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Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network

Spatially resolved transcriptomics (SRT) provides an unprecedented opportunity to investigate the complex and heterogeneous tissue organization. However, it is challenging for a single model to learn an effective representation within and across spatial contexts. To solve the issue, we develop a nov...

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Autores principales: Li, Xinxing, Huang, Wendong, Xu, Xuan, Zhang, Hong-Yu, Shi, Qianqian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10248005/
https://www.ncbi.nlm.nih.gov/pubmed/37303949
http://dx.doi.org/10.3389/fgene.2023.1202409
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author Li, Xinxing
Huang, Wendong
Xu, Xuan
Zhang, Hong-Yu
Shi, Qianqian
author_facet Li, Xinxing
Huang, Wendong
Xu, Xuan
Zhang, Hong-Yu
Shi, Qianqian
author_sort Li, Xinxing
collection PubMed
description Spatially resolved transcriptomics (SRT) provides an unprecedented opportunity to investigate the complex and heterogeneous tissue organization. However, it is challenging for a single model to learn an effective representation within and across spatial contexts. To solve the issue, we develop a novel ensemble model, AE-GCN (autoencoder-assisted graph convolutional neural network), which combines the autoencoder (AE) and graph convolutional neural network (GCN), to identify accurate and fine-grained spatial domains. AE-GCN transfers the AE-specific representations to the corresponding GCN-specific layers and unifies these two types of deep neural networks for spatial clustering via the clustering-aware contrastive mechanism. In this way, AE-GCN accommodates the strengths of both AE and GCN for learning an effective representation. We validate the effectiveness of AE-GCN on spatial domain identification and data denoising using multiple SRT datasets generated from ST, 10x Visium, and Slide-seqV2 platforms. Particularly, in cancer datasets, AE-GCN identifies disease-related spatial domains, which reveal more heterogeneity than histological annotations, and facilitates the discovery of novel differentially expressed genes of high prognostic relevance. These results demonstrate the capacity of AE-GCN to unveil complex spatial patterns from SRT data.
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spelling pubmed-102480052023-06-09 Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network Li, Xinxing Huang, Wendong Xu, Xuan Zhang, Hong-Yu Shi, Qianqian Front Genet Genetics Spatially resolved transcriptomics (SRT) provides an unprecedented opportunity to investigate the complex and heterogeneous tissue organization. However, it is challenging for a single model to learn an effective representation within and across spatial contexts. To solve the issue, we develop a novel ensemble model, AE-GCN (autoencoder-assisted graph convolutional neural network), which combines the autoencoder (AE) and graph convolutional neural network (GCN), to identify accurate and fine-grained spatial domains. AE-GCN transfers the AE-specific representations to the corresponding GCN-specific layers and unifies these two types of deep neural networks for spatial clustering via the clustering-aware contrastive mechanism. In this way, AE-GCN accommodates the strengths of both AE and GCN for learning an effective representation. We validate the effectiveness of AE-GCN on spatial domain identification and data denoising using multiple SRT datasets generated from ST, 10x Visium, and Slide-seqV2 platforms. Particularly, in cancer datasets, AE-GCN identifies disease-related spatial domains, which reveal more heterogeneity than histological annotations, and facilitates the discovery of novel differentially expressed genes of high prognostic relevance. These results demonstrate the capacity of AE-GCN to unveil complex spatial patterns from SRT data. Frontiers Media S.A. 2023-05-25 /pmc/articles/PMC10248005/ /pubmed/37303949 http://dx.doi.org/10.3389/fgene.2023.1202409 Text en Copyright © 2023 Li, Huang, Xu, Zhang and Shi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Li, Xinxing
Huang, Wendong
Xu, Xuan
Zhang, Hong-Yu
Shi, Qianqian
Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title_full Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title_fullStr Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title_full_unstemmed Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title_short Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
title_sort deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10248005/
https://www.ncbi.nlm.nih.gov/pubmed/37303949
http://dx.doi.org/10.3389/fgene.2023.1202409
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