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Mise K, Long J, Galvan DL, Ye Z, Fan G, Sharma R, Serysheva II, Moore TI, Jeter CR, Anna Zal M, Araki M, Wada J, Schumacker PT, Chang BH, Danesh FR. NDUFS4 regulates cristae remodeling in diabetic kidney disease. Nat Commun 2024; 15:1965. [PMID: 38438382 PMCID: PMC10912198 DOI: 10.1038/s41467-024-46366-w] [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: 06/19/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generate diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that conditional male mice with genetic overexpression of Ndufs4 exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping protein STOML2 in linking NDUFS4 with improved cristae morphology. Together, we provide the evidence on the central role of NDUFS4 as a regulator of cristae remodeling and mitochondrial function in kidney podocytes. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
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Affiliation(s)
- Koki Mise
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jianyin Long
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel L Galvan
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zengchun Ye
- Division of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rajesh Sharma
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Travis I Moore
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Collene R Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Anna Zal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Motoo Araki
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Paul T Schumacker
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Benny H Chang
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farhad R Danesh
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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2
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McCall AD. Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy. BMC Bioinformatics 2024; 25:55. [PMID: 38308215 PMCID: PMC10837882 DOI: 10.1186/s12859-024-05675-z] [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: 10/04/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND A common goal of scientific microscopic imaging is to determine if a spatial correlation exists between two imaged structures. This is generally accomplished by imaging fluorescently labeled structures and measuring their spatial correlation with a class of image analysis algorithms known as colocalization. However, the most commonly used methods of colocalization have strict limitations, such as requiring overlap in the fluorescent markers and reporting requirements for accurate interpretation of the data, that are often not met. Due to the development of novel super-resolution techniques, which reduce the overlap of the fluorescent signals, a new colocalization method is needed that does not have such strict requirements. RESULTS In order to overcome the limitations of other colocalization algorithms, I developed a new ImageJ/Fiji plugin, Colocalization by cross-correlation (CCC). This method uses cross-correlation over space to identify spatial correlations as a function of distance, removing the overlap requirement and providing more comprehensive results. CCC is compatible with 3D and time-lapse images, and was designed to be easy to use. CCC also generates new images that only show the correlating labeled structures from the input images, a novel feature among the cross-correlating algorithms. CONCLUSIONS CCC is a versatile, powerful, and easy to use colocalization and spatial correlation tool that is available through the Fiji update sites. Full and up to date documentation can be found at https://imagej.net/plugins/colocalization-by-cross-correlation . CCC source code is available at https://github.com/andmccall/Colocalization_by_Cross_Correlation .
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Affiliation(s)
- Andrew D McCall
- Optical Imaging and Analysis Facility, School of Dental Medicine, University at Buffalo, Buffalo, NY, USA.
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3
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Liang Z, Solano A, Lou J, Hinde E. Histone FRET reports the spatial heterogeneity in nanoscale chromatin architecture that is imparted by the epigenetic landscape at the level of single foci in an intact cell nucleus. Chromosoma 2024; 133:5-14. [PMID: 38265456 PMCID: PMC10904561 DOI: 10.1007/s00412-024-00815-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Genome sequencing has identified hundreds of histone post-translational modifications (PTMs) that define an open or compact chromatin nanostructure at the level of nucleosome proximity, and therefore serve as activators or repressors of gene expression. Direct observation of this epigenetic mode of transcriptional regulation in an intact single nucleus, is however, a complex task. This is because despite the development of fluorescent probes that enable observation of specific histone PTMs and chromatin density, the changes in nucleosome proximity regulating gene expression occur on a spatial scale well below the diffraction limit of optical microscopy. In recent work, to address this research gap, we demonstrated that the phasor approach to fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between fluorescently labelled histones core to the nucleosome, is a readout of chromatin nanostructure that can be multiplexed with immunofluorescence (IF) against specific histone PTMs. Here from application of this methodology to gold standard gene activators (H3K4Me3 and H3K9Ac) versus repressors (e.g., H3K9Me3 and H3K27Me), we find that while on average these histone marks do impart an open versus compact chromatin nanostructure, at the level of single chromatin foci, there is significant spatial heterogeneity. Collectively this study illustrates the importance of studying the epigenetic landscape as a function of space within intact nuclear architecture and opens the door for the study of chromatin foci sub-populations defined by combinations of histone marks, as is seen in the context of bivalent chromatin.
