactome and pathways analyses also support a regulatory role for Ly-GDI in platelets, as Ly-GDI is phosphorylated at PKC substrate motifs in a PKC-dependent manner in response to the platelet collagen receptor glycoprotein (GP)VI-specific agonist collagen-related peptide. Notably, inhibition of PKC diffuses the polarized organization of Ly-GDI in spread platelets relative to its colocalization with Rac1 and Cdc42.
Conclusion:
In conclusion, our results support roles for Ly-GDI as a localized regulator of Rho GTPases in platelets and link PKC and Rho GTPase signaling systems to platelet function.
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Affiliation(s)
- Anh T Ngo
- Oregon Health & Science Univ, Portland, OR
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35
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Bittel AM, Davis A, Huang T, Nan X, Gibbs SL. Expanding the Spectral Resolution of Single-Molecule Localization Microscopy with Bodipy-Based Photoswitchable Fluorophores. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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36
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Ngo ATP, Thierheimer MLD, Babur Ö, Rocheleau AD, Huang T, Pang J, Rigg RA, Mitrugno A, Theodorescu D, Burchard J, Nan X, Demir E, McCarty OJT, Aslan JE. Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach. Am J Physiol Cell Physiol 2017; 312:C527-C536. [PMID: 28148498 PMCID: PMC5407014 DOI: 10.1152/ajpcell.00274.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 12/29/2022]
Abstract
On activation at sites of vascular injury, platelets undergo morphological alterations essential to hemostasis via cytoskeletal reorganizations driven by the Rho GTPases Rac1, Cdc42, and RhoA. Here we investigate roles for Rho-specific guanine nucleotide dissociation inhibitor proteins (RhoGDIs) in platelet function. We find that platelets express two RhoGDI family members, RhoGDI and Ly-GDI. Whereas RhoGDI localizes throughout platelets in a granule-like manner, Ly-GDI shows an asymmetric, polarized localization that largely overlaps with Rac1 and Cdc42 as well as microtubules and protein kinase C (PKC) in platelets adherent to fibrinogen. Antibody interference and platelet spreading experiments suggest a specific role for Ly-GDI in platelet function. Intracellular signaling studies based on interactome and pathways analyses also support a regulatory role for Ly-GDI, which is phosphorylated at PKC substrate motifs in a PKC-dependent manner in response to the platelet collagen receptor glycoprotein (GP) VI-specific agonist collagen-related peptide. Additionally, PKC inhibition diffuses the polarized organization of Ly-GDI in spread platelets relative to its colocalization with Rac1 and Cdc42. Together, our results suggest a role for Ly-GDI in the localized regulation of Rho GTPases in platelets and hypothesize a link between the PKC and Rho GTPase signaling systems in platelet function.
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Affiliation(s)
- Anh T P Ngo
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Marisa L D Thierheimer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon.,School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon; and
| | - Özgün Babur
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon.,Computational Biology Program, Oregon Health & Science University, Portland, Oregon
| | - Anne D Rocheleau
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Jiaqing Pang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Rachel A Rigg
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Annachiara Mitrugno
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Dan Theodorescu
- Department of Surgery, Department of Pharmacology, and Comprehensive Cancer Center University of Colorado, Aurora, Colorado
| | - Julja Burchard
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Emek Demir
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon.,Computational Biology Program, Oregon Health & Science University, Portland, Oregon
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon.,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Joseph E Aslan
- Knight Cardiovascular Institute, School of Medicine, Oregon Health & Science University, Portland, Oregon;
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37
