{"entity": "journal", "iuid": "0bbd1bbb6d6b4bb09e87518d6ebe1a03", "timestamp": "2026-07-12T08:44:33.664Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Cell%20Stem%20Cell.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Cell%20Stem%20Cell"}}, "title": "Cell Stem Cell", "issn": "1934-5909", "issn-l": "1875-9777", "publications_count": 6, "publications": [{"entity": "publication", "iuid": "5cb642ba606340c383ccccef9091ae0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cb642ba606340c383ccccef9091ae0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cb642ba606340c383ccccef9091ae0c"}}, "title": "Spatiotemporal single-cell roadmap of human skin wound healing.", "authors": [{"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Bian", "given": "Xiaowei", "initials": "X"}, {"family": "Luo", "given": "Lihua", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Li", "given": "Li", "initials": "L"}, {"family": "Zhang", "given": "Letian", "initials": "L"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Guo", "given": "Lei", "initials": "L"}, {"family": "Gao", "given": "Juan", "initials": "J"}, {"family": "Cao", "given": "Chunyan", "initials": "C"}, {"family": "Wang", "given": "Jiating", "initials": "J"}, {"family": "He", "given": "Wenjun", "initials": "W"}, {"family": "Xiao", "given": "Yunting", "initials": "Y"}, {"family": "Zhu", "given": "Liping", "initials": "L"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "Gopee", "given": "Nusayhah Hudaa", "initials": "NH"}, {"family": "Basurto-Lozada", "given": "Daniela", "initials": "D"}, {"family": "Horsfall", "given": "David", "initials": "D"}, {"family": "Bennett", "given": "Clare L", "initials": "CL"}, {"family": "Kasper", "given": "Maria", "initials": "M"}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Li", "given": "Dongqing", "initials": "D"}, {"family": "Land\u00e9n", "given": "Ning Xu", "initials": "NX"}], "type": "journal article", "published": "2024-12-18", "journal": {"title": "Cell Stem Cell", "issn": "1875-9777", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Wound healing is vital for human health, yet the details of cellular dynamics and coordination in human wound repair remain largely unexplored. To address this, we conducted single-cell multi-omics analyses on human skin wound tissues through inflammation, proliferation, and remodeling phases of wound repair from the same individuals, monitoring the cellular and molecular dynamics of human skin wound healing at an unprecedented spatiotemporal resolution. This singular roadmap reveals the cellular architecture of the wound margin and identifies FOSL1 as a critical driver of re-epithelialization. It shows that pro-inflammatory macrophages and fibroblasts sequentially support keratinocyte migration like a relay race across different healing stages. Comparison with single-cell data from venous and diabetic foot ulcers uncovers a link between failed keratinocyte migration and impaired inflammatory response in chronic wounds. Additionally, comparing human and mouse acute wound transcriptomes underscores the indispensable value of this roadmap in bridging basic research with clinical innovations.", "doi": "10.1016/j.stem.2024.11.013", "pmid": "39729995", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(24)00412-0"}], "notes": [], "created": "2025-01-02T10:30:31.039Z", "modified": "2025-01-20T13:20:10.129Z"}, {"entity": "publication", "iuid": "6348dc1af1b14d5a8d9c28f3df10d966", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6348dc1af1b14d5a8d9c28f3df10d966.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6348dc1af1b14d5a8d9c28f3df10d966"}}, "title": "A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.", "authors": [{"family": "Johansson", "given": "Pia A", "initials": "PA"}, {"family": "Bratt\u00e5s", "given": "Per Ludvik", "initials": "PL"}, {"family": "Douse", "given": "Christopher H", "initials": "CH"}, {"family": "Hsieh", "given": "PingHsun", "initials": "P"}, {"family": "Adami", "given": "Anita", "initials": "A"}, {"family": "Pontis", "given": "Julien", "initials": "J"}, {"family": "Grassi", "given": "Daniela", "initials": "D"}, {"family": "Garza", "given": "Raquel", "initials": "R"}, {"family": "Sozzi", "given": "Edoardo", "initials": "E"}, {"family": "Cataldo", "given": "Rodrigo", "initials": "R"}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME"}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM"}, {"family": "Pircs", "given": "Karolina", "initials": "K"}, {"family": "Eren", "given": "Feride", "initials": "F"}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "Johansson", "given": "Jenny", "initials": "J"}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A"}, {"family": "Parmar", "given": "Malin", "initials": "M"}, {"family": "Fex", "given": "Malin", "initials": "M"}, {"family": "Trono", "given": "Didier", "initials": "D"}, {"family": "Eichler", "given": "Evan E", "initials": "EE"}, {"family": "Jakobsson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Cell Stem Cell", "issn": "1875-9777", "volume": "29", "issue": "1", "pages": "52-69.e8", "issn-l": null}, "abstract": "The human forebrain has expanded in size and complexity compared to chimpanzees