What types of cells are in which human tissue and where? What genes are active in individual cells and what proteins are there? A specialist atlas will provide answers to these questions and more – particularly how different tissues form during embryonic development and what causes diseases. In creating this atlas, researchers aim not only to identify tissues isolated directly from humans, but also structures called organelles. These are 3D clumps of tissue that are grown in a lab and develop in a similar way to human organs, but on a smaller scale.
“The advantage of organelles is that we can interfere with their development and test active substances on them, which allows us to learn more about healthy tissues as well as diseases,” explains Barbara Treutlin, associate professor of quantitative developmental biology in the Department of Biosystem Sciences. and engineering at ETH Zurich in Basel.
To help produce such an atlas, Treutlein, together with researchers from the Universities of Zurich and Basel, developed an approach to collect and compile a large amount of information about organelles and their evolution. The research team applied this approach to the organelles of the retina, which they derived from stem cells.
Several proteins are visible at once
At the heart of 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 Lukas Pilkmans, a professor at the University of Zurich and co-author of the study that has just been published in the scientific journal Nature Biotechnology. In this study, the researchers applied this method to organelles for the first time.
Typically, researchers use fluorescence microscopy to highlight three proteins in tissue, each with a different fluorescent dye. For technical reasons, no more than five proteins can be stained at a time. In the 4i technique, three dyes are used, but these are washed off from the tissue sample after measurements are 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, the computer merges the individual images into a single micrograph showing 53 different proteins. They provide information on the function of the individual cell types that make up the retina; For example, rods, cones, and ganglion cells.
The researchers complemented this visual information of retinal proteins with information about which genes are read in individual cells.
High spatial and temporal resolution
The scientists performed all these analyzes on organelles 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 full 39-week development of the retinal organoids. “We can use this time series to show how organ tissue slowly builds up, where and when cell types reproduce, and where synapses are located. These processes are comparable to the processes of retinal formation during embryonic development,” says Gray Camp, professor at the University of Basel and senior author for this article. the study.
The researchers posted their information about the images and more findings about the development of the retina on a publicly available website: EyeSee4is.
Other planned tissue types
So far, scientists are studying how a healthy retina develops, but in the future they hope to intentionally disrupt the growth of retinal organelles using drugs or genetic modifications. “This will give us new insights into diseases such as retinitis pigmentosa, a genetic condition that causes deterioration of the light-sensitive receptors in the retina, which ultimately leads to blindness,” Camp says. Researchers want to know when this process starts and how it can be stopped.
Treutlein and her colleagues are also working on applying the new detailed mapping approach to other tissue types, such as different sections of the human brain and different tumor tissues. Step by step, this will create an atlas that provides information on the development of human organs and tissues.