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Zhang JX, Tan XH, Yuan Z, Li YH, Qi Y, Nan X, Qi MJ, Gao H, Lian FZ, Yang L. [Let-7 miRNA silencing promotes Kaposi's sarcoma-associated herpesvirus lytic replication via activating mitogen-activated protein kinase kinase kinase kinase 4 and its downstream factors]. Zhonghua Zhong Liu Za Zhi 2017; 38:485-91. [PMID: 27531260 DOI: 10.3760/cma.j.issn.0253-3766.2016.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To explore the effect of let-7 miRNA silencing on Kaposi's sarcoma-associated herpesvirus (KSHV) lytic replication and the underling mechanism. METHODS The pEGFP-C2-let-7 sponge vector was transfected into BCBL-1 and 293T cells with Lipofectamine 2000 to silence the expression of let-7 miRNAs. Quantitative real-time PCR (qRT-PCR) was used to quantify the expression of let-7 miRNAs, the transcriptional levels of mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), cyclooxygenase-2 (COX-2) and matrix metalloproteinase 13 (MMP-13), and the DNA copy numbers of KSHV open reading frame 50 (ORF50) and open reading frame 72 (ORF72). Western blot was used to detect the total and phosphorylated protein levels of MAP4K4, COX-2, extracellular regulated protein kinases (ERK1/2), c-Jun N-terminal kinase (JNK) and p38 MAPK. RESULTS The expression of let-7 miRNAs was dramatically decreased in the let-7 sponge transfected BCBL-1 and 293T cells compared with that in the vector-transfected cells (P<0.05 for all). The gene copy number and mRNA transcriptional level of KSHV ORF50 were significantly increased in the let-7 sponge transfected BCBL-1 cells compared with that in the vector-transfected cells (1.00±0.10 vs. 2.33±0.18 and 1.08±0.48 vs 3.22±0.27, respectively,P<0.001 for both). The gene copy number and mRNA transcriptional level of KSHV ORF72 were also significantly increased in let-7 sponge transfected BCBL-1 cells compared with those in the vector-transfected cells(1.07±0.49 vs 1.67±0.45 and 1.01±0.19 vs 1.54±0.11, respectively,P<0.05 for both). Furthermore, the mRNA transcriptional levels of MAP4K4, COX-2 and MMP-13 were significantly increased in the let-7 sponge transfected BCBL-1 cells compared with those in the vector-transfected cells (1.00±0.05 vs 5.73±0.96, 1.00±0.05 vs 2.68±0.19, 1.00±0.02 vs 2.69±0.25, respectively,P<0.001 for all). Let-7 miRNAs silencing also increased the protein expression levels of MAP4K4, COX-2 and phospho-ERK1/2, while the phospho-JNK and phospho-p38 were not changed in the BCBL-1 and 293T cells. CONCLUSIONS Let-7 silencing may activate the replication of KSHV, possibly through up-regulating MAP4K4 and its downstream molecules COX-2, MMP-13, and phosphorylation of ERK1/2, finally results in the progression of Kaposi sarcoma.
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Affiliation(s)
- J X Zhang
- School of Medicine, Shihezi University, Shihezi 832000, China
| | - X H Tan
- Department of Preventive Medicine, School of Clinical Medicine, Hangzhou Normal University, Hangzhou 310018, China
| | - Z Yuan
- Department of Preventive Medicine, School of Clinical Medicine, Hangzhou Normal University, Hangzhou 310018, China
| | - Y H Li
- School of Medicine, Shihezi University, Shihezi 832000, China
| | - Y Qi
- Department of Preventive Medicine, School of Clinical Medicine, Hangzhou Normal University, Hangzhou 310018, China
| | - X Nan
- School of Medicine, Shihezi University, Shihezi 832000, China
| | - M J Qi
- School of Medicine, Shihezi University, Shihezi 832000, China
| | - H Gao
- School of Medicine, Shihezi University, Shihezi 832000, China
| | - F Z Lian
- Department of Preventive Medicine, School of Clinical Medicine, Hangzhou Normal University, Hangzhou 310018, China
| | - L Yang
- Department of Preventive Medicine, School of Clinical Medicine, Hangzhou Normal University, Hangzhou 310018, China
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38
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Li J, Wang YY, Tian XF, Nan X, Yan T, Wang P, Fu YL, Wang GQ. HPV genotype analysis for women in Shaanxi Province of China. Genet Mol Res 2016; 15:gmr-15-gmr15047178. [PMID: 27819735 DOI: 10.4238/gmr15047178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this study was to examine the subtype distribution of human papilloma virus (HPV) in women in the Shaanxi Province of China. A DNA chip, along with polymerase chain reaction amplification and reverse dot blot technology, was adopted to analyze the HPV genotypes of 22,937 cases of cervical cell specimens. The HPV infection rate was 18.70%, wherein high-risk, low-risk, and high- and low-risk multiple infection rates were 15.75, 2.96 and 1.91%, respectively. High-risk infections accounted for 84.20% of total infections. The rate of HPV infection in women with rural residence, high school education or less, a low income, or age over 40 years was significantly higher than that in the control