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Huang Z, Wu Z, Yan H. A convex-hull based method with manifold projections for detecting cell protrusions. Comput Biol Med 2024; 173:108350. [PMID: 38555705 DOI: 10.1016/j.compbiomed.2024.108350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/25/2024] [Accepted: 03/17/2024] [Indexed: 04/02/2024]
Abstract
Cell protrusions play an important role in a variety of cell physiological processes. In this paper, we propose a convex-hull based method, combined with manifold projections, to detect cell protrusions. A convex hull is generated based on the cell surface. We consider the cell surface and the boundary of its convex hull as two manifolds, which are diffeomorphic, and define a depth function based on the distance between the cell surface and its convex hull boundary. The extreme points of the depth function represent the positions of cell protrusions. To find the extreme points easily, we project the points on the cell surface onto the boundary of the convex hull and expand them in spherical polar coordinates. We conducted experiments on three types of cell protrusions. The proposed method achieved the average precision of 98.9%, 95.6%, and 94.7% on blebs, filopodia, and lamellipodia, respectively. Experiments on three datasets show that the proposed method has a robust performance.
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Affiliation(s)
- Zhaoke Huang
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region of China.
| | - Zihan Wu
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Hong Yan
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region of China
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2
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Yang S, Shi Z. Quantification of membrane geometry and protein sorting on cell membrane protrusions using fluorescence microscopy. Methods Enzymol 2024; 700:385-411. [PMID: 38971608 DOI: 10.1016/bs.mie.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Plasma membranes are flexible and can exhibit numerous shapes below the optical diffraction limit. The shape of cell periphery can either induce or be a product of local protein density changes, encoding numerous cellular functions. However, quantifying membrane curvature and the ensuing sorting of proteins in live cells remains technically demanding. Here, we demonstrate the use of simple widefield fluorescence microscopy to study the geometrical properties (i.e., radius, length, and number) of thin membrane protrusions. Importantly, the quantification of protrusion radius establishes a platform for studying the curvature preferences of membrane proteins.
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Affiliation(s)
- Shilong Yang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, United States
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, United States.
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3
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Eddington C, Schwartz JK, Titus MA. filoVision - using deep learning and tip markers to automate filopodia analysis. J Cell Sci 2024; 137:jcs261274. [PMID: 38264939 PMCID: PMC10941656 DOI: 10.1242/jcs.261274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
Filopodia are slender, actin-filled membrane projections used by various cell types for environment exploration. Analyzing filopodia often involves visualizing them using actin, filopodia tip or membrane markers. Due to the diversity of cell types that extend filopodia, from amoeboid to mammalian, it can be challenging for some to find a reliable filopodia analysis workflow suited for their cell type and preferred visualization method. The lack of an automated workflow capable of analyzing amoeboid filopodia with only a filopodia tip label prompted the development of filoVision. filoVision is an adaptable deep learning platform featuring the tools filoTips and filoSkeleton. filoTips labels filopodia tips and the cytosol using a single tip marker, allowing information extraction without actin or membrane markers. In contrast, filoSkeleton combines tip marker signals with actin labeling for a more comprehensive analysis of filopodia shafts in addition to tip protein analysis. The ZeroCostDL4Mic deep learning framework facilitates accessibility and customization for different datasets and cell types, making filoVision a flexible tool for automated analysis of tip-marked filopodia across various cell types and user data.
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Affiliation(s)
- Casey Eddington
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jessica K. Schwartz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret A. Titus
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Graduate Program in Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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4
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Desroches S, Harris AR. Quantifying cytoskeletal organization from optical microscopy data. Front Cell Dev Biol 2024; 11:1327994. [PMID: 38234685 PMCID: PMC10792062 DOI: 10.3389/fcell.2023.1327994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024] Open
Abstract
The actin cytoskeleton plays a pivotal role in a broad range of physiological processes including directing cell shape and subcellular organization, determining cell mechanical properties, and sensing and transducing mechanical forces. The versatility of the actin cytoskeleton arises from the ability of actin filaments to assemble into higher order structures through their interaction with a vast set of regulatory proteins. Actin filaments assemble into bundles, meshes, and networks, where different combinations of these structures fulfill specific functional roles. Analyzing the organization and abundance of different actin structures from optical microscopy data provides a valuable metric for assessing cell physiological function and changes associated with disease. However, quantitative measurements of the size, abundance, orientation, and distribution of different types of actin structure remains challenging both from an experimental and image analysis perspective. In this review, we summarize image analysis methods for extracting quantitative values that can be used for characterizing the organization of actin structures and provide selected examples. We summarize the potential sample types and metric reported with different approaches as a guide for selecting an image analysis strategy.
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Affiliation(s)
- Sarah Desroches
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
- Ottawa-Carleton Institute for Biomedical Engineering Graduate Program, Ottawa, ON, Canada
| | - Andrew R. Harris
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
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Li W, Chung WL, Kozlov MM, Medalia O, Geiger B, Bershadsky AD. Chiral growth of adherent filopodia. Biophys J 2023; 122:3704-3721. [PMID: 37301982 PMCID: PMC10541518 DOI: 10.1016/j.bpj.2023.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/03/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023] Open
Abstract
Adherent filopodia are elongated finger-like membrane protrusions, extending from the edges of diverse cell types and participating in cell adhesion, spreading, migration, and environmental sensing. The formation and elongation of filopodia are driven by the polymerization of parallel actin filaments, comprising the filopodia cytoskeletal core. Here, we report that adherent filopodia, formed during the spreading of cultured cells on galectin-8-coated substrates, tend to change the direction of their extension in a chiral fashion, acquiring a left-bent shape. Cryoelectron tomography examination indicated that turning of the filopodia tip to the left is accompanied by the displacement of the actin core bundle to the right of the filopodia midline. Reduction of the adhesion to galectin-8 by treatment with thiodigalactoside abolished this filopodia chirality. By modulating the expression of a variety of actin-associated filopodia proteins, we identified myosin-X and formin DAAM1 as major filopodia chirality promoting factors. Formin mDia1, actin filament elongation factor VASP, and actin filament cross-linker fascin were also shown to be involved. Thus, the simple actin cytoskeleton of filopodia, together with a small number of associated proteins are sufficient to drive a complex navigation process, manifested by the development of left-right asymmetry in these cellular protrusions.
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Affiliation(s)
- Wenhong Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Wen-Lu Chung
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Geiger
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Alexander D Bershadsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
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Membrane curvature governs the distribution of Piezo1 in live cells. Nat Commun 2022; 13:7467. [PMID: 36463216 PMCID: PMC9719557 DOI: 10.1038/s41467-022-35034-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Piezo1 is a bona fide mechanosensitive ion channel ubiquitously expressed in mammalian cells. The distribution of Piezo1 within a cell is essential for various biological processes including cytokinesis, cell migration, and wound healing. However, the underlying principles that guide the subcellular distribution of Piezo1 remain largely unexplored. Here, we demonstrate that membrane curvature serves as a key regulator of the spatial distribution of Piezo1 in the plasma membrane of living cells. Piezo1 depletes from highly curved membrane protrusions such as filopodia and enriches to nanoscale membrane invaginations. Quantification of the curvature-dependent sorting of Piezo1 directly reveals the in situ nano-geometry of the Piezo1-membrane complex. Piezo1 density on filopodia increases upon activation, independent of calcium, suggesting flattening of the channel upon opening. Consequently, the expression of Piezo1 inhibits filopodia formation, an effect that diminishes with channel activation.
