空间转录组学测序 z-bio 2024-12-17 506

　　Schematic diagram of Decoder Seq technology for spatial transcriptome sequencing

　　With the support of the National Natural Science Foundation of China (Grant No. 21927806) and other grants, Professor Yang Chaoyong's team at Xiamen University has made progress in the technology and application of spatial transcriptome sequencing. The related research results, titled "Decoder seq enhances mRNA capture efficiency in spatial RNA sequencing", were published in the journal Nature Biotechnology. Paper link: https://www.nature.com/articles/s41587-023-02086-y .

　　Space transcriptomics technology is a powerful tool for describing the spatial expression patterns of genes within tissues, revealing cell composition, spatial arrangement, and interactions. It has important application value in major research areas such as organ structure, embryonic development, neuroscience, life evolution, and human diseases. In recent years, sequencing methods based on spatial barcode arrays have received great attention from researchers due to their ability to provide preference free, high-throughput spatial transcriptome analysis. However, this technology still faces bottlenecks such as high cost, insufficient sensitivity, and low resolution.

　　The team utilized microfluidic assisted orthogonal coding strategy to generate an array of high-density spatial barcodes on a three-dimensional (3D) nano substrate, achieving low-cost, high-sensitivity, and high-resolution spatial transcriptomics research. Firstly, the work constructed a 3D tree like nano substrate, which increased the modification density of barcodes by about an order of magnitude, thereby improving mRNA capture efficiency. Secondly, by designing two microchannel chips with channels perpendicular to each other and adjusting the number and width of channels on the chips, DNA coordinate barcode lattices with different capture areas and spatial resolutions (50, 25, 15, and 10 μ m) were flexibly generated. Finally, the deterministic combination barcode generated based on the orthogonal encoding strategy significantly reduces the number of encoded DNA types, eliminating the need for decoding steps and significantly reducing experimental costs. The sensitivity of Decoder seq with near single-cell resolution (15 μ m) is as high as 40.1 mRNA molecules per μ m2, which is much higher than other similar methods and achieves accurate mapping of tissue single-cell spatial maps. Thanks to the significant improvement in detection sensitivity, the team has discovered and confirmed for the first time a new pattern of layered distribution of two Olfr genes, revealing spatial immune heterogeneity in the microenvironment of different subtypes of renal cell carcinoma tissues and identifying a set of genes associated with clinical staging and prognosis evaluation of renal cell carcinoma.