group (negative HPV infection women). Of the 18 detected high-risk HPV subtypes, the most common in single infections were, in the order of prevalence, HPV16, 58, 18, 52, 33, and 56. For multiple high-risk infections, the most common subtypes in the order of prevalence were HPV16, 52, 58, 18, 56, and 33. Age was a factor in the rate of infection, as the 41-50-year age group had a significantly higher risk of infection than the other groups (P < 0.05). In multiple infections, double infections were common, accounting for 77.10% of multiple infections, and triple or more infections were more common in women aged 51-60 years. In Shaanxi Province, high-risk HPV infection in women was mainly attributed to rural residence, age over 40 years, low income, and low education level.
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Affiliation(s)
- J Li
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Y Y Wang
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - X F Tian
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - X Nan
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - T Yan
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - P Wang
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Y L Fu
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - G Q Wang
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
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Chen M, Peters A, Huang T, Nan X. Ras Dimer Formation as a New Signaling Mechanism and Potential Cancer Therapeutic Target. Mini Rev Med Chem 2016; 16:391-403. [PMID: 26423697 PMCID: PMC5421135 DOI: 10.2174/1389557515666151001152212] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/31/2015] [Accepted: 09/18/2015] [Indexed: 12/12/2022]
Abstract
The K-, N-, and HRas small GTPases are key regulators of cell physiology and are frequently mutated in human cancers. Despite intensive research, previous efforts to target hyperactive Ras based on known mechanisms of Ras signaling have been met with little success. Several studies have provided compelling evidence for the existence and biological relevance of Ras dimers, establishing a new mechanism for regulating Ras activity in cells additionally to GTP-loading and membrane localization. Existing data also start to reveal how Ras proteins dimerize on the membrane. We propose a dimer model to describe Ras-mediated effector activation, which contrasts existing models of Ras signaling as a monomer or as a 5-8 membered multimer. We also discuss potential implications of this model in both basic and translational Ras biology.
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Affiliation(s)
| | | | | | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR.
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40
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Gao S, Guo J, Quan S, Nan X, Baumgard LH, Bu D. 1507 The effects of heat stress on protein metabolism in lactating Holstein cows. J Anim Sci 2016. [DOI: 10.2527/jam2016-1507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Abstract
MicroRNA (miRNA) deregulation has been previously linked to the initiation and development of breast cancer. Although miR-99a is aberrantly expressed in many types of cancers, including breast cancer, the serum miR-99a expression level in breast cancer and its clinical significance remains unknown. Blood samples were obtained from 72 patients with breast cancer and 40 healthy volunteers, and subjected to real-time polymerase chain reaction to evaluate the level of expression of serum miR-99a in the study participants. Furthermore, we investigated the association between serum miR-99a and the clinical outcome of breast cancer. Serum miR-99a expression was significantly downregulated in patients with breast cancer, compared to that in healthy controls (P < 0.01). Moreover, the serum miR-99a was correlated with various clinical parameters of breast cancer, including lymph node metastasis (P = 0.0194), distant metastasis (P = 0.0037), Ki67 intensity (P = 0.0164), TNM stage (P = 0.0096), and histological grade (P = 0.0051) of cancer. Additionally, breast cancer patients displaying lower miR-99a levels showed poorer overall survival rates (P = 0.0411). The serum miR-99a level was also found to be an independent risk factor for breast cancer (hazard ratio = 3.176, 95% confidence interval = 1.543-7.360, P = 0.023). Our data indicated that serum miR-99a expression was downregulated in breast cancer patients; moreover, this downregulation was associated with poor prognosis, suggesting that serum miR-99a could function as a tumor suppressor in breast cancer.
