{"entity": "researcher", "timestamp": "2026-07-11T14:14:23.260Z", "family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "affiliations": ["Department of Medical Biochemistry and Biophysics, Division of Molecular Neurobiology, Karolinska Institutet, 17177 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22"}}, "publications": [{"entity": "publication", "iuid": "e5ec787139724ab0bcd41b3b3b928147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147"}}, "title": "Persistent interferon signaling causes sensory neuron plasticity and pain before and during arthritis.", "authors": [{"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Kwak", "given": "Dongoh", "initials": "D"}, {"family": "Picton", "given": "Laurence", "initials": "L"}, {"family": "Xu", "given": "Bingze", "initials": "B"}, {"family": "do Nascimento", "given": "Leandro Flores", "initials": "LF"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Gonzalez", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-7513-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/df94b05dc87c4d5f9e9939170f4d001f.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Xu", "given": "Zhongwei", "initials": "Z", "orcid": "0000-0001-5178-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/f056000b3af842bda8cdd411da7d44ad.json"}}, {"family": "Szczot", "given": "Marcin", "initials": "M", "orcid": "0000-0002-3902-059X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4fef830b2914f37b100c433fbdd4fd0.json"}}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A", "orcid": "0000-0001-5920-9384", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c6e1ed8fbb547b1844b979220d8514a.json"}}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2026-03-10", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Although inflammatory processes in rheumatoid arthritis have been described, mechanisms driving pain are poorly defined. Here, we used a multitude of approaches to uncover the neural basis and causes of inflammatory pain. We show in mice with cartilage autoantibody-induced arthritis that early immune activation and a cytokine storm were mainly driven by vascular cells and monocytes/macrophages in the dorsal root ganglion. However, persistently elevated interferons and receptor activation of the MNK1/MNK2-eIF4E signaling pathway at all disease phases caused sensory-motor dysfunction and pain by inducing hyperexcitability and sensitization of a GFRA3+ C-fiber subtype of joint-innervating sensory neurons. Signaling pathway inhibition in vivo reversed pain and restored limb function. Like mice, human sensory neurons expressed interferon receptors, and type 1 interferons and signaling were increased only in individuals with painful rheumatoid arthritis. The finding that joint pain before and during arthritis is caused by a defined cytokine and signaling pathway holds promise for targeted therapies for pain relief in arthritis.", "doi": "10.1038/s41593-026-02234-y", "pmid": "41807847", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02234-y"}], "notes": [], "created": "2026-03-23T15:25:03.672Z", "modified": "2026-03-23T15:25:04.053Z"}, {"entity": "publication", "iuid": "7f700b3e5e634b2295705bc2ae62f3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb"}}, "title": "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.", "authors": [{"family": "Krauter", "given": "Doris", "initials": "D", "orcid": "0000-0002-1779-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/631f89b570c44663b8c6a29f0759aca2.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "908", "issn-l": "2399-3642"}, "abstract": "Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we present an integrated atlas from published high-quality scRNA-seq datasets and resequencing the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirms cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We present a cell type specific open chromatin atlas revealing enhancer driven regulons and gene-regulatory networks organized into co-regulated gene-programs that together define sensory neuron diversity. Cell type complexity is shown to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.", "doi": "10.1038/s42003-025-08315-1", "pmid": "40500276", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12159162"}, {"db": "pii", "key": "10.1038/s42003-025-08315-1"}], "notes": [], "created": "2025-07-18T10:23:45.299Z", "modified": "2025-11-14T11:07:16.782Z"}, {"entity": "publication", "iuid": "7a9207954e064e188159483708b530ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef"}}, "title": "Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord.", "authors": [{"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Magnusson", "given": "Kajsa A", "initials": "KA", "orcid": "0000-0001-9159-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf40497aadb44dabafaba5e8126d68a.