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Affiliation(s)
- Zhen Liang
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
- Cancer and RNA Laboratory, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medicine, Melbourne Medical School, St Vincent's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth Hinde
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia.
- School of Physics, University of Melbourne, Melbourne, VIC, Australia.
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4
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Pierzynska-Mach A, Cainero I, Oneto M, Ferrando-May E, Lanzanò L, Diaspro A. Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. Sci Rep 2023; 13:12749. [PMID: 37550322 PMCID: PMC10406876 DOI: 10.1038/s41598-023-38685-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein-a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns-alongside breast cancer progression-leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
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Affiliation(s)
| | - Isotta Cainero
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Oneto
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
| | - Elisa Ferrando-May
- Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Luca Lanzanò
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy.
- DIFILAB, Department of Physics, University of Genoa, Genoa, Italy.
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5
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Mise K, Long J, Galvan DL, Ye Z, Fan G, Serysheva II, Moore TI, Wada J, Schumacker PT, Chang BH, Danesh FR. NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease. RESEARCH SQUARE 2023:rs.3.rs-3070079. [PMID: 37461606 PMCID: PMC10350115 DOI: 10.21203/rs.3.rs-3070079/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generated diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model to investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that these conditional mice exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping proteins in linking NDUFS4 with improved cristae morphology. Taken together, we discover the central role of NDUFS4 as a powerful regulator of cristae remodeling, respiratory supercomplexes assembly, and mitochondrial ultrastructure in vitro and in vivo. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
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Affiliation(s)
- Koki Mise
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Jianyin Long
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel L. Galvan
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zengchun Ye
- Division of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Irina I. Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Travis I. Moore
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology & Metabolism, Okayama University Graduate School of Medicine, Dentistry & Pharmaceutical Sciences, Okayama, Japan
| | - Paul T. Schumacker
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Benny H. Chang
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farhad R. Danesh
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX
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6
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Cerutti E, D'Amico M, Cainero I, Pelicci PG, Faretta M, Dellino GI, Diaspro A, Lanzanò L. Alterations induced by the PML-RARα oncogene revealed by image cross correlation spectroscopy. Biophys J 2022; 121:4358-4367. [PMID: 36196056 PMCID: PMC9703036 DOI: 10.1016/j.bpj.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanisms that underlie oncogene-induced genomic damage are still poorly understood. To understand how oncogenes affect chromatin architecture, it is important to visualize fundamental processes such as DNA replication and transcription in intact nuclei and quantify the alterations of their spatiotemporal organization induced by oncogenes. Here, we apply superresolution microscopy in combination with image cross correlation spectroscopy to the U937-PR9 cell line, an in vitro model of acute promyelocytic leukemia that allows us to activate the expression of the PML-RARα oncogene and analyze its effects on the spatiotemporal organization of functional nuclear processes. More specifically, we perform Tau-stimulated emission depletion imaging, a superresolution technique based on the concept of separation of photons by lifetime tuning. Tau-stimulated emission depletion imaging is combined with a robust image analysis protocol that quickly produces a value of colocalization fraction on several hundreds of single cells and allows observation of cell-to-cell variability. Upon activation of the oncogene, we detect a significant increase in the fraction of transcription sites colocalized with PML/PML-RARα. This increase of colocalization can be ascribed to oncogene-induced disruption of physiological PML bodies and the abnormal occurrence of a relatively large number of PML-RARα microspeckles. We also detect a significant cell-to-cell variability of this increase of colocalization, which can be ascribed, at least in part, to a heterogeneous response of the cells to the activation of the oncogene. These results prove that our method efficiently reveals oncogene-induced alterations in the spatial organization of nuclear processes and suggest that the abnormal localization of PML-RARα could interfere with the transcription machinery, potentially leading to DNA damage and genomic instability.
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Affiliation(s)
- Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy; DIFILAB, Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.