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Zhang ZD, Li RR, Chen JY, Huang HX, Cheng YW, Xu LY, Li EM. The post-translational modification of Fascin: impact on cell biology and its associations with inhibiting tumor metastasis. Amino Acids 2022; 54:1541-1552. [PMID: 35939077 DOI: 10.1007/s00726-022-03193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023]
Abstract
The post-translational modifications (PTMs), which are crucial in the regulation of protein functions, have great potential as biomarkers of cancer status. Fascin (Fascin actin-bundling protein 1, FSCN1), a key protein in the formation of filopodia that is structurally based on actin filaments (F-actin), is significantly associated with tumor invasion and metastasis. Studies have revealed various regulatory mechanisms of human Fascin, including PTMs. Although a number of Fascin PTM sites have been identified, their exact functions and clinical significance are much less explored. This review explores studies on the functions of Fascin and briefly discusses the regulatory mechanisms of Fascin. Next, to review the role of Fascin PTMs in cell biology and their associations with metastatic disease, we discuss the advances in the characterization of Fascin PTMs, including phosphorylation, ubiquitination, sumoylation, and acetylation, and the main regulatory mechanisms are discussed. Fascin PTMs may be potential targets for therapy for metastatic disease.
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Affiliation(s)
- Zhi-Da Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
| | - Rong-Rong Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
| | - Jia-You Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
| | - Hong-Xin Huang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
| | - Yin-Wei Cheng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, China
- Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, China
- Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, Guangdong, China
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TNTdetect.AI: A Deep Learning Model for Automated Detection and Counting of Tunneling Nanotubes in Microscopy Images. Cancers (Basel) 2022; 14:cancers14194958. [PMID: 36230881 PMCID: PMC9562025 DOI: 10.3390/cancers14194958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Microscopy is central to many areas of biomedical science research, including cancer research, and is critical for understanding basic pathophysiology, mechanisms of action, and treatment response. However, analysis of the numerous images generated from microscopy readouts is usually performed manually, a process that is tedious and time-consuming. Moreover, manual analysis of microscopy images may limit both accuracy and reproducibility. Here, we used an artificial intelligence approach to analyze tunnelling nanotubes (TNTs), a feature of cancer cells that may contribute to their aggressiveness, but which are hard to identify and count. Our approach labeled and detected TNTs and cancer cells from microscopy images and generated TNT-to-cell ratios comparable to those of human experts. Continued refinement of this process will provide a new approach to the analysis of TNTs. Additionally, this approach has the potential to enhance drug screens intended to assess therapeutic efficacy of experimental agents and to reproducibly assess TNTs as a potential biomarker of response to cancer therapy. Abstract Background: Tunneling nanotubes (TNTs) are cellular structures connecting cell membranes and mediating intercellular communication. TNTs are manually identified and counted by a trained investigator; however, this process is time-intensive. We therefore sought to develop an automated approach for quantitative analysis of TNTs. Methods: We used a convolutional neural network (U-Net) deep learning model to segment phase contrast microscopy images of both cancer and non-cancer cells. Our method was composed of preprocessing and model development. We developed a new preprocessing method to label TNTs on a pixel-wise basis. Two sequential models were employed to detect TNTs. First, we identified the regions of images with TNTs by implementing a classification algorithm. Second, we fed parts of the image classified as TNT-containing into a modified U-Net model to estimate TNTs on a pixel-wise basis. Results: The algorithm detected 49.9% of human expert-identified TNTs, counted TNTs, and calculated the number of TNTs per cell, or TNT-to-cell ratio (TCR); it detected TNTs that were not originally detected by the experts. The model had 0.41 precision, 0.26 recall, and 0.32 f-1 score on a test dataset. The predicted and true TCRs were not significantly different across the training and test datasets (p = 0.78). Conclusions: Our automated approach labeled and detected TNTs and cells imaged in culture, resulting in comparable TCRs to those determined by human experts. Future studies will aim to improve on the accuracy, precision, and recall of the algorithm.
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Yang HI, Huang PY, Chan SC, Tung CW, Cheng PH, Chen CM, Yang SH. miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in Huntington's disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:286-299. [PMID: 36320323 PMCID: PMC9593307 DOI: 10.1016/j.omtn.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022]
Abstract
Huntington's disease (HD) is one of the inheritable neurodegenerative diseases, and these diseases share several similar pathological characteristics, such as abnormal neuronal morphology. miR-196a is a potential target to provide neuroprotective functions, and has been reported to enhance polymerization of neuronal microtubules in HD. While microtubules and microfilaments are two important components of the neuronal cytoskeleton, whether miR-196a improves neuronal microfilaments is still unknown. Here, we identify insulin-like growth factor 2 mRNA binding protein 3 (IMP3), and show that miR-196a directly suppresses IMP3 to increase neurite outgrowth in neurons. In addition, IMP3 disturbs neurite outgrowth in vitro and in vivo, and worsens the microfilament polymerization. Moreover, insulin-like growth factor-II (IGF2) is identified as the downstream target of IMP3, and miR-196a downregulates IMP3 to upregulate IGF2, which increases microfilamental filopodia numbers and activates Cdc42 to increase neurite outgrowth. Besides, miR-196a increases neurite outgrowth through IGF2 in different HD models. Finally, higher expression of IMP3 and lower expression IGF2 are observed in HD transgenic mice and patients, and increase the formation of aggregates in the HD cell model. Taken together, miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in HD, supporting the neuroprotective functions of miR-196a through neuronal cytoskeleton in HD.
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Affiliation(s)
- Han-In Yang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pin-Yu Huang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Siew Chin Chan
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chih-Wei Tung
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pei-Hsun Cheng
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chuan-Mu Chen
- Department of Life Sciences, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shang-Hsun Yang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan,Corresponding author Shang-Hsun Yang, Ph.D., Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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Huang C, Fukushi K, Wang Z, Nihey F, Kajitani H, Nakahara K. Method for Estimating Temporal Gait Parameters Concerning Bilateral Lower Limbs of Healthy Subjects Using a Single In-Shoe Motion Sensor through a Gait Event Detection Approach. SENSORS 2022; 22:s22010351. [PMID: 35009893 PMCID: PMC8749800 DOI: 10.3390/s22010351] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/22/2021] [Accepted: 01/01/2022] [Indexed: 12/20/2022]
Abstract
To expand the potential use of in-shoe motion sensors (IMSs) in daily healthcare or activity monitoring applications for healthy subjects, we propose a real-time temporal estimation method for gait parameters concerning bilateral lower limbs (GPBLLs) that uses a single IMS and is based on a gait event detection approach. To validate the established methods, data from 26 participants recorded by an IMS and a reference 3D motion analysis system were compared. The agreement between the proposed method and the reference system was evaluated by the intraclass correlation coefficient (ICC). The results showed that, by averaging over five continuous effective strides, all time parameters achieved precisions of no more than 30 ms and agreement at the “excellent” level, and the symmetry indexes of the stride time and stance phase time achieved precisions of 1.0% and 3.0%, respectively, and agreement at the “good” level. These results suggest our method is effective and shows promise for wide use in many daily healthcare or activity monitoring applications for healthy subjects.
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Sasaki S, Takahashi R, Luo Y, Chujo K, Sera T, Kudo S. Spatiotemporal distribution of PKCα, Cdc42, and Rac1 before directed cell migration. Biochem Biophys Res Commun 2021; 584:26-31. [PMID: 34753065 DOI: 10.1016/j.bbrc.2021.10.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 11/19/2022]
Abstract
Cdc42 is a key factor in directed cell migration and accumulates at the leading edge of migrating cells. However, what kind of proteins control Cdc42 and when is unclear. After mechanical wounding, protein kinase C α (PKCα), a conventional PKC isozyme, begins to accumulate at the edges of cells adjacent to the wounded cells (WCs). In this study, we hypothesized that PKCα may be implicated in directed cell migration at an early stage before Cdc42 controls the migration. We focused on the spatiotemporal distribution of PKCα, Cdc42, and Rac1 before cell migration. After wounding, at the edges of cells adjacent to the WCs, PKCα accumulation, Cdc42 accumulation, Rac1 accumulation, and filopodia formation occurred in that order. The PKCα inhibitor suppressed Cdc42 accumulation at the cell edges. These results suggest that inhibition of PKCα activity inhibits cell migration. In addition, it is not Cdc42 but PKCα that may decide the direction of cell migration.
