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Huang HN, Kuo CW, Hung YL, Yang CH, Hsieh YH, Lin YC, Chang MDT, Lin YY, Ko JC. Optimizing immunofluorescence with high-dynamic-range imaging to enhance PD-L1 expression evaluation for 3D pathology assessment from NSCLC tumor tissue. Sci Rep 2024; 14:15176. [PMID: 38956114 PMCID: PMC11219731 DOI: 10.1038/s41598-024-65187-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: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
Assessing programmed death ligand 1 (PD-L1) expression through immunohistochemistry (IHC) is the golden standard in predicting immunotherapy response of non-small cell lung cancer (NSCLC). However, observation of heterogeneous PD-L1 distribution in tumor space is a challenge using IHC only. Meanwhile, immunofluorescence (IF) could support both planar and three-dimensional (3D) histological analyses by combining tissue optical clearing with confocal microscopy. We optimized clinical tissue preparation for the IF assay focusing on staining, imaging, and post-processing to achieve quality identical to traditional IHC assay. To overcome limited dynamic range of the fluorescence microscope's detection system, we incorporated a high dynamic range (HDR) algorithm to restore the post imaging IF expression pattern and further 3D IF images. Following HDR processing, a noticeable improvement in the accuracy of diagnosis (85.7%) was achieved using IF images by pathologists. Moreover, 3D IF images revealed a 25% change in tumor proportion score for PD-L1 expression at various depths within tumors. We have established an optimal and reproducible process for PD-L1 IF images in NSCLC, yielding high quality data comparable to traditional IHC assays. The ability to discern accurate spatial PD-L1 distribution through 3D pathology analysis could provide more precise evaluation and prediction for immunotherapy targeting advanced NSCLC.
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Affiliation(s)
- Hsien-Neng Huang
- Department of Pathology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
- Department and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Wei Kuo
- Department of Pathology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | | | | | | | | | | | | | - Jen-Chung Ko
- Department of Internal Medicine, National Taiwan University HospitalHsin-Chu Branch, No. 25, Ln. 442, Sec. 1, Jingguo Rd., North Dist., Hsinchu City, 300, Taiwan, ROC.
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Abu-Humaidan AH, Ismail MA, Ahmad FM, Al Shboul S, Barham R, Tadros JS, Alhesa A, El-Sadoni M, Alotaibi MR, Ababneh NA, Saleh T. Therapy-induced senescent cancer cells exhibit complement activation and increased complement regulatory protein expression. Immunol Cell Biol 2024; 102:240-255. [PMID: 38265162 DOI: 10.1111/imcb.12727] [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: 08/31/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
Therapy-induced senescence (TIS) is a primary response to chemotherapy, contributing to untoward treatment outcomes such as evasion of immunosurveillance. Despite the established role of the complement system in the immune response to cancer, the role of complement in mediating the immune response against senescent tumor cells remains poorly understood. To explore this relationship, we exposed lung adenocarcinoma (A549), breast adenocarcinoma (MCF7) and pancreatic carcinoma (Panc-1) cell lines to sublethal doses of either etoposide or doxorubicin to trigger TIS. Identification of TIS was based on morphological changes, upregulation of the senescence-associated β-galactosidase, p21Cip1 induction and lamin B1 downregulation. Using immunofluorescence microscopy, quantitative PCR, ELISA of conditioned media and in silico analysis, we investigated complement activation, complement protein expression, C3 levels in the conditioned media of senescent cells and secreted complement proteins as part of the senescence-associated secretory phenotype (SASP), respectively. In cell lines undergoing TIS, complement-related changes included (i) activation of the terminal pathway, evidenced by the deposition of C5b-9 on senescent cells; (ii) an increase in the expression of CD59 and complement factor H and (iii) in A549 cells, an elevation in the expression of C3 with its secretion into the medium. In addition, increased C3 expression was observed in breast cancer samples expressing TIS hallmarks following exposure to neoadjuvant chemotherapy. In conclusion, TIS led to the activation of complement, upregulation of complement regulatory proteins and increased C3 expression. Complement appears to play a role in shaping the cancer microenvironment upon senescence induction.
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Affiliation(s)
- Anas Ha Abu-Humaidan
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mohammad A Ismail
- Cell Therapy Center, The University of Jordan, Amman, Jordan
- South Australian ImmunoGENomics Cancer Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Fatima M Ahmad
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of the Clinical Laboratory Sciences, School of Science, The University of Jordan, Amman, Jordan
| | - Sofian Al Shboul
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Raghad Barham
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Joud S Tadros
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Ahmad Alhesa
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Mohammed El-Sadoni
- Department of Pathology, Microbiology, and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Moureq R Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Nidaa A Ababneh
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Tareq Saleh
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
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Honzel E, Joshi A, Hernandez-Morato I, Pennington-FitzGerald W, Pitman MJ. A comparison of confocal and epifluorescence microscopy for quantification of RNAScope and immunohistochemistry fluorescent images. J Neurosci Methods 2024; 403:110050. [PMID: 38145719 PMCID: PMC10874114 DOI: 10.1016/j.jneumeth.2023.110050] [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: 08/14/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Quantification of RNA expression and protein production in fluorescent stainings provides critical information concerning neurodevelopment. A trustable independent quantification technique requires acquisition of reliable images prior to image processing. There is uncertainty in existing literature regarding the use of confocal microscopy compared to standard epifluorescence microscopy, especially in the context of RNA in situ hybridization protocols. NEW METHOD The hindbrains of developing rat embryos from embryologic day 14 (E14) to E20 were sectioned and stained for expression of Hoxb1, Hoxb2, and Phox2b using both RNAScope and immunohistochemistry. Islet1 was used for identification of hindbrain motoneuron cell bodies. Slides were imaged using both confocal and epifluorescence microscopy. RESULTS Expression patterns of both mRNA and protein were similar in both imaging modalities. Analyses of Hoxb1 and Hoxb2 mRNA expression were particularly concordant between-scopes, with similar p-values and posthoc differences between timepoints. Confocal imaging of Hoxb2 protein yielded a significant peak at E18, but this level of significance was not reached using epifluorescence microscopy. Although similar trends were observed, only Phox2b RNAScope results were statistically significant when analyzed with confocal microscopy. In contrast, Phox2b immunostaining analyses showed significant differences using both microscopes. COMPARISON WITH EXISTING METHODS Researchers may save time and financial resources if epifluorescence microscopy provides comparable or equal results as confocal. CONCLUSIONS Epifluorescence microscopy appears sufficient for quantification of RNAScope experiments with relatively low puncta per cell, while confocal microscopy gives clearer definition to immunohistochemical protein relationships and may be preferable especially in targets with low protein production.
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Affiliation(s)
- Emily Honzel
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, United States.
| | - Abhinav Joshi
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, United States.
| | - Ignacio Hernandez-Morato
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, United States.
| | - William Pennington-FitzGerald
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, United States.
| | - Michael J Pitman
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, United States.
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Lee YH, Huang CY, Hsieh YH, Yang CH, Hung YL, Chen YA, Lin YC, Lin CH, Lee JH, Wang MY, Kuo WH, Lin YY, Lu YS. A novel computer-assisted tool for 3D imaging of programmed death-ligand 1 expression in immunofluorescence-stained and optically cleared breast cancer specimens. BMC Cancer 2024; 24:121. [PMID: 38267903 PMCID: PMC10807239 DOI: 10.1186/s12885-023-11748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) are the two most common immune checkpoints targeted in triple-negative breast cancer (BC). Refining patient selection for immunotherapy is non-trivial and finding an appropriate digital pathology framework for spatial analysis of theranostic biomarkers for PD-1/PD-L1 inhibitors remains an unmet clinical need. METHODS We describe a novel computer-assisted tool for three-dimensional (3D) imaging of PD-L1 expression in immunofluorescence-stained and optically cleared BC specimens (n = 20). The proposed 3D framework appeared to be feasible and showed a high overall agreement with traditional, clinical-grade two-dimensional (2D) staining techniques. Additionally, the results obtained for automated immune cell detection and analysis of PD-L1 expression were satisfactory. RESULTS The spatial distribution of PD-L1 expression was heterogeneous across various BC tissue layers in the 3D space. Notably, there were six cases (30%) wherein PD-L1 expression levels along different layers crossed the 1% threshold for admitting patients to PD-1/PD-L1 inhibitors. The average PD-L1 expression in 3D space was different from that of traditional immunohistochemistry (IHC) in eight cases (40%). Pending further standardization and optimization, we expect that our technology will become a valuable addition for assessing PD-L1 expression in patients with BC. CONCLUSION Via a single round of immunofluorescence imaging, our approach may provide a considerable improvement in patient stratification for cancer immunotherapy as compared with standard techniques.
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Affiliation(s)
- Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Yen Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | | | | | | | | | | | - Ching-Hung Lin
- Department of Medical Oncology, Cancer Center Branch, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jih-Hsiang Lee
- Department of Oncology, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
| | - Ming-Yang Wang
- Department of Surgical Oncology, Cancer Center Branch, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Yen-Shen Lu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
- Department of Oncology, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 100225, Taiwan.
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Hu Y, Li CY, Lu Q, Kuang Y. Multiplex miRNA reporting platform for real-time profiling of living cells. Cell Chem Biol 2024; 31:150-162.e7. [PMID: 38035883 DOI: 10.1016/j.chembiol.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Accurately characterizing cell types within complex cell structures provides invaluable information for comprehending the cellular status during biological processes. In this study, we have developed an miRNA-switch cocktail platform capable of reporting and tracking the activities of multiple miRNAs (microRNAs) at the single-cell level, while minimizing disruption to the cell culture. Drawing on the principles of traditional miRNA-sensing mRNA switches, our platform incorporates subcellular tags and employs intelligent engineering to segment three subcellular regions using two fluorescent proteins. These designs enable the quantification of multiple miRNAs within the same cell. Through our experiments, we have demonstrated the platform's ability to track marker miRNA levels during cell differentiation and provide spatial information of heterogeneity on outlier cells exhibiting extreme miRNA levels. Importantly, this platform offers real-time and in situ miRNA reporting, allowing for multidimensional evaluation of cell profile and paving the way for a comprehensive understanding of cellular events during biological processes.
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Affiliation(s)
- Yaxin Hu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qiuyu Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yi Kuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.
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Ahmadian M, Rickert C, Minic A, Wrobel J, Bitler BG, Xing F, Angelo M, Hsieh EWY, Ghosh D, Jordan KR. A platform-independent framework for phenotyping of multiplex tissue imaging data. PLoS Comput Biol 2023; 19:e1011432. [PMID: 37733781 PMCID: PMC10547204 DOI: 10.1371/journal.pcbi.1011432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/03/2023] [Accepted: 08/14/2023] [Indexed: 09/23/2023] Open
Abstract
Multiplex imaging is a powerful tool to analyze the structural and functional states of cells in their morphological and pathological contexts. However, hypothesis testing with multiplex imaging data is a challenging task due to the extent and complexity of the information obtained. Various computational pipelines have been developed and validated to extract knowledge from specific imaging platforms. A common problem with customized pipelines is their reduced applicability across different imaging platforms: Every multiplex imaging technique exhibits platform-specific characteristics in terms of signal-to-noise ratio and acquisition artifacts that need to be accounted for to yield reliable and reproducible results. We propose a pixel classifier-based image preprocessing step that aims to minimize platform-dependency for all multiplex image analysis pipelines. Signal detection and noise reduction as well as artifact removal can be posed as a pixel classification problem in which all pixels in multiplex images can be assigned to two general classes of either I) signal of interest or II) artifacts and noise. The resulting feature representation maps contain pixel-scale representations of the input data, but exhibit significantly increased signal-to-noise ratios with normalized pixel values as output data. We demonstrate the validity of our proposed image preprocessing approach by comparing the results of two well-accepted and widely-used image analysis pipelines.