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Calvo-Enrique", "given": "Laura", "initials": "L", "orcid": "0000-0002-9428-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/42206cbfcbb04c0188bea08535937cec.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Albisetti", "given": "Gioele W", "initials": "GW"}, {"family": "Ceder", "given": "Mikaela M", "initials": "MM"}, {"family": "Henriksson", "given": "Katharina", "initials": "K"}, {"family": "Leavitt", "given": "Andrew D", "initials": "AD"}, {"family": "Zeilhofer", "given": "Hanns Ulrich", "initials": "HU", "orcid": "0000-0001-6954-4629", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c122280e0449e6bcdc144cfdf2ebd8.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T", "orcid": "0000-0002-3587-0116", "researcher": {"href": "https://publications.scilifelab.se/researcher/e228cd63f3a84d999ca3781c53a18f27.json"}}, {"family": "Lagerstr\u00f6m", "given": "Malin C", "initials": "MC"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "28", "issue": "5", "pages": "1012-1023", "issn-l": "1097-6256"}, "abstract": "Acute pain is an unpleasant experience caused by noxious stimuli. How the spinal neural circuits attribute differences in quality of noxious information remains unknown. By means of genetic capturing, activity manipulation and single-cell RNA sequencing, we identified distinct neural ensembles in the adult mouse spinal cord encoding mechanical and heat pain. Reactivation or silencing of these ensembles potentiated or stopped, respectively, paw shaking, lifting and licking within but not across the stimuli modalities. Within ensembles, polymodal Gal+ inhibitory neurons with monosynaptic contacts to A-fiber sensory neurons gated pain transmission independent of modality. Peripheral nerve injury led to inferred microglia-driven inflammation and an ensemble transition with decreased recruitment of Gal+ inhibitory neurons and increased excitatory drive. Forced activation of Gal+ neurons reversed hypersensitivity associated with neuropathy. Our results reveal the existence of a spinal representation that forms the neural basis of the discriminative and defensive qualities of acute pain, and these neurons are under the control of a shared feed-forward inhibition.", "doi": "10.1038/s41593-025-01921-6", "pmid": "40128392", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12081300"}, {"db": "pii", "key": "10.1038/s41593-025-01921-6"}], "notes": [], "created": "2025-04-07T09:57:28.435Z", "modified": "2025-11-28T10:46:43.366Z"}, {"entity": "publication", "iuid": "b0a1735fa3c94ba19d53f47c45ce60c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0a1735fa3c94ba19d53f47c45ce60c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0a1735fa3c94ba19d53f47c45ce60c3"}}, "title": "Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation.", "authors": [{"family": "Yu", "given": "Huasheng", "initials": "H", "orcid": "0000-0001-5641-2512", "researcher": {"href": "https://publications.scilifelab.se/researcher/49eee43185cb4ce2840ff16d92691667.json"}}, {"family": "Nagi", "given": "Saad S", "initials": "SS", "orcid": "0000-0001-8773-8232", "researcher": {"href": "https://publications.scilifelab.se/researcher/65b6a02b5f684a94afe0bf52ec1c3737.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Bouchatta", "given": "Otmane", "initials": "O", "orcid": "0000-0002-1639-0600", "researcher": {"href": "https://publications.scilifelab.se/researcher/f720171d0efa4bbc9b08e3e36a7097ae.json"}}, {"family": "Yan", "given": "Hanying", "initials": "H", "orcid": "0000-0002-9227-1742", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a215de0dd63457caa5d2fc3bd569e74.json"}}, {"family": "Cranfill", "given": "Suna Li", "initials": "SL"}, {"family": "Gautam", "given": "Mayank", "initials": "M", "orcid": "0000-0002-7257-5837", "researcher": {"href": "https://publications.scilifelab.se/researcher/4328ae71eb5342e5821c64e715f10213.json"}}, {"family": "Su", "given": "Yijing", "initials": "Y", "orcid": "0000-0002-4146-0068", "researcher": {"href": "https://publications.scilifelab.se/researcher/f928e5321c694db5bd5adafdace2744b.json"}}, {"family": "Lu", "given": "You", "initials": "Y"}, {"family": "Wymer", "given": "James", "initials": "J"}, {"family": "Glanz", "given": "Max", "initials": "M"}, {"family": "Albrecht", "given": "Phillip", "initials": "P"}, {"family": "Song", "given": "Hongjun", "initials": "H", "orcid": "0000-0002-8720-5310", "researcher": {"href": "https://publications.scilifelab.se/researcher/639950331afb4a438698bbba5a832e32.json"}}, {"family": "Ming", "given": "Guo-Li", "initials": "GL", "orcid": "0000-0002-2517-6075", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2cbf0b747b54a099eb460966a4963d0.json"}}, {"family": "Prouty", "given": "Stephen", "initials": "S"}, {"family": "Seykora", "given": "John", "initials": "J"}, {"family": "Wu", "given": "Hao", "initials": "H", "orcid": "0000-0003-4395-6929", "researcher": {"href": "https://publications.scilifelab.se/researcher/6984bc1467cb411ea939f6c16c666be5.json"}}, {"family": "Ma", "given": "Minghong", "initials": "M", "orcid": "0000-0002-5027-9623", "researcher": {"href": "https://publications.scilifelab.se/researcher/05c889e0338440f0ae420738e686e411.json"}}, {"family": "Marshall", "given": "Andrew", "initials": "A", "orcid": "0000-0001-8273-7089", "researcher": {"href": "https://publications.scilifelab.se/researcher/79300c405b1546c89d5a9858bc729c0a.json"}}, {"family": "Rice", "given": "Frank L", "initials": "FL"}, {"family": "Li", "given": "Mingyao", "initials": "M", "orcid": "0000-0003-2422-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bab87c8d264240a71dd1142cb4db48.json"}}, {"family": "Olausson", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-6319-1786", "researcher": {"href": "https://publications.scilifelab.se/researcher/02cd686b0d8e43df980217b9cc70718d.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Luo", "given": "Wenqin", "initials": "W", "orcid": "0000-0002-2486-807X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd94cdc96d07408187b5e61cf126ce4f.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "27", "issue": "12", "pages": "2326-2340", "issn-l": "1097-6256"}, "abstract": "The versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human (h)DRG neurons-critical information to decipher their functions-are lacking due to technical difficulties. In this study, we isolated somata from individual hDRG neurons and conducted deep RNA sequencing (RNA-seq) to detect, on average, over 9,000 unique genes per neuron, and we identified 16 neuronal types. These results were corroborated and validated by spatial transcriptomics and RNAscope in situ hybridization. Cross-species analyses revealed divergence among potential pain-sensing neurons and the likely existence of human-specific neuronal types. Molecular-profile-informed microneurography recordings revealed temperature-sensing properties across human sensory afferent types. In summary, by employing single-soma deep RNA-seq and spatial transcriptomics, we generated an hDRG neuron atlas, which provides insights into human somatosensory physiology and serves as a foundation for translational work.", "doi": "10.1038/s41593-024-01794-1", "pmid": "39496796", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11614738"}, {"db": "pii", "key": "10.1038/s41593-024-01794-1"}], "notes": [], "created": "2025-02-28T14:15:48.562Z", "modified": "2025-02-28T14:15:49.449Z"}, {"entity": "publication", "iuid": "4333ee23db77472a96803fe7220c99ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4333ee23db77472a96803fe7220c99ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4333ee23db77472a96803fe7220c99ff"}}, "title": "Glioblastoma cytotoxicity conferred through dual disruption of endolysosomal homeostasis by Vacquinol-1.", "authors": [{"family": "Kwak", "given": "Dongoh", "initials": "D"}, {"family": "Hammarstr\u00f6m", "given": "Lars G J", "initials": "LGJ"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2021-10-15", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "issn-l": null, "volume": "3", "issue": "1", "pages": "vdab152"}, "abstract": "Increased membrane trafficking is observed in numerous cancer types, including glioblastoma. Targeting the oncogenic driven acquired alterations in membrane trafficking by synthetic cationic amphiphilic small molecules has recently been shown to induce death of glioblastoma cells, although the molecular targets are unknown.\r\n\r\nThe mechanism of action of the cationic amphiphilic drug Vacquinol-1 (Vacq1)-induced cytotoxicity was investigated using cell biology, biochemistry, functional experiments, chemical biology, unbiased antibody-based post-translation modification profiling, and mass spectrometry-based chemical proteomic analysis on patient-derived glioblastoma cells.\r\n\r\nVacq1 induced two types of abnormal endolysosomal vesicles, enlarged vacuoles and acidic vesicle organelles (AVOs). Mechanistically, enlarged vacuoles were formed by the impairment of lysosome reformation through the direct interaction and inhibition of calmodulin (CaM) by Vacq1, while AVO formation was induced by Vacq1 accumulation and acidification in the endosomal compartments through its activation of the v-ATPase. As a consequence of v-ATPase activation, cellular ATP consumption markedly increased, causing cellular energy shortage and cytotoxicity. This effect of Vacq1 was exacerbated by its inhibitory effects on calmodulin, causing lysosomal depletion and a failure of acidic vesicle organelle clearance.