Specific oncogene activation of the cell of origin in mucosal melanoma

Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we developed a zebrafish model in which all melanocytes experienced CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only developed from melanocytes lining internal organs, analogous to the location of patient MM. We found that zebrafish MMs had a unique chromatin landscape from cutaneous melanoma. Internal melanocytes could be labeled using a MM-specific transcriptional enhancer. Normal zebrafish internal melanocytes shared a gene expression signature with MMs. Patient and zebrafish MMs have increased migratory neural crest gene and decreased antigen presentation gene expression, consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors, allowing this model to be used for MM therapeutic discovery.

Voices: Challenges and opportunities in RNA biology

In the first of many thematic issues marking the 30th anniversary of Cell Chemical Biology, we highlight the contribution of chemical biology to RNA biology in a special issue on RNA modulation. We asked several leaders in the field to share their opinions on the current challenges and opportunities in RNA biology.

Oncogenic CDK13 mutations impede nuclear RNA surveillance

RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 (CDK13) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.

Abstract 2846: Stereotypic patterns and genomic correlates of organotropism in metastatic melanoma

Despite the major role that metastasis plays in the morbidity and mortality of melanoma, stereotyped patterns of metastasis and drivers of its organotropism in melanoma are still not well characterized, limited by a dearth of sequencing data in well-annotated clinical melanoma samples. To address these open questions, we performed an integrative analysis of clinical and genomic features from 243 patients with metastatic melanoma treated at Dana Farber Cancer Institute (DFCI). Tumor biopsies were sequenced with OncoPanel, a next-generation sequencing panel that identifies mutations in 331 cancer genes. Presence of site metastases was evaluated radiographically pre-treatment for each patient; sites include lymph node (64% of cohort), soft tissue (59%), lung (57%), liver (32%), brain (24%), bone (22%), mesentery (12%), adrenal gland (9%), spleen (7%), and other metastatic sites (13%).

Metastases showed significant co-occurrences (e.g. bone and lung, OR 2.8, 95% CI = [2.3, 3.3], p < 0.01; adrenal and mesentery, OR 4.4, 95% CI = [3.8, 5.0], p < 0.01) and exclusions (lymph node and brain, OR 0.5, 95% CI = [0.2, 0.8], p = 0.02). We performed unsupervised hierarchical clustering of patients with cutaneous melanoma (n = 203) by metastatic site pattern using a Euclidean distance metric weighted to favor uncommon metastatic sites, yielding five stereotypic patterns of metastasis, characterized by: (1) co-occurrence of adrenal, mesenteric, and abdominal metastases (n=19); (2) liver metastases (n=33); (3) low metastatic burden (n=80); (4) co-occurrence of lung, brain, and mesentery metastases (n=42); and (5) co-occurrence of bone and lung metastases (n=29). Clustering is stable, with highly concordant cluster assignments in repeated subsampling of the data.

Patients with cutaneous melanoma (n=203) exhibited both site-specific and pattern-specific genomic correlates of metastatic organotropism that persist after correction for mutational burden. Tumors from patients with liver metastases showed significantly higher prevalence (p < 0.05) of mutation compared to patients without liver metastases in KMT2D (56% vs 18%), BCL6 (22% vs 0%), TMPRSS2 (22% vs 0%), ARID1B (33% vs 4%), MET (33% vs 4%), and AXL (44% vs 11%), with similar enrichment in the liver met-predominant metastatic cluster, implicating dysregulation of histone and protein deacetylation pathways in liver metastatic organotropism (p < 0.01). Numerous additional mutational correlates were found for the remaining nine metastatic sites and all five metastatic patterns, and validation in an orthogonal dataset is ongoing.

We present robust stereotypic patterns of metastasis and both site- and pattern-specific genomic correlates of organotropism in metastatic melanoma. By leveraging a valuable clinical/genomic data set, we nominate genetic correlates of organotropism for functional validation and potential therapeutic targets.

Citation Format: William H. Ge, Giuseppe Tarantino, Emily Robitschek, Michael P. Manos, Lauren Eastman, Olivia Ouyang, Patrick Ott, Ann W. Silk, Osama E. Rahma, Alexander Gusev, Rizwan Haq, Elizabeth I. Buchbinder, Megan L. Insco, Stephen Hodi, Eliezer Van Allen, David Liu. Stereotypic patterns and genomic correlates of organotropism in metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2846.

Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis

Epigenetic regulators, when genomically altered, may become driver oncogenes that mediate otherwise unexplained pro-oncogenic changes lacking a clear genetic stimulus, such as activation of the WNT/β-catenin pathway in melanoma. This study identifies previously unrecognized recurrent activating mutations in the G9a histone methyltransferase gene, as well as G9a genomic copy gains in approximately 26% of human melanomas, which collectively drive tumor growth and an immunologically sterile microenvironment beyond melanoma. Furthermore, the WNT pathway is identified as a key tumorigenic target of G9a gain-of-function, via suppression of the WNT antagonist DKK1. Importantly, genetic or pharmacologic suppression of mutated or amplified G9a using multiple in vitro and in vivo models demonstrates that G9a is a druggable target for therapeutic intervention in melanoma and other cancers harboring G9a genomic aberrations. SIGNIFICANCE: Oncogenic G9a abnormalities drive tumorigenesis and the "cold" immune microenvironment by activating WNT signaling through DKK1 repression. These results reveal a key druggable mechanism for tumor development and identify strategies to restore "hot" tumor immune microenvironments.This article is highlighted in the In This Issue feature, p. 890.

Severe Radiation Necrosis Refractory to Surgical Resection in Patients with Melanoma and Brain Metastases Managed with Ipilimumab/Nivolumab and Brain-Directed Stereotactic Radiation Therapy

BACKGROUND

The use of targeted therapies and immune checkpoint inhibitors has drastically changed the management of patients with melanoma and brain metastases. Specifically, combination therapy with ipilimumab, a cytotoxic T-lymphocyte antigen 4 inhibitor, and nivolumab, a programmed cell death protein 1 inhibitor, has become a preferred systemic therapy option for patients with melanoma and asymptomatic brain metastases. However, the efficacy and toxicity profile of these agents in combination with brain-directed radiation therapy is not well described.

CASE DESCRIPTION

In this case series, we highlight a series of patients with melanoma demonstrating severe radiation necrosis immediately refractory to surgical resection following brain-directed stereotactic radiation therapy with concurrent ipilimumab and nivolumab. Three patients described in this series each received stereotactic radiation therapy to a dose of 30 Gy in 5 fractions to a melanoma brain metastasis. These areas developed radiographic evidence of necrosis, which was managed surgically and progressed immediately and rapidly after resection. Re-resection, bevacizumab, steroids, and/or discontinuation of nivolumab was used to mitigate further necrosis with varying efficacy.

CONCLUSIONS

Patients with metastatic melanoma receiving brain-directed radiation therapy with concurrent ipilimumab and nivolumab are at risk for developing severe, surgically refractory radiation necrosis and should be closely followed clinically and with imaging. The exact mechanism for such severe necrosis is unknown, and future studies are needed to better understand this pathophysiology and identify optimal treatment strategies.

A self-limiting switch based on translational control regulates the transition from proliferation to differentiation in an adult stem cell lineage

In adult stem cell lineages, progenitor cells commonly undergo mitotic transit amplifying (TA) divisions before terminal differentiation, allowing production of many differentiated progeny per stem cell division. Mechanisms that limit TA divisions and trigger the switch to differentiation may protect against cancer by preventing accumulation of oncogenic mutations in the proliferating population. Here we show that the switch from TA proliferation to differentiation in the Drosophila male germline stem cell lineage is mediated by translational control. The TRIM-NHL tumor suppressor homolog Mei-P26 facilitates accumulation of the differentiation regulator Bam in TA cells. In turn, Bam and its partner Bgcn bind the mei-P26 3' untranslated region and repress translation of mei-P26 in late TA cells. Thus, germ cells progress through distinct, sequential regulatory states, from Mei-P26 on/Bam off to Bam on/Mei-P26 off. TRIM-NHL homologs across species facilitate the switch from proliferation to differentiation, suggesting a conserved developmentally programmed tumor suppressor mechanism.

Novelty seeking and stereotypic activation of behavior in mice with disruption of the Dat1 gene

Disruption of the dopamine (DA) transporter (Dat1) gene in mice leads to a 50% reduction or complete elimination of Dat1 expression in striatum of respective heterozygous (HZ) and knockout (KO) mice. Compared to wild-type (WT) controls, extracellular DA is increased approximately two- and five-fold in the mutants. Although open field (OF) activity is similar for WT and HZ animals, it is enhanced for KO mice. The purpose of the present investigations was to study spontaneously emitted behaviors and to determine the behavioral and neurochemical mechanisms that may contribute to the hyperactivity of KO animals. Heterozygotes are less anxious than other genotypes and they engage in novelty-seeking behaviors that include increased time spent in the center of the OF, enhanced investigation of objects, and augmented free exploration of a novel environment. By comparison, KO mice display neophobia when initially exposed to novel conditions. Over time the anxiety-like response habituates and behaviors become activated and stereotyped; these responses are unrelated to exploration or novelty seeking. No alterations in extracellular DA levels or tissue contents from several brain regions are detected at the time of stereotypic activation of KO mice. By contrast, this behavior is accompanied by changes in serotonin metabolism in basal ganglia. This feature may contribute to the behavioral inflexibility of KO mice in different experimental contexts. Collectively, these findings suggest that disruption of the Dat1 gene in mice leads to two different phenotypes; one related to anxiety-reducing and novelty seeking, while the other has some homology to disorders with a stereotypical-perseverative spectrum.