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7
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Hetero-pentamerization determines mobility and conductance of Glycine receptor α3 splice variants. Cell Mol Life Sci 2022; 79:540. [PMID: 36197517 PMCID: PMC9534812 DOI: 10.1007/s00018-022-04506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/05/2022]
Abstract
Glycine receptors (GlyRs) are ligand-gated pentameric chloride channels in the central nervous system. GlyR-α3 is a possible target for chronic pain treatment and temporal lobe epilepsy. Alternative splicing into K or L variants determines the subcellular fate and function of GlyR-α3, yet it remains to be shown whether its different splice variants can functionally co-assemble, and what the properties of such heteropentamers would be. Here, we subjected GlyR-α3 to a combined fluorescence microscopy and electrophysiology analysis. We employ masked Pearson’s and dual-color spatiotemporal correlation analysis to prove that GlyR-α3 splice variants heteropentamerize, adopting the mobility of the K variant. Fluorescence-based single-subunit counting experiments revealed a variable and concentration ratio dependent hetero-stoichiometry. Via cell-attached single-channel electrophysiology we show that heteropentamers exhibit currents in between those of K and L variants. Our data are compatible with a model where α3 heteropentamerization fine-tunes mobility and activity of GlyR-α3 channels, which is important to understand and tackle α3 related diseases.
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8
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Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy. NANOMATERIALS 2022; 12:nano12040686. [PMID: 35215014 PMCID: PMC8875509 DOI: 10.3390/nano12040686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023]
Abstract
Super Resolution Microscopy revolutionized the approach to the study of molecular interactions by providing new quantitative tools to describe the scale below 100 nanometers. Single Molecule Localization Microscopy (SMLM) reaches a spatial resolution less than 50 nm with a precision in calculating molecule coordinates between 10 and 20 nanometers. However new procedures are required to analyze data from the list of molecular coordinates created by SMLM. We propose new tools based on Image Cross Correlation Spectroscopy (ICCS) to quantify the colocalization of fluorescent signals at single molecule level. These analysis procedures have been inserted into an experimental pipeline to optimize the produced results. We show that Fluorescent NanoDiamonds targeted to an intracellular compartment can be employed (i) to correct spatial drift to maximize the localization precision and (ii) to register confocal and SMLM images in correlative multiresolution, multimodal imaging. We validated the ICCS based approach on defined biological control samples and showed its ability to quantitatively map area of interactions inside the cell. The produced results show that the ICCS analysis is an efficient tool to measure relative spatial distribution of different molecular species at the nanoscale.
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9
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Russo GI, Musso N, Romano A, Caruso G, Petralia S, Lanzanò L, Broggi G, Camarda M. The Role of Dielectrophoresis for Cancer Diagnosis and Prognosis. Cancers (Basel) 2021; 14:198. [PMID: 35008359 PMCID: PMC8750463 DOI: 10.3390/cancers14010198] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy is emerging as a potential diagnostic tool for prostate cancer (PC) prognosis and diagnosis. Unfortunately, most circulating tumor cells (CTC) technologies, such as AdnaTest or Cellsearch®, critically rely on the epithelial cell adhesion molecule (EpCAM) marker, limiting the possibility of detecting cancer stem-like cells (CSCs) and mesenchymal-like cells (EMT-CTCs) that are present during PC progression. In this context, dielectrophoresis (DEP) is an epCAM independent, label-free enrichment system that separates rare cells simply on the basis of their specific electrical properties. As compared to other technologies, DEP may represent a superior technique in terms of running costs, cell yield and specificity. However, because of its higher complexity, it still requires further technical as well as clinical development. DEP can be improved by the use of microfluid, nanostructured materials and fluoro-imaging to increase its potential applications. In the context of cancer, the usefulness of DEP lies in its capacity to detect CTCs in the bloodstream in their epithelial, mesenchymal, or epithelial-mesenchymal phenotype forms, which should be taken into account when choosing CTC enrichment and analysis methods for PC prognosis and diagnosis.