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Affiliation(s)
- Mansooreh Ahmadian
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christian Rickert
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Angela Minic
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Julia Wrobel
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of OB/GYN, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Fuyong Xing
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Elena W. Y. Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Pediatrics, Section of Allergy and Immunology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kimberly R. Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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Daigle N, Duan S, Song H, Lima N, Sontz R, Merchant JL, Sawyer TW. Wide field-of-view fluorescence imaging for organ-level lineage tracing of rare intestinal stem cell populations. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:096004. [PMID: 37711357 PMCID: PMC10499363 DOI: 10.1117/1.jbo.28.9.096004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Significance Lineage tracing using fluorescent reporters is a common tool for monitoring the expression of genes and transcription factors in stem cell populations and their progeny. The zinc-binding protein 89 (ZBP-89/Zfp148 mouse gene) is a transcription factor that plays a role in gastrointestinal (GI) stem cell maintenance and cellular differentiation and has been linked to the progression of colon cancer. While lineage tracing is a useful tool, it is commonly performed with high-magnification microscopy on a small field of view within tissue sections, thereby limiting the ability to resolve reporter expression at the organ level. Furthermore, this technique requires extensive tissue processing, which is time consuming and requires euthanizing the animal. Further knowledge could be elucidated by measuring the expression of fluorescent reporters across entire organs with minimal tissue processing. Aim We present the application of wide-field fluorescence imaging for whole-organ lineage tracing of an inducible Zfp148-tdTomato-expressing transgenic mouse line to assess the expression of ZBP-89/Zfp148 in the GI tract. Approach We measured tdTomato fluorescence in ex vivo organs at time points between 24 h and 6 months post-induction. Fluctuations in tdTomato expression were validated by fluorescence microscopy of tissue sections. Results Quantification of the wide field-of-view images showed a statistically significant increase in fluorescent signal across the GI tract between transgenic mice and littermate controls. The results also showed a gradient of decreasing reporter expression from proximal to distal intestine, suggesting a higher abundance of ZBP-89 expressing stem cells, or higher expression of ZBP-89 within the stem cells, in the proximal intestine. Conclusions We demonstrate that wide-field fluorescence imaging is a valuable tool for monitoring whole-organ expression of fluorescent reporters. This technique could potentially be applied in vivo for longitudinal assessment of a single animal, further enhancing our ability to resolve rare stem cell lineages spatially and temporally.
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Affiliation(s)
- Noelle Daigle
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Suzann Duan
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Heyu Song
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Natzem Lima
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Ricky Sontz
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | | | - Travis W. Sawyer
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
- University of Arizona, College of Medicine, Tucson, Arizona, United States
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Machado M, Klaus S, Klaschka D, Guizetti J, Ganter M. Plasmodium falciparum CRK4 links early mitotic events to the onset of S-phase during schizogony. mBio 2023; 14:e0077923. [PMID: 37345936 PMCID: PMC10470535 DOI: 10.1128/mbio.00779-23] [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: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
Plasmodium falciparum proliferates through schizogony in the clinically relevant blood stage of infection. During schizogony, consecutive rounds of DNA replication and nuclear division give rise to multinucleated stages before cellularization occurs. Although these nuclei reside in a shared cytoplasm, DNA replication and nuclear division occur asynchronously. Here, by mapping the proteomic context of the S-phase-promoting kinase PfCRK4, we show that it has a dual role for nuclear-cycle progression: PfCRK4 orchestrates not only DNA replication, but in parallel also the rearrangement of intranuclear microtubules from hemispindles into early mitotic spindles. Live-cell imaging of a reporter parasite showed that these microtubule rearrangements coincide with the onset of DNA replication. Together, our data render PfCRK4 a key factor for nuclear-cycle progression, linking entry into S-phase with the initiation of mitotic events. In part, such links may compensate for the absence of canonical cell cycle checkpoints in P. falciparum. IMPORTANCE The human malaria parasite Plasmodium falciparum proliferates in erythrocytes through schizogony, forming multinucleated stages before cellularization occurs. In marked contrast to the pattern of proliferation seen in most model organisms, P. falciparum nuclei multiply asynchronously despite residing in a shared cytoplasm. This divergent mode of replication is, thus, a good target for therapeutic interventions. To exploit this potential, we investigated a key regulator of the parasite's unusual cell cycle, the kinase PfCRK4 and found that this kinase regulated not only DNA replication but also in parallel the rearrangement of nuclear microtubules into early mitotic spindles. Since canonical cell cycle checkpoints have not been described in P. falciparum parasites, linking entry into S-phase and the initiation of mitotic events via a kinase, may be an alternative means to exert control, which is typically achieved by checkpoints.
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Affiliation(s)
- Marta Machado
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Severina Klaus
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Darius Klaschka
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Julien Guizetti
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ganter
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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Uzhytchak M, Lunova M, Smolková B, Jirsa M, Dejneka A, Lunov O. Iron oxide nanoparticles trigger endoplasmic reticulum damage in steatotic hepatic cells. NANOSCALE ADVANCES 2023; 5:4250-4268. [PMID: 37560414 PMCID: PMC10408607 DOI: 10.1039/d3na00071k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Iron oxide nanoparticles (IONPs) are being actively researched in various biomedical applications, particularly as magnetic resonance imaging (MRI) contrast agents for diagnosing various liver pathologies like nonalcoholic fatty liver diseases, nonalcoholic steatohepatitis, and cirrhosis. Emerging evidence suggests that IONPs may exacerbate hepatic steatosis and liver injury in susceptible livers such as those with nonalcoholic fatty liver disease. However, our understanding of how IONPs may affect steatotic cells at the sub-cellular level is still fragmented. Generally, there is a lack of studies identifying the molecular mechanisms of potential toxic and/or adverse effects of IONPs on "non-heathy" in vitro models. In this study, we demonstrate that IONPs, at a dose that does not cause general toxicity in hepatic cells (Alexander and HepG2), induce significant toxicity in steatotic cells (cells loaded with non-toxic doses of palmitic acid). Mechanistically, co-treatment with PA and IONPs resulted in endoplasmic reticulum (ER) stress, accompanied by the release of cathepsin B from lysosomes to the cytosol. The release of cathepsin B, along with ER stress, led to the activation of apoptotic cell death. Our results suggest that it is necessary to consider the interaction between IONPs and the liver, especially in susceptible livers. This study provides important basic knowledge for the future optimization of IONPs as MRI contrast agents for various biomedical applications.
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Affiliation(s)
- Mariia Uzhytchak
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences Prague 18221 Czech Republic
| | - Mariia Lunova
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences Prague 18221 Czech Republic
- Institute for Clinical & Experimental Medicine (IKEM) Prague 14021 Czech Republic
| | - Barbora Smolková
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences Prague 18221 Czech Republic
| | - Milan Jirsa
- Institute for Clinical & Experimental Medicine (IKEM) Prague 14021 Czech Republic
| | - Alexandr Dejneka
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences Prague 18221 Czech Republic
| | - Oleg Lunov
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences Prague 18221 Czech Republic
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Helmbrecht H, Lin TJ, Janakiraman S, Decker K, Nance E. Prevalence and practices of immunofluorescent cell image processing: a systematic review. Front Cell Neurosci 2023; 17:1188858. [PMID: 37545881 PMCID: PMC10400723 DOI: 10.3389/fncel.2023.1188858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Background We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescent microscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field. Methods We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software. Results Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research. Discussion Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods. Conclusion Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor.
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Affiliation(s)
- Hawley Helmbrecht
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Teng-Jui Lin
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Sanjana Janakiraman
- Paul G. Allen School of Computer Science & Engineering, Seattle, WA, United States
| | - Kaleb Decker
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Elizabeth Nance
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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Li N, Wang T, Wang N, Fan M, Cui X. A Substituted-Rhodamine-Based Reversible Fluorescent Probe for In Vivo Quantification of Glutathione. Angew Chem Int Ed Engl 2023; 62:e202217326. [PMID: 36564368 DOI: 10.1002/anie.202217326] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
Quantifying glutathione (GSH) in cells and organisms is of great significance for understanding the mechanism of oxidative stress in various physiological and pathological processes. However, the quantification by fluorescence bioimaging in living tissues has much stricter requirements than the "Petri dish"-cultured cells in flat plates. Based on the evaluation of the electronic structure and steric hindrance-tuned reactivity of phospha-substituted rhodamine with GSH, a reversible Förster resonance energy transfer (FRET) probe ZpSiP with a distinct performance (Kd =4.9 mM, t1/2 =0.57 s, k=81 M-1 s-1 ) is developed for real time quantifying GSH in living cells. Furthermore, the near-infrared (NIR) probe succeeded in sensitively tracking the dynamics of GSH in the real organisms bearing tumors, chronic renal failure, and liver fibrosis for unveiling the related pathological processes. We believe that the advance in chemistry with quantitative analysis methods will initiate more promising progress and broad applications.
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Affiliation(s)
- Ni Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Ting Wang
- Department of Organic Chemistry, College of Pharmacy, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, P. R. China
| | - Ning Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Mengting Fan
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Xiaoyan Cui
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
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12
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Hirano R, Okamoto K, Shinke M, Sato M, Watanabe S, Watanabe H, Kondoh G, Kadonosono T, Kizaka-Kondoh S. Tissue-resident macrophages are major tumor-associated macrophage resources, contributing to early TNBC development, recurrence, and metastases. Commun Biol 2023; 6:144. [PMID: 36737474 PMCID: PMC9898263 DOI: 10.1038/s42003-023-04525-7] [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: 09/22/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive and highly heterogenous disease with no well-defined therapeutic targets. Treatment options are thus limited and mortality is significantly higher compared with other breast cancer subtypes. Mammary gland tissue-resident macrophages (MGTRMs) are found to be the most abundant stromal cells in early TNBC before angiogenesis. We therefore aimed to explore novel therapeutic approaches for TNBC by focusing on MGTRMs. Local depletion of MGTRMs in mammary gland fat pads the day before TNBC cell transplantation significantly reduced tumor growth and tumor-associated macrophage (TAM) infiltration in mice. Furthermore, local depletion of MGTRMs at the site of TNBC resection markedly reduced recurrence and distant metastases, and improved chemotherapy outcomes. This study demonstrates that MGTRMs are a major TAM resource and play pivotal roles in the growth and malignant progression of TNBC. The results highlight a possible novel anti-cancer approach targeting tissue-resident macrophages.
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Affiliation(s)
- Ryuichiro Hirano
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Koki Okamoto
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Miyu Shinke
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Marika Sato
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Shigeaki Watanabe
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Hitomi Watanabe
- grid.258799.80000 0004 0372 2033Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, 606-8507 Japan
| | - Gen Kondoh
- grid.258799.80000 0004 0372 2033Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, 606-8507 Japan
| | - Tetsuya Kadonosono
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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13
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Hunt GJ, Dane MA, Korkola JE, Heiser LM, Gagnon-Bartsch JA. Systematic replication enables normalization of high-throughput imaging assays. Bioinformatics 2022; 38:4934-4940. [PMID: 36063034 PMCID: PMC9620822 DOI: 10.1093/bioinformatics/btac606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION High-throughput fluorescent microscopy is a popular class of techniques for studying tissues and cells through automated imaging and feature extraction of hundreds to thousands of samples. Like other high-throughput assays, these approaches can suffer from unwanted noise and technical artifacts that obscure the biological signal. In this work, we consider how an experimental design incorporating multiple levels of replication enables the removal of technical artifacts from such image-based platforms. RESULTS We develop a general approach to remove technical artifacts from high-throughput image data that leverages an experimental design with multiple levels of replication. To illustrate the methods, we consider microenvironment microarrays (MEMAs), a high-throughput platform designed to study cellular responses to microenvironmental perturbations. In application to MEMAs, our approach removes unwanted spatial artifacts and thereby enhances the biological signal. This approach has broad applicability to diverse biological assays. AVAILABILITY AND IMPLEMENTATION Raw data are on synapse (syn2862345), analysis code is on github: gjhunt/mema_norm, a reproducible Docker image is available on dockerhub: gjhunt/mema_norm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gregory J Hunt
- Department of Mathematics, College of William & Mary, Williamsburg, VA 23185, USA
| | - Mark A Dane
- Department of Biomedical Engineering, Knight Cancer Institute OHSU Center for Spatial Systems Biomedicine Oregon Health and Science University, Portland, OR 97201, USA
| | - James E Korkola
- Department of Biomedical Engineering, Knight Cancer Institute OHSU Center for Spatial Systems Biomedicine Oregon Health and Science University, Portland, OR 97201, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute OHSU Center for Spatial Systems Biomedicine Oregon Health and Science University, Portland, OR 97201, USA
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14
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Tayal S, Singh V, Kaur T, Singh N, Mehta DS. Multimodal biomicroscopic system for the characterization of cells with high spatial phase sensitivity and sub-pixel accuracy. JOURNAL OF BIOPHOTONICS 2022; 15:e202100258. [PMID: 34855288 DOI: 10.1002/jbio.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/13/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Multimodal analysis is highly advantageous for various biomedical applications including cancer and brain studies. Simultaneous measurement of quantitative phase with sub-pixel accuracy and fluorescence image is difficult to achieve in single measurement. Conventionally, off-axis interferograms are analyzed using the Fourier-transform method which limits the accuracy of the phase maps by pixel size, and usually the location of the carrier peak is in sub-pixel. We report a multimodal microscopic system consisting of high-resolution (HR) quantitative phase interferometer to retrieve sub-pixel accuracy in phase imaging and an oblique-illumination-based fluorescence imaging system which decouples the excited light from emitted signal light to avoid saturation of the camera, both integrated into a single unit. Here, highly resolved phase maps are obtained using a two-step process. First, using a speckle-free illumination which offers high spatial phase sensitivity. Second, using a hamming window for accurate estimation of original signal frequency information and HR discrete Fourier transform (DFT) which offers sub-pixel accuracy in phase measurements. HR-DFT has computational load of OABβ , where A×B is the size of the interferogram and β is the upsampling factor, making system computationally more robust and efficient compared to zero-padded FFT. The experiment is conducted on MG63 osteosarcoma and human mesenchymal stem cells (hMSCs) and their quantitative parameters are extracted with significantly improved accuracy. The average phase for MG63 cells and hMSCs, for nucleus is obtained to be 8.02 rad ± 0.80 rad and 4.29 rad ± 0.43 rad, respectively, and for cytoplasm is obtained to be 2.63 rad ± 0.96 rad and 1.73 rad ± 0.57 rad, respectively.
