{"entity": "researcher", "timestamp": "2026-08-08T15:55:19.245Z", "family": "Sounart", "given": "Hailey", "initials": "H", "orcid": "0009-0000-5772-3961", "affiliations": ["Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089"}}, "publications": [{"entity": "publication", "iuid": "59d7ae58ceea4c3bb2eb1e766d18641a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a"}}, "title": "Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitis", "authors": [{"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Castillo", "given": "Francisca", "initials": "F"}, {"family": "Chi", "given": "Yuhao", "initials": "Y"}, {"family": "He", "given": "Ning", "initials": "N"}, {"family": "Suarez-Alvarez", "given": "Martin", "initials": "M"}, {"family": "Ulloa", "given": "Maria Alejandra", "initials": "MA"}, {"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Okhovat", "given": "Ali", "initials": "A"}, {"family": "Sounart", "given": "Hailey", "initials": "H", "orcid": "0009-0000-5772-3961", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089.json"}}, {"family": "Zagami", "given": "Chiara", "initials": "C"}, {"family": "Cardoso", "given": "Rebeca F", "initials": "RF"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Mechling", "given": "Anna", "initials": "A"}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH"}, {"family": "Smith", "given": "Philip", "initials": "P"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}], "type": "journal-article", "published": "2026-06-00", "journal": {"title": "Immunity", "issn": "1074-7613", "volume": "59", "issue": "6", "pages": "1599-1615.e5", "issn-l": null}, "abstract": "Inflammatory bowel disease (IBD) is a complex disorder that is often resistant to immunomodulatory treatments. Here, to understand how immune, epithelial, and stromal compartments are rewired during disease initiation and progression, we leveraged T cell transfer and Il10-/- spontaneous colitis models, including anti-IL-12p40 intervention, and integrated time-course transcriptomic analyses at bulk, single-cell, and spatial resolution. These well-established models exhibited conserved features of chronic inflammation, including neutrophil infiltration, and impaired tissue regeneration. Comparison of murine transcriptional programs and human IBD datasets revealed neutrophil-associated inflammation and cytokine signaling as the most conserved pathways across species. We identified spatial heterogeneity in inflammatory modules and described three gene programs with differential spatial and temporal distributions, including one corresponding to tertiary lymphoid structures. When used together, these models recapitulate complementary aspects of human disease at both cellular and transcriptional levels. This high-resolution spatiotemporal atlas will guide future translational research aimed at optimizing therapeutic strategies for IBD.", "doi": "10.1016/j.immuni.2026.04.005", "pmid": "42097141", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(26)00167-6"}], "notes": [], "created": "2026-05-11T11:50:48.709Z", "modified": "2026-06-29T07:40:31.984Z"}, {"entity": "publication", "iuid": "61870ecf000246d1bfc7c1a38844d67c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61870ecf000246d1bfc7c1a38844d67c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61870ecf000246d1bfc7c1a38844d67c"}}, "title": "Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale.", "authors": [{"family": "Sounart", "given": "Hailey", "initials": "H", "orcid": "0009-0000-5772-3961", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089.json"}}, {"family": "Voronin", "given": "Denis", "initials": "D"}, {"family": "Masarapu", "given": "Yuvarani", "initials": "Y", "orcid": "0000-0002-3267-2085", "researcher": {"href": "https://publications.scilifelab.se/researcher/055fa17f6cdd490e87182c94c847c440.json"}}, {"family": "Chung", "given": "Matthew", "initials": "M"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "Ghedin", "given": "Elodie", "initials": "E", "orcid": "0000-0002-1515-725X", "researcher": {"href": "https://publications.scilifelab.se/researcher/999da8f68b344372874fec159e5a986b.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}], "type": "journal article", "published": "2023-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6500", "issn-l": "2041-1723"}, "abstract": "Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization; to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia. However, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we spatially explored how Wolbachia interacts with the worm's reproductive system by performing a spatial characterization using Spatial Transcriptomics (ST) across a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method's ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions, also under antibiotic treatment. We envision our approach will open up new avenues for the study of infectious diseases caused by micro-scale parasitic worms.", "doi": "10.1038/s41467-023-42237-y", "pmid": "37838705", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10576761"}, {"db": "pii", "key": "10.1038/s41467-023-42237-y"}], "notes": [], "created": "2024-11-25T10:16:00.794Z", "modified": "2024-11-25T10:16:00.902Z"}]}