{"entity": "researcher", "timestamp": "2026-08-20T21:01:27.419Z", "family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6"}}, "publications": [{"entity": "publication", "iuid": "82365bc3e6554f9aa7b4675638a38f12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/82365bc3e6554f9aa7b4675638a38f12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/82365bc3e6554f9aa7b4675638a38f12"}}, "title": "Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts.", "authors": [{"family": "Mayr", "given": "Christoph H", "initials": "CH"}, {"family": "Sengupta", "given": "Arunima", "initials": "A"}, {"family": "Asgharpour", "given": "Sara", "initials": "S"}, {"family": "Ansari", "given": "Meshal", "initials": "M"}, {"family": "Pestoni", "given": "Jeanine C", "initials": "JC"}, {"family": "Ogar", "given": "Paulina", "initials": "P"}, {"family": "Angelidis", "given": "Ilias", "initials": "I", "orcid": "0000-0002-0549-8878", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f7214e4f34ae4ffeb20e38a3001271f0.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Rodriguez-Castillo", "given": "Jos\u00e9 Alberto", "initials": "JA"}, {"family": "Lang", "given": "Niklas J", "initials": "NJ"}, {"family": "Strunz", "given": "Maximilian", "initials": "M"}, {"family": "Porras-Gonzalez", "given": "Diana", "initials": "D"}, {"family": "Gerckens", "given": "Michael", "initials": "M", "orcid": "0000-0002-2251-4382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49a61c301eb04c2f9f31c2a607839d0a.json"}}, {"family": "De Sadeleer", "given": "Laurens J", "initials": "LJ", "orcid": "0000-0003-1237-7369", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91bb16436f50405c82ff257f48e3648f.json"}}, {"family": "Oehrle", "given": "Bettina", "initials": "B"}, {"family": "Viteri-Alvarez", "given": "Valeria", "initials": "V"}, {"family": "Fernandez", "given": "Isis E", "initials": "IE"}, {"family": "Tallquist", "given": "Michelle", "initials": "M"}, {"family": "Irmler", "given": "Martin", "initials": "M", "orcid": "0000-0003-3169-479X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b41c9238685342509b29d897bde74364.json"}}, {"family": "Beckers", "given": "Johannes", "initials": "J"}, {"family": "Eickelberg", "given": "Oliver", "initials": "O"}, {"family": "Stoleriu", "given": "Gabriel Mircea", "initials": "GM"}, {"family": "Behr", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Kneidinger", "given": "Nikolaus", "initials": "N", "orcid": "0000-0001-7583-0453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c3a20dc5f2b4a13b90eb4aed378c3c8.json"}}, {"family": "Wuyts", "given": "Wim A", "initials": "WA", "orcid": "0000-0001-9648-3497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cf1630c2efc461fb133bf3c45225da5.json"}}, {"family": "Wasnick", "given": "Roxana Maria", "initials": "RM", "orcid": "0000-0003-1114-7799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0332cbf0ab174e3f8ed96227f95fc361.json"}}, {"family": "Yildirim", "given": "Ali \u00d6nder", "initials": "A\u00d6", "orcid": "0000-0003-1969-480X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0bbd67703284c328b715cdbb29a0391.json"}}, {"family": "Ahlbrecht", "given": "Katrin", "initials": "K"}, {"family": "Morty", "given": "Rory E", "initials": "RE", "orcid": "0000-0003-0833-9749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26760356c3d24c0c98f98035cdc57bad.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Theis", "given": "Fabian J", "initials": "FJ"}, {"family": "Burgstaller", "given": "Gerald", "initials": "G"}, {"family": "Schiller", "given": "Herbert B", "initials": "HB"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Eur. Respir. J.", "issn": "1399-3003", "volume": "63", "issue": "2", "issn-l": "0903-1936"}, "abstract": "Fibroblast-to-myofibroblast conversion is a major driver of tissue remodelling in organ fibrosis. Distinct lineages of fibroblasts support homeostatic tissue niche functions, yet their specific activation states and phenotypic trajectories during injury and repair have remained unclear.\n\nWe combined spatial transcriptomics, multiplexed immunostainings, longitudinal single-cell RNA-sequencing and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. Our findings were validated in idiopathic pulmonary fibrosis patient tissues in situ as well as in cell differentiation and invasion assays using patient lung fibroblasts. Cell differentiation and invasion assays established a function of SFRP1 in regulating human lung fibroblast invasion in response to transforming growth factor (TGF)\u03b21.\n\nWe discovered a transitional fibroblast state characterised by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1 + cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage-specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1 + transitional fibroblasts and Cthrc1 + myofibroblasts. TGF\u03b21 downregulated SFRP1 in noninvasive transitional cells and induced their switch to an invasive CTHRC1+ myofibroblast identity. Finally, using loss-of-function studies we showed that SFRP1 modulates TGF\u03b21-induced fibroblast invasion and RHOA pathway activity.