{"entity": "researcher", "timestamp": "2026-09-26T23:31:12.272Z", "family": "Grahn", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-8048-9058", "affiliations": ["Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.", "Department of Urology, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc646e7a3254639afe2a7bb1d78f444.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc646e7a3254639afe2a7bb1d78f444"}}, "publications": [{"entity": "publication", "iuid": "95cc3614dd2b45898ad25951221bed13", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/95cc3614dd2b45898ad25951221bed13.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/95cc3614dd2b45898ad25951221bed13"}}, "title": "Genomic profile - a possible diagnostic and prognostic marker in upper tract urothelial carcinoma.", "authors": [{"family": "Grahn", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-8048-9058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc646e7a3254639afe2a7bb1d78f444.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Malm", "given": "Camilla", "initials": "C"}, {"family": "Foroughi Asl", "given": "Hassan", "initials": "H"}, {"family": "Jaremko", "given": "Georg", "initials": "G"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Brehmer", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "BJU Int", "issn": "1464-410X", "volume": "130", "issue": "1", "pages": "92-101", "issn-l": null}, "abstract": "To investigate gene alterations as diagnostic and prognostic markers in upper tract urothelial carcinoma (UTUC).\n\nPatients with UTUC who underwent nephroureterectomy between 2005 and 2012 were followed until November 2020. DNA was extracted from paraffin-embedded tumour tissue. Next-generation sequencing using a 388-gene panel was performed. First a blinded analysis using principal component analysis and hierarchical clustering was used to search for patterns of mutations. Then a comparative analysis using analysis of variance (ANOVA) was used to search for mutations enriched in groups of various grades, stages, and survival. In addition, careful manual annotation was used to identify pathogenic mutations over-represented in tumours of high grade/stage and/or poor survival.\n\nA total of 39 patients were included. All tumour stages and grades were represented in the cohort. The median follow-up was 10.6 years. In all, 11 patients died from UTUC during the follow-up. Tumour mutational burden showed a statistically significant correlation with stage, grade, and stage + grade. Grade 1, Grade 2, and Grade 3 tumours had different mutational patterns. Patients who died from UTUC had pathogenic mutations in specific genes e.g. tumour protein p53 (TP53) and HRas proto-oncogene, GTPase (HRAS). Patients with Ta Grade 1 tumours with a known pathogenic fibroblast growth factor receptor 3 (FGFR3) mutation did not die from UTUC.\n\nThe genetic analysis was highly concordant with histopathological features and added prognostic information in some cases. Thus, results from genomic profiling may contribute to the choice of treatment and follow-up regimens in the future.", "doi": "10.1111/bju.15566", "pmid": "34375486", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T12:50:14.536Z", "modified": "2026-09-23T12:50:14.638Z"}, {"entity": "publication", "iuid": "580e442cf10f4a459619b385bbe3dd12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/580e442cf10f4a459619b385bbe3dd12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/580e442cf10f4a459619b385bbe3dd12"}}, "title": "Volumetric imaging: a potential tool to stage upper tract urothelial carcinoma.", "authors": [{"family": "Grahn", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-8048-9058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc646e7a3254639afe2a7bb1d78f444.json"}}, {"family": "Tanaka", "given": "Nobuyuki", "initials": "N", "orcid": "0000-0003-0841-9167", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/764447a2897d46afb2f96fddeb3e6dee.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ad7d29180614f89800a512887eeedd1.json"}}, {"family": "Brehmer", "given": "Marianne", "initials": "M", "orcid": "0000-0001-9232-363X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0f84fc5cbaa41da809815756a5ae21d.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "World J Urol", "issn": "1433-8726", "volume": "37", "issue": "11", "pages": "2297-2302", "issn-l": null}, "abstract": "To investigate whether volumetric imaging of tumor vasculature can be used to phenotypically characterize advanced upper tract urothelial carcinoma, and if this technique can distinguish aggressive invasive tumors from non-aggressive superficial ones.\n\nIn a pilot study, two TaG1 and two T3G3 formalin-fixed paraffin-embedded (FFPE) tumor samples were examined using the DIPCO pipeline (Tanaka et al. in Nature Biomed Eng 1(10):796-806. https://doi.org/10.1038/s41551-017-0139-0 , 2017). Briefly, punch biopsies of FFPE tumors were deparaffinized, cleared, immunolabeled with the vessel marker CD34 and imaged with a light-sheet microscope. Thereafter, the three-dimensional (3D) vasculature of the tumors was analyzed and characterized using a specialized image processing software.\n\nWe found that T3G3 tumors had increased CD34 density kurtosis and skewness compared to TaG1 tumors. This suggests that analysis of the 3D vasculature can distinguish between high-grade invasive and low-grade superficial tumors.\n\nVolumetric imaging of tumor samples may represent novel methodology that can complement conventional histopathology. Volumetric imaging enabled us to differentiate between invasive and non-invasive upper tract urothelial carcinoma. The method is of particular interest in diagnostic work-up of patients with upper tract urothelial carcinoma as previous findings indicate that volumetric imaging of vascular patterns could be used to differentiate superficial and invasive urothelial carcinoma, irrespective of if the tumor sample was deep or superficial. However, further and more extensive studies are required before this method can be applied clinically.", "doi": "10.1007/s00345-019-02682-1", "pmid": "30820651", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6825635"}, {"db": "pii", "key": "10.1007/s00345-019-02682-1"}], "notes": [], "created": "2026-09-23T13:30:35.511Z", "modified": "2026-09-23T13:30:35.678Z"}]}