ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [RNA-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. Overall design: ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The transcriptomes of the ZNF180 KD cells were compared to the respective non-transfected controls.