Spotiphy integrative analysis tool turns spatial RNA sequencing into imager

(Press-News.org) Spatial transcriptomics is a cutting-edge technique that characterizes gene expression within sections of tissue, such as heart, skin or liver tissue. These snapshots provide insights into how spatial organization affects cellular functions across the spectrum of biology and disease. Up to now, researchers conducting spatial transcriptomics have had to choose between two options based on their needs: genome-wide coverage or single-cell resolution. To solve this tradeoff, scientists at St. Jude Children’s Research Hospital and the University of Wisconsin-Madison have created a computational tool that uses generative artificial intelligence (AI) to enhance the resolution of sequencing-based spatial transcriptomics without sacrificing gene coverage. The algorithm and its first findings were published today in Nature Methods. 

“We’ve made the first generative algorithm that can predict spatial gene expression of whole transcriptomics at the single-cell level,” said co-senior and corresponding author Jiyang Yu, PhD, St. Jude Department of Computational Biology interim chair. “The key is to borrow information from single-cell RNA-seq atlas and histology imaging data with this generative modeling approach, giving full transcriptome coverage and single-cell resolution in spatial RNA-sequencing.” 

The new computational tool, Spot imager with pseudo single-cell resolution histology (Spotiphy), employs a machine learning algorithm to improve conventional spatial transcriptomics technologies significantly. Those technologies look at predefined “spots” on a grid to capture gene expression. These are essentially the pixels that form the final gene expression image across the entire tissue section. Each spot typically contains multiple, often heterogeneous, cells, making them difficult to classify and analyze into single cells.  

Spotiphy uses machine learning that extrapolates cell-type proportions and gene expression data to fill the space between “spots.” The program knows what to fill these gaps with because it was trained on vast spatial transcriptomics databases paired with histological images.  

“Imagine a picture of a hand, but the middle is missing,” said co-senior author Junmin Peng, PhD, St. Jude Departments of Structural Biology and Developmental Neurobiology. “The algorithm has acquired general rules from its training so that it can impute the missing part of the picture — like reconstructing where and what the palm should look like, or in reality, the space between imaging spots.” 

Spotiphy finds new insights from spatial transcriptomics data  Peng, who studies neurobiology, explained how single-cell spatial transcriptomics provides an opportunity to understand neurodegenerative diseases better, including Alzheimer’s, especially aberrant cells and their gene expression. However, “previous spatial transcriptomics data for Alzheimer’s have not truly resolved single-cell data,” Peng said. “Existing methods result in a low-resolution output, often clustering multiple cells into a single spot. We merged adjacent sections for RNA analysis and imaging one-to-one with Spotiphy, truly reaching a clean single-cell resolution with high gene coverage.

Applied to a mouse model of Alzheimer’s Disease, Spotiphy confirmed the findings of previous studies, validating the tool’s ability to pinpoint cell location and gene expression patterns accurately. This increased confidence in the technique. In addition, the researchers deployed Spotiphy in new experiments, finding that subsets of astrocytes, a common cell type in the central nervous system, are associated with specific brain regions. They also found that disease-associated microglia, a rare type of immune cells, had a greater presence in brains affected by Alzheimer’s, supporting previous findings that microglial dysfunction may be involved in the disease.  

“The real power of this algorithm is its ability to distinguish subtle differences within the same cell type that previous technologies could not detect,” Yu said. “For example, identifying sub-populations of astrocytes located in certain areas of the brain.” 

Findings were not limited to neurobiology. The scientists also showed that Spotiphy could be used to analyze other tissues, including cancer samples. The tool successfully identified different spatial domains and alterations in tumor-tumor microenvironment interactions.  

“We saw the data reflected known breast cancer heterogeneity,” said co-first author Jiyuan Yang, PhD, St. Jude Department of Computational Biology. “We also invested significant efforts to generating the matched datasets for mouse brains, which we believe will be a valuable resource for the spatial omics community.” 

“We’ve made a tool that can resolve single-cell spatial transcriptomics of any given tissue,” Yu said. “In other words, Spotiphy lets scientists see things that they could not see before.” 

Spotiphy is freely available at https://github.com/jyyulab/Spotiphy. 

Authors and funding  The study’s other co-first author is Ziqian Zheng, University of Wisconsin-Madison. The study’s other co-senior author is Kaibo Liu, University of Wisconsin-Madison. The study’s other authors are Yun Jiao, Kaiwen Yu, Sheetal Bhatara, Xu Yang, Sivaraman Natarajan, John Easton and Koon-Kiu Yan, all of St. Jude; and Jiahui Zhang, University of Wisconsin-Madison. 

This work is supported in part by grants from National Institutes of Health (R01GM134382, U01CA264610, U01CA281868, R01CA274251, RF1AG068581 and ALSAC, the fundraising and awareness organization of St. Jude. 

St. Jude Children's Research Hospital St. Jude Children's Research Hospital is leading the way the world understands, treats and cures childhood cancer, sickle cell disease, and other life-threatening disorders. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20% to 80% since the hospital opened more than 60 years ago. St. Jude shares the breakthroughs it makes to help doctors and researchers at local hospitals and cancer centers around the world improve the quality of treatment and care for even more children. To learn more, visit stjude.org, read St. Jude Progress, a digital magazine, and follow St. Jude on social media at @stjuderesearch.

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