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Mao K, Jing X, Wang G, Chang Y, Liu J, Zhao Y, Yu S, Liu J. A novel open-source CADs platform for 3D CT pulmonary analysis. Comput Biol Med 2024; 169:107878. [PMID: 38141446 DOI: 10.1016/j.compbiomed.2023.107878] [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: 10/12/2023] [Revised: 11/10/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Computer-aided diagnosis (CAD) systems play vital roles in the early detection of pulmonary nodules for reducing lung cancer mortality rates. To provide better services for professional doctors, this paper proposes an efficient open-source CAD platform with flexible equipments, user-friendly interfaces, and completed functions for 3D CT pulmonary nodule analysis. For the platform's design and implementation, we fully consider application scenarios and system requirements. The platform supplies core functions for (1) Basic Image Processing, (2) Intelligent Image Analysis, (3) Multi-View Image Visualization, (4) Report Editing and Generation, (5) User Information Management, and (6) Inference Service Monitoring. Specifically, other state-of-the-art or user-defined algorithms can be integrated as plugin modules with no interference for system architecture. System evaluation with use-case testing demonstrates the effectiveness and universality of the proposed platform.
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Affiliation(s)
- Keming Mao
- Software College, Northeastern University, Shenyang, China
| | - Xin Jing
- Software College, Northeastern University, Shenyang, China
| | - Gao Wang
- Software College, Northeastern University, Shenyang, China
| | - Yachen Chang
- School of Software Technology, Zhejiang University, Ningbo, China
| | - Jiale Liu
- Software College, Northeastern University, Shenyang, China.
| | - Yuhai Zhao
- College of Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Shiyu Yu
- China Mobile Group Liaoning Company Limited, Shenyang, China
| | - Jingyu Liu
- China Mobile Group Liaoning Company Limited, Shenyang, China
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2
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Piemonte KM, Webb BM, Bobbitt JR, Majmudar PR, Cuellar-Vite L, Bryson BL, Latina NC, Seachrist DD, Keri RA. Disruption of CDK7 signaling leads to catastrophic chromosomal instability coupled with a loss of condensin-mediated chromatin compaction. J Biol Chem 2023; 299:104834. [PMID: 37201585 PMCID: PMC10300262 DOI: 10.1016/j.jbc.2023.104834] [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: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Chromatin organization is highly dynamic and modulates DNA replication, transcription, and chromosome segregation. Condensin is essential for chromosome assembly during mitosis and meiosis, as well as maintenance of chromosome structure during interphase. While it is well established that sustained condensin expression is necessary to ensure chromosome stability, the mechanisms that control its expression are not yet known. Herein, we report that disruption of cyclin-dependent kinase 7 (CDK7), the core catalytic subunit of CDK-activating kinase, leads to reduced transcription of several condensin subunits, including structural maintenance of chromosomes 2 (SMC2). Live and static microscopy revealed that inhibiting CDK7 signaling prolongs mitosis and induces chromatin bridge formation, DNA double-strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Affirming the importance of condensin regulation by CDK7, genetic suppression of the expression of SMC2, a core subunit of this complex, phenocopies CDK7 inhibition. Moreover, analysis of genome-wide chromatin conformation using Hi-C revealed that sustained activity of CDK7 is necessary to maintain chromatin sublooping, a function that is ascribed to condensin. Notably, the regulation of condensin subunit gene expression is independent of superenhancers. Together, these studies reveal a new role for CDK7 in sustaining chromatin configuration by ensuring the expression of condensin genes, including SMC2.
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Affiliation(s)
- Katrina M Piemonte
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Bryan M Webb
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jessica R Bobbitt
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Parth R Majmudar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Leslie Cuellar-Vite
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Benjamin L Bryson
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicholas C Latina
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ruth A Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of General Medical Sciences-Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
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3
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Matlock A, Zhu J, Tian L. Multiple-scattering simulator-trained neural network for intensity diffraction tomography. OPTICS EXPRESS 2023; 31:4094-4107. [PMID: 36785385 DOI: 10.1364/oe.477396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Recovering 3D phase features of complex biological samples traditionally sacrifices computational efficiency and processing time for physical model accuracy and reconstruction quality. Here, we overcome this challenge using an approximant-guided deep learning framework in a high-speed intensity diffraction tomography system. Applying a physics model simulator-based learning strategy trained entirely on natural image datasets, we show our network can robustly reconstruct complex 3D biological samples. To achieve highly efficient training and prediction, we implement a lightweight 2D network structure that utilizes a multi-channel input for encoding the axial information. We demonstrate this framework on experimental measurements of weakly scattering epithelial buccal cells and strongly scattering C. elegans worms. We benchmark the network's performance against a state-of-the-art multiple-scattering model-based iterative reconstruction algorithm. We highlight the network's robustness by reconstructing dynamic samples from a living worm video. We further emphasize the network's generalization capabilities by recovering algae samples imaged from different experimental setups. To assess the prediction quality, we develop a quantitative evaluation metric to show that our predictions are consistent with both multiple-scattering physics and experimental measurements.
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4
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Schirmer EC, Latonen L, Tollis S. Nuclear size rectification: A potential new therapeutic approach to reduce metastasis in cancer. Front Cell Dev Biol 2022; 10:1022723. [PMID: 36299481 PMCID: PMC9589484 DOI: 10.3389/fcell.2022.1022723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 03/07/2024] Open
Abstract
Research on metastasis has recently regained considerable interest with the hope that single cell technologies might reveal the most critical changes that support tumor spread. However, it is possible that part of the answer has been visible through the microscope for close to 200 years. Changes in nuclear size characteristically occur in many cancer types when the cells metastasize. This was initially discarded as contributing to the metastatic spread because, depending on tumor types, both increases and decreases in nuclear size could correlate with increased metastasis. However, recent work on nuclear mechanics and the connectivity between chromatin, the nucleoskeleton, and the cytoskeleton indicate that changes in this connectivity can have profound impacts on cell mobility and invasiveness. Critically, a recent study found that reversing tumor type-dependent nuclear size changes correlated with reduced cell migration and invasion. Accordingly, it seems appropriate to now revisit possible contributory roles of nuclear size changes to metastasis.
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Affiliation(s)
- Eric C. Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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Sandlin CW, Gu S, Xu J, Deshpande C, Feldman MD, Good MC. Epithelial cell size dysregulation in human lung adenocarcinoma. PLoS One 2022; 17:e0274091. [PMID: 36201559 PMCID: PMC9536599 DOI: 10.1371/journal.pone.0274091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Human cells tightly control their dimensions, but in some cancers, normal cell size control is lost. In this study we measure cell volumes of epithelial cells from human lung adenocarcinoma progression in situ. By leveraging artificial intelligence (AI), we reconstruct tumor cell shapes in three dimensions (3D) and find airway type 2 cells display up to 10-fold increases in volume. Surprisingly, cell size increase is not caused by altered ploidy, and up to 80% of near-euploid tumor cells show abnormal sizes. Size dysregulation is not explained by cell swelling or senescence because cells maintain cytoplasmic density and proper organelle size scaling, but is correlated with changes in tissue organization and loss of a novel network of processes that appear to connect alveolar type 2 cells. To validate size dysregulation in near-euploid cells, we sorted cells from tumor single-cell suspensions on the basis of size. Our study provides data of unprecedented detail for cell volume dysregulation in a human cancer. Broadly, loss of size control may be a common feature of lung adenocarcinomas in humans and mice that is relevant to disease and identification of these cells provides a useful model for investigating cell size control and consequences of cell size dysregulation.
