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Medicine, Research & Experimental
Joseph Curry et al.
Summary: This study analyzed the cellular density and intercellular distances of CD8+ and FoxP3+ T-cells in head and neck squamous cell carcinoma samples. The results showed that the distribution of CD8+ and FoxP3+ cells was associated with treatment outcomes and pathological treatment response. Increased CD8+-FoxP3+ intercellular distances were closely related to pathological treatment response.
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Medicine, Research & Experimental
Yuyu Zhu et al.
Summary: The study identified SHP2 as a novel regulator of psoriasis, showing that SHP2 inhibition can reduce skin inflammation and may be a promising therapeutic approach for psoriatic patients.
EMBO MOLECULAR MEDICINE
(2022)
Review
Dermatology
Georgios Theocharidis et al.
Summary: Single-cell technologies, particularly single-cell RNA sequencing, have revolutionized research in skin biology by enabling the assessment of cell-to-cell variation and elucidation of cellular heterogeneity in human diseases. These technologies have found wide applications in inflammatory skin disorders, fibrotic skin diseases, wound healing complications, and cutaneous neoplasms.
EXPERIMENTAL DERMATOLOGY
(2022)
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Dermatology
Joonho Shim et al.
Summary: In this study, single-cell RNA sequencing and spatial transcriptomics were used to uncover the underlying pathophysiology of keloids. The results revealed cellular heterogeneity, cell-cell interactions, and mesenchymal activation of endothelial cells, which may play a role in the development of keloids.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
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Dermatology
Maija Kiuru et al.
Summary: Early diagnosis of melanoma is crucial for patient survival. However, the biomarkers and origin of early melanoma evolution, such as keratinocytes, within the tumor and its microenvironment are still unclear. This study used spatial transcript profiling to measure RNA expression in patient-derived tissue sections and found distinct expression patterns across cell types and tumor types during melanoma development. The study also discovered the expression of S100A8 by keratinocytes in the tumor microenvironment, suggesting it could be an early indicator of melanoma development. These findings provide a framework for studying gene expression in archival tissue and the characterization of tumor microenvironment interactions.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
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Multidisciplinary Sciences
S. Vickovic et al.
Summary: The spatial organization of cells and molecules is crucial for tissue function and disease. Spatial transcriptomics, a technique for capturing and locating RNA in tissues, has been advanced with the development of a fully automated platform called Spatial Multi-Omics (SM-Omics). SM-Omics combines spatial transcriptomics and antibody-based protein measurement, allowing high-throughput analysis of multiple omics in a short time.
NATURE COMMUNICATIONS
(2022)
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Multidisciplinary Sciences
Georgios Theocharidis et al.
Summary: This study utilizes single-cell RNA sequencing to reveal the distribution of specific populations of fibroblasts and macrophages in diabetic foot ulceration (DFU) patients and identifies their crucial roles in wound healing.
NATURE COMMUNICATIONS
(2022)
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Biology
Sanja Vickovic et al.
Summary: Spatial transcriptomics is used to study the local interactions in synovial tissue of rheumatoid arthritis patients. The results provide valuable insights into the spatial organization of cell populations and inflammation associated with rheumatoid arthritis.
COMMUNICATIONS BIOLOGY
(2022)
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Biochemistry & Molecular Biology
Ao Chen et al.
Summary: Spatially resolved transcriptomic technologies enable us to study complex biological processes such as mammalian embryogenesis. However, current methods have limitations in resolution, gene capture, and field of view, which hinders their systematic application to large and three-dimensional mid- and late-gestation embryos. In this study, we developed Stereo-seq, a spatially enhanced resolution omics-sequencing method, by combining DNA nanoball-patterned arrays and in situ RNA capture. We used Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas, MOSTA, which provides single cell resolution and high sensitivity for mapping the kinetics and directionality of transcriptional variation during mouse organogenesis. By utilizing this atlas, we investigated the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues like the dorsal midbrain. Our panoramic atlas will facilitate in-depth research into long-standing questions about normal and abnormal mammalian development.
Review
Biochemical Research Methods
Lambda Moses et al.
Summary: This article reviews spatial transcriptomics research since 1987 and provides a detailed analysis of trends and applications of related technologies and methods. The study offers historical context and guidance for current research.
Article
Biochemistry & Molecular Biology
Jana Biermann et al.
Summary: This study provides comprehensive insights into the biology of melanoma brain metastasis (MBM) and reveals the distinct characteristics of cancer cells in MBM, including chromosomal instability and neuronal-like cell state. The study also identifies the presence of monocyte-derived macrophages and dysfunctional T cells in MBM, as well as the geographic differences in cancer immune evasion. These findings contribute to a better understanding of MBM and have implications for future therapeutic exploration.
Article
Multidisciplinary Sciences
A. Schabitz et al.
Summary: This study investigates non-communicable inflammatory skin diseases (ncISD) through spatial transcriptomics and finds abundant heterogeneous immune cell infiltrates. Despite the presence of immune cell infiltration, the number of pathogenic disease promoting cytokine transcripts is relatively low in lesional skin sections, and their expression is limited to lesional skin in a disease-specific pattern.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Andreas Mund et al.
