{"entity": "researcher", "timestamp": "2026-09-23T18:33:39.283Z", "family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.", "Division of Medical Systems Bioengineering, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/013ce63a80ce45339125f0594cb78bc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/013ce63a80ce45339125f0594cb78bc2"}}, "publications": [{"entity": "publication", "iuid": "b04fc38ca1bc41219c5789a45d512463", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b04fc38ca1bc41219c5789a45d512463.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b04fc38ca1bc41219c5789a45d512463"}}, "title": "The regulatory code of injury-responsive enhancers enables precision cell-state targeting in the CNS.", "authors": [{"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Mart\u00ednez-Mart\u00edn", "given": "Adri\u00e1n", "initials": "A", "orcid": "0009-0008-2335-6460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/482a7b0867014f11a9996fd581b4f705.json"}}, {"family": "Rydholm", "given": "Gabriel", "initials": "G", "orcid": "0009-0006-1667-1214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/794282761ade47e59420d9ed7b2bf164.json"}}, {"family": "H\u00e4neke", "given": "Timm", "initials": "T", "orcid": "0000-0002-9734-8307", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ce2f05758324386bd21211f0ccd53ac.json"}}, {"family": "Pintado Almeida", "given": "Laura", "initials": "L"}, {"family": "Se\u00e7ilmi\u015f", "given": "Deniz", "initials": "D"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/013ce63a80ce45339125f0594cb78bc2.json"}}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}}], "type": "journal article", "published": "2026-02-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "29", "issue": "2", "pages": "337-349", "issn-l": "1097-6256"}, "abstract": "Enhancer elements direct cell-type-specific gene expression programs. After injury, cells change their transcriptional state to adapt to stress and initiate repair. Here we investigate how injury-induced transcriptional programs are encoded within enhancers in the mammalian CNS. Leveraging single-nucleus transcriptomics and chromatin accessibility profiling, we identify thousands of injury-induced, cell-type-specific enhancers in the mouse spinal cord after a contusion injury. These are abundant in glial cells and retain cell-type specificity, even when regulating shared wound response genes. By modeling glial injury-responsive enhancers using deep learning, we reveal that their architecture encodes cell-type specificity by integrating generic stimulus response elements with cell identity programs. Finally, through in vivo enhancer screening, we demonstrate that injury-responsive enhancers can selectively target reactive astrocytes across the CNS using therapeutically relevant gene delivery vectors. Our decoding of the principles of injury-responsive enhancers enables the design of sequences that can be programmed to target disease-associated cell states.", "doi": "10.1038/s41593-025-02131-w", "pmid": "41331142", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12880913"}, {"db": "pii", "key": "10.1038/s41593-025-02131-w"}], "notes": [], "created": "2026-09-23T12:34:13.828Z", "modified": "2026-09-23T12:34:14.007Z"}, {"entity": "publication", "iuid": "74b0dacf09d840d796bfe2142a7a64ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74b0dacf09d840d796bfe2142a7a64ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74b0dacf09d840d796bfe2142a7a64ff"}}, "title": "RNA BaseCode: Long-Read RNA Sequences with Short-Read Accuracy", "authors": [{"family": "Hendriks", "given": "Gert Jan", "initials": "GJ", "orcid": "0000-0001-8798-1443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da2c12860dab436f8ba91afc907c516f.json"}}, {"family": "Larsson", "given": "Anton J M", "initials": "AJM", "orcid": "0000-0001-5876-7763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a15fd73b06b44e8bf412c21caf1f054.json"}}, {"family": "de Castroviejo Teba", "given": "Paloma Ruiz", "initials": "PR", "orcid": "0000-0002-7104-1681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1995e28583349738c7e3a041184d88f.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/013ce63a80ce45339125f0594cb78bc2.