{"entity": "researcher", "timestamp": "2026-08-14T13:08:23.556Z", "family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "affiliations": ["Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, 17164 Stockholm, Sweden.", "Astrid Lindgren Children's Hospital , Karolinska University Hospital, Region Stockholm, 17164 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7"}}, "publications": [{"entity": "publication", "iuid": "2c3956defcf44e96ad1976508cd8f7ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed"}}, "title": "Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.", "authors": [{"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Mazan-Mamczarz", "given": "Krystyna", "initials": "K", "orcid": "0009-0005-1545-0500", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c526906891841359c173a86c8ab6414.json"}}, {"family": "Martindale", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0002-3234-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/46adaad64bfc479eb2452956f6a25cc3.json"}}, {"family": "Ye", "given": "Xuan", "initials": "X"}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Banskota", "given": "Nirad", "initials": "N"}, {"family": "Gorospe", "given": "Myriam", "initials": "M", "orcid": "0000-0001-5439-3434", "researcher": {"href": "https://publications.scilifelab.se/researcher/d946f33774fc424fa0ae365eb8079646.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2026-02-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "4", "issn-l": "0305-1048"}, "abstract": "HNRNPU is an RNA-binding protein with diverse roles in transcriptional and post-transcriptional regulation. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we comprehensively investigate the HNRNPU molecular interactome by integrating protein-protein interaction (PPI) mapping, RNA target identification, and genome-wide DNA methylation profiling in human neuroepithelial stem cells and differentiating neural cells. We identified extensive HNRNPU-centered networks, including an association with the mammalian SWI/SNF chromatin-remodeling complex, and uncovered a previously unrecognized role in translation. We present evidence that HNRNPU associates with messenger RNAs (mRNAs) encoding proteins important for neuronal development, including several linked to NDDs. Silencing HNRNPU reprogrammed methylation dynamics at regulatory regions, particularly at active and bivalent promoters of neurodevelopmental transcription factors. Integrative analysis across PPI, RNA, and methylome datasets identified 19 converging genes at all three molecular levels, including NDD genes within the SWI/SNF complex, SMARCA4 and SMARCC2, and RNA-processing machinery such as SYNCRIP. Together, these data showcase HNRNPU as a central coordinator of RNA metabolism and epigenetic remodeling during neural differentiation, linking RNA-binding, chromatin organization, and DNA methylation to the pathogenesis of HNRNPU-related NDDs.", "doi": "10.1093/nar/gkag107", "pmid": "41674383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12895067"}, {"db": "pii", "key": "8474399"}], "notes": [], "created": "2026-02-27T13:05:08.621Z", "modified": "2026-03-24T09:06:45.961Z"}, {"entity": "publication", "iuid": "1885732477df47578922cf7104309bdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1885732477df47578922cf7104309bdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1885732477df47578922cf7104309bdb"}}, "title": "Urine metabolomic profiles of autism and autistic traits-A twin study.", "authors": [{"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/bead50319cae447f90bcf7658d9edf56.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2024-09-03", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "9", "pages": "e0308224", "issn-l": "1932-6203"}, "abstract": "Currently, there are no reliable biomarkers for autism diagnosis. The heterogeneity of autism and several co-occurring conditions are key challenges to establishing these. Here, we used untargeted mass spectrometry-based urine metabolomics to investigate metabolic differences for autism diagnosis and autistic traits in a well-characterized twin cohort (N = 105). We identified 208 metabolites in the urine samples of the twins. No clear, significant metabolic drivers for autism diagnosis were detected when controlling for other neurodevelopmental conditions. However, we identified nominally significant changes for several metabolites. For instance, phenylpyruvate (p = 0.019) and taurine (p = 0.032) were elevated in the autism group, while carnitine (p = 0.047) was reduced. We