RT Journal Article SR Electronic T1 In situ electro-sequencing in three-dimensional tissues JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.04.22.440941 DO 10.1101/2021.04.22.440941 A1 Qiang Li A1 Zuwan Lin A1 Ren Liu A1 Xin Tang A1 Jiahao Huang A1 Yichun He A1 Haowen Zhou A1 Hao Sheng A1 Hailing Shi A1 Xiao Wang A1 Jia Liu YR 2021 UL http://biorxiv.org/content/early/2021/04/23/2021.04.22.440941.abstract AB Pairwise mapping of single-cell gene expression and electrophysiology in intact three-dimensional (3D) tissues is crucial for studying electrogenic organs (e.g., brain and heart)1–5. Here, we introduce in situ electro-sequencing (electro-seq), combining soft bioelectronics with in situ RNA sequencing to stably map millisecond-timescale cellular electrophysiology and simultaneously profile a large number of genes at single-cell level across 3D tissues. We applied in situ electro-seq to 3D human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) patches, precisely registering the CM gene expression with electrophysiology at single-cell level, enabling multimodal in situ analysis. Such multimodal data integration substantially improved the dissection of cell types and the reconstruction of developmental trajectory from spatially heterogeneous tissues. Using machine learning (ML)-based cross-modal analysis, in situ electro-seq identified the gene-to-electrophysiology relationship over the time course of cardiac maturation. Further leveraging such a relationship to train a coupled autoencoder, we demonstrated the prediction of single-cell gene expression profile evolution using long-term electrical measurement from the same cardiac patch or 3D millimeter-scale cardiac organoids. As exemplified by cardiac tissue maturation, in situ electro-seq will be broadly applicable to create spatiotemporal multimodal maps and predictive models in electrogenic organs, allowing discovery of cell types and gene programs responsible for electrophysiological function and dysfunction.Competing Interest StatementA patent application has been filed by Broad Institute of MIT and Harvard related to this work; all methods and protocols are freely available.