scholarly journals Integrative data analysis predicts YY1 as a Cis-regulator in the 3D Cell Culture Models of MCF10A at the Stiffness Level of High Mammographic Density

2018 ◽  
Author(s):  
Qingsu Cheng ◽  
Mina Khoshdeli ◽  
Chongzhi Zang ◽  
Bahram Parvin
Keyword(s):  
Cell Culture ◽  
Transcription Factors ◽  
Mammographic Density ◽  
Regulation Of Gene Expression ◽  
3D Culture ◽  
3D Cell Culture ◽  
Transcriptome Data ◽  
High Mammographic Density ◽  
Culture Models ◽  
Cell Culture Models

AbstractPrevious studies have shown that in 3D cell culture models of human mammary cells (HMEC) (i) colony organizations are heterogeneous, and (ii) ERBB2 is overexpressed in MCF10A when the stiffness of the microenvironment is increased to that of high mammographic density (MD). The goal of the current study is to identify transcription factors that regulate processes associated with the increased stiffness of the microenvironment. Two HMEC premalignant lines of MCF7 and 184A1 are cultured in 3D, colonies are imaged using confocal microscopy, and colony organizations and heterogeneity are quantified as a function of the stiffness of the microenvironment. In parallel and surrogate assays, colony organizations are profiled by transcriptomics. Transcriptome data are enriched by correlative analysis with the computed morphometric indices, from 3D culture, and a subset of transcriptome data is selected. This subset is then processed with Model-based Analysis of Regulation of Gene Expression (MARGE) and publicly available ChIP-seq data to predict regulatory transcription factors. The integrative analysis indicated that YY1 regulates ERBB2 in the 3D cell culture of MCF10A when the stiffness of the microenvironment is increased to that of high MD. Subsequent experimental validation confirmed that YY1 is only expressed at the high stiffness value of the microenvironment concomitant with the overexpression of ERBB2 in MCF10A. Furthermore, using ERBB2 positive SKBR3 cell line, co-expression of YY1 and ERBB2 is absent, which indicates that YY1 regulates tumorigenicity through multiple pathways.Author’s summaryMCF10A is a premalignant immortalized human mammary cell that has been isolated from a patient with fibrocystic and lost several barriers toward transformation. In an earlier study, we showed that ERBB2 is upregulated in 3D cultures of MCF10A when the stiffness of the microenvironment is increased to that of high mammographic density. Here, we leverage publicly available ChIP-seq data to predict and validate the cis-regulator of ERBB2. Our integrated experimental and computation protocol provides a pathway for elucidating regulators that can potentially be targeted for intervention.

scholarly journals The Communication between Ocular Surface and Nasal Epithelia in 3D Cell Culture Technology for Translational Research: A Narrative Review

2021 ◽  
Vol 22 (23) ◽  
pp. 12994
Author(s):  
Malik Aydin ◽  
Jana Dietrich ◽  
Joana Witt ◽  
Maximiliane S. C. Finkbeiner ◽  
Jonas J.-H. Park ◽  
...  
Keyword(s):  
Cell Culture ◽  
Nasal Cavity ◽  
Ocular Surface ◽  
Measles Virus ◽  
3D Culture ◽  
3D Cell Culture ◽  
Narrative Review ◽  
Culture Models ◽  
Cell Culture Models

There is a lack of knowledge regarding the connection between the ocular and nasal epithelia. This narrative review focuses on conjunctival, corneal, ultrastructural corneal stroma, and nasal epithelia as well as an introduction into their interconnections. We describe in detail the morphology and physiology of the ocular surface, the nasolacrimal ducts, and the nasal cavity. This knowledge provides a basis for functional studies and the development of relevant cell culture models that can be used to investigate the pathogenesis of diseases related to these complex structures. Moreover, we also provide a state-of-the-art overview regarding the development of 3D culture models, which allow for addressing research questions in models resembling the in vivo situation. In particular, we give an overview of the current developments of corneal 3D and organoid models, as well as 3D cell culture models of epithelia with goblet cells (conjunctiva and nasal cavity). The benefits and shortcomings of these cell culture models are discussed. As examples for pathogens related to ocular and nasal epithelia, we discuss infections caused by adenovirus and measles virus. In addition to pathogens, also external triggers such as allergens can cause rhinoconjunctivitis. These diseases exemplify the interconnections between the ocular surface and nasal epithelia in a molecular and clinical context. With a final translational section on optical coherence tomography (OCT), we provide an overview about the applicability of this technique in basic research and clinical ophthalmology. The techniques presented herein will be instrumental in further elucidating the functional interrelations and crosstalk between ocular and nasal epithelia.

scholarly journals Factors to consider when interrogating 3D culture models with plate readers or automated microscopes

2021 ◽  
Author(s):  
Terry Riss ◽  
O. Joseph Trask
Keyword(s):  
Cell Culture ◽  
Three Dimensional ◽  
3D Culture ◽  
Fluorescent Imaging ◽  
Culture Models ◽  
Assay Methods ◽  
Diffusion Rates ◽  
Cell Culture Models ◽  
Dimensional Cell ◽  
Cells Cultured

AbstractAlong with the increased use of more physiologically relevant three-dimensional cell culture models comes the responsibility of researchers to validate new assay methods that measure events in structures that are physically larger and more complex compared to monolayers of cells. It should not be assumed that assays designed using monolayers of cells will work for cells cultured as larger three-dimensional masses. The size and barriers for penetration of molecules through the layers of cells result in a different microenvironment for the cells in the outer layer compared to the center of three-dimensional structures. Diffusion rates for nutrients and oxygen may limit metabolic activity which is often measured as a marker for cell viability. For assays that lyse cells, the penetration of reagents to achieve uniform cell lysis must be considered. For live cell fluorescent imaging assays, the diffusion of fluorescent probes and penetration of photons of light for probe excitation and fluorescent emission must be considered. This review will provide an overview of factors to consider when implementing assays to interrogate three dimensional cell culture models.