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Affiliation(s)
- J Li
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Z J Song
- Breast Surgery Center, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Y Y Wang
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Y Yin
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Y Liu
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - X Nan
- Tumor Research Department, Shaanxi Provincial Tumor Hospital, Xi'an, China
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42
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Bittel AM, Nickerson A, Saldivar IS, Dolman NJ, Nan X, Gibbs SL. Methodology for Quantitative Characterization of Fluorophore Photoswitching to Predict Superresolution Microscopy Image Quality. Sci Rep 2016; 6:29687. [PMID: 27412307 PMCID: PMC4944197 DOI: 10.1038/srep29687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/23/2016] [Indexed: 01/05/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) image quality and resolution strongly depend on the photoswitching properties of fluorophores used for sample labeling. Development of fluorophores with optimized photoswitching will considerably improve SMLM spatial and spectral resolution. Currently, evaluating fluorophore photoswitching requires protein-conjugation before assessment mandating specific fluorophore functionality, which is a major hurdle for systematic characterization. Herein, we validated polyvinyl alcohol (PVA) as a single-molecule environment to efficiently quantify the photoswitching properties of fluorophores and identified photoswitching properties predictive of quality SMLM images. We demonstrated that the same fluorophore photoswitching properties measured in PVA films and using antibody adsorption, a protein-conjugation environment analogous to labeled cells, were significantly correlated to microtubule width and continuity, surrogate measures of SMLM image quality. Defining PVA as a fluorophore photoswitching screening platform will facilitate SMLM fluorophore development and optimal image buffer assessment through facile and accurate photoswitching property characterization, which translates to SMLM fluorophore imaging performance.
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Affiliation(s)
- Amy M Bittel
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Andrew Nickerson
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Isaac S Saldivar
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | | | - Xiaolin Nan
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
| | - Summer L Gibbs
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
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43
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Nan X, Qin S, Yuan Z, Li Y, Zhang J, Li C, Tan X, Yan Y. Hsa-miRNA-31 regulates epithelial cell barrier function by inhibiting TNFSF15 expression. Cell Mol Biol (Noisy-le-grand) 2016; 62:104-110. [PMID: 27188743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Ulcerative colitis (UC) is characterized by epithelial barrier disruption and alterations in immune regulation but with the etiology unknown. MicroRNA-31 is the most consistent differentially expressed miRNA in ulcerative colitis tissue. The aim of this project is to study the important roles of miRNA-31 in regulation of intestinal epithelial barrier function. We found that expression of miRNA-31 is proportional to the proliferation of Caco2-BBE cells and overexpression of miRNA-31 can increase its trans-epithelial resistance (TER) by decreasing the transepithelial permeability. miRNA-31 can directly bind to the 3-UTR of TNFSF15, thereafter negatively regulating its expression in Caco2-BBE cells. BrdU and TUNEL analysis demonstrated that transfection of miRNA-31 stimulates proliferation or apoptosis-resistance. Taken together, these results revealed a novel mecha-nism underlying the regulation of epithelial barrier function by miRNA-31 during its regulation on proliferation of epithelial cells.
