Year: 2021
Type: article
Abstract: Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.
Source: Cell Genomics
Authors: Eva Gracia Villacampa, Ludvig Larsson, Reza Mirzazadeh, Linda Kvastad, Alma Andersson, Annelie Mollbrink, Georgia Kokaraki, Vanessa Monteil, Niklas Schultz, Karin Sofia Appelberg, Nuria Montserrat, Haibo Zhang, Josef M. Penninger, Wolfgang Miesbach, Ali Mirazimi, Joseph Carlson, Joakim Lundeberg
Institutions: Science for Life Laboratory, KTH Royal Institute of Technology, Karolinska Institutet, Karolinska University Hospital, Public Health Agency of Sweden, Institució Catalana de Recerca i Estudis Avançats, Barcelona Institute of Science and Technology, Institute for Bioengineering of Catalonia, University of Toronto, Unity Health Toronto, Keenan Research Centre for Biomedical Science, Institute of Molecular Biotechnology, Austrian Academy of Sciences, University of British Columbia, University Hospital Frankfurt, Swedish Veterinary Agency
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $8,900
Funders: Familjen Erling-Perssons Stiftelse, European Commission, Stiftelsen för Strategisk Forskning, Cancerfonden, Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, Science for Life Laboratory, Stiftelsen för Strategisk Forskning, Horizon 2020 Framework Programme, HORIZON EUROPE Framework Programme, Horizon 2020
OpenAlex ID: W4200565305