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Affiliation(s)
- Shilpa Tayal
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
| | - Veena Singh
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
| | - Tejinder Kaur
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Neetu Singh
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Dalip Singh Mehta
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
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15
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Engineered barriers regulate osteoblast cell migration in vertical direction. Sci Rep 2022; 12:4459. [PMID: 35292702 PMCID: PMC8924172 DOI: 10.1038/s41598-022-08262-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/01/2022] [Indexed: 11/29/2022] Open
Abstract
Considering cell migration is essential for understanding physiological processes and diseases. The vertical migration of cells in three dimensions is vital, but most previous studies on cell migration have only focused on two-dimensional horizontal migration. In this paper, cell migration in the vertical direction was studied. Barriers with a height of 1, 5, 10, and 25 µm with grating and arrows in channels as guiding patterns were fabricated. The effects of barrier height and guiding patterns on the vertical migration of MC3T3 cells were explored. The study revealed that taller barriers hinder vertical migration of MC3T3 cells, whereas grating and arrows in channels promote it. The time-lapse and micrograph images showed that as the barrier height increased, the cell climbing angle along the barrier sidewall decreased, and the time taken to climb over the barrier increased. These results indicate that taller barriers increase the difficulty of vertical migration by MC3T3 cells. To promote the vertical migration of MC3T3 cells, 10 µm tall barriers with 18° and 40° sloped sidewalls were fabricated. For barriers with 18° sloped sidewalls, the probability for MC3T3 cells to climb up and down the 10 µm tall barriers was 40.6% and 20.3%, respectively; this is much higher than the migration probability over vertical barriers. This study shows topographic guidance on the vertical migration of MC3T3 cells and broadens the understanding of cell migration in the vertical direction.
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16
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Pierzchala K, Simicic D, Sienkiewicz A, Sessa D, Mitrea S, Braissant O, McLin VA, Gruetter R, Cudalbu C. Central nervous system and systemic oxidative stress interplay with inflammation in a bile duct ligation rat model of type C hepatic encephalopathy. Free Radic Biol Med 2022; 178:295-307. [PMID: 34890769 DOI: 10.1016/j.freeradbiomed.2021.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
The role and coexistence of oxidative stress (OS) and inflammation in type C hepatic encephalopathy (C HE) is a subject of intense debate. Under normal conditions the physiological levels of intracellular reactive oxygen species are controlled by the counteracting antioxidant response to maintain redox homeostasis. Our previous in-vivo1H-MRS studies revealed the longitudinal impairment of the antioxidant system (ascorbate) in a bile-duct ligation (BDL) rat model of type C HE. Therefore, the aim of this work was to examine the course of central nervous system (CNS) OS and systemic OS, as well as to check for their co-existence with inflammation in the BDL rat model of type C HE. To this end, we implemented a multidisciplinary approach, including ex-vivo and in-vitro electron paramagnetic resonance spectroscopy (EPR) spin-trapping, which was combined with UV-Vis spectroscopy, and histological assessments. We hypothesized that OS and inflammation act synergistically in the pathophysiology of type C HE. Our findings point to an increased CNS- and systemic-OS and inflammation over the course of type C HE progression. In particular, an increase in the CNS OS was observed as early as 2-weeks post-BDL, while the systemic OS became significant at week 6 post-BDL. The CNS EPR measurements were further validated by a substantial accumulation of 8-Oxo-2'-deoxyguanosine (Oxo-8-dG), a marker of oxidative DNA/RNA modifications on immunohistochemistry (IHC). Using IHC, we also detected increased synthesis of antioxidants, glutathione peroxidase 1 (GPX-1) and superoxide dismutases (i.e.Cu/ZnSOD (SOD1) and MnSOD (SOD2)), along with proinflammatory cytokine interleukin-6 (IL-6) in the brains of BDL rats. The presence of systemic inflammation was observed already at 2-weeks post-surgery. Thus, these results suggest that CNS OS is an early event in type C HE rat model, which seems to precede systemic OS. Finally, our results suggest that the increase in CNS OS is due to enhanced formation of intra- and extra-cellular ROS rather than due to reduced antioxidant capacity, and that OS in parallel with inflammation plays a significant role in type C HE.
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Affiliation(s)
- K Pierzchala
- Center for Biomedical Imaging, EPFL, Lausanne, Switzerland; Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Laboratory of Functional and Metabolic Imaging, EPFL, Lausanne, Switzerland.
| | - D Simicic
- Center for Biomedical Imaging, EPFL, Lausanne, Switzerland; Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Laboratory of Functional and Metabolic Imaging, EPFL, Lausanne, Switzerland
| | - A Sienkiewicz
- Laboratory for Quantum Magnetism, Institute of Physics, EPFL, Lausanne, Switzerland; ADSresonances Sàrl, Préverenges, Switzerland
| | - D Sessa
- Swiss Pediatric Liver Center, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals Geneva and University of Geneva, Geneva, Switzerland
| | - S Mitrea
- Center for Biomedical Imaging, EPFL, Lausanne, Switzerland; Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - O Braissant
- Service of Clinical Chemistry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - V A McLin
- Swiss Pediatric Liver Center, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals Geneva and University of Geneva, Geneva, Switzerland
| | - R Gruetter
- Center for Biomedical Imaging, EPFL, Lausanne, Switzerland; Laboratory of Functional and Metabolic Imaging, EPFL, Lausanne, Switzerland
| | - C Cudalbu
- Center for Biomedical Imaging, EPFL, Lausanne, Switzerland; Animal Imaging and Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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17
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McClelland RD, Culp TN, Marchant DJ. Imaging Flow Cytometry and Confocal Immunofluorescence Microscopy of Virus-Host Cell Interactions. Front Cell Infect Microbiol 2021; 11:749039. [PMID: 34712624 PMCID: PMC8546218 DOI: 10.3389/fcimb.2021.749039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Viruses are diverse pathogens that use host factors to enter cells and cause disease. Imaging the entry and replication phases of viruses and their interactions with host factors is key to fully understanding viral infections. This review will discuss how confocal microscopy and imaging flow cytometry are used to investigate virus entry and replication mechanisms in fixed and live cells. Quantification of viral images and the use of cryo-electron microscopy to gather structural information of viruses is also explored. Using imaging to understand how viruses replicate and interact with host factors, we gain insight into cellular processes and identify novel targets to develop antiviral therapeutics and vaccines.
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Affiliation(s)
- Ryley D McClelland
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
| | - Tyce N Culp
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
| | - David J Marchant
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, Katz Center for Health Research, University of Alberta, Edmonton, AB, Canada
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18
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Smolková B, MacCulloch T, Rockwood TF, Liu M, Henry SJW, Frtús A, Uzhytchak M, Lunova M, Hof M, Jurkiewicz P, Dejneka A, Stephanopoulos N, Lunov O. Protein Corona Inhibits Endosomal Escape of Functionalized DNA Nanostructures in Living Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:46375-46390. [PMID: 34569777 PMCID: PMC9590277 DOI: 10.1021/acsami.1c14401] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNA nanostructures (DNs) can be designed in a controlled and programmable manner, and these structures are increasingly used in a variety of biomedical applications, such as the delivery of therapeutic agents. When exposed to biological liquids, most nanomaterials become covered by a protein corona, which in turn modulates their cellular uptake and the biological response they elicit. However, the interplay between living cells and designed DNs are still not well established. Namely, there are very limited studies that assess protein corona impact on DN biological activity. Here, we analyzed the uptake of functionalized DNs in three distinct hepatic cell lines. Our analysis indicates that cellular uptake is linearly dependent on the cell size. Further, we show that the protein corona determines the endolysosomal vesicle escape efficiency of DNs coated with an endosome escape peptide. Our study offers an important basis for future optimization of DNs as delivery systems for various biomedical applications.
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Affiliation(s)
- Barbora Smolková
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Tyler F Rockwood
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Minghui Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Skylar J W Henry
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Adam Frtús
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
| | - Mariia Uzhytchak
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
| | - Mariia Lunova
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
- Institute for Clinical & Experimental Medicine (IKEM), Prague 14021, Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague 18223, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague 18223, Czech Republic
| | - Alexandr Dejneka
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Oleg Lunov
- Department of Optical and Biophysical Systems, Institute of Physics of the Czech Academy of Sciences, Prague 18221, Czech Republic
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19
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Gopal A, Herr AE. Segmentation-based analysis of single-cell immunoblots. Electrophoresis 2021; 42:2070-2080. [PMID: 34357587 PMCID: PMC8526408 DOI: 10.1002/elps.202100144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 11/11/2022]
Abstract
From genomics to transcriptomics to proteomics, microfluidic tools underpin recent advances in single-cell biology. Detection of specific proteoforms-with single-cell resolution-presents challenges in detection specificity and sensitivity. Miniaturization of protein immunoblots to single-cell resolution mitigates these challenges. For example, in microfluidic western blotting, protein targets are separated by electrophoresis and subsequently detected using fluorescently labeled antibody probes. To quantify the expression level of each protein target, the fluorescent protein bands are fit to Gaussians; yet, this method is difficult to use with noisy, low-abundance, or low-SNR protein bands, and with significant band skew or dispersion. In this study, we investigate segmentation-based approaches to robustly quantify protein bands from single-cell protein immunoblots. As compared to a Gaussian fitting pipeline, the segmentation pipeline detects >1.5× more protein bands for downstream quantification as well as more of the low-abundance protein bands (i.e., with SNR ∼3). Utilizing deep learning-based segmentation approaches increases the recovery of low-SNR protein bands by an additional 50%. However, we find that segmentation-based approaches are less robust at quantifying poorly resolved protein bands (separation resolution, Rs < 0.6). With burgeoning needs for more single-cell protein analysis tools, we see microfluidic separations as benefitting substantially from segmentation-based analysis approaches.
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Affiliation(s)
- Anjali Gopal
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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20
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Drees D, Scherzinger A, Hägerling R, Kiefer F, Jiang X. Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets. BMC Bioinformatics 2021; 22:346. [PMID: 34174827 PMCID: PMC8236169 DOI: 10.1186/s12859-021-04262-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/11/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent advances in 3D imaging technologies provide novel insights to researchers and reveal finer and more detail of examined specimen, especially in the biomedical domain, but also impose huge challenges regarding scalability for automated analysis algorithms due to rapidly increasing dataset sizes. In particular, existing research towards automated vessel network analysis does not always consider memory requirements of proposed algorithms and often generates a large number of spurious branches for structures consisting of many voxels. Additionally, very often these algorithms have further restrictions such as the limitation to tree topologies or relying on the properties of specific image modalities. RESULTS We propose a scalable iterative pipeline (in terms of computational cost, required main memory and robustness) that extracts an annotated abstract graph representation from the foreground segmentation of vessel networks of arbitrary topology and vessel shape. The novel iterative refinement process is controlled by a single, dimensionless, a-priori determinable parameter. CONCLUSIONS We are able to, for the first time, analyze the topology of volumes of roughly 1 TB on commodity hardware, using the proposed pipeline. We demonstrate improved robustness in terms of surface noise, vessel shape deviation and anisotropic resolution compared to the state of the art. An implementation of the presented pipeline is publicly available in version 5.1 of the volume rendering and processing engine Voreen.
