{"entity": "label", "iuid": "1cfc7d177ba64cac8b74cf98279d7d3a", "timestamp": "2026-07-20T12:30:51.293Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/Clinical%20Proteomics%20Lund.json"}, "display": {"href": "https://publications.scilifelab.se/label/Clinical%20Proteomics%20Lund"}}, "value": "Clinical Proteomics Lund", "started": "2025", "ended": null, "created": "2025-10-17T12:12:20.825Z", "modified": "2025-10-17T12:13:04.852Z", "accounts": [{"entity": "account", "iuid": "3c17080d257a45c0b852d4413175690f", "timestamp": "2026-07-20T12:30:51.293Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/anahita.bakochi%40med.lu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/anahita.bakochi%40med.lu.se"}}, "email": "anahita.bakochi@med.lu.se", "name": "Anahita Bakochi", "orcid": "0000-0001-8144-8525", "role": "curator", "status": "enabled", "login": "2026-07-01T10:40:17.991Z", "created": "2025-10-20T17:21:31.044Z", "modified": "2026-07-01T10:40:17.991Z"}, {"entity": "account", "iuid": "6a38350bd21f4fb6aeeb1530037a99ae", "timestamp": "2026-07-20T12:30:51.293Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:37.113Z", "created": "2024-08-16T10:01:02.800Z", "modified": "2025-10-31T11:15:37.113Z"}], "publications_count": 13, "publications": [{"entity": "publication", "iuid": "166b088f32524d54834a4f3d40280ff2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/166b088f32524d54834a4f3d40280ff2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/166b088f32524d54834a4f3d40280ff2"}}, "title": "Fibroblast growth factor signals drive the metastatic behavior in small cell lung cancer.", "authors": [{"family": "Ernhofer", "given": "B\u00fcsra", "initials": "B"}, {"family": "Solta", "given": "Anna", "initials": "A"}, {"family": "Sinner", "given": "Julia", "initials": "J"}, {"family": "Megyesfalvi", "given": "Zsolt", "initials": "Z"}, {"family": "Deloria", "given": "Abigail J", "initials": "AJ"}, {"family": "Boettiger", "given": "Kristiina", "initials": "K"}, {"family": "Glatt", "given": "Lisa", "initials": "L"}, {"family": "Horvath", "given": "Lilla", "initials": "L"}, {"family": "Sturtzel", "given": "Caterina", "initials": "C"}, {"family": "Wenninger-Weinzierl", "given": "Andrea", "initials": "A"}, {"family": "Distel", "given": "Martin", "initials": "M"}, {"family": "Grusch", "given": "Michael", "initials": "M", "orcid": "0000-0001-5486-9340", "researcher": {"href": "https://publications.scilifelab.se/researcher/33d23db694784675b9bd43c5a325a11e.json"}}, {"family": "Szeitz", "given": "Beata", "initials": "B"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Aigner", "given": "Clemens", "initials": "C", "orcid": "0000-0002-7787-991X", "researcher": {"href": "https://publications.scilifelab.se/researcher/247257fbcb174339a5d0a16eecaafcca.json"}}, {"family": "Dome", "given": "Balazs", "initials": "B", "orcid": "0000-0001-8799-8624", "researcher": {"href": "https://publications.scilifelab.se/researcher/a76111211b8e4c44a556da4ca321811c.json"}}, {"family": "Schelch", "given": "Karin", "initials": "K", "orcid": "0000-0001-8742-1737", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb1707596834e4cbec4850d46d220c4.json"}}], "type": "journal article", "published": "2026-02-00", "journal": {"title": "Br. J. Cancer", "issn": "1532-1827", "volume": "134", "issue": "4", "pages": "543-554", "issn-l": "0007-0920"}, "abstract": "Early metastatic spread represents a challenge in fighting small cell lung cancer (SCLC). The molecular mechanisms underlying metastatic dissemination remain unclear in this devastating disease.\n\nInvasive traits were investigated in 13 SCLC cell lines using 3D-spheroid formation, sprouting assays, co-cultures and a zebrafish xenograft model. Proteomic analysis was performed to unravel metastatic drivers, which were validated by qPCR, growth factor arrays and specific inhibitors.\n\nOverall, 8 cell lines formed spheroids, and half of these displayed invasive sprouting in collagen. The 'sprouter' SCLC cells, which all had a YAP1-dominant subtype, showed increased migration in zebrafish larvae and penetrated endothelial cell monolayers to a higher extent, thereby mimicking intra- and extravasation. Proteomics revealed differences in adhesion properties, oncogenic pathways and receptor tyrosine kinase signalling. Sprouter cells showed higher expression levels of mesenchymal cell state markers. Stimulation with fibroblast growth factor 2 (FGF2) further induced invasive sprouting, while blocking the FGF/R axis resulted in a significant reduction of sprouting in vitro and in vivo.