Biochemical Pharmacology, Journal Year: 2023, Volume and Issue: 209, P. 115441 - 115441
Published: Jan. 30, 2023
Language: Английский
Theranostics, Journal Year: 2024, Volume and Issue: 14(7), P. 2946 - 2968
Published: Jan. 1, 2024
Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy accelerating discovery process. With evolution spatial (ST) technology emerged as a derivative approach. Spatial hot topic field omics research recent years; it not only provides information on gene expression levels but also offers expression. This shown tremendous potential disease understanding In this article, we introduce analytical strategies review its applications novel target mechanism unravelling. Moreover, discuss current challenges issues that need be addressed. conclusion, new perspective
Language: Английский
Citations
16
Frontiers in Oncology, Journal Year: 2022, Volume and Issue: 12
Published: Oct. 13, 2022
In recent years, spatial transcriptomics (ST) technologies have developed rapidly and been widely used in constructing tissue atlases characterizing spatiotemporal heterogeneity of cancers. Currently, ST has to profile multiple cancer types. Besides, is a benefit for identifying comprehensively understanding special areas such as tumor interface tertiary lymphoid structures (TLSs), which exhibit unique microenvironments (TMEs). Therefore, also shown great potential improve pathological diagnosis identify novel prognostic factors cancer. This review presents advances prospects applications on research based well the challenges.
Language: Английский
Citations
44
Advanced Science, Journal Year: 2023, Volume and Issue: 10(16)
Published: April 7, 2023
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization transcripts and related analyses in various applications for biological systems. By transitioning from conventional studies to "in situ" biology, can provide transcriptome-scale information. Currently, ability simultaneously characterize gene expression profiles cells relevant cellular environment paradigm shift studies. In this review, recent progress its neuroscience cancer are highlighted. Technical aspects existing technologies future directions new developments (as March 2023), computational analysis transcriptome data, application notes studies, discussions regarding multi-omics their expanding roles biomedical emphasized.
Language: Английский
Citations
40
Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)
Published: Nov. 22, 2023
Abstract Spatial transcriptomics (ST) technologies detect mRNA expression in single cells/spots while preserving their two-dimensional (2D) spatial coordinates, allowing researchers to study the distribution of transcriptome tissues; however, joint analysis multiple ST slices and aligning them construct a three-dimensional (3D) stack tissue still remain challenge. Here, we introduce architecture characterization by deep learning (SPACEL) for data analysis. SPACEL comprises three modules: Spoint embeds multiple-layer perceptron with probabilistic model deconvolute cell type composition each spot slice; Splane employs graph convolutional network approach an adversarial algorithm identify domains that are transcriptomically spatially coherent across slices; Scube automatically transforms coordinate systems consecutive stacks together 3D tissue. Comparisons against 19 state-of-the-art methods using both simulated real datasets from various tissues demonstrate outperforms others deconvolution, domain identification, alignment, thus showcasing as valuable integrated toolkit processing
Language: Английский
Citations
37
Biochemical Pharmacology, Journal Year: 2023, Volume and Issue: 209, P. 115441 - 115441
Published: Jan. 30, 2023
Language: Английский
Citations
31