\r\n\r\nOur study identifies the targets of Vacq1 and the mechanisms underlying its selective cytotoxicity in glioblastoma cells. The dual function of Vacq1 sets in motion a glioblastoma-specific vicious cycle of ATP consumption resulting in cellular energy crisis and cell death.", "doi": "10.1093/noajnl/vdab152", "pmid": "34765974", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "vdab152"}, {"db": "pmc", "key": "PMC8577523"}], "notes": [], "created": "2022-02-21T09:19:05.112Z", "modified": "2025-10-17T13:04:28.013Z"}, {"entity": "publication", "iuid": "634a4941b9a3488cb12cafd4aab1d5e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2"}}, "title": "Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.", "authors": [{"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D"}, {"family": "Parisien", "given": "Marc", "initials": "M", "orcid": "0000-0003-2924-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/046deabca7484670a0c9f7378580d7f5.json"}}, {"family": "Lou", "given": "Daohua", "initials": "D"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Fatt", "given": "Michael", "initials": "M"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Sp\u00e5ngberg", "given": "Mats", "initials": "M"}, {"family": "Eriksson", "given": "Bengt", "initials": "B"}, {"family": "Barkas", "given": "Nikolaos", "initials": "N", "orcid": "0000-0002-4675-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/969cdbac84bb434d865b99c3d21be988.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}, {"family": "Khoury", "given": "Samar", "initials": "S"}, {"family": "Diatchenko", "given": "Luda", "initials": "L", "orcid": "0000-0002-1350-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ff8b8cc7d444732a4dfcb0c9e3d8507.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1510", "issn-l": "2041-1723"}, "abstract": "Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.", "doi": "10.1038/s41467-021-21725-z", "pmid": "33686078", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21725-z"}, {"db": "pmc", "key": "PMC7940623"}], "notes": [], "created": "2021-06-09T12:16:22.425Z", "modified": "2024-01-16T13:48:40.539Z"}, {"entity": "publication", "iuid": "1cffa41cd92b4f0aad44c320905ffe52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1cffa41cd92b4f0aad44c320905ffe52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1cffa41cd92b4f0aad44c320905ffe52"}}, "title": "Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing.", "authors": [{"family": "Morarach", "given": "Khomgrit", "initials": "K"}, {"family": "Mikhailova", "given": "Anastassia", "initials": "A"}, {"family": "Knoflach", "given": "Viktoria", "initials": "V"}, {"family": "Memic", "given": "Fatima", "initials": "F", "orcid": "0000-0002-8876-1212", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5dcdcbf16f4caab9cea24133389afb.json"}}, {"family": "Kumar", "given": "Rakesh", "initials": "R"}, {"family": "Li", "given": "Wei", "initials": "W"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Marklund", "given": "Ulrika", "initials": "U", "orcid": "0000-0003-1426-1271", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f82ee40ccd49adbbb72d2994df6cb9.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "24", "issue": "1", "pages": "34-46"}, "abstract": "Autonomous regulation of the intestine requires the combined activity of functionally distinct neurons of the enteric nervous system (ENS). However, the variety of enteric neuron types and how they emerge during development remain largely unknown. Here, we define a molecular taxonomy of 12 enteric neuron classes within the myenteric plexus of the mouse small intestine using single-cell RNA sequencing. We present cell-cell communication features and histochemical markers for motor neurons, sensory neurons and interneurons, together with transgenic tools for class-specific targeting. Transcriptome analysis of the embryonic ENS uncovers a novel principle of neuronal diversification, where two neuron classes arise through a binary neurogenic branching and all other identities emerge through subsequent postmitotic differentiation. We identify generic and class-specific transcriptional regulators and functionally connect Pbx3 to a postmitotic fate transition. Our results offer a conceptual and molecular resource for dissecting ENS circuits and predicting key regulators for directed differentiation of distinct enteric neuron