Single-cell RNA sequencing analyses on the human epidermis have given new insights into cell fates of the tissue by characterizing the precise transcriptomic profile at the single-cell scale. Nevertheless, the information of the spatial localizations of transcripts in each single cell s is lacking. Three dimension transcriptomic analyses are therefore of great importance to characterize cell fates of the epidermis with spatial information.
To study human epidermal biology and diseases, organotypic models can be grown using primary or immortalized keratinocytes. These models have been shown to recapitulate the structure of the epidermis with the different cell layers and architecture. These 3D human epidermal equivalent (3D HEE) allow the modelling of epidermal biology and related diseases caused by genetic defects as well as environmental signals and insults such as cytokines and microbes. However, 3D HEEs need to further be validated at the singe cell transcriptomic level with spatial information to demonstrate that they can recapitulate the in vivo epidermal biology.
Here we applied a novel technology of spatial transcriptomic analyses to the 3D HEEs. This technology is based on synthetic aperture optics and cyclical single-molecule fluorescence in-situ hybridization, enabling the analyses of up to 30 genes in a single experiment using RNA probes linked to fluorochromes.
Using a panel of well characterized marker genes for different epidermal layers, we detected expression of these marker genes in the expected epidermal layers, showing that the designed probe set is able to characterize 3D HEEs. We also included genes that are known to be involved in different cell cycle phases, aiming to test this spatial transcriptomic technology for detecting rare cell fates in HEEs. Notably, with the use of MKI67, markers of proliferating cells, we detected clear but a few cycling cells in the stratum basale.
We thus show that we have established the spatial transcriptomic technology that can be applied to human epidermal organotypic models. This powerful technique can further be used to dissect cell fates of the human epidermis in 3 dimensional space that are affected by diseases or environmental cues.

E2BRN006 - Spatial transcriptomics on human epidermal equivalents

The scientific meeting of the European Society for Dermatological Research (ESDR) is held yearly, usually in September. With an international attendance of more than 1000 skin scientists from around the globe, the four-day event includes short oral presentations from peer-reviewed abstracts, keynote lectures from international experts, sponsored symposia, satellite programs, educational events as well as an important focus on posters, networking and building collaborations amongst scientists. For more information about this year’s meeting visit our website.