{"entity": "researcher", "timestamp": "2026-08-15T06:14:22.548Z", "family": "\u00d6stman", "given": "Arne", "initials": "A", "orcid": "0000-0003-3993-0021", "affiliations": ["Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab"}}, "publications": [{"entity": "publication", "iuid": "36f146b5c7b14bbca774b45612b1d3ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec"}}, "title": "An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.", "authors": [{"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6863-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/216d382919954ccfb4b47458bb3d9b08.json"}}, {"family": "Geyer", "given": "Natalie", "initials": "N"}, {"family": "Harrizi", "given": "Sara", "initials": "S"}, {"family": "Hamidi", "given": "Yousra", "initials": "Y"}, {"family": "S\u00f6derqvist", "given": "Sara", "initials": "S"}, {"family": "Kuznyecov", "given": "Danyil", "initials": "D", "orcid": "0009-0007-8218-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b48e050665d04e4da8484bcf6da5cc96.json"}}, {"family": "Tidholm Qvist", "given": "Evelina", "initials": "E"}, {"family": "Salmonson Schaad", "given": "Media", "initials": "M"}, {"family": "Hermann", "given": "Laura", "initials": "L"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Heuchel", "given": "Rainer L", "initials": "RL", "orcid": "0000-0002-2782-585X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf96c4ef4e8c4d64bcbffdcaa994258b.json"}}, {"family": "Mart\u00edn-Bernab\u00e9", "given": "Alfonso", "initials": "A"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Navis", "given": "Anna C", "initials": "AC", "orcid": "0000-0002-5267-4678", "researcher": {"href": "https://publications.scilifelab.se/researcher/e89ad1a255984dd2ba50d83c3c0c628f.json"}}, {"family": "Villard", "given": "Christina", "initials": "C"}, {"family": "Del Valle", "given": "Andrea C", "initials": "AC", "orcid": "0000-0002-1698-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/52990e30c09c48cbbd0f39f90ab25994.json"}}, {"family": "Boz\u00f3ky", "given": "Lorand", "initials": "L"}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Dirix", "given": "Luc", "initials": "L", "orcid": "0000-0002-6248-1677", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1a10889290412e9257e79899aef2e9.json"}}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A", "orcid": "0000-0003-3993-0021", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab.json"}}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Vermeulen", "given": "Peter B", "initials": "PB"}, {"family": "Engstrand", "given": "Jennie", "initials": "J", "orcid": "0000-0003-1123-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef6292473b94b3b90e78745841cdeaa.json"}}, {"family": "Boz\u00f3ky", "given": "B\u00e9la", "initials": "B"}, {"family": "Gerling", "given": "Marco", "initials": "M", "orcid": "0000-0002-1810-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f9aa5d37124e379eb160737d657bab.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5024", "issn-l": "2041-1723"}, "abstract": "A perimetastatic capsule is a strong positive prognostic factor in liver metastases, but its origin remains unclear. Here, we systematically quantify the capsule's extent and cellular composition in 263 patients with colorectal cancer liver metastases to investigate its clinical significance and origin. We show that survival improves proportionally with increasing encapsulation and decreasing tumor-hepatocyte contact. Immunostaining reveals the gradual zonation of the capsule, transitioning from benign-like NGFRhigh stroma at the liver edge to FAPhigh stroma towards the tumor. Encapsulation correlates with decreased tumor viability and preoperative chemotherapy. In mice, chemotherapy and tumor cell ablation induce capsule formation. Our results suggest that encapsulation develops where tumor invasion into the liver plates stalls, representing a reparative process rather than tumor-induced desmoplasia. We propose a model of metastases growth, where the efficient tumor colonization of the liver parenchyma and a reparative liver injury reaction are opposing determinants of metastasis aggressiveness.", "doi": "10.1038/s41467-023-40688-x", "pmid": "37596278", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10439160"}, {"db": "pii", "key": "10.1038/s41467-023-40688-x"}], "notes": [], "created": "2023-08-20T11:51:56.440Z", "modified": "2023-10-19T12:56:35.044Z"}, {"entity": "publication", "iuid": "c20fafa5b31244a9ab60fc632f64d9c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c20fafa5b31244a9ab60fc632f64d9c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c20fafa5b31244a9ab60fc632f64d9c3"}}, "title": "Machine learning for cell classification and neighborhood analysis in glioma tissue.", "authors": [{"family": "Solorzano", "given": "Leslie", "initials": "L", "orcid": "0000-0001-8658-6417", "researcher": {"href": "https://publications.scilifelab.se/researcher/24c62ca6579b4055a95d0dba53722939.json"}}, {"family": "Wik", "given": "Lina", "initials": "L", "orcid": "0000-0001-8406-1828", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae592fc4e7404511a39f79638003a7aa.json"}}, {"family": "Olsson Bontell", "given": "Thomas", "initials": "T"}, {"family": "Wang", "given": "Yuyu", "initials": "Y"}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "\u00d6fverstedt", "given": "Johan", "initials": "J", "orcid": "0000-0003-0253-9037", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ade42e706714d9b8f0b9e7b8b26890d.json"}}, {"family": "Jakola", "given": "Asgeir S", "initials": "AS", "orcid": "0000-0002-2860-9331", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2ebf72073a64dad9f5b16b38754d905.json"}}, {"family": "\u00d6stman", "given": "Arne", "initials": "A", "orcid": "0000-0003-3993-0021", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}], "type": "journal article", "published": "2021-06-04", "journal": {"title": "Cytometry A", "issn": "1552-4930", "issn-l": "1552-4922"}, "abstract": "Multiplexed and spatially resolved single-cell analyses that intend to study tissue heterogeneity and cell organization invariably face as a first step the challenge of cell classification. Accuracy and reproducibility are important for the downstream process of counting cells, quantifying cell-cell interactions, and extracting information on disease-specific localized cell niches. Novel staining techniques make it possible to visualize and quantify large numbers of cell-specific molecular markers in parallel. However, due to variations in sample handling and artifacts from staining and scanning, cells of the same type may present different marker profiles both within and across samples. We address multiplexed immunofluorescence data from tissue microarrays of low-grade gliomas and present a methodology using two different machine learning architectures and features insensitive to illumination to perform cell classification. The fully automated cell classification provides a measure of confidence for the decision and requires a comparably small annotated data set for training, which can be created using freely available tools. Using the proposed method, we reached an accuracy of 83.1% on cell classification without the need for standardization of samples. Using our confidence measure, cells with low-confidence classifications could be excluded, pushing the classification accuracy to 94.5%. Next, we used the cell classification results to search for cell niches with an unsupervised learning approach based on graph neural networks. We show that the approach can re-detect specialized tissue niches in previously published data, and that our proposed cell classification leads to niche definitions that may be relevant for sub-groups of glioma, if applied to larger data sets.", "doi": "10.1002/cyto.a.24467", "pmid": "34089228", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-29T12:36:20.429Z", "modified": "2021-11-29T12:36:20.618Z"}]}