Computational solutions for spatial transcriptomics

Kleino, Iivari; Frolovaitė, Paulina; Suomi, Tomi; Elo, Laura L.

doi:10.1016/j.csbj.2022.08.043

Cited by 72 publications

(45 citation statements)

References 152 publications

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“…A volcano plot was drawn to represent the up-regulated and down-regulated genes under acute UVB exposure and chronic UVB exposure to determine the probabilistic significance [ 37 ]. Uniform manifold approximation and projection computed that the UVB exposure samples were distinct from the control samples generally for selection [ 38 ]. Heatmap research analysis was enforced to illustrate the differences between expression data of DEGs under acute and chronic UVB exposure.…”

Section: Acute and Chronic Uvb Exposure-dependent Expression Analysismentioning

confidence: 99%

A Genomic Approach to Identify the Different between Acute and Chronic UVB Exposures in the Causation of Inflammation and Cancer

et al. 2022

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As a principal component of solar radiation, ultraviolet B (UVB) exposure can be harmful depending on the duration and intensity because the human body can easily be exposed to it. Many studies have demonstrated that UVB causes a series of inflammatory and other skin disorders. UVB has been classified as the Group 1 carcinogen by the International Agency for Research on Cancer. Diverse studies have focused on UVB exposure but the complex perspective of acute and chronic UVB exposure is still lacking. This review presents the differences between acute and chronic exposure to UVB and summarizes public information in terms of toxicogenomic characteristics. We also demonstrated the differences between adverse effects of acute and chronic UVB exposure on the skin system. From the published literatures, we compared the biological pathways predict of the adverse effects caused by each UVB exposure type. Furthermore, our review not only clarifies the differences in each UVB exposure network but also suggests major hub genes related to cellular mechanisms and diseases that are thought to be affected by acute and chronic UVB exposure.

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Section: Acute and Chronic Uvb Exposure-dependent Expression Analysismentioning

confidence: 99%

A Genomic Approach to Identify the Different between Acute and Chronic UVB Exposures in the Causation of Inflammation and Cancer

et al. 2022

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“…1D and Supplemental Videos). Importantly, UMAP analysis 14,15 computed using immunohistochemistry-based cell identification (Fig. 1E, right panel) matched that of cell identification via Insitutype (Fig.…”

mentioning

confidence: 66%

Spatial molecular imaging of the human type 2 diabetic islet

Kolar

Ross

Killingbeck

et al. 2023

Preprint

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The islets of Langerhans are complex micro-organs comprised of multiple cell types essential for the maintenance of glucose homeostasis. The endocrine cell types of the islets engage in intimate, intercellular communication that is necessary for normal secretory activity. Disruption of this intercellular communication, which is at least partially dependent upon the spatial organization of individual islets, leads to secretory dysfunction and exacerbation of the symptomology of disease states such as type 2 diabetes. However, the molecular determinants of the mechanisms underlying disrupted intercellular communication remain incompletely understood. Herein we describe the utilization of spatial molecular imaging to interrogate transcriptomic changes associated with the transition from the obese, prediabetic state to overt type 2 diabetes. Using this technology, we verified previously reported findings regarding islet composition in the obese and type 2 diabetic state, including loss of beta cells and expansion of alpha cell mass. In addition, we identified changes in the islet neighborhood that could have implications for the function of islet endocrine cells. To our knowledge, this is the first study utilizing spatial molecular imaging to investigate single cell transcriptomics of individual islets. Further exploration of the intersection of islet architecture and gene expression using this and other, related technologies, is expected to yield novel insights into the mechanisms underlying the development and progression of metabolic diseases like type 2 diabetes.

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“…After that, the amplicons are cross-linked to the cell matrix to prevent translocation and the barcodes are detected by fluorescence in situ hybridization (FISH) or sequenced in situ to obtain genetic information about the bases they encode. BOLORAMIS is more sensitive than non-targeting methods like FISSEQ, Slide-seq, and high-definition spatial transcriptomic (HDST) because it targets specific genes of interest in a highly multiplexed manner (Kleino et al, 2022;Moffitt et al, 2022). By employing SplintR ligase, BOLORAMIS eliminates the need for RT in comparison to in situ padlock probe methods, thereby reducing the potential for detection bias and the cost of experiments associated.…”

Section: In Situ Sequencing-based Spatial Transcriptome Technologymentioning

confidence: 99%

Application of spatial transcriptome technologies to neurological diseases

Zhang²,

Chen³

et al. 2023

Front. Cell Dev. Biol.

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Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.

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Computational solutions for spatial transcriptomics

Cited by 72 publications

References 152 publications

A Genomic Approach to Identify the Different between Acute and Chronic UVB Exposures in the Causation of Inflammation and Cancer

A Genomic Approach to Identify the Different between Acute and Chronic UVB Exposures in the Causation of Inflammation and Cancer

Spatial molecular imaging of the human type 2 diabetic islet

Application of spatial transcriptome technologies to neurological diseases

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