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/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T18/A_57.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T12/A_24.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T14/A_27.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/ACM67/A_42.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/ACM36/A_53.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/ACM67/A_18.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T14/A_43.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T12/A_32.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/ACM36/A_61.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T14/A_35.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/ACM67/A_34.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322/FILES/RAW_FILES/T12/A_40.rawprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15322<p>Metabolite identification used accurate-mass MS1 features from MSI and fragment-ion MS/MS data from LC-MS/MS analysis of adjacent tissue sections. Features were compared with HMDB, METLIN, and MJDB; metabolite classification and pathway enrichment used KEGG, HMDB, and ClassyFire.</p>MetaboLightsPublicMS Imaging - negativeSingle-cell and spatial multi-omics reveal a recurrent multicellular niche at the tumor-stroma interface in multidrug resistance.fudan universityKangjie Shenskin of bodymass spectrometry assayHomo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS15322Kangjie Shen. fudan university. kjshen21@m.fudan.edu.cn.<p>Thermo RAW files were converted to imzML format using imzMLConverter and imported into the Cardinal package in R for background correction, peak alignment, total-peak-area normalization, smoothing, and molecular imaging. UMAP, PCA, PLS-DA, and OPLS-DA were used for downstream analyses, including ropls v1.40.0 and the R stats package.</p>Multidrug resistance statuskjshen21@m.fudan.edu.cn<p>Six human malignant melanoma tissue samples (three treatment-naive and three multidrug-resistant) were selected from the Visium cohort for AFADESI mass spectrometry imaging.</p>Metabolomics<p>Ten-micrometer cryosections mounted on Superfrost Plus slides were stained with hematoxylin and eosin and imaged before AFADESI mass spectrometry imaging.</p><p>Frozen tissue was thawed at -20 °C for 30 min, embedded in 5% sodium carboxymethyl cellulose, and cryosectioned at 10 μm using a Leica CM1950. Sections were mounted on Superfrost Plus slides, stained with hematoxylin and eosin, imaged, and stored at -80 °C. Before MSI, sections were dried at -20 °C for 30 min and equilibrated to room temperature.</p>Metabolomicsdesorption electrospray ionisation mass spectrometryQ Exactive HF-XThermo Fisher Scientificuntargeted analysisHomo sapiensmelanomaexperimental blankskin of bodyMetabolomicsdesorption electrospray ionisation mass spectrometryQ Exactive HF-XThermo Fisher Scientificuntargeted analysisHomo sapiensmelanomaexperimental blankskin of body<p>AFADESI mass spectrometry imaging was performed in negative-ion mode on a Thermo Scientific Q Exactive HF-X with a desorption electrospray ionization source. The spray solvent was 80% acetonitrile and 20% water (v/v) at 4 μL/min; spray voltage was -4500 V; capillary temperature was 350 °C; scan range was m/z 70-1050; and resolving power was 60,000. Xcalibur was used for data processing.</p>falseSingle-cell and spatial multi-omics reveal a recurrent multicellular niche at the tumor-stroma interface in multidrug resistanceMulti-drug resistance (MDR) is an almost inevitable end point of cancer therapy, driving rapid tumor progression, yet its evolutionary logic remains unclear because MDR tumors are rarely resected. Using paired therapy-naive and MDR melanoma specimens from a clinical trial, integrated with single-cell and spatial multi-omics and evaluated together with datasets from ten additional cancer types, we identify a recurrent MDR-associated spatial nexus along the tumor-stroma interface. This niche juxtaposes CXCL14+ inflammatory cancer-associated fibroblasts (iCAFs), TREM2+ tumor-associated macrophages (TAMs), and AXL+ dedifferentiated tumor cells, and is accompanied by loss of tumor-reactive CXCL13+ CD8+ T cells. In vitro, CXCL14 promotes macrophage migration and TREM2 induction, while TREM2+ TAMs suppress CXCL13+ CD8+ T cells via CD86-CTLA4 signaling. TREM2+ TAMs also promote tumor dedifferentiation through oleic acid-driven GAS6-AXL activation. We develop an FAP/TREM2-targeting bispecific antibody to disrupt this spatial nexus and restore therapeutic sensitivity in MDR patient-derived xenograft models with favorable safety.2027-08-132026-08-13MTBLS15322