classes.", "doi": "10.1038/s41593-020-00736-x", "pmid": "33288908", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-020-00736-x"}, {"db": "pmc", "key": "PMC7610403"}, {"db": "mid", "key": "EMS118468"}], "notes": [], "created": "2020-12-10T11:10:40.536Z", "modified": "2024-01-16T13:48:41.067Z"}, {"entity": "publication", "iuid": "5772fc9a0bde4a55bcf300028482da2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e"}}, "title": "Spatiotemporal structure of cell fate decisions in murine neural crest", "authors": [{"family": "Soldatov", "given": "Ruslan", "initials": "R", "orcid": "0000-0002-5670-5881", "researcher": {"href": "https://publications.scilifelab.se/researcher/3800b61f5f7042e89514b439e9532a97.json"}}, {"family": "Kaucka", "given": "Marketa", "initials": "M", "orcid": "0000-0002-8781-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/933187e42ddc4ab6a29c46d5cca411e6.json"}}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Petersen", "given": "Julian", "initials": "J", "orcid": "0000-0002-7444-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d20bbfd5a540a58aac82ada8d80b0d.json"}}, {"family": "Chontorotzea", "given": "Tatiana", "initials": "T", "orcid": "0000-0002-6134-1365", "researcher": {"href": "https://publications.scilifelab.se/researcher/7426e1056a94430bb9ab69191e623fd2.json"}}, {"family": "Englmaier", "given": "Lukas", "initials": "L", "orcid": "0000-0002-0082-2616", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba3d0eb3f634ccda4e6562c37bd77f2.json"}}, {"family": "Akkuratova", "given": "Natalia", "initials": "N", "orcid": "0000-0001-6733-8119", "researcher": {"href": "https://publications.scilifelab.se/researcher/68fc565dc99b4e8eb61d39dcef0f3a48.json"}}, {"family": "Yang", "given": "Yunshi", "initials": "Y", "orcid": "0000-0003-0396-5257", "researcher": {"href": "https://publications.scilifelab.se/researcher/4663511b58bd4c0f9c69da8445c7974b.json"}}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M", "orcid": "0000-0003-4949-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafb570acc6d40159228d08f9dcc985f.json"}}, {"family": "Dyachuk", "given": "Viacheslav", "initials": "V", "orcid": "0000-0001-8100-7367", "researcher": {"href": "https://publications.scilifelab.se/researcher/a32abc6aafed40e382beb35f873ae91c.json"}}, {"family": "Bock", "given": "Christoph", "initials": "C", "orcid": "0000-0001-6091-3088", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab95ee1c8284fa7bf2e5a2ee987c835.json"}}, {"family": "Farlik", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0698-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/906ad9a447b64e028f9cf41fbeaea108.json"}}, {"family": "Piacentino", "given": "Michael L", "initials": "ML", "orcid": "0000-0003-1773-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75e58e24dbcf4b8ba91ce39db1491c69.json"}}, {"family": "Boismoreau", "given": "Franck", "initials": "F"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Bronner", "given": "Marianne E", "initials": "ME", "orcid": "0000-0003-4274-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/56516b93bfb047aeab63c9d2fee21d4a.json"}}, {"family": "Croci", "given": "Laura", "initials": "L", "orcid": "0000-0002-7826-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e08f8646894441297506e2a3eb5fb57.json"}}, {"family": "Hsiao", "given": "Wen Yu", "initials": "WY"}, {"family": "Guertin", "given": "David A", "initials": "DA"}, {"family": "Brunet", "given": "Jean Francois", "initials": "JF", "orcid": "0000-0002-1985-6103", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e7516ee3e5a47ed9b6163b10d5baf9a.json"}}, {"family": "Consalez", "given": "Gian Giacomo", "initials": "GG", "orcid": "0000-0003-4594-6273", "researcher": {"href": "https://publications.scilifelab.se/researcher/1eabaebce3194d9c93e65ce4123f4254.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Fried", "given": "Kaj", "initials": "K", "orcid": "0000-0002-9997-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eaae026524ee6b9b589f12846b458.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal-article", "published": "2019-06-07", "journal": {"volume": "364", "issn": "0036-8075", "issue": "6444", "pages": "eaas9536", "title": "Science", "issn-l": null}, "abstract": "Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor Twist1. The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial coactivation of bipotential properties followed by gradual shifts toward commitment. Competing fate programs are coactivated before cells acquire fate-specific phenotypic traits. Determination of a specific fate is achieved by increased synchronization of relevant programs and concurrent repression of competing fate programs.", "doi": "10.1126/science.aas9536", "pmid": "31171666", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "364/6444/eaas9536"}], "notes": [], "created": "2019-06-12T08:11:45.162Z", "modified": "2025-10-17T13:02:18.356Z"}]}