Fig. 2: Determining circadian clock strength in cancer and healthy tissue cell models.
From: Time-of-day effects of cancer drugs revealed by high-throughput deep phenotyping
a Schematic of the deep circadian phenotyping approach. b Simplified circadian feedback loops involving Bmal1 and Per2. c Raw and processed signals from MDAMB468-Bmal1/Per2-Luc cells. d Example of autocorrelation (AC) analysis. The arrow indicates 2nd peak and abscissa (lag). Dashed lines = 95% CI. e Boxplot of AC values and (f) lags of signals from various cell models. g Wavelet power spectrum (bottom) from continuous wavelet transform (CWT) showing time-resolved periods of detrended-amplitude-normalized signals from MDAMB468-Bmal1-Luc cells (top). Red line = main oscillatory component (ridge). h Boxplot of CWT ridge lengths from various cell models. Box bounds in (e, f, h) are defined by the 25th and 75th percentiles. Extending whiskers represent data points within 1.5 times the interquartile range from lower and upper quartiles. Red lines and crosses denote the median and outliers, respectively. n = 12 samples, collected from Bmal1-/Per2-reporters, with 6 samples per reporter (n = 2 biological replicates á technical triplicates or duplicates [HCC1806 Per2-Luc]). n = 6 for U-2 OS KO-lines (Bmal1-Luc-only) and MCF10A (single experiment). n = 9 for MDAMB468 (Per2-Luc: single experiment). n = 17 for SH-SY5Y (biological triplicates with technical triplicates or duplicates). i Multiresolution analysis (MRA) of detrended MDAMB468-Bmal1-Luc signal. % = fraction to signal. j Scatterplot of normalized MRA noise versus circadianicity components from the indicated cell models. The shaded area covers an unattainable range. Data represents the mean ± s.d. of multiple samples per reporter cell line (see above). k Bar diagram ranking cell models by global circadian strength, integrating min-max scaled parameters from AC (peak), CWT (ridge), and MRA (circadianicity) for Bmal1-Luc and, where applicable, Per2-Luc signals. Data represents mean ± s.d of scaled parameters (n = 6, except U-2 OS knockouts where n = 3 parameters). Only the positive s.d. is shown. Color coding in (b–I, k) corresponds to Bmal1 (yellow) and Per2 (blue) reporters. Color coding of cell models in (e, f, h, j, k) corresponds to tissue origin. One-way ANOVA and Tukey’s post-hoc test compared U-2 OS WT and KO cell lines, where **, ***, and **** indicate p-values of 5.7 × 10−3, 4.8 × 10−4 and ≤ 0.0001, respectively. n.s. = non-significant. Source data for (c–k) are provided as a Source Data file.