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Affiliation(s)
- Dominik Drees
- Faculty of Mathematics and Computer Science, University of Münster, Münster, Germany
| | | | | | | | - Xiaoyi Jiang
- Faculty of Mathematics and Computer Science, University of Münster, Münster, Germany
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21
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Pilevar M, Kim KT, Lee WH. Recent advances in biosensors for detecting viruses in water and wastewater. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124656. [PMID: 33308919 DOI: 10.1016/j.jhazmat.2020.124656] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 05/09/2023]
Abstract
As there is a considerable number of virus particles in wastewater which cause numerous infectious diseases, it is necessary to eliminate viruses from domestic wastewater before it is released in the environment. In addition, on-site detection of viruses in wastewater can provide information on possible virus exposures in the community of a given wastewater catchment. For this purpose, the pre-detection of different strains of viruses in wastewaters is an essential environmental step. Epidemiological studies illustrate that viruses are the most challenging pathogens to be detected in water samples because of their nano sizes, discrete distribution, and low infective doses. Over the past decades, several methods have been applied for the detection of waterborne viruses which include polymerase chain reaction-based methods (PCR), enzyme-linked immunosorbent assay (ELISA), and nucleic acid sequence-based amplification (NASBA). Although they have shown acceptable performance in virus measurements, their drawbacks such as complicated and time-consuming procedures, low sensitivity, and high analytical cost call for alternatives. Although biosensors are still in an early stage for practical applications, they have shown great potential to become an alternative means for virus detection in water and wastewater. This comprehensive review addresses the different types of viruses found in water and the recent development of biosensors for detecting waterborne viruses.
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Affiliation(s)
- Mohsen Pilevar
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Keug Tae Kim
- Department of Environmental & Energy Engineering, The University of Suwon, 17 Wauan-gil, Bongdam-eup, Hwaseong-si, Gyeonggi-do 18323, South Korea
| | - Woo Hyoung Lee
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL 32816, USA.
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22
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Kim BH, Jeziorek M, Kanal HD, Contu VR, Dobrowolski R, Levison SW. Moderately Inducing Autophagy Reduces Tertiary Brain Injury after Perinatal Hypoxia-Ischemia. Cells 2021; 10:898. [PMID: 33919804 PMCID: PMC8070811 DOI: 10.3390/cells10040898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/13/2023] Open
Abstract
Recent studies of cerebral hypoxia-ischemia (HI) have highlighted slowly progressive neurodegeneration whose mechanisms remain elusive, but if blocked, could considerably improve long-term neurological function. We previously established that the cytokine transforming growth factor (TGF)β1 is highly elevated following HI and that delivering an antagonist for TGFβ receptor activin-like kinase 5 (ALK5)-SB505124-three days after injury in a rat model of moderate pre-term HI significantly preserved the structural integrity of the thalamus and hippocampus as well as neurological functions associated with those brain structures. To elucidate the mechanism whereby ALK5 inhibition reduces cell death, we assessed levels of autophagy markers in neurons and found that SB505124 increased numbers of autophagosomes and levels of lipidated light chain 3 (LC3), a key protein known to mediate autophagy. However, those studies did not determine whether (1) SB was acting directly on the CNS and (2) whether directly inducing autophagy could decrease cell death and improve outcome. Here we show that administering an ALK5 antagonist three days after HI reduced actively apoptotic cells by ~90% when assessed one week after injury. Ex vivo studies using the lysosomal inhibitor chloroquine confirmed that SB505124 enhanced autophagy flux in the injured hemisphere, with a significant accumulation of the autophagic proteins LC3 and p62 in SB505124 + chloroquine treated brain slices. We independently activated autophagy using the stimulatory peptide Tat-Beclin1 to determine if enhanced autophagy is directly responsible for improved outcomes. Administering Tat-Beclin1 starting three days after injury preserved the structural integrity of the hippocampus and thalamus with improved sensorimotor function. These data support the conclusion that intervening at this phase of injury represents a window of opportunity where stimulating autophagy is beneficial.
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Affiliation(s)
- Brian H. Kim
- Department of Pharmacology, Physiology and Neuroscience, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA; (B.H.K.); (H.D.K.)
| | - Maciej Jeziorek
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Rutgers University, Newark, NJ 07102, USA; (M.J.); (V.R.C.); (R.D.)
| | - Hur Dolunay Kanal
- Department of Pharmacology, Physiology and Neuroscience, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA; (B.H.K.); (H.D.K.)
| | - Viorica Raluca Contu
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Rutgers University, Newark, NJ 07102, USA; (M.J.); (V.R.C.); (R.D.)
| | - Radek Dobrowolski
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Rutgers University, Newark, NJ 07102, USA; (M.J.); (V.R.C.); (R.D.)
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX 78229, USA
| | - Steven W. Levison
- Department of Pharmacology, Physiology and Neuroscience, Rutgers-New Jersey Medical School, Newark, NJ 07103, USA; (B.H.K.); (H.D.K.)
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23
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Luo S, Zhang Y, Nguyen KT, Feng S, Shi Y, Liu Y, Hutchinson P, Chierchia G, Talbot H, Bourouina T, Jiang X, Liu AQ. Machine Learning-Based Pipeline for High Accuracy Bioparticle Sizing. MICROMACHINES 2020; 11:mi11121084. [PMID: 33297515 PMCID: PMC7762436 DOI: 10.3390/mi11121084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022]
Abstract
High accuracy measurement of size is essential in physical and biomedical sciences. Various sizing techniques have been widely used in sorting colloidal materials, analyzing bioparticles and monitoring the qualities of food and atmosphere. Most imaging-free methods such as light scattering measure the averaged size of particles and have difficulties in determining non-spherical particles. Imaging acquisition using camera is capable of observing individual nanoparticles in real time, but the accuracy is compromised by the image defocusing and instrumental calibration. In this work, a machine learning-based pipeline is developed to facilitate a high accuracy imaging-based particle sizing. The pipeline consists of an image segmentation module for cell identification and a machine learning model for accurate pixel-to-size conversion. The results manifest a significantly improved accuracy, showing great potential for a wide range of applications in environmental sensing, biomedical diagnostical, and material characterization.
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Affiliation(s)
- Shaobo Luo
- ESIEE, Universite Paris-Est, CEDEX 93162 Noisy-le-Grand, France; (S.L.); (G.C.)
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore;
| | - Yi Zhang
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Correspondence: (Y.Z.); (T.B.); (X.J.); (A.Q.L.)
| | - Kim Truc Nguyen
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore;
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
| | - Shilun Feng
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
- Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Beijing 200050, China
| | - Yuzhi Shi
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
| | - Yang Liu
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
| | - Paul Hutchinson
- Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore;
| | - Giovanni Chierchia
- ESIEE, Universite Paris-Est, CEDEX 93162 Noisy-le-Grand, France; (S.L.); (G.C.)
| | - Hugues Talbot
- CentraleSupelec, Universite Paris-Saclay, 91190 Saint-Aubin, France;
| | - Tarik Bourouina
- ESIEE, Universite Paris-Est, CEDEX 93162 Noisy-le-Grand, France; (S.L.); (G.C.)
- Correspondence: (Y.Z.); (T.B.); (X.J.); (A.Q.L.)
| | - Xudong Jiang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
- Correspondence: (Y.Z.); (T.B.); (X.J.); (A.Q.L.)
| | - Ai Qun Liu
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore;
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore; (S.F.); (Y.S.); (Y.L.)
- Correspondence: (Y.Z.); (T.B.); (X.J.); (A.Q.L.)
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24
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Lunde A, Glover JC. A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis. Sci Rep 2020; 10:19027. [PMID: 33149236 PMCID: PMC7643144 DOI: 10.1038/s41598-020-75835-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/14/2020] [Indexed: 11/09/2022] Open
Abstract
Differential fluorescence labeling and multi-fluorescence imaging followed by colocalization analysis is commonly used to investigate cellular heterogeneity in situ. This is particularly important when investigating the biology of tissues with diverse cell types. Object-based colocalization analysis (OBCA) tools can employ automatic approaches, which are sensitive to errors in cell segmentation, or manual approaches, which can be impractical and tedious. Here, we present a novel set of tools for OBCA using a semi-automatic approach, consisting of two ImageJ plugins, a Microsoft Excel macro, and a MATLAB script. One ImageJ plugin enables customizable processing of multichannel 3D images for enhanced visualization of features relevant to OBCA, and another enables semi-automatic colocalization quantification. The Excel macro and the MATLAB script enable data organization and 3D visualization of object data across image series. The tools are well suited for experiments involving complex and large image data sets, and can be used in combination or as individual components, allowing flexible, efficient and accurate OBCA. Here we demonstrate their utility in immunohistochemical analyses of the developing central nervous system, which is characterized by complexity in the number and distribution of cell types, and by high cell packing densities, which can both create challenging situations for OBCA.
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Affiliation(s)
- Anders Lunde
- Laboratory of Neural Development and Optical Recording (NDEVOR), Division of Physiology, Department of Molecular Medicine, University of Oslo, Blindern, 1105, Oslo, Norway
| | - Joel C Glover
- Laboratory of Neural Development and Optical Recording (NDEVOR), Division of Physiology, Department of Molecular Medicine, University of Oslo, Blindern, 1105, Oslo, Norway.
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25
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Xue R, Cartmell S. A simple in vitro biomimetic perfusion system for mechanotransduction study. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2020; 21:635-640. [PMID: 33061836 PMCID: PMC7534211 DOI: 10.1080/14686996.2020.1808432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
In mechanotransduction studies, flow-induced shear stress (FSS) is often applied to two-dimensional (2D) cultured cells with a parallel-plate flow chamber (PPFC) due to its simple FSS estimation. However, cells behave differently under FSS inside a 3D scaffold (e.g. 10 mPa FSS was shown to induce osteogenesis of human mesenchymal stem cells (hMSC) in 3D but over 900 mPa was needed for 2D culture). Here, a simple in vitro biomimetic perfusion system using borosilicate glass capillary tubes has been developed to study the cellular behaviour under low-level FSS that mimics 3D culture. It has been shown that, compared to cells in the PPFC, hMSC in the capillary tubes had upregulated Runx-2 expression and osteogenic cytoskeleton actin network under 10 mPa FSS for 24 h. Also, an image analysis method based on Haralick texture measurement has been used to identify osteogenic actin network. The biomimetic perfusion system can be a valuable tool to study mechanotransduction in 3D for more clinical relevant tissue-engineering applications.
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Affiliation(s)
- Ruikang Xue
- Department of Materials, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Sarah Cartmell
- Department of Materials, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
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26
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Dallas SL, Moore DS. Using confocal imaging approaches to understand the structure and function of osteocytes and the lacunocanalicular network. Bone 2020; 138:115463. [PMID: 32512167 PMCID: PMC7423610 DOI: 10.1016/j.bone.2020.115463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023]
Abstract
Although overlooked in the past, osteocytes have come to the forefront of skeletal biology and are now recognized as a key cell type that integrates hormonal, mechanical and other signals to control bone mass through regulation of both osteoblast and osteoclast activity. With the surge of recent interest in osteocytes as bone regulatory cells and the discovery that they also function as endocrine regulators of phosphate homeostasis, there has been renewed interest in understanding the structure and function of these unique and relatively inaccessible cells. Osteocytes are embedded within the mineralized bone matrix and are housed within a complex lacunocanalicular system which connects them with the circulation and with other organ systems. This has presented unique challenges for imaging these cells. This review summarizes recent advances in confocal imaging approaches for visualizing osteocytes and their lacunocanalicular networks in both living and fixed bone specimens and discusses how computational approaches can be combined with live and fixed cell imaging techniques to generate quantitative outputs and predictive models. The integration of advanced imaging with computational approaches promises to lead to a more in depth understanding of the structure and function of osteocyte networks and the lacunocanalicular system in the healthy and aging state as well as in pathological conditions in bone.
