{"entity": "journal", "iuid": "7a53f67416cc4f1b976897c72c264643", "timestamp": "2026-08-15T06:52:39.754Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Am.%20J.%20Pathol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Am.%20J.%20Pathol."}}, "title": "Am. J. Pathol.", "issn": "1525-2191", "issn-l": "0002-9440", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "00a23e638c504441b0a54f8ee8dec96b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b"}}, "title": "Single-Cell Triomics Analysis of Tumor Cells Infiltrating Patient-Derived Breast Cancer Scaffolds", "authors": [{"family": "Filges", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5994-6699", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d546bd6e774a639c45968aa81c0c1b.json"}}, {"family": "Jonasson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0463-9373", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddcca3a85ea848c5afdae4d5cf066b44.json"}}, {"family": "Leiva Arrabal", "given": "Maria Del Carmen", "initials": "MDC"}, {"family": "Andersson", "given": "Lisa", "initials": "L"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Dhingra", "given": "Dalia", "initials": "D"}, {"family": "Mendez", "given": "Pedro", "initials": "P"}, {"family": "Ooi", "given": "Aik", "initials": "A", "orcid": "0000-0002-9101-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/817965235259489cb9e029059b9451e3.json"}}, {"family": "Sciambi", "given": "Adam", "initials": "A"}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9004-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3b79caacba4566897f136a1200476f.json"}}, {"family": "Ruff", "given": "David", "initials": "D", "orcid": "0000-0003-2260-3163", "researcher": {"href": "https://publications.scilifelab.se/researcher/f48bd314d7494e819be6ae6d4d2ea1ca.json"}}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal-article", "published": "2026-04-00", "journal": {"title": "Am. J. Pathol.", "issn": "0002-9440", "volume": "196", "issue": "4", "pages": "1016-1027", "issn-l": null}, "abstract": "Cellular heterogeneity plays a critical role in tissues and diseases, including cancer. Single-cell technologies are required to provide detailed information about the phenotype and genotype of individual cells. Despite several approaches to analyzing different analytes at the single-cell level, it is challenging to assess DNA, RNA, and protein simultaneously. Here, a single-cell triomics method to assess DNA, RNA, and proteins from the same cell using a targeted sequencing approach is shown. Breast cancer cells cultured in monolayers and in patient-derived scaffolds that mimic in vivo-like growth conditions, both with and without chemotherapy treatment, were analyzed. Data showed that DNA, RNA, and protein biomarkers could be reliably analyzed, providing biological insights into breast cancer cell heterogeneity. In addition, chemotherapy treatment caused changes in subpopulations and expressions of biomarkers. Furthermore, cells growing in patient-derived scaffolds generated from various breast cancers affected cell heterogeneity and drug resistance differently as a result of the unique tumor-specific microenvironments. The data show that single-cell triomics provides new means to assess cancer cell heterogeneity at DNA, RNA, and protein levels.", "doi": "10.1016/j.ajpath.2025.12.013", "pmid": "41580235", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9440(26)00008-8"}], "notes": [], "created": "2026-02-09T12:51:37.488Z", "modified": "2026-03-24T09:14:15.522Z"}, {"entity": "publication", "iuid": "e842d4e2fc484d519d7074d4e56d443c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e842d4e2fc484d519d7074d4e56d443c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e842d4e2fc484d519d7074d4e56d443c"}}, "title": "Defective Uterine Spiral Artery Remodeling and Placental Senescence in a Pregnant Rat Model of Polycystic Ovary Syndrome.", "authors": [{"family": "Hu", "given": "Min", "initials": "M"}, {"family": "Zhang", "given": "Yuehui", "initials": "Y"}, {"family": "Zhang", "given": "Xu", "initials": "X"}, {"family": "Zhang", "given": "XiuYing", "initials": "X"}, {"family": "Huang", "given": "Xinyue", "initials": "X"}, {"family": "Lu", "given": "Yaxing", "initials": "Y"}, {"family": "Li", "given": "Yijia", "initials": "Y"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Sferruzzi-Perri", "given": "Amanda N", "initials": "AN"}, {"family": "Shao", "given": "Linus R", "initials": "LR"}, {"family": "Billig", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Am. J. Pathol.", "issn": "1525-2191", "volume": "193", "issue": "12", "pages": "1916-1935", "issn-l": "0002-9440"}, "abstract": "Pregnancy-related problems have been linked to impairments in maternal uterine spiral artery (SpA) remodeling. The mechanisms underlying this association are still unclear. It is also unclear whether hyperandrogenism and insulin resistance, the two common manifestations of polycystic ovary syndrome, affect uterine SpA remodeling. We verified previous work in which exposure to 5-dihydrotestosterone (DHT) and insulin (INS) in rats during pregnancy resulted in hyperandrogenism, insulin intolerance, and higher fetal mortality. Exposure to DHT and INS dysregulated the expression of angiogenesis-related genes in the uterus and placenta and also decreased expression of endothelial nitric oxide synthase and matrix metallopeptidases 2 and 9, increased fibrotic collagen deposits in the uterus, and reduced expression of marker genes for SpA-associated trophoblast giant cells. These changes were related to a greater proportion of unremodeled uterine SpAs and a smaller