{"entity": "researcher", "timestamp": "2026-08-20T20:27:32.201Z", "family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "affiliations": ["Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25"}}, "publications": [{"entity": "publication", "iuid": "07172111441645cb84cf0dcbc8a39a5a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07172111441645cb84cf0dcbc8a39a5a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07172111441645cb84cf0dcbc8a39a5a"}}, "title": "Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.", "authors": [{"family": "Kang", "given": "Wenjing", "initials": "W", "orcid": "0000-0001-8732-9631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3dd251e7961740f28c25a0580ec314cb.json"}}, {"family": "Yip", "given": "Wing Hin", "initials": "WH", "orcid": "0000-0002-4282-9453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4078204293b34e1c99f0ebd6bee0e732.json"}}, {"family": "Li-Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e2947dca1e4467aef5342387c5ca7d.json"}}, {"family": "Pedrotti", "given": "Simona", "initials": "S", "orcid": "0000-0001-9502-8556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb6ce1669fc847c5b77fdd25cecd176e.json"}}, {"family": "Yaghi", "given": "Andrea Abou", "initials": "AA"}, {"family": "Murata", "given": "Mitsuyoshi", "initials": "M", "orcid": "0000-0001-9706-8797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604c59620bf844d29dc71c61c40f7bb8.json"}}, {"family": "Salviati", "given": "Lorenzo", "initials": "L", "orcid": "0000-0001-5467-2003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4da8fe43b8474e509e9d83e114e70f91.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Zhang", "given": "Yali", "initials": "Y", "orcid": "0009-0005-8066-1224", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/64d782b175424aca9e73a04890eb64ad.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M"}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F"}, {"family": "Shu", "given": "Xufeng", "initials": "X", "orcid": "0009-0009-0984-5417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f17d670db1f426a9ecaaaaea97a52f5.json"}}, {"family": "Pracana", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-2492-4067", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beea520d340947cb90f1c60bf060feb2.json"}}, {"family": "Shin", "given": "Jay W", "initials": "JW", "orcid": "0000-0003-4037-3533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49d50db4d37d44b4bb8a8f361cbeb2e5.json"}}, {"family": "Kasukawa", "given": "Takeya", "initials": "T", "orcid": "0000-0001-5085-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa0101e9716b4452a07a08e4c1fa22c3.json"}}, {"family": "Yip", "given": "Chi Wai", "initials": "CW", "orcid": "0000-0003-3327-5695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a8cd02560534539a2d7cfdd5ef2cf6b.json"}}, {"family": "Kato", "given": "Masaki", "initials": "M", "orcid": "0009-0006-0846-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384c4d198690412589c72779f0794358.json"}}, {"family": "Takahashi", "given": "Hazuki", "initials": "H", "orcid": "0000-0001-7315-7349", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d834f1581a6b451bb1954d7743a566ab.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/480cdbabfc57460f967e6921f12e6ec4.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9101681a8aa41dab4a9345dfd03add4.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b8da7a1f8524d0e812c83b1f5e20ef6.json"}}], "type": "journal article", "published": "2026-05-27", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be important regulators of such changes; however, the type, abundance, and role of these RNAs during neuronal differentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes occurring during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We reveal a previously unreported phenomenon, in which intronic RNAs engage in long-distance contacts with DNA loci distributed all over the genome. These trans-contacting intronic RNAs (TIRs) are produced from exceptionally long (mean length: 750 kilobases, kb) protein-coding genes that carry ultra-long introns and are selectively expressed in neurons. We show that TIRs do not undergo rapid co-transcriptional degradation but rather accumulate in the nucleus of neuronal cells, forming large 'dot clouds' around their source loci and spreading across the nucleus, as visualized by single-molecule RNA fluorescence in situ hybridization. TIRs engage in contacts with a set