RET Kinase is transcriptionally regulated by ASCL1 in Neuroendocrine Prostate Cancer and Small Cell Lung Cancer

Abstract

Resistance to second-generation androgen deprivation therapies often causes neuroendocrine prostate cancer (NEPC), an aggressive disease variant, in castration-resistant prostate cancer patients. Due to low survival outcomes and limited therapeutic interventions for patients, it is imperative to study the molecular basis of NEPC. Studies have shown that NEPC can be categorized into two subtypes based on the expression of ASCL1 or NEUROD1, two proneuronaltranscription factors. In this study, we aim to find cell surface markers specific to ASCL+ NEPC which can be used as a biomarker or a druggable target. Analysis of parental and siASCL1 NCIH660 cells nominated RET as the top hit gene strongly correlated to ASCL1. In previous studies, we have shown that RET kinase is implicated as a mechanism of treatment resistance contributing to NEPC survival or growth. Here, we see that RET gene expression strongly correlates to ASCL1 but not NEUROD1 in various NEPC patient samples and mouse models. This data was corroborated by scRNA-seq data in CRPC-NEPC samples, whereas there was no expression of RET or ASCL1 in CRPC-Adeno samples. We also analyzed temporal gene expression data from PARCB xenograft models, and observed that the gene expression of RET mirrors the gene expression of ASCL1, and increases as the tumor progresses towards a neuroendocrine phenotype. Informatics modeling of whole transcriptome sequencing data from patient samples indicates that RET and ASCL1 has substantially similar gene network signatures in NEPC than ADCA, implying that these genes reside in the same gene ecosystem in NEPC. Remarkably, we did not notice correlations between RET and NEUROD1 gene networks in both subtypes. We saw increased ASCL1 recruitment and H3K27ac marks at the RET transcription sites in ASCL1- positive PDXs, but not in CRPC or NEUROD1-positive PDXs. We also demonstrated a similar relationship between RET and ASCL1 in Small Cell Lung Cancer, a neuroendocrine cancer type using publicly available bulk RNA-seq, scRNA-seq, as well as ChIP-seq data. These results highlight the critical role of ASCL1 in mediating RET signaling in NEPC and will be crucial to stratify patients and develop novel therapeutic interventions.