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Affiliation(s)
- X Nan
- Shihezi University Shihezi China
| | - S Qin
- Hangzhou Normal University School of Medicine Hangzhou China
| | - Z Yuan
- Hangzhou Normal University School of Medicine Hangzhou China
| | - Y Li
- Hangzhou Normal University School of Medicine Hangzhou China
| | - J Zhang
- Hangzhou Normal University School of Medicine Hangzhou China
| | - C Li
- Hangzhou Normal University School of Medicine Hangzhou China
| | - X Tan
- Hangzhou Normal University School of Medicine Hangzhou China
| | - Y Yan
- Hangzhou Normal University School of Medicine Hangzhou China
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44
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Li J, Wang YY, Nan X, Tian XF, Yan T, Wang P, Yin Y, Liu Y, Yuan R, Wang GQ, Fu YL. Prevalence of human papillomavirus genotypes among women with cervical lesions in the Shaanxi Province of China. Genet Mol Res 2016; 15:gmr7181. [PMID: 27051020 DOI: 10.4238/gmr.15017181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study aimed to investigate human papilloma virus (HPV) genotypes among women with cervical lesions in Shaanxi Province, China, to obtain information regarding cervical lesion prevention and treatment. The study included 4508 HPV-positive subjects; cervical swab specimens were collected and tested for HPV infection status and HPV genotypes using polymerase chain reaction and reverse dot-blot hybridization. Women positive for HPV with cervical lesions, including chronic cervicitis, cervical intraepithelial neoplasia, and cervical squamous cell carcinoma (SCC), were examined; HPV-positive women with no cervical lesions were controls. Data were pooled and weighted estimates have been presented. For women with no cervical lesions and positive for one HPV genotype, HPV 52, 16, 58, 81, 33, and 56 were the most common; for multiple-HPV genotype infection, HPV 16, 52, 6, 18, 58, and 66 were the most common. Collectively, HPV 16, 58, 52, 18, 33, and 81 were the most common in women with cervical lesions. HPV 16 comprised 26.71% of single-genotype and 15.64% of multiple-genotype infections. The proportion of HPV-16-positive cases was 29.15%, which was the highest among all HPV genotypes (P < 0.01). Single-HPV genotype infection was the most common in cervical HPV infection (77.48%); infection with two HPV genotypes comprised 72.22% of multiple-genotype infections. The proportion of single-low-risk HPV genotype infections decreased with increase in cervical lesion severity; there were no single- or multiple-low-risk genotype HPV infections in cervical SCC patients. The proportion of multiple-genotype HPV infections with at least one high-risk genotype increased with cervical lesion severity.
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Affiliation(s)
- J Li
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Y Y Wang
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - X Nan
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - X F Tian
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - T Yan
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - P Wang
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Y Yin
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Y Liu
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - R Yuan
- Basic Research Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - G Q Wang
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Y L Fu
- Gynecologic Oncology Center, Shaanxi Provincial Tumor Hospital, Xi'an Jiaotong University, Xi'an, China
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45
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Peng S, Wang K, Gu Y, Chen Y, Nan X, Xing J, Cui Q, Chen Y, Ge Q, Zhao H. TRAF3IP3, a novel autophagy up-regulated gene, is involved in marginal zone B lymphocyte development and survival. Clin Exp Immunol 2015; 182:57-68. [PMID: 26011558 DOI: 10.1111/cei.12658] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/26/2022] Open
Abstract
Tumour necrosis factor receptor-associated factor 3 (TRAF3) interacting protein 3 (TRAF3IP3; also known as T3JAM) is expressed specifically in immune organs and tissues. To investigate the impact of TRAF3IP3 on immunity, we generated Traf3ip3 knock-out (KO) mice. Interestingly, these mice exhibited a significant reduction in the number of common lymphoid progenitors (CLPs) and inhibition of B cell development in the bone marrow. Furthermore, Traf3ip3 KO mice lacked marginal zone (MZ) B cells in the spleen. Traf3ip3 KO mice also exhibited a reduced amount of serum natural antibodies and impaired T cell-independent type II (TI-II) responses to trinitrophenol (TNP)-Ficoll antigen. Additionally, our results showed that Traf3ip3 promotes autophagy via an ATG16L1-binding motif, and MZ B cells isolated from mutant mice showed a diminished level of autophagy and a high rate of apoptosis. These results suggest that TRAF3IP3 contributes to MZ B cell survival by up-regulating autophagy, thereby promoting the TI-II immune response.