despite limited changes in protein-coding genes, suggesting that gene expression regulation is an important driver of brain evolution. Here, we identify a KRAB-ZFP transcription factor, ZNF558, that is expressed in human but not chimpanzee forebrain neural progenitor cells. ZNF558 evolved as a suppressor of LINE-1 transposons but has been co-opted to regulate a single target, the mitophagy gene SPATA18. ZNF558 plays a role in mitochondrial homeostasis, and loss-of-function experiments in cerebral organoids suggests that ZNF558 influences developmental timing during early human brain development. Expression of ZNF558 is controlled by the size of a variable number tandem repeat that is longer in chimpanzees compared to humans, and variable in the human population. Thus, this work provides mechanistic insight into how a cis-acting structural variation establishes a regulatory network that affects human brain evolution.", "doi": "10.1016/j.stem.2021.09.008", "pmid": "34624206", "labels": {"Clinical Genomics Lund": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1934-5909(21)00384-2"}], "notes": [], "created": "2021-11-23T14:23:20.527Z", "modified": "2024-01-16T13:48:37.814Z"}, {"entity": "publication", "iuid": "e7b62282c0ab4fa298b3a15c0daefd80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7b62282c0ab4fa298b3a15c0daefd80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7b62282c0ab4fa298b3a15c0daefd80"}}, "title": "The Molecular Anatomy of Mouse Skin during Hair Growth and Rest.", "authors": [{"family": "Joost", "given": "Simon", "initials": "S"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "Jacob", "given": "Tina", "initials": "T"}, {"family": "Sun", "given": "Xiaoyan", "initials": "X"}, {"family": "Dalessandri", "given": "Tim", "initials": "T"}, {"family": "Sivan", "given": "Unnikrishnan", "initials": "U"}, {"family": "Sequeira", "given": "In\u00eas", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Kasper", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2020-03-05", "journal": {"volume": "26", "issn": "1875-9777", "issue": "3", "pages": "441-457.e7", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Skin homeostasis is orchestrated by dozens of cell types that together direct stem cell renewal, lineage commitment, and differentiation. Here, we use single-cell RNA sequencing and single-molecule RNA FISH to provide a systematic molecular atlas of full-thickness skin, determining gene expression profiles and spatial locations that define 56 cell types and states during hair growth and rest. These findings reveal how the outer root sheath (ORS) and inner hair follicle layers coordinate hair production. We found that the ORS is composed of two intermingling but transcriptionally distinct cell types with differing capacities for interactions with stromal cell types. Inner layer cells branch from transcriptionally uncommitted progenitors, and each lineage differentiation passes through an intermediate state. We also provide an online tool to explore this comprehensive skin cell atlas, including epithelial and stromal cells such as fibroblasts, vascular, and immune cells, to spur further discoveries in skin biology.", "doi": "10.1016/j.stem.2020.01.012", "pmid": "32109378", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1934-5909(20)30012-6"}], "notes": [], "created": "2020-03-02T10:57:50.903Z", "modified": "2024-01-16T13:48:42.819Z"}, {"entity": "publication", "iuid": "562df6d302fc4fa2bea64241772afbdc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/562df6d302fc4fa2bea64241772afbdc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/562df6d302fc4fa2bea64241772afbdc"}}, "title": "Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy.", "authors": [{"family": "\u010can\u010der", "given": "Matko", "initials": "M"}, {"family": "Hutter", "given": "Sonja", "initials": "S"}, {"family": "Holmberg", "given": "Karl O", "initials": "KO"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Tailor", "given": "Jignesh", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Garancher", "given": "Alexandra", "initials": "A"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}], "type": "journal article", "published": "2019-12-05", "journal": {"volume": "25", "issn": "1875-9777", "issue": "6", "pages": "855-870.e11", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Medulloblastoma (MB), the most frequent malignant childhood brain tumor, can arise from cellular malfunctions during hindbrain development. Here we generate humanized models for Sonic Hedgehog (SHH)-subgroup MB via MYCN overexpression in primary human hindbrain-derived neuroepithelial stem (hbNES) cells or iPSC-derived NES cells, which display a range of aggressive phenotypes upon xenografting. iPSC-derived NES tumors develop quickly with leptomeningeal dissemination, whereas hbNES-derived cells exhibit delayed tumor formation with less dissemination. Methylation and expression profiling show that tumors from both origins recapitulate hallmarks of infant SHH MB and reveal that mTOR activation, as a result of increased Oct4, promotes aggressiveness of human SHH tumors. Targeting mTOR decreases cell viability and prolongs survival, showing the