The force loading rate drives cell mechanosensing through both reinforcement and cytoskeletal softening.

Cell response to force regulates essential processes in health and disease. However, the fundamental mechanical variables that cells sense and respond to remain unclear. Here we show that the rate of force application (loading rate) drives mechanosensing, as predicted by a molecular clutch model. By applying dynamic force regimes to cells through substrate stretching, optical tweezers, and atomic force microscopy, we find that increasing loading rates trigger talin-dependent mechanosensing, leading to adhesion growth and reinforcement, and YAP nuclear localization. However, above a given threshold the actin cytoskeleton softens, decreasing loading rates and preventing reinforcement. By stretching rat lungs in vivo, we show that a similar phenomenon may occur. Our results show that cell sensing of external forces and of passive mechanical parameters (like tissue stiffness) can be understood through the same mechanisms, driven by the properties under force of the mechanosensing molecules involved.

Streamlining Quantitative Analysis of Long RNA Sequencing Reads.

Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often lacks cost- and time-efficient workflows. Although kit-based workflows and benchtop platforms for RNA sequencing provide software options, e.g., cloud-based tools to analyze basecalled reads, quantitative, and easy-to-use solutions for transcriptome analysis, especially for non-human data, are missing. We therefore developed a user-friendly tool, termed Alignator, for rapid analysis of long RNA reads requiring only FASTQ files and an Ensembl cDNA database reference. After successful mapping, Alignator generates quantitative information for each transcript and provides a table in which sequenced and aligned RNA are stored for further comparative analyses.

The Focinator v2-0 - Graphical Interface, Four Channels, Colocalization Analysis and Cell Phase Identification.

The quantitative analysis of foci plays an important role in various cell biological methods. In the fields of radiation biology and experimental oncology, the effect of ionizing radiation, chemotherapy or molecularly targeted drugs on DNA damage induction and repair is frequently performed by the analysis of protein clusters or phosphorylated proteins recruited to so called repair foci at DNA damage sites, involving for example γ-H2A.X, 53BP1 or RAD51. We recently developed "The Focinator" as a reliable and fast tool for automated quantitative and qualitative analysis of nuclei and DNA damage foci. The refined software is now even more user-friendly due to a graphical interface and further features. Thus, we included an R-script-based mode for automated image opening, file naming, progress monitoring and an error report. Consequently, the evaluation no longer required the attendance of the operator after initial parameter definition. Moreover, the Focinator v2-0 is now able to perform multi-channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of a specific cell cycle phase.

Role of SGK1 for fatty acid uptake, cell survival and radioresistance of NCI-H460 lung cancer cells exposed to acute or chronic cycling severe hypoxia.

BACKGROUND: Unsaturated fatty acids (FA) are required for cancer cell growth. In normoxia cells can generate unsaturated FA from saturated stearic and palmitic acid by desaturation. However, since the desaturation step is oxygen-dependent hypoxic cancer cells display an increased dependence on the uptake of unsaturated FA. Up to now the mechanism of increased FA uptake in hypoxia is largely unknown. Here we aimed to study the role of human serum and glucocorticoid-inducible kinase (SGK1) in the regulation of FA uptake in cancer cells exposed to acute or chronic cycling hypoxia and explore its use as target for the radiosensitization of hypoxic cancer cells. METHODS: The effect of SGK1-inhibition (GSK650394) on NCI-H460 lung adenocarcinoma cells exposed to normoxia, acute or chronic cycling hypoxia was analyzed under standard and serum-deprived conditions by short-term proliferation, apoptosis and cell death assays. The impact of SGK1-inhibition on radiation sensitivity was determined by standard colony formation assays. The effect of GSK650394 on FA uptake was quantified by measuring intracellular accumulation of fluorescent FA (C1-BODIPY®-C12). RESULTS: Exposure to acute or chronic cycling hypoxia was associated with up-regulated expression of SGK1 in NCI-H460 cells, increased uptake of FA from the culture medium, and increased sensitivity to serum deprivation. Survival of serum-deprived hypoxic NCI-H460 cells was rescued by the addition of the unsaturated FA, oleic acid, whereas the saturated FA, palmitic acid was highly toxic to the hypoxic cancer cells. Interestingly, SGK1 inhibition abrogated the rescue effect of oleic acid in serum-deprived hypoxic cancer cells and this effect was associated with a reduction in FA uptake particularly in anoxia-tolerant cancer cells exposed to severe hypoxia. Finally, SKG1 inhibition decreased long-term survival and potently sensitized the parental and anoxia-tolerant NCI-H460 cells to the cytotoxic effects of ionizing radiation in normoxia as well as the anoxia-tolerant cancer cells in severe hypoxia. CONCLUSIONS: Our data suggest that SGK1 plays a role in the regulation of FA uptake that becomes essential under conditions of acute or chronic cycling hypoxia. We assume that SGK1 may represent a promising therapeutic target for the eradication of hypoxic cancer cells.