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Affiliation(s)
- Sarah L Dallas
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri Kansas City, Kansas City, MO 64108, United States of America.
| | - David S Moore
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri Kansas City, Kansas City, MO 64108, United States of America
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27
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Ashdown GW, Dimon M, Fan M, Sánchez-Román Terán F, Witmer K, Gaboriau DCA, Armstrong Z, Ando DM, Baum J. A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens. SCIENCE ADVANCES 2020; 6:6/39/eaba9338. [PMID: 32978158 PMCID: PMC7518791 DOI: 10.1126/sciadv.aba9338] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Drug resistance threatens the effective prevention and treatment of an ever-increasing range of human infections. This highlights an urgent need for new and improved drugs with novel mechanisms of action to avoid cross-resistance. Current cell-based drug screens are, however, restricted to binary live/dead readouts with no provision for mechanism of action prediction. Machine learning methods are increasingly being used to improve information extraction from imaging data. These methods, however, work poorly with heterogeneous cellular phenotypes and generally require time-consuming human-led training. We have developed a semi-supervised machine learning approach, combining human- and machine-labeled training data from mixed human malaria parasite cultures. Designed for high-throughput and high-resolution screening, our semi-supervised approach is robust to natural parasite morphological heterogeneity and correctly orders parasite developmental stages. Our approach also reproducibly detects and clusters drug-induced morphological outliers by mechanism of action, demonstrating the potential power of machine learning for accelerating cell-based drug discovery.
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Affiliation(s)
- George W Ashdown
- Department of Life Sciences, Imperial College London, London, UK
| | | | | | | | - Kathrin Witmer
- Department of Life Sciences, Imperial College London, London, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, Imperial College London, London, UK
| | | | | | - Jake Baum
- Department of Life Sciences, Imperial College London, London, UK.
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28
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Meijering E. A bird's-eye view of deep learning in bioimage analysis. Comput Struct Biotechnol J 2020; 18:2312-2325. [PMID: 32994890 PMCID: PMC7494605 DOI: 10.1016/j.csbj.2020.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/26/2020] [Accepted: 08/01/2020] [Indexed: 02/07/2023] Open
Abstract
Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with potentially far-reaching consequences for healthcare. In this mini-review, we take a bird's-eye view at the past, present, and future developments of deep learning, starting from science at large, to biomedical imaging, and bioimage analysis in particular.
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Affiliation(s)
- Erik Meijering
- School of Computer Science and Engineering & Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia
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29
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Lunova M, Smolková B, Uzhytchak M, Janoušková KŽ, Jirsa M, Egorova D, Kulikov A, Kubinová Š, Dejneka A, Lunov O. Light-induced modulation of the mitochondrial respiratory chain activity: possibilities and limitations. Cell Mol Life Sci 2020; 77:2815-2838. [PMID: 31583425 PMCID: PMC11104903 DOI: 10.1007/s00018-019-03321-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/11/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022]
Abstract
Biological effects of high fluence low-power (HFLP) lasers have been reported for some time, yet the molecular mechanisms procuring cellular responses remain obscure. A better understanding of the effects of HFLP lasers on living cells will be instrumental for the development of new experimental and therapeutic strategies. Therefore, we investigated sub-cellular mechanisms involved in the laser interaction with human hepatic cell lines. We show that mitochondria serve as sub-cellular "sensor" and "effector" of laser light non-specific interactions with cells. We demonstrated that despite blue and red laser irradiation results in similar apoptotic death, cellular signaling and kinetic of biochemical responses are distinct. Based on our data, we concluded that blue laser irradiation inhibited cytochrome c oxidase activity in electron transport chain of mitochondria. Contrary, red laser triggered cytochrome c oxidase excessive activation. Moreover, we showed that Bcl-2 protein inhibited laser-induced toxicity by stabilizing mitochondria membrane potential. Thus, cells that either overexpress or have elevated levels of Bcl-2 are protected from laser-induced cytotoxicity. Our findings reveal the mechanism how HFLP laser irradiation interfere with cell homeostasis and underscore that such laser irradiation permits remote control of mitochondrial function in the absence of chemical or biological agents.
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Affiliation(s)
- Mariia Lunova
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic
- Institute for Clinical and Experimental Medicine (IKEM), 14021, Prague, Czech Republic
| | - Barbora Smolková
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Mariia Uzhytchak
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Klára Žofie Janoušková
- Institute for Clinical and Experimental Medicine (IKEM), 14021, Prague, Czech Republic
- First Faculty of Medicine, Charles University, 12108, Prague, Czech Republic
| | - Milan Jirsa
- Institute for Clinical and Experimental Medicine (IKEM), 14021, Prague, Czech Republic
| | | | | | - Šárka Kubinová
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic
- Institute of Experimental Medicine, Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Alexandr Dejneka
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Oleg Lunov
- Institute of Physics, Czech Academy of Sciences, 18221, Prague, Czech Republic.
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30
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ZNF322A-mediated protein phosphorylation induces autophagosome formation through modulation of IRS1-AKT glucose uptake and HSP-elicited UPR in lung cancer. J Biomed Sci 2020; 27:75. [PMID: 32576196 PMCID: PMC7310457 DOI: 10.1186/s12929-020-00668-5] [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: 01/06/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background ZNF322A is an oncogenic transcription factor that belongs to the Cys2His2-type zinc-finger protein family. Accumulating evidence suggests that ZNF322A may contribute to the tumorigenesis of lung cancer, however, the ZNF322A-mediated downstream signaling pathways remain unknown. Methods To uncover ZNF322A-mediated functional network, we applied phosphopeptide enrichment and isobaric labeling strategies with mass spectrometry-based proteomics using A549 lung cancer cells, and analyzed the differentially expressed proteins of phosphoproteomic and proteomic profiles to determine ZNF322A-modulated pathways. Results ZNF322A highlighted a previously unidentified insulin signaling, heat stress, and signal attenuation at the post-translational level. Consistently, protein-phosphoprotein-kinase interaction network analysis revealed phosphorylation of IRS1 and HSP27 were altered upon ZNF322A-silenced lung cancer cells. Thus, we further investigated the molecular regulation of ZNF322A, and found the inhibitory transcriptional regulation of ZNF322A on PIM3, which was able to phosphorylate IRS1 at serine1101 in order to manipulate glucose uptake via the PI3K/AKT/mTOR signaling pathway. Moreover, ZNF322A also affects the unfolded protein response by phosphorylation of HSP27S82 and eIF2aS51, and triggers autophagosome formation in lung cancer cells. Conclusions These findings not only give new information about the molecular regulation of the cellular proteins through ZNF322A at the post-translational level, but also provides a resource for the study of lung cancer therapy.
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31
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Martín MJ, Gentili C, Lassalle V. In vitro Biological Tests as the First Tools To Validate Magnetic Nanotheranostics for Colorectal Cancer Models. ChemMedChem 2020; 15:1003-1017. [PMID: 32365271 DOI: 10.1002/cmdc.202000119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/03/2020] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) remains a leading cause of cancer death. Nanotechnology has focused on reaching more effective treatments. In this concern, magnetic nanoparticles (MNPs) have been studied for a wide range of biomedical applications related to CRC, such as diagnostic imaging, drug delivery and thermal therapy. However, limited research is currently found in the open literature that refers to nanosystems combining all these mentioned areas (theranostics). When developing nanosystems intended as theranostics applied to CRC, possible variations between patients must be considered. Therefore, multiple in vitro assays are required as guidance for future preclinical and clinical trials. The objective of this contribution is to evaluate the available and recent literature regarding the interactions of MNP and CRC models, aiming to critically analyze the information given by the commonly used assays and evaluate the data provided by each one with a view to implementing this novel technology in CRC diagnostics and therapy.
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Affiliation(s)
- María Julia Martín
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (CONICET-UNS), Alem 1253, Bahía Blanca, Argentina.,INBIOSUR, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (CONICET-UNS), San Juan 670, Bahía Blanca, Argentina
| | - Claudia Gentili
- INBIOSUR, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (CONICET-UNS), San Juan 670, Bahía Blanca, Argentina
| | - Verónica Lassalle
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (CONICET-UNS), Alem 1253, Bahía Blanca, Argentina
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32
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Corso G, Montagna G, Figueiredo J, La Vecchia C, Fumagalli Romario U, Fernandes MS, Seixas S, Roviello F, Trovato C, Guerini-Rocco E, Fusco N, Pravettoni G, Petrocchi S, Rotili A, Massari G, Magnoni F, De Lorenzi F, Bottoni M, Galimberti V, Sanches JM, Calvello M, Seruca R, Bonanni B. Hereditary Gastric and Breast Cancer Syndromes Related to CDH1 Germline Mutation: A Multidisciplinary Clinical Review. Cancers (Basel) 2020; 12:E1598. [PMID: 32560361 PMCID: PMC7352390 DOI: 10.3390/cancers12061598] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
E-cadherin (CDH1 gene) germline mutations are associated with the development of diffuse gastric cancer in the context of the so-called hereditary diffuse gastric syndrome, and with an inherited predisposition of lobular breast carcinoma. In 2019, the international gastric cancer linkage consortium revised the clinical criteria and established guidelines for the genetic screening of CDH1 germline syndromes. Nevertheless, the introduction of multigene panel testing in clinical practice has led to an increased identification of E-cadherin mutations in individuals without a positive family history of gastric or breast cancers. This observation motivated us to review and present a novel multidisciplinary clinical approach (nutritional, surgical, and image screening) for single subjects who present germline CDH1 mutations but do not fulfil the classic clinical criteria, namely those identified as-(1) incidental finding and (2) individuals with lobular breast cancer without family history of gastric cancer (GC).
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Affiliation(s)
- Giovanni Corso
- Division of Breast Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (G.M.); (F.M.); (V.G.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.G.-R.); (N.F.); (G.P.)
| | - Giacomo Montagna
- Breast Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Joana Figueiredo
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (J.F.); (M.S.F.); (S.S.); (R.S.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Carlo La Vecchia
- Department of Clinical Sciences and Community Health, University of Milan, 20133 Milan, Italy;
| | - Uberto Fumagalli Romario
- Department of Digestive Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy;
| | - Maria Sofia Fernandes
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (J.F.); (M.S.F.); (S.S.); (R.S.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Susana Seixas
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (J.F.); (M.S.F.); (S.S.); (R.S.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Franco Roviello
- Departments of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy;
| | - Cristina Trovato
- Division of Endoscopy, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy;
| | - Elena Guerini-Rocco
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.G.-R.); (N.F.); (G.P.)
- Division of Pathology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.G.-R.); (N.F.); (G.P.)
- Division of Pathology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy
| | - Gabriella Pravettoni
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.G.-R.); (N.F.); (G.P.)
- Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy;
| | - Serena Petrocchi
- Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy;
| | - Anna Rotili
- Division of Breast Imaging, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy;
| | - Giulia Massari
- Division of Breast Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (G.M.); (F.M.); (V.G.)
| | - Francesca Magnoni
- Division of Breast Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (G.M.); (F.M.); (V.G.)
| | - Francesca De Lorenzi
- Division of Plastic Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (F.D.L.); (M.B.)
| | - Manuela Bottoni
- Division of Plastic Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (F.D.L.); (M.B.)
| | - Viviana Galimberti
- Division of Breast Surgery, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (G.M.); (F.M.); (V.G.)
| | - João Miguel Sanches
- Institute for Systems and Robotics, Instituto Superior Técnico, 1049-001 Lisboa, Portugal;
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (M.C.); (B.B.)
| | - Raquel Seruca
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal; (J.F.); (M.S.F.); (S.S.); (R.S.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Medical Faculty, University of Porto, 4099-002 Porto, Portugal
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy; (M.C.); (B.B.)
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Di Rosa G, Brunetti G, Scuto M, Trovato Salinaro A, Calabrese EJ, Crea R, Schmitz-Linneweber C, Calabrese V, Saul N. Healthspan Enhancement by Olive Polyphenols in C. elegans Wild Type and Parkinson's Models. Int J Mol Sci 2020; 21:E3893. [PMID: 32486023 PMCID: PMC7312680 DOI: 10.3390/ijms21113893] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is the second most prevalent late-age onset neurodegenerative disorder, affecting 1% of the population after the age of about 60 years old and 4% of those over 80 years old, causing motor impairments and cognitive dysfunction. Increasing evidence indicates that Mediterranean diet (MD) exerts beneficial effects in maintaining health, especially during ageing and by the prevention of neurodegenerative disorders. In this regard, olive oil and its biophenolic constituents like hydroxytyrosol (HT) have received growing attention in the past years. Thus, in the current study we test the health-promoting effects of two hydroxytyrosol preparations, pure HT and Hidrox® (HD), which is hydroxytyrosol in its "natural" environment, in the established invertebrate model organism Caenorhabditis elegans. HD exposure led to much stronger beneficial locomotion effects in wild type worms compared to HT in the same concentration. Consistent to this finding, in OW13 worms, a PD-model characterized by α-synuclein expression in muscles, HD exhibited a significant higher effect on α-synuclein accumulation and swim performance than HT, an effect partly confirmed also in swim assays with the UA44 strain, which features α-synuclein expression in DA-neurons. Interestingly, beneficial effects of HD and HT treatment with similar strength were detected in the lifespan and autofluorescence of wild-type nematodes, in the neuronal health of UA44 worms as well as in the locomotion of rotenone-induced PD-model. Thus, the hypothesis that HD features higher healthspan-promoting abilities than HT was at least partly confirmed. Our study demonstrates that HD polyphenolic extract treatment has the potential to partly prevent or even treat ageing-related neurodegenerative diseases and ageing itself. Future investigations including mammalian models and human clinical trials are needed to uncover the full potential of these olive compounds.