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Affiliation(s)
- Clifford W. Sandlin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
| | - Song Gu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Jun Xu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Charuhas Deshpande
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
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La Torre M, Merigliano C, Maccaroni K, Chojnowski A, Goh WI, Giubettini M, Vernì F, Capanni C, Rhodes D, Wright G, Burke B, Soddu S, Burla R, Saggio I. Combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. J Exp Clin Cancer Res 2022; 41:273. [PMID: 36096808 PMCID: PMC9469526 DOI: 10.1186/s13046-022-02480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Lamins, key nuclear lamina components, have been proposed as candidate risk biomarkers in different types of cancer but their accuracy is still debated. AKTIP is a telomeric protein with the property of being enriched at the nuclear lamina. AKTIP has similarity with the tumor susceptibility gene TSG101. AKTIP deficiency generates genome instability and, in p53−/− mice, the reduction of the mouse counterpart of AKTIP induces the exacerbation of lymphomas. Here, we asked whether the distribution of AKTIP is altered in cancer cells and whether this is associated with alterations of lamins. Methods We performed super-resolution imaging, quantification of lamin expression and nuclear morphology on HeLa, MCF7, and A549 tumor cells, and on non-transformed fibroblasts from healthy donor and HGPS (LMNA c.1824C > T p.Gly608Gly) and EDMD2 (LMNA c.775 T > G) patients. As proof of principle model combining a defined lamin alteration with a tumor cell setting, we produced HeLa cells exogenously expressing the HGPS lamin mutant progerin that alters nuclear morphology. Results In HeLa cells, AKTIP locates at less than 0.5 µm from the nuclear rim and co-localizes with lamin A/C. As compared to HeLa, there is a reduced co-localization of AKTIP with lamin A/C in both MCF7 and A549. Additionally, MCF7 display lower amounts of AKTIP at the rim. The analyses in non-transformed fibroblasts show that AKTIP mislocalizes in HGPS cells but not in EDMD2. The integrated analysis of lamin expression, nuclear morphology, and AKTIP topology shows that positioning of AKTIP is influenced not only by lamin expression, but also by nuclear morphology. This conclusion is validated by progerin-expressing HeLa cells in which nuclei are morphologically altered and AKTIP is mislocalized. Conclusions Our data show that the combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. The results also point to the fact that lamin alterations per se are not predictive of AKTIP mislocalization, in both non-transformed and tumor cells. In more general terms, this study supports the thesis that a combined analytical approach should be preferred to predict lamin-associated changes in tumor cells. This paves the way of next translational evaluation to validate the use of this combined analytical approach as risk biomarker. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02480-5.
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Gurova K. Can aggressive cancers be identified by the "aggressiveness" of their chromatin? Bioessays 2022; 44:e2100212. [PMID: 35452144 DOI: 10.1002/bies.202100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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8
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Leveraging cellular mechano-responsiveness for cancer therapy. Trends Mol Med 2021; 28:155-169. [PMID: 34973934 DOI: 10.1016/j.molmed.2021.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 12/21/2022]
Abstract
Cells sense the biophysical properties of the tumor microenvironment (TME) and adopt these signals in their development, progression, and metastatic dissemination. Recent work highlights the mechano-responsiveness of cells in tumors and the underlying mechanisms. Furthermore, approaches to mechano-modulating diverse types of cell have emerged aiming to inhibit tumor growth and metastasis. These include targeting mechanosensitive machineries in cancer cells to induce apoptosis, intervening matrix stiffening incurred by cancer-associated fibroblasts (CAFs) in both primary and metastatic tumor sites, and modulating matrix mechanics to improve immune cell therapeutic efficacy. This review is envisaged to help scientists and clinicians in cancer research to advance understanding of the cellular mechano-responsiveness in TME, and to harness these concepts for cancer mechanotherapies.
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9
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Sebastian JA, Moore MJ, Berndl ESL, Kolios MC. An image-based flow cytometric approach to the assessment of the nucleus-to-cytoplasm ratio. PLoS One 2021; 16:e0253439. [PMID: 34166419 PMCID: PMC8224973 DOI: 10.1371/journal.pone.0253439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Abstract
The nucleus-to-cytoplasm ratio (N:C) can be used as one metric in histology for grading certain types of tumor malignancy. Current N:C assessment techniques are time-consuming and low throughput. Thus, in high-throughput clinical contexts, there is a need for a technique that can assess cell malignancy rapidly. In this study, we assess the N:C ratio of four different malignant cell lines (OCI-AML-5-blood cancer, CAKI-2-kidney cancer, HT-29-colon cancer, SK-BR-3-breast cancer) and a non-malignant cell line (MCF-10A -breast epithelium) using an imaging flow cytometer (IFC). Cells were stained with the DRAQ-5 nuclear dye to stain the cell nucleus. An Amnis ImageStreamX® IFC acquired brightfield/fluorescence images of cells and their nuclei, respectively. Masking and gating techniques were used to obtain the cell and nucleus diameters for 5284 OCI-AML-5 cells, 1096 CAKI-2 cells, 6302 HT-29 cells, 3159 SK-BR-3 cells, and 1109 MCF-10A cells. The N:C ratio was calculated as the ratio of the nucleus diameter to the total cell diameter. The average cell and nucleus diameters from IFC were 12.3 ± 1.2 μm and 9.0 ± 1.1 μm for OCI-AML5 cells, 24.5 ± 2.6 μm and 15.6 ± 2.1 μm for CAKI-2 cells, 16.2 ± 1.8 μm and 11.2 ± 1.3 μm for HT-29 cells, 18.0 ± 3.7 μm and 12.5 ± 2.1 μm for SK-BR-3 cells, and 19.4 ± 2.2 μm and 10.1 ± 1.8 μm for MCF-10A cells. Here we show a general N:C ratio of ~0.6-0.7 across varying malignant cell lines and a N:C ratio of ~0.5 for a non-malignant cell line. This study demonstrates the use of IFC to assess the N:C ratio of cancerous and non-cancerous cells, and the promise of its use in clinically relevant high-throughput detection scenarios to supplement current workflows used for cancer cell grading.