scholarly journals Conjunctival melanoma and electrochemotherapy: preliminary results using 2D and 3D cell culture models in vitro

2018 ◽  
Vol 97 (4) ◽  
pp. e632-e640 ◽  
Author(s):  
Miltiadis Fiorentzis ◽  
Periklis Katopodis ◽  
Helen Kalirai ◽  
Berthold Seitz ◽  
Arne Viestenz ◽  
...  
Keyword(s):  
Cell Culture ◽  
3D Cell Culture ◽  
Conjunctival Melanoma ◽  
Preliminary Results ◽  
Culture Models ◽  
2D And 3D ◽  
Cell Culture Models

Organotypic 3D cell culture models: using the rotating wall vessel to study host–pathogen interactions

2010 ◽  
Vol 8 (11) ◽  
pp. 791-801 ◽  
Author(s):  
Jennifer Barrila ◽  
Andrea L. Radtke ◽  
Aurélie Crabbé ◽  
Shameema F. Sarker ◽  
Melissa M. Herbst-Kralovetz ◽  
...  
Keyword(s):  
Cell Culture ◽  
3D Cell Culture ◽  
Host Pathogen Interactions ◽  
Rotating Wall ◽  
Rotating Wall Vessel ◽  
Host Pathogen ◽  
Culture Models ◽  
Cell Culture Models

Length vs. stiffness: which plays a dominant role in the cellular uptake of fructose-based rod-like micelles by breast cancer cells in 2D and 3D cell culture models?

2018 ◽  
Vol 6 (25) ◽  
pp. 4223-4231 ◽  
Author(s):  
Jiacheng Zhao ◽  
Hongxu Lu ◽  
Yin Yao ◽  
Sylvia Ganda ◽  
Martina H. Stenzel
Keyword(s):  
Breast Cancer ◽  
Cell Culture ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Dominant Role ◽  
3D Cell Culture ◽  
Culture Models ◽  
Nano Rods ◽  
2D And 3D ◽  
Cell Culture Models

Internalization of rod-like micelles by breast cancer cells is significantly affected by the stiffness of nano-rods.

scholarly journals YY1 is a cis-regulator in the organoid models of high mammographic density

2019 ◽  
Vol 36 (6) ◽  
pp. 1663-1667 ◽  
Author(s):  
Qingsu Cheng ◽  
Mina Khoshdeli ◽  
Bradley S Ferguson ◽  
Kosar Jabbari ◽  
Chongzhi Zang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Lines ◽  
Mammographic Density ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Human Mammary Epithelial Cell ◽  
Mammary Epithelial ◽  
Supplementary Information ◽  
Mrna Levels ◽  
High Mammographic Density

Abstract Motivation Our previous study has shown that ERBB2 is overexpressed in the organoid model of MCF10A when the stiffness of the microenvironment is increased to that of high mammographic density (MD). We now aim to identify key transcription factors (TFs) and functional enhancers that regulate processes associated with increased stiffness of the microenvironment in the organoid models of premalignant human mammary cell lines. Results 3D colony organizations and the cis-regulatory networks of two human mammary epithelial cell lines (184A1 and MCF10A) are investigated as a function of the increased stiffness of the microenvironment within the range of MD. The 3D colonies are imaged using confocal microscopy, and the morphometries of colony organizations and heterogeneity are quantified as a function of the stiffness of the microenvironment using BioSig3D. In a surrogate assay, colony organizations are profiled by transcriptomics. Transcriptome data are enriched by correlative analysis with the computed morphometric indices. Next, a subset of enriched data are processed against publicly available ChIP-Seq data using Model-based Analysis of Regulation of Gene Expression to predict regulatory transcription factors. This integrative analysis of morphometric and transcriptomic data predicted YY1 as one of the cis-regulators in both cell lines as a result of the increased stiffness of the microenvironment. Subsequent experiments validated that YY1 is expressed at protein and mRNA levels for MCF10A and 184A1, respectively. Also, there is a causal relationship between activation of YY1 and ERBB2 when YY1 is overexpressed at the protein level in MCF10A. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Untargeted Metabolite Mapping in 3D Cell Culture Models Using High Spectral Resolution FT-ICR Mass Spectrometry Imaging

2019 ◽  
Vol 91 (15) ◽  
pp. 9522-9529 ◽  
Author(s):  
Lulu H. Tucker ◽  
Gregory R. Hamm ◽  
Rebecca J. E. Sargeant ◽  
Richard J. A. Goodwin ◽  
C. Logan Mackay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cell Culture ◽  
Spectral Resolution ◽  
Mass Spectrometry Imaging ◽  
3D Cell Culture ◽  
High Spectral Resolution ◽  
Culture Models ◽  
Cell Culture Models ◽  
Ft Icr

Effect of cell culture models on the evaluation of anticancer activity and mechanism analysis of the potential bioactive compound, iturin A, produced by Bacillus subtilis

2019 ◽  
Vol 10 (3) ◽  
pp. 1478-1489 ◽  
Author(s):  
Haobin Zhao ◽  
Xixi Zhao ◽  
Shuzhen Lei ◽  
Yawen Zhang ◽  
Dongyan Shao ◽  
...  
Keyword(s):  
Cell Culture ◽  
Bacillus Subtilis ◽  
3D Culture ◽  
Bioactive Compound ◽  
Mechanism Analysis ◽  
Iturin A ◽  
Culture Cells ◽  
Culture Models ◽  
Cell Culture Models ◽  
Cells Cultured

Compared to 2D culture, cells cultured in 3D culture were more resistant to iturin A from Bacillus.

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