gaussian population modeling  (GraphPad Software Inc)

Journal: Scientific Reports

Article Title: Subclonal response heterogeneity to define cancer organoid therapeutic sensitivity

doi: 10.1038/s41598-025-96204-2

Figure Lengend Snippet: FOLFOX resistance monitoring reveals subclonal resistance from a patient with familial adenomatous polyposis. ( a ) Representative therapeutic study (patient LC1) with FOLFOX imaged with brightfield microscopy at 0 h and 48 h annotated with percent difference in individual organoid diameter and ( b ) representative images of organoids with two-photon ORR at 48 h. ( c ) Comparison of PCO location perpendicular to the matrix edge correlated against growth with FOLFOX treatment across three independent cultures (LR4, LR5, MC7) along with the coefficient of determinant (R 2 ). ( d ) Sites of tissue sampling from patient with multiple site polyp (n = 4) and tumor sampling (n = 5). ( e ) Heatmap of pathologic alterations of PCOs derived from individual polyps (P1–P4) and tumors (T1–T5) compared between primary tissue (black, T) and organoids (gray, O) plotted as relative variant allele frequency (rVAF). Denoted are tumor suppressor genes (green) and oncogenes (red) plotted as a function of rVAR. ( f ) Heatmap of expanded PCO subclones selected by individual spikes using NGS profiling. ( g ) Comparison of normalized Δ diameter and FLIRR at 48 h stratified by parent culture, FBXW7 WT (wild type, WT), and FBXW7 R479Q (mutant, MT) using two-sided student t-test ( p > 0.05). ( h ) Representative PCOs metabolism assessed at 48 h by ORR (NAD(P)H/FAD) for control (top panel) and FOLFOX stratified by FBXW7 profile. Scale bar represents 100 µm. ( i ) Heatmap of OMI parameters by FBXW7 status stratified with respective Z-score as compared to parent culture. Significance noted for |GΔ| > 0.75 for individual OMI parameters with corresponding positive (black *) or negative (white *) effect size. Z-score defined by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\overline{\text{x}}}_{{{\text{PCO}}}}$$\end{document} (average value of individual OMI parameter for individual PCO culture), \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\overline{\text{x}}}_{{{\text{population}}}}$$\end{document} (average value of individual OMI parameter across the control population), σ population (standard deviation of an individual OMI parameter across the control population) for the control conditions \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\overline{\text{x}}}_{{{\text{population}}}}$$\end{document} and σ population refer to parent culture values. ( j,k ) Gaussian distribution plots of normalized PCO diameter change assessed from 0 to 48 h including control (gray), 5-FU (blue), oxaliplatin (red), and FOLFOX (purple). Molecular profile at FBXW7 denoted wildtype (WT, solid line) and mutant FBXW7 R479Q (MT, dashed line). Response assessed using effect size (GΔ) relative to untreated control stratified by molecular profile at FBXW7 for ( j ) normalized Δ diameter and ( k ) ORR at 48 h. Scale bars for brightfield (black bar) represent 200 µm, scale bars for OMI (white bar) represent 100 μm.

Article Snippet: Due to expected heterogeneity across mixed populations, the pooled analyses of multiple cultures in response to EGFR inhibition was performed by Gaussian population modeling using GraphPad Prism 9 (GraphPad Software, Boston, MA, USA, www.graphpad.com ).

Techniques: Microscopy, Comparison, Sampling, Derivative Assay, Variant Assay, Mutagenesis, Control, Standard Deviation

Journal: Scientific Reports

Article Title: Subclonal response heterogeneity to define cancer organoid therapeutic sensitivity

doi: 10.1038/s41598-025-96204-2

Figure Lengend Snippet: Validation of PCO response for clinical prediction. ( a ) Representative brightfield microscopy from MTB-3 ovarian (Ov) PCOs at baseline and 48 h; scale bar represents 200 μm for each panel. ( b ) Gaussian distributions for growth at 48 h with respective effect sizes (GΔ) for MTB-3 Ov PCOs treated with gemcitabine 50 μm (24 h, green), paclitaxel 50 nM (48 h, gold) or control (black) as assessed at 48 h. ( c ) Clinical response from the initial restaging CT scan of subject MTB-3 confirming the disease with enlarging retroperitoneal adenopathy after treatment with single agent gemcitabine on CT imaging. ( d ) Representative brightfield microscopy for MC7 PCOs treated with control (top panels), or FOLFOX (5-FU 10 μm and oxaliplatin 5 mμ ( e ) Gaussian distributions of MC7 for Δ diameter over 48 h and respective effect sizes (GΔ) for 5-FU 10 μm (blue), oxaliplatin 5 μm (red), and FOLFOX (violet). ( f ) Restaging CT scan of MC7 shows partial response after FOLFOX. ( g ) Experimental sensitivity with clinical outcome or canonical mechanism of resistance labeled by treatment type including chemotherapy (purple), targeted therapy (blue), canonical EGFRi resistance (RAS MT or RAF MT , red), and radiation (black) with reported significance by two-sided student t-test. ( h,i ) Comparison of FOLFOX effect size (GΔ) between PCOs with disease progression after FOLFOX chemotherapy versus subjects without prior drug exposure assessed using two-sided student t-test with prior established sensitivity thresholds (shaded region). ( h ) Absolute diameter effect size assessed at 48 h for single agent 5-FU (ns), oxaliplatin (ns) and FOLFOX (* p < 0.05) between clinically resistant and unknown cohorts. ( i Effect size of growth (percent Δ diameter) tracked from 0 to 48 h for single agent 5-FU (* p < 0.05), oxaliplatin (** p < 0.005) and FOLFOX (*** p < 0.0005) between clinically resistant and unknown cohorts. ( j ) Bar plot of negative predictive value (NPV) and positive predictive value (PPV) for prospectively treated subjects. ( k ) Receiver operator curve (ROC) in response prediction plotted as false positive rate versus sensitivity with the colored line showing the continuum of effect size (GΔ) for change in diameter and corresponding area under the curve (AUC).

Article Snippet: Due to expected heterogeneity across mixed populations, the pooled analyses of multiple cultures in response to EGFR inhibition was performed by Gaussian population modeling using GraphPad Prism 9 (GraphPad Software, Boston, MA, USA, www.graphpad.com ).

Techniques: Biomarker Discovery, Microscopy, Control, Computed Tomography, Imaging, Labeling, Comparison