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Affiliation(s)
- Joseph A. Sebastian
- Department of Physics, Ryerson University, Toronto, Canada
- Institute of Biomedical Engineering, Science and Technology (iBEST), A Partnership Between Ryerson University and St. Michael’s Hospital, Toronto, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
| | - Michael J. Moore
- Department of Physics, Ryerson University, Toronto, Canada
- Institute of Biomedical Engineering, Science and Technology (iBEST), A Partnership Between Ryerson University and St. Michael’s Hospital, Toronto, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
| | - Elizabeth S. L. Berndl
- Department of Physics, Ryerson University, Toronto, Canada
- Institute of Biomedical Engineering, Science and Technology (iBEST), A Partnership Between Ryerson University and St. Michael’s Hospital, Toronto, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
| | - Michael C. Kolios
- Department of Physics, Ryerson University, Toronto, Canada
- Institute of Biomedical Engineering, Science and Technology (iBEST), A Partnership Between Ryerson University and St. Michael’s Hospital, Toronto, Canada
- Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
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A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proc Natl Acad Sci U S A 2021; 118:2021571118. [PMID: 33990464 DOI: 10.1073/pnas.2021571118] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
YAP/TAZ is a master regulator of mechanotransduction whose functions rely on translocation from the cytoplasm to the nucleus in response to diverse physical cues. Substrate stiffness, substrate dimensionality, and cell shape are all input signals for YAP/TAZ, and through this pathway, regulate critical cellular functions and tissue homeostasis. Yet, the relative contributions of each biophysical signal and the mechanisms by which they synergistically regulate YAP/TAZ in realistic tissue microenvironments that provide multiplexed input signals remain unclear. For example, in simple two-dimensional culture, YAP/TAZ nuclear localization correlates strongly with substrate stiffness, while in three-dimensional (3D) environments, YAP/TAZ translocation can increase with stiffness, decrease with stiffness, or remain unchanged. Here, we develop a spatial model of YAP/TAZ translocation to enable quantitative analysis of the relationships between substrate stiffness, substrate dimensionality, and cell shape. Our model couples cytosolic stiffness to nuclear mechanics to replicate existing experimental trends, and extends beyond current data to predict that increasing substrate activation area through changes in culture dimensionality, while conserving cell volume, forces distinct shape changes that result in nonlinear effect on YAP/TAZ nuclear localization. Moreover, differences in substrate activation area versus total membrane area can account for counterintuitive trends in YAP/TAZ nuclear localization in 3D culture. Based on this multiscale investigation of the different system features of YAP/TAZ nuclear translocation, we predict that how a cell reads its environment is a complex information transfer function of multiple mechanical and biochemical factors. These predictions reveal a few design principles of cellular and tissue engineering for YAP/TAZ mechanotransduction.
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Prognostic Value of the Diversity of Nuclear Chromatin Compartments in Gynaecological Carcinomas. Cancers (Basel) 2020; 12:cancers12123838. [PMID: 33352679 PMCID: PMC7766595 DOI: 10.3390/cancers12123838] [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: 11/26/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
Statistical texture analysis of cancer cell nuclei stained for DNA has recently been used to develop a pan-cancer prognostic marker of chromatin heterogeneity. In this study, we instead analysed chromatin organisation by automatically quantifying the diversity of chromatin compartments in cancer cell nuclei. The aim was to investigate the prognostic value of such an assessment in relation to chromatin heterogeneity and as a potential supplement to pathological risk classifications in gynaecological carcinomas. The diversity was quantified by calculating the entropy of both chromatin compartment sizes and optical densities within compartments. We analysed a median of 281 nuclei (interquartile range (IQR), 273 to 289) from 246 ovarian carcinoma patients and a median of 997 nuclei (IQR, 502 to 1452) from 791 endometrial carcinoma patients. The prognostic value of the entropies and chromatin heterogeneity was moderately strongly correlated (r ranged from 0.68 to 0.73), but the novel marker was observed to provide additional prognostic information. In multivariable analysis with clinical and pathological markers, the hazard ratio associated with the novel marker was 2.1 (95% CI, 1.3 to 3.5) in ovarian carcinoma and 2.4 (95% CI, 1.5 to 3.9) in endometrial carcinoma. Integration with pathological risk classifications gave three risk groups with distinctly different prognoses. This suggests that the novel marker of diversity of chromatin compartments might possibly contribute to the selection of high-risk stage I ovarian carcinoma patients for adjuvant chemotherapy and low-risk endometrial carcinoma patients for less extensive surgery.
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Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics 2020; 21:511. [PMID: 33167851 PMCID: PMC7654587 DOI: 10.1186/s12859-020-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations. RESULTS A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells. CONCLUSIONS Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.
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Affiliation(s)
- Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Tongye Shen
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
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Matlock A, Tian L. High-throughput, volumetric quantitative phase imaging with multiplexed intensity diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2019; 10:6432-6448. [PMID: 31853409 PMCID: PMC6913397 DOI: 10.1364/boe.10.006432] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 05/06/2023]
Abstract
Intensity diffraction tomography (IDT) provides quantitative, volumetric refractive index reconstructions of unlabeled biological samples from intensity-only measurements. IDT is scanless and easily implemented in standard optical microscopes using an LED array but suffers from large data requirements and slow acquisition speeds. Here, we develop multiplexed IDT (mIDT), a coded illumination framework providing high volume-rate IDT for evaluating dynamic biological samples. mIDT combines illuminations from an LED grid using physical model-based design choices to improve acquisition rates and reduce dataset size with minimal loss to resolution and reconstruction quality. We analyze the optimal design scheme with our mIDT framework in simulation using the reconstruction error compared to conventional IDT and theoretical acquisition speed. With the optimally determined mIDT scheme, we achieve hardware-limited 4Hz acquisition rates enabling 3D refractive index distribution recovery on live Caenorhabditis elegans worms and embryos as well as epithelial buccal cells. Our mIDT architecture provides a 60 × speed improvement over conventional IDT and is robust across different illumination hardware designs, making it an easily adoptable imaging tool for volumetrically quantifying biological samples in their natural state.
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Affiliation(s)
- Alex Matlock
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
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14
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Characterization of 3D matrix conditions for cancer cell migration with elasticity/porosity-independent tunable microfiber gels. Polym J 2019. [DOI: 10.1038/s41428-019-0283-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Moore MJ, Sebastian JA, Kolios MC. Determination of cell nucleus-to-cytoplasmic ratio using imaging flow cytometry and a combined ultrasound and photoacoustic technique: a comparison study. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-10. [PMID: 31625322 PMCID: PMC7000884 DOI: 10.1117/1.jbo.24.10.106502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/09/2019] [Indexed: 05/09/2023]
Abstract
While the nucleus-to-cytoplasmic (N:C) ratio has traditionally been used for assessing cell malignancy, most N:C measurement techniques are time-consuming and performed on thin histological sections, which prohibit assessment of three-dimensional cell structure. A combined ultrahigh frequency ultrasound (US) and photoacoustic (PA) technique was used to assess the size and N:C ratio of cultured cancer cells in three dimensions (3D). The diameters of the cells and their stained nuclei were obtained by fitting the power spectrum of backscattered US pulses and emitted PA waves, respectively, to well-established theoretical models. For comparison, an imaging flow cytometer (IFC) was also used to determine the two-dimensional cell and nucleus sizes from large cell populations using brightfield and fluorescence images, respectively. An N:C ratio was calculated for each cell using the quotient of the measured nucleus diameter and the total cell diameter. The mean N:C ratios calculated using the sound-based approach were 0.68, 0.66, and 0.54 for MCF-7, PC-3, and MDA-MB-231 cells, respectively, and were in good agreement with the corresponding values of 0.68, 0.67, and 0.68 obtained using the IFC. The combined US and PA technique, which assesses cellular N:C ratio in 3D, has potential applications in the detection of circulating tumor cells in liquid biopsies.