of genomic regions (TIR-contacted regions or TIRCs) that carry much shorter (mean length: ~30 kb) neuronally expressed genes forming high-connectivity hubs. We also show that the expression of genes within TIRCs contacted by the same set of TIRs is highly co-varied, and that TIR source genes, especially their introns, are enriched in genetic risk loci for neurodevelopmental and neuropsychiatric disorders. Our findings point to a functional role of the persistence of long intronic RNAs in the nucleus of neuronal cells and might contribute to explain why neurons uniquely express many ultra-long genes. We propose a model in which TIRs form pan-nuclear scaffolds-which we propose to name introsomes-that constitute a dynamically self-renewing regulatory layer, where transcription itself continuously regenerates the very scaffold that organizes genome function in neurons, and that might be involved in the pathogenesis of neurodevelopmental and neuropsychiatric disorders.", "doi": "10.1101/2025.03.13.641826", "pmid": "42244686", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC13232347"}, {"db": "pii", "key": "2025.03.13.641826"}], "notes": [], "created": "2026-08-20T11:01:31.285Z", "modified": "2026-08-20T11:01:31.656Z"}, {"entity": "publication", "iuid": "2e468fb6ee84403d9cddc6c5ef0a7713", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2e468fb6ee84403d9cddc6c5ef0a7713.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2e468fb6ee84403d9cddc6c5ef0a7713"}}, "title": "Modulation of lytic molecules restrain serial killing in \u03b3\u03b4 T lymphocytes.", "authors": [{"family": "Sandoz", "given": "Patrick A", "initials": "PA", "orcid": "0000-0002-8379-7267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d309ec0cb74f41a49a18e226079e6787.json"}}, {"family": "Kuhnigk", "given": "Kyra", "initials": "K", "orcid": "0000-0002-2265-8204", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c9038f497daf47f4b001942f2d6a5788.json"}}, {"family": "Szabo", "given": "Edina K", "initials": "EK"}, {"family": "Thunberg", "given": "Sarah", "initials": "S", "orcid": "0000-0001-6912-6048", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c1a27ca8cd2429098eeb6bbebaa73f5.json"}}, {"family": "Erikson", "given": "Elina", "initials": "E"}, {"family": "Sandstr\u00f6m", "given": "Niklas", "initials": "N", "orcid": "0000-0001-6443-878X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b65278c9896e466f92f62f3ba1e58136.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}}, {"family": "Brech", "given": "Andreas", "initials": "A"}, {"family": "Watzl", "given": "Carsten", "initials": "C", "orcid": "0000-0001-5195-0995", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/705dc690627d4843a59d21e3f2b62ea6.json"}}, {"family": "Wagner", "given": "Arnika K", "initials": "AK"}, {"family": "Alici", "given": "Evren", "initials": "E"}, {"family": "Malmberg", "given": "Karl-Johan", "initials": "KJ", "orcid": "0000-0002-8718-9373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1b891c497ca402aaff79e8082f22553.json"}}, {"family": "Uhlin", "given": "Michael", "initials": "M", "orcid": "0000-0002-2177-6727", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/116cfe482bb941159ee2e7175f1cd095.json"}}, {"family": "\u00d6nfelt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-5178-7593", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b4b8fcbedb54e2ba38633687f417ae8.json"}}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6035", "issn-l": "2041-1723"}, "abstract": "\u03b3\u03b4 T cells play a pivotal role in protection against various types of infections and tumours, from early childhood on and throughout life. They consist of several subsets characterised by adaptive and innate-like functions, with V\u03b39V\u03b42 being the largest subset in human peripheral blood. Although these cells show signs of cytotoxicity, their modus operandi remains poorly understood. Here we explore, using live single-cell imaging, the cytotoxic functions of \u03b3\u03b4 T cells upon interactions with tumour target cells with high temporal and spatial resolution. While \u03b3\u03b4 T cell killing is dominated by degranulation, the availability of lytic molecules appears tightly regulated in time and space. In particular, the limited co-occurrence of granzyme B and perforin restrains serial killing of tumour cells by \u03b3\u03b4 T cells. Thus, our data provide new insights into the cytotoxic arsenal and functions of \u03b3\u03b4 T cells, which may guide the development of more efficient \u03b3\u03b4 T cell based adoptive immunotherapies.", "doi": "10.1038/s41467-023-41634-7", "pmid": "37758698", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10533871"}, {"db": "pii", "key": "10.1038/s41467-023-41634-7"}], "notes": [], "created": "2026-08-20T08:52:55.661Z", "modified": "2026-08-20T08:52:56.006Z"}, {"entity": "publication", "iuid": "2903d3c2bd7c4394976557c749d39360", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2903d3c2bd7c4394976557c749d39360.