CAR-T cells rest to get back in the race: Chimeric antigen receptor (CAR)–T cells, which are engineered to target specific tumor antigens, are increasingly used as an immunotherapy. CAR-T cells have shown promising results in patients, particularly in hematologic cancers, but their anticancer activity can be limited by the onset of exhaustion and the loss of effectiveness. Weber et al. characterized the phenotypic and epigenomic changes associated with CAR-T cell exhaustion caused by continuous activity and the beneficial effects of transient rest periods (see the Perspective by Mamonkin and Brenner). The authors tested different approaches for providing these rest periods, such as using the drug dasatinib to temporarily suppress T cell activity, which helped to prevent exhaustion and improved antitumor activity in mouse models. Science , this issue p. eaba1786 ; see also p. 34

William Harbour, Anne Bowcock and colleagues identify recurrent mutations at codon 625 of SF3B1 in uveal melanomas. These mutations occur in low-grade tumors and are associated with favorable prognosis. Uveal melanoma is the most common primary cancer of the eye and often results in fatal metastasis. Here, we describe mutations occurring exclusively at codon 625 of the SF3B1 gene, encoding splicing factor 3B subunit 1, in low-grade uveal melanomas with good prognosis. Thus, uveal melanoma is among a small group of cancers associated with SF3B1 mutations, and these mutations denote a distinct molecular subset of uveal melanomas.

Uveal melanoma (UM) is the most common primary cancer of the eye and has a propensity for fatal hematogenous metastasis.¹ Uveal melanomas can be stratified by gene expression profile (GEP) classification into 2 prognostically significant molecular classes. Class 1 UMs have a low metastatic risk, whereas class 2 UMs have a high metastatic risk.² Class 1 tumors retain a differentiated melanocytic phenotype, whereas class 2 tumors exhibit a dedifferentiated stem cell–like phenotype.³ After it was shown by multiple groups that the prognostic accuracy of GEP outperforms clinicopathologic features and chromosomal gains and losses,^4-6 our group developed a GEP classifier for routine clinical use in which expression of 12 discriminating genes and 3 control genes is measured by quantitative polymerase chain reaction (PCR) on a microfluidics platform after targeted amplification. The result was an ultrahigh-performance assay that accurately measures gene expression from fine-needle biopsy samples that are too small to be reliably assessed using chromosome-based assays.⁷ A prospective multicenter study⁸ was performed, which confirmed the assay’s prognostic accuracy and showed it to be superior to chromosome 3 testing. To date, this assay is the only prognostic test for UM ever to undergo prospective multicenter validation, which is required for a cancer biomarker to achieve the highest level I evidence according to the National Comprehensive Cancer Network Task Force on cancer biomarkers and the Tumor Marker Utility Grading System.⁹

Cancer is thought to arise through the accumulation of genomic aberrations evolving under Darwinian selection. However, it remains unclear when the aberrations associated with metastasis emerge during tumor evolution. Uveal melanoma (UM) is the most common primary eye cancer and frequently leads to metastatic death, which is strongly linked to BAP1 mutations. Accordingly, UM is ideally suited for studying the clonal evolution of metastatic competence. Here we analyze sequencing data from 151 primary UM samples using a customized bioinformatic pipeline, to improve detection of BAP1 mutations and infer the clonal relationships among genomic aberrations. Strikingly, we find BAP1 mutations and other canonical genomic aberrations usually arise in an early punctuated burst, followed by neutral evolution extending to the time of clinical detection. This implies that the metastatic proclivity of UM is “set in stone” early in tumor evolution and may explain why advances in primary treatment have not improved survival.

Pediatric cancers often mimic fetal tissues and express proteins normally silenced postnatally that could serve as immune targets. We developed T cells expressing Chimeric Antigen Receptors (CAR) targeting glypican-2 (GPC2), a fetal antigen expressed on neuroblastoma (NB) and several other solid tumors. CARs engineered using standard designs control NBs with transgenic GPC2 overexpression but not those expressing clinically relevant GPC2 site densities (~5000 molecules/cell, range 1–6 ×10³). Iterative engineering of transmembrane (TM) and costimulatory domains plus overexpression of c-Jun lowered the GPC2-CAR antigen density threshold, enabling potent and durable eradication of NBs expressing clinically relevant GPC2 antigen densities, without toxicity. These studies highlight the critical interplay between CAR design and antigen density threshold, demonstrate potent efficacy and safety of a lead GPC2-CAR candidate suitable for clinical testing and credential oncofetal antigens as a promising class of targets for CAR T cell therapy of solid tumors.

Purpose: Uveal melanoma is a primary malignancy of the eye with oncogenic mutations in GNAQ, GNA11, or CYSLTR2, and additional mutations in BAP1 (usually associated with LOH of Chr 3), SF3B1, or EIF1AX. There are other characteristic chromosomal alterations, but their significance is not clear. Experimental Design: To investigate genes driving chromosomal alterations, we integrated copy number, transcriptome, and mutation data from three cohorts and followed up key findings. Results: We observed significant enrichment of transcripts on chromosomes 1p, 3, 6, 8, and 16q and identified seven shared focal copy number alterations (FCNAs) on Chr 1p36, 2q37, 3, 6q25, 6q27, and 8q24. Integrated analyses revealed clusters of genes in focal copy number regions whose expression was associated with metastasis and worse overall survival. This included genes from Chr 1p36, 3p21, and 8q24.3. At Chr 6q27, we identified two tumors with homozygous deletion of PHF10/BAF45a and one with a frameshift mutation with concomitant loss of the wild-type allele. Downregulation of PHF10 in uveal melanoma cell lines and tumors altered a number of biological pathways including development and adhesion. These findings provide support for a role for PHF10 as a novel tumor suppressor at Chr 6q27. Conclusions: Integration of copy number, transcriptome, and mutation data revealed novel candidate genes playing a role in uveal melanoma pathogenesis and a potential tumor suppressor role for PHF10.