Characterization of the phenotypic profile in tumor microenvironments in CD163-rich and CD163-sparse segments. (A) CD20⁺ MCL cells and infiltrating CD3⁺ cells were sampled in 56 patients with CD163-sparse (left) and 44 patients with CD163-rich (right) MCL TIMEs. IF staining of CD20⁺ cells are shown in red, CD3⁺ cells are shown in light blue, CD163⁺ cells are shown in yellow, and nuclear staining is in dark blue. Marked segments to be collected are shown in orange for CD20⁺ cells and turquoise for CD3⁺ cells. (B,C) Significantly deregulated proteins were visualized by plotting the LMM coefficients (x-axis) against the FDR–adjusted P values (y-axis), and proteins (shown in blue) in the right part of the plot are higher in CD163-rich MCL TIMEs and proteins (shown in red) in the left part of the plot are higher in CD163-sparse MCL TIMEs. Expression of the 63 targeted proteins in either (B) CD20⁺ cells or (C) CD3⁺ cell segments are compared. The LMM model included patient as a random effect, and proteins that were significantly differentially expressed (FDR < 0.1) are indicated by name. Coefficients and FDR values are listed in supplemental Tables 5 and 6. (D) Schematic representation of the MAPK pathway. Highlighted in red are proteins that showed increased levels in CD20⁺ cell segments in CD163-rich MCL. Highlighted in light blue are proteins that show increased levels in CD3⁺ cell segments in CD163-rich MCL TIMEs.