utility of these varied models for dissecting mechanisms mediating tumor aggression and demonstrating the value of humanized models for a better understanding of pediatric cancers.", "doi": "10.1016/j.stem.2019.10.005", "pmid": "31786016", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1934-5909(19)30426-6"}, {"db": "pmc", "key": "PMC6900751"}], "notes": [], "created": "2019-12-03T09:31:02.184Z", "modified": "2024-01-16T13:48:43.324Z"}, {"entity": "publication", "iuid": "ef9cd281e9f048cdb7b6541b0876e08a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef9cd281e9f048cdb7b6541b0876e08a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef9cd281e9f048cdb7b6541b0876e08a"}}, "title": "Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.", "authors": [{"family": "Guo", "given": "Jingtao", "initials": "J"}, {"family": "Grow", "given": "Edward J", "initials": "EJ"}, {"family": "Yi", "given": "Chongil", "initials": "C"}, {"family": "Mlcochova", "given": "Hana", "initials": "H"}, {"family": "Maher", "given": "Geoffrey J", "initials": "GJ"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Murphy", "given": "Patrick J", "initials": "PJ"}, {"family": "Wike", "given": "Candice L", "initials": "CL"}, {"family": "Carrell", "given": "Douglas T", "initials": "DT"}, {"family": "Goriely", "given": "Anne", "initials": "A"}, {"family": "Hotaling", "given": "James M", "initials": "JM"}, {"family": "Cairns", "given": "Bradley R", "initials": "BR"}], "type": "journal article", "published": "2017-10-05", "journal": {"volume": "21", "issn": "1875-9777", "issue": "4", "pages": "533-546.e6", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4(+) hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4(+) hSSCs and differentiating c-KIT(+) spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic \"poising\" in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed. Interestingly, open chromatin in hSSCs was strikingly enriched in binding sites for pioneer factors (NFYA/B, DMRT1, and hormone receptors). Remarkably, single-cell RNA-seq clustering analysis identified four cellular/developmental states during hSSC differentiation, involving major transitions in cell-cycle and transcriptional regulators, splicing and signaling factors, and glucose/mitochondria regulators. Overall, our results outline the dynamic chromatin/transcription landscape operating in hSSCs and identify crucial molecular pathways that accompany the transition from quiescence to proliferation and differentiation.", "doi": "10.1016/j.stem.2017.09.003", "pmid": "28985528", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(17)30370-3"}, {"db": "GEO", "description": "Genomic profiling of human spermatogonial stem cells", "key": "GSE92280"}, {"db": "GEO", "description": "scRNA-Seq", "key": "GSE92276"}, {"db": "GEO", "description": "BulkRNA-Seq", "key": "GSE92277"}, {"db": "GEO", "description": "Whole genome bisulfite sequencing", "key": "GSE92278"}], "notes": [], "created": "2017-11-05T13:07:00.197Z", "modified": "2018-11-14T11:32:27.610Z"}, {"entity": "publication", "iuid": "389c89b5cd9f4e68b0b97447e9fdcb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/389c89b5cd9f4e68b0b97447e9fdcb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/389c89b5cd9f4e68b0b97447e9fdcb93"}}, "title": "Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.", "authors": [{"family": "Kee", "given": "Nigel", "initials": "N"}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Kirkeby", "given": "Agnete", "initials": "A"}, {"family": "Dahl", "given": "Lina", "initials": "L"}, {"family": "Storvall", "given": "Helena", "initials": "H"}, {"family": "Nolbrant", "given": "Sara", "initials": "S"}, {"family": "Lahti", "given": "Laura", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Joodmardi", "given": "Eliza", "initials": "E"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2017-01-05", "journal": {"volume": "20", "issn": "1875-9777", "issue": "1", "pages": "29-40", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons is a promising strategy for brain repair in Parkinson's disease (PD). Refinement of differentiation protocols to optimize this approach will require deeper understanding of mesDA neuron development. Here, we studied this process using transcriptome-wide single-cell RNA sequencing of mouse neural progenitors expressing the mesDA neuron determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons, while also highlighting a distinct transcription factor set that can distinguish between them. While previous hESC mesDA differentiation protocols have relied on markers that are shared between the two lineages, we found that application of these highlighted markers can help to refine current stem cell engineering protocols, increasing the proportion of appropriately patterned mesDA progenitors. Our results, therefore, have important implications for cell replacement therapy in PD.", "doi": "10.1016/j.stem.2016.10.003", "pmid": "28094018", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(16)30343-5"}], "notes": [], "created": "2017-05-03T13:00:32.781Z", "modified": "2021-07-07T11:46:33.581Z"}], "created": "2017-05-09T09:12:54.893Z", "modified": "2020-11-27T13:14:08.167Z"}