Journal: Nature Communications
Article Title: Longitudinal plasma proteome profiling reveals the diversity of biomarkers for diagnosis and cetuximab therapy response of colorectal cancer
doi: 10.1038/s41467-024-44911-1
Figure Lengend Snippet: A Association of proteomic subtypes with therapy response (two-sided Fisher’s exact test). B Correlation of the pathways of the G-III subtype (two-sided Pearson’s correlation test). C , E Boxplots for immune score among G-I ( N = 24), G-II ( N = 34), and G-III ( N = 31) ( P = 0.042) ( C ), and CD8+Tem score between S and NS groups in plasma samples (N (S) = 16, N (NS) = 15; P = 0.035) and tissue samples (N (S) = 12, N (NS) = 19; P = 0.005) (two-sided Student’s t test). D Differential cell types between G-III and other subtypes (two-sided Student’s t test). F Qualification of CD44 ( P = 1.0E-5) and GZMK ( P = 8.0E-6) stained by IHC in representative examples (two-sided Student’s t test). Data are shown as mean ± SD ( n = 3 independent experiments). G Association between CD8+Tem score (Z score) with tumor size (cm), and S/NS group. H Correlation of CD8+Tem score and tumor size (two-sided Pearson’s correlation test). Data are presented as Pearson r with 95%CI. I Diagram showing the potential mechanism of cetuximab sensitivity. The little heatmap depicted the log-transformed fold-change of S versus NS groups. J Correlation of CD8+Tem score and RPTOR/IMPDH2 (two-sided Pearson’s correlation test). K Kaplan–Meier curves of Overall survival (OS) in the CPTAC cohort (two-sided log rank test). L Differential expression of RPTOR ( P = 8.9E-5, 2.9E-5) and IMPDH2 ( P = 4.2E-8, 3.4E-6) in discovery cohort (N (S) = 31, N (NS) = 45) and validation cohort (N (S) = 16, N (NS) = 15) (two-sided Wilcoxon rank-sum test). PRM, parallel reaction monitoring. Boxplots show median (central line), upper and lower quartiles (box limits), 1.5×interquartile range (whiskers) ( C , E , and L ). Source data are provided as a file.
Article Snippet: A standard IHC protocol was followed to stain the tumor tissue samples of the CD8+ Tem markers by using the rabbit monoclonal antibody against CD44 (1:200, Signalway Antibody, catalog No: 48911-1), and the rabbit polyclonal antibody against GZMK (1:300, Signalway Antibody, catalog No: 40985-1).
Techniques: Clinical Proteomics, Staining, Transformation Assay, Quantitative Proteomics, Biomarker Discovery, Targeted Proteomics