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Technology Development Initiative – Paper of the Month – February 2023

 A figure from this article. Image – Copyright Cell.

Image – Copyright Cell.

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

Published in Cell.

Authors

Xiaonan Fu, Li Sun, Runze Dong, Jane Y Chen, Runglawan Silakit, Logan F Condon, Yiing Lin, Shin Lin, Richard D Palmiter, Liangcai Gu

Paper presented by Dr. Katherine Savell and selected by the NIDA TDI Paper of the Month Committee

Background and Technological Advancement

Advances in spatial transcriptomics offer transcriptional characterization of complex tissues, such as the brain. However, most existing methods only provide a spatial resolution of 100-200 µm, with gene expression representing multiple cells in proximity. Higher resolution is possible but requires specialized equipment and expensive reagents. Fu*, Sun*, Dong* et. al. generated and validated a novel polony-based ‘stamp gel’ that uses common lab equipment and enzymatic replication to produce copies of the 1 µm resolution barcoded array slide that is used for spatial transcriptomic capture. The authors demonstrate that the stamping fidelity is robust and consistent over many cycles, and the slides capture the top layer of RNA on a tissue slice. The authors created a new bioinformatics tool called “V-seg” to assign transcripts to single cells which they used to investigate the effects of chronic pain on cell-type transcriptomes in the parabrachial nucleus.  Taken together, polony gel stamping is poised to increase accessibility of high-resolution spatial transcriptomics.


Fu, Xiaonan; Sun, Li; Dong, Runze; Chen, Jane Y; Silakit, Runglawan; Condon, Logan F; Lin, Yiing; Lin, Shin; Palmiter, Richard D; Gu, Liangcai

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain Journal Article

In: Cell, vol. 185, no. 24, pp. 4621–4633.e17, 2022, ISSN: 1097-4172.

Abstract | Links

@article{pmid36368323,
title = {Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain},
author = {Xiaonan Fu and Li Sun and Runze Dong and Jane Y Chen and Runglawan Silakit and Logan F Condon and Yiing Lin and Shin Lin and Richard D Palmiter and Liangcai Gu},
url = {https://pubmed.ncbi.nlm.nih.gov/36368323/},
doi = {10.1016/j.cell.2022.10.021},
issn = {1097-4172},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
journal = {Cell},
volume = {185},
number = {24},
pages = {4621--4633.e17},
abstract = {Methods for acquiring spatially resolved omics data from complex tissues use barcoded DNA arrays of low- to sub-micrometer features to achieve single-cell resolution. However, fabricating such arrays (randomly assembled beads, DNA nanoballs, or clusters) requires sequencing barcodes in each array, limiting cost-effectiveness and throughput. Here, we describe a vastly scalable stamping method to fabricate polony gels, arrays of ∼1-micrometer clonal DNA clusters bearing unique barcodes. By enabling repeatable enzymatic replication of barcode-patterned gels, this method, compared with the sequencing-dependent array fabrication, reduced cost by at least 35-fold and time to approximately 7 h. The gel stamping was implemented with a simple robotic arm and off-the-shelf reagents. We leveraged the resolution and RNA capture efficiency of polony gels to develop Pixel-seq, a single-cell spatial transcriptomic assay, and applied it to map the mouse parabrachial nucleus and analyze changes in neuropathic pain-regulated transcriptomes and cell-cell communication after nerve ligation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

Methods for acquiring spatially resolved omics data from complex tissues use barcoded DNA arrays of low- to sub-micrometer features to achieve single-cell resolution. However, fabricating such arrays (randomly assembled beads, DNA nanoballs, or clusters) requires sequencing barcodes in each array, limiting cost-effectiveness and throughput. Here, we describe a vastly scalable stamping method to fabricate polony gels, arrays of ∼1-micrometer clonal DNA clusters bearing unique barcodes. By enabling repeatable enzymatic replication of barcode-patterned gels, this method, compared with the sequencing-dependent array fabrication, reduced cost by at least 35-fold and time to approximately 7 h. The gel stamping was implemented with a simple robotic arm and off-the-shelf reagents. We leveraged the resolution and RNA capture efficiency of polony gels to develop Pixel-seq, a single-cell spatial transcriptomic assay, and applied it to map the mouse parabrachial nucleus and analyze changes in neuropathic pain-regulated transcriptomes and cell-cell communication after nerve ligation.

Close

  • https://pubmed.ncbi.nlm.nih.gov/36368323/
  • doi:10.1016/j.cell.2022.10.021

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