Figure 3.

Proteomic analysis of human (tumor) versus mouse (stroma) of BM18 and LAPC9 tumors. (A) Experimental separation of human from mouse cell suspensions from fresh tumor isolations by MACS mouse depletion sorting. Cell fractions from intact/replaced (n = 3 each), castrated (n = 4) biological replicates were pooled into a single replicate (n = 1) to achieve an adequate cell number for the proteomic analysis (1 × 10⁶ cells). Protein lysates from the different fractions of BM18/LAPC9 (intact, castrated and replaced) were subjected to Tandem Mass Tag (TMT) labeling (all-mouse or all-human samples were multiplexed in one TMT experiment each), followed by mass spectrometry. (B) Detected peptides from human and mouse fractions were searched against a combined human and mouse protein database. Number of species specific or shared proteins is indicated in different colors. (C) KLK3 (PSA; Prostate Serum Antigen) protein levels (log₂ normalized TMT signal sum values) in human cell isolations (left) and in mouse cell isolations (right), and the protein sequence was predicted as human-specific (spheres indicate Homo Sapiens sequence). Seven-up Ob-BMST signature markers POSTN, PDGFRB and MCAM protein levels were absent in human cell isolations (left) and present in mouse cell isolations (right), while all the protein sequences were mouse-specific (triangles indicate Mus Musculus sequences).