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Affiliation(s)
- Michael J. Moore
- Ryerson University, Department of Physics, Faculty of Science, Toronto, Ontario, Canada
- Ryerson University and St. Michael’s Hospital, Institute for Biomedical Engineering and Science Technology, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, Keenan Research Center for Biomedical Science, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Joseph A. Sebastian
- Ryerson University, Department of Physics, Faculty of Science, Toronto, Ontario, Canada
- Ryerson University and St. Michael’s Hospital, Institute for Biomedical Engineering and Science Technology, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, Keenan Research Center for Biomedical Science, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Michael C. Kolios
- Ryerson University, Department of Physics, Faculty of Science, Toronto, Ontario, Canada
- Ryerson University and St. Michael’s Hospital, Institute for Biomedical Engineering and Science Technology, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, Keenan Research Center for Biomedical Science, St. Michael’s Hospital, Toronto, Ontario, Canada
- Address all correspondence to Michael C. Kolios, E-mail:
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16
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Damodaran K, Crestani M, Jokhun DS, Shivashankar GV. Nuclear morphometrics and chromatin condensation patterns as disease biomarkers using a mobile microscope. PLoS One 2019; 14:e0218757. [PMID: 31314779 PMCID: PMC6636717 DOI: 10.1371/journal.pone.0218757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/08/2019] [Indexed: 12/26/2022] Open
Abstract
Current cancer diagnosis involves the use of nuclear morphology and chromatin condensation signatures for accurate advanced stage classification. While such diagnostic approaches rely on high resolution imaging of the cell nucleus using expensive microscopy systems, developing portable mobile microscopes to visualize nuclear and chromatin condensation patterns is desirable at clinical settings with limited infrastructure. In this study, we develop a portable fluorescent mobile microscope capable of acquiring high resolution images of the nucleus and chromatin. Using this we extracted nuclear morphometric and chromatin texture based features and were able to discriminate between normal and cancer cells with similar accuracy as wide-field fluorescence microscopy. We were also able to detect subtle changes in nuclear and chromatin features in cells subjected to compressive forces, cytoskeletal perturbations and cytokine stimulation, thereby highlighting the sensitivity of the portable microscope. Taken together, we present a versatile platform to exploit nuclear morphometrics and chromatin condensation features as physical biomarkers for point-of-care diagnostic solutions.
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Affiliation(s)
- Karthik Damodaran
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Michele Crestani
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Doorgesh Sharma Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - G. V. Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular Oncology, Italian Foundation for Cancer Research, Milan, Italy
- * E-mail:
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17
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Mai S. The three-dimensional cancer nucleus. Genes Chromosomes Cancer 2019; 58:462-473. [PMID: 30536826 DOI: 10.1002/gcc.22720] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
Research into the three-dimensional (3D) organization of the cancer cell genome started over 100 years ago. We follow an exciting avenue of research in this field, from Hansemann's early observations of aberrant mitoses and nuclei in cancer cells in the late 19th century to Boveri's theory of the cancer cell in the early 20th century, to current views of nuclear organization and its changes in cancer. Molecular and imaging methods go hand in hand with providing us with a better understanding of the spatial nature of the cancer cell genome. This has led to the concept that the structural order of the nucleus can be used as cancer cell biomarker.
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Affiliation(s)
- Sabine Mai
- Cell Biology, Research Institute for Oncology and Hematology, CancerCare Manitoba, The University of Manitoba, Winnipeg, Manitoba, Canada
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18
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Zhikhoreva AA, Belashov AV, Bespalov VG, Semenov AL, Semenova IV, Tochilnikov GV, Zhilinskaya NT, Vasyutinskii OS. Morphological changes in the ovarian carcinoma cells of Wistar rats induced by chemotherapy with cisplatin and dioxadet. BIOMEDICAL OPTICS EXPRESS 2018; 9:5817-5827. [PMID: 30460164 PMCID: PMC6238906 DOI: 10.1364/boe.9.005817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 06/09/2023]
Abstract
The development of new express methods for the analysis of the efficacy of anti-cancer therapy on the cellular level is highly desirable for the analysis of chemotherapeutic agent performance. In this paper we suggest the use of parameters of cell morphology determined by holographic microscopy and tomography for the effective label free quantitative analysis of cell viability under antitumor chemotherapy and thus of cytostatic agent efficacy. As shown, measured phase shifts and cell morphology change dramatically as a result of chemotherapy and depend strongly on the cell type and agent applied. Experimentally, a comparative analysis of the antitumor efficacy of the two cytostatics, cisplatin and dioxadet, that are commonly used for chemotherapy of disseminated ovarian carcinoma has been performed. The experiments were carried out on the Wistar rat model. An essential difference in the morphology of cells, both normal (erythrocytes) and cancerous, present in ascitic fluid taken from the non-treated group of rats and the groups treated with either dioxadet or cisplatin, has been observed. The results obtained can be interpreted as an indication of the antitumor performance of both cytostatics at the cellular level and as a demonstration of the higher efficacy of therapy with dioxadet as compared to that with cisplatin. Differences in cell morphology are suggested to be applied as quantitative markers of cell viability and cytostatic agent efficacy. The conclusions made are supported by a comparison with the results of recent experiments based on survival rates of laboratory animals treated with these agents..
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Affiliation(s)
- A. A. Zhikhoreva
- Ioffe Institute; 26 Polytekhnicheskaya, St.Petersburg, 194021,
Russia
| | - A. V. Belashov
- Ioffe Institute; 26 Polytekhnicheskaya, St.Petersburg, 194021,
Russia
| | - V. G. Bespalov
- ITMO University; Kronverkskiy pr., 49, St. Petersburg, 197101,
Russia
- N. N. Petrov National Medical Research Center of Oncology, 68, Leningradskaya ul., Pesochnyi, St. Petersburg, 197758,
Russia
| | - A. L. Semenov
- N. N. Petrov National Medical Research Center of Oncology, 68, Leningradskaya ul., Pesochnyi, St. Petersburg, 197758,
Russia
| | - I. V. Semenova
- Ioffe Institute; 26 Polytekhnicheskaya, St.Petersburg, 194021,
Russia
| | - G. V. Tochilnikov
- N. N. Petrov National Medical Research Center of Oncology, 68, Leningradskaya ul., Pesochnyi, St. Petersburg, 197758,
Russia
| | - N. T. Zhilinskaya
- N. N. Petrov National Medical Research Center of Oncology, 68, Leningradskaya ul., Pesochnyi, St. Petersburg, 197758,
Russia
- Peter the Great St.Petersburg Polytechnic University; 29, Polytekhnicheskaya, St. Petersburg, 195251,
Russia
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19
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Cao B, Shetty R, Smith D, Kelbauskas L, Meldrum DR. Integrating fluorescence computed tomography with optical sheet illumination for imaging of live single cells. OPTICS EXPRESS 2018; 26:24020-24030. [PMID: 30184895 DOI: 10.1364/oe.26.024020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/12/2018] [Indexed: 05/24/2023]
Abstract
We present a new approach for three-dimensional (3D) live single-cell imaging with isotropic sub-micron spatial resolution using fluorescence computed tomography (fCT). A thin, highly inclined and laminated optical (HILO) sheet of light is used for fluorescence excitation in live single cells that are rotated around an axis perpendicular to the optical axis. During a full rotation, 400-500 two-dimensional (2D) projection images of the cell are acquired from multiple viewing perspectives by rapidly scanning the HILO light sheet along the optical axis. We report technical characteristics of the HILO approach and the results of a quantitative comparison with conventional epi fCT, demonstrating that HILO fCT offers significantly (about 17 times) reduced photobleaching and a two-fold improvement in 3D imaging contrast. We discuss potential application areas of the method for cell structure studies in live single cells with isotropic 3D spatial resolution.
