{"entity": "researcher", "timestamp": "2026-09-23T22:40:00.794Z", "family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "affiliations": ["Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2"}}, "publications": [{"entity": "publication", "iuid": "1d629cb35a5146c787baaa4ade6dd381", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1d629cb35a5146c787baaa4ade6dd381.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1d629cb35a5146c787baaa4ade6dd381"}}, "title": "Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.", "authors": [{"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa189d497af4380b7db4c1aba55ae80.json"}}, {"family": "Adler", "given": "Andrew F", "initials": "AF"}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M"}, {"family": "van Lunteren", "given": "Josina Anna", "initials": "JA"}, {"family": "Nolbrant", "given": "Sara", "initials": "S", "orcid": "0000-0003-2184-1741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4659a9108d743a59cf24d5a5df71582.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Vasylovska", "given": "Svitlana", "initials": "S", "orcid": "0000-0003-0682-3449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f1b1e3a159d40679255275a858f6fec.json"}}, {"family": "Yoshitake", "given": "Takashi", "initials": "T"}, {"family": "Kehr", "given": "Jan", "initials": "J"}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5bb1bfff3214cca8753a75f5a251b93.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8078f1505d9747e1ac76cf2f6d4ee606.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8d36e78309f45f8879f07e42682b29d.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2963ca6a73bb409baea88ca67eeca936.json"}}], "type": "journal article", "published": "2022-06-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "3046", "issn-l": "2041-1723"}, "abstract": "Stem cell therapies for Parkinson's disease (PD) have entered first-in-human clinical trials using a set of technically related methods to produce mesencephalic dopamine (mDA) neurons from human pluripotent stem cells (hPSCs). Here, we outline an approach for high-yield derivation of mDA neurons that principally differs from alternative technologies by utilizing retinoic acid (RA) signaling, instead of WNT and FGF8 signaling, to specify mesencephalic fate. Unlike most morphogen signals, where precise concentration determines cell fate, it is the duration of RA exposure that is the key-parameter for mesencephalic specification. This concentration-insensitive patterning approach provides robustness and reduces the need for protocol-adjustments between hPSC-lines. RA-specified progenitors promptly differentiate into functional mDA neurons in vitro, and successfully engraft and relieve motor deficits after transplantation in a rat PD model. Our study provides a potential alternative route for cell therapy and disease modelling that due to its robustness could be particularly expedient when use of autologous- or immunologically matched cells is considered.", "doi": "10.1038/s41467-022-30777-8", "pmid": "35650213", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9160024"}, {"db": "pii", "key": "10.1038/s41467-022-30777-8"}], "notes": [], "created": "2026-09-23T09:56:17.450Z", "modified": "2026-09-23T10:30:52.184Z"}, {"entity": "publication", "iuid": "6b6e8a7e8697435baaa36054b1576495", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6b6e8a7e8697435baaa36054b1576495.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6b6e8a7e8697435baaa36054b1576495"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baa189d497af4380b7db4c1aba55ae80.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b4fc8d2ae534ff3aa7ee88457346a16.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J", "orcid": "0000-0001-8341-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2613649376a74ff1b465b1876298b6f6.json"}}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad46be6158194a729e4286901403c2e7.json"}}, {"family": "Wang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5444-1579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f37c92155e4494390f02d6f59e821ac.json"}}, {"family": "Matise", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-2998-9927", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b141693f76654b30be9ab0324f43df86.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8078f1505d9747e1ac76cf2f6d4ee606.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/634585a0768c4149ac5287d0bed67c30.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2963ca6a73bb409baea88ca67eeca936.