Summary: Mass spectrometry-based proteomics is a powerful technology for quantifying proteins in cells or tissues. Single-cell transcriptomes are influenced by stochastic noise due to low transcript numbers, whereas single-cell proteomes appear to be more complete. With the combination of imaging and spatial transcriptomics, the spatial organization of cells in tissues can be studied alongside ultra-sensitive proteomics.
Article
Multidisciplinary Sciences
Laura Yerly et al.
Summary: By utilizing single-cell and spatial transcriptomics, this study identifies the cellular contributors and their transcriptional reprogramming in the spatial organization of the invasive niche in basal cell carcinomas. The findings demonstrate the potential of integrated multi-omics approaches in deciphering cancer-specific invasive properties and developing targeted therapies.
NATURE COMMUNICATIONS
(2022)
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Medicine, Research & Experimental
Yan Ding et al.
Summary: This study reveals that SHP2 and neutrophils play crucial roles in the progression of psoriasis. SHP2 promotes the formation of NETs in neutrophils, which enhances the inflammatory response and aggravates psoriasis. The findings suggest that SHP2 may be a promising therapeutic target for psoriasis.
Editorial Material
Biochemical Research Methods
Vivien Marx
Summary: Nature Methods has named spatially resolved transcriptomics as Method of the Year 2020.
Article
Biochemistry & Molecular Biology
Ruben Dries et al.
Summary: Spatial transcriptomics is a rapidly growing field that characterizes tissue organization and architecture comprehensively at single-cell or subcellular resolution, providing a foundation for mechanistic understanding of biological processes. Computational methods play crucial roles in extracting biological signals from data, while various approaches have been developed to overcome technology-specific limitations. Downstream analysis tools quantify spatial organization and cell-cell communications, and integrative pipelines assemble multiple tools for convenient data analysis.
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Biochemical Research Methods
Tommaso Biancalani et al.
Summary: Tangram is a versatile tool that aligns single-cell and single-nucleus RNA-seq data to spatially resolved transcriptomics data using deep learning. By addressing the loss of spatial information in single-cell data and overcoming technical limitations, this method demonstrates genome-wide anatomically integrated spatial mapping at single-cell resolution on healthy mouse brain tissue.
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Multidisciplinary Sciences
Deshka S. Foster et al.
Summary: This study introduces a multimodal -omics platform to comprehensively study cell populations involved in wound healing across both time and space. By analyzing single cell chromatin landscapes and gene expression states, potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury have been revealed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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Multidisciplinary Sciences
Casey A. Thornton et al.
Summary: High-throughput single-cell epigenomic assays may lose spatial orientation, but sciMAP-ATAC is introduced to produce spatially resolved single-cell ATAC-seq data with retained positional information for assessing cell types and chromatin states in different tissues.
NATURE COMMUNICATIONS
(2021)
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Multidisciplinary Sciences
Miranda V. Hunter et al.
Summary: By integrating spatially resolved transcriptomics and single-cell RNA-seq, this study reveals a distinct cilia-enriched interface cell state at the tumor-microenvironment boundary in melanoma, suggesting a conserved feature in human melanoma. This interface is regulated by ETS-family transcription factors and demonstrates the power of spatially resolved transcriptomics in uncovering mechanisms that allow tumors to adapt to new environments.
NATURE COMMUNICATIONS
(2021)
Review
Dermatology
Shishiria R. Jartarkar et al.
Summary: Advancements in dermatology have led to newer technologies such as confocal microscopy, digital photographic imaging, optical coherence tomography, high frequency ultrasonography, and artificial intelligence for improved diagnosis and therapy. The use of artificial intelligence/machine-learning software is expected to have a significant impact on dermatological practice.
JOURNAL OF COSMETIC DERMATOLOGY
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Biochemistry & Molecular Biology
Chun-Seok Cho et al.
Summary: Seq-Scope is a spatial barcoding technology with resolution comparable to an optical microscope, allowing visualization of spatial transcriptome heterogeneity at multiple histological scales from tissue sections. The technology works by processing DNA clusters to expose RNA-capture moiety, making cell analysis simpler and more accurate.
Review
Multidisciplinary Sciences
Anjali Rao et al.
Summary: Spatial transcriptomic technologies have revolutionized the field of biological research by systematically measuring gene expression levels throughout tissue space. In addition to generating biological insights, these technologies can be used for exploratory data analysis, hypothesis testing, and integration with other data modalities, providing a framework for understanding tissue organization.
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Immunology
Feiyang Ma et al.
Summary: The study identified a set of genes involved in antimicrobial responses that are differentially expressed in reversal reactions (RRs) lesions compared to lepromatous leprosy (L-lep) lesions, regulated by interferon-gamma and interleukin-1 beta. By integrating spatial coordinates of key cell types and antimicrobial gene expression, a map depicting the organized architecture of granulomas in RR and T-lep lesions was constructed, showing compositional and functional layers contributing to the antimicrobial response. Modlin and colleagues utilized single-cell RNA sequencing with cellular spatial mapping to examine the architecture of granulomas in leprosy lesions, providing insights from localized disease (tuberculoid leprosy, reversal reaction) to progressive infection (lepromatous leprosy).
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Multidisciplinary Sciences
Sanjay R. Srivatsan et al.
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