{"entity": "researcher", "timestamp": "2026-06-15T17:37:41.794Z", "family": "Sherif", "given": "Amir", "initials": "A", "orcid": "0000-0002-3675-3050", "affiliations": ["Department of Surgical and Perioperative Sciences, Urology and Andrology, Ume\u00e5 University, 907 36 Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2"}}, "publications": [{"entity": "publication", "iuid": "b69e3a293cb74fbc9c8c46ecf0a78fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b69e3a293cb74fbc9c8c46ecf0a78fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b69e3a293cb74fbc9c8c46ecf0a78fbb"}}, "title": "Imaging Single Particle Profiler to Study Nanoscale Bioparticles Using Conventional Confocal Microscopy.", "authors": [{"family": "Sych", "given": "Taras", "initials": "T", "orcid": "0000-0002-7330-9063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d104a7d8096b4a4ab2a9fe618489fc7e.json"}}, {"family": "G\u00f6rgens", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-9198-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5f85e2c23a4515a39a2fa23d665a99.json"}}, {"family": "Steiner", "given": "Lo\u00efc", "initials": "L", "orcid": "0000-0001-6640-3513", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6ac5c6f9324434b11fc1cccd0a9027.json"}}, {"family": "Gucluler", "given": "Gozde", "initials": "G"}, {"family": "Huge", "given": "Ylva", "initials": "Y"}, {"family": "Alamdari", "given": "Farhood", "initials": "F"}, {"family": "Johansson", "given": "Markus", "initials": "M"}, {"family": "Aljabery", "given": "Firas", "initials": "F"}, {"family": "Sherif", "given": "Amir", "initials": "A", "orcid": "0000-0002-3675-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2.json"}}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1771-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d446cb52d7e4a01ad8478a9cfe22ae1.json"}}, {"family": "El Andaloussi", "given": "Samir", "initials": "S", "orcid": "0000-0003-4468-9113", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1036a42043441da3e444f4eac58010.json"}}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Nano Lett.", "issn": "1530-6992", "volume": "25", "issue": "6", "pages": "2173-2180", "issn-l": "1530-6984"}, "abstract": "Single particle profiling (SPP) is a unique methodology to study nanoscale bioparticles such as liposomes, lipid nanoparticles, extracellular vesicles, and lipoproteins in a single particle and high throughput manner. The initial version requires the single photon counting modules for data acquisition, which limits its adoptability. Here, we present imaging-based SPP (iSPP) that can be performed by imaging a spot over time in the common imaging mode with confocal detectors. We also provide user-friendly software with a graphical user interface to analyze such data and give quantitative insights on the content and properties of nanoscale bioparticles. We use iSPP to decipher lipid-protein interactions, membrane modifications by drugs, and the heterogeneity of extracellular vesicles isolated from cell lines and human urine. This easily applicable modality of the single particle profiler will facilitate nanoscale bioparticle research in laboratories with access to any confocal microscope.", "doi": "10.1021/acs.nanolett.4c05117", "pmid": "39878336", "labels": {"Integrated Microscopy Technologies Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11827106"}], "notes": [], "created": "2025-03-11T12:50:21.409Z", "modified": "2025-03-24T08:21:15.353Z"}, {"entity": "publication", "iuid": "2faf5fd60f764dfa92d3120f79803dd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2faf5fd60f764dfa92d3120f79803dd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2faf5fd60f764dfa92d3120f79803dd2"}}, "title": "Immune-Activated B Cells Are Dominant in Prostate Cancer.", "authors": [{"family": "Saudi", "given": "Aws", "initials": "A"}, {"family": "Banday", "given": "Viqar", "initials": "V", "orcid": "0000-0002-5081-2272", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e62d1e1569648a3905f3eb8b4d1469a.json"}}, {"family": "Zirakzadeh", "given": "A Ali", "initials": "AA", "orcid": "0000-0002-1568-1430", "researcher": {"href": "https://publications.scilifelab.se/researcher/2092f6ff059c465fb725d34f4640ff19.json"}}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc68cdd8b8d748499e552a6e700d7e55.json"}}, {"family": "Forsberg", "given": "Jon", "initials": "J"}, {"family": "Holmbom", "given": "Martin", "initials": "M", "orcid": "0000-0002-3706-2294", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0f3c0d388144a9d90b6f95e2f721f43.