furthermore accounted for the shared factors, such as genetics within the twin pairs, and report additional metabolite differences. Based on the nominally significant metabolites for autism diagnosis, the arginine and proline metabolism pathway (p = 0.024) was enriched. We also investigated the association between quantitative autistic traits, as measured by the Social Responsiveness Scale 2nd Edition, and metabolite differences, identifying a greater number of nominally significant metabolites and pathways. A significant positive association between indole-3-acetate and autistic traits was observed within the twin pairs (adjusted p = 0.031). The utility of urine biomarkers in autism, therefore, remains unclear, with mixed findings from different study populations.", "doi": "10.1371/journal.pone.0308224", "pmid": "39226293", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11371219"}, {"db": "pii", "key": "PONE-D-23-39743"}], "notes": [], "created": "2024-11-27T13:00:35.687Z", "modified": "2024-11-27T13:00:35.789Z"}, {"entity": "publication", "iuid": "34c38b3d3f564542956074b47323ddb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c38b3d3f564542956074b47323ddb5"}}, "title": "Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.", "authors": [{"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Soldini", "given": "Cristina", "initials": "C"}, {"family": "Alatar", "given": "Shemim", "initials": "S", "orcid": "0009-0009-0738-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/0500cee4755b46479d0818314e5c05a7.json"}}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Molinari", "given": "Maya", "initials": "M"}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Poulet", "given": "Axel", "initials": "A", "orcid": "0000-0002-3415-8960", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4dfc191bbfd4ed6922008f10531835c.json"}}, {"family": "Watts", "given": "Michelle", "initials": "M", "orcid": "0000-0002-3178-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/28a00d3b8c3e40e1b68fc333a7aa4fb7.json"}}, {"family": "Rabkina", "given": "Ielyzaveta", "initials": "I", "orcid": "0000-0001-5890-4115", "researcher": {"href": "https://publications.scilifelab.se/researcher/509d3fdbf53b45acbae3ddea4903a0ba.json"}}, {"family": "Becker", "given": "Martin", "initials": "M", "orcid": "0000-0001-8442-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/85eaa4173364473d83506125206a7193.json"}}, {"family": "Li", "given": "Danyang", "initials": "D", "orcid": "0000-0001-7470-6645", "researcher": {"href": "https://publications.scilifelab.se/researcher/01900295a1904ac886960b3eea5915f0.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM", "orcid": "0000-0002-2488-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c8590243874a0a9f18b9e7138ce9a9.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J", "orcid": "0000-0003-1033-2618", "researcher": {"href": "https://publications.scilifelab.se/researcher/af22620f762a4a5e80dca3f546223caa.json"}}, {"family": "Lundin Remnelius", "given": "Karl", "initials": "K"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Jacob", "given": "Yannick", "initials": "Y", "orcid": "0000-0003-4741-0755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f553bc5034e4768bad65bf8b1236e6a.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Santini", "given": "Emanuela", "initials": "E", "orcid": "0000-0002-8948-9652", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d176892d0f14922bab782fe4cd69e90.json"}}, {"family": "Borgkvist", "given": "Anders", "initials": "A", "orcid": "0000-0003-1698-0288", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c0f5180d7a74249bcfeb59386a7c65d.json"}}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S", "orcid": "0000-0002-4579-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/bead50319cae447f90bcf7658d9edf56.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2023-10-15", "journal": {"title": "Biol Open", "issn": "2046-6390", "volume": "12", "issue": "10", "issn-l": "2046-6390"}, "abstract": "Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level HNRNPU downregulation leads to an increased fraction of neural progenitors in the maturing neuronal population. We conclude that the HNRNPU locus is involved in delayed commitment of neural progenitors to differentiate in cell types with hindbrain profile.", "doi": "10.1242/bio.060113", "pmid": "37815090", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581386"}, {"db": "pii", "key": "330791"}], "notes": [], "created": "2023-11-16T12:03:03.393Z", "modified": "2024-01-16T13:48:31.943Z"}]}