Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

Abstract

Transcriptome profiling is an indispensable tool in advancing the understanding of single cell biology, but depends upon methods capable of isolating mRNA at the spatial resolution of a single cell. Current capture methods lack sufficient spatial resolution to isolate mRNA from individual in vivo resident cells without damaging adjacent tissue. Because of this limitation, it has been difficult to assess the influence of the microenvironment on the transcriptome of individual neurons. Here, we engineered a Transcriptome In Vivo Analysis (TIVA)-tag, which upon photoactivation enables mRNA capture from single cells in live tissue. Using the TIVA-tag in combination with RNA-seq to analyze transcriptome variance among single dispersed cells and in vivo resident mouse and human neurons, we show that the tissue microenvironment shapes the transcriptomic landscape of individual cells. The TIVA methodology provides the first noninvasive approach for capturing mRNA from single cells in their natural microenvironment.

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

“…Recently, alternative approaches for profiling the transcriptomes of spatially referenced cells have been proposed 5,20 . Transcriptome in vivo analysis (TIVA) 20 allows individual cells to be fluorescently labeled within a tissue, visualized and then sequenced after capture.…”

“…Transcriptome in vivo analysis (TIVA) 20 allows individual cells to be fluorescently labeled within a tissue, visualized and then sequenced after capture. In practice, this is extremely useful when a particular cell, or small npg a n a ly s i s number of cells, is of interest.…”

Stochastic electrotransport selectively enhances the transport of highly electromobile molecules

“…Diverse methods of tissue labeling are used in many areas of biological research and medical diagnosis for visualizing various biomolecules of interest. However, these techniques have been mostly confined to small samples owing to the difficulty of labeling and examining deep structures in large-scale intact tissues (6,(27)(28)(29)(30)(31). CLARITY and other emerging tissue-clearing techniques (2,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25) render intact tissues optically transparent and macromolecule-permeable, allowing examination deep inside Significance Many chemical and biomedical techniques rely on slow diffusive transport because existing pressure-based methods or electrokinetic methods can incidentally damage the sample.…”

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

“…Even more difficult is the task of capturing the precise time when a cell undergoes a cell-fate transition. Recently, new technologies are being rapidly developed to quantify gene expression at the single-cell resolution (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23), providing an unprecedented opportunity for the detection of such rare events. Nonetheless, interpretation of these novel kinds of data remains a difficult task owing to the lack of suitable computational methods.…”