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SPADE:面向特定领域细胞类型估计的空间去卷积。

SPADE: spatial deconvolution for domain specific cell-type estimation.

机构信息

Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, 85721, USA.

College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.

出版信息

Commun Biol. 2024 Apr 17;7(1):469. doi: 10.1038/s42003-024-06172-y.


DOI:10.1038/s42003-024-06172-y
PMID:38632414
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11024133/
Abstract

Understanding gene expression in different cell types within their spatial context is a key goal in genomics research. SPADE (SPAtial DEconvolution), our proposed method, addresses this by integrating spatial patterns into the analysis of cell type composition. This approach uses a combination of single-cell RNA sequencing, spatial transcriptomics, and histological data to accurately estimate the proportions of cell types in various locations. Our analyses of synthetic data have demonstrated SPADE's capability to discern cell type-specific spatial patterns effectively. When applied to real-life datasets, SPADE provides insights into cellular dynamics and the composition of tumor tissues. This enhances our comprehension of complex biological systems and aids in exploring cellular diversity. SPADE represents a significant advancement in deciphering spatial gene expression patterns, offering a powerful tool for the detailed investigation of cell types in spatial transcriptomics.

摘要

理解不同细胞类型在其空间背景下的基因表达是基因组学研究的一个关键目标。我们提出的 SPADE(空间去卷积)方法通过将空间模式纳入细胞类型组成的分析中来解决这个问题。该方法结合了单细胞 RNA 测序、空间转录组学和组织学数据,以准确估计不同位置的细胞类型比例。我们对合成数据的分析表明,SPADE 能够有效地辨别细胞类型特异性的空间模式。当应用于真实数据集时,SPADE 提供了对细胞动态和肿瘤组织组成的深入了解。这增强了我们对复杂生物系统的理解,并有助于探索细胞多样性。SPADE 代表了破译空间基因表达模式的重大进展,为空间转录组学中对细胞类型的详细研究提供了强大的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/f3ded03ec2a1/42003_2024_6172_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/6d98021902b7/42003_2024_6172_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/eb885a798da0/42003_2024_6172_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/c8353c1c7fe0/42003_2024_6172_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/0e996d6dd95c/42003_2024_6172_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/8227ba77aace/42003_2024_6172_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/f3ded03ec2a1/42003_2024_6172_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/6d98021902b7/42003_2024_6172_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/eb885a798da0/42003_2024_6172_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/c8353c1c7fe0/42003_2024_6172_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/0e996d6dd95c/42003_2024_6172_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/8227ba77aace/42003_2024_6172_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/83ac/11024133/f3ded03ec2a1/42003_2024_6172_Fig6_HTML.jpg

相似文献

[1]
SPADE: spatial deconvolution for domain specific cell-type estimation.

Commun Biol. 2024-4-17

[2]
SPADE: Spatial Deconvolution for Domain Specific Cell-type Estimation.

bioRxiv. 2023-4-17

[3]
Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach.

BMC Bioinformatics. 2025-1-31

[4]
Dual decoding of cell types and gene expression in spatial transcriptomics with PANDA.

Nucleic Acids Res. 2024-11-11

[5]
STPDA: Leveraging spatial-temporal patterns for downstream analysis in spatial transcriptomic data.

Comput Biol Chem. 2024-10

[6]
SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning.

Commun Biol. 2023-4-7

[7]
STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution.

Brief Bioinform. 2024-11-22

[8]
Spatially Aware Domain Adaptation Enables Cell Type Deconvolution from Multi-Modal Spatially Resolved Transcriptomics.

Small Methods. 2024-12-2

[9]
Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks.

Brief Bioinform. 2024-5-23

[10]
EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning.

Bioinformatics. 2023-1-1

引用本文的文献

[1]
High-resolution mapping of single cells in spatial context.

Nat Commun. 2025-7-15

[2]
Deconvolution and inference of spatial communication through optimization algorithm for spatial transcriptomics.

Commun Biol. 2025-2-14

[3]
Spall: accurate and robust unveiling cellular landscapes from spatially resolved transcriptomics data using a decomposition network.

BMC Bioinformatics. 2024-12-18

[4]
IL1RAP Blockade With a Monoclonal Antibody Reduces Cardiac Inflammation and Preserves Heart Function in Viral and Autoimmune Myocarditis.

Circ Heart Fail. 2024-12

[5]
Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics.

Bioinformatics. 2024-10-1

本文引用的文献

[1]
Semi-reference based cell type deconvolution with application to human metastatic cancers.

NAR Genom Bioinform. 2023-12-23

[2]
A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology.

Front Immunol. 2022

[3]
Spatial transcriptomics technology in cancer research.

Front Oncol. 2022-10-13

[4]
Computational solutions for spatial transcriptomics.

Comput Struct Biotechnol J. 2022-9-1

[5]
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies.

Genome Biol. 2022-8-4

[6]
An introduction to spatial transcriptomics for biomedical research.

Genome Med. 2022-6-27

[7]
A comprehensive comparison on cell-type composition inference for spatial transcriptomics data.

Brief Bioinform. 2022-7-18

[8]
Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor.

Nat Commun. 2022-6-6

[9]
Spatially informed cell-type deconvolution for spatial transcriptomics.

Nat Biotechnol. 2022-9

[10]
Causal mapping of human brain function.

Nat Rev Neurosci. 2022-6

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