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Spatially resolved gene expression patterns are emerging as a key component of medical studies, including companion diagnostics, but technologies for quantification and multiplexing are limited. We present a method to perform spatially resolved and multiplexed microRNA (miRNA) measurements from formalin-fixed, paraffin-embedded (FFPE) tissue. Using nanoliter well arrays to pixelate the tissue section and photopatterned hydrogels to quantify miRNA, we identified differentially expressed miRNAs in tumors from a genetically engineered mouse model for non-small cell lung cancer (K-ras LSL-G12D/+ ; p53 fl/fl ). This technology could be used to quantify heterogeneities in tissue samples and lead to informed, biomarker-based diagnostics.

Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays