Journal: Nature Communications

Article Title: Exploring the role of stromal osmoregulation in cancer and disease using executable modelling

doi: 10.1038/s41467-018-05414-y

Figure Lengend Snippet: The qualitative network explains cellular phenotypes of Stromal cells in varying experimental conditions. Membrane proteins deregulated under varying stimuli, showing a Transport proteins deregulated in Early (ETDLN) and Late (LTDLN) stage after exposure to TFs, and after exposure to LPS. Proteins are upregulated (red arrows), downregulated (blue arrows), or unchanged (grey) in response to TFs or LPS. b Phenotype change for FRCs upon exposure to TFs for Early (ETDLN) and Late (LTDLN) stage. The Model output represents the physiological behaviour predicted by the model, and the experimental output represents the behaviour observed or implied at the cellular level from experiments or the gene array, and is independent of the model (see methods). Boxes containing two colours indicate phenotypes where there is contradictions/data is unclear. The model predicts an increase in viability, and a sustained increase in attachment and movement/membrane dynamics. Specific protein activity loss predictions are verified with experiments. c , d Knockdown of genes for ( c ) ATP2A3 , and its effect on cellular attachment. The cascade predicted by the model to be underpinning this behaviour change is seen in part ( d ). e , f Also shown are siRNA knockdowns for SLC9A1 and its effect on cell viability ( e ), and FXYD5 and its effect on viability and attachment ( f ). Predicted mechanisms for these knockdowns are included in Supplementary Fig. . * P < 0.05, ** P < 0.01, *** P < 0.001 using two-tailed unpaired t -test. Error bars represent standard deviation. Shown are 11 replicates ( c ), and 9 replicates ( e , f )

Article Snippet: One microgram of total RNA was reverse transcribed using the First Strand cDNA synthesis Kit (Thermo Scientific) with oligo(dT) primers. qRT-PCR was performed using TaqMan assays ( ATP2A3 (Mm00443911_m1), FXYD5 (Mm00435435_m1), SLC9A1 (Mm00444270_m1)) and a StepOne Real Time PCR System instrument (both Life Technologies).

Techniques: Membrane, Activity Assay, Knockdown, Cell Attachment Assay, Two Tailed Test, Standard Deviation

Journal: BMC Cancer

Article Title: Receptor and secreted targets of Wnt-1/β-catenin signalling in mouse mammary epithelial cells

doi: 10.1186/1471-2407-5-3

Figure Lengend Snippet: (a) Analysis of HIG2 mRNA expression on a human cDNA array containing matched tumour and normal samples from 68 patients. For each pair, the tumour sample is on top. The bottom row of the array contains cDNA from cell lines (left to right: HeLa, Daudi, K562, HL-60, G361, A549, MOLT-4, SW480 and Raji). (b) Quantitative analysis by phosphorimager. Vertical dashed lines indicate ± 2-fold difference. HIG2 expression is broadly similar in most pairs, but is strongly and consistently downregulated in most of the kidney and stomach tumours analysed.

Article Snippet: Total RNA was isolated, from which mRNA was purified. cDNAs were labelled and hybridized to an 8962 element Incyte mouse GEM1 cDNA microarray (Incyte Genomics, Palo Alto, CA).

Techniques: Expressing