TMExplorer: A Tumour Microenvironment Single-Cell RNAseq Database and Search Tool: A Summary

Christensen, Erik, Alaine Naidas, David Chen, Mia Husic, and Parisa Shooshtari 

Cancer research has made tremendous progress in recent years, thanks to new technologies that allow scientists to study the complexity of a tumour. One of these technologies, called single-cell RNA sequencing (scRNA-seq), allows researchers to measure the expression of thousands of genes in individual cells. This can be used to understand the different types of cells present in a tumour and how they interact with each other. This information is important because the mix of cells in a tumour, known as the tumour microenvironment (TME), influences how the cancer grows and how new therapies can target it. 

Despite the availability of many scRNA-seq datasets, accessing and analyzing this data can be a significant challenge for researchers. Many of these datasets are scattered across various sources, making it very time-consuming and difficult to find the right information. To address this problem, our group created TMExplorer, a specialized database that collects and organizes TME scRNA-seq data from different studies worldwide. This database brings the datasets together from multiple cancer types (i.e. breast cancer, lung cancer, pancreatic cancer etc.) and makes it easy to search and access specific data needed to answer difficult research questions.  

The TMExplorer database is available for download to be used within R, a common programming software. This allows researchers to explore the TME data and incorporate it into their research. Understanding the TME is important because it can reveal why some tumours become more aggressive, spread to other body parts, or develop resistance to treatments. Ultimately, TMExplorer helps scientists better understand how the cellular environment around tumours shapes cancer behavior, paving the way for improved cancer therapies and more personalized treatment strategies.  

Link to full text: https://doi.org/10.1371/journal.pone.0272302