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20
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Uhler C, Shivashankar GV. Nuclear Mechanopathology and Cancer Diagnosis. Trends Cancer 2018; 4:320-331. [PMID: 29606315 DOI: 10.1016/j.trecan.2018.02.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
Abstract
Abnormalities in nuclear and chromatin organization are hallmarks of many diseases including cancer. In this review, we highlight our understanding of how the cellular microenvironment regulates nuclear morphology and, with it, the spatial organization of chromosomes and genes, resulting in cell type-specific genomic programs. We also discuss the molecular basis for maintaining nuclear and genomic integrity and how alterations in nuclear mechanotransduction pathways result in various diseases. Finally, we highlight the importance of digital pathology based on nuclear morphometric features combined with single-cell genomics for early cancer diagnostics.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering & Computer Science, Institute for Data, Systems & Society, MIT, Cambridge, MA, USA
| | - G V Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore; FIRC Institute of Molecular Oncology (IFOM), Milan, Italy.
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21
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Radhakrishnan A, Damodaran K, Soylemezoglu AC, Uhler C, Shivashankar GV. Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis. Sci Rep 2017; 7:17946. [PMID: 29263424 PMCID: PMC5738417 DOI: 10.1038/s41598-017-17858-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 12/04/2022] Open
Abstract
Current cancer diagnosis employs various nuclear morphometric measures. While these have allowed accurate late-stage prognosis, early diagnosis is still a major challenge. Recent evidence highlights the importance of alterations in mechanical properties of single cells and their nuclei as critical drivers for the onset of cancer. We here present a method to detect subtle changes in nuclear morphometrics at single-cell resolution by combining fluorescence imaging and deep learning. This assay includes a convolutional neural net pipeline and allows us to discriminate between normal and human breast cancer cell lines (fibrocystic and metastatic states) as well as normal and cancer cells in tissue slices with high accuracy. Further, we establish the sensitivity of our pipeline by detecting subtle alterations in normal cells when subjected to small mechano-chemical perturbations that mimic tumor microenvironments. In addition, our assay provides interpretable features that could aid pathological inspections. This pipeline opens new avenues for early disease diagnostics and drug discovery.
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Affiliation(s)
- Adityanarayanan Radhakrishnan
- Department of Electrical Engineering and Computer Science, Laboratory for Information and Decision Systems, Institute for Data, Systems and Society, MIT, Cambridge, MA, USA
| | - Karthik Damodaran
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ali C Soylemezoglu
- Department of Electrical Engineering and Computer Science, Laboratory for Information and Decision Systems, Institute for Data, Systems and Society, MIT, Cambridge, MA, USA
| | - Caroline Uhler
- Department of Electrical Engineering and Computer Science, Laboratory for Information and Decision Systems, Institute for Data, Systems and Society, MIT, Cambridge, MA, USA.
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore. .,FIRC Institute for Molecular Oncology (IFOM), Milan, Italy.
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22
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Breaking the scale: how disrupting the karyoplasmic ratio gives cancer cells an advantage for metastatic invasion. Biochem Soc Trans 2017; 45:1333-1344. [PMID: 29150524 DOI: 10.1042/bst20170153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 01/03/2023]
Abstract
Nuclear size normally scales with the size of the cell, but in cancer this 'karyoplasmic ratio' is disrupted. This is particularly so in more metastatic tumors where changes in the karyoplasmic ratio are used in both diagnosis and prognosis for several tumor types. However, the direction of nuclear size changes differs for particular tumor types: for example in breast cancer, larger nuclear size correlates with increased metastasis, while for lung cancer smaller nuclear size correlates with increased metastasis. Thus, there must be tissue-specific drivers of the nuclear size changes, but proteins thus far linked to nuclear size regulation are widely expressed. Notably, for these tumor types, ploidy changes have been excluded as the basis for nuclear size changes, and so, the increased metastasis is more likely to have a basis in the nuclear morphology change itself. We review what is known about nuclear size regulation and postulate how such nuclear size changes can increase metastasis and why the directionality can differ for particular tumor types.
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23
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Xu M. Plum pudding random medium model of biological tissue toward remote microscopy from spectroscopic light scattering. BIOMEDICAL OPTICS EXPRESS 2017; 8:2879-2895. [PMID: 28663913 PMCID: PMC5480436 DOI: 10.1364/boe.8.002879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 05/02/2023]
Abstract
Biological tissue has a complex structure and exhibits rich spectroscopic behavior. There has been no tissue model until now that has been able to account for the observed spectroscopy of tissue light scattering and its anisotropy. Here we present, for the first time, a plum pudding random medium (PPRM) model for biological tissue which succinctly describes tissue as a superposition of distinctive scattering structures (plum) embedded inside a fractal continuous medium of background refractive index fluctuation (pudding). PPRM faithfully reproduces the wavelength dependence of tissue light scattering and attributes the "anomalous" trend in the anisotropy to the plum and the powerlaw dependence of the reduced scattering coefficient to the fractal scattering pudding. Most importantly, PPRM opens up a novel venue of quantifying the tissue architecture and microscopic structures on average from macroscopic probing of the bulk with scattered light alone without tissue excision. We demonstrate this potential by visualizing the fine microscopic structural alterations in breast tissue (adipose, glandular, fibrocystic, fibroadenoma, and ductal carcinoma) deduced from noncontact spectroscopic measurement.
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Affiliation(s)
- Min Xu
- Department of Physics, Fairfield University, 1073 North Benson Road, Fairfield, CT 06824,
USA
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24
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dos Santos AF, Terra LF, Wailemann RAM, Oliveira TC, Gomes VDM, Mineiro MF, Meotti FC, Bruni-Cardoso A, Baptista MS, Labriola L. Methylene blue photodynamic therapy induces selective and massive cell death in human breast cancer cells. BMC Cancer 2017; 17:194. [PMID: 28298203 PMCID: PMC5353937 DOI: 10.1186/s12885-017-3179-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/08/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Breast cancer is the main cause of mortality among women. The disease presents high recurrence mainly due to incomplete efficacy of primary treatment in killing all cancer cells. Photodynamic therapy (PDT), an approach that causes tissue destruction by visible light in the presence of a photosensitizer (Ps) and oxygen, appears as a promising alternative therapy that could be used adjunct to chemotherapy and surgery for curing cancer. However, the efficacy of PDT to treat breast tumours as well as the molecular mechanisms that lead to cell death remain unclear. METHODS In this study, we assessed the cell-killing potential of PDT using methylene blue (MB-PDT) in three breast epithelial cell lines that represent non-malignant conditions and different molecular subtypes of breast tumours. Cells were incubated in the absence or presence of MB and irradiated or not at 640 nm with 4.5 J/cm2. We used a combination of imaging and biochemistry approaches to assess the involvement of classical autophagic and apoptotic pathways in mediating the cell-deletion induced by MB-PDT. The role of these pathways was investigated using specific inhibitors, activators and gene silencing. RESULTS We observed that MB-PDT differentially induces massive cell death of tumour cells. Non-malignant cells were significantly more resistant to the therapy compared to malignant cells. Morphological and biochemical analysis of dying cells pointed to alternative mechanisms rather than classical apoptosis. MB-PDT-induced autophagy modulated cell viability depending on the cell model used. However, impairment of one of these pathways did not prevent the fatal destination of MB-PDT treated cells. Additionally, when using a physiological 3D culture model that recapitulates relevant features of normal and tumorous breast tissue morphology, we found that MB-PDT differential action in killing tumour cells was even higher than what was detected in 2D cultures. CONCLUSIONS Finally, our observations underscore the potential of MB-PDT as a highly efficient strategy which could use as a powerful adjunct therapy to surgery of breast tumours, and possibly other types of tumours, to safely increase the eradication rate of microscopic residual disease and thus minimizing the chance of both local and metastatic recurrence.