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Affiliation(s)
- Gabriele Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.D.R.); (G.B.); (M.S.); (A.T.S.)
| | - Giovanni Brunetti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.D.R.); (G.B.); (M.S.); (A.T.S.)
| | - Maria Scuto
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.D.R.); (G.B.); (M.S.); (A.T.S.)
| | - Angela Trovato Salinaro
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.D.R.); (G.B.); (M.S.); (A.T.S.)
| | - Edward J. Calabrese
- Department of Environmental Health Sciences, Morrill I, N344, University of Massachusetts, Amherst, MA 01003, USA;
| | - Roberto Crea
- Oliphenol LLC., 26225 Eden Landing Road, Unit C, Hayward, CA 94545, USA;
| | - Christian Schmitz-Linneweber
- Faculty of Life Sciences, Institute of Biology, Molecular Genetics Group, Humboldt University of Berlin, Philippstr. 13, House 22, 10115 Berlin, Germany; (C.S.-L.); (N.S.)
| | - Vittorio Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.D.R.); (G.B.); (M.S.); (A.T.S.)
| | - Nadine Saul
- Faculty of Life Sciences, Institute of Biology, Molecular Genetics Group, Humboldt University of Berlin, Philippstr. 13, House 22, 10115 Berlin, Germany; (C.S.-L.); (N.S.)
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Tayal S, Singh V, Kaur T, Singh N, Mehta DS. Simultaneous fluorescence and quantitative phase imaging of MG63 osteosarcoma cells to monitor morphological changes with time using partially spatially coherent light source. Methods Appl Fluoresc 2020; 8:035004. [PMID: 32325433 DOI: 10.1088/2050-6120/ab8c5d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Quantitative phase imaging (QPI) technique is used to determine various biophysical parameters, such as refractive index, cell thickness, morphology, etc. On the other hand, fluorescence microscopy is used to acquire information regarding molecular specificity of the biological cells and tissues. Conventionally, a fully coherent light source such as laser is used in QPI technique to obtain the interference fringes with ease; however, its high coherence is also responsible for the generation of speckle and spurious fringes, which results in degraded image quality and affects the phase measurement results too. In this paper, we report a multi-modal system that can be effectively utilized to acquire time varied diverse information about the biological specimen with high spatial phase sensitivity. Herein, a single unit comprising of a fluorescence microscope and the Linnik based interferometer specially equipped with a partially spatially coherent light source illumination was developed. The integrated system is capable to procure molecular specificity and phase information of biological specimen, in a single shot, utilizing a single-chip color CCD camera. Here, we performed experiments on MG63 osteosarcoma cells, and the composite interferometric-fluorescence images were obtained and then digitally decomposed into red and green colors; and, the phase maps were reconstructed using the Fourier fringe analysis method. Furthermore, the cultured cells were monitored over a time-span to observe and investigate the time dependent morphological changes along with the quantification of cellular adhesion and spreading. Hence, the proposed system can be utilized to quantify time dependent changes in the cell's morphology and in cell adhesion which can be an indicator for the detection of various range of diseases such as arthritis, cancer, osteoporosis and atherosclerosis.
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Affiliation(s)
- Shilpa Tayal
- Bio-Photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
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Levada K, Pshenichnikov S, Omelyanchik A, Rodionova V, Nikitin A, Savchenko A, Schetinin I, Zhukov D, Abakumov M, Majouga A, Lunova M, Jirsa M, Smolková B, Uzhytchak M, Dejneka A, Lunov O. Progressive lysosomal membrane permeabilization induced by iron oxide nanoparticles drives hepatic cell autophagy and apoptosis. NANO CONVERGENCE 2020; 7:17. [PMID: 32424769 PMCID: PMC7235155 DOI: 10.1186/s40580-020-00228-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/29/2020] [Indexed: 05/02/2023]
Abstract
Iron oxide nanoparticles (IONs) are frequently used in various biomedical applications, in particular as magnetic resonance imaging contrast agents in liver imaging. Indeed, number of IONs have been withdrawn due to their poor clinical performance. Yet comprehensive understanding of their interactions with hepatocytes remains relatively limited. Here we investigated how iron oxide nanocubes (IO-cubes) and clusters of nanocubes (IO-clusters) affect distinct human hepatic cell lines. The viability of HepG2, Huh7 and Alexander cells was concentration-dependently decreased after exposure to either IO-cubes or IO-clusters. We found similar cytotoxicity levels in three cell lines triggered by both nanoparticle formulations. Our data indicate that different expression levels of Bcl-2 predispose cell death signaling mediated by nanoparticles. Both nanoparticles induced rather apoptosis than autophagy in HepG2. Contrary, IO-cubes and IO-clusters trigger distinct cell death signaling events in Alexander and Huh7 cells. Our data clarifies the mechanism by which cubic nanoparticles induce autophagic flux and the mechanism of subsequent toxicity. These findings imply that the cytotoxicity of ION-based contrast agents should be carefully considered, particularly in patients with liver diseases.
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Affiliation(s)
- Kateryna Levada
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Stanislav Pshenichnikov
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alexander Omelyanchik
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Valeria Rodionova
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Aleksey Nikitin
- National University of Science and Technology "MISIS", Moscow, Russia
| | | | - Igor Schetinin
- National University of Science and Technology "MISIS", Moscow, Russia
| | - Dmitry Zhukov
- National University of Science and Technology "MISIS", Moscow, Russia
| | - Maxim Abakumov
- National University of Science and Technology "MISIS", Moscow, Russia
| | - Alexander Majouga
- National University of Science and Technology "MISIS", Moscow, Russia
| | - Mariia Lunova
- Institute of Physics of the Czech Academy of Sciences, 18221, Prague, Czech Republic
- Institute for Clinical & Experimental Medicine (IKEM), Prague, Czech Republic
| | - Milan Jirsa
- Institute for Clinical & Experimental Medicine (IKEM), Prague, Czech Republic
| | - Barbora Smolková
- Institute of Physics of the Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Mariia Uzhytchak
- Institute of Physics of the Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, 18221, Prague, Czech Republic
| | - Oleg Lunov
- Institute of Physics of the Czech Academy of Sciences, 18221, Prague, Czech Republic.
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Babii O, Wang Z, Liu G, Martinez EC, van Drunen Littel-van den Hurk S, Chen L. Low molecular weight chitosan nanoparticles for CpG oligodeoxynucleotides delivery: Impact of molecular weight, degree of deacetylation, and mannosylation on intracellular uptake and cytokine induction. Int J Biol Macromol 2020; 159:46-56. [PMID: 32437810 DOI: 10.1016/j.ijbiomac.2020.05.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Although synthetic CpG oligodeoxynucleotides (ODNs) have shown substantial potential as immunotherapeutic agents, their effective intracellular delivery remains challenging. In this work, nanoparticles prepared from low-molecular weight (LMW) chitosans were investigated as CpG ODN delivery systems. Chitosan samples with a molecular weight (Mw) of 5 and 15 kDa and degree of deacetylation (DDA) of 50 and 80% were prepared. Additionally, mannosylated chitosans with a substitution degree of 15% were synthesized. The impact of LMW chitosan Mw and DDA on nanoparticle physical properties and the associated immunostimulatory effect in RAW 264.7 cells was studied. Nanoparticles prepared with chitosan of higher DDA and larger Mw exhibited better CpG ODN binding ability and intracellular uptake. Nevertheless, the most efficient immunostimulatory effect was observed while using 50% acetylated and mannosylated samples. The decreased charge density on chitosan backbone resulted in the enhanced intracellular CpG ODN release, which promoted in vitro cytokine secretion. Moreover, mannose ligand grafting promoted nanoparticle uptake through receptor-mediated recognition. Overall, this research suggests that chitosan structural parameters can be modulated to prepare LMW chitosan nanoparticles that first efficiently encapsulate CpG ODN, and then release it in immune cells, thus may be used as an efficient vector for intracellular CpG ODN delivery.
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Affiliation(s)
- Oksana Babii
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Zhenggang Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Guangyu Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Elisa C Martinez
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada; Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E3, Canada
| | | | - Lingyun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada.
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Iron Oxide Nanoparticle-Induced Autophagic Flux Is Regulated by Interplay between p53-mTOR Axis and Bcl-2 Signaling in Hepatic Cells. Cells 2020; 9:cells9041015. [PMID: 32325714 PMCID: PMC7226334 DOI: 10.3390/cells9041015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Iron oxide-based nanoparticles have been repeatedly shown to affect lysosomal-mediated signaling. Recently, nanoparticles have demonstrated an ability to modulate autophagic flux via lysosome-dependent signaling. However, the precise underlying mechanisms of such modulation as well as the impact of cellular genetic background remain enigmatic. In this study, we investigated how lysosomal-mediated signaling is affected by iron oxide nanoparticle uptake in three distinct hepatic cell lines. We found that nanoparticle-induced lysosomal dysfunction alters sub-cellular localization of pmTOR and p53 proteins. Our data indicate that alterations in the sub-cellular localization of p53 protein induced by nanoparticle greatly affect the autophagic flux. We found that cells with high levels of Bcl-2 are insensitive to autophagy initiated by nanoparticles. Altogether, our data identify lysosomes as a central hub that control nanoparticle-mediated responses in hepatic cells. Our results provide an important fundamental background for the future development of targeted nanoparticle-based therapies.
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Geissinger SE, Schreiber A, Huber MC, Stühn LG, Schiller SM. Adjustable Bioorthogonal Conjugation Platform for Protein Studies in Live Cells Based on Artificial Compartments. ACS Synth Biol 2020; 9:827-842. [PMID: 32130855 DOI: 10.1021/acssynbio.9b00494] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The investigation of complex biological processes in vivo often requires defined multiple bioconjugation and positioning of functional entities on 3D structures. Prominent examples include spatially defined protein complexes in nature, facilitating efficient biocatalysis of multistep reactions. Mimicking natural strategies, synthetic scaffolds should comprise bioorthogonal conjugation reactions and allow for absolute stoichiometric quantification as well as facile scalability through scaffold reproduction. Existing in vivo scaffolding strategies often lack covalent conjugations on geometrically confined scaffolds or precise quantitative characterization. Addressing these shortcomings, we present a bioorthogonal dual conjugation platform based on genetically encoded artificial compartments in vivo, comprising two distinct genetically encoded covalent conjugation reactions and their precise stoichiometric quantification. The SpyTag/SpyCatcher (ST/SC) bioconjugation and the controllable strain-promoted azide-alkyne cycloaddition (SPAAC) were implemented on self-assembled protein membrane-based compartments (PMBCs). The SPAAC reaction yield was quantified to be 23% ± 3% and a ST/SC surface conjugation yield of 82% ± 9% was observed, while verifying the compatibility of both chemical reactions as well as enhanced proteolytic stability. Using tandem mass spectrometry, absolute concentrations of the proteinaceous reactants were calculated to be 0.11 ± 0.05 attomol/cell for PMBC surface-tethered mCherry-ST-His and 0.22 ± 0.09 attomol/cell for PMBC-constituting pAzF-SC-E20F20-His. The established in vivo conjugation platform enables quantifiable protein-protein interaction studies on geometrically defined scaffolds and paves the road to investigate effects of scaffold-tethering on enzyme activity.