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Wald\u00e9n", "given": "Mauritz", "initials": "M"}, {"family": "Alamdari", "given": "Farhood", "initials": "F"}, {"family": "Aljabery", "given": "Firas", "initials": "F"}, {"family": "Winqvist", "given": "Ola", "initials": "O"}, {"family": "Sherif", "given": "Amir", "initials": "A", "orcid": "0000-0002-3675-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2.json"}}], "type": "journal article", "published": "2023-02-01", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "3", "issn-l": "2072-6694"}, "abstract": "B cells are multifaceted immune cells responding robustly during immune surveillance against tumor antigens by presentation to T cells and switched immunoglobulin production. However, B cells are unstudied in prostate cancer (PCa). We used flow cytometry to analyze B-cell subpopulations in peripheral blood and lymph nodes from intermediate-high risk PCa patients. B-cell subpopulations were related to clinicopathological factors. B-cell-receptor single-cell sequencing and VDJ analysis identified clonal B-cell expansion in blood and lymph nodes. Pathological staging was pT2 in 16%, pT3a in 48%, and pT3b in 36%. Lymph node metastases occurred in 5/25 patients (20%). Compared to healthy donors, the peripheral blood CD19+ B-cell compartment was significantly decreased in PCa patients and dominated by na\u00efve B cells. The nodal B-cell compartment had significantly increased fractions of CD19+ B cells and switched memory B cells. Plasmablasts were observed in tumor-draining sentinel lymph nodes (SNs). VDJ analysis revealed clonal expansion in lymph nodes. Thus, activated B cells are increased in SNs from PCa patients. The increased fraction of switched memory cells and plasmablasts together with the presence of clonally expanded B cells indicate tumor-specific T-cell-dependent responses from B cells, supporting an important role for B cells in the protection against tumors.", "doi": "10.3390/cancers15030920", "pmid": "36765877", "labels": {"Clinical Genomics Ume\u00e5": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9913271"}, {"db": "pii", "key": "cancers15030920"}], "notes": [], "created": "2023-11-27T22:02:05.675Z", "modified": "2024-01-16T13:48:34.002Z"}, {"entity": "publication", "iuid": "394b989e896342f8a803356dbb5e5c2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/394b989e896342f8a803356dbb5e5c2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/394b989e896342f8a803356dbb5e5c2f"}}, "title": "Proteomic Profiling of Tissue Exosomes Indicates Continuous Release of Malignant Exosomes in Urinary Bladder Cancer Patients, Even with Pathologically Undetectable Tumour.", "authors": [{"family": "Eldh", "given": "Maria", "initials": "M"}, {"family": "Mints", "given": "Michael", "initials": "M"}, {"family": "Hiltbrunner", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3415-7992", "researcher": {"href": "https://publications.scilifelab.se/researcher/b80636a6106f48d5892e99e58249412e.json"}}, {"family": "Ladjevardi", "given": "Sam", "initials": "S"}, {"family": "Alamdari", "given": "Farhood", "initials": "F"}, {"family": "Johansson", "given": "Markus", "initials": "M"}, {"family": "Jakubczyk", "given": "Tomasz", "initials": "T"}, {"family": "Veerman", "given": "Rosanne E", "initials": "RE"}, {"family": "Winqvist", "given": "Ola", "initials": "O"}, {"family": "Sherif", "given": "Amir", "initials": "A", "orcid": "0000-0002-3675-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/e27ad5d3def147849d4821d86075c3d2.json"}}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1771-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d446cb52d7e4a01ad8478a9cfe22ae1.json"}}], "type": "journal article", "published": "2021-06-29", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "13", "issue": "13", "issn-l": "2072-6694"}, "abstract": "Invasive urothelial bladder cancer (UBC) has high recurrence rates even after radical cystectomy (RC). Exosomes are membrane-bound nanovesicles, which have been shown to contribute to carcinogenesis and metastasis. We previously showed that urinary exosomes display a malignant profile in UBC patients despite the absence of detectable tumour. Here, we investigated exosomes from sampling sites close to or distant from the former tumour, aiming to understand the effect of the tumour on the local milieu. Ten patients scheduled for cystectomy after transurethral bladder resection (TUR-B), without remaining detectable tumour, were included. Exosomes were isolated from tissue explants of both the previous tumour site and distant bladder tissue. Proteins were quantified by mass spectrometry in seven patients. Exosomes from the previous tumour site were enriched in inflammatory but not cancer-related pathways compared to distant tissue. However, the 69 most abundant proteins in tissue-derived exosomes regardless of site, 20 of which were also found in urinary exosomes from our previous study, were enriched for cancer-related metabolic pathways and associated with poor prognosis in an external mRNA dataset. The enrichment of cancer-related pathways in the most abundant proteins, regardless of sampling site, confirms our hypothesis that despite the absence of detectable tumour, the entire bladder releases exosomes that contribute to metastasis and highlights the need for early RC.", "doi": "10.3390/cancers13133242", "pmid": "34209558", "labels": {"Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "cancers13133242"}, {"db": "pmc", "key": "PMC8267924"}], "notes": [], "created": "2022-03-29T12:09:27.244Z", "modified": "2022-03-29T12:09:27.355Z"}]}