Spatial oncology: Translating contextual biology to the clinic

Cancer Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

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Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 6, 2025

Language: Английский

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Protein molecular structures of USP53, NPY2R, and DCTN1-AS1 and impact on tumors: Analysis of prognostic biomarkers for diffuse large B-cell lymphoma

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: 297, P. 139910 - 139910

Published: Jan. 14, 2025

Language: Английский

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Clonal Heterogeneity in Human Pancreatic Ductal Adenocarcinoma and Its Impact on Tumor Progression

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 15, 2025

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer characterized by profound desmoplasia and cellular heterogeneity, which cannot be fully resolved using traditional bulk sequencing approaches. To understand the contribution of this heterogeneity to PDAC biology, we analyzed a large cohort primary human samples (n = 62), profiling 443,451 single cells 53,236 spatial transcriptomic spots combined single-cell RNA transcriptomics approach. Our analysis revealed significant intratumoral with multiple genetically distinct neoplastic clones co-existing within individual tumors. These exhibited diverse transcriptional states subtype profiles, challenging binary classification into basal classical subtypes; instead, our findings support continuum influenced clonal evolution organization. Additionally, these each interacted uniquely surrounding cell types in tumor microenvironment. Phylogenetic uncovered rare but consistent classical-to-basal transition associated MYC amplification immune response depletion, were validated experimentally, suggesting mechanism driving emergence more phenotype. Spatial analyses further dispersed enriched for epithelial-to-mesenchymal (EMT) activity suppression, correlating metastatic potential colonization lymph node niches. tended toward phenotype, contributing disease progression. highlight critical role diversity, plasticity, TME interactions shaping biology. This work provides new insights molecular offers avenues therapeutic intervention targeting mechanisms metastasis.

Language: Английский

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From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

Molecular Cancer, Journal Year: 2025, Volume and Issue: 24(1)

Published: March 3, 2025

Language: Английский

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Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 14, 2025

Analyses of patient-derived cell lines have greatly enhanced discovery molecular biomarkers and therapeutic targets. However, characterization cellular morphological properties is limited. We studied morphologies human pancreatic adenocarcinoma (PDAC) their associations with drug sensitivity, gene expression, functional properties. By integrating live spatial mRNA imaging, we identified KRAS inhibitor-induced changes specific for drug-resistant cells that correlated expression changes. then categorized a large panel PDAC into (e.g., polygonal, irregular, spheroid) organizational tightly aggregated, multilayered, dispersed) subtypes found differences in targeting potential, metastatic proclivity. In tissues, prognostic signatures associated distinct cancer organization patterns. summary, highlight the potential information rapid, cost-effective assays to aid precision oncology efforts leveraging vitro models tissues.

Language: Английский

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Immune-Based Therapies in Pancreatic Cancer: a Systematic Review of Ongoing Clinical Trials (2020–2022)

Journal of Gastrointestinal Cancer, Journal Year: 2025, Volume and Issue: 56(1)

Published: April 22, 2025

Language: Английский

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InSituCor: exploring spatially correlated genes conditional on the cell type landscape

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 24, 2025

Language: Английский

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Learning tissue representation by identification of persistent local patterns in spatial omics data

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 30, 2025

Language: Английский

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Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 25, 2024

Abstract Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collected clinical samples from three cancer types – colon adenocarcinoma, hepatocellular carcinoma, ovarian generated serial tissue sections evaluation. Using these uniformly processed samples, data across five high-throughput platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, FF, CosMx 6K, Xenium 5K. establish ground truth datasets, profiled proteins adjacent corresponding to all using CODEX performed single-cell RNA sequencing on the same samples. Leveraging manual cell segmentation detailed annotations, systematically assessed each platform’s performance key metrics, including capture sensitivity, specificity, diffusion control, segmentation, annotation, clustering, transcript-protein alignment CODEX. The generated, processed, annotated multi-omics dataset is valuable advancing computational method development biological discoveries. accessible via SPATCH, a user-friendly web server visualization download ( http://spatch.pku-genomics.org/ ).

Language: Английский

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