美国华盛顿大学Liangcai Gu研究组利用新方法实现可扩增的DNA印刷和慢性疼痛的空间转录组学。该研究于2022年11月10日在线发表于国际一流学术期刊《细胞》。

研究人员描述了一种巨大的可扩展的印刷方法来制造多聚物凝胶，即带有独特条形码的1微米左右的克隆DNA簇的阵列。通过实现条形码图案凝胶的可重复酶促复制，该方法与依赖测序的阵列制造相比，成本至少降低了35倍，时间缩短到约7小时。研究人员利用多聚物凝胶的分辨率和RNA捕获效率开发了Pixel-seq，一种单细胞空间转录组检测方法，并将其应用于小鼠臂旁核的测绘，以及分析了神经结扎后神经痛调节的转录组和细胞-细胞通讯的变化。

据介绍，从复杂组织中获取空间分辨率的全息数据的方法，使用低至亚微米特征的条码DNA阵列来实现单细胞分辨率。然而，制造这种阵列（随机组装的珠子、DNA纳米球或集群）需要对每个阵列中的条形码进行排序，限制了成本效益和产量。

附：英文原文

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

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

Issue&Volume: 2022-11-10

Abstract: Methods for acquiring spatially resolved omics data from complex tissues use barcodedDNA arrays of low- to sub-micrometer features to achieve single-cell resolution. However,fabricating such arrays (randomly assembled beads, DNA nanoballs, or clusters) requiressequencing 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 repeatableenzymatic replication of barcode-patterned gels, this method, compared with the sequencing-dependentarray 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 parabrachialnucleus and analyze changes in neuropathic pain-regulated transcriptomes and cell-cellcommunication after nerve ligation.

DOI: 10.1016/j.cell.2022.10.021

Source: https://www.cell.com/cell/fulltext/S0092-8674(22)01367-8