Genome-wide spatial expression profiling in formalin-fixed tissues

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

doi:10.1016/j.xgen.2021.100065

Genome-wide spatial expression profiling in formalin-fixed tissues

Cell Genom. 2021 Dec 8;1(3):100065. doi: 10.1016/j.xgen.2021.100065.

Authors

Eva Gracia Villacampa¹, Ludvig Larsson¹, Reza Mirzazadeh¹, Linda Kvastad¹, Alma Andersson¹, Annelie Mollbrink¹, Georgia Kokaraki², Vanessa Monteil³, Niklas Schultz^{2

4}, Karin Sofia Appelberg⁵, Nuria Montserrat^{6

7}, Haibo Zhang⁸, Josef M Penninger^{9

10}, Wolfgang Miesbach¹¹, Ali Mirazimi^{3

5

12}, Joseph Carlson², Joakim Lundeberg¹

Affiliations

¹ Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Stockholm, Sweden.
² Department of Oncology-Pathology, Karolinska Institute, 17176 Stockholm, Sweden.
³ Department of Laboratory Medicine, Unit of Clinical Microbiology Karolinska Institutet and Karolinska University Hospital, 17177 Stockholm, Sweden.
⁴ Department of Pathology and Cytology, Karolinska University Hospital, 17176 Stockholm, Sweden.
⁵ Public Health Agency of Sweden, 17182, Solna, Sweden.
⁶ Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Technology (BIST), Barcelona, Spain.
⁷ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
⁸ Departments of Anesthesia, Medicine, and Physiology, University of Toronto, Keenan Research Centre for Biomedical Science, Unity Health Toronto, Toronto, ON, Canada.
⁹ Department of Medical Genetics, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada.
¹⁰ Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
¹¹ Department of Haemostaseology and Haemophilia Center, Institute of Transfusion Medicine, Medical Clinic 2, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany.
¹² National Veterinary Institute, 751 89 Uppsala, Sweden.

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.

Keywords: COVID-19; FFPE; PFA; SARS-CoV-2; Visium; genome-wide; mouse brain; organoids; ovarian carcinosarcoma; spatial transcriptomics.