Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer, with a 10% five-year survival rate. However, little is known about its origin and the mechanisms governing its emergence. Our study characterized ADPC and NEPC in prostate tumors from 7 patients using scRNA-seq. First, we identified two NEPC gene expression signatures representing different phases of trans-differentiation. New marker genes we identified may be used for clinical diagnosis. Second, integrative analyses combining expression and subclonal architecture revealed different paths by which NEPC diverges from the original ADPC, either directly from treatment-naïve tumor cells or from specific intermediate states of treatment-resistance. Third, we inferred a hierarchical transcription factor (TF) network underlying the progression, which involves constitutive regulation by ASCL1, FOXA2, and selective regulation by NKX2-2, POU3F2, and SOX2. Together, these results defined the complex expression profiles and advanced our understanding of the genetic and transcriptomic mechanisms leading to NEPC differentiation.

While single-cell technologies have advanced bladder cancer research, the microenvironment of lymph node metastases and its role in progression remain uncl

Transposable elements (TEs) can provide ectopic promoters to drive the expression of oncogenes in cancer, a mechanism known as onco-exaptation. Onco-exaptation events have been extensively identified in various cancers, with bladder cancer showing a high frequency of onco-exaptation events (77%). However, the effect of most of these events in bladder cancer remains unclear. This study identified 44 onco-exaptation events in 44 bladder cancer cell lines in 137 RNA-seq datasets from six publicly available cohorts, with L1PA2 contributing the most events. L1PA2-SYT1, L1PA2-MET, and L1PA2-XCL1 had the highest frequency not only in cell lines but also in TCGA-BLCA samples. L1PA2-SYT1 showed significant tumor specificity and was found to be activated by CpG island demethylation in its promoter. The upregulation of L1PA2-SYT1 enhances the in vitro invasion of bladder cancer and is an independent risk factor for patient’s overall survival, suggesting L1PA2-SYT1 being an important event that promotes the development of bladder cancer.

Background: Molecular subtyping of bladder cancer (BCa) using bulk transcriptomic data is hindered by tumor microenvironment (TME) contamination and intra-tumoral heterogeneity. These factors also contribute to variable responses to immune checkpoint inhibitor (ICI) therapy. Single-cell RNA sequencing offers a high-resolution approach to overcome these limitations by enabling tumor-specific analysis and improving therapeutic target identification. Materials and methods: We constructed a large multicenter single-cell atlas of BCa by integrating nine cohorts comprising 123 samples and 842 127 cells. Tumor epithelial cells ( n = 265 962) were identified via copy number variation (CNV) analysis using inferCNV. Pseudobulk RNA profiles were generated to simulate conventional bulk samples (Pseudobulk _all ) and purified tumor profiles (Pseudobulk _tumor ), enabling systematic evaluation of bulk-based classifiers. Inter-tumoral and intra-tumoral heterogeneity programs were defined based on transcriptional profiles and validated through in vitro and in vivo experiments. Additionally, we cross-analyzed five immunotherapy datasets encompassing 13 immune response phenotypes to identify molecular features associated with therapeutic resistance and sensitivity. Results: Unsupervised clustering identified 11 major cell types and 55 non-epithelial subtypes, with TME heterogeneity driven by tissue origin and malignancy status. Existing molecular classifiers UNC (University of North Carolina at Chapel Hill) showed compromised concordance between Pseudobulk _all and Pseudobulk _tumor , particularly in stroma-rich samples. We defined three inter-tumoral (GE _inter 2–4) subtypes with distinct CNV and transcription factor signatures that remained stable even at low tumor purity. Seven intra-tumoral (GE _intra ) programs captured key biological states, including an EMT/Stem-like module associated with immunosuppression and ICI resistance. Mechanistically, TGF-β1 induced expression of EMT/Stem-like genes (e.g., PTHLH ), while Pthlh knockdown synergized with anti-PD-L1 therapy in murine models by enhancing T cell cytotoxicity without altering T cell infiltration. Conclusions: This study provides a robust single-cell framework for resolving inter- and intra-tumoral heterogeneity in BCa, overcoming limitations of bulk-based subtyping. The TGF-β1-PTHLH axis contributes to ICI resistance, positioning PTHLH as a promising therapeutic target. These findings offer new insights for improving immunotherapeutic strategies in BCa.

Li Z, et al. World J Mens Health. 2024 Sep;42:e84. https://doi.org/10.5534/wjmh.240062