Published on Fri Mar 19 2021

Micro-region transcriptomics of fixed human tissue using Pick-Seq

Maliga, Z., Nirmal, A. J., Ericson, N. G., Boswell, S. A., U'Ren, L., Podyminogin, R., Chow, J., Chen, Y.-A., Chen, A. A., Weinstock, D. M., Lian, C. G., Murphy, G. F., Kaldjian, E. P., Santagata, S., Sorger, P. K.

Pick-Seq is a form of micro-region sequencing in which small regions of tissue, containing 5-20 cells, are mechanically isolated on a microscope and then sequenced. Application of Pick- Seq to a human melanoma with complex histology reveals significant differences in transcriptional programs.

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Abstract

Spatial transcriptomics and multiplexed imaging are complementary methods for studying tissue biology and disease. Recently developed spatial transcriptomic methods use fresh-frozen specimens but most diagnostic specimens, clinical trials, and tissue archives rely on formaldehyde-fixed tissue. Here we describe the Pick-Seq method for deep spatial transcriptional profiling of fixed tissue. Pick-Seq is a form of micro-region sequencing in which small regions of tissue, containing 5-20 cells, are mechanically isolated on a microscope and then sequenced. We demonstrate the use of Pick-Seq with several different fixed and frozen human specimens. Application of Pick-Seq to a human melanoma with complex histology reveals significant differences in transcriptional programs associated with tumor invasion, proliferation, and immuno-editing. Parallel imaging confirms changes in immuno-phenotypes and cancer cell states. This work demonstrates the ability of Pick-Seq to generate deep spatial transcriptomic data from fixed and archival tissue with multiplexed imaging in parallel.