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Affiliation(s)
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, 95123 Catania, Italy
- STLab s.r.l., Via Anapo 53, 95126 Catania, Italy;
| | - Alessandra Romano
- Haematological Section, University of Catania, 95125 Catania, Italy;
| | - Giuseppe Caruso
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy; (G.C.); (S.P.)
| | - Salvatore Petralia
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy; (G.C.); (S.P.)
| | - Luca Lanzanò
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy;
| | - Giuseppe Broggi
- Pathology Section, Department of Medical, Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy;
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10
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Sato Y, Mustafina KR, Luo Y, Martini C, Thomas DY, Wiseman PW, Hanrahan JW. Nonspecific binding of common anti-CFTR antibodies in ciliated cells of human airway epithelium. Sci Rep 2021; 11:23256. [PMID: 34853321 PMCID: PMC8636639 DOI: 10.1038/s41598-021-02420-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/11/2021] [Indexed: 11/10/2022] Open
Abstract
There is evidence that the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is highly expressed at the apical pole of ciliated cells in human bronchial epithelium (HBE), however recent studies have detected little CFTR mRNA in those cells. To understand this discrepancy we immunostained well differentiated primary HBE cells using CFTR antibodies. We confirmed apical immunofluorescence in ciliated cells and quantified the covariance of the fluorescence signals and that of an antibody against the ciliary marker centrin-2 using image cross-correlation spectroscopy (ICCS). Super-resolution stimulated emission depletion (STED) imaging localized the immunofluorescence in distinct clusters at the bases of the cilia. However, similar apical fluorescence was observed when the monoclonal CFTR antibodies 596, 528 and 769 were used to immunostain ciliated cells expressing F508del-CFTR, or cells lacking CFTR due to a Class I mutation. A BLAST search using the CFTR epitope identified a similar amino acid sequence in the ciliary protein rootletin X1. Its expression level correlated with the intensity of immunostaining by CFTR antibodies and it was detected by 596 antibody after transfection into CFBE cells. These results may explain the high apparent expression of CFTR in ciliated cells and reports of anomalous apical immunofluorescence in well differentiated cells that express F508del-CFTR.
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Affiliation(s)
- Yukiko Sato
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Kamila R Mustafina
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Chemistry, McGill University, Montréal, Canada
| | - Yishan Luo
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - Carolina Martini
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada.,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada
| | - David Y Thomas
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Biochemistry, McGill University, Montréal, Canada
| | - Paul W Wiseman
- Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada.,Department of Chemistry, McGill University, Montréal, Canada.,Department of Physics, McGill University, Montréal, Canada
| | - John W Hanrahan
- Department of Physiology, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, QC, H3G 1Y6, Canada. .,Cystic Fibrosis Translational Research Centre, McGill University, Montréal, Canada. .,Research Institute - McGill University Health Centre, Montréal, Canada.
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11
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Cerutti E, D'Amico M, Cainero I, Dellino GI, Faretta M, Vicidomini G, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Evaluation of sted super-resolution image quality by image correlation spectroscopy (QuICS). Sci Rep 2021; 11:20782. [PMID: 34675304 PMCID: PMC8531054 DOI: 10.1038/s41598-021-00301-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Quantifying the imaging performances in an unbiased way is of outmost importance in super-resolution microscopy. Here, we describe an algorithm based on image correlation spectroscopy (ICS) that can be used to assess the quality of super-resolution images. The algorithm is based on the calculation of an autocorrelation function and provides three different parameters: the width of the autocorrelation function, related to the spatial resolution; the brightness, related to the image contrast; the relative noise variance, related to the signal-to-noise ratio of the image. We use this algorithm to evaluate the quality of stimulated emission depletion (STED) images of DNA replication foci in U937 cells acquired under different imaging conditions. Increasing the STED depletion power improves the resolution but may reduce the image contrast. Increasing the number of line averages improves the signal-to-noise ratio but facilitates the onset of photobleaching and subsequent reduction of the image contrast. Finally, we evaluate the performances of two different separation of photons by lifetime tuning (SPLIT) approaches: the method of tunable STED depletion power and the commercially available Leica Tau-STED. We find that SPLIT provides an efficient way to improve the resolution and contrast in STED microscopy.