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Affiliation(s)
- Saori Sasaki
- Department of Mechanical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
| | - Ryu Takahashi
- Department of Mechanical Engineering, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Yangfeng Luo
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Kengo Chujo
- Department of Mechanical Engineering, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Toshihiro Sera
- Department of Mechanical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
| | - Susumu Kudo
- Department of Mechanical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan.
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AGO2 localizes to cytokinetic protrusions in a p38-dependent manner and is needed for accurate cell division. Commun Biol 2021; 4:726. [PMID: 34117353 PMCID: PMC8196063 DOI: 10.1038/s42003-021-02130-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Argonaute 2 (AGO2) is an indispensable component of the RNA-induced silencing complex, operating at the translational or posttranscriptional level. It is compartmentalized into structures such as GW- and P-bodies, stress granules and adherens junctions as well as the midbody. Here we show using immunofluorescence, image and bioinformatic analysis and cytogenetics that AGO2 also resides in membrane protrusions such as open- and close-ended tubes. The latter are cytokinetic bridges where AGO2 colocalizes at the midbody arms with cytoskeletal components such as α-Τubulin and Aurora B, and various kinases. AGO2, phosphorylated on serine 387, is located together with Dicer at the midbody ring in a manner dependent on p38 MAPK activity. We further show that AGO2 is stress sensitive and important to ensure the proper chromosome segregation and cytokinetic fidelity. We suggest that AGO2 is part of a regulatory mechanism triggered by cytokinetic stress to generate the appropriate micro-environment for local transcript homeostasis. Pantazopoulou et al. find that AGO2 resides in open-ended tunneling nanotubes and close-ended cytokinetic bridges. At the latter location, AGO2 colocalizes with cell division components and the authors show that AGO2 depletion impairs cell division fidelity.
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Li W, Sancho A, Chung WL, Vinik Y, Groll J, Zick Y, Medalia O, Bershadsky AD, Geiger B. Differential cellular responses to adhesive interactions with galectin-8- and fibronectin-coated substrates. J Cell Sci 2021; 134:jcs252221. [PMID: 33722978 PMCID: PMC8106957 DOI: 10.1242/jcs.252221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 03/03/2021] [Indexed: 12/16/2022] Open
Abstract
The mechanisms underlying the cellular response to extracellular matrices (ECMs) that consist of multiple adhesive ligands are still poorly understood. Here, we address this topic by monitoring specific cellular responses to two different extracellular adhesion molecules - the main integrin ligand fibronectin and galectin-8, a lectin that binds β-galactoside residues - as well as to mixtures of the two proteins. Compared with cell spreading on fibronectin, cell spreading on galectin-8-coated substrates resulted in increased projected cell area, more-pronounced extension of filopodia and, yet, the inability to form focal adhesions and stress fibers. These differences can be partially reversed by experimental manipulations of small G-proteins of the Rho family and their downstream targets, such as formins, the Arp2/3 complex and Rho kinase. We also show that the physical adhesion of cells to galectin-8 was stronger than adhesion to fibronectin. Notably, galectin-8 and fibronectin differently regulate cell spreading and focal adhesion formation, yet act synergistically to upregulate the number and length of filopodia. The physiological significance of the coherent cellular response to a molecularly complex matrix is discussed. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Wenhong Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ana Sancho
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, Würzburg, 97070, Germany
- Department of Automatic Control and Systems Engineering, University of the Basque Country UPV/EHU, San Sebastian, 20018, Spain
| | - Wen-Lu Chung
- Department of Biochemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Yaron Vinik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jürgen Groll
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, Würzburg, 97070, Germany
| | - Yehiel Zick
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Alexander D. Bershadsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Benjamin Geiger
- Department of Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
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14
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Vemula SK, Malci A, Junge L, Lehmann AC, Rama R, Hradsky J, Matute RA, Weber A, Prigge M, Naumann M, Kreutz MR, Seidenbecher CI, Gundelfinger ED, Herrera-Molina R. The Interaction of TRAF6 With Neuroplastin Promotes Spinogenesis During Early Neuronal Development. Front Cell Dev Biol 2020; 8:579513. [PMID: 33363141 PMCID: PMC7755605 DOI: 10.3389/fcell.2020.579513] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/11/2020] [Indexed: 11/22/2022] Open
Abstract
Correct brain wiring depends on reliable synapse formation. Nevertheless, signaling codes promoting synaptogenesis are not fully understood. Here, we report a spinogenic mechanism that operates during neuronal development and is based on the interaction of tumor necrosis factor receptor-associated factor 6 (TRAF6) with the synaptic cell adhesion molecule neuroplastin. The interaction between these proteins was predicted in silico and verified by co-immunoprecipitation in extracts from rat brain and co-transfected HEK cells. Binding assays show physical interaction between neuroplastin’s C-terminus and the TRAF-C domain of TRAF6 with a Kd value of 88 μM. As the two proteins co-localize in primordial dendritic protrusions, we used young cultures of rat and mouse as well as neuroplastin-deficient mouse neurons and showed with mutagenesis, knock-down, and pharmacological blockade that TRAF6 is required by neuroplastin to promote early spinogenesis during in vitro days 6-9, but not later. Time-framed TRAF6 blockade during days 6–9 reduced mEPSC amplitude, number of postsynaptic sites, synapse density and neuronal activity as neurons mature. Our data unravel a new molecular liaison that may emerge during a specific window of the neuronal development to determine excitatory synapse density in the rodent brain.
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Affiliation(s)
- Sampath Kumar Vemula
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Ayse Malci
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Lennart Junge
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Anne-Christin Lehmann
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Ramya Rama
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Johannes Hradsky
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Ricardo A Matute
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.,Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O'Higgins, Santiago, Chile
| | - André Weber
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Matthias Prigge
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Michael R Kreutz
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Constanze I Seidenbecher
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Eckart D Gundelfinger
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany.,Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Rodrigo Herrera-Molina
- Laboratory of Synaptic Signaling, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O'Higgins, Santiago, Chile.,Center for Behavioral Brain Sciences, Magdeburg, Germany
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15
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Kyykallio H, Oikari S, Bueno Álvez M, Gallardo Dodd CJ, Capra J, Rilla K. The Density and Length of Filopodia Associate with the Activity of Hyaluronan Synthesis in Tumor Cells. Cancers (Basel) 2020; 12:cancers12071908. [PMID: 32679746 PMCID: PMC7409202 DOI: 10.3390/cancers12071908] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
Filopodia are multifunctional finger-like plasma membrane protrusions with bundles of actin filaments that exist in virtually all cell types. It has been known for some time that hyaluronan synthesis activity induces filopodial growth. However, because of technical challenges in the studies of these slender and fragile structures, no quantitative analyses have been performed so far to indicate their association with hyaluronan synthesis. In this work we comprehensively address the direct quantification of filopodial traits, covering for the first time length and density measurements in a series of human cancer cell lines with variable levels of hyaluronan synthesis. The synthesis and plasma membrane binding of hyaluronan were manipulated with hyaluronan synthase 3 (HAS3) and hyaluronan receptor CD44 overexpression, and treatments with mannose, 4-methylumbelliferone (4-MU), and glucosamine. The results of this work show that the growth of filopodia was associated with the levels of hyaluronan synthesis but was not dependent on CD44 expression. The results confirm the hypothesis that abundance and length of filopodia in cancer cells is associated with the activity of hyaluronan synthesis.