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2903d3c2bd7c4394976557c749d39360"}}, "title": "NK cells integrate signals over large areas when building immune synapses but require local stimuli for degranulation", "authors": [{"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}}, {"family": "Forslund", "given": "Elin", "initials": "E"}, {"family": "Brandt", "given": "Ludwig", "initials": "L"}, {"family": "Leino", "given": "Mattias", "initials": "M"}, {"family": "Frisk", "given": "Thomas W", "initials": "TW"}, {"family": "Olofsson", "given": "Per E", "initials": "PE", "orcid": "0000-0002-6019-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56eaefeebb1e49628dd3cf68c47541fa.json"}}, {"family": "\u00d6nfelt", "given": "Bj\u00f6rn", "initials": "B"}], "type": "posted-content", "published": "2020-07-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.07.29.224618", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:58:27.737Z", "modified": "2026-08-20T09:58:27.804Z"}, {"entity": "publication", "iuid": "e8ff69c347d040da88e3f25d7aafc45a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e8ff69c347d040da88e3f25d7aafc45a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e8ff69c347d040da88e3f25d7aafc45a"}}, "title": "NK cells switch from granzyme B to death receptor-mediated cytotoxicity during serial killing.", "authors": [{"family": "Prager", "given": "Isabel", "initials": "I"}, {"family": "Liesche", "given": "Clarissa", "initials": "C"}, {"family": "van Ooijen", "given": "Hanna", "initials": "H"}, {"family": "Urlaub", "given": "Doris", "initials": "D"}, {"family": "Verron", "given": "Quentin", "initials": "Q", "orcid": "0000-0001-5800-4379", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/31de7b29ad984949bc1901417bc7ed25.json"}}, {"family": "Sandstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Fasbender", "given": "Frank", "initials": "F"}, {"family": "Claus", "given": "Maren", "initials": "M", "orcid": "0000-0001-8732-0645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5fe94feaa4d4ed8929a35838e2c6915.json"}}, {"family": "Eils", "given": "Roland", "initials": "R"}, {"family": "Beaudouin", "given": "Jo\u00ebl", "initials": "J"}, {"family": "\u00d6nfelt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Watzl", "given": "Carsten", "initials": "C", "orcid": "0000-0001-5195-0995", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/705dc690627d4843a59d21e3f2b62ea6.json"}}], "type": "journal article", "published": "2019-09-02", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "216", "issue": "9", "pages": "2113-2127", "issn-l": "0022-1007"}, "abstract": "NK cells eliminate virus-infected and tumor cells by releasing cytotoxic granules containing granzyme B (GrzB) or by engaging death receptors that initiate caspase cascades. The orchestrated interplay between both cell death pathways remains poorly defined. Here we simultaneously measure the activities of GrzB and caspase-8 in tumor cells upon contact with human NK cells. We observed that NK cells switch from inducing a fast GrzB-mediated cell death in their first killing events to a slow death receptor-mediated killing during subsequent tumor cell encounters. Target cell contact reduced intracellular GrzB and perforin and increased surface-CD95L in NK cells over time, showing how the switch in cytotoxicity pathways is controlled. Without perforin, NK cells were unable to perform GrzB-mediated serial killing and only killed once via death receptors. In contrast, the absence of CD95 on tumor targets did not impair GrzB-mediated serial killing. This demonstrates that GrzB and death receptor-mediated cytotoxicity are differentially regulated during NK cell serial killing.", "doi": "10.1084/jem.20181454", "pmid": "31270246", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6719417"}, {"db": "pii", "key": "jem.20181454"}], "notes": [], "created": "2026-08-20T09:38:15.463Z", "modified": "2026-08-20T09:38:15.563Z"}]}