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Affiliation(s)
- S Peng
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,Human Disease Genomics Center, Peking University, Beijing, China
| | - K Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Y Gu
- Human Disease Genomics Center, Peking University, Beijing, China.,Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Y Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,Human Disease Genomics Center, Peking University, Beijing, China
| | - X Nan
- Human Disease Genomics Center, Peking University, Beijing, China.,Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - J Xing
- Human Disease Genomics Center, Peking University, Beijing, China.,Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Q Cui
- Human Disease Genomics Center, Peking University, Beijing, China.,Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Y Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Q Ge
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - H Zhao
- Human Disease Genomics Center, Peking University, Beijing, China.,Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
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46
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Baker-Groberg SM, Phillips KG, Healy LD, Itakura A, Porter JE, Newton PK, Nan X, McCarty OJT. Critical behavior of subcellular density organization during neutrophil activation and migration. Cell Mol Bioeng 2015; 8:543-552. [PMID: 26640599 DOI: 10.1007/s12195-015-0400-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Physical theories of active matter continue to provide a quantitative understanding of dynamic cellular phenomena, including cell locomotion. Although various investigations of the rheology of cells have identified important viscoelastic and traction force parameters for use in these theoretical approaches, a key variable has remained elusive both in theoretical and experimental approaches: the spatiotemporal behavior of the subcellular density. The evolution of the subcellular density has been qualitatively observed for decades as it provides the source of image contrast in label-free imaging modalities (e.g., differential interference contrast, phase contrast) used to investigate cellular specimens. While these modalities directly visualize cell structure, they do not provide quantitative access to the structures being visualized. We present an established quantitative imaging approach, non-interferometric quantitative phase microscopy, to elucidate the subcellular density dynamics in neutrophils undergoing chemokinesis following uniform bacterial peptide stimulation. Through this approach, we identify a power law dependence of the neutrophil mean density on time with a critical point, suggesting a critical density is required for motility on 2D substrates. Next we elucidate a continuum law relating mean cell density, area, and total mass that is conserved during neutrophil polarization and migration. Together, our approach and quantitative findings will enable investigators to define the physics coupling cytoskeletal dynamics with subcellular density dynamics during cell migration.
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Affiliation(s)
- Sandra M Baker-Groberg
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239
| | - Kevin G Phillips
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239
| | - Laura D Healy
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239
| | - Asako Itakura
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239
| | - Juliana E Porter
- Viterbi School of Engineering, Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089
| | - Paul K Newton
- Viterbi School of Engineering, Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, CA 90089 ; Department of Mathematics, University of Southern California, Los Angeles, CA 90089 ; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239 ; Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239 ; Division of Hematology and Medical Oncology, School of Medicine, Oregon Health & Science University, Portland, OR 97239
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47
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Bittel AM, Saldivar I, Dolman N, Nickerson A, Lin LJ, Nan X, Gibbs SL. Effect of Labeling Density and Time Post Labeling on Quality of Antibody-Based Super Resolution Microscopy Images. Proc SPIE Int Soc Opt Eng 2015; 9331. [PMID: 32280156 PMCID: PMC7148159 DOI: 10.1117/12.2083209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Super resolution microscopy (SRM) has overcome the historic spatial resolution limit of light microscopy, enabling fluorescence visualization of intracellular structures and multi-protein complexes at the nanometer scale. Using single-molecule localization microscopy, the precise location of a stochastically activated population of photoswitchable fluorophores is determined during the collection of many images to form a single image with resolution of ~10-20 nm, an order of magnitude improvement over conventional microscopy. One of the key factors in achieving such resolution with single-molecule SRM is the ability to accurately locate each fluorophore while it emits photons. Image quality is also related to appropriate labeling density of the entity of interest within the sample. While ease of detection improves as entities are labeled with more fluorophores and have increased fluorescence signal, there is potential to reduce localization precision, and hence resolution, with an increased number of fluorophores that are on at the same time in the same relative vicinity. In the current work, fixed microtubules were antibody labeled using secondary antibodies prepared with a range of Alexa Fluor 647 conjugation ratios to compare image quality of microtubules to the fluorophore labeling density. It was found that image quality changed with both the fluorophore labeling density and time between completion of labeling and performance of imaging study, with certain fluorophore to protein ratios giving optimal imaging results.
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Affiliation(s)
- Amy M Bittel
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201
| | - Isaac Saldivar
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201
| | - Nicholas Dolman
- Molecular Probes Labeling and Detection Technologies, Thermo Fisher Scientific, Eugene, Oregon 97402
| | - Andrew Nickerson
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201
| | - Li-Jung Lin
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201.,Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97201.,Oregon Center for Spatial Systems Biology, Oregon Health and Science University, Portland, Oregon 97201
| | - Summer L Gibbs
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97201.,Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97201.,Oregon Center for Spatial Systems Biology, Oregon Health and Science University, Portland, Oregon 97201
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48
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Nickerson A, Huang T, Lin LJ, Nan X. Photoactivated localization microscopy with bimolecular fluorescence complementation (BiFC-PALM) for nanoscale imaging of protein-protein interactions in cells. PLoS One 2014; 9:e100589. [PMID: 24963703 PMCID: PMC4070983 DOI: 10.1371/journal.pone.0100589] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/26/2014] [Indexed: 01/07/2023] Open
Abstract
Bimolecular fluorescence complementation (BiFC) has been widely used to visualize protein-protein interactions (PPIs) in cells. Until now, however, the resolution of BiFC has been limited by the diffraction of light to ∼250 nm, much larger than the nanometer scale at which PPIs occur or are regulated. Cellular imaging at the nanometer scale has recently been realized with single molecule superresolution imaging techniques such as photoactivated localization microscopy (PALM). Here we have combined BiFC with PALM to visualize PPIs inside cells with nanometer spatial resolution and single molecule sensitivity. We demonstrated that PAmCherry1, a photoactivatable fluorescent protein commonly used for PALM, can be used as a BiFC probe when split between residues 159 and 160 into two fragments. PAmCherry1 BiFC exhibits high specificity and high efficiency even at 37°C in detecting PPIs with virtually no background from spontaneous reconstitution. Moreover, the reconstituted protein maintains the fast photoconversion, high contrast ratio, and single molecule brightness of the parent PAmCherry1, which enables selective PALM localization of PPIs with ∼18 nm spatial precision. With BiFC-PALM, we studied the interactions between the small GTPase Ras and its downstream effector Raf, and clearly observed nanoscale clustering and diffusion of individual KRas G12D/CRaf RBD (Ras-binding domain) complexes on the cell membrane. These observations provided novel insights into the regulation of Ras/Raf interaction at the molecular scale, which would be difficult with other techniques such as conventional BiFC, fluorescence co-localization or FRET.
