# Molecular Mechanisms Underlying Luminal- Neuroendocrine Transdifferentiation

> **NIH NIH R01** · EMORY UNIVERSITY · 2024 · $541,236

## Abstract

Summary
The objective of this proposal is to determine the molecular mechanisms underlying luminal-to-neuroendocrine
transdifferentiation (NET) of prostate cancer (PCa). NET underlines the critical progression of prostate
adenocarcinoma (AdPC) to neuroendocrine PCa (NEPC), a lethal disease with no cure. Understanding the
molecular mechanisms that drive NET may pave the way to discovering critical druggable steps and identifying
biomarkers of NEPC progression. In our preliminary studies, we generated a model system where we push the
prostate luminal epithelial cell LNCaP towards NE cell type over a period of 28 days via the overexpression
(OE) of a single gene FOXA2, a chromatin-pioneering factor. Time-course RNA-seq analyses of FOXA2-OE
cells revealed a gradual loss of epithelial gene expression and gain of NE transcriptional program. This
transcriptomic shift is accompanied by substantial alterations in TF binding and chromatin remodeling at
luminal and NE enhancers, accompanied by remarkable changes in DNA methylation and 3D chromatin
architecture. Interestingly, FOXA2 induced the transcription of a neural TF called NKX2-1 on day 14 (D14) of
OE, and the expression of NKX2-1 is required for the completion of FOXA2-driven NET. Further, NKX2-1 and
FOXA2 bind to promoters and enhancers, respectively, and they interact with each other through chromatin
looping to co-occupy active enhancers. Further, we found regional DNA demethylation around FOXA2-binding
sites and a remarkable up-regulation of TET1, the key enzyme that catalyzes DNA demethylation, on D14
following FOXA2 OE. These preliminary data lead to our central hypothesis that enhancer-bound FOXA2
interacts with promoter-bound NKX2-1 to drive luminal-to-NE transdifferentiation, involving 3D chromatin
reorganization and enhancer priming and activation, which requires regional DNA demethylation mediated by
TET1. To test these hypotheses, Aim 1 will first determine whether the abilities of NKX2-1 to bind DNA and
interact with FOXA2 are both required for its role in facilitating FOXA2-induced NET and then validate this
pathway in additional NEPC models. Aim 2 will evaluate whether TET1 induction at D14 is required for FOXA2-
driven NET through modulating regional DNA demethylation and NE enhancer priming. Lastly, Aim 3 will
validate the genomic and epigenomic reprogramming in clinical samples by comparative analyses of the
spatial transcriptome, whole-genome DNA methylation, and 3D chromatin structure in AdPC vs. NEPC
samples. We will also examine the downstream genes regulated by a TET1 inhibitor and test its efficacy in
suppressing NEPC growth in vitro and in vivo.

## Key facts

- **NIH application ID:** 10982139
- **Project number:** 1R01CA286147-01A1
- **Recipient organization:** EMORY UNIVERSITY
- **Principal Investigator:** Jindan Yu
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $541,236
- **Award type:** 1
- **Project period:** 2024-09-01 → 2029-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10982139

## Citation

> US National Institutes of Health, RePORTER application 10982139, Molecular Mechanisms Underlying Luminal- Neuroendocrine Transdifferentiation (1R01CA286147-01A1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10982139. Licensed CC0.

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