proportion of highly remodeled arteries in DHT + INS-exposed rats. Placentas from DHT + INS-exposed rats exhibited decreased basal and labyrinth zone regions, reduced maternal blood spaces, diminished labyrinth vascularity, and an imbalance in the abundance of vascular and smooth muscle proteins. Furthermore, placentas from DHT + INS-exposed rats showed expression of placental insufficiency markers and a significant increase in cell senescence-associated protein levels. Altogether, this work demonstrates that increased pregnancy complications in polycystic ovary syndrome may be mediated by problems with uterine SpA remodeling, placental functionality, and placental senescence.", "doi": "10.1016/j.ajpath.2023.08.008", "pmid": "37689383", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9440(23)00315-2"}], "notes": [], "created": "2023-12-01T10:46:37.723Z", "modified": "2023-12-01T10:46:37.727Z"}, {"entity": "publication", "iuid": "e05c733036464f4295919979fdbb89c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e05c733036464f4295919979fdbb89c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e05c733036464f4295919979fdbb89c8"}}, "title": "Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers.", "authors": [{"family": "Kiflemariam", "given": "Sara", "initials": "S"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2015-06-00", "journal": {"title": "Am. J. Pathol.", "issn": "1525-2191", "volume": "185", "issue": "6", "pages": "1600-1609", "issn-l": "0002-9440"}, "abstract": "The tyrosine kinome and phosphatome harbor oncogenes and tumor suppressor genes and important regulators of angiogenesis and tumor stroma formation. To provide a better understanding of their potential roles in cancer, we analyzed the expression of 85 tyrosine kinases and 42 tyrosine phosphatases by in situ hybridization 48 human normal and 24 tumor tissue specimens. Nine-tenths of the\u00a0assessed transcripts had tumor cell expression concordant with expression array databases. Further, pan-cancer expression of AATK, PTPRK, and PTPRU and expression of PTPRS in a subset of tumors were observed. To demonstrate tumor subcompartment resolution, we validated the predicted tumor stroma-specific markers HTRA1, HTRA3, MXRA5, MXRA8, and SERPING1 in situ. In addition to known vascular and stromal markers such as PDGFRB, we observed stromal expression of PTK6 and TNS1 and vascular expression of INSR, PTPRF, PTPRG, PTPRU, and TNS1, of which INSR emerged as a tumor-specific vessel marker. This study demonstrates the feasibility of large-scale analyses to chart the transcriptome in situ in human cancers and their ability to identify novel cancer biomarkers.", "doi": "10.1016/j.ajpath.2015.02.019", "pmid": "25864925", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0002-9440(15)00154-6"}], "notes": [], "created": "2017-11-05T13:00:50.218Z", "modified": "2017-11-05T13:00:50.239Z"}, {"entity": "publication", "iuid": "2c0244ff53ae45abbec01053a02856a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c0244ff53ae45abbec01053a02856a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c0244ff53ae45abbec01053a02856a8"}}, "title": "Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.", "authors": [{"family": "Skog", "given": "Oskar", "initials": "O"}, {"family": "Korsgren", "given": "Stella", "initials": "S"}, {"family": "Wiberg", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edwin", "given": "Bj\u00f8rn", "initials": "B"}, {"family": "Buanes", "given": "Trond", "initials": "T"}, {"family": "Krogvold", "given": "Lars", "initials": "L"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Dahl-J\u00f8rgensen", "given": "Knut", "initials": "K"}], "type": "journal article", "published": "2015-01-00", "journal": {"volume": "185", "issn": "1525-2191", "issue": "1", "pages": "129-138", "title": "Am. J. Pathol.", "issn-l": "0002-9440"}, "abstract": "The cause of type 1 diabetes remains unknown. To dissect the link between hyperexpression of human leukocyte antigen (HLA) class I on the islet cells, we examined its expression in subjects with recent-onset type 1 diabetes. IHC showed seemingly pronounced hyperexpression in subjects with recent-onset type 1 diabetes, as well as in some nondiabetic subjects. In all subjects, HLA class I expression on exocrine tissue was low. However, no difference in the level of HLA class I expression was found between islet and exocrine tissue using Western blot, flow cytometry, real-time quantitative PCR, or RNA sequencing analyses. Also, the level of HLA class I expression on the messenger level was not increased in islets from subjects with recent-onset type 1 diabetes compared with that in nondiabetic subjects. Consistently, the HLA class I specific enhanceosome (NLRC5) and related transcription factors, as well as interferons, were not enhanced in islets from recent-onset type 1 diabetic subjects. In conclusion, a discrepancy in HLA class I expression in islets assessed by IHC was observed compared with that using quantitative techniques showing similar expression of HLA class I in islets and exocrine tissue in subjects with recent-onset type 1 diabetes, nor could any differences be found between type 1 diabetic and nondiabetic subjects. Results presented provide important clues for a better understanding on how this complex disease develops.", "doi": "10.1016/j.ajpath.2014.09.004", "pmid": "25524212", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0002-9440(14)00548-3"}], "notes": [], "created": "2017-05-02T12:58:12.774Z", "modified": "2020-01-21T13:56:01.273Z"}], "created": "2017-05-09T09:12:15.225Z", "modified": "2020-11-27T13:14:04.556Z"}