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16
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Zhu S, Eldeeb MA, Pang SW. 3D nanoplasmonic biosensor for detection of filopodia in cells. LAB ON A CHIP 2020; 20:2188-2196. [PMID: 32421116 DOI: 10.1039/d0lc00173b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filopodia are thin finger-like protrusions from cells and they are hard to detect using electrical, mechanical, or optical sensors because of their nanometer scale features. Besides, the signals from filopodia and the cell membrane are often mixed together which makes the detection of filopodia challenging. Here, a 3D nanoplasmonic biosensor with microposts is proposed to overcome these limitations. By using suitable chemical coating and physical dimensions, the signals from filopodia and the cell membrane were separated by having the microposts keep the cell membrane from making contact with the nanoplasmonic biosensor. The filopodia were detected by the 3D asymmetrical nanopillars with sharp Fano resonance. The sensitivity and figure of merit of the nanoplasmonic biosensor were 650 nm per refractive index unit and 28.3, respectively. A large peak shift of 6 nm was observed for the detection of MC3T3 osteoblastic cell filopodia at a concentration of 1300 cells per mm2. To the best of our knowledge, this is the first demonstration of filopodia detection using nanoplasmonic biosensors, where microposts were used to separate the cell membrane from filopodia and the 3D nanoplasmonic biosensors were used to monitor filopodia on the nanometer scale. These combined 3D micro- and nano-structures allow filopodia to be detected using different sensors without interference from the cell membrane.
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Affiliation(s)
- Shuyan Zhu
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong.
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17
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Mousavi SI, Pearce KM, Scarlata S, Tüzel E. Re-track: Software to analyze the retraction and protrusion velocities of neurites, filopodia and other structures. Anal Biochem 2020; 596:113626. [PMID: 32081618 PMCID: PMC9195366 DOI: 10.1016/j.ab.2020.113626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/23/2022]
Abstract
We have developed new software, Re-track, that will quantify the rates of retraction and protrusion of structures emanating from the central core of a cell, such as neurites or filopodia. Re-Track, uses time-lapse images of cells in TIFF format and calculates the velocity of retraction or protrusion of a selected structure. The software uses a flexible moving boundary and has the ability to correct this boundary throughout analysis. Re-Track is fast, platform independent, and user friendly, and it can be used to follow biological events such as changes in neuronal connections, tip-growing cells such as moss, adaptive migration of cells, and similar behavior in non-biological systems.
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Affiliation(s)
- Sayed Iman Mousavi
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Katherine M Pearce
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Suzanne Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA.
| | - Erkan Tüzel
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA.
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18
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Breuer A, Lauritsen L, Bertseva E, Vonkova I, Stamou D. Quantitative investigation of negative membrane curvature sensing and generation by I-BARs in filopodia of living cells. SOFT MATTER 2019; 15:9829-9839. [PMID: 31728468 DOI: 10.1039/c9sm01185d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane curvature has recently been recognized as an active regulator of cellular function, with several protein families identified as sensors and generators of membrane curvature. Amongst them, the inverse Bin/Amphiphysin/Rvs (I-BAR) domain family has been implicated in the sensing and generation of membrane structures with negative membrane curvature e.g. filopodia or dendritic spines. However, to date, quantitative biophysical investigations of I-BAR domains have mostly taken place in reconstitution. Here, we use fluorescence microscopy to quantitatively investigate membrane curvature sensing and generation by I-BARs in filopodia of living cells. As a model system, we selected two prototypic members of the I-BAR family, the insulin receptor substrate p53 and missing-in-metastasis. Our data demonstrated how I-BARs sense negative membrane curvature in the complex environment of live cells by revealing a dependence on membrane curvature for both their binding affinity to membranes and their saturation density. The non-monotonic dependence of protein sorting with negative membrane curvature allowed us to apply previously developed thermodynamic models to provide estimates of the effective intrinsic curvature and bending rigidity of the two I-BARs bound at the plasma membrane. Our results agree with studies performed on the insulin receptor substrate p53 in reconstitution. To quantitate membrane curvature generation by I-BARs we measured how their overexpression reduces the peak and the width of the size distribution of filopodia, resulting in filopodia populations with smaller and more uniform diameters. Our findings provide a quantitative biophysical insight in the ability of I-BARs to sense and generate negative membrane curvature in the crowded environment of living cells.
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Affiliation(s)
- Artù Breuer
- Bionanotechnology and Nanomedicine Laboratory, Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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19
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Bagonis MM, Fusco L, Pertz O, Danuser G. Automated profiling of growth cone heterogeneity defines relations between morphology and motility. J Cell Biol 2019; 218:350-379. [PMID: 30523041 PMCID: PMC6314545 DOI: 10.1083/jcb.201711023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 09/26/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022] Open
Abstract
Growth cones are complex, motile structures at the tip of an outgrowing neurite. They often exhibit a high density of filopodia (thin actin bundles), which complicates the unbiased quantification of their morphologies by software. Contemporary image processing methods require extensive tuning of segmentation parameters, require significant manual curation, and are often not sufficiently adaptable to capture morphology changes associated with switches in regulatory signals. To overcome these limitations, we developed Growth Cone Analyzer (GCA). GCA is designed to quantify growth cone morphodynamics from time-lapse sequences imaged both in vitro and in vivo, but is sufficiently generic that it may be applied to nonneuronal cellular structures. We demonstrate the adaptability of GCA through the analysis of growth cone morphological variation and its relation to motility in both an unperturbed system and in the context of modified Rho GTPase signaling. We find that perturbations inducing similar changes in neurite length exhibit underappreciated phenotypic nuance at the scale of the growth cone.
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Affiliation(s)
- Maria M Bagonis
- Departments of Bioinformatics and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Ludovico Fusco
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Olivier Pertz
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Gaudenz Danuser
- Departments of Bioinformatics and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Cell Biology, Harvard Medical School, Boston, MA
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20
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Abstract
Filopodia are fingerlike membrane protrusions that are extended by cells in vitro and in vivo. Due to important roles in sensing the extracellular microenvironment, filopodia and filopodia-like protrusions have been implicated in numerous biological processes including epithelial sheet zippering in development and wound healing and in cancer progression. Recently, there has been an explosion in the number of software available to analyze specific features of cell protrusions with the aim of gaining mechanistic insights into the action of filopodia and filopodia-like structures. In this methods chapter, we highlight an open-access software called FiloQuant that has been developed to specifically quantify the length, density, and dynamics of filopodia and filopodia-like structures from in vitro and in vivo generated samples. We provide step-by-step protocols on (i) how to install FiloQuant in the ImageJ platform (Fiji), (ii) how to quantify filopodia and filopodia-like protrusions from single images using FiloQuant, and (iii) how to track filopodial protrusions from live-cell imaging experiments using FiloQuant and TrackMate.
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Affiliation(s)
- Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Hellyeh Hamidi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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21
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Martínez-Vieyra I, Pacheco-Tapia G, Reyes-López C, Méndez-Méndez JV, Cerecedo D. Role of α-Dystrobrevin in the differentiation process of HL-60 cells. Exp Cell Res 2018; 370:591-600. [PMID: 30026031 DOI: 10.1016/j.yexcr.2018.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/28/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
The α-Dystrobrevin gene encodes at least five different protein isoforms, expressed in diverse tissues. The α-Dystrobrevin-1 isoform (α-Db-1) is a member of the cytoplasmic dystrophin-associated protein complex, which has a C-terminal extension comprising at least three tyrosine residues susceptible to phosphorylation in vivo. We previously described α-Db in stem-progenitor cells and blood neutrophils as playing a scaffolding role and, in association with kinesin and microtubules, α-Db promotes platelet-granule trafficking. Additionally, the microtubules must establish a balanced interaction with the lamina A/C network for appropriate nuclear morphology. Considering that the most outstanding feature during neutrophil differentiation is nuclei lobulation, we hypothesized that α-Db might possess a pivotal function during the neutrophil differentiation process. Western Blot (WB) and confocal microscope assays evidenced a differential pattern expression and a subcellular redistribution of α-Db in neutrophils derived from HL-60 cells. At the end of the differentiation process, we detected an important diminution in the expression of tubulin, kinesin, and α-Db-1. Knockdown of α-Db prevented nuclei lobulation, increased Lamin A/C and syne1 expression and augmented the roughness of derived neutrophil membrane and disturbed filopodia assembly. Our results suggest that HL-60 cells undergo extensive cytoskeletal reorganization including α-Db in order to possess lobulated nuclei when they further differentiate into neutrophils.