The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damage.

BACKGROUND: The quantitative analysis of foci plays an important role in many cell biological methods such as counting of colonies or cells, organelles or vesicles, or the number of protein complexes. In radiation biology and molecular radiation oncology, DNA damage and DNA repair kinetics upon ionizing radiation (IR) are evaluated by counting protein clusters or accumulations of phosphorylated proteins recruited to DNA damage sites. Consistency in counting and interpretation of foci remains challenging. Many current software solutions describe instructions for time-consuming and error-prone manual analysis, provide incomplete algorithms for analysis or are expensive. Therefore, we aimed to develop a tool for costless, automated, quantitative and qualitative analysis of foci. METHODS: For this purpose we integrated a user-friendly interface into ImageJ and selected parameters to allow automated selection of regions of interest (ROIs) depending on their size and circularity. We added different export options and a batch analysis. The use of the Focinator was tested by analyzing γ-H2.AX foci in murine prostate adenocarcinoma cells (TRAMP-C1) at different time points after IR with 0.5 to 3 Gray (Gy). Additionally, measurements were performed by users with different backgrounds and experience. RESULTS: The Focinator turned out to be an easily adjustable tool for automation of foci counting. It significantly reduced the analysis time of radiation-induced DNA-damage foci. Furthermore, different user groups were able to achieve a similar counting velocity. Importantly, there was no difference in nuclei detection between the Focinator and ImageJ alone. CONCLUSIONS: The Focinator is a costless, user-friendly tool for fast high-throughput evaluation of DNA repair foci. The macro allows improved foci evaluation regarding accuracy, reproducibility and analysis speed compared to manual analysis. As innovative option, the macro offers a combination of multichannel evaluation including colocalization analysis and the possibility to run all analyses in a batch mode.

Biphasic response of cell invasion to matrix stiffness in three-dimensional biopolymer networks.

When cells come in contact with an adhesive matrix, they begin to spread and migrate with a speed that depends on the stiffness of the extracellular matrix. On a flat surface, migration speed decreases with matrix stiffness mainly due to an increased stability of focal adhesions. In a three-dimensional (3-D) environment, cell migration is thought to be additionally impaired by the steric hindrance imposed by the surrounding matrix. For porous 3-D biopolymer networks such as collagen gels, however, the effect of matrix stiffness on cell migration is difficult to separate from effects of matrix pore size and adhesive ligand density, and is therefore unknown. Here we used glutaraldehyde as a crosslinker to increase the stiffness of self-assembled collagen biopolymer networks independently of collagen concentration or pore size. Breast carcinoma cells were seeded onto the surface of 3-D collagen gels, and the invasion depth was measured after 3 days of culture. Cell invasion in gels with pore sizes >5 µm increased with higher gel stiffness, whereas invasion in gels with smaller pores decreased with higher gel stiffness. These data show that 3-D cell invasion is enhanced by higher matrix stiffness, opposite to cell behavior in two dimensions, as long as the pore size does not fall below a critical value where it causes excessive steric hindrance. These findings may be important for optimizing the recellularization of soft tissue implants or for the design of 3-D invasion models in cancer research.