Prostate cancer (PCa) is a malignancy with high heterogeneity arising from tumor microenvironment and histological subtypes. Identifying conserved progression drivers within such heterogeneity is essential for improving clinical outcomes. Using imaging mass cytometry, this study analyzes 38 proteins across paracancerous tissue and four histological subtypes: low-grade prostate acinar adenocarcinoma (LgPAC), high-grade PAC (HgPAC), intraductal carcinoma (IDC), and ductal adenocarcinoma (DAC). Results reveal that eIF1A is overexpressed in high-risk subtypes including HgPAC, IDC, and DAC and correlates with poor prognosis. In luminal cells, EIF1A knockdown and the translation inhibitor homoharringtonine (HHT) both suppress HIF-1α translation and tumor growth, while promoting infiltration of anticancer immune cells including PD-1- T cells and CD163- macrophages. Clinically, neoadjuvant HHT combined with androgen deprivation therapy reduces hypoxia and enhances immune cell infiltration, as shown by single-cell RNA sequencing. Collectively, this work defines conserved molecular features across PCa subtypes, providing promising insights for clinical management. This study was registered at Clinicaltrials.gov (NCT06834321).

Prostate cancer resistance to androgen deprivation therapy often involves neuroendocrine transformation. Using single-cell RNA sequencing of transgenic adenocarcinoma of the mouse prostate (TRAMP) mice across pathological stages (early adenocarcinoma to late neuroendocrine prostate cancer [NEPC]), we find an early neuroendocrine-initiating cluster marked by elevated HOXD11, conserved in human NEPC. Genetic suppression of HOXD11 blocks neuroendocrine differentiation and restores androgen receptor (AR) signaling. Mechanistically, HOXD11 directly activates FOXA2 and N-methyl-D-aspartate receptor (NMDAR) subunits (GRIN1/GRIN3A), pathways upregulated in NEPC and linked to poor prognosis. Pharmacological NMDAR inhibition with memantine suppresses NEPC progression preclinically. Notably, a preliminary clinical observation in one evaluable patient with chemotherapy-failed NEPC shows radiographic regression of primary and metastatic lesions after memantine treatment. These findings establish HOXD11 as a driver of neuroendocrine transformation and support further investigation of memantine as a candidate therapeutic strategy for NEPC.

Loss of major histocompatibility complex (MHC)-I is a hallmark of prostate cancer (PCa) immune evasion and immunotherapy failure. Here, we identify ZNF263 as a transcriptional repressor that silences MHC-I by recruiting nucleosome-remodeling and deacetylase (NuRD) to the STAT1 promoter, reducing STAT1 and MHC-I expression. Hypoxia enhances this repression through two ZNF263 modifications: phosphorylation-driven phase separation that strengthens NuRD interaction and O-GlcNAcylation at S662 that aids STAT1 promoter binding. O-GlcNAcylation also promotes interaction with protein kinase, DNA‑activated catalytic subunit (PRKDC), amplifying phosphorylation. Interferon‑gamma (IFN‑γ)‑induced MHC-I induction is augmented upon ZNF263 loss. In silico docking identified Viroptic as a Krüppel‑associated box (KRAB) pocket binder disrupting ZNF263-NuRD, derepressing STAT1, and potentiating IFN-γ antitumor immunity in vivo. High ZNF263 correlates with low MHC-I, scarce CD8+ T cells, and poor survival, providing rationale for targeting ZNF263 in PCa immunotherapy.

Tubulointerstitial fibrosis is a critical and irreversible process of chronic kidney disease. Dedifferentiated proximal tubular cells (PTCs) after injury are important for tubulointerstitial fibrosis. Hepatocyte nuclear factor 4 alpha (HNF4A) is the main regulatory factor for PTC differentiation. However, its role in PTC dedifferentiation and kidney fibrosis remains unclear. To investigate the role of HNF4A in kidney fibrosis, bioinformatics analysis and in vivo models were used to evaluate its expression in kidney tissues. The mechanisms through which the HNF4A P2 isoform inhibits kidney fibrosis were examined by using both in vivo and in vitro models. In this study, we revealed that the sustained downregulation of HNF4A expression was a key characteristic of abnormally repaired PTCs after injury and was associated with cell dedifferentiation. It was confirmed that the HNF4A P2 isoform, rather than the P1 isoform, inhibited TGF-β1-induced PTC dedifferentiation. The activation of fibroblasts, which was induced by dedifferentiated PTCs through paracrine signalling, was also inhibited. In vivo experiments confirmed that HNF4A P2 was more effective than HNF4A P1 was in alleviating kidney fibrosis. Mechanistically, on one hand, HNF4A P2 antagonized the TGF-β1-induced dedifferentiation of PTCs by inhibiting the JAG1/NOTCH pathway. On the other hand, the distinct structure of HNF4A P2 from that of P1 made it unaffected by TGF-β1-activated SRC, allowing HNF4A P2 to perform transcriptional regulatory functions. These findings suggest that targeting the HNF4A P2 isoform could serve as a novel therapeutic strategy to alleviate kidney fibrosis.

