Unraveling the Mysteries of Human Tissue: A Comprehensive Atlas

Detail of a cross section of a retinal organoid. Different tissue structures are made visible with different colors. Credit: Wahle et al. natural biotechnology 2023

What types of cells can be found in various human tissues and where? Which genes show activity in these single cells and which proteins can be identified within them? Detailed answers to these and other questions should be provided by a specialized atlas. This atlas will specifically clarify how different tissues take shape during embryonic development and the underlying causes of disease.

In the process of developing this atlas, the researchers aim to track not only tissues purchased directly from humans, but also structures called organoids. These are three-dimensional tissue aggregates that are grown in a laboratory and develop in a similar way to human organs, albeit on a smaller scale.

The advantage of organoids is that we can intervene in their development and test active substances on them, which allows us to learn more about healthy tissue and disease, explains Barbara Treutlein, a professor of quantitative developmental biology in the Department of Science and Health. biosystems engineering at ETH Zurich in Basel.

To help produce such an atlas, Treutlein, together with researchers from the Universities of Zurich and Basel, has now developed an approach to collect and compile a wealth of information about organoids and their development. The research team applied this approach to human retinal organoids, which they derived from stem cells.

Many visible proteins at once

Central to the methods the scientists used for their approach was 4i technology: iterative indirect immunofluorescence imaging. This new imaging technique can visualize several dozen proteins in a thin tissue section at high resolution using fluorescence microscopy. The 4i technology was developed a few years ago by Lucas Pelkmans, a professor at the University of Zurich and co-author of the study just published in the scientific journal natural biotechnology. It is in this study that the researchers first applied this method to organoids.

Typically, researchers use fluorescence microscopy to highlight three proteins in a tissue, each with a different fluorescent dye. For technical reasons, it is not possible to color more than five proteins at a time. Three dyes are used in the 4i technology, but these are washed out of the tissue sample after measurements have been taken and three new proteins are stained. This step was performed 18 times by a robot and the process took a total of 18 days. Finally, a computer stitches the individual images into a single microscope image on which 53 different proteins are visible. They provide information about the function of the individual cell types that make up the retina; for example, rods, cones and ganglion cells.

The researchers supplemented this visual information of retinal proteins with information about which genes are being read in individual cells.

High spatial and temporal resolution

The scientists performed all of these analyzes on organoids of different ages and therefore at different stages of development. In this way, they were able to create a time series of images and genetic information describing the entire 39-week development of retinal organoids. We can use this time series to show how slowly organoid tissue accumulates, where cell types proliferate and when, and where synapses are located. The processes are comparable to those of retinal formation during embryonic development, says Gray Camp, a professor at the University of Basel and senior author of this study.

The researchers have published their image information and additional findings on retinal development on a publicly accessible website: EyeSee4is.

Further types of fabric planned

So far, scientists have studied how a healthy retina develops, but in the future they hope to deliberately disrupt the development of retinal organoids with drugs or genetic modifications. This will give us new insights into diseases such as retinitis pigmentosa, an inherited condition that causes the light-sensing receptors of the retina to gradually degrade and ultimately leads to blindness, Camp says. Researchers want to find out when this process starts and how it can be stopped.

Treutlein and his colleagues are also working to apply the new detailed mapping approach to other tissue types, such as different sections of the human brain and various tumor tissues. Step by step, this will create an atlas that provides insight into the development of human organoids and tissues.

Reference: Multimodal Spatiotemporal Phenotyping of Human Retinal Organoid Development by Philipp Wahle, Giovanna Brancati, Christoph Harmel, Zhisong He, Gabriele Gut, Jacobo Sarabia del Castillo, Aline Xavier da Silveira dos Santos, Qianhui Yu, Pascal Noser, Jonas Simon Fleck, Bruno Gjeta , Dinko Pavlini, Simone Picelli, Max Hess, Gregor W. Schmidt, Tom TA Lummen, Yanyan Hou, Patricia Galliker, David Goldblum, Marton Balogh, Cameron S. Cowan, Hendrik PN Scholl, Botond Roska, Magdalena Renner, Lucas Pelkmans, Barbara Treutlein and J. Gray Camp, May 8, 2023, natural biotechnology.
DOI: 10.1038/s41587-023-01747-2