\n\nOur study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies SFRP1 as a modulator of TGF\u03b21-driven fibroblast phenotypes in fibrogenesis. These findings are relevant in the context of therapeutic interventions that aim at limiting or reversing fibroblast foci formation.", "doi": "10.1183/13993003.01326-2023", "pmid": "38212077", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10850614"}, {"db": "pii", "key": "13993003.01326-2023"}], "notes": [], "created": "2026-08-20T12:19:08.176Z", "modified": "2026-08-20T12:19:08.584Z"}, {"entity": "publication", "iuid": "57b68793aa824f6f891b6f7e0f485c6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/57b68793aa824f6f891b6f7e0f485c6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/57b68793aa824f6f891b6f7e0f485c6d"}}, "title": "Postnatal FGFR-signaling establishes gradients of secretory cell identities along the proximal-distal axis of the lung airways", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3ffb6926be74c11928edb174a245718.json"}}, {"family": "Koepke", "given": "Janine", "initials": "J"}, {"family": "Millar-B\u00fcchner", "given": "Pamela", "initials": "P", "orcid": "0000-0002-0079-6200", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c1d73ee7c0004665af7e3406a2e3b9a9.json"}}, {"family": "Manner\u00e5s-Holm", "given": "Louise", "initials": "L", "orcid": "0000-0001-8783-6107", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1da5a99df644b72adf7bd3524dbdfa3.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cfd05eeb19640eea44f996699f998f0.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Gaengel", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-2682-2833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/725dce05043142eca1ebfa7c05494037.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6340409dae344947868b4d6c79413cb5.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C", "orcid": "0000-0002-8494-971X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7839aedc01354442a552955542cfc754.json"}}, {"family": "Seeger", "given": "Werner", "initials": "W", "orcid": "0000-0003-1946-0894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59c1a6af6c4240a89064d5a0b5abfc25.json"}}, {"family": "Bellusci", "given": "Saverio", "initials": "S", "orcid": "0000-0001-5987-4579", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/775bd6384dc94fc98c87fef871bcaba3.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "posted-content", "published": "2023-12-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.11.571142", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:55.983Z", "modified": "2026-08-20T10:50:56.293Z"}, {"entity": "publication", "iuid": "bcb3f1bfd9ec4b6d814f092b14d5823a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb3f1bfd9ec4b6d814f092b14d5823a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb3f1bfd9ec4b6d814f092b14d5823a"}}, "title": "SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Nguyen", "given": "Hong Phuong", "initials": "HP", "orcid": "0000-0001-9170-9303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91241fcfd1404122a8849adab383514c.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37300f2654d74a5c9b81dd287d47768a.json"}}, {"family": "Seeger", "given": "Werner", "initials": "W"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "18", "issue": "11", "pages": "e3000675", "issn-l": "1544-9173"}, "abstract": "Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.", "doi": "10.1371/journal.pbio.3000675", "pmid": "33216742", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7717588"}, {"db": "pii", "key": "PBIOLOGY-D-20-00202"}], "notes": [], "created": "2026-08-20T12:42:40.156Z", "modified": "2026-08-20T12:42:40.301Z"}, {"entity": "publication", "iuid": "9c33bdfb53214af0a4dba29f6385f0ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c33bdfb53214af0a4dba29f6385f0ed"}}, "title": "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/618bb4684ceb4d839a2a83d4a7bca479.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5690cc0920d42aaae3dae9eaaedd2e6.json"}}, {"family": "Nguyen", "given": "Hong Phuong", "initials": "HP", "orcid": "0000-0001-9170-9303", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91241fcfd1404122a8849adab383514c.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/60b52d4946b347c5b99cab25b958cc43.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "Seeger", "given": "Werner", "initials": "W"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3311155f09a64b4f88d673da2a40627b.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d8ef864cc7c34dba830faa9caeafc3e7.json"}}], "type": "posted-content", "published": "2020-02-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.02.07.938571", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:55:54.959Z", "modified": "2026-08-20T09:55:55.187Z"}]}