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Affiliation(s)
- Ivette Martínez-Vieyra
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Giselle Pacheco-Tapia
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - César Reyes-López
- Laboratorio de Bioquímica Estructural, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Juan Vicente Méndez-Méndez
- Centro de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Doris Cerecedo
- Laboratorio de Hematobiología, Escuela Nacional de Medicina y Homeopatía (ENMH), Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
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22
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Zhou XL, Guo X, Song YP, Zhu CY, Zou W. The LPI/GPR55 axis enhances human breast cancer cell migration via HBXIP and p-MLC signaling. Acta Pharmacol Sin 2018; 39:459-471. [PMID: 29188802 DOI: 10.1038/aps.2017.157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/09/2017] [Indexed: 01/06/2023] Open
Abstract
The G protein-coupled receptor 55 (GPR55) is expressed in multiple tissues, and has been implicated in cancer pathogenesis, but little is known about its role in the migratory behavior of cancer cells, particularly breast cancer cells. In this study we first showed that GPR55 expression levels in 38 metastatic lymph nodes of breast cancer patients were profoundly elevated, and were positively associated in human breast cancer cells with their migratory ability. Moreover, the plasma levels of GPR55 endogenous agonist L-a-lysophosphatidylinositol (LPI) were significantly increased in breast cancer patients compared with healthy individuals. In human breast cancer LM-MCF-7 and MDA-MB-231 cells, treatment with LPI (2.5 μmol/L) significantly increased filopodia formation and resulted in cell migration, which could be blocked either by the GPR55 antagonist CID16020046 or by siRNA-mediated GPR55 knockdown. Furthermore, dual-luciferase report gene assays showed that GPR55 upregulated HBXIP at the promoter; GPR55 expression levels were positively correlated with HBXIP expression levels in breast cancer tissues and 8 breast cancer cell lines. We also showed that the LPI/GPR55 axis promoted the migration of breast cancer cells via two mutually exclusive pathways - the HBXIP/p-ERK1/2/Capn4 and MLCK/MLC signaling pathways. In xenograft nude mouse model, loss of GPR55 mainly affected breast cancer cell metastasis and the formation of metastatic foci. Thus, GPR55 is involved in the migratory behavior of human breast cancer cells and could serve as a pharmacological target for preventing metastasis.
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23
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Urbančič V, Butler R, Richier B, Peter M, Mason J, Livesey FJ, Holt CE, Gallop JL. Filopodyan: An open-source pipeline for the analysis of filopodia. J Cell Biol 2017; 216:3405-3422. [PMID: 28760769 PMCID: PMC5626553 DOI: 10.1083/jcb.201705113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/28/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023] Open
Abstract
Filopodia have important sensory and mechanical roles in motile cells. The recruitment of actin regulators, such as ENA/VASP proteins, to sites of protrusion underlies diverse molecular mechanisms of filopodia formation and extension. We developed Filopodyan (filopodia dynamics analysis) in Fiji and R to measure fluorescence in filopodia and at their tips and bases concurrently with their morphological and dynamic properties. Filopodyan supports high-throughput phenotype characterization as well as detailed interactive editing of filopodia reconstructions through an intuitive graphical user interface. Our highly customizable pipeline is widely applicable, capable of detecting filopodia in four different cell types in vitro and in vivo. We use Filopodyan to quantify the recruitment of ENA and VASP preceding filopodia formation in neuronal growth cones, and uncover a molecular heterogeneity whereby different filopodia display markedly different responses to changes in the accumulation of ENA and VASP fluorescence in their tips over time.
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Affiliation(s)
- Vasja Urbančič
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Richard Butler
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
| | - Benjamin Richier
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Manuel Peter
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Julia Mason
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Frederick J Livesey
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Christine E Holt
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, England, UK
| | - Jennifer L Gallop
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, England, UK
- Department of Biochemistry, University of Cambridge, Cambridge, England, UK
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24
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Jacquemet G, Paatero I, Carisey AF, Padzik A, Orange JS, Hamidi H, Ivaska J. FiloQuant reveals increased filopodia density during breast cancer progression. J Cell Biol 2017; 216:3387-3403. [PMID: 28765364 PMCID: PMC5626550 DOI: 10.1083/jcb.201704045] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
Defective filopodia formation is linked to pathologies such as cancer, wherein actively protruding filopodia, at the invasive front, accompany cancer cell dissemination. Despite wide biological significance, delineating filopodia function in complex systems remains challenging and is particularly hindered by lack of compatible methods to quantify filopodia properties. Here, we present FiloQuant, a freely available ImageJ plugin, to detect filopodia-like protrusions in both fixed- and live-cell microscopy data. We demonstrate that FiloQuant can extract quantifiable information, including protrusion dynamics, density, and length, from multiple cell types and in a range of microenvironments. In cellular models of breast ductal carcinoma in situ, we reveal a link between filopodia formation at the cell-matrix interface, in collectively invading cells and 3D tumor spheroids, and the in vitro invasive capacity of the carcinoma. Finally, using intravital microscopy, we observe that tumor spheroids display filopodia in vivo, supporting a potential role for these protrusions during tumorigenesis.
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Affiliation(s)
- Guillaume Jacquemet
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ilkka Paatero
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Alexandre F Carisey
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Artur Padzik
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jordan S Orange
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Hellyeh Hamidi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Biochemistry, University of Turku, Turku, Finland
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25
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Moriconi C, Palmieri V, Di Santo R, Tornillo G, Papi M, Pilkington G, De Spirito M, Gumbleton M. INSIDIA: A FIJI Macro Delivering High-Throughput and High-Content Spheroid Invasion Analysis. Biotechnol J 2017; 12. [PMID: 28786556 DOI: 10.1002/biot.201700140] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/05/2017] [Indexed: 01/18/2023]
Abstract
Time-series image capture of in vitro 3D spheroidal cancer models embedded within an extracellular matrix affords examination of spheroid growth and cancer cell invasion. However, a customizable, comprehensive and open source solution for the quantitative analysis of such spheroid images is lacking. Here, the authors describe INSIDIA (INvasion SpheroID ImageJ Analysis), an open-source macro implemented as a customizable software algorithm running on the FIJI platform, that enables high-throughput high-content quantitative analysis of spheroid images (both bright-field gray and fluorescent images) with the output of a range of parameters defining the spheroid "tumor" core and its invasive characteristics.
