Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Jessica Svedlund &
Department of Immunology, Genetics, and Pathology, the Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
Johan Botling &
Science for Life Laboratory, Centre for Image Analysis, Uppsala University, Uppsala, Sweden.
Alexandra Pacureanu &
Imaging Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
R.K. and M.M. designed and performed the experiments. J.B. provided tissue sections and pathology examination of the tissue. C.W. designed the image analysis pipelines and performed the image analysis together with A.P. J.S. performed the correlation between in situ sequencing and RNA-seq data. R.K., M.M., C.W. and M.N. wrote the manuscript. All authors commented on and revised the manuscript. M.N. conceived the idea and supervised the project.
Competing financial interests
M.N. owns shares in the company Olink AB, Uppsala, Sweden, which holds patents whose value may be affected by publication of these results.