metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels

Sep 23, 2026

Uploaded by Logic

Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, causes most cancer-related deaths. A systematic analysis compiles 1786 bulk tissue samples from 13 cancer types, 988,463 single cells from 17 cancer types, and 40,252 spatial spots from 45 slides across 10 cancer types. These results are integrated into metsDB, supporting cell or gene searches to retrieve multi-view, multi-scale metastasis data and insights into constitutions, relationships, pathways, biomarkers, and drug responses.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages8

Reading Time20 min

AccessFree to download

Abstract

Graphical abstract

Introduction

Related metastasis databases

Materials and methods

Collection of sequencing samples

Nucleic Acids Research, 2025, 53, D1427–D1434 [https://doi.org/10.1093/nar/gkae916](https://doi.org/10.1093/nar/gkae916) Advance access publication date: 22 October 2024 Database issue metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels Sijia Wu 1 , *, Jiajin Zhang1 , Yanfei Wang2 , Xinyu Qin1 , Zhaocan Zhang1 , Zhennan Lu 1 , Pora Kim 2 , Xiaobo Zhou 2 , * and Liyu Huang 1 , * 1 School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, PR China 2 School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA * To whom correspondence should be addressed. Tel: +86 29 8189 1070; Fax: +86 29 8189 1070; Email: [huangly@mail.xidian.edu.cn](huangly@mail.xidian.edu.cn) Correspondence may also be addressed to Xiaobo Zhou. Tel: +1 713 500 3923/3636; Fax: +1 713 500 3923/3636; [Email: xiaobo.zhou@uth.tmc.edu](Email: xiaobo.zhou@uth.tmc.edu) Correspondence may also be addressed to [Sijia Wu. Email: wusijia@xidian.edu.cn](Sijia Wu. Email: wusijia@xidian.edu.cn) Abstract Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, is responsible for the majority of cancer-related deaths. Understanding the cellular and molecular mechanisms underlying this complex process is essential for developing effective metastasis prevention and therapy strategies. To this end, we systematically analysed 1786 bulk tissue samples from 13 cancer types, 988 463 single cells from 17 cancer types, and 40 252 spots from 45 spatial slides across 10 cancer types. The results of these analyses are compiled in the metsDB database, accessible at [https://relab.xidian.edu.cn/metsDB/](https://relab.xidian.edu.cn/metsDB/. This)[. This](https://relab.xidian.edu.cn/metsDB/. This) database provides insights into alterations in cell constitutions, cell relationships, biological pathways, molecular biomarkers, and drug responses during cancer metastasis at bulk, single-cell, and spatial levels. Users can perform cell or gene searches to obtain multi-view and multi-scale metastasis-related data. This comprehensive resource is invaluable for understanding the metastasis process and for designing molecular therapies. Graphical abstract Introduction Cancer metastasis involves the movement of tumour cells from a primary site to progressively colonize distant organs, a complex process responsible for the majority of cancer-related deaths (1). This process encompasses numerous molecular and cellular changes that facilitate tumour cell migration from the primary site, survival in hostile environments, evasion of immune attacks, and colonization of foreign organs (2) . Understanding the dynamics of metastasis is crucial for identifying molecular targets that could potentially halt or reverse cancer progression (2) . The database study aims to integrate information and provide a comprehensive map related to cancer metastasis. Existing metastasis-related databases include HCMDB (3), CMGene (4), dbEMT (5), TMMGdb (6) and Mets (Supplementary Table S1 ) . HCMDB analysed and compared genes from bulk data between primary tumours and metastases, but Its website is no longer accessible. CMGene, dbEMT and TMMGdb archive metastatic genes identified through literature searches. Mets gathers data on metastatic patterns and frequencies across cancers. Despite these resources, there remains an urgent need for a comprehensive metastasis- Received: July 28, 2024. Revised: September 18, 2024. Editorial Decision: October 2, 2024. Accepted: October 18, 2024 © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ([https:](https://creativecommons.org/licenses/by-nc/4.0/)[//](https://creativecommons.org/licenses/by-nc/4.0/)[creativecommons.org](https://creat

FAQs

What datasets are integrated into metsDB?

metsDB compiles 1786 bulk tissue samples from 13 cancer types, 988,463 single cells from 17 cancer types, and 40,252 spatial spots from 45 spatial slides across 10 cancer types.

What types of analyses and insights does metsDB provide?

The database provides multi-view, multi-scale insights into changes in cell constitutions and relationships, biological pathways, molecular biomarkers, and drug responses during metastasis.

How can users query metsDB data?

Users can perform cell or gene searches to retrieve metastasis-related data across bulk, single-cell, and spatial levels.

Sep 23, 2026

Uploaded by Logic