Mineotaur: a tool for high-content microscopy screen sharing and visual analytics

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From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

Abstract In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular—powered by breakthroughs in computer vision, large-scale image analysis and machine learning—high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell ‘omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function

Dynamics of cell shape inheritance in fission yeast.

Every cell has a characteristic shape key to its fate and function. That shape is not only the product of genetic design and of the physical and biochemical environment, but it is also subject to inheritance. However, the nature and contribution of cell shape inheritance to morphogenetic control is mostly ignored. Here, we investigate morphogenetic inheritance in the cylindrically-shaped fission yeast Schizosaccharomyces pombe. Focusing on sixteen different 'curved' mutants--a class of mutants which often fail to grow axially straight--we quantitatively characterize their dynamics of cell shape inheritance throughout generations. We show that mutants of similar machineries display similar dynamics of cell shape inheritance, and exploit this feature to show that persistent axial cell growth in S. pombe is secured by multiple, separable molecular pathways. Finally, we find that one of those pathways corresponds to the swc2-swr1-vps71 SWR1/SRCAP chromatin remodelling complex, which acts additively to the known mal3-tip1-mto1-mto2 microtubule and tea1-tea2-tea4-pom1 polarity machineries.This is the published manuscript. It has been published by PLoS in PLoS ONE and is available online here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0106959

Mineotaur:a tool for high-content microscopy screen sharing and visual analytics

High-throughput/high-content microscopy-based screens are powerful tools for functional genomics, yielding intracellular information down to the level of single-cells for thousands of genotypic conditions. However, accessing their data requires specialized knowledge and most often that data is no longer analyzed after initial publication. We describe Mineotaur (http://www.mineotaur.org), a open-source, downloadable web application that allows easy online sharing and interactive visualisation of large screen datasets, facilitating their dissemination and further analysis, and enhancing their impact. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0836-5) contains supplementary material, which is available to authorized users

Molecular Insights into Division of Single Human Cancer Cells in On-Chip Transparent Microtubes.

In vivo, mammalian cells proliferate within 3D environments consisting of numerous microcavities and channels, which contain a variety of chemical and physical cues. External environments often differ between normal and pathological states, such as the unique spatial constraints that metastasizing cancer cells experience as they circulate the vasculature through arterioles and narrow capillaries, where they can divide and acquire elongated cylindrical shapes. While metastatic tumors cause most cancer deaths, factors impacting early cancer cell proliferation inside the vasculature and those that can promote the formation of secondary tumors remain largely unknown. Prior studies investigating confined mitosis have mainly used 2D cell culture systems. Here, we mimic aspects of metastasizing tumor cells dividing inside blood capillaries by investigating single-cell divisions of living human cancer cells, trapped inside 3D rolled-up, transparent nanomembranes. We assess the molecular effects of tubular confinement on key mitotic features, using optical high- and super-resolution microscopy. Our experiments show that tubular confinement affects the morphology and dynamics of the mitotic spindle, chromosome arrangements, and the organization of the cell cortex. Moreover, we reveal that membrane blebbing and/or associated processes act as a potential genome-safety mechanism, limiting the extent of genomic instability caused by mitosis in confined circumstances, especially in tubular 3D microenvironments. Collectively, our study demonstrates the potential of rolled-up nanomembranes for gaining molecular insights into key cellular events occurring in tubular 3D microenvironments in vivo.The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 311529 (S.S.) and the Volkswagen Foundation no. 86 362 (S.S. and W.X.), a FEBS Return-to-Europe fellowship (C.K.S.), the Wellcome Trust (092096/Z/10/Z for N.L.; 094587/Z/10/Z for R.B.), and a European Research Council (ERC) Starting Researcher Grant (R.E.C.-S.; SYSGRO). O.G.S. acknowledges financial support from the DFG Research Unit 1713 “Sensorische Mikro und Nanosysteme”. D.H.G. acknowledges funding from the Alexander von Humboldt Foundation and the U.S. National Science Foundation (Grants: CMMI 1200241 and CBET-1442014). Research in the S.P.J. laboratory is funded by Cancer Research U.K., the ERC, and the European Community Seventh Framework Programme (DDResponse), with core infrastructure provided by Cancer Research U.K. and the Wellcome Trust.This is the final version of the article. It first appeared from the American Chemical Society via http://dx.doi.org/10.1021/acsnano.6b0046

Mechanical cell competition kills cells via induction of lethal p53 levels.

Cell competition is a quality control mechanism that eliminates unfit cells. How cells compete is poorly understood, but it is generally accepted that molecular exchange between cells signals elimination of unfit cells. Here we report an orthogonal mechanism of cell competition, whereby cells compete through mechanical insults. We show that MDCK cells silenced for the polarity gene scribble (scrib(KD)) are hypersensitive to compaction, that interaction with wild-type cells causes their compaction and that crowding is sufficient for scrib(KD) cell elimination. Importantly, we show that elevation of the tumour suppressor p53 is necessary and sufficient for crowding hypersensitivity. Compaction, via activation of Rho-associated kinase (ROCK) and the stress kinase p38, leads to further p53 elevation, causing cell death. Thus, in addition to molecules, cells use mechanical means to compete. Given the involvement of p53, compaction hypersensitivity may be widespread among damaged cells and offers an additional route to eliminate unfit cells.This work was supported by a Cancer Research UK Programme Grant (EP and LW A12460), a Royal Society University Research fellowship to EP (UF0905080), a Wellcome Trust PhD studentship to I.K, a Cambridge Cancer Centre PhD studentship to MG and Core grant funding from the Wellcome Trust (092096) and CRUK (C6946/A14492).This is the final version of the article. It first appeared from Nature Publishing Group via https://doi.org/10.1038/ncomms1137

Publisher Correction: Image Data Resource: a bioimage data integration and publication platform

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