Abstract 3013: Acquired resistance to immune checkpoint inhibition by melanoma phenotypic transformation
Authors: Mehta Arnav , Liu David , Shi Alvin , Frederick Dennie T. , Ho Li-Lun , Larque Ana B. , Miao Benchun , Raghavan Rumya S. , Sharova Tatyana , Shin John H. , Rinaldi Nicola , Chebib Ivan A. , Kellis Manolis , Allen Eliezer Van , Hacohen Nir , Flaherty Keith T. , Boland Genevieve M. , Sullivan Ryan J. 
Published: August 2019

Immune checkpoint blockade (ICB) has revolutionized the treatment of metastatic melanoma, however, cases of resistance have now begun to emerge. We report here a case of acquired resistance by melanoma phenotypic transformation in a patient treated on a Phase 1b/2 clinical trial (NCT02437136) with anti-PD1 (Pembrolizumab) and a histone deacetylase (HDAC) inhibitor (Entinostat). The patient presented to MGH with metastatic melanoma confirmed by core-needle biopsy of a liver lesion. A PET/CT scan one month after starting the trial revealed interval regression of liver and bone lesions, however, four months later the patient presented with disease progression. A tumor debulked from the L2 vertebral body at that time revealed the presence of a pleomorphic rhabdomyosarcoma. The patient was started on anti-CTLA4 (Ipilumimab) with further disease progression, and surgical specimens thereafter revealed either melanoma or rhabdomyosarcoma. Tumor tissue was evaluated for markers by immunohistochemistry. All tumors (5 specimens in total) were subjected to whole exosome sequencing (WES), RNA-sequencing (RNAseq) and epigenomic sequencing (ATACseq). WES revealed 844 mutations were shared between all tumors, suggesting a common ancestor including driver mutations in NRAS (G13D), NF1 (E1121* and W1314*) and the TERT2 promoter, among others. The pre-treatment melanoma biopsy had positive staining for S100 and MART-1, nuclear staining patterns for SOX10 and MITF, and were BRAF V600E negative. Importantly, 80% of the tumor cells had strong staining for PD-L1 expression and CD8 CTL infiltration was associated with 25% of the tumor. The post-treatment rhabdomyosarcoma biopsy was notable for diffusely positive staining for Desmin and MyoD1, and multifocal positivity for myogenin. The tumor stained negative for S100 and SOX10, and there was no PD-L1 staining and less than 5% tumor CD8 CTL infiltration. Gene expression analysis revealed distinct expression patterns between melanoma and rhabdomyosarcoma samples, with 150 differentially expressed genes implicated in processes such as antigen presentation, T cell activation, cell death and protein metabolism. In addition, each tumor was found to have a unique immune cell composition and T-cell receptor repertoire, suggesting an interplay between phenotypic transformation and immune response. Results from epigenomic sequencing are pending, but may shed light on the mechanisms of transformation leading to resistance. These data therefore elucidate a previously undescribed mechanism of acquired resistance to ICB through melanoma phenotypic transformation to a rhabdomyosarcoma. Whereas these tumors were genetically similar, they expressed distinct gene expression patterns suggestive of underlying epigenomic differences in the setting of an HDAC inhibitor.

Citation Format: Arnav Mehta, David Liu, Alvin Shi, Dennie T. Frederick, Li-Lun Ho, Ana B. Larque, Benchun Miao, Rumya S. Raghavan, Tatyana Sharova, John H. Shin, Nicola Rinaldi, Ivan A. Chebib, Manolis Kellis, Eliezer Van Allen, Nir Hacohen, Keith T. Flaherty, Genevieve M. Boland, Ryan J. Sullivan. Acquired resistance to immune checkpoint inhibition by melanoma phenotypic transformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3013.