{"entity": "researcher", "timestamp": "2026-08-20T21:11:18.140Z", "family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e"}}, "publications": [{"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": "47481be28e614b77bbbfb235f7d459c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47481be28e614b77bbbfb235f7d459c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47481be28e614b77bbbfb235f7d459c3"}}, "title": "Clathrin-Mediated Albumin Clearance in Alveolar Epithelial Cells of Murine Precision-Cut Lung Slices.", "authors": [{"family": "Kryvenko", "given": "Vitalii", "initials": "V", "orcid": "0000-0002-5683-4990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65bc8406d7354cfb9b62af8f98c3957b.json"}}, {"family": "Alberro-Brage", "given": "Andr\u00e9s", "initials": "A", "orcid": "0000-0001-8158-544X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd2d3fdfc590460caa364683733e05d1.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fbd975bb6524e31a9ee8f079bc1513e.json"}}, {"family": "Wessendorf", "given": "Miriam", "initials": "M"}, {"family": "Tello", "given": "Khodr", "initials": "K"}, {"family": "Morty", "given": "Rory E", "initials": "RE"}, {"family": "Herold", "given": "Susanne", "initials": "S"}, {"family": "Seeger", "given": "Werner", "initials": "W"}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Vad\u00e1sz", "given": "Istv\u00e1n", "initials": "I"}], "type": "journal article", "published": "2023-01-31", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "3", "issn-l": null}, "abstract": "A hallmark of acute respiratory distress syndrome (ARDS) is an accumulation of protein-rich alveolar edema that impairs gas exchange and leads to worse outcomes. Thus, understanding the mechanisms of alveolar albumin clearance is of high clinical relevance. Here, we investigated the mechanisms of the cellular albumin uptake in a three-dimensional culture of precision-cut lung slices (PCLS). We found that up to 60% of PCLS cells incorporated labeled albumin in a time- and concentration-dependent manner, whereas virtually no uptake of labeled dextran was observed. Of note, at a low temperature (4 \u00b0C), saturating albumin receptors with unlabeled albumin and an inhibition of clathrin-mediated endocytosis markedly decreased the endocytic uptake of the labeled protein, implicating a receptor-driven internalization process. Importantly, uptake rates of albumin were comparable in alveolar epithelial type I (ATI) and type II (ATII) cells, as assessed in PCLS from a SftpcCreERT2/+: tdTomatoflox/flox mouse strain (defined as EpCAM+CD31-CD45-tdTomatoSPC-T1\u03b1+ for ATI and EpCAM+CD31-CD45-tdTomatoSPC+T1\u03b1- for ATII cells). Once internalized, albumin was found in the early and recycling endosomes of the alveolar epithelium as well as in endothelial, mesenchymal, and hematopoietic cell populations, which might indicate transcytosis of the protein. In summary, we characterize albumin uptake in alveolar epithelial cells in the complex setting of PCLS. These findings may open new possibilities for pulmonary drug delivery that may improve the outcomes for patients with respiratory failure.", "doi": "10.3390/ijms24032644", "pmid": "36768968", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9916738"}, {"db": "pii", "key": "ijms24032644"}], "notes": [], "created": "2026-08-20T13:41:34.565Z", "modified": "2026-08-20T13:41:34.708Z"}, {"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"}]}