Lineage commitment pathways epigenetically oppose oncogenic Gαq/11-YAP signaling in dormant disseminated uveal melanoma

The mechanisms driving late relapse in uveal melanoma (UM) patients remains a medical mystery and major challenge. Clinically it is inferred that UM disseminated cancer cells (DCCs) persist asymptomatic for years-to-decades mainly in the liver before they manifest as symptomatic metastasis. Here we reveal using Gαq/11 ^mut /BAP ^wt human uveal melanoma models and human UM metastatic samples, that the neural crest lineage commitment nuclear receptor NR2F1 is a key regulator of spontaneous UM DCC dormancy in the liver. Using a quiescence reporter, RNA-seq and multiplex imaging we revealed that rare dormant UM DCCs upregulate NR2F1 expression and genes related to neural crest programs while repressing gene related to cell cycle progression. Gain and loss of function assays showed that NR2F1 silences YAP1/TEAD1 transcription downstream of Gαq/11 signaling and that NR2F1 expression can also be repressed by YAP1. YAP1 expression is repressed by NR2F1 binding to its promoter and changing the histone H3 tail activation marks to repress YAP1 transcription. In vivo CRISPR KO of NR2F1 led dormant UM DCCs to awaken and initiate relentless liver metastatic growth. Cut&Run and bulk RNA sequencing further confirmed that NR2F1 epigenetically stimulates neuron axon guidance and neural lineage programs, and it globally represses gene expression linked to G-protein signaling to drive dormancy. Pharmacological inhibition of Gαq/11 ^mut signaling resulted in NR2F1 upregulation and robust UM growth arrest, which was also achieved using a novel NR2F1 agonist. Our work sheds light on the molecular underpinnings of UM dormancy revealing that transcriptional programs driven by NR2F1 epigenetically short-circuit Gαq/11 signaling to its downstream target YAP1.

Highlights

• Quiescent solitary uveal melanoma (UM) DCCs in the liver up- and down-regulate neural crest and cell cycle progression programs, respectively.

• NR2F1 drives solitary UM DCC dormancy by antagonizing the Gαq/11-YAP1 pathway; small molecule Gαq/11 inhibition restores NR2F1 expression and quiescence.

• NR2F1 short-circuits oncogenic YAP1 and G-protein signaling via a chromatin remodeling program.

• Loss of function of NR2F1 in dormant UM DCCs leads to aggressive liver metastasis.

UM cells disseminate to the liver and stay dormant for a prolonged period before manifesting as overt metastasis(A). Dormant UM DCCs express high levels of NR2F1 which induces transcriptional repression of YAP1 by binding to its promoter (B). Binding of NR2F1 inhibits recruitment of H3K4me3 and H3K27ac gene activation marks onto YAP1 promoter and globally represses programs related to cell cycle proliferation, transcriptional initiation and GPCR signaling while activating axonal guidance and neural crest migration pathways in dormant UM DCCs (B). With time, dormant UM DCCs lose NR2F1 expression (C) and are reawakened to give rise to overt metastasis as NR2F1 binding onto the YAP promoter is reduced leading to activation of YAP1 oncogenic signaling (C). Also, YAP1 inhibits NR2F1 expression through unknown mechanisms causing activation of cell cycle proliferation, transcriptional initiation and GPCR pathways and inhibition of neuronal programs (C).