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Affiliation(s)
- Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy.,Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.,DIFILAB, Department of Physics, University of Genoa, via Dodecaneso 33, 16143, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy. .,Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
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12
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Label-free two-photon imaging of mitochondrial activity in murine macrophages stimulated with bacterial and viral ligands. Sci Rep 2021; 11:14081. [PMID: 34234166 PMCID: PMC8263786 DOI: 10.1038/s41598-021-93043-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/16/2021] [Indexed: 11/12/2022] Open
Abstract
Mitochondria are the metabolic hub of the cell, playing a central role in regulating immune responses. Dysfunction of mitochondrial reprogramming can occur during bacterial and viral infections compromising hosts’ immune signaling. Comparative evaluation of these alterations in response to bacterial and viral ligands can provide insights into a cell’s ability to mount pathogen-specific responses. In this study, we used two-photon excitation fluorescence (TPEF) imaging to quantify reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H) and flavin adenine dinucleotide (FAD) levels in the cell and to calculate the optical redox ratio (ORR), an indicator of mitochondrial dysfunction. Analyses were performed on RAW264.7 cells and murine bone marrow derived macrophages (BMM) stimulated with bacterial (LPS) and viral (Poly(I:C)) ligands. Responses were cell type dependent, with primary cells having significantly higher levels of FAD and higher oxygen consumption rates suggesting BMM may be more dependent on mitochondrial metabolism. Our findings also suggest that FAD-TPEF intensity may be a better predictor of mitochondrial activity and localization since it demonstrates unique mitochondrial clustering patterns in LPS vs. Poly(I:C) stimulated macrophages. Collectively, we demonstrate that TPEF imaging is a powerful label-free approach for quantifying changes in mitochondrial function and organization in macrophages following bacterial and viral stimuli.
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13
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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14
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Cainero I, Cerutti E, Faretta M, Dellino GI, Pelicci PG, Bianchini P, Vicidomini G, Diaspro A, Lanzanò L. Chromatin investigation in the nucleus using a phasor approach to structured illumination microscopy. Biophys J 2021; 120:2566-2576. [PMID: 33940021 PMCID: PMC8390874 DOI: 10.1016/j.bpj.2021.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/14/2021] [Accepted: 04/26/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin in the nucleus is organized in functional sites at variable level of compaction. Structured illumination microscopy (SIM) can be used to generate three-dimensional super-resolution (SR) imaging of chromatin by changing in phase and in orientation a periodic line illumination pattern. The spatial frequency domain is the natural choice to process SIM raw data and to reconstruct an SR image. Using an alternative approach, we demonstrate that the additional spatial information encoded in the knowledge of the position of the illumination pattern can be efficiently decoded using a generalized version of separation of photon by lifetime tuning (SPLIT) that does not require lifetime measurements. In the resulting SPLIT-SIM, the SR image is obtained by isolating a fraction of the intensity corresponding to the center of the diffraction-limited point spread function. This extends the use of the SPLIT approach from stimulated emission depletion microscopy to SIM. The SPLIT-SIM algorithm is based only on phasor analysis and does not require deconvolution. We show that SPLIT-SIM can be used to generate SR images of chromatin organizational motifs with tunable resolution and can be a valuable tool for the imaging of functional sites in the nucleus.
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Affiliation(s)
- Isotta Cainero
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Elena Cerutti
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.
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15
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Cainero I, Cerutti E, Faretta M, Dellino GI, Pelicci PG, Diaspro A, Lanzanò L. Measuring Nanoscale Distances by Structured Illumination Microscopy and Image Cross-Correlation Spectroscopy (SIM-ICCS). SENSORS (BASEL, SWITZERLAND) 2021; 21:2010. [PMID: 33809144 PMCID: PMC8001887 DOI: 10.3390/s21062010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/27/2022]
Abstract
Since the introduction of super-resolution microscopy, there has been growing interest in quantifying the nanoscale spatial distributions of fluorescent probes to better understand cellular processes and their interactions. One way to check if distributions are correlated or not is to perform colocalization analysis of multi-color acquisitions. Among all the possible methods available to study and quantify the colocalization between multicolor images, there is image cross-correlation spectroscopy (ICCS). The main advantage of ICCS, in comparison with other co-localization techniques, is that it does not require pre-segmentation of the sample into single objects. Here we show that the combination of structured illumination microscopy (SIM) with ICCS (SIM-ICCS) is a simple approach to quantify colocalization and measure nanoscale distances from multi-color SIM images. We validate the SIM-ICCS analysis on SIM images of optical nanorulers, DNA-origami-based model samples containing fluorophores of different colors at a distance of 80 nm. The SIM-ICCS analysis is compared with an object-based analysis performed on the same samples. Finally, we show that SIM-ICCS can be used to quantify the nanoscale spatial distribution of functional nuclear sites in fixed cells.
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Affiliation(s)
- Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Elena Cerutti
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
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