{"entity": "researcher", "timestamp": "2026-06-15T17:48:18.575Z", "family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "affiliations": ["Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden. karin.nilsson@igp.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176"}}, "publications": [{"entity": "publication", "iuid": "833c3f2b059a4f12856d43fb4a7e02e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3"}}, "title": "Rare germline variants contribute to glioma predisposition: Whole-genome analysis of a regional cohort of glioma patients.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A", "orcid": "0009-0003-4573-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6fcd448d744a99945a361353add88f.json"}}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Hammermeister Suger", "given": "Austin", "initials": "A", "orcid": "0000-0002-6599-2202", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5c4526d1504762a430373285155fab.json"}}, {"family": "Pensch", "given": "Raphaela", "initials": "R", "orcid": "0000-0002-0313-8369", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfb52298bf146c9a327c2fbe2e5e7cb.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4201-8204", "researcher": {"href": "https://publications.scilifelab.se/researcher/086ede39254945288fb9c708f98eb0cd.json"}}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Dahlin", "given": "Anna Margareta", "initials": "AM"}, {"family": "Melin", "given": "Beatrice", "initials": "B", "orcid": "0000-0002-9982-3757", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ee34db763294de2b7dec15a9ffe8aee.json"}}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "8", "issue": "1", "pages": "vdag038", "issn-l": null}, "abstract": "Gliomas are the most common malignant primary tumor of the central nervous system and show a high mortality, particularly at higher grades. Cancer predisposition syndromes and common low-penetrance single nucleotide polymorphisms have been shown to contribute to glioma risk, but the contribution of rare germline variants remains incompletely understood. Here, we investigated rare germline variants in glioma patients.\n\nWe performed whole-genome sequencing on 113 glioma patients from Northern Sweden, analyzing rare germline variants across 651 genes. Variants were compared to population controls (ACpop, gnomAD) and validated in TCGA glioma data, a UK Biobank glioma nested case-control study, and a separate cohort of 105 Swedish glioblastomas.\n\n17.6% of glioma cases carried a Pathogenic or Likely Pathogenic (P/LP) variant within 1 of the 651 genes, and the number of alleles carrying a P/LP was significantly more than in the reference data (P = ). Many of the observed candidate genes also harbored P/LP variants in our Swedish validation cohort. Overall, gene-based comparison of rare coding variants indicated an enrichment in several genes, including 3.2 \u00d7 10 - 3TP53, CREBBP, and DNMT3A.\n\nRare P/LP germline variants were more frequent among glioma patients than in the reference population within our predefined gene set. These results suggest a contribution of rare germline variants to glioma risk, particularly in genes involved in DNA repair. While several genes are indicated as enriched with rare variants, only TP53 validates across all 3 patient sets.", "doi": "10.1093/noajnl/vdag038", "pmid": "41878702", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13007284"}, {"db": "pii", "key": "vdag038"}], "notes": [], "created": "2026-03-26T20:20:23.541Z", "modified": "2026-03-26T20:20:24.274Z"}, {"entity": "publication", "iuid": "b7086e5f716e435090388237fe0eaeb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5"}}, "title": "Lack of ST2 aggravates glioma invasiveness, vascular abnormality, and immune suppression.", "authors": [{"family": "Wicher", "given": "Grzegorz", "initials": "G"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Vaccaro", "given": "Alessandra", "initials": "A"}, {"family": "Vemuri", "given": "Kalyani", "initials": "K"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Imbria", "given": "Rebeca-Noemi", "initials": "RN"}, {"family": "Belting", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2025-01-27", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "7", "issue": "1", "pages": "vdaf010", "issn-l": null}, "abstract": "Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, characterized by aggressive growth and a dismal prognosis. Interleukin-33 (IL-33) and its receptor ST2 have emerged as regulators of glioma growth, but their exact function in tumorigenesis has not been deciphered. Indeed, previous studies on IL-33 in cancer have yielded somewhat opposing results as to whether it is pro- or anti-tumorigenic.\n\nIL-33 expression was assessed in a GBM tissue microarray and public databases. As in vivo models we used orthotopic xenografts of patient-derived GBM cells, and syngenic models with grafted mouse glioma cells.