Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis

Zhenzhen Xun; Xinyu Ding; Yao Zhang; Benyan Zhang; Shujing Lai; Duowu Zou; Junke Zheng; Guoqiang Chen; Bing Su; Leng Han; Youqiong Ye

doi:10.1038/s41467-023-36560-7

Nature Communications (Feb 2023)

Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis

Zhenzhen Xun,
Xinyu Ding,
Yao Zhang,
Benyan Zhang,
Shujing Lai,
Duowu Zou,
Junke Zheng,
Guoqiang Chen,
Bing Su,
Leng Han,
Youqiong Ye

Affiliations

Zhenzhen Xun: Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
Xinyu Ding: Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
Yao Zhang: Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
Benyan Zhang: Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
Shujing Lai: Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine
Duowu Zou: Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
Junke Zheng: Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine
Guoqiang Chen: State Key Laboratory of Oncogenes and Related Genes, and Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM)
Bing Su: Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
Leng Han: Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University
Youqiong Ye: Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

DOI: https://doi.org/10.1038/s41467-023-36560-7
Journal volume & issue: Vol. 14, no. 1
pp. 1 – 16

Abstract

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Delineating the cellular composition of tumour boundaries in spatial transcriptomics (ST) data is challenging. Here, the authors develop Cottrazm to integrate ST with histological imaging and single-cell data, identify the malignant and non-malignant tissue boundaries, deconvolute cell-type composition, and reconstruct cell type-specific gene expression profiles.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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