{"entity": "researcher", "timestamp": "2026-09-23T18:46:06.259Z", "family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547"}}, "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": "89b02873950641b4a86f525a057a7572", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/89b02873950641b4a86f525a057a7572.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/89b02873950641b4a86f525a057a7572"}}, "title": "Solid-phase capture and profiling of open chromatin by spatial ATAC.", "authors": [{"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/037e17f3f330479fa3bd48fcd0c55684.json"}}, {"family": "Bhalla", "given": "Nayanika", "initials": "N", "orcid": "0000-0002-6800-0432", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8973efc3bbd44e5fb4124583d2c75502.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/132000c8241249d9b2c4cfeb4a058862.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "41", "issue": "8", "pages": "1085-1088", "issn-l": "1087-0156"}, "abstract": "Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.", "doi": "10.1038/s41587-022-01603-9", "pmid": "36604544", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10421738"}, {"db": "pii", "key": "10.1038/s41587-022-01603-9"}], "notes": [], "created": "2026-09-23T07:41:35.186Z", "modified": "2026-09-23T07:41:35.296Z"}, {"entity": "publication", "iuid": "7a9e2a0e40e24344bad397c54a74123a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a9e2a0e40e24344bad397c54a74123a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a9e2a0e40e24344bad397c54a74123a"}}, "title": "Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.", "authors": [{"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Sabelstr\u00f6m", "given": "Hanna", "initials": "H"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04321d9fb805493db538489927a42c8f.json"}}, {"family": "Zhang", "given": "Shupei", "initials": "S"}, {"family": "Basak", "given": "Onur", "initials": "O"}, {"family": "Clevers", "given": "Hans", "initials": "H", "orcid": "0000-0002-3077-5582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1064100a57194938b25d307e5f069b20.json"}}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C", "orcid": "0000-0003-0799-766X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2cb28cab7a447cdb6a627d59ea5f562.json"}}, {"family": "Barnab\u00e9-Heider", "given": "Fanie", "initials": "F"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}], "type": "journal article", "published": "2022-03-01", "journal": {"title": "Cell Reports", "issn": "2211-1247", "volume": "38", "issue": "9", "pages": "110440", "issn-l": null}, "abstract": "Spinal cord ependymal cells display neural stem cell properties in vitro and generate scar-forming astrocytes and remyelinating oligodendrocytes after injury. We report that ependymal cells are functionally heterogeneous and identify a small subpopulation (8% of ependymal cells and 0.1% of all cells in a spinal cord segment), which we denote ependymal A (EpA) cells, that accounts for the in vitro stem cell potential in the adult spinal cord. After spinal cord injury, EpA cells undergo self-renewing cell division as they give rise to differentiated progeny. Single-cell transcriptome analysis revealed a loss of ependymal cell gene expression programs as EpA cells gained signaling entropy and dedifferentiated to a stem-cell-like transcriptional state after an injury. We conclude that EpA cells are highly differentiated cells that can revert to a stem cell state and constitute a therapeutic target for spinal cord repair.", "doi": "10.1016/j.celrep.2022.110440", "pmid": "35235796", "labels": [], "xrefs": [{"db": "pii", "key": "S2211-1247(22)00167-X"}], "notes": [], "created": "2026-09-23T08:44:04.526Z", "modified": "2026-09-23T14:50:42.296Z"}, {"entity": "publication", "iuid": "1e753e21d17c43859a69bddf57c856cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1e753e21d17c43859a69bddf57c856cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1e753e21d17c43859a69bddf57c856cb"}}, "title": "Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.", "authors": [{"family": "Floriddia", "given": "Elisa M", "initials": "EM", "orcid": "0000-0003-2304-8114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70a1f02f113240dba707ef4674f2ee33.json"}}, {"family": "Louren\u00e7o", "given": "T\u00e2nia", "initials": "T"}, {"family": "Zhang", "given": "Shupei", "initials": "S"}, {"family": "van Bruggen", "given": "David", "initials": "D", "orcid": "0000-0001-6794-7731", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28de015d20c0494b9e03eac607cdcfa4.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec435b1759284c98aa17c7dfd11c3617.json"}}, {"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb68d959131542c0bf7e8335a45cadfc.json"}}, {"family": "Gon\u00e7alves Dos Santos", "given": "Jo\u00e3o P", "initials": "JP"}, {"family": "Alt\u0131nk\u00f6k", "given": "M\u00fcge", "initials": "M"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}}, {"family": "Mulinyawe", "given": "Sara B", "initials": "SB"}, {"family": "Gr\u00e3os", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-2707-1488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bb016e746114c0db3a8f2043c36a736.json"}}, {"family": "Sun", "given": "Lu O", "initials": "LO", "orcid": "0000-0002-9293-7241", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a0d175bf20a4f3897753c1ed530b07c.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50ede6d74fde420f8139cef3f0a1ff5e.json"}}], "type": "journal article", "published": "2020-11-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5860", "issn-l": "2041-1723"}, "abstract": "Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.", "doi": "10.1038/s41467-020-19453-x", "pmid": "33203872", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7673029"}, {"db": "pii", "key": "10.1038/s41467-020-19453-x"}], "notes": [], "created": "2026-09-23T06:48:24.545Z", "modified": "2026-09-23T06:48:24.832Z"}, {"entity": "publication", "iuid": "3f7fda5f5f5f4ff28ffe9ee70124a091", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3f7fda5f5f5f4ff28ffe9ee70124a091.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3f7fda5f5f5f4ff28ffe9ee70124a091"}}, "title": "A latent lineage potential in resident neural stem cells enables spinal cord repair.", "authors": [{"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/796c6813bb64461485d5e0c966d46547.json"}}, {"family": "Chell", "given": "James M", "initials": "JM", "orcid": "0000-0003-3019-4750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/093ecd9cbe01413b95212a80988e8367.json"}}, {"family": "Le Merre", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4205-7411", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ebebeabbd3a4bc89ea05d00cc47013a.json"}}, {"family": "Wu", "given": "Yicheng", "initials": "Y"}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Sopova", "given": "Elena", "initials": "E", "orcid": "0000-0001-7561-331X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff45a8ead3b440cba414cc1ec7775268.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Shupliakov", "given": "Oleg", "initials": "O", "orcid": "0000-0001-5352-6848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7c2034256bf49d4a810b5df729703f6.json"}}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5bb1bfff3214cca8753a75f5a251b93.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c428941167b42c495b9fcdb6eb85729.json"}}], "type": "journal article", "published": "2020-10-02", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "370", "issue": "6512", "issn-l": "0036-8075"}, "abstract": "Injuries to the central nervous system (CNS) are inefficiently repaired. Resident neural stem cells manifest a limited contribution to cell replacement. We have uncovered a latent potential in neural stem cells to replace large numbers of lost oligodendrocytes in the injured mouse spinal cord. Integrating multimodal single-cell analysis, we found that neural stem cells are in a permissive chromatin state that enables the unfolding of a normally latent gene expression program for oligodendrogenesis after injury. Ectopic expression of the transcription factor OLIG2 unveiled abundant stem cell-derived oligodendrogenesis, which followed the natural progression of oligodendrocyte differentiation, contributed to axon remyelination, and stimulated functional recovery of axon conduction. Recruitment of resident stem cells may thus serve as an alternative to cell transplantation after CNS injury.", "doi": "10.1126/science.abb8795", "pmid": "33004487", "labels": [], "xrefs": [{"db": "pii", "key": "370/6512/eabb8795"}], "notes": [], "created": "2026-09-23T06:48:00.569Z", "modified": "2026-09-23T06:48:00.861Z"}]}