Single-cell analysis reveals new evolutionary complexity in uveal melanoma

Michael A Durante,J William Harbour,Stefan Kurtenbach,Christina L Decatur,Helen Snyder,Alan S Livingstone,Jeffim N Kuznetsov,Daniel A Rodriguez,Lynn G Feun,Margaret I Sanchez

doi:10.1038/s41467-019-14256-1

Abstract

Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. Here, we interrogate the tumor microenvironment at single-cell resolution using scRNA-seq of 59,915 tumor and non-neoplastic cells from 8 primary and 3 metastatic samples. Tumor cells reveal novel subclonal genomic complexity and transcriptional states. Tumor-infiltrating immune cells comprise a previously unrecognized diversity of cell types, including CD8+ T cells predominantly expressing the checkpoint marker LAG3, rather than PD1 or CTLA4. V(D)J analysis shows clonally expanded T cells, indicating that they are capable of mounting an immune response. An indolent liver metastasis from a class 1B UM is infiltrated with clonally expanded plasma cells, indicative of antibody-mediated immunity. This complex ecosystem of tumor and immune cells provides new insights into UM biology, and LAG3 is identified as a potential candidate for immune checkpoint blockade in patients with high risk UM.

Highlights

Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy
Tumor cells cluster most strongly according to the GEPbased clinical prognostic classifier, with the primary division occurring between class 1 (BAP1 wild-type) and class 2 (BAP1 mutant) tumors (Fig. 1c)
Previous studies showed that canonical genomic aberrations arise early in UM and give rise to one of three principal evolutionary trajectories associated with signature driver mutations—EIF1AX in class 1 A, SF3B1 and other splicing mutations in class 1B, and BAP1 in class 2 tumors[9,10], yet the single-cell resolution of our current findings reveal that these tumors continue to evolve with the development of heretofore unrecognized non-canonical copy number variations (CNVs) subclones that may contribute to tumor progression, as suggested by recent work[13]

Summary

Introduction

Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. We interrogate the tumor microenvironment at single-cell resolution using scRNA-seq of 59,915 tumor and nonneoplastic cells from 8 primary and 3 metastatic samples. An indolent liver metastasis from a class 1B UM is infiltrated with clonally expanded plasma cells, indicative of antibody-mediated immunity. This complex ecosystem of tumor and immune cells provides new insights into UM biology, and LAG3 is identified as a potential candidate for immune checkpoint blockade in patients with high risk UM. UMs with the class 1 GEP typically harbor mutations in EIF1AX (class 1A, low metastatic risk), SF3B1, or other splicing factors (class 1B, intermediate metastatic risk), and exhibit chromosomal gains of 6p and 8q. Based on computational inference from bulk sequencing data, UM appears to undergo an early punctuated evolutionary burst in which a full set of canonical aberrations arises specifying a particular subtype, after which further aberrations accrue as neutral passenger events[10]

Methods

Results

Conclusion