\n\nThe FGF/R axis is a key driver of SCLC metastatic spread in the YAP1-dominant subtype. These data might facilitate the development of potential future therapies targeting FGF/R signalling to prevent SCLC progression and metastasis.", "doi": "10.1038/s41416-025-03276-y", "pmid": "41390896", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12859120"}, {"db": "pii", "key": "10.1038/s41416-025-03276-y"}], "notes": [], "created": "2026-07-01T10:52:55.099Z", "modified": "2026-07-01T10:53:38.296Z"}, {"entity": "publication", "iuid": "84576d4b89174b05be4e264f7d9736a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84576d4b89174b05be4e264f7d9736a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84576d4b89174b05be4e264f7d9736a6"}}, "title": "Accessing the proteome of extracellular vesicles via rapid acoustic isolation of a minute human blood plasma sample.", "authors": [{"family": "Havers", "given": "Megan", "initials": "M"}, {"family": "Scott", "given": "Aaron M", "initials": "AM"}, {"family": "Ortenl\u00f6f", "given": "Niklas", "initials": "N"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}, {"family": "Baasch", "given": "Thierry", "initials": "T"}, {"family": "Evander", "given": "Mikael", "initials": "M"}, {"family": "Lenshof", "given": "Andreas", "initials": "A"}, {"family": "Gram", "given": "Magnus", "initials": "M"}, {"family": "Laurell", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2025-12-15", "journal": {"title": "Anal. Chim. Acta", "issn": "1873-4324", "volume": "1379", "pages": "344661", "issn-l": "0003-2670"}, "abstract": "Despite substantial progress in the field of mass spectrometry, there remain barriers to measuring the extracellular vesicles (EVs) proteome in blood plasma. Recent work has shown that isolating EVs can make it possible to detect proteins that have low abundance in plasma. Commonly used EV isolation methods either require large sample volumes and long ultracentrifugation times, or else result in population bias via targeted isolation. There is a great need for fast and easy methods to isolate EVs from small volumes of plasma, <10 \u03bcL, enabling biomarker discovery, e.g. in biobanked samples, where mass spectrometry can play an important role.\n\nWe unveil the extracellular vesicle proteome by using seed particle enhanced acoustic trapping to purify EVs from minute blood plasma samples (8 \u03bcL) in 6 min per sample. The differential mass spectrometry results find proteins which are significantly enriched (FDR-adjusted p-values<0.05) in acoustically trapped samples compared to raw (unprocessed) plasma, more than two thirds of those proteins have been associated with EVs previously. Additionally, we are able to increase the depth of analysis by detecting 51 low abundance proteins not detected in raw plasma, half of which are tagged with the gene ontology (GO) tag \"extracellular exosome\" (GO:0070062). Finally, we validate the novel use of neutrally charged silica seed particles paired with a washing flowrate of 200 \u03bcL/min, enabling the processing time to be halved and finding the same proteome as for tried-and-tested polystyrene seed particles with washing at 30 \u03bcL/min.\n\nOur microfluidics-based approach to EV isolation enables rapid processing of an individual minute blood plasma sample, demonstrating that personal proteomic information associated with EVs can be detected when acoustic trapping is used as a pre-processing step. By applying this technique to plasma from patient cohorts or mouse models, future studies may offer new insights into the role of EVs in the progression of diseases and reveal new diagnostic targets in the proteomic cargo of EVs.", "doi": "10.1016/j.aca.2025.344661", "pmid": "41167904", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-2670(25)01055-4"}], "notes": [], "created": "2025-11-28T10:03:49.935Z", "modified": "2025-11-28T10:03:49.946Z"}, {"entity": "publication", "iuid": "83806efbc25545839421c1bd304539b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83806efbc25545839421c1bd304539b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83806efbc25545839421c1bd304539b4"}}, "title": "MHC I of the Great Reed Warbler Promotes a Flat Peptide Binding Mode.", "authors": [{"family": "Venskutonyt\u0117", "given": "Raminta", "initials": "R"}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "O'Connor", "given": "Emily Amelia", "initials": "EA"}, {"family": "Westerdahl", "given": "Helena", "initials": "H"}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Immunology", "issn": "1365-2567", "volume": "176", "issue": "4", "pages": "508-519", "issn-l": "0019-2805"}, "abstract": "The major histocompatibility complex (MHC) plays a key role in pathogen recognition as part