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}], "type": "posted-content", "published": "2025-12-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.64898/2025.12.09.693136", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:56:04.855Z", "modified": "2026-09-23T15:56:04.963Z"}, {"entity": "publication", "iuid": "b81751065aef4f29a2e84e4f4eee4cda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b81751065aef4f29a2e84e4f4eee4cda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b81751065aef4f29a2e84e4f4eee4cda"}}, "title": "Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells.", "authors": [{"family": "Carrelha", "given": "Joana", "initials": "J", "orcid": "0000-0002-0324-2617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faab09289b454503bc5f7d6081bc0139.json"}}, {"family": "Mazzi", "given": "Stefania", "initials": "S"}, {"family": "Winroth", "given": "Axel", "initials": "A", "orcid": "0009-0002-3314-7781", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82c81bffb2084c2db009202dfdf8182b.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a67d94769764d37a2bf3febd4f79101.json"}}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/013ce63a80ce45339125f0594cb78bc2.json"}}, {"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Seki", "given": "Masafumi", "initials": "M", "orcid": "0000-0003-4671-7026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/874ec57589844c3a96c2719df63353cd.json"}}, {"family": "Brennan", "given": "Margs S", "initials": "MS"}, {"family": "Lehander", "given": "Madeleine", "initials": "M"}, {"family": "Wu", "given": "Bishan", "initials": "B"}, {"family": "Meng", "given": "Yiran", "initials": "Y", "orcid": "0000-0002-9333-2383", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c8b748e8780437295ab3dbca9e66c17.json"}}, {"family": "Markljung", "given": "Ellen", "initials": "E"}, {"family": "Norfo", "given": "Ruggiero", "initials": "R"}, {"family": "Ishida", "given": "Hisashi", "initials": "H", "orcid": "0000-0002-3391-8403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a296b8844bcf482288ee5a8fd3d35726.json"}}, {"family": "Belander Str\u00e5lin", "given": "Karin", "initials": "K", "orcid": "0000-0002-8190-513X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23d1b4284a84e7d92e51855b867ece4.json"}}, {"family": "Grasso", "given": "Francesca", "initials": "F"}, {"family": "Simoglou Karali", "given": "Christina", "initials": "C"}, {"family": "Aliouat", "given": "Affaf", "initials": "A"}, {"family": "Hillen", "given": "Amy", "initials": "A", "orcid": "0000-0002-8567-1545", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e3a8b7ea3184eff95abc40e5b0f6bc9.json"}}, {"family": "Chari", "given": "Edwin", "initials": "E"}, {"family": "Siletti", "given": "Kimberly", "initials": "K"}, {"family": "Thongjuea", "given": "Supat", "initials": "S"}, {"family": "Mead", "given": "Adam J", "initials": "AJ", "orcid": "0000-0001-8522-1002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3d6130b489c440ca31c4998c5820108.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/638b2874e1144bf497bc96f9bce5ccb9.json"}}, {"family": "Nerlov", "given": "Claus", "initials": "C", "orcid": "0000-0002-0544-735X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a91ceeda951400fa27db77db6534ca3.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55acae2b727144ddac3ac6bfe51fc74d.json"}}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32797bad8e1645a881f6b010e604e596.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc8b31b0c69144b89e595fbcb4343717.json"}}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a57175f43784cc2b545be052d6790c8.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Nat. Immunol.", "issn": "1529-2916", "volume": "25", "issue": "6", "pages": "1007-1019", "issn-l": "1529-2908"}, "abstract": "Rare multipotent stem cells replenish millions of blood cells per second through a time-consuming process, passing through multiple stages of increasingly lineage-restricted progenitors. Although insults to the blood-forming system highlight the need for more rapid blood replenishment from stem cells, established models of hematopoiesis implicate only one mandatory differentiation pathway for each blood cell lineage. Here, we establish a nonhierarchical relationship between distinct stem cells that replenish all blood cell lineages and stem cells that replenish almost exclusively platelets, a lineage essential for hemostasis and with important roles in both the innate and adaptive immune systems. These distinct stem cells use cellularly, molecularly and functionally separate pathways for the replenishment of molecularly distinct megakaryocyte-restricted progenitors: a slower steady-state multipotent pathway and a fast-track emergency-activated platelet-restricted pathway. These findings provide a framework for enhancing platelet replenishment in settings in which slow recovery of platelets remains a major clinical challenge.", "doi": "10.1038/s41590-024-01845-6", "pmid": "38816617", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11147777"}, {"db": "pii", "key": "10.1038/s41590-024-01845-6"}], "notes": [], "created": "2026-09-23T08:51:37.070Z", "modified": "2026-09-23T08:51:37.545Z"}]}