PCa is a malignancy with high heterogeneity arises from both tumor microenvironment (TME) and histological subtypes. To achieve superior clinical efficacy, it is imperative to identify unified progression drivers within such heterogeneity in PCa, thereby enabling the development of more consistent and effective therapeutic strategies. In this study, we applied imaging mass cytometry to stain 39 proteins on 71 tissues comprising para-cancer, low-grade acinar adenocarcinoma (LgPAC), high-grade PAC (HgPAC), intraductal carcinoma (IDC) and ductal adenocarcinoma (DAC) tissues, obtaining the spatial proteomic landscape of 345,233 single cells. We discovered a hypoxic eIF1A+ luminal epithelial (LE) cluster exhibiting both translational activation and immunosuppressive properties, which was enriched in high-risk PCa including HgPAC, IDC and DAC, and associated which tumor progression and unfavorable prognosis. Additionally, eIF1A+ LE orchestrates the formation of an immunologically “cold” TME, characterized by the low infiltration of anti-cancer immune cells including PD1- T cells CD163- macrophages. Through in vivo validation and investigator-initiated study, we further found that Homoharringtonine, an inhibitor targeting protein translation process, effectively inhibited PCa growth, alleviated hypoxic microenvironment, and enhanced immune cell infiltration. This study is the first to apply spatial proteomics to delineate consistent molecular features across histological subtypes, providing transformative insights for clinical management of PCa. ### Competing Interest Statement The authors have declared no competing interest.

The clustering of multiple transcription factor binding sites (TFBSs) for the same TF has proved to be a pervasive feature of cis-regulatory elements in the eukaryotic genome. However, the contribution of binding sites within the homotypic clusters of TFBSs (HCTs) to TF binding and target gene expression remains to be understood. Here, we characterize the CHD4 enhancers that harbor unique functional ZNF410 HCTs genome wide. We uncover that ZNF410 controls chromatin accessibility and activity of the CHD4 enhancer regions. We demonstrate that ZNF410 binds to the HCTs in a collaborative fashion, further conferring transcriptional activation. In particular, three ZNF410 motifs (sub-HCTs) located at 3' end of the distal enhancer act as "switch motifs" to control chromatin accessibility and enhancer activity. Mechanistically, the SWI/SNF complex is selectively required to mediate cooperative ZNF410 binding for CHD4 expression. Together, our findings expose a complex functional hierarchy of homotypic clustered motifs, which cooperate to fine-tune target gene expression.

Benign prostatic hyperplasia (BPH), a prevalent urological condition affecting aging males globally, significantly impairs urinary function and quality of life. This study evaluates the capacity of large language models (LLMs) to deliver reliable BPH-related information through a curated dataset of 235 clinically relevant questions, systematically categorized into Primary Questions (PQ), Extended Questions (EQ), and six subdomains encompassing disease mechanisms to therapeutic strategies. Eight open-source LLMs, including general-purpose models (Llama, DeepSeek, Intern) and medical-specialized models (PMCLlama, Meditron, MedAlpaca, BioMedGpt, BioMistral), were rigorously assessed using a multimodal evaluation framework integrating expert-led subjective assessments, ChatGPT-4o simulated evaluations, and quantitative metrics (ROUGE-L-f1, BLEU-4 g, METEOR, BERTScore-f1). The results revealed significant disparities among the models, with general-purpose models, particularly Llama, outperforming some specialized medical models. This suggests that advanced general LLMs can provide valuable reference answers for routine clinical queries. Although statistical analysis did not show significant differences between PQ and EQ, the general trend indicated that simpler queries were more effectively handled by LLMs. Given the increasing demand for accurate and accessible medical information, these findings highlight the importance of flexible and reliable AI tools in patient education. By demonstrating the potential of general LLMs and identifying the limitations of specialized models, this study offers insights for future research and underscores the growing role of AI in supporting patient-centered healthcare communication.

