Making rare cell types visible: Researchers develop new method

The human body contains more than 30 trillion cells. Until recently, the sheer number of cells in an organism meant that approaches to understanding human disease and developmental processes based on analysis of single cells were a vision of the future. The development of new sequencing methods is currently revolutionizing our understanding of cellular heterogeneity. These technologies can detect rare or new cell types by extracting and sequencing genetic information from cells based on RNA sequences.

In collaboration with Helmholtz Munich, Professor Matthias Meyer of the Center for Biotechnology and Biomedicine at the University of Leipzig and his research group have developed a new, efficient and relatively inexpensive method for making rare cell types, types of cellular communication and disease patterns visible in tissues. The researchers have now published their findings in the journal Nature Communications.

All methods of single-cell analysis require separation of cells from the tissue complex, losing spatial information about cell types and thus information about the cellular environment or cellular communication pathways or functions. To obtain spatially resolved information about individual cells, imaging and sequencing techniques must be used together. In recent years, several approaches have been developed to standardize the integration of imaging and sequencing data.

Depending on the research question, different parameters such as spatial resolution, detection limit, RNA accessibility and cost were weighed against each other. An earlier analysis method was based on the idea of ​​attaching local information to RNAs using barcodes based on the sequence of DNA bases. After extraction of all RNAs and subsequent comprehensive sequencing, barcodes can be used to generate a synthetic image.

This is where Johannes Wirth’s work came in. As a PhD researcher in Matthias Meyer’s lab, the Helmholtz Munich researcher has developed an advanced workflow that makes it possible to obtain locally resolved genomic data combined with high-quality microscopic images. This enables the visualization of rare cell types, types of cell communication, and disease patterns in tissues. The focus has been on developing a new microfluidic chip that makes it possible to analyze RNA sequences in large tissue sections at low cost.

“Compared to the original method, the new method increased the amount of image information per pixel by six or twelve. This means that we can resolve about 5,000 genes per pixel, allowing us to visualize rare cell types in the kidney or liver,” Wirth explains. In comparison, a standard HD display can only display the three primary colors with 256 different brightness levels for each pixel.

In addition to technical developments, the team also introduced an open source analysis pipeline to make the method more accessible. As the method is suitable for a wide range of tissues, it will facilitate studies of complex diseases, multi-organ functions and dysfunctions.

“The method we developed, which combines imaging and sequencing techniques, was visionary until recently. It revolutionized our understanding of cellular heterogeneity and allowed us to find new types of cells in all organisms,” says Professor Meyer. With the development of single-cell sequencing methods, it is now possible to better understand pathways of cellular development and how diseases develop.