Neuroendocrine tumors (NETs) comprise a heterogeneous family of malignancies of wide anatomic distribution but shared clinical and molecular features. Although tissue-specific biology has been well characterized for some common primary sites, comprehensive analyses capable of defining biologically meaningful, site-independent subtypes are lacking. This study aimed to identify and validate cross-site molecular subtypes of NETs and to evaluate their clinical relevance. Multi-omic factor analysis (MOFA) and unsupervised clustering were used to integrate tumor gene expression and DNA methylation data from 194 patients with lung, stomach, pancreas, small intestine, and colorectal NETs. Latent factors representing biologically meaningful sources of variation were leveraged to generate a robust consensus clustering derived from eight unsupervised algorithms. Each molecular subtype was comprehensively characterized by integrating clinical, pathological and molecular features with survival through multivariable Cox proportional hazards models. Validation was performed in independent external cohorts of lung, small intestine, and pancreatic NETs with publicly available multi-omic datasets. We identified three distinct molecular subtypes (NS1–3). NS1 exhibited a strong immune phenotype and was enriched in metabolic and nutrient-digestion pathways. NS2 showed pronounced neuroendocrine differentiation with enrichment of neuronal and secretory programs. NS3 was characterized by global DNA hypermethylation, enrichment in DNA-replication pathways, and significantly poorer prognosis (10-year OS: 51.9
The dissemination of carbapenem-resistant Pseudomonas aeruginosa (CRPA) across human, environmental, and agricultural interfaces represents an increasing One Health challenge. We analyzed 716 P. aeruginosa isolates collected over four seasons from hospitals, farms, and wastewater treatment plants in five provinces of China using whole-genome sequencing, clonal network analysis, and comparative genomics. Among the collected isolates, 477 (66.62
Choroid plexus tumours (CPTs) are rare intraventricular brain neoplasms derived from choroid plexus epithelium, predominantly affecting young children. They include benign choroid plexus papilloma (CPP), atypical CPP (aCPP), and malignant choroid plexus carcinoma (CPC) and segregate into three DNA-methylation subgroups: paediatric A (pedA), paediatric B (pedB), and adult. To resolve subtype-specific biology, we performed single-nucleus RNA sequencing on 43 CPTs and integrated 12 non-neoplastic foetal, paediatric, and adult choroid plexus references, complemented by spatial transcriptomics in a subset of 16 tumour sections and 2 normal choroid plexus samples. Tumour embeddings and correlation analyses demonstrated that CPTs cluster by methylation subtype rather than WHO grade, revealing epigenetically driven relationships despite divergent histology. We identified 10 tumour metaprograms spanning epithelial differentiation, ciliogenesis, proliferation, extra cellular matrix remodelling, and stress responses. PedA and adult tumours showed relatively homogeneous program distribution dominated by differentiation or ciliation states, whereas pedB tumours exhibited marked heterogeneity with selective enrichment of hypoxia, interferon signalling, early stress response, and TGF-β signalling. Spatial mapping revealed consistent anticorrelation of these programs with ciliogenesis and differentiation programs, suggesting stress-associated dedifferentiation. Elevated stress and hypoxia scores correlated with poorer survival. PedB tumours showed enrichment of interferon- and lipid-associated myeloid populations, that carried pro-angiogenic signatures. They were spatially co-localised with hypoxic and interferon I expressing tumour areas, that were predicted to interact with myeloid cells via immunosuppressive cues, shaping a pro-angiogenic, pro-tumour environment. This study identifies stress- and hypoxia-associated dedifferentiation programs that are selectively enriched in pedB tumours, correlate with poor clinical outcome, and antagonise multiciliogenesis and epithelial differentiation. Their spatial co-localisation with immunosuppressive, pro-angiogenic macrophage populations links developmental arrest to microenvironmental remodelling and aggressive behaviour. These findings provide a biologically grounded framework for risk stratification and highlight hypoxia, angiogenesis and macrophage polarisation as candidate therapeutic targets in high-risk CPTs.
Neuroendocrine prostate cancer (NEPC), a lethal outcome of androgen deprivation, arises through neuroendocrine transdifferentiation (NEtD) of prostate adenocarcinoma (PRAD), yet its initiating drivers and their temporal order remain only partially defined. Clinical single-cell studies primarily capture established PRAD or NEPC at single timepoints, so they cannot directly resolve transitional states or the order and direction of transdifferentiation. We generated longitudinal single-cell RNA sequencing of the LTL331 patient-derived xenograft across eight timepoints spanning pre-castration PRAD to relapsed NEPC (51,726 cells) with matched whole-exome sequencing, integrating inferred single-cell copy-number profiles, trajectory inference, regulon and transcription-factor-activity analysis, and chromatin-accessibility data from a clinical metastatic castration-resistant prostate cancer atlas. Lineage states were tested for replication in two clinical single-cell cohorts by embedding-free, label-level comparison. NEtD proceeded by transcriptional reprogramming of a single clone, not clonal outgrowth: PRAD and NEPC shared copy-number architecture and a truncal TMPRSS2::ERG rearrangement, with the androgen receptor (AR) locus copy-number stable despite loss of AR transcription. Every PRAD-to-NEPC path funneled through one transient, obligate mesenchymal gateway ( 0.25
While the association between gut microbiota and cholangiocarcinoma (CCA) has been explored, existing research has been limited to bacterial components. The alterations in non-bacterial members (fungi, archaea, and viruses) and their functional characteristics in CCA remain unclear. This study aimed to comprehensively characterize the multi-kingdom gut microbiota and functional profiles in CCA patients and develop a non-invasive diagnostic model. We performed metagenomic sequencing on 700 fecal samples collected from three distinct regions in China, comprising 289 CCA patients, 312 healthy controls, and 99 hepatocellular carcinoma (HCC) patients. Multi-kingdom microbial composition and functional profiles were analyzed. We integrated multiple machine learning algorithms to generate 117 distinct modeling schemes for constructing and screening the optimal CCA diagnostic model. The model was validated across three independent cohorts and tested for specificity against HCC. We also benchmarked the model against established diagnostic approaches by reviewing 15 CCA clinical practice guidelines/consensus statements and their cited evidence and by evaluating model detection in CA19-9-positive and CA19-9-negative patients. Extensive alterations were identified in CCA patients across multi-kingdom and functional layers, including 198 archaeal, 154 bacterial, 78 fungal, and 120 viral species, as well as 278 genes, 99 pathways, and 151 carbohydrate-active enzymes (CAZymes). A panel of 21 multi-kingdom and functional markers demonstrated superior diagnostic accuracy with an average AUC of 91