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Affiliation(s)
- Chiara Moriconi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Valentina Palmieri
- Physics Institute, Catholic University of Sacred Hearth, Rome, Italy.,Institute for Complex Systems, National Research Council (CNR), Rome, Italy
| | - Riccardo Di Santo
- Physics Institute, Catholic University of Sacred Hearth, Rome, Italy
| | - Giusy Tornillo
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
| | - Massimiliano Papi
- Physics Institute, Catholic University of Sacred Hearth, Rome, Italy.,Institute for Complex Systems, National Research Council (CNR), Rome, Italy
| | - Geoff Pilkington
- Institute of Biomedical and Biomolecular Science, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Marco De Spirito
- Physics Institute, Catholic University of Sacred Hearth, Rome, Italy
| | - Mark Gumbleton
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
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26
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Palmieri V, Bozzi M, Signorino G, Papi M, De Spirito M, Brancaccio A, Maulucci G, Sciandra F. α-Dystroglycan hypoglycosylation affects cell migration by influencing β-dystroglycan membrane clustering and filopodia length: A multiscale confocal microscopy analysis. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2182-2191. [DOI: 10.1016/j.bbadis.2017.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 05/05/2017] [Accepted: 05/28/2017] [Indexed: 12/26/2022]
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27
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Schenk LK, Möller-Kerutt A, Klosowski R, Wolters D, Schaffner-Reckinger E, Weide T, Pavenstädt H, Vollenbröker B. Angiotensin II regulates phosphorylation of actin-associated proteins in human podocytes. FASEB J 2017; 31:5019-5035. [PMID: 28768720 DOI: 10.1096/fj.201700142r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/17/2017] [Indexed: 02/02/2023]
Abstract
Within the kidney, angiotensin II (AngII) targets different cell types in the vasculature, tubuli, and glomeruli. An important part of the renal filtration barrier is composed of podocytes with their actin-rich foot processes. In this study, we used stable isotope labeling with amino acids in cell culture coupled to mass spectrometry to characterize relative changes in the phosphoproteome of human podocytes in response to short-term treatment with AngII. In 4 replicates, we identified a total of 17,956 peptides that were traceable to 2081 distinct proteins. Bioinformatic analyses revealed that among the increasingly phosphorylated peptides are predominantly peptides that are related to actin filaments, cytoskeleton, lamellipodia, mammalian target of rapamycin, and MAPK signaling. Among others, this screening approach highlighted the increased phosphorylation of actin-bundling protein, l-plastin (LCP1). AngII-dependent phosphorylation of LCP1 in cultured podocytes was mediated by the kinases ERK, p90 ribosomal S6 kinase, PKA, or PKC. LCP1 phosphorylation increased filopodia formation. In addition, treatment with AngII led to LCP1 redistribution to the cell margins, membrane ruffling, and formation of lamellipodia. Our data highlight the importance of AngII-triggered actin cytoskeleton-associated signal transduction in podocytes.-Schenk, L. K., Möller-Kerutt, A., Klosowski, R., Wolters, D., Schaffner-Reckinger, E., Weide, T., Pavenstädt, H., Vollenbröker, B. Angiotensin II regulates phosphorylation of actin-associated proteins in human podocytes.
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Affiliation(s)
- Laura K Schenk
- Medizinischen Klinik und Poliklinik D, Universitätsklinikum Münster, Munster, Germany
| | - Annika Möller-Kerutt
- Medizinischen Klinik und Poliklinik D, Universitätsklinikum Münster, Munster, Germany
| | - Rafael Klosowski
- Analytische Chemie, Biomolekulare Massenspektrometrie, Ruhr-Universität Bochum, Bochum, Germany
| | - Dirk Wolters
- Analytische Chemie, Biomolekulare Massenspektrometrie, Ruhr-Universität Bochum, Bochum, Germany
| | - Elisabeth Schaffner-Reckinger
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Thomas Weide
- Medizinischen Klinik und Poliklinik D, Universitätsklinikum Münster, Munster, Germany
| | - Hermann Pavenstädt
- Medizinischen Klinik und Poliklinik D, Universitätsklinikum Münster, Munster, Germany
| | - Beate Vollenbröker
- Medizinischen Klinik und Poliklinik D, Universitätsklinikum Münster, Munster, Germany;
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A role for dystroglycan in the pathophysiology of acute leukemic cells. Life Sci 2017; 182:1-9. [DOI: 10.1016/j.lfs.2017.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/30/2017] [Accepted: 06/03/2017] [Indexed: 11/21/2022]
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Saha T, Rathmann I, Galic M. A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions. J Vis Exp 2017. [PMID: 28745622 DOI: 10.3791/55653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.
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Affiliation(s)
- Tanumoy Saha
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), Institute of Medical Physics and Biophysics, University of Muenster
| | - Isabel Rathmann
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), Institute of Medical Physics and Biophysics, University of Muenster
| | - Milos Galic
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), Institute of Medical Physics and Biophysics, University of Muenster;
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Stutchbury B, Atherton P, Tsang R, Wang DY, Ballestrem C. Distinct focal adhesion protein modules control different aspects of mechanotransduction. J Cell Sci 2017; 130:1612-1624. [PMID: 28302906 DOI: 10.1242/jcs.195362] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022] Open
Abstract
Focal adhesions (FAs) are macromolecular complexes that regulate cell adhesion and mechanotransduction. By performing fluorescence recovery after photobleaching (FRAP) and fluorescence loss after photoactivation (FLAP) experiments, we found that the mobility of core FA proteins correlates with their function. Structural proteins such as tensin, talin and vinculin are significantly less mobile in FAs than signaling proteins such as FAK (also known as PTK2) and paxillin. The mobilities of the structural proteins are directly influenced by substrate stiffness, suggesting that they are involved in sensing the rigidity of the extracellular environment. The turnover rates of FAK and paxillin, as well as kindlin2 (also known as FERMT2), are not influenced by substrate stiffness. By using specific Src and FAK inhibitors, we reveal that force-sensing by vinculin occurs independently of FAK and paxillin phosphorylation. However, their phosphorylation is required for downstream Rac1-driven cellular processes, such as protrusion and cell migration. Overall, we show that the FA is composed of different functional modules that separately control mechanosensing and the cellular mechano-response.
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Affiliation(s)
- Ben Stutchbury
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
| | - Paul Atherton
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
| | - Ricky Tsang
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
| | - De-Yao Wang
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
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31
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Quantifying Filopodia in Cultured Astrocytes by an Algorithm. Neurochem Res 2017; 42:1795-1809. [PMID: 28243788 DOI: 10.1007/s11064-017-2193-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/06/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Astrocytes in vivo extend thin processes termed peripheral astrocyte processes (PAPs), in particular around synapses where they can mediate glia-neuronal communication. The relation of PAPs to synapses is not based on coincidence, but it is not clear which stimuli and mechanisms lead to their formation and are active during process extension/ retraction in response to neuronal activity. Also, the molecular basis of the extremely fine PAP morphology (often 50 to 100 nm) is not understood. These open questions can be best investigated under in vitro conditions studying glial filopodia. We have previously analyzed filopodial mechanisms (Lavialle et al. PNAS 108:12915) applying an automated method for filopodia morphometry, which is now described in greater detail. The Filopodia Specific Shape Factor (FSSF) developed integrates number and length of filopodia. It quantifies filopodia independent of overall astrocytic shape or size, which can be intricate in itself. The algorithm supplied here permits automated image processing and measurements using ImageJ. Cells have to be sampled in higher numbers to obtain significant results. We validate the FSSF, and characterize the systematic influence of thresholding and camera pixel grid on measurements. We provide exemplary results of substance-induced filopodia dynamics (glutamate, mGluR agonists, EGF), and show that filopodia formation is highly sensitive to medium pH (CO2) and duration of cell culture. Although the FSSF was developed to study astrocyte filopodia with focus on the perisynaptic glial sheath, we expect that this parameter can also be applied to neuronal growth cones, non-neural cell types, or cell lines.
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Bird JE, Barzik M, Drummond MC, Sutton DC, Goodman SM, Morozko EL, Cole SM, Boukhvalova AK, Skidmore J, Syam D, Wilson EA, Fitzgerald T, Rehman AU, Martin DM, Boger ET, Belyantseva IA, Friedman TB. Harnessing molecular motors for nanoscale pulldown in live cells. Mol Biol Cell 2016; 28:463-475. [PMID: 27932498 PMCID: PMC5341729 DOI: 10.1091/mbc.e16-08-0583] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 11/13/2022] Open
Abstract
Nanoscale pulldown (NanoSPD) miniaturizes the concept of affinity pulldown to detect protein–protein interactions in live cells. NanoSPD hijacks the myosin-based intracellular trafficking machinery to assess interactions under physiological buffer conditions and is microscopy-based, allowing for sensitive detection and quantification. Protein–protein interactions (PPIs) regulate assembly of macromolecular complexes, yet remain challenging to study within the native cytoplasm where they normally exert their biological effect. Here we miniaturize the concept of affinity pulldown, a gold-standard in vitro PPI interrogation technique, to perform nanoscale pulldowns (NanoSPDs) within living cells. NanoSPD hijacks the normal process of intracellular trafficking by myosin motors to forcibly pull fluorescently tagged protein complexes along filopodial actin filaments. Using dual-color total internal reflection fluorescence microscopy, we demonstrate complex formation by showing that bait and prey molecules are simultaneously trafficked and actively concentrated into a nanoscopic volume at the tips of filopodia. The resulting molecular traffic jams at filopodial tips amplify fluorescence intensities and allow PPIs to be interrogated using standard epifluorescence microscopy. A rigorous quantification framework and software tool are provided to statistically evaluate NanoSPD data sets. We demonstrate the capabilities of NanoSPD for a range of nuclear and cytoplasmic PPIs implicated in human deafness, in addition to dissecting these interactions using domain mapping and mutagenesis experiments. The NanoSPD methodology is extensible for use with other fluorescent molecules, in addition to proteins, and the platform can be easily scaled for high-throughput applications.