\n\nWe analyzed the role of IL-33 and its receptor ST2 in nonmalignant cells of the glioma microenvironment and found that IL-33 levels are increased in cells surrounding the tumor. Protein complexes of IL-33 and ST2 are mainly found outside of the tumor core. The IL-33-producing cells consist primarily of oligodendrocytes. To determine the function of IL-33 in the tumor microenvironment, we used mice lacking the ST2 receptor. When glioma cells were grafted to ST2-deficient mouse brains, the resulting tumors exhibited a more invasive growth pattern, and are associated with poorer survival, compared to wild-type mice. Tumors in ST2-deficient hosts are more invasive, with increased expression of extracellular matrix remodeling enzymes and enhanced tumor angiogenesis. Furthermore, the absence of ST2 leads to a more immunosuppressive environment.\n\nOur findings reveal that glia-derived IL-33 and its receptor ST2 participate in modulating tumor invasiveness, tumor vasculature, and immunosuppression in glioma.", "doi": "10.1093/noajnl/vdaf010", "pmid": "39931535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11808570"}, {"db": "pii", "key": "vdaf010"}], "notes": [], "created": "2025-09-08T11:37:18.675Z", "modified": "2025-09-08T11:37:18.685Z"}, {"entity": "publication", "iuid": "6cea0eb350cd40bba54717d8b627da6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b"}}, "title": "Leveraging base-pair mammalian constraint to understand genetic variation and human disease.", "authors": [{"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f84c888473d45ea8d8e97945d508705.json"}}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S", "orcid": "0000-0002-7746-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/538c86311b2549d6a5214a5562578cc2.json"}}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/087384bb1f8743158b76352c8847d48d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Xue", "given": "James", "initials": "J", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Yao", "given": "Shuyang", "initials": "S", "orcid": "0000-0001-9669-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcd036ee020e4622ad16d020bfcd7b38.json"}}, {"family": "Sun", "given": "Quan", "initials": "Q", "orcid": "0000-0001-8324-2803", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed5ee3899858449cae82e6be2e6faca6.json"}}, {"family": "Szatkiewicz", "given": "Jin", "initials": "J", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}, {"family": "Wen", "given": "Jia", "initials": "J"}, {"family": "Huckins", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-5369-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/aef1cd06be604bc9ac483e888bf2235d.json"}}, {"family": "Lawler", "given": "Alyssa", "initials": "A", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications.scilifelab.se/researcher/60254d61d3d64a8e80eee17c1e3d24db.json"}}, {"family": "Zheng", "given": "Zhili", "initials": "Z", "orcid": "0000-0003-2102-221X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6856724cd504fca8624fc001f9e6381.json"}}, {"family": "Zeng", "given": "Jian", "initials": "J", "orcid": "0000-0001-8801-5220", "researcher": {"href": "https://publications.scilifelab.se/researcher/483f4a2875dd42a68b4f6f4e18c503ec.json"}}, {"family": "Wray", "given": "Naomi R", "initials": "NR", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "Li", "given": "Yun", "initials": "Y", "orcid": "0000-0002-9275-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/c294ce82ce8946428048b9b4e3e9cad8.json"}}, {"family": "Johnson", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4519-3120", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2cc5da674c44d4cb58c1f98d145043a.json"}}, {"family": "Chen", "given": "Jiawen", "initials": "J", "orcid": "0000-0002-6193-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39de15a492f34e4b8e237e748c38524b.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2937"}, "abstract": "Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2023-12-01T08:54:10.456Z", "modified": "2024-01-16T13:48:33.619Z"}, {"entity": "publication", "iuid": "e913056a4e7f4aad822efbc06d4f28d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e913056a4e7f4aad822efbc06d4f28d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e913056a4e7f4aad822efbc06d4f28d5"}}, "title": "Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes.", "authors": [{"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Haseeb", "given": "Lulu", "initials": "L"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2020-06-09", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "21", "issue": "1", "pages": "127", "issn-l": "1474-7596"}, "abstract": "Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions.\n\nWe validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites.\n\nThese results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.", "doi": "10.1186/s13059-020-02035-x", "pmid": "32513296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-020-02035-x"}, {"db": "pmc", "key": "PMC7281935"}], "notes": [], "created": "2020-06-10T22:06:24.696Z", "modified": "2024-01-16T13:48:42.389Z"}]}