TISMorph: A tool to quantify texture, irregularity and spreading of single cells

A number of recent studies have shown that cell shape and cytoskeletal texture can be used as sensitive readouts of the physiological state of the cell. However, utilization of this information requires the development of quantitative measures that can describe relevant aspects of cell shape. In this paper we develop a toolbox, TISMorph, to calculate set of quantitative measures to address this need. Some of the measures introduced here are used previously and others are new and have desirable properties for shape and texture quantification of cells. These measures, broadly classifiable into the categories of textural, spreading and irregularity measures, are tested by using them to discriminate between osteosarcoma cell lines treated with different cytoskeletal drugs. We find that even though specific classification tasks often rely on a few measures, these are not the same between all classification tasks, thus requiring the use of the entire suite of measures for classification and discrimination. We provide detailed descriptions of the measures, well as TISMorph package to implement them. Image based quantitative analysis has the potential to become a new field of biological data (“image-omics”), providing quantitative insight into cellular processes.

A Cell Profiling Framework for Modeling Drug Responses from HCS Imaging

The authors present an unsupervised, scalable, and interpretable cell profiling framework that is compatible with data gathered from high-content screening. They demonstrate the effectiveness of their framework by modeling drug differential effects of IC-21 macrophages treated with microtubule and actin disrupting drugs. They identify significant features of cell phenotypes for unsupervised learning based on maximum relevancy and minimum redundancy criteria. A 2-stage clustering approach annotates, clusters cells, and then merges them together to form super-clusters. An interpretable cell profile consisting of super-cluster proportions profiled at each drug treatment, concentration, or duration is obtained. Differential changes in super-cluster profiles are the basis for understanding the drug’s differential effect and biology. The authors’ method is validated by significant chi-squared statistics obtained from similar drug-treated super-cluster profiles from a 5-fold cross-validation. In addition, drug profiles of 2 microtubule drugs with equivalent mechanisms of action are statistically similar. Several distinct trends are identified for the 5 cytoskeletal drugs profiled under different conditions.

Microtubules and microfilaments in tip growth: evidence that microtubules impose polarity on protonemal growth in Physcomitrella patens

In this study we compare the contributions of Factin and microtubules to tip growth in filamentous cells of the moss Physcomitrella patens. In tip growth, expansion seems to be restricted to the hemispherical apical dome. Cytoskeletal elements have been suspected, from drug studies, to be involved in this but electron microscopy has generally not confirmed the presence of an apical cytoskeleton. However, in a previous immunofluorescence study we reported that microtubules could be seen to focus upon the apical dome in tip cells of the moss P. patens. In the present investigation F-actin has also been detected at the apices of these cells. Anti-cytoskeletal drugs were therefore used to differentiate between the roles of actin filaments and microtubules in tip growth. At high concentrations (30μM), the herbicide cremart de-polymerized microtubules and caused tip swelling. F-actin was still present under such conditions but its fragmentation by cytochalasin D suppressed this herbicide-induced swelling. On its own, cytochalasin D arrested tip growth without causing swollen tips. At lower concentrations, cremart disorganized microtubules rather than causing their complete depolymerization. Under these conditions, new but swollen growing points were initiated along the filament. The addition of taxol to cremart-treated filaments tended to reduce swelling and to re-polarize outgrowth. With particular combinations of these drugs, multiple lateral out-growths were initiated in the vicinity of the nucleus. It is concluded: (1) that F-actin is present at the tips of Physcomitrella caulonemal apical cells; (2) that unfragmented F-actin is necessary for outgrowth; (3) that even disorganized microtubules permit some degree of outgrowth but that an unperturbed distribution of axial microtubules, focussing upon an apex, is essential in order to impose tubular shape and directionality upon expansion.