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Affiliation(s)
- Ancély F. dos Santos
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Letícia F. Terra
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Rosangela A. M. Wailemann
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Talita C. Oliveira
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Vinícius de Morais Gomes
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Marcela Franco Mineiro
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Flávia Carla Meotti
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Alexandre Bruni-Cardoso
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Maurício S. Baptista
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
| | - Leticia Labriola
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo, 05508-000 SP Brazil
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25
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Pradhan S, Clary JM, Seliktar D, Lipke EA. A three-dimensional spheroidal cancer model based on PEG-fibrinogen hydrogel microspheres. Biomaterials 2016; 115:141-154. [PMID: 27889665 DOI: 10.1016/j.biomaterials.2016.10.052] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/26/2016] [Accepted: 10/29/2016] [Indexed: 12/11/2022]
Abstract
Three-dimensional (3D) in vitro cancer models offer an attractive approach towards the investigation of tumorigenic phenomena and other cancer studies by providing dimensional context and higher degree of physiological relevance than that offered by conventional two-dimensional (2D) models. The multicellular tumor spheroid model, formed by cell aggregation, is considered to be the "gold standard" for 3D cancer models, due to its ease and simplicity of use. Although better than 2D models, tumor spheroids are unable to replicate key features of the native tumor microenvironment, particularly due to a lack of surrounding extracellular matrix components and heterogeneity in shape, size and aggregate forming tendencies. In order to address this issue, we have developed a 3D "tumor microsphere" model, formed by a dual-photoinitiator, aqueous-oil emulsion technique, for the encapsulation of cancer cells within PEG-fibrinogen hydrogel microspheres and for subsequent long-term 3D culture. In comparison to self-aggregated tumor spheroids, the tumor microspheres displayed a higher degree of size and shape homogeneity throughout long-term culture. In sharp contrast to cells in tumor spheroids, cells within tumor microspheres demonstrated significant loss in apico-basal polarity and cellular architecture, cellular and nuclear atypia, increased disorganization, elevated nuclear cytoplasmic ratio and nuclear volume density and reduction in cell-cell junction length, all of which are hallmarks of malignant transformation and tumorigenic progression. Additionally, the tumor microsphere model was extended for the 3D encapsulation and maintenance of a wide range of other cancer cell (metastatic and non-metastatic) types. Taken together, our results reinforce the importance of incorporating a biomimetic matrix in the cellular microenvironment of 3D tumor models and the influential effects of the matrix on the tumorigenic morphology of 3D cultured cells. The tumor microsphere system established in this study has the potential to be used in future investigations of 3D cancer cell-cell and cell-ECM interactions and in drug-testing applications.
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Affiliation(s)
- Shantanu Pradhan
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
| | - Jacob M Clary
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
| | - Dror Seliktar
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Elizabeth A Lipke
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA.
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26
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Mueller JL, Gallagher JE, Chitalia R, Krieger M, Erkanli A, Willett RM, Geradts J, Ramanujam N. Rapid staining and imaging of subnuclear features to differentiate between malignant and benign breast tissues at a point-of-care setting. J Cancer Res Clin Oncol 2016; 142:1475-86. [PMID: 27106032 DOI: 10.1007/s00432-016-2165-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/11/2016] [Indexed: 01/01/2023]
Abstract
PURPOSE Histopathology is the clinical standard for tissue diagnosis; however, it requires tissue processing, laboratory personnel and infrastructure, and a highly trained pathologist to diagnose the tissue. Optical microscopy can provide real-time diagnosis, which could be used to inform the management of breast cancer. The goal of this work is to obtain images of tissue morphology through fluorescence microscopy and vital fluorescent stains and to develop a strategy to segment and quantify breast tissue features in order to enable automated tissue diagnosis. METHODS We combined acriflavine staining, fluorescence microscopy, and a technique called sparse component analysis to segment nuclei and nucleoli, which are collectively referred to as acriflavine positive features (APFs). A series of variables, which included the density, area fraction, diameter, and spacing of APFs, were quantified from images taken from clinical core needle breast biopsies and used to create a multivariate classification model. The model was developed using a training data set and validated using an independent testing data set. RESULTS The top performing classification model included the density and area fraction of smaller APFs (those less than 7 µm in diameter, which likely correspond to stained nucleoli).When applied to the independent testing set composed of 25 biopsy panels, the model achieved a sensitivity of 82 %, a specificity of 79 %, and an overall accuracy of 80 %. CONCLUSIONS These results indicate that our quantitative microscopy toolbox is a potentially viable approach for detecting the presence of malignancy in clinical core needle breast biopsies.
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Affiliation(s)
- Jenna L Mueller
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall Box 90281, Durham, NC, 27708, USA.
| | - Jennifer E Gallagher
- Department of Surgery, Duke University Medical Center, 30 Medicine Drive White Zone, 3rd Floor, Suite 3570, Durham, NC, 27710, USA
| | - Rhea Chitalia
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall Box 90281, Durham, NC, 27708, USA
| | - Marlee Krieger
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall Box 90281, Durham, NC, 27708, USA
| | - Alaattin Erkanli
- Department of Biostatistics and Bioinformatics, Duke University, Brightleaf Square Suite 22B, 905 West Main Street, Durham, NC, 27701, USA
| | - Rebecca M Willett
- Department of Electrical and Computer Engineering, University of Wisconsin - Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Joseph Geradts
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Nimmi Ramanujam
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall Box 90281, Durham, NC, 27708, USA
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27
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Vuković LD, Jevtić P, Edens LJ, Levy DL. New Insights into Mechanisms and Functions of Nuclear Size Regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:1-59. [PMID: 26940517 DOI: 10.1016/bs.ircmb.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear size is generally maintained within a defined range in a given cell type. Changes in cell size that occur during cell growth, development, and differentiation are accompanied by dynamic nuclear size adjustments in order to establish appropriate nuclear-to-cytoplasmic volume relationships. It has long been recognized that aberrations in nuclear size are associated with certain disease states, most notably cancer. Nuclear size and morphology must impact nuclear and cellular functions. Understanding these functional implications requires an understanding of the mechanisms that control nuclear size. In this review, we first provide a general overview of the diverse cellular structures and activities that contribute to nuclear size control, including structural components of the nucleus, effects of DNA amount and chromatin compaction, signaling, and transport pathways that impinge on the nucleus, extranuclear structures, and cell cycle state. We then detail some of the key mechanistic findings about nuclear size regulation that have been gleaned from a variety of model organisms. Lastly, we review studies that have implicated nuclear size in the regulation of cell and nuclear function and speculate on the potential functional significance of nuclear size in chromatin organization, gene expression, nuclear mechanics, and disease. With many fundamental cell biological questions remaining to be answered, the field of nuclear size regulation is still wide open.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America.
