Nanoscale in situ Sequencing of Tissues from Patients

Next-generation sequencing of RNA from tissues and single cells has transformed biology by starting to provide the molecular basis behind the function of cells and tissues. However, so far sequencing methods involved grinding up or dissociating the cells before sequencing, thereby destroying all spatial information. We have developed a new technology, expansion sequencing (ExSeq), which enables to resolve transcripts in situ, throughout entire cells and tissues. With ExSeq a genome-wide snapshot of the transcriptome is obtained, and indeed we find that the correlation between the information obtained with standard sequencing and ExSeq is very high. In addition, as ExSeq is done in physically expanded samples, a subcellular resolution for the locations of the sequencing reads is obtained. ExSeq was utilized to globally quantify RNA subcellular localization and expression using data generated from metastatic breast cancer, thereby allowing to map the microenvironment of the tumor.