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Affiliation(s)
- Jonathan E Bird
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Melanie Barzik
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Meghan C Drummond
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Daniel C Sutton
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Spencer M Goodman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Eva L Morozko
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Stacey M Cole
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | | | - Jennifer Skidmore
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109
| | - Diana Syam
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109
| | - Elizabeth A Wilson
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Tracy Fitzgerald
- Mouse Auditory Testing Core Facility, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20814
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109.,Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Erich T Boger
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
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Saha T, Rathmann I, Viplav A, Panzade S, Begemann I, Rasch C, Klingauf J, Matis M, Galic M. Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking. Mol Biol Cell 2016; 27:3616-3626. [PMID: 27535428 PMCID: PMC5221593 DOI: 10.1091/mbc.e16-06-0406] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/11/2016] [Indexed: 12/05/2022] Open
Abstract
A novel approach based on the convex-hull algorithm is used for parallel analysis of growth dynamics and relative spatiotemporal protein concentration along flexible filopodial protrusions. Testing of filopodia formation in silico, in vitro, and in vivo validates the robustness and sensitivity of the proposed approach. Filopodia are dynamic, actin-rich structures that transiently form on a variety of cell types. To understand the underlying control mechanisms requires precise monitoring of localization and concentration of individual regulatory and structural proteins as filopodia elongate and subsequently retract. Although several methods exist that analyze changes in filopodial shape, a software solution to reliably correlate growth dynamics with spatially resolved protein concentration along the filopodium independent of bending, lateral shift, or tilting is missing. Here we introduce a novel approach based on the convex-hull algorithm for parallel analysis of growth dynamics and relative spatiotemporal protein concentration along flexible filopodial protrusions. Detailed in silico tests using various geometries confirm that our technique accurately tracks growth dynamics and relative protein concentration along the filopodial length for a broad range of signal distributions. To validate our technique in living cells, we measure filopodial dynamics and quantify spatiotemporal localization of filopodia-associated proteins during the filopodial extension–retraction cycle in a variety of cell types in vitro and in vivo. Together these results show that the technique is suitable for simultaneous analysis of growth dynamics and spatiotemporal protein enrichment along filopodia. To allow readily application by other laboratories, we share source code and instructions for software handling.
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Affiliation(s)
- Tanumoy Saha
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Isabel Rathmann
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Abhiyan Viplav
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Sadhana Panzade
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Cell Biology, University of Münster, 48149 Münster, Germany
| | - Isabell Begemann
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Christiane Rasch
- Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Jürgen Klingauf
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
| | - Maja Matis
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany.,Institute of Cell Biology, University of Münster, 48149 Münster, Germany
| | - Milos Galic
- DFG Cluster of Excellence Cells in Motion (EXC 1003), University of Münster, 48149 Münster, Germany .,Institute of Medical Physics and Biophysics, University of Münster, 48149 Münster, Germany
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Dystroglycan Depletion Impairs Actin-Dependent Functions of Differentiated Kasumi-1 Cells. PLoS One 2015; 10:e0144078. [PMID: 26630171 PMCID: PMC4668107 DOI: 10.1371/journal.pone.0144078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/12/2015] [Indexed: 01/20/2023] Open
Abstract
Background Dystroglycan has recently been characterised in blood tissue cells, as part of the dystrophin glycoprotein complex involved in the differentiation process of neutrophils. Purpose In the present study we have investigated the role of dystroglycan in the human promyelocytic leukemic cell line Kasumi-1 differentiated to macrophage-like cells. Methods We characterised the pattern expression and subcellular distribution of dystroglycans in non-differentiated and differentiated Kasumi-1 cells. Results Our results demonstrated by WB and flow cytometer assays that during the differentiation process to macrophages, dystroglycans were down-regulated; these results were confirmed with qRT-PCR assays. Additionally, depletion of dystroglycan by RNAi resulted in altered morphology and reduced properties of differentiated Kasumi-1 cells, including morphology, migration and phagocytic activities although secretion of IL-1β and expression of markers of differentiation are not altered. Conclusion Our findings strongly implicate dystroglycan as a key membrane adhesion protein involved in actin-based structures during the differentiation process in Kasumi-1 cells.
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Dong Q, Brenneman B, Fields C, Srivastava A. A Cathepsin-L is required for invasive behavior during Air Sac Primordium development in Drosophila melanogaster. FEBS Lett 2015; 589:3090-7. [PMID: 26341534 DOI: 10.1016/j.febslet.2015.08.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/16/2015] [Accepted: 08/25/2015] [Indexed: 12/14/2022]
Abstract
The Drosophila Air Sac Primordium (ASP) has emerged as an important structure where cellular, genetic and molecular events responsible for invasive behavior and branching morphogenesis can be studied. In this report we present data which demonstrate that a Cathepsin-L encoded by the gene CP1 in Drosophila is necessary for invasive behavior during ASP development. We find that CP1 is expressed in ASP and knockdown of CP1 results in suppression of migratory and invasive behavior observed during ASP development. We further show that CP1 possibly regulates invasive behavior by promoting degradation of Basement Membrane. Our data provide clues to the possible role of Cathepsin L in human lung development and tumor invasion, especially, given the similarities between human lung and Drosophila ASP development.
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Affiliation(s)
- Qian Dong
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY 42101, USA
| | - Breanna Brenneman
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY 42101, USA
| | - Christopher Fields
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY 42101, USA
| | - Ajay Srivastava
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY 42101, USA.
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Nilufar S, Perkins TJ. Learning a cost function for microscope image segmentation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:5506-9. [PMID: 25571241 DOI: 10.1109/embc.2014.6944873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative analysis of microscopy images is increasingly important in clinical researchers' efforts to unravel the cellular and molecular determinants of disease, and for pathological analysis of tissue samples. Yet, manual segmentation and measurement of cells or other features in images remains the norm in many fields. We report on a new system that aims for robust and accurate semi-automated analysis of microscope images. A user interactively outlines one or more examples of a target object in a training image. We then learn a cost function for detecting more objects of the same type, either in the same or different images. The cost function is incorporated into an active contour model, which can efficiently determine optimal boundaries by dynamic programming. We validate our approach and compare it to some standard alternatives on three different types of microscopic images: light microscopy of blood cells, light microscopy of muscle tissue sections, and electron microscopy cross-sections of axons and their myelin sheaths.
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Selfridge A, Hyun N, Chiang CC, Reyna SM, Weissmiller AM, Shi LZ, Preece D, Mobley WC, Berns MW. Rat embryonic hippocampus and induced pluripotent stem cell derived cultured neurons recover from laser-induced subaxotomy. NEUROPHOTONICS 2015; 2:015006. [PMID: 26157985 PMCID: PMC4487718 DOI: 10.1117/1.nph.2.1.015006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
Axonal injury and stress have long been thought to play a pathogenic role in a variety of neurodegenerative diseases. However, a model for studying single-cell axonal injury in mammalian cells and the processes of repair has not been established. The purpose of this study was to examine the response of neuronal growth cones to laser-induced axonal damage in cultures of embryonic rat hippocampal neurons and induced pluripotent stem cell (iPSC) derived human neurons. A 532-nm pulsed [Formula: see text] picosecond laser was focused to a diffraction limited spot at a precise location on an axon using a laser energy/power that did not rupture the cell membrane (subaxotomy). Subsequent time series images were taken to follow axonal recovery and growth cone dynamics. After laser subaxotomy, axons thinned at the damage site and initiated a dynamic cytoskeletal remodeling process to restore axonal thickness. The growth cone was observed to play a role in the repair process in both hippocampal and iPSC-derived neurons. Immunofluorescence staining confirmed structural tubulin damage and revealed initial phases of actin-based cytoskeletal remodeling at the damage site. The results of this study indicate that there is a repeatable and cross-species repair response of axons and growth cones after laser-induced damage.