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28
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Cell type-specific adaptation of cellular and nuclear volume in micro-engineered 3D environments. Biomaterials 2015; 69:121-32. [DOI: 10.1016/j.biomaterials.2015.08.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/14/2022]
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Dobbs JL, Mueller JL, Krishnamurthy S, Shin D, Kuerer H, Yang W, Ramanujam N, Richards-Kortum R. Micro-anatomical quantitative optical imaging: toward automated assessment of breast tissues. Breast Cancer Res 2015; 17:105. [PMID: 26290094 PMCID: PMC4545917 DOI: 10.1186/s13058-015-0617-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Pathologists currently diagnose breast lesions through histologic assessment, which requires fixation and tissue preparation. The diagnostic criteria used to classify breast lesions are qualitative and subjective, and inter-observer discordance has been shown to be a significant challenge in the diagnosis of selected breast lesions, particularly for borderline proliferative lesions. Thus, there is an opportunity to develop tools to rapidly visualize and quantitatively interpret breast tissue morphology for a variety of clinical applications. METHODS Toward this end, we acquired images of freshly excised breast tissue specimens from a total of 34 patients using confocal fluorescence microscopy and proflavine as a topical stain. We developed computerized algorithms to segment and quantify nuclear and ductal parameters that characterize breast architectural features. A total of 33 parameters were evaluated and used as input to develop a decision tree model to classify benign and malignant breast tissue. Benign features were classified in tissue specimens acquired from 30 patients and malignant features were classified in specimens from 22 patients. RESULTS The decision tree model that achieved the highest accuracy for distinguishing between benign and malignant breast features used the following parameters: standard deviation of inter-nuclear distance and number of duct lumens. The model achieved 81 % sensitivity and 93 % specificity, corresponding to an area under the curve of 0.93 and an overall accuracy of 90 %. The model classified IDC and DCIS with 92 % and 96 % accuracy, respectively. The cross-validated model achieved 75 % sensitivity and 93 % specificity and an overall accuracy of 88 %. CONCLUSIONS These results suggest that proflavine staining and confocal fluorescence microscopy combined with image analysis strategies to segment morphological features could potentially be used to quantitatively diagnose freshly obtained breast tissue at the point of care without the need for tissue preparation.
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Affiliation(s)
- Jessica L Dobbs
- Department of Bioengineering, Rice University, 6500 Main Street, BRC 502, Houston, TX, 77030, USA.
| | - Jenna L Mueller
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708, USA.
| | - Savitri Krishnamurthy
- Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1350, Houston, TX, 77030, USA.
| | - Dongsuk Shin
- Department of Bioengineering, Rice University, 6500 Main Street, BRC 502, Houston, TX, 77030, USA.
| | - Henry Kuerer
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 0444, Houston, TX, 77030, USA.
| | - Wei Yang
- Department of Diagnostic Radiology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1350, Houston, TX, 77030, USA.
| | - Nirmala Ramanujam
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708, USA.
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University, 6500 Main Street, BRC 502, Houston, TX, 77030, USA.
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Characterization of Dynamic Behaviour of MCF7 and MCF10A Cells in Ultrasonic Field Using Modal and Harmonic Analyses. PLoS One 2015; 10:e0134999. [PMID: 26241649 PMCID: PMC4524665 DOI: 10.1371/journal.pone.0134999] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/15/2015] [Indexed: 12/25/2022] Open
Abstract
Treatment options specifically targeting tumour cells are urgently needed in order to reduce the side effects accompanied by chemo- or radiotherapy. Differences in subcellular structure between tumour and normal cells determine their specific elasticity. These structural differences can be utilised by low-frequency ultrasound in order to specifically induce cytotoxicity of tumour cells. For further evaluation, we combined in silico FEM (finite element method) analyses and in vitro assays to bolster the significance of low-frequency ultrasound for tumour treatment. FEM simulations were able to calculate the first resonance frequency of MCF7 breast tumour cells at 21 kHz in contrast to 34 kHz for the MCF10A normal breast cells, which was due to the higher elasticity and larger size of MCF7 cells. For experimental validation of the in silico-determined resonance frequencies, equipment for ultrasonic irradiation with distinct frequencies was constructed. Differences for both cell lines in their response to low-frequent ultrasonic treatment were corroborated in 2D and in 3D cell culture assays. Treatment with ~ 24.5 kHz induced the death of MCF7 cells and MDA-MB-231 metastases cells possessing a similar elasticity; frequencies of > 29 kHz resulted in cytotoxicity of MCF10A. Fractionated treatments by ultrasonic irradiation of suspension myeloid HL60 cells resulted in a significant decrease of viable cells, mostly significant after threefold irradiation in intervals of 3 h. Most importantly in regard to a clinical application, combined ultrasonic treatment and chemotherapy with paclitaxel showed a significantly increased killing of MCF7 cells compared to both monotherapies. In summary, we were able to determine for the first time for different tumour cell lines a specific frequency of low-intensity ultrasound for induction of cell ablation. The cytotoxic effect of ultrasonic irradiation could be increased by either fractionated treatment or in combination with chemotherapy. Thus, our results will open new perspectives in tumour treatment.
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Lobo J, See EYS, Biggs M, Pandit A. An insight into morphometric descriptors of cell shape that pertain to regenerative medicine. J Tissue Eng Regen Med 2015; 10:539-53. [DOI: 10.1002/term.1994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/25/2014] [Accepted: 12/09/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Joana Lobo
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Eugene Yong-Shun See
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Manus Biggs
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Abhay Pandit
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
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Chiotaki R, Polioudaki H, Theodoropoulos PA. Differential nuclear shape dynamics of invasive andnon-invasive breast cancer cells are associated with actin cytoskeleton organization and stability. Biochem Cell Biol 2014; 92:287-95. [PMID: 25053513 DOI: 10.1139/bcb-2013-0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cancer cells often exhibit characteristic aberrations in their nuclear architecture, which are indicative of their malignant potential. In this study, we have examined the nuclear and cytoskeletal composition, attachment configuration dynamics, and osmotic or drug treatment response of invasive (Hs578T and MDA-MB-231) and non-invasive (MCF-10A and MCF-7) breast cancer cell lines. Unlike MCF-10A and MCF-7, Hs578T and MDA-MB-231 cells showed extensive nuclear elasticity and deformability and displayed distinct kinetic profiles during substrate attachment. The nuclear shape of MCF-10A and MCF-7 cells remained almost unaffected upon detachment, hyperosmotic shock, or cytoskeleton depolymerization, while Hs578T and MDA-MB-231 revealed dramatic nuclear contour malformations following actin reorganization.
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Affiliation(s)
- Rena Chiotaki
- Department of Biochemistry, School of Medicine, University of Crete, Heraklion 71003, Greece
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33
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Sizing and shaping the nucleus: mechanisms and significance. Curr Opin Cell Biol 2014; 28:16-27. [PMID: 24503411 DOI: 10.1016/j.ceb.2014.01.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/07/2014] [Accepted: 01/11/2014] [Indexed: 01/14/2023]
Abstract
The size and shape of the nucleus are tightly regulated, indicating the physiological significance of proper nuclear morphology, yet the mechanisms and functions of nuclear size and shape regulation remain poorly understood. Correlations between altered nuclear morphology and certain disease states have long been observed, most notably many cancers are diagnosed and staged based on graded increases in nuclear size. Here we review recent studies investigating the mechanisms regulating nuclear size and shape, how mitotic events influence nuclear morphology, and the role of nuclear size and shape in subnuclear chromatin organization and cancer progression.
