Assessing the Viability of Inferential Spatial Transcriptomics Data for Studying Skin Photoaging
Victoria Zhang
Lay Summary:
This project tests the capabilities of synthetic spatial data to study how sunlight affects skin aging at the molecular level. The data, though created through artificial means, proved to be effective in biological analysis and reveals new spatial insights in how sun damage progresses in the skin.
Abstract:
As skin is exposed chronically to the sun’s UV rays, various skin processes are disrupted and skin immunity worsens. This may lead to photoaging, or age acceleration caused by sun damage, visible through wrinkles and skin elasticity, which increases the risk for major diseases such as skin cancer. Previous analyses of photoaging, particularly in the construction of age acceleration clocks, have used data such as DNAm and scRNA-seq. The viability of spatial transcriptomics data, particularly of ST data generated through inference methods, have been unexplored in photoaging, despite having the potential to reveal new spatial markers and relationships in photoaging. This study uses synthetic spatial transcriptomics data to identify key gene markers and cell types in aging on the spot level, as well as to create one of the first spatially informed aging clock models. The leading aging clock was a CNN, which used gene expression and spatial coordinates to predict age. The model’s performance is on-par with DNAm-based aging clocks in literature, suggesting that synthetic ST data can be used to give an opinion on photoaging. Spatial transcriptomics remains a valuable contender to give unique insights on photoaging and can be used in additional analyses to infer biological relationships.
Q&A:
Bios: Victoria Zhang
Program Track: Advanced Research
GitHub Username:
victoriiz -Victoria Zhang
What was your favorite seminar? Why?
I really enjoyed Alos Diallo’s presentation on adaptive immunity. The presentation was very clear and definitely sparked my interest in learning more about the biological background of the immune system. I also learned of the potential for gene markers to be used to regulate immune response, which inspired me to do something similar for my summer project. -Victoria Zhang
If you were to summarize your summer internship experience in one sentence, what would it be?
Learning through trial and error; trying many things at once and figuring out what works. -Victoria Zhang