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Affiliation(s)
- Aaron Selfridge
- University of California, San Diego, Department of Bioengineering, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nicholas Hyun
- University of California, San Diego, Department of Bioengineering, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Chai-Chun Chiang
- University of California, San Diego, Department of Neurosciences, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sol M. Reyna
- University of California, San Diego, Department of Biomedical Sciences, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - April M. Weissmiller
- University of California, San Diego, Department of Neurosciences, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Linda Z. Shi
- University of California, San Diego, Institute of Engineering in Medicine, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Daryl Preece
- University of California, San Diego, Department of NanoEngineering, 9500 Gilman Drive La Jolla, California 92093, United States
| | - William C. Mobley
- University of California, San Diego, Department of Neurosciences, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael W. Berns
- University of California, San Diego, Department of Bioengineering, 9500 Gilman Drive, La Jolla, California 92093, United States
- University of California, San Diego, Institute of Engineering in Medicine, 9500 Gilman Drive, La Jolla, California 92093, United States
- University of California, Irvine, Beckman Laser Institute, 1002 Health Sciences Road, Irvine, California 92612, United States
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Li Y, Zhang Z, Zhou X, Li L, Liu Q, Wang Z, Bai X, Zhao Y, Shi H, Zhang X, Ye L. The oncoprotein HBXIP enhances migration of breast cancer cells through increasing filopodia formation involving MEKK2/ERK1/2/Capn4 signaling. Cancer Lett 2014; 355:288-96. [DOI: 10.1016/j.canlet.2014.09.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/03/2014] [Accepted: 09/28/2014] [Indexed: 12/01/2022]
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39
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Martínez-Zárate AD, Martínez-Vieyra I, Alonso-Rangel L, Cisneros B, Winder SJ, Cerecedo D. Dystroglycan depletion inhibits the functions of differentiated HL-60 cells. Biochem Biophys Res Commun 2014; 448:274-80. [DOI: 10.1016/j.bbrc.2014.04.110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 12/16/2022]
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40
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Jeon JS, Bersini S, Whisler JA, Chen MB, Dubini G, Charest JL, Moretti M, Kamm RD. Generation of 3D functional microvascular networks with human mesenchymal stem cells in microfluidic systems. Integr Biol (Camb) 2014; 6:555-63. [PMID: 24676392 PMCID: PMC4307755 DOI: 10.1039/c3ib40267c] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The generation of functional microvascular networks is critical for the development of advanced in vitro models to replicate pathophysiological conditions. Mural cells provide structural support to blood vessels and secrete biomolecules contributing to vessel stability and functionality. We investigated the role played by two endothelium-related molecules, angiopoietin (Ang-1) and transforming growth factor (TGF-β1), on bone marrow-derived human mesenchymal stem cell (BM-hMSC) phenotypic transition toward a mural cell lineage, both in monoculture and in direct contact with human endothelial cells (ECs), within 3D fibrin gels in microfluidic devices. We demonstrated that the effect of these molecules is dependent on direct heterotypic cell-cell contact. Moreover, we found a significant increase in the amount of α-smooth muscle actin in microvascular networks with added VEGF and TGF-β1 or VEGF and Ang-1 compared to networks with added VEGF alone. However, the addition of TGF-β1 generated a non-interconnected microvasculature, while Ang-1 promoted functional networks, confirmed by microsphere perfusion and permeability measurements. The presence of mural cell-like BM-hMSCs coupled with the addition of Ang-1 increased the number of network branches and reduced mean vessel diameter compared to EC only vasculature. This system has promising applications in the development of advanced in vitro models to study complex biological phenomena involving functional and perfusable microvascular networks.
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Affiliation(s)
- Jessie S Jeon
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA 02139.
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Jeon JS, Bersini S, Whisler JA, Chen MB, Dubini G, Charest JL, Moretti M, Kamm RD. Generation of 3D functional microvascular networks with human mesenchymal stem cells in microfluidic systems. Integr Biol (Camb) 2014. [PMID: 24676392 DOI: 10.1039/b000000x/nih-pa] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The generation of functional microvascular networks is critical for the development of advanced in vitro models to replicate pathophysiological conditions. Mural cells provide structural support to blood vessels and secrete biomolecules contributing to vessel stability and functionality. We investigated the role played by two endothelium-related molecules, angiopoietin (Ang-1) and transforming growth factor (TGF-β1), on bone marrow-derived human mesenchymal stem cell (BM-hMSC) phenotypic transition toward a mural cell lineage, both in monoculture and in direct contact with human endothelial cells (ECs), within 3D fibrin gels in microfluidic devices. We demonstrated that the effect of these molecules is dependent on direct heterotypic cell-cell contact. Moreover, we found a significant increase in the amount of α-smooth muscle actin in microvascular networks with added VEGF and TGF-β1 or VEGF and Ang-1 compared to networks with added VEGF alone. However, the addition of TGF-β1 generated a non-interconnected microvasculature, while Ang-1 promoted functional networks, confirmed by microsphere perfusion and permeability measurements. The presence of mural cell-like BM-hMSCs coupled with the addition of Ang-1 increased the number of network branches and reduced mean vessel diameter compared to EC only vasculature. This system has promising applications in the development of advanced in vitro models to study complex biological phenomena involving functional and perfusable microvascular networks.
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Affiliation(s)
- Jessie S Jeon
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA 02139.
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Patnala R, Lee SH, Dahlstrom JE, Ohms S, Chen L, Dheen ST, Rangasamy D. Inhibition of LINE-1 retrotransposon-encoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells. Breast Cancer Res Treat 2013; 143:239-53. [PMID: 24337508 PMCID: PMC3889873 DOI: 10.1007/s10549-013-2812-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 12/04/2013] [Indexed: 12/31/2022]
Abstract
Long Interspersed Elements (L1 elements) are biologically active retrotransposons that are capable of autonomous replication using their own reverse transcriptase (RT) enzyme. Expression of the normally repressed RT has been implicated in cancer cell growth. However, at present, little is known about the expression of L1-encoded RT activity or the molecular changes that are associated with RT activity in the development of breast cancer. Here, we report that RT activity is widespread in breast cancer cells. The expression of RT protein decreased markedly in breast cancer cells after treatment with the antiretroviral drug, efavirenz. While the majority of cells showed a significant reduction in proliferation, inhibition of RT was also accompanied by cell-specific differences in morphology. MCF7 cells displayed elongated microtubule extensions that adhered tightly to their substrate, while a large fraction of the T47D cells that we studied formed long filopodia projections. These morphological changes were reversible upon cessation of RT inhibition, confirming their dependence on RT activity. We also carried out gene expression profiling with microarrays and determined the genes that were differentially expressed during the process of cellular differentiation. Genes involved in proliferation, cell migration, and invasive activity were repressed in RT-inhibited cells. Concomitantly, genes involved in cell projection, formation of vacuolar membranes, and cell-to-cell junctions were significantly upregulated in RT-inhibited cells. qRT-PCR examination of the mRNA expression of these genes in additional cell lines yielded close correlation between their differential expression and the degree of cellular differentiation. Our study demonstrates that the inhibition of L1-encoded RT can reduce the rate of proliferation and promote differentiation of breast cancer cells. Together, these results provide a direct functional link between the expression of L1 retrotransposons and the development of breast cancer.
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Affiliation(s)
- Radhika Patnala
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
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