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Jevtić P, Levy DL. Mechanisms of nuclear size regulation in model systems and cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:537-69. [PMID: 24563365 DOI: 10.1007/978-1-4899-8032-8_25] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Changes in nuclear size have long been used by cytopathologists as an important parameter to diagnose, stage, and prognose many cancers. Mechanisms underlying these changes and functional links between nuclear size and malignancy are largely unknown. Understanding mechanisms of nuclear size regulation and the physiological significance of proper nuclear size control will inform the interplay between altered nuclear size and oncogenesis. In this chapter we review what is known about molecular mechanisms of nuclear size control based on research in model experimental systems including yeast, Xenopus, Tetrahymena, Drosophila, plants, mice, and mammalian cell culture. We discuss how nuclear size is influenced by DNA ploidy, nuclear structural components, cytoplasmic factors and nucleocytoplasmic transport, the cytoskeleton, and the extracellular matrix. Based on these mechanistic insights, we speculate about how nuclear size might impact cell physiology and whether altered nuclear size could contribute to cancer development and progression. We end with some outstanding questions about mechanisms and functions of nuclear size regulation.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA,
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de Las Heras JI, Schirmer EC. The nuclear envelope and cancer: a diagnostic perspective and historical overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:5-26. [PMID: 24563341 DOI: 10.1007/978-1-4899-8032-8_1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer has been diagnosed for millennia, but its cellular nature only began to be understood in the mid-nineteenth century when advances in microscopy allowed detailed specimen observations. It was soon noted that cancer cells often possessed nuclei that were altered in size and/or shape. This became an important criterion for cancer diagnosis that continues to be used today. The mechanisms linking nuclear abnormalities and cancer only started to be understood in the second half of the twentieth century, with the discovery of nuclear lamina composition differences in cancer cells compared to normal cells. The nuclear envelope, rather than providing a mere physical barrier between the genetic material in the nucleus and the cytoplasm, is a very important functional hub for many cellular processes. In this review we give an overview of the links between cancer biology and nuclear envelope, from the early days of microscopy until the present day's understanding of some of the molecular mechanisms behind those links.
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Affiliation(s)
- Jose I de Las Heras
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Building, Room 5.21, Edinburgh, EH9 3JR, UK,
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36
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Kumar VS, Webster M. The automated pathologist. Clin Chem 2013; 59:1418-20. [PMID: 23986508 DOI: 10.1373/clinchem.2013.210260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vikram Sheel Kumar
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
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37
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Song W, Liu W, Niu X, Wang Q, Sun L, Liu M, Fan Y. Three-dimensional morphometric comparison of normal and apoptotic endothelial cells based on laser scanning confocal microscopy observation. Microsc Res Tech 2013; 76:1154-62. [PMID: 23955846 DOI: 10.1002/jemt.22279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/18/2013] [Accepted: 07/29/2013] [Indexed: 01/29/2023]
Abstract
Three-dimensional (3D) morphometric analysis of cellular and subcellular structures provides an effective method for spatial cell biology. Here, 3D cellular and nuclear morphologies are reconstructed to quantify and compare morphometric differences between normal and apoptotic endothelial cells. Human umbilical vein endothelial cells (HUVECs) are treated with 60 μM H2 O2 to get apoptotic cell model and then a series of sectional images are acquired from laser scanning confocal microscopy. The 3D cell model containing plasma membrane and cell nucleus is reconstructed and fused utilizing three sequential softwares or packages (Mimics, Geomagic, and VTK). The results reveal that H2 O2 can induce apoptosis effectively by regulating the activity of apoptosis-related biomolecules, including pro-apoptotic factors p53 and Bax, and anti-apoptotic factor Bcl-2. Compared with the normal HUVECs, the apoptotic cells exhibit significant 3D morphometric parameters (height, volume and nucleus-to-cytoplasm ratio) variation. The present research provides a new perspective on comparative quantitative analysis associated with cell apoptosis and points to the value of LSCM as an objective tool for 3D cell reconstruction.
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Affiliation(s)
- Wei Song
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
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Abuhattoum S, Weihs D. Location-dependent intracellular particle tracking using a cell-based coordinate system. Comput Methods Biomech Biomed Engin 2013; 16:1042-9. [PMID: 23452183 DOI: 10.1080/10255842.2012.761694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Intracellular structure and active processes have been studied by particle tracking using the motion of internalised probes. Intracellular particle motion is driven by a complex combination of active and thermal processes within heterogeneous and dynamically changing micro-environments. Regions in the cells may react differently to environmental changes or following treatment, exhibiting location-dependent responses. Hence, to reveal such responses, we introduce cell-specific polar coordinate systems. The coordinates are defined for each cell by its nucleus location and orientation, providing relative particle locations in the cytoplasm. The utility of our approach is demonstrated by comparing Adenosine Triphosphate (ATP)-depleted and control cells. In both cells, we observe differences in particle transport with the distance from the nucleus. Following ATP depletion, basic particle motion analysis shows an expected reduction in activity driving particle transport. However, it is our location-dependent approach which reveals that while morphology changes primarily at the cortex, the cell response is actually nearly uniform across the cytoplasm.
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Affiliation(s)
- Shada Abuhattoum
- a Faculty of Biomedical Engineering, Technion-Israel Institute of Technology , Haifa , 32000 , Israel
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40
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Fleischer DE. Comparing apples with apples and oranges: the role of radiofrequency ablation alone versus radiofrequency ablation plus EMR for endoscopic management of Barrett's esophagus with advanced neoplasia. Gastrointest Endosc 2012; 76:740-2. [PMID: 22985641 DOI: 10.1016/j.gie.2012.07.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 07/16/2012] [Indexed: 02/04/2023]
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41
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Kshitiz, Park J, Kim P, Helen W, Engler AJ, Levchenko A, Kim DH. Control of stem cell fate and function by engineering physical microenvironments. Integr Biol (Camb) 2012; 4:1008-18. [PMID: 23077731 PMCID: PMC3476065 DOI: 10.1039/c2ib20080e] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The phenotypic expression and function of stem cells are regulated by their integrated response to variable microenvironmental cues, including growth factors and cytokines, matrix-mediated signals, and cell–cell interactions. Recently, growing evidence suggests that matrix-mediated signals include mechanical stimuli such as strain, shear stress, substrate rigidity and topography, and these stimuli have a more profound impact on stem cell phenotypes than had previously been recognized, e.g. self-renewal and differentiation through the control of gene transcription and signaling pathways. Using a variety of cell culture models enabled by micro and nanoscale technologies, we are beginning to systematically and quantitatively investigate the integrated response of cells to combinations of relevant mechanobiological stimuli. This paper reviews recent advances in engineering physical stimuli for stem cell mechanobiology and discusses how micro- and nanoscale engineered platforms can be used to control stem cell niche environments and regulate stem cell fate and function.
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Affiliation(s)
- Kshitiz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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