Proteomic Comparison of 3D and 2D Glioma Models Reveals Increased HLA‑E Expression in 3D Models is Associated with Resistance to NK Cell-Mediated Cytotoxicity

Three-dimensional cell culture techniques can better reflect the
in vivo characteristics of tumor cells compared with traditional monolayer
cultures. Compared with their 2D counterparts, 3D-cultured tumor cells
showed enhanced resistance to the cytotoxic T cell-mediated immune
response. However, it remains unclear whether 3D-cultured tumor cells
have an enhanced resistance to NK cell cytotoxicity. In this study,
a total of 363 differentially expressed proteins were identified between
the 2D- and 3D-cultured U251 cells by comparative proteomics, and
an immune-associated protein–protein interaction (PPI) network
based on these differential proteins was constructed by bioinformatics.
Within the network, HLA-E, as a molecule for inhibiting NK cell activation,
was significantly up-regulated in the 3D-cultured tumor cells. Then,
we found that the 3D-cultured U251 cells exhibited potent resistance
to NK cell cytotoxicity in vitro and were prone to tumor formation
in vivo. The resistance of the 3D-cultured tumor cells to NK cell
lysis was mediated by the HLA-E/NKG2A interaction because the administration
of antibodies that block either HLA-E or NKG2A completely eliminated
this resistance and significantly decreased tumor formation. Taken
together, our findings indicate that HLA-E up-regulation in 3D-cultured
cells may result in enhanced tumor resistance to NK cell-mediated
immune response.