ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [ATAC-seq]

Through analyzing publicly available single-cell and bulk sequencing data from ICI-treated cohorts, ZNF180-regulome was predictive of ICI responses in independent bulk sequencing cohorts, and ZNF180+ tumors persisted after the therapy with immune-suppressive features such as MHC-I loss and CD155 expressions, the primary ligand to TIGIT inhibitory receptor. To investigate regulatory roles of ZNF180 to confer these immune suppressive phenotypes, we performed ZNF180 knock-down in melanoma cells in vitro with different genetic backgrounds, namely A375 (BRAF-mutant) and SKMEL147 (NRAS-mutant) cells, and performed RNA- and ATAC-sequencing. The integrative analysis revealed ZNF180 silencing promoted tumor immunogenicity through gain of accessibility on MHC-I/-II coding genes, CD155 down-regulation to avoid TIGIT/CD155 checkpoint signaling, and suppressed AP-1 transcription factor activities as the drivers of melanoma reprogramming towards MITFlowAXLhigh de-differentiated cells. Further, ZNF180 silencing increased CD4 helper T-cell infiltrations in tumors and regressed the tumors in vivo. Collectively, these results indicate ZNF180 is a tumor intrinsic regulator of melanoma plasticity to drive de-differentiated phenotypes with immune-suppressive features including loss of immunogenicity, T-cell inhibitory signals through TIGIT/CD155 checkpoint and exclusion of CD4 helper T-cells. As ZNF180-regulome manifests in non-metastatic melanoma in contrast to the current focus of standard-of-care ICI on the metastatic disease, these results establish ZNF180-regulome as a biomarker and novel therapeutic avenue for early stage melanoma to intervene ICI resistance. ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The ATAC-seq was performed on the ZNF180 KD cells and the respective non-transfected controls.