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Affiliation(s)
- Süreyya E. Geissinger
- Zentrum für Biosystemanalyse (ZBSA), University of Freiburg, Habsburgerstraße 49, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA), University of Freiburg, Habsburgerstraße 49, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Matthias C. Huber
- Zentrum für Biosystemanalyse (ZBSA), University of Freiburg, Habsburgerstraße 49, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Lara G. Stühn
- Zentrum für Biosystemanalyse (ZBSA), University of Freiburg, Habsburgerstraße 49, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Stefan M. Schiller
- Zentrum für Biosystemanalyse (ZBSA), University of Freiburg, Habsburgerstraße 49, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstraße 19, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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Guerreiro DN, Wu J, Dessaux C, Oliveira AH, Tiensuu T, Gudynaite D, Marinho CM, Boyd A, García-Del Portillo F, Johansson J, O'Byrne CP. Mild Stress Conditions during Laboratory Culture Promote the Proliferation of Mutations That Negatively Affect Sigma B Activity in Listeria monocytogenes. J Bacteriol 2020; 202:e00751-19. [PMID: 32094160 PMCID: PMC7148139 DOI: 10.1128/jb.00751-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/01/2020] [Indexed: 12/18/2022] Open
Abstract
In Listeria monocytogenes, the full details of how stress signals are integrated into the σB regulatory pathway are not yet available. To help shed light on this question, we investigated a collection of transposon mutants that were predicted to have compromised activity of the alternative sigma factor B (σB). These mutants were tested for acid tolerance, a trait that is known to be under σB regulation, and they were found to display increased acid sensitivity, similar to a mutant lacking σB (ΔsigB). The transposon insertions were confirmed by whole-genome sequencing, but in each case, the strains were also found to carry a frameshift mutation in the sigB operon. The changes were predicted to result in premature stop codons, with negative consequences for σB activation, independently of the transposon location. Reduced σB activation in these mutants was confirmed. Growth measurements under conditions similar to those used during the construction of the transposon library revealed that the frameshifted sigB operon alleles conferred a growth advantage at higher temperatures, during late exponential phase. Mixed-culture experiments at 42°C demonstrated that the loss of σB activity allowed mutants to take over a population of parental bacteria. Together, our results suggest that mutations affecting σB activity can arise during laboratory culture because of the growth advantage conferred by these mutations under mild stress conditions. The data highlight the significant cost of stress protection in this foodborne pathogen and emphasize the need for whole-genome sequence analysis of newly constructed strains to confirm the expected genotype.IMPORTANCE In the present study, we investigated a collection of Listeria monocytogenes strains that all carried sigB operon mutations. The mutants all had reduced σB activity and were found to have a growth advantage under conditions of mild heat stress (42°C). In mixed cultures, these mutants outcompeted the wild type when mild heat stress was present but not at an optimal growth temperature. An analysis of 22,340 published L. monocytogenes genome sequences found a high rate of premature stop codons present in genes positively regulating σB activity. Together, these findings suggest that the occurrence of mutations that attenuate σB activity can be favored under conditions of mild stress, probably highlighting the burden on cellular resources that stems from deploying the general stress response.
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Affiliation(s)
- Duarte N Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jialun Wu
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Charlotte Dessaux
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology (CNB)-CSIC, Madrid, Spain
| | - Ana H Oliveira
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Teresa Tiensuu
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Diana Gudynaite
- Molecular Microbiology Department, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catarina M Marinho
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Université Bourgogne Franche-Conté, Dijon, France
- Institut National de la Recherche Agronomique, UMR Agroécologie, Dijon, France
| | - Aoife Boyd
- Pathogenic Mechanisms Research Group, National University of Ireland, Galway, Ireland
| | | | - Jörgen Johansson
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Conor P O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Brunetti G, Di Rosa G, Scuto M, Leri M, Stefani M, Schmitz-Linneweber C, Calabrese V, Saul N. Healthspan Maintenance and Prevention of Parkinson's-like Phenotypes with Hydroxytyrosol and Oleuropein Aglycone in C. elegans. Int J Mol Sci 2020; 21:ijms21072588. [PMID: 32276415 PMCID: PMC7178172 DOI: 10.3390/ijms21072588] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
Numerous studies highlighted the beneficial effects of the Mediterranean diet (MD) in maintaining health, especially during ageing. Even neurodegeneration, which is part of the natural ageing process, as well as the foundation of ageing-related neurodegenerative disorders like Alzheimer’s and Parkinson’s disease (PD), was successfully targeted by MD. In this regard, olive oil and its polyphenolic constituents have received increasing attention in the last years. Thus, this study focuses on two main olive oil polyphenols, hydroxytyrosol (HT) and oleuropein aglycone (OLE), and their effects on ageing symptoms with special attention to PD. In order to avoid long-lasting, expensive, and ethically controversial experiments, the established invertebrate model organism Caenorhabditis elegans was used to test HT and OLE treatments. Interestingly, both polyphenols were able to increase the survival after heat stress, but only HT could prolong the lifespan in unstressed conditions. Furthermore, in aged worms, HT and OLE caused improvements of locomotive behavior and the attenuation of autofluorescence as a marker for ageing. In addition, by using three different C. elegans PD models, HT and OLE were shown i) to enhance locomotion in worms suffering from α-synuclein-expression in muscles or rotenone exposure, ii) to reduce α-synuclein accumulation in muscles cells, and iii) to prevent neurodegeneration in α-synuclein-containing dopaminergic neurons. Hormesis, antioxidative capacities and an activity-boost of the proteasome & phase II detoxifying enzymes are discussed as potential underlying causes for these beneficial effects. Further biological and medical trials are indicated to assess the full potential of HT and OLE and to uncover their mode of action.
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Affiliation(s)
- Giovanni Brunetti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.B.); (G.D.R.); (M.S.)
| | - Gabriele Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.B.); (G.D.R.); (M.S.)
| | - Maria Scuto
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.B.); (G.D.R.); (M.S.)
| | - Manuela Leri
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy; (M.L.); (M.S.)
- Department of Neuroscience, Psychology, Area of Medicine and Health of the Child of the University of Florence, Viale Pieraccini, 6 - 50139 Florence, Italy
| | - Massimo Stefani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy; (M.L.); (M.S.)
| | - Christian Schmitz-Linneweber
- Humboldt University of Berlin, Faculty of Life Sciences, Institute of Biology, Molecular Genetics Group, Philippstr. 13, House 22, 10115 Berlin, Germany;
| | - Vittorio Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy; (G.B.); (G.D.R.); (M.S.)
- Correspondence: (V.C.); (N.S.)
| | - Nadine Saul
- Humboldt University of Berlin, Faculty of Life Sciences, Institute of Biology, Molecular Genetics Group, Philippstr. 13, House 22, 10115 Berlin, Germany;
- Correspondence: (V.C.); (N.S.)
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Koldej R, Ritchie D. High multiplex analysis of the immune microenvironment in bone marrow trephine samples using GeoMX™ digital spatial profiling. IMMUNO-ONCOLOGY TECHNOLOGY 2020; 5:1-9. [PMID: 35756143 PMCID: PMC9216341 DOI: 10.1016/j.iotech.2020.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background To date, studies into the bone marrow (BM) immune microenvironment have been limited due to reliance on the analysis of BM aspirates in which the microenvironmental context is lost. GeoMX™ digital spatial profiling (DSP) is a new technique developed for the analysis of formalin-fixed paraffin-embedded tissue samples which allows high multiplex analysis of protein expression in multiple user-defined regions within a tissue section. We examined the applicability of this technique to the analysis of protein expression in diagnostic BM trephine samples. Materials and methods Archival BM trephines were obtained from patient groups (normal, myelodysplasia and aplastic anaemia). Regions of interest in each section were identified by dual CD3+/CD45+ immunohistochemistry staining to identify immune infiltrates, and DSP was applied. Results Due to variability in cell number within regions of interest and differing cellular composition of the BM trephines, raw protein expression counts were normalised by internal controls and nuclei count to determine the expression level of each protein within each region of interest. In heat map analysis using Spearman's rank correlation, aplastic anaemia samples clustered away from both normal and myelodysplasia samples, demonstrating significant differences in their BM immunology. Conclusions GeoMX™ DSP is an innovative new technique that, for the first time, allows the analysis of archival BM trephines at an unprecedented level of detail. It will allow investigations in large cohorts of patients with haematological malignancies to identify new biomarkers, new mechanisms of disease pathogenesis and new drug targets.
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Affiliation(s)
- R.M. Koldej
- ACRF Translational Haematology Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - D.S. Ritchie
- ACRF Translational Haematology Research Laboratory, Royal Melbourne Hospital, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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Lunov O, Uzhytchak M, Smolková B, Lunova M, Jirsa M, Dempsey NM, Dias AL, Bonfim M, Hof M, Jurkiewicz P, Petrenko Y, Kubinová Š, Dejneka A. Remote Actuation of Apoptosis in Liver Cancer Cells via Magneto-Mechanical Modulation of Iron Oxide Nanoparticles. Cancers (Basel) 2019; 11:cancers11121873. [PMID: 31779223 PMCID: PMC6966689 DOI: 10.3390/cancers11121873] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023] Open
Abstract
Lysosome-activated apoptosis represents an alternative method of overcoming tumor resistance compared to traditional forms of treatment. Pulsed magnetic fields open a new avenue for controlled and targeted initiation of lysosomal permeabilization in cancer cells via mechanical actuation of magnetic nanomaterials. In this study we used a noninvasive tool; namely, a benchtop pulsed magnetic system, which enabled remote activation of apoptosis in liver cancer cells. The magnetic system we designed represents a platform that can be used in a wide range of biomedical applications. We show that liver cancer cells can be loaded with superparamagnetic iron oxide nanoparticles (SPIONs). SPIONs retained in lysosomal compartments can be effectively actuated with a high intensity (up to 8 T), short pulse width (~15 µs), pulsed magnetic field (PMF), resulting in lysosomal membrane permeabilization (LMP) in cancer cells. We revealed that SPION-loaded lysosomes undergo LMP by assessing an increase in the cytosolic activity of the lysosomal cathepsin B. The extent of cell death induced by LMP correlated with the accumulation of reactive oxygen species in cells. LMP was achieved for estimated forces of 700 pN and higher. Furthermore, we validated our approach on a three-dimensional cellular culture model to be able to mimic in vivo conditions. Overall, our results show that PMF treatment of SPION-loaded lysosomes can be utilized as a noninvasive tool to remotely induce apoptosis.
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Affiliation(s)
- Oleg Lunov
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
- Correspondence: ; Tel.: +42-026-6052-131
| | - Mariia Uzhytchak
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
| | - Barbora Smolková
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
| | - Mariia Lunova
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
- Institute for Clinical & Experimental Medicine (IKEM), 14021 Prague, Czech Republic;
| | - Milan Jirsa
- Institute for Clinical & Experimental Medicine (IKEM), 14021 Prague, Czech Republic;
| | - Nora M. Dempsey
- Institut Néel, Grenoble INP, CNRS, Université Grenoble Alpes, 38000 Grenoble, France; (N.M.D.); (A.L.D.)
| | - André L. Dias
- Institut Néel, Grenoble INP, CNRS, Université Grenoble Alpes, 38000 Grenoble, France; (N.M.D.); (A.L.D.)
| | - Marlio Bonfim
- Universidade Federal do Paraná, DELT, Curitiba 81531-980, Brazil;
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 18223 Prague, Czech Republic; (M.H.); (P.J.)
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 18223 Prague, Czech Republic; (M.H.); (P.J.)
| | - Yuri Petrenko
- Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Šárka Kubinová
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
- Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, 18221 Prague, Czech Republic; (M.U.); (B.S.); (M.L.); (Š.K.); (A.D.)
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Abstract
Over the past two decades there have been unprecedented advances in the capabilities for live cell imaging using light and confocal microscopy. Together with the discovery of green fluorescent protein and its derivatives and the development of a vast array of fluorescent imaging probes and conjugates, it is now possible to image virtually any intracellular or extracellular protein or structure. Traditional static imaging of fixed bone cells and tissues takes a snapshot view of events at a specific time point, but can often miss the dynamic aspects of the events being investigated. This chapter provides an overview of the application of live cell imaging approaches for the study of bone cells and bone organ cultures. Rather than emphasizing technical aspects of the imaging equipment, which may vary in different laboratories, we focus on what we consider to be the important principles that are of most practical use for an investigator setting up these techniques in their own laboratory. We also provide detailed protocols that our laboratory has used for live imaging of bone cell and organ cultures.
