Fig. 1: In situ segmentation of multiclonal mammary tumors.
From: Vitamin B5 supports MYC oncogenic metabolism and tumor progression in breast cancer
a, Polar and apolar fractions of WMhigh, WMlow and WMmix tumors were analyzed with LC–MS (10 mg dry tissue from each sample was taken for the extraction) and plotted on a radial plot using the R package volcano3D. The radial angle ρ represents relative affiliation of metabolites to the individual samples and the distance from center the relative amounts. Colors indicate statistically significant affiliation to one or two samples. Significance was calculated with an unpaired two-tailed t-test (WMhigh, n = 4; WMlow, n = 4; WMmix, n = 8 tumors from independent animals). b, Metabolic pathways analysis of the data in a showing several significantly changed pathways and numbers of identified members against the pathway size. c, Schematic of tissue processing and DEFFI imaging. d,e, Levels and distribution of two selected ions as measured by DEFFI (d) or LC–MS (e) show concordance between the methodologies. Significance was calculated with an unpaired two-tailed t-test (WMhigh, n = 4; WMlow, n = 4; WMmix, n = 8 tumors from independent animals (WMhigh versus WMlow, P = 0.00234; WMhigh versus WMmix, P = 0.0089 (left); WMhigh versus WMlow, P = 0.0047; WMhigh versus WMmix, P = 0.0154 (right)). f, Post-DEFFI fluorescent microscopy of WMhigh, WMlow and WMmix tumors show clonal distribution (top). Ion colocalization analysis of DEFFI acquired images of WMhigh, WMlow and WMmix tumors reveal a WMhigh module (green) and a WMlow module (red) (bottom). g, Circos plot representing all metabolites found in the WMhigh module. Nodes represent the metabolites in the module. Node size is proportional to module membership, which represents a given metabolite’s strength of the colocalization index and is calculated as Pearson’s correlation between the spatial intensities of the corresponding metabolite and the module’s eigenmetabolites. Arc lines connect node pairs corresponding to colocalized metabolites with Pearson’s correlation >0.7. The nodes are color-grouped according to metabolite class based on Human Metabolome Database putative annotations (|m/z error| < 10 ppm). All box-and-whisker plots represent the following: line, median; box, interquartile range (IQR); whiskers, 1.5 × IQR limited by largest/smallest non-extreme value (NEV). In all DEFFI-MSI experiments n = 3 tumors from independent animals for each WM tumor type. P values indicated by *<0.05, ** 0.001, ***<0.0001, ****<0.00001.