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Affiliation(s)
- Andrew Nickerson
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Tao Huang
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Li-Jung Lin
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States of America
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49
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Bittel AM, Nickerson AK, Lin LJ, Nan X, Gibbs SL. Design and development of BODIPY-based photoswitchable fluorophores to visualize cell signaling with multispectral super resolution microscopy. ACTA ACUST UNITED AC 2014; 8950. [PMID: 32273645 PMCID: PMC7144406 DOI: 10.1117/12.2040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Super resolution microscopy (SRM) has overcome the historic spatial resolution limit of light microscopy, enabling fluorescence visualization of cellular structures and multi-protein complexes at the nanometer scale. Using single-molecule localization microscopy, the precise location of a stochastically activated population of photoswitchable fluorophores is determined during the collection of many images to form a single image with resolution of ~10-20 nm, an order of magnitude improvement over conventional microscopy. However, the spectral resolution of current SRM techniques are limited by existing fluorophores with only up to four colors imaged simultaneously, limiting the number of intracellular components that can be studied in a single sample. In the current work, a library of novel BODIPY-based fluorophores was synthesized using a solid phase synthetic platform with the goal of creating a set of photoswitchable fluorophores that can be excited by 5 distinct laser lines but emit throughout the spectral range (450-850 nm) enabling multispectral super resolution microscopy (MSSRM). The photoswitching properties of all new fluorophores were quantified for the following key photoswitching characteristics: (1) the number of photons per on cycle (2) the number of on cycles (switching events), (3) the percentage of time the fluorophore spends in the fluorescent on and off states, and (4) the susceptibility of the fluorophore to photobleaching (time of last event). To ensure the accuracy of our photoswitching measurements, our methodology to detect and quantitate the photoswitching properties of individual fluorophore molecules was validated by comparing measured photoswitching properties of three commercial dyes to published results.1 We also identified two efficient methods to positionally isolate fluorophores on coverglass for screening of the BODIPY-based library.
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Affiliation(s)
- Amy M Bittel
- Oregon Health & Science University, Department of Biomedical Engineering, 3303 SW Bond Ave., Portland, OR 97239
| | - Andrew K Nickerson
- Oregon Health & Science University, Department of Biomedical Engineering, 3303 SW Bond Ave., Portland, OR 97239
| | - Li-Jung Lin
- Oregon Health & Science University, Department of Biomedical Engineering, 3303 SW Bond Ave., Portland, OR 97239
| | - Xiaolin Nan
- Oregon Health & Science University, Department of Biomedical Engineering, 3303 SW Bond Ave., Portland, OR 97239
| | - Summer L Gibbs
- Oregon Health & Science University, Department of Biomedical Engineering, 3303 SW Bond Ave., Portland, OR 97239
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50
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Itakura A, Aslan JE, Kusanto BT, Phillips KG, Porter JE, Newton PK, Nan X, Insall RH, Chernoff J, McCarty OJT. p21-Activated kinase (PAK) regulates cytoskeletal reorganization and directional migration in human neutrophils. PLoS One 2013; 8:e73063. [PMID: 24019894 PMCID: PMC3760889 DOI: 10.1371/journal.pone.0073063] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/15/2013] [Indexed: 01/11/2023] Open
Abstract
Neutrophils serve as a first line of defense in innate immunity owing in part to their ability to rapidly migrate towards chemotactic factors derived from invading pathogens. As a migratory function, neutrophil chemotaxis is regulated by the Rho family of small GTPases. However, the mechanisms by which Rho GTPases orchestrate cytoskeletal dynamics in migrating neutrophils remain ill-defined. In this study, we characterized the role of p21-activated kinase (PAK) downstream of Rho GTPases in cytoskeletal remodeling and chemotactic processes of human neutrophils. We found that PAK activation occurred upon stimulation of neutrophils with f-Met-Leu-Phe (fMLP), and PAK accumulated at the actin-rich leading edge of stimulated neutrophils, suggesting a role for PAK in Rac-dependent actin remodeling. Treatment with the pharmacological PAK inhibitor, PF3758309, abrogated the integrity of RhoA-mediated actomyosin contractility and surface adhesion. Moreover, inhibition of PAK activity impaired neutrophil morphological polarization and directional migration under a gradient of fMLP, and was associated with dysregulated Ca(2+) signaling. These results suggest that PAK serves as an important effector of Rho-family GTPases in neutrophil cytoskeletal reorganization, and plays a key role in driving efficient directional migration of human neutrophils.
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Affiliation(s)
- Asako Itakura
- Department of Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joseph E. Aslan
- Department of Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Branden T. Kusanto
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Kevin G. Phillips
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Juliana E. Porter
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Paul K. Newton
- Department of Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Robert H. Insall
- CRUK Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Jonathan Chernoff
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Owen J. T. McCarty
- Department of Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
- Division of Hematology and Medical Oncology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
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