Spatial Transcriptomics: Technical Aspects of Recent Developments and Their Applications in Neuroscience and Cancer Research
Sign Up to like & getrecommendations! Published in 2023 at "Advanced Science"
DOI: 10.1002/advs.202206939
Abstract: Spatial transcriptomics is a newly emerging field that enables high‐throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional biological studies to “in situ”… read more here.
Keywords: transcriptomics technical; technical aspects; neuroscience cancer; applications neuroscience ... See more keywords
Multiscale Cell–Cell Interactive Spatial Transcriptomics Analysis
Sign Up to like & getrecommendations! Published in 2025 at "Advanced Science"
DOI: 10.1002/advs.202508358
Abstract: Spatial transcriptomics data analysis integrates gene expression profiles with their corresponding spatial locations to identify spatial domains, infer cell‐type dynamics, and detect gene expression patterns within tissues. However, the current spatial transcriptomics analysis neglects the… read more here.
Keywords: cell cell; spatial transcriptomics; analysis; multiscale cell ... See more keywords
Spatial Transcriptomics and snRNA-seq Expose CAF Niches Orchestrating Dual Stromal-Immune Barriers in Hepatocellular Carcinoma.
Sign Up to like & getrecommendations! Published in 2025 at "Advanced science"
DOI: 10.1002/advs.202514661
Abstract: Hepatocellular carcinoma (HCC) exhibits profound spatial heterogeneity driving therapeutic resistance, while the role of cancer‐associated fibroblasts (CAFs) in orchestrating immunosuppressive niches remains incompletely defined. This study integrates single‐nucleus RNA sequencing (snRNA‐seq) and spatial transcriptomics (stRNA‐seq)… read more here.
Keywords: snrna seq; spatial transcriptomics; hepatocellular carcinoma; cell ... See more keywords
Spatial Transcriptomics of Patients With Kaposi Sarcoma Identifies Mechanisms of Immune Evasion
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Medical Virology"
DOI: 10.1002/jmv.70728
Abstract: To identify the cell types that are infected with KSHV and the immune interactions in Kaposi sarcoma (KS) lesions, we performed spatial transcriptomics with seven KS skin tumors. We used a single‐cell RNA‐sequencing reference data… read more here.
Keywords: spatial transcriptomics; kaposi sarcoma; transcriptomics patients; expression ... See more keywords
Improving Spatial Transcriptomics with Membrane‐Based Boundary Definition and Enhanced Single‐Cell Resolution
Sign Up to like & getrecommendations! Published in 2025 at "Small Methods"
DOI: 10.1002/smtd.202401056
Abstract: Accurately defining cell boundaries for spatial transcriptomics is technically challenging. The current major approaches are nuclear staining or mathematical inference, which either exclude the cytoplasm or determine a hypothetical boundary. Here, a new method is… read more here.
Keywords: membrane based; spatial transcriptomics; single cell; cell resolution ... See more keywords
STExplore: An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data
Sign Up to like & getrecommendations! Published in 2025 at "Small Methods"
DOI: 10.1002/smtd.202401272
Abstract: Spatial transcriptomics revolutionizes the understanding of tissue organization and cellular interactions by combining high‐resolution spatial information with gene expression profiles. Existing spatial transcriptomics analysis platforms face challenges in accommodating diverse techniques, integrating multi‐omics data, and… read more here.
Keywords: spatial transcriptomics; online platform; analysis; integrated online ... See more keywords
Unraveling Tissue Complexity Through Single‐Cell and Spatial Transcriptomics
Sign Up to like & getrecommendations! Published in 2025 at "Small Methods"
DOI: 10.1002/smtd.202500710
Abstract: We are pleased to present this special section of Small Methods , which highlights the rapidly advancing fields of single-cell and spatial transcriptomics. Single-cell transcriptomics and spatial transcriptomics have emerged as transformative tools for high-resolution… read more here.
Keywords: spatial transcriptomics; single cell; biology; cell ... See more keywords
Navigating the landscapes of spatial transcriptomics: How computational methods guide the way
Sign Up to like & getrecommendations! Published in 2024 at "Wiley Interdisciplinary Reviews: RNA"
DOI: 10.1002/wrna.1839
Abstract: Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single‐cell, multi‐cellular, or sub‐cellular resolution, while retaining the information of geometric localizations of cells in complex… read more here.
Keywords: transcriptomics computational; spatial transcriptomics; computational methods; landscapes spatial ... See more keywords
Spatial transcriptomics in cancer research and potential clinical impact: a narrative review
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Cancer Research and Clinical Oncology"
DOI: 10.1007/s00432-024-05816-0
Abstract: Spatial transcriptomics (ST) provides novel insights into the tumor microenvironment (TME). ST allows the quantification and illustration of gene expression profiles in the spatial context of tissues, including both the cancer cells and the microenvironment… read more here.
Keywords: oncology; cancer; spatial transcriptomics; review ... See more keywords
Neurobiological subtypes of adolescent depression: a multimodal integration of morphometric similarity network and spatial transcriptomics
Sign Up to like & getrecommendations! Published in 2025 at "Molecular Psychiatry"
DOI: 10.1038/s41380-025-03133-7
Abstract: Adolescent major depressive disorder (AMDD) is a heterogeneous condition with rising global prevalence and limited treatment efficacy. This study integrates morphometric similarity networks (MSN) and spatial transcriptomics to identify neurobiologically distinct AMDD subtypes and their… read more here.
Keywords: spatial transcriptomics; network; adolescent depression; morphometric similarity ... See more keywords
Role for kappa-opioid system in stress-induced cocaine use uncovered with PET
Sign Up to like & getrecommendations! Published in 2019 at "Neuropsychopharmacology"
DOI: 10.1038/s41386-019-0512-7
Abstract: 1. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenomewide association studies. Genome Biol. 2014;15:R31. 2. Zheng SC, Breeze CE, Beck S, Teschendorff AE. Identification of differentially methylated cell types in epigenome-wide… read more here.
Keywords: science; spatial transcriptomics; opioid system; role kappa ... See more keywords