Molecular profiling of driver events and tumor-infiltrating lymphocytes in metastatic uveal melanoma

Abstract

Uveal melanoma (UM) is a rare form of melanoma with a genetics and immunology that is different from skin melanoma. Previous studies have identified genetic driver events of early stage disease when the tumor is confined to the eye. However due to lack of a clinical rationale to biopsy metastatic disease, access to tumor material to perform molecular profiling of metastases has been limited. In this study, we have characterized genomic events in UM metastases using whole-genome sequencing of fresh frozen biopsies from thirty-two patients and profiled the transcriptomes of individual tumor infiltrating lymphocytes in eight patients by single-cell sequencing. We find that 91% of the patients have metastases carrying inactivating events in the tumor suppressor BAP1 and this coincided with somatic alterations in GNAQ, GNA11, CYSLTR2, PLCB4, SF3B1 and/or CDKN2A. Mutational signature analysis revealed a rare subset of tumors with prominent signs of UV damage, associated with outlier mutational burden. We study copy number variations (CNV) and find overrepresented events, some of which were not altered in matched primary eye tumors. A focused siRNA screen identified functionally significant genes of some of the segments recurrently gained. We reintroduced a functional copy of BAP1 into a patient-derived BAP1 deficient tumor cell line and found broad transcriptomic changes of genes associated with subtype distinction and prognosis in primary UM. Lastly, our analysis of the immune microenvironments of metastases revealed a presence of tumor-reactive T cells. However, a majority expressed the immune checkpoint receptors TIM-3, LAG3 and TIGIT, and to a lesser extent PD-1. These results provide an updated view of genomic events represented in metastatic UM and immune interactions in advanced lesions.

Prognostic utility of TME-associated genes in pancreatic cancer

“…Combining regimens, Frontiers in Genetics frontiersin.org with inhibitors of TIGIT and PD-1 plus CD40 agonism, in preclinical models exhibited encouraging tumor suppression (Freed-Pastor et al, 2021). In the TME, T-cell exhaustion is caused by LAG-3 that cooperates with a pile of blockade receptors (Chihara et al, 2018;Edwards et al, 2018;Karlsson et al, 2020). In mice, treatment with anti-LAG-3 and anti-PD-1 antibodies also showed a strong anti-tumor effect (Woo et al, 2012).…”

Improving therapy in metastatic uveal melanoma by understanding prior failures

“…One issue that has potentially limited the field to date has been a reliance upon primary disease to design therapeutic approaches in the metastatic setting. Recently The Cancer Genome Atlas [3] has described the genomics of primary UM, however studies of metastatic disease are only starting to emerge [4][5][6]. While analyses of primary UM have been insightful in the prognostication of primary tumor features associated with higher risks of metastases and poor clinical outcomes [7], these efforts may not have been optimal toward elucidating the next generation of therapeutic targets in metastatic UM .…”