Mapping human tissues with highly multiplexed RNA in situ hybridization

Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard Que, Carter R. Palmer, Yixu Yuan, Yida Zhang, Xuwen Li, Jinghui Song, Amanda Knoten, Blue B. Lake, Joseph P. Gaut, C. Dirk Keene, Ed Lein, Peter V. Kharchenko, Jerold Chun, Sanjay Jain, Jian-Bing Fan and Kun Zhang ()
Additional contact information
Kian Kalhor: University of California San Diego
Chien-Ju Chen: University of California San Diego
Ho Suk Lee: University of California San Diego
Matthew Cai: University of California San Diego
Mahsa Nafisi: University of California San Diego
Richard Que: University of California San Diego
Carter R. Palmer: Sanford Burnham Prebys Medical Discovery Institute
Yixu Yuan: University of California San Diego
Yida Zhang: Harvard Medical School
Xuwen Li: Altos Labs
Jinghui Song: University of California San Diego
Amanda Knoten: Washington University School of Medicine
Blue B. Lake: University of California San Diego
Joseph P. Gaut: Washington University School of Medicine
C. Dirk Keene: University of Washington School of Medicine
Ed Lein: Allen Institute for Brain Science
Peter V. Kharchenko: Harvard Medical School
Jerold Chun: Sanford Burnham Prebys Medical Discovery Institute
Sanjay Jain: Washington University School of Medicine
Jian-Bing Fan: Illumina
Kun Zhang: University of California San Diego

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in 20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.

Date: 2024
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DOI: 10.1038/s41467-024-46437-y

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