HOXD11 drives NMDAR signaling activation and the neuroendocrine transition in prostate cancer epithelium

Prostate cancer frequently develops resistance to androgen deprivation therapy (ADT), with adenocarcinoma-neuroendocrine prostate cancer (NEPC) lineage plasticity representing a critical yet mechanistically unclear driver of therapeutic failure. Here, we employ single-cell transcriptomic analysis of 29,436 cells from transgenic adenocarcinoma of mouse prostate (TRAMP), recapitulating the full clinical progression of human prostate cancer-NEPC evolution, to dissect the molecular dynamics underlying lineage transition. We identify Hoxd11 as a key transcriptional driver of adenocarcinoma-NEPC plasticity, with its expression and regulatory activity markedly upregulated during early NEPC transformation. Genetic suppression of Hoxd11 reversed lineage plasticity and delayed ADT-induced neuroendocrine differentiation. Mechanistically, HOXD11 directly activates the NMDAR signaling pathway (via GRIN1/GRIN3A), which is hyperactivated in NEPC and correlates with poor prognosis. Pharmacological inhi..., Sequencing Protocol:
scRNA-seq for TRAMP and human PCa tissue: Fresh tumor specimens were preserved in GEXSCOPE Tissue Preservation Solution under ice-cold transport conditions. Subsequent processing involved sequential steps: (1) washing in Hanks Balanced Salt Solution, (2) mechanical mincing coupled with enzymatic digestion using GEXSCOPE Tissue Dissociation Solution, (3) centrifugation and resuspension, followed by (4) erythrocyte depletion with GEXSCOPE Red Blood Cell Lysis Buffer. Single-cell suspensions derived from this workflow were converted into barcoded libraries employing the Chromium Single Cell Kit (10x Genomics). Final libraries were prepared with 10x Genomics Library Kits and subjected to paired-end 150 bp (PE150) sequencing on an Illumina NovaSeq 6000 platform, strictly adhering to manufacturer protocols.
RNA-seq for HEK-293T and LNCaP cells: Total RNA was isolated from HEK-293T cells using Trizol reagent according to the manufacturer's protocol, followed by purificatio..., # HOXD11 drives NMDAR signaling activation and the neuroendocrine transition in prostate cancer epithelium

Dataset DOI: [10.5061/dryad.kkwh70sgd](10.5061/dryad.kkwh70sgd)

## Description of the data and file structure

This dataset includes a single-cell RNA sequencing (scRNA-seq) count matrix of prostate tissues from Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) mice across four distinct disease stages (one at 8 week, one at 20 week, one at 25 week and one at 30 week) in a csv file, generated to resolve lineage dynamics during neuroendocrine prostate cancer (NEPC) progression, as well as four standard formatted matrices for scRNA-seq data corresponding to these four ages, relatively. This dataset also includes scRNA-seq of two *de novo* human NEPC samples from clinical biopsy. Furthermore, this dataset contains the bulk RNA-seq count matrix and bigwig files of ATAC-seq from HEK-293T cells following HOXD11 knockdown, as well as the bulk RNA-seq count matrix and bigwig files of CU...,