Immune checkpoint therapy for prostate cancer (PCa), a classic 'immune-cold' tumor characterized by an immunosuppressive tumor microenvironment, failed previously in clinical trials, but the underlying causes remain elusive. Here we find that YY1+, immunosuppressive macrophages aggregate in the hypoxic areas of PCa. Mechanistically, hypoxia promotes the phase separation of YY1 in the nucleus, where YY1 binds to NUSAP1 and promotes the SUMOylation, phase separation and stabilization of HIF-1α. Either myeloid-specific conditional knockout of YY1 or a treatment with tenapanor for decreasing the YY1-NUSAP1-HIF-1α interaction impairs subcutaneous PCa tumor formation in mouse prostate tumor models. Lastly, a first-generation tetrahedral DNA nanostructure based on the proteolysis targeting chimera technique, termed YY1-DcTAC, allows targeting and degrading YY1 in tumor-associated macrophages for inducing antitumor effects and CD8+ T cell tumor infiltration in mouse tumor models. In summary, our findings underscore the pivotal role of YY1 in the hypoxia/HIF-1α pathway in tumor-associated macrophages and support the targeting of YY1 for treating PCa.

Circular RNA (circRNA) plays a pivotal role in the pathogenesis of renal cell carcinoma (RCC). CircRNAs regulate gene expression via RNA-binding proteins (RBPs) and also exert biological effects through peptide encoding. CircPVT1 has been previously identified as an oncogenic circRNA. This study identified that circPVT1 encodes a 104-amino acid peptide, termed cP104aa. Functional assays showed that circPVT1 and the cP104aa peptide enhance RCC cell proliferation, invasion, migration, and lung metastasis both in vitro and in vivo. Mechanistically, the cP104aa peptide interacts with HNRNPK, leading to reduced c-MYC ubiquitination and increased c-MYC expression. Additionally, circPVT1 directly associates with EIF4A3, facilitating the expression of the target gene c-MYC. Furthermore, axitinib is shown to target the degradation of the cP104aa peptide. These findings reveal a novel mechanism by which circPVT1 contributes to RCC, highlighting the potential of the cP104aa peptide as a therapeutic target. Axitinib may serve as an effective therapeutic agent for patients with advanced RCC exhibiting high cP104aa expression.

The rational design of organic phototheranostic agents that combine diagnostic and therapeutic capabilities for cancer treatment remains challenging due to the inherent competition between radiative and non-radiative energy dissipation pathways. Herein, a novel molecule, TQP-TTPA, is strategically designed by incorporating a bulky electron donor and extended π-bridge, resulting in red-shifted absorption and emission in the second near-infrared window (NIR-II), along with prominent NIR-IIa emission (1300-1500 nm), a high NIR-II extinction coefficient, and enhanced NIR-IIa fluorescence brightness and photothermal conversion efficiency (43.8 %). These favorable properties are attributed to the strong donor-acceptor (D-A) interaction and enhanced intramolecular motion. Quantum chemical calculations provide insights into the excited-state energy dissipation mechanism and the role of intramolecular motion in modulating photophysical behavior. Furthermore, the femtosecond transient absorption (fs-TA) spectroscopy reveals that the performance enhancement originates from efficient intramolecular charge transfer (ICT) and promoted intramolecular motion by rational donor/π-bridge engineering. Based on these advantages, alendronate-functionalized TQP-TTPA nanoparticles (TQP-TTPA@ALD NPs) are developed for precise and high-resolution NIR-II fluorescence (FLI), photoacoustic (PAI), and phototherml (PTI) trimodal imaging-guided high-efficiency photothermal therapy (PTT) of prostate cancer bone metastases. This work offers a molecular-level design strategy for organic phototheranostics with tunable radiative/non-radiative decay balance, bridging fundamental photophysics and precision cancer theranostics.

Mounting evidence has implicated the RNA m(6)A methylation catalyzed by METTL3 in a wide range of physiological and pathological processes, including tumorigenesis. The detailed m(6)A landscape and molecular mechanism of METTL3 in prostate cancer (PCa) remains ill-defined. We find that METTL3 is overexpressed in PCa and correlates with worse patient survival. Functional studies establish METTL3 as an oncoprotein dependent on its m(6)A enzymatic activity in both AR(+) and AR(-) PCa cells. To dissect the regulatory network of m(6)A pathway in PCa, we map the m(6)A landscape in clinical tumor samples using m(6)A-seq and identify genome-wide METTL3-binding transcripts via RIP-seq. Mechanistically, we discover RRBP1 as a direct METTL3 target in which METTL3 stabilizes RRBP1 mRNA in an m(6)A-dependent manner. RRBP1 positively correlates with METTL3 expression in PCa cohorts and exerts an oncogenic role in aggressive PCa cells. Leveraging the 3D structural protein-protein interaction between METTL3 and METTL14, we successfully develop two potential METTL3 peptide inhibitors (RM3 and RSM3) that effectively suppress cancer cell proliferation in vitro and tumor growth in vivo. Collectively, our study reveals a novel METTL3/m(6)A/RRBP1 axis in enhancing aggressive traits of PCa, which can be therapeutically targeted by small-peptide METTL3 antagonists.