of the adaptive immune system. MHC I gene copy numbers in birds of the order Passeriformes (songbirds) are substantially larger compared to other birds. MHC I diversity and antigen presentation have been carefully characterised in chicken Gallus gallus of the order Galliformes; chickens express few MHC I genes and often present antigens that bulge out of the peptide binding cleft. This observation raises the question of whether MHC I presents antigens in a similar way in species with many MHC genes? Here, we present the X-ray structure of MHC I from the great reed warbler Acrocephalus arundinaceus (Acar3) a long-distance migratory songbird. Structural analysis shows that MHC I binds the antigen in a flat conformation due to a sequentially well-conserved restriction point, acting like a pair of tweezers, within the peptide binding grove, created by Arg97 and Arg155. This more stringent antigen presentation by Acar MHC I molecules may partly explain the high MHC gene copy numbers seen in the great reed warbler.", "doi": "10.1111/imm.70015", "pmid": "40643222", "labels": {"Clinical Proteomics Lund": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12583234"}, {"db": "PDB", "key": "9QG8"}, {"db": "Dryad", "key": "cvdncjtg1"}], "notes": [], "created": "2026-07-01T10:50:43.948Z", "modified": "2026-07-01T10:50:44.013Z"}, {"entity": "publication", "iuid": "62b08b8c76874e48bea117c92bd8ecb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62b08b8c76874e48bea117c92bd8ecb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62b08b8c76874e48bea117c92bd8ecb8"}}, "title": "Commensal Peptoniphilus harei induce activation of monocytes via TLR2/CD14 signalling in whole blood.", "authors": [{"family": "Schmidt", "given": "Tobias", "initials": "T"}, {"family": "Frick", "given": "Inga-Maria", "initials": "IM"}, {"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "Neumann", "given": "Ariane", "initials": "A"}], "type": "journal article", "published": "2025-11-27", "journal": {"title": "Med Microbiol Immunol", "issn": "1432-1831", "volume": "214", "issue": "1", "pages": "52", "issn-l": null}, "abstract": "Myeloid cells, such as monocytes, are central in the immune response to infections. However, limited knowledge exists regarding the inflammatory response to Gram-positive anaerobic cocci (GPAC).To explore the ability of GPACs to induce monocyte activation, we compared two GPAC species, Parvimonas micra and Peptoniphilus harei, with E. coli, a major cause of bloodstream infections. We stimulated whole blood with heat-killed bacteria or conditioned medium (CM) and analysed monocytes for signs of activation by flow cytometry. The mechanisms were explored using anti-CD14- or anti-TLR2 antibodies. Finally, to investigate potential pathogen-associated molecular patterns in CM, we performed mass spectrometry (MS).Our findings revealed that P. harei significantly induced activation of monocytes, as evidenced by increased expression of activation markers (PDL1, HLA-DR and CD11b), phosphorylation of members of signalling pathways (NF\u03baBp65, p38 and Akt) and production of cytokines (IL-1\u03b2, TNF, IL-6). Interestingly, P. micra had minimal impact on monocyte activation, and we thus focused on P. harei. Pre-treatment with anti-CD14 attenuated the activation of monocytes by heat-killed P. harei. Moreover, P. harei CM also induced clear monocyte activation, though, in contrast to heat-killed P. harei, this activation was dependent on TLR2 signalling. MS analysis of CM primarily identified four proteins possibly associated with monocyte activation. Finally, we also explored neutrophil activation and found a similar activation pattern to that of monocytes, suggesting that our observations are not exclusive to monocytes.Our study demonstrates that P. harei induce prominent activation of monocytes in blood, highlighting a pathogenic potential of these otherwise harmless perceived bacteria.", "doi": "10.1007/s00430-025-00859-7", "pmid": "41307706", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12660362"}, {"db": "pii", "key": "10.1007/s00430-025-00859-7"}], "notes": [], "created": "2026-07-01T10:51:16.191Z", "modified": "2026-07-01T10:51:16.217Z"}, {"entity": "publication", "iuid": "7b5288037215436796bda7010f8cde84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b5288037215436796bda7010f8cde84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b5288037215436796bda7010f8cde84"}}, "title": "Characterisation of airway inflammation and proteomes associated with cystic fibrosis-related diabetes.", "authors": [{"family": "Diemer", "given": "Stefanie", "initials": "S", "orcid": "0009-0006-3319-611X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b68575ebda04f75861e4c75e729e9bd.json"}}, {"family": "Chowdhury", "given": "Sounak", "initials": "S"}, {"family": "Sahl", "given": "Cecilia", "initials": "C"}, {"family": "Happonen", "given": "Lotta", "initials": "L"}, {"family": "P\u00e5hlman", "given": "Lisa I", "initials": "LI", "orcid": "0000-0001-6366-2309", "researcher": {"href": "https://publications.scilifelab.se/researcher/f58db990776f4e228707df2502d44728.