{"entity": "researcher", "timestamp": "2026-06-15T16:52:12.678Z", "family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713"}}, "publications": [{"entity": "publication", "iuid": "663259e242554c7aa13f3a0303e14035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035"}}, "title": "Classification of Paediatric Celiac Disease Using RNA Sequencing and Real-Time PCR of Duodenal Biomarkers.", "authors": [{"family": "Bragde", "given": "Hanna Gustafsson", "initials": "HG", "orcid": "0000-0001-9104-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/7192535c27614e7a81122bef9fee9d42.json"}}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "S\u00f6derman", "given": "Jan", "initials": "J", "orcid": "0000-0001-7505-7210", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e27f9f58384d158dc7bb019e4a97db.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "J. Cell. Mol. Med.", "issn": "1582-4934", "volume": "29", "issue": "18", "pages": "e70854", "issn-l": "1582-1838"}, "abstract": "Celiac disease (CD) diagnosis in children with sub-threshold tissue transglutaminase autoantibody (anti-TG2) levels requires a small intestinal biopsy. Through RNA sequencing and real-time PCR of small intestinal biopsies, gene expression in such children was compared with the expression in children with active CD and anti-TG2 levels above the threshold, and with non-CD children. The study also included CD children with a non-diagnostic first biopsy to explore early gene expression changes in CD. The aim of the study was to explore gene expression in relation to anti-TG2 levels, investigate gene expression in Potential CD, and provide a gene expression profile to aid in CD diagnostics. The results showed that in active CD, expression changes involved genes associated with e.g., immune response, transport, angiogenesis, and epithelial barrier function, with even more pronounced changes of genes associated with cell cycle progression, absorption, lipid and lipoprotein processes, and retinoid metabolism in the active CD group with higher anti-TG2 levels. Gene expression changes in CD children with a non-diagnostic first biopsy showed large inter-individual variations, but in general, gene expressions were associated with many of the same biological contexts as in active CD, including epithelial barrier function. Overall, the results show that gene expression profiling has great potential as a complement to the histopathologic assessment in CD diagnostics, even early in the disease course, but probably cannot be used for prognostic purposes.", "doi": "10.1111/jcmm.70854", "pmid": "40977520", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12451401"}], "notes": [], "created": "2025-09-30T13:39:32.092Z", "modified": "2025-11-28T10:51:11.561Z"}, {"entity": "publication", "iuid": "a38ee778ff164c3f81c0f75f0c598e62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62"}}, "title": "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.", "authors": [{"family": "Mazzurana", "given": "Luca", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Wigge", "given": "Leif", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Williams", "given": "Teresa C", "initials": "TC"}, {"family": "Ravindran", "given": "Avinash", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "S\u00e4fholm", "given": "Jesper", "initials": "J"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "Orre", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "H\u00f6\u00f6g", "given": "Charlotte", "initials": "C"}, {"family": "Hedin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-4921-8516", "researcher": {"href": "https://publications.scilifelab.se/researcher/d451be670f7f456ebca935690af79076.json"}}, {"family": "Szczegielniak", "given": "Sylwester", "initials": "S"}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Cell Res", "issn": "1001-0602", "issn-l": null, "volume": "31", "issue": "5", "pages": "554-568"}, "abstract": "The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident na\u00efve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2- ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-\u03b4 rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.", "doi": "10.1038/s41422-020-00445-x", "pmid": "33420427", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41422-020-00445-x"}, {"db": "pmc", "key": "PMC8089104"}], "notes": [], "created": "2021-01-11T12:39:39.962Z", "modified": "2024-01-16T13:48:39.843Z"}]}