Bladder Ewing sarcoma/primitive neuroectodermal tumor (bladder ES/PNET) is a rare and highly malignant tumor associated with a poor prognosis, yet its underlying mechanisms remain poorly understood. Here, we employed a combination of single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), and functional analyses to delve into the pathogenesis of bladder ES/PNET. The investigation revealed the presence of specialized types of epithelial cells (referred to as bladder ES-Epi) and mast cells (referred to as bladder ES-Mast) within bladder ES/PNET in comparison to urothelial carcinoma. Notably, TNFRSF12A exhibited significant upregulation in bladder ES/PNET. Furthermore, mast cells possessed the ability to activate epithelial cells through the TNFSF12-TNFRSF12A ligand-receptor signaling pattern. In addition, Enavatuzumab can significantly inhibit the migratory ability of the Ewing sarcoma cell line RD-ES. This groundbreaking study provides unprecedented mechanistic insights into the progression of bladder ES/PNET and introduces a potential therapeutic avenue for treating this challenging malignancy.

Protein arginine methylation is a common post-translational modification (PTM) catalyzed by nine protein arginine methyltransferases (PRMTs). As the major symmetric arginine methyltransferase that methylates both histone and non-histone substrates, PRMT5 plays key roles in a number of biological processes critical for development and tumorigenesis. PRMT5 overexpression has been reported in multiple cancer types including prostate cancer (PCa), but the exact biological and mechanistic understanding of PRMT5 in aggressive PCa remains ill-defined. Here, we show that PRMT5 is upregulated in PCa, correlates with worse patient survival, promotes corrupted RNA splicing, and functionally cooperates with an array of pro-tumorigenic pathways to enhance oncogenesis. PRMT5 inhibition via either genetic knockdown or pharmacological inhibition reduces stemness with paralleled differentiation and arrests cell cycle progression without causing appreciable apoptosis. Strikingly, the severity of antitumor effect of PRMT5 inhibition correlates with disease aggressiveness, with AR+ PCa being less affected. Molecular characterization pinpoints MYC, but not (or at least to a lesser degree) AR, as the main partner of PRMT5 to form a positive feedback loop to exacerbate malignancy in both AR+ and AR— PCa cells. Inspired by the surprising finding that PRMT5 negatively correlates with tumor immune infiltration and transcriptionally suppresses an immune-gene program, we further show that although PRMT5 inhibitor (PRMT5i) EPZ015666 or anti-PD-1 immunotherapy alone exhibits limited antitumor effects, combination of PRMT5i with anti-PD-1 displays superior efficacy in inhibiting castration-resistant PCa (CRPC) in vivo. Finally, to expand the potential use of PRMT5i through a synthetic lethality concept, we also perform a global CRISPR/Cas9 knockout screen to unravel that many clinical-grade drugs of known oncogenic pathways can be repurposed to target CRPC when used in combination with PRMT5i at low doses. Collectively, our findings establish a rationale to exploit PRMT5i in combination with immunotherapy or other targeted therapies to treat aggressive PCa.

Immune checkpoint therapy for prostate cancer (PCa) has failed in clinical trials; however, the precise underlying mechanisms involved remain elusive. PCa, a classic "immune-cold" tumor, is characterized by an immunosuppressive tumor microenvironment. Within this milieu, macrophages, the predominant immune cell population, have a propensity to infiltrate the hypoxic zones of tumors. In a previous study, we showed that Yin Yang 1 (YY1) is highly expressed in macrophages in PCa tissues. Here, through multiplexed imaging mass cytometry (IMC) of a PCa tissue microarray, we further demonstrate that YY1+ macrophages aggregate in hypoxic areas of tumors and that hypoxia promotes the phase separation of YY1 in the nucleus by increasing YY1 tyrosine phosphorylation in macrophages. Furthermore, YY1 binds to NUSAP1 and promotes the SUMOylation of HIF-1α, which promotes phase separation and stabilization of the HIF-1α protein. We also demonstrated that either treatment with a small molecule inhibitor (tenapanor) to decrease the YY1-NUSAP1-HIF-1α interaction or myeloid-specific YY1 gene knockout impairs subcutaneous PCa tumor formation. Furthermore, we present a first-generation tetrahedral DNA nanostructure (TDN) based on the proteolysis targeting chimera (PROTAC) technique, named YY1-DcTAC, which targets and degrades YY1 in tumor-associated macrophages. In a PCa mouse model, YY1-DcTAC exhibited prolonged drug efficacy, robust macrophage-specific responsiveness, potent antitumor effects, and increased CD8+ T cell tumor infiltration. In summary, our findings underscore the pivotal role of YY1 within the hypoxia/HIF-1α pathway in tumor-associated macrophages and affirm the therapeutic potential of targeting YY1 for treating PCa. ### Competing Interest Statement The authors have declared no competing interest.