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Affiliation(s)
- Sarah L Dallas
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA.
| | - Patricia A Veno
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA
| | - LeAnn M Tiede-Lewis
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, Kansas City, MO, USA
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44
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Wilson RL, François M, Jankovic-Karasoulos T, McAninch D, McCullough D, Leifert WR, Roberts CT, Bianco-Miotto T. Characterization of 5-methylcytosine and 5-hydroxymethylcytosine in human placenta cell types across gestation. Epigenetics 2019; 14:660-671. [PMID: 31038385 DOI: 10.1080/15592294.2019.1609866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The placenta is an important organ in pregnancy, however, very little is understood about placental development at a molecular level. This includes the role of epigenetic mechanisms and how they change throughout gestation. DNA methylation studies in this organ are complicated by the different cell types that make up the placenta, each with their own unique transcriptome and epigenome. Placental dysfunction is often associated with pregnancy complications such as preeclampsia (PE). Aberrant DNA methylation in the placenta has been identified in pregnancy complications. We used immunohistochemistry (IHC) and immunofluorescence (IF) to localize 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in placenta tissue from first and second trimester as well as uncomplicated term and PE samples. IHC analysis of whole placental tissues showed 5-mC increased across gestation. When cytotrophoblasts (CTB) and syncytiotrophoblasts (STB) were isolated and assessed using IF, both 5-mC and 5-hmC increased in term CTBs compared to first/second-trimester samples. Staining intensity of 5-hmC was higher in first/second trimester STBs compared to CTBs (P = 0.0011). Finally, IHC staining of term tissue from PE and uncomplicated pregnancies revealed higher 5-mC staining intensity in placentas from PE pregnancies (P = 0.028). Our study has shown increased 5-mC and 5-hmC staining intensities across gestation and differed between two trophoblast populations. Differences in DNA methylation profiles between placental cell types may be indicative of different functions and requires further study to elucidate what changes accompany placental pathologies.
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Affiliation(s)
- Rebecca L Wilson
- a Center for Fetal and Placental Research , Cincinnati Children's Hospital and Medical Research Center , Cincinnati , OH , USA.,b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Maxime François
- d CSIRO Health and Biosecurity , Future Science Platforms Probing Biosystems , Adelaide , Australia.,e School of Biological Sciences , University of Adelaide , Adelaide , Australia
| | - Tanja Jankovic-Karasoulos
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Dale McAninch
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Dylan McCullough
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Wayne R Leifert
- d CSIRO Health and Biosecurity , Future Science Platforms Probing Biosystems , Adelaide , Australia.,e School of Biological Sciences , University of Adelaide , Adelaide , Australia
| | - Claire T Roberts
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Tina Bianco-Miotto
- c Robinson Research Institute , University of Adelaide , Adelaide , Australia.,f School of Agriculture, Food and Wine, Waite Research Institute , University of Adelaide , Adelaide , Australia
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45
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Wiercigroch E, Stepula E, Mateuszuk L, Zhang Y, Baranska M, Chlopicki S, Schlücker S, Malek K. ImmunoSERS microscopy for the detection of smooth muscle cells in atherosclerotic plaques. Biosens Bioelectron 2019; 133:79-85. [PMID: 30909016 DOI: 10.1016/j.bios.2019.02.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/19/2023]
Abstract
We investigated the suitability of immuno-SERS (iSERS) microscopy for imaging of smooth muscle cells (SMCs) in atherosclerotic plaques. Localization of SMCs is achieved by using SERS-labelled antibodies direct against alpha-smooth muscle actin (SMA). The staining quality of the false-colour iSERS images obtained by confocal Raman microscopy with point mapping is compared with wide-field immunofluorescence images. Both direct (labelled primary antibody) and indirect iSERS staining (unlabelled primary and labelled secondary antibody) techniques were employed. Direct iSERS staining yields results comparable to indirect IF staining, demonstrating the suitability of iSERS in research on atherosclerosis and paving the way for future multiplexed imaging experiments.
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Affiliation(s)
- Ewelina Wiercigroch
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Elzbieta Stepula
- Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Lukasz Mateuszuk
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Yuying Zhang
- Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland; Chair of Pharmacology, Jagiellonian University, Medical College, Grzegorzecka 16, 31-531 Krakow, Poland
| | - Sebastian Schlücker
- Department of Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Kamilla Malek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow 30-348, Poland.
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46
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Kelley JB, Paschal BM. Fluorescence-based quantification of nucleocytoplasmic transport. Methods 2018; 157:106-114. [PMID: 30419335 DOI: 10.1016/j.ymeth.2018.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 02/02/2023] Open
Abstract
The sequestration of DNA within the membrane-bound nucleus is a defining characteristic of eukaryotic cells. Replication and transcription are therefore restricted to the nucleus, however, the regulation of these events relies on cytoplasmic processes including protein synthesis and signal transduction pathways. Because a variety of cellular activities depend on nuclear transport, researchers from diverse fields have found it useful to examine the nuclear localization of proteins of interest. Here we present some important technical considerations for studying nuclear and cytoplasmic localization, and provide guidance for quantifying protein levels using fluorescence microscopy and ImageJ software. We include discussion of the use of regions of interest and image segmentation for quantification of protein localization. Nucleocytoplasmic transport is fundamentally important for controlling protein levels and activity in the nucleus or cytoplasm, and quantitative analysis can provide insight into how biological output is achieved.
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Affiliation(s)
- Joshua B Kelley
- Department of Molecular and Biomedical Sciences, University of Maine, United States.
| | - Bryce M Paschal
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, University of Virginia, United States
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47
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Hosseini ZF, Nelson DA, Moskwa N, Larsen M. Generating Embryonic Salivary Gland Organoids. ACTA ACUST UNITED AC 2018; 83:e76. [PMID: 30394683 DOI: 10.1002/cpcb.76] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Organoids are important research tools for studying organ morphogenesis and differentiation because they recapitulate ex vivo the native 3D organization of cells that is essential for proper cell and organ function. The composition of organoids can be manipulated to incorporate specific cell types to facilitate molecular interrogation of cell-cell interactions during organoid formation. A method for generating organoids derived from both embryonic salivary gland epithelial progenitor cells and mesenchymal support cells is described. Methods for isolating enriched populations of the epithelial cells as clusters and the mesenchyme cells as single cells from mouse embryonic submandibular salivary glands are also provided. Separating the epithelial and mesenchymal cell populations allows for independent molecular manipulation of each cell type. In addition, methods for lentiviral transduction of the mesenchyme cells and quantitative image analysis of organoids are provided. The methods described here are useful for exploring mechanisms driving organ formation. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zeinab F Hosseini
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York.,Graduate Program in Molecular, Cellular, Developmental and Neural Biology, University at Albany, State University of New York, Albany, New York
| | - Deirdre A Nelson
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York
| | - Nicholas Moskwa
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York.,Graduate Program in Molecular, Cellular, Developmental and Neural Biology, University at Albany, State University of New York, Albany, New York
| | - Melinda Larsen
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York
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48
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Geometric compensation applied to image analysis of cell populations with morphological variability: a new role for a classical concept. Sci Rep 2018; 8:10266. [PMID: 29980764 PMCID: PMC6035232 DOI: 10.1038/s41598-018-28570-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/06/2018] [Indexed: 02/06/2023] Open
Abstract
Immunofluorescence is the gold standard technique to determine the level and spatial distribution of fluorescent-tagged molecules. However, quantitative analysis of fluorescence microscopy images faces crucial challenges such as morphologic variability within cells. In this work, we developed an analytical strategy to deal with cell shape and size variability that is based on an elastic geometric alignment algorithm. Firstly, synthetic images mimicking cell populations with morphological variability were used to test and optimize the algorithm, under controlled conditions. We have computed expression profiles specifically assessing cell-cell interactions (IN profiles) and profiles focusing on the distribution of a marker throughout the intracellular space of single cells (RD profiles). To experimentally validate our analytical pipeline, we have used real images of cell cultures stained for E-cadherin, tubulin and a mitochondria dye, selected as prototypes of membrane, cytoplasmic and organelle-specific markers. The results demonstrated that our algorithm is able to generate a detailed quantitative report and a faithful representation of a large panel of molecules, distributed in distinct cellular compartments, independently of cell’s morphological features. This is a simple end-user method that can be widely explored in research and diagnostic labs to unravel protein regulation mechanisms or identify protein expression patterns associated with disease.
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49
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Kudryavtsev DS, Spirova EN, Shelukhina IV, Son LV, Makarova YV, Utkina NK, Kasheverov IE, Tsetlin VI. Makaluvamine G from the Marine Sponge Zyzzia fuliginosa Inhibits Muscle nAChR by Binding at the Orthosteric and Allosteric Sites. Mar Drugs 2018; 16:md16040109. [PMID: 29597332 PMCID: PMC5923396 DOI: 10.3390/md16040109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/16/2018] [Accepted: 03/23/2018] [Indexed: 12/19/2022] Open
Abstract
Diverse ligands of the muscle nicotinic acetylcholine receptor (nAChR) are used as muscle relaxants during surgery. Although a plethora of such molecules exists in the market, there is still a need for new drugs with rapid on/off-set, increased selectivity, and so forth. We found that pyrroloiminoquinone alkaloid Makaluvamine G (MG) inhibits several subtypes of nicotinic receptors and ionotropic γ-aminobutiric acid receptors, showing a higher affinity and moderate selectivity toward muscle nAChR. The action of MG on the latter was studied by a combination of electrophysiology, radioligand assay, fluorescent microscopy, and computer modeling. MG reveals a combination of competitive and un-competitive inhibition and caused an increase in the apparent desensitization rate of the murine muscle nAChR. Modeling ion channel kinetics provided evidence for MG binding in both orthosteric and allosteric sites. We also demonstrated that theα1 (G153S) mutant of the receptor, associated with the myasthenic syndrome, is more prone to inhibition by MG. Thus, MG appears to be a perspective hit molecule for the design of allosteric drugs targeting muscle nAChR, especially for treating slow-channel congenital myasthenic syndromes.
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Affiliation(s)
- Denis S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Ekaterina N Spirova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Irina V Shelukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Lina V Son
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
- Moscow Institute of Physics and Technology, Institutsky Per. 9, Dolgoprudny, 141700 Moscow Region, Russia.
| | - Yana V Makarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Natalia K Utkina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry (PIBOC), Russian Academy of Sciences, Prospect 100 let Vladivostoku, 159, 690022 Vladivostok, Russia.
| | - Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
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50
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Faraco CCF, Faria JAQA, Kunrath-Lima M, Miranda MCD, de Melo MIA, Ferreira ADF, Rodrigues MA, Gomes DA. Translocation of Epidermal Growth Factor (EGF) to the nucleus has distinct kinetics between adipose tissue-derived mesenchymal stem cells and a mesenchymal cancer cell lineage. J Struct Biol 2017; 202:61-69. [PMID: 29277356 DOI: 10.1016/j.jsb.2017.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 01/09/2023]
Abstract
Nuclear Epidermal Growth Factor Receptor (EGFR) has been associated with worse prognosis and treatment resistance for several cancer types. After Epidermal Growth Factor (EGF) binding, the ligand-receptor complex can translocate to the nucleus where it functions in oncological processes. By three-dimensional quantification analysis of super-resolution microscopy images, we verified the translocation kinetics of fluorescent conjugated EGF to the nucleus in two mesenchymal cell types: human adipose tissue-derived stem cells (hASC) and SK-HEP-1 tumor cells. The number of EGF clusters in the nucleus does not change after 10 min of stimulation with EGF in both cells. The total volume occupied by EGF clusters in the nucleus of hASC also does not change after 10 min of stimulation with EGF. However, the total volume of EGF clusters increases only after 20 min in SK-HEP-1 cells nuclei. In these cells the nuclear volume occupied by EGF is 3.2 times higher than in hASC after 20 min of stimulation, indicating that translocation kinetics of EGF differs between these two cell types. After stimulation, EGF clusters assemble in larger clusters in the cell nucleus in both cell types, which suggests specific sub-nuclear localizations of the receptor. Super-resolution microscopy images show that EGF clusters are widespread in the nucleoplasm, and can be localized in nuclear envelope invaginations, and in the nucleoli. The quantitative study of EGF-EGFR complex translocation to the nucleus may help to unravel its roles in health and pathological conditions, such as cancer.
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Affiliation(s)
- Camila Cristina Fraga Faraco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Marianna Kunrath-Lima
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcelo Coutinho de Miranda
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariane Izabella Abreu de Melo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andrea da Fonseca Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michele Angela Rodrigues
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Dawidson Assis Gomes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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