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

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

doi:10.1016/j.cell.2022.10.021

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

Cell. 2022 Nov 23;185(24):4621-4633.e17. doi: 10.1016/j.cell.2022.10.021. Epub 2022 Nov 10.

Authors

Xiaonan Fu¹, Li Sun², Runze Dong³, Jane Y Chen⁴, Runglawan Silakit⁵, Logan F Condon⁶, Yiing Lin⁷, Shin Lin⁸, Richard D Palmiter⁴, Liangcai Gu⁹

Affiliations

¹ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
² Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; TopoGene Inc., Seattle, WA 98195, USA.
³ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.
⁴ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
⁵ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
⁶ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Graduate Programs in Medical Scientist Training and Neuroscience, University of Washington, Seattle, WA, USA.
⁷ Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA.
⁸ Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
⁹ Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Electronic address: gulc@uw.edu.

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: DNA array; DNA stamping; Pixel-seq; chronic pain; microcontact printing; olfactory bulb; parabrachial nucleus; polony gel; polony sequencing; spatial transcriptomics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chronic Pain*
DNA
Gels
Mice
RNA
Transcriptome*

Substances

DNA
RNA
Gels

Abstract

Publication types

MeSH terms

Substances

Grants and funding