Exploring the world of cells with scProAtlas: A new map of human tissues

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Overview of scProAtlas's: (A) Public resources and tissues used in scProAtlas. (B) Basic function of scProAtlas. scProAtlas supports browsing, downloading and searching (C) Analysis module in scProAtlas. Image credit: Nucleic Acids Research. https://doi.org/10.1093/nar/gkae990

Have you ever wondered what’s happening inside your body at the tiniest level? Scientists are now able to look at tissues in amazing detail, all the way down to individual cells. This is thanks to something called spatial proteomics, which lets us see where different proteins are within tissues. Think of it like having a super-powered microscope that not only sees cells but also identifies what they are doing.

The challenge is that there is so much data, that it can be difficult to make sense of it all. This is where scProAtlas comes in. scProAtlas is a special online database that brings together a lot of spatial proteomics information. It’s like a map of the human body, but instead of showing roads and cities, it shows cells and proteins. This tool is designed to help researchers explore the complex world within our tissues.

What Does scProAtlas Do?

ScProAtlas is more than just a collection of data. It is a tool that helps us understand what is going on inside our tissues. It includes information from eight different spatial protein imaging methods. These methods allow scientists to look at many different proteins within 15 different types of human tissues, which are divided into 945 regions of interest.

Here are some of the key things scProAtlas can do:

  • Integrate data: It combines spatial proteomics data with single-cell RNA sequencing (scRNA-seq) data. This helps to make sense of the spatial information by linking it to gene expression. This is important because spatial proteomics can only look at a limited number of proteins, while scRNA-seq can give a much wider view of genes.
  • Identify cell neighbourhoods: scProAtlas identifies groups of cells that are close together and seem to work as a unit. This helps us to understand the functional structures in the tissue. It looks at what types of cells are found together in local regions, and what their spatial patterns might mean for their function.
  • Show how regions communicate: The tool also shows how different regions within a tissue communicate with each other. This helps us understand how cells coordinate their actions across the tissue.
  • Find spatial patterns in genes: scProAtlas also identifies genes that show specific spatial patterns within tissues. This helps us see how certain genes are expressed in different locations and cell types.
  • Study cell-to-cell interactions: By examining ligand-receptor pairs, scProAtlas enables the study of communication between cells. This helps us to understand how cells "talk" to each other.

Why is scProAtlas important?

Understanding the spatial organization of cells is crucial because it helps us learn about how tissues work and what can go wrong in diseases. For example, knowing how immune cells are located in tissues can help us understand how the body fights off infections or cancer.

The database can help us understand the role of specific proteins, like MZB1, which is important in plasma cells, and its expression pattern in different tissues. It also helps us see how genes like TSPAN8 play a role in maintaining the intestinal barrier.

ScProAtlas is also a valuable tool for researchers. It allows them to explore large datasets, find new insights, and design new experiments. The database is user-friendly and is constantly being updated with new data.

In conclusion

ScProAtlas is a significant step forward in our understanding of the human body. By providing a detailed spatial view of our tissues, it gives researchers a new way to study health and disease. It's like having a detailed map of the human body's inner workings. As the database grows and develops, it’s expected to play a vital role in future biomedical discoveries.

Additional information: Wang, T., Chen, X., Han, Y., Yi, J., Liu, X., Kim, P., Huang, L., Huang, K., & Zhou, X. (2024). scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues. Nucleic Acids Research. https://doi.org/10.1093/nar/gkae990

Journal information: https://academic.oup.com/nar

Explore atlas: https://relab.xidian.edu.cn/scProAtlas/#/


Location: Oxford, UK

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