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "38", "issn-l": "2375-2548"}, "abstract": "How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modeling, we define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through down-regulation of Gli transcription. The circuitry conforms an incoherent feed-forward loop, whereby Gli proteins not only promote expression of Phox2b and thereby MN-fate but also account for a delayed activation of a self-promoting transforming growth factor-\u03b2 (Tgf\u03b2) node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf\u03b2 counteract noise and increase temporal accuracy at the population level, providing a functional rationale for the intrinsically programmed activation of extrinsic switch signals in temporal patterning. Our study defines how time is reliably encoded during the sequential specification of neurons.", "doi": "10.1126/sciadv.aba8196", "pmid": "32938678", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7494341"}, {"db": "pii", "key": "6/38/eaba8196"}], "notes": [], "created": "2026-09-23T12:02:37.544Z", "modified": "2026-09-23T12:02:37.826Z"}, {"entity": "publication", "iuid": "b0d815ccfad3407a96c595bb20f1148d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b0d815ccfad3407a96c595bb20f1148d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b0d815ccfad3407a96c595bb20f1148d"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b4fc8d2ae534ff3aa7ee88457346a16.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J"}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad46be6158194a729e4286901403c2e7.json"}}, {"family": "Wang", "given": "Hui", "initials": "H"}, {"family": "Matise", "given": "Michael P", "initials": "MP"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8078f1505d9747e1ac76cf2f6d4ee606.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/634585a0768c4149ac5287d0bed67c30.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0135-3871", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/297463631cb34278a96a50aba9a849a3.json"}}], "type": "posted-content", "published": "2019-10-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/809418", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:01:12.393Z", "modified": "2026-09-23T15:01:12.478Z"}, {"entity": "publication", "iuid": "c26df83ccecb41168cbc36f5852daa8d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c26df83ccecb41168cbc36f5852daa8d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c26df83ccecb41168cbc36f5852daa8d"}}, "title": "Sequentially acting SOX proteins orchestrate astrocyte- and oligodendrocyte-specific gene expression.", "authors": [{"family": "Klum", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1316-2175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0cd527b84454d6ea40c80304e07b0f2.json"}}, {"family": "Zaouter", "given": "C\u00e9cile", "initials": "C", "orcid": "0000-0002-0359-4866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/510dc63840e74d9fb7a83df8b6883acc.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/445652e37bbe48729174f49e389b79b2.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cfd05eeb19640eea44f996699f998f0.json"}}, {"family": "Hagey", "given": "Daniel W", "initials": "DW"}, {"family": "Ericson", "given": "Johan", "initials": "J"}, {"family": "Muhr", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0704-0788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e647b598c244a7d8c3cc9f82de41e6e.json"}}, {"family": "Bergsland", "given": "Maria", "initials": "M", "orcid": "0000-0003-2720-388X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4267ee899c054f96967e1b913776c7c8.json"}}], "type": "journal article", "published": "2018-11-00", "journal": {"title": "EMBO Rep.", "issn": "1469-3178", "volume": "19", "issue": "11", "issn-l": "1469-221X"}, "abstract": "SOX transcription factors have important roles during astrocyte and oligodendrocyte development, but how glial genes are specified and activated in a sub-lineage-specific fashion remains unknown. Here, we define glial-specific gene expression in the developing spinal cord using single-cell RNA-sequencing. Moreover, by ChIP-seq analyses we show that these glial gene sets are extensively preselected already in multipotent neural precursor cells through prebinding by SOX3. In the subsequent lineage-restricted glial precursor cells, astrocyte genes become additionally targeted by SOX9 at DNA regions strongly enriched for Nfi binding motifs. Oligodendrocyte genes instead are prebound by SOX9 only, at sites which during oligodendrocyte maturation are targeted by SOX10. Interestingly, reporter gene assays and functional studies in the spinal cord reveal that SOX3 binding represses the synergistic activation of astrocyte genes by SOX9 and NFIA, whereas oligodendrocyte genes are activated in a combinatorial manner by SOX9 and SOX10. These genome-wide studies demonstrate how sequentially expressed SOX proteins act on lineage-specific regulatory DNA elements to coordinate glial gene expression both in a temporal and in a sub-lineage-specific fashion.", "doi": "10.15252/embr.201846635", "pmid": "30166336", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6216240"}, {"db": "pii", "key": "embr.201846635"}], "notes": [], "created": "2026-09-23T09:20:19.515Z", "modified": "2026-09-23T09:20:19.781Z"}]}