{"entity": "publication", "iuid": "f2fbb06f1e4747a99932396a216fa5b1", "timestamp": "2026-09-01T08:24:41.009Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2fbb06f1e4747a99932396a216fa5b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2fbb06f1e4747a99932396a216fa5b1"}}, "title": "Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.", "authors": [{"family": "Sounart", "given": "Hailey", "initials": "H"}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E"}, {"family": "Masarapu", "given": "Yuvarani", "initials": "Y"}, {"family": "Wu", "given": "Jian", "initials": "J"}, {"family": "V\u00e1rkonyi", "given": "Tibor", "initials": "T"}, {"family": "Glasz", "given": "Tibor", "initials": "T"}, {"family": "Kiss", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Hill", "given": "Andrew", "initials": "A"}, {"family": "Rezene", "given": "Sefanit", "initials": "S"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Jurek", "given": "Aleksandra", "initials": "A"}, {"family": "Niesnerov\u00e1", "given": "Anezka", "initials": "A"}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a9c4a7494ba4284ab52158e6cbc85da.json"}}], "type": "journal article", "published": "2023-10-19", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "24", "issue": "1", "pages": "237", "issn-l": "1474-7596"}, "abstract": "Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.", "doi": "10.1186/s13059-023-03080-y", "pmid": "37858234", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10588020"}, {"db": "pii", "key": "10.1186/s13059-023-03080-y"}], "notes": [], "created": "2026-08-20T12:21:47.688Z", "modified": "2026-08-20T12:21:47.727Z"}