Nat Commun. 2025 Sep 25;16(1):8388. doi: 10.1038/s41467-025-63050-9.

ABSTRACT

Spatial technologies examining the cell and tissue microenvironment at near single-cell resolution are revealing important molecular insights. However, few tools enable integrated, interactive analysis of spatial-omics with tissue morphology in the same functional tissue unit. Here, we present FUSION (Functional Unit State Identification in Whole Slide Images), a web-based platform for visualizing and analyzing spatial-omics data with high-resolution histology. FUSION provides workflows for assessing cell compositions, quantitative morphometrics, and comparative tissue analyses. We demonstrate applicability across spatial assays, including 10x Visium, Visium HD, 10x Xenium, Cell DIVE, and PhenoCycler, applied to healthy and diseased tissues from kidney, small intestine, lung, and skin in the Human BioMolecular Atlas Program. FUSION is cloud-based, open-source, and accessible at https://fusion.hubmapconsortium.org/ , hosting over 50 paired datasets and tutorials. In a series of use cases, we show its capacity to distinguish renal glomeruli injury states, quantify morphometric changes, and characterize fibrosis with immune infiltration.

PMID:40998789 | PMC:PMC12462499 | DOI:10.1038/s41467-025-63050-9

J Transl Med. 2025 Aug 7;23(1):877. doi: 10.1186/s12967-025-06725-7.

ABSTRACT

BACKGROUND: Gastric cancer (GC) is characterized by significant intertumoral heterogeneity, which often leads to the development of resistance to platinum-based chemotherapy. Combining platinum drugs with other therapeutic strategies may improve treatment efficacy; however, the mechanisms underlying platinum resistance in GC remain unclear.

METHODS: Key genes related to platinum resistance in GC were selected from the platinum resistance gene database and GC resistance datasets. The Similarity Network Fusion (SNF) algorithm was employed, along with prognosis-related methylation data and somatic mutation data, to classify the molecular subtypes of GC based on GC platinum resistance genes. Gene expression profiles, prognosis, immune cell infiltration, chemotherapy sensitivity, and immunotherapy responsiveness were comprehensively evaluated for each subtype. Localization and functional evaluation were conducted at the single-cell and spatial transcriptomics levels, and predictive models were developed using machine learning techniques. These functional differences in platinum resistance gene models were further explored in GC. Moreover, experimental validation was conducted to elucidate the mechanisms of key genes involved in platinum resistance in GC.

RESULTS: Stomach adenocarcinoma (STAD) patients were classified into three subtypes using the SNF algorithm and multiomics data. Patients with subtype CS2 exhibited a significantly poorer prognosis than those with subtypes CS1 and CS3 (p < 0.05). Subtype CS1 was characterized as immune-deprived, CS2 as stroma-enriched, and CS3 as immune-enriched. Patients with subtype CS2 also exhibited the most adverse therapeutic responses to docetaxel, cisplatin, and gemcitabine. Single-cell analysis revealed high enrichment of M1 module cells with elevated expression of resistance genes, including the transcription factor KLF9. Spatial transcriptomic analysis further confirmed the independent spatial distribution of malignant cells with high expression of drug resistance genes (DRGs). Predictive models based on machine learning demonstrated excellent prognostic performance. Patients in the high DRG group also exhibited poorer responses to immunotherapy. Cellular experiments revealed that KLF9 overexpression significantly inhibited the proliferation of AGS cells (p < 0.05), reduced their resistance to platinum-based drugs, and markedly decreased the levels of inflammatory cytokines in them.

CONCLUSION: KLF9 was identified as a promising therapeutic target for overcoming platinum resistance in GC, warranting further investigation into its role and potential clinical applications.

PMID:40775648 | PMC:PMC12330134 | DOI:10.1186/s12967-025-06725-7