Comparisons of transcriptional activity for genotyped WM patient samples and healthy donor B cells. (A) Multidimensional scaling of the top 500 genes for all HD and WM samples using Voom transformed expression values in Limma’s plotMDS function.24 (B) Pearson correlation coefficients from the correlation matrix of gene expression were averaged over all the samples for each major group. Correlation values with the HD samples were higher for those WM patients with CXCR4 mutations (P = .025 and P = .036 for HD PB and HD MB cells, respectively). (C) The 596 genes differentially expressed between the HD PB and HD MB cells were analyzed across all samples using PCA. No preferential relationship between WM samples and HD B-cell type was observed. The first 3 principal components were used to plot the samples representing 54% of the overall variability. (D) Median expression levels for 19 genes known to regulate B-cell to plasma cell transition for HD B-cell and genotyped WM samples. Error bars represent full data range per for each group. (E) PCA of the 19 genes related to B-cell to plasma cell transition shown in panel D depicting the first 3 principal components which covered over 65% of the overall gene expression variability.