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "ERJ Open Res", "issn": "2312-0541", "volume": "11", "issue": "6", "issn-l": "2312-0541"}, "abstract": "Cystic fibrosis (CF)-related diabetes (CFRD) is the most common extrapulmonary complication in CF. CFRD is associated with low lung function, but the underlying mechanisms are poorly understood. The aim of the present study was to compare airway inflammation and the airway proteome in people with CF (pwCF) with and without CFRD.\n\nSputum samples from pwCF were analysed for neutrophil elastase (NE) activity with a chromogenic assay, inflammatory cytokines using Meso Scale and bacterial load via quantitative PCR of the 16S rRNA gene. The sputum proteome was characterised by liquid chromatography-mass spectrometry.\n\n33 pwCF were included in the study, of which 55% had CFRD. The CFRD group had significantly lower lung function and higher sputum levels of NE, interleukin (IL)-8 and IL-1\u03b2, whereas IL-6 levels were lower compared to pwCF without CFRD. Proteome analysis identified 27 sputum proteins linked to CFRD, mainly involved in neutrophil degranulation. Given that lung function could be a possible confounding factor, we matched pwCF with and without CFRD based on lung function. In these lung function-matched cohorts, IL-8 and IL-6 levels did not differ significantly, but IL-1\u03b2 showed a trend towards higher levels in the CFRD group. 10 CFRD-associated proteins were significantly more abundant in the CFRD group, including prothymosin \u03b1, which plays a role in diabetes and insulin release.\n\nCFRD is associated with lower lung function, increased sputum levels of NE, IL-8 and IL-1\u03b2, and specific protein profiles.", "doi": "10.1183/23120541.00290-2025", "pmid": "41220822", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12598600"}, {"db": "pii", "key": "00290-2025"}], "notes": [], "created": "2025-11-28T10:17:17.675Z", "modified": "2025-11-28T10:17:17.777Z"}, {"entity": "publication", "iuid": "b7e17533eee14fb99c7a12b71c7c780d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7e17533eee14fb99c7a12b71c7c780d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7e17533eee14fb99c7a12b71c7c780d"}}, "title": "Retinal tau phosphorylation in Alzheimer's disease: A mass spectrometry study.", "authors": [{"family": "Santiago", "given": "Jessica", "initials": "J"}, {"family": "Pocevi\u010di\u016bt\u0117", "given": "Dovil\u0117", "initials": "D"}, {"family": "Vogel", "given": "Jacob", "initials": "J"}, {"family": "Netherlands Brain Bank", "given": "", "initials": ""}, {"family": "Brinkmalm", "given": "Gunnar", "initials": "G"}, {"family": "Wennstr\u00f6m", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Neurobiol. Dis.", "issn": "1095-953X", "volume": "215", "pages": "107057", "issn-l": "0969-9961"}, "abstract": "Most neurodegenerative diseases, including Alzheimer's disease (AD) and multiple sclerosis (MS), feature abnormal tau phosphorylation (p-tau) in the brain. Prior immunostaining studies have shown p-tau accumulation in the AD retina, suggesting it may mirror brain tau pathology.\n\nWe used mass spectrometry to quantify p-tau peptides in matched retinal and hippocampal samples from non-demented controls (NC, n = 8), AD (n = 12), and MS (n = 4). We compared p-tau levels across diagnoses and analysed correlations between retinal p-tau variants, hippocampal p-tau, and neuropathological changes.\n\nTau peptides phosphorylated at T181, S199/S202, T231, T231 + T235, S396 + T403/S404, and T403/S404 were detected in retinas. Total tau phosphorylation and phosphorylation at S199/S202 and T231 were significantly higher in AD cases compared to NC. These two, along with p-tau S396 + T403/S404, were also higher in cases with high amyloid-beta (A\u03b2) Braak stages compared to those with low A\u03b2 Braak stages. Higher A\u03b2 stages were also correlated with higher peak intensities of p-tau S199/S202 and S396 + T403/S404, and retinal p-tau S396 + T403/S404 and T403/S404 correlated with neurofibrillary tangle (NFT) Braak stages. Additionally, p-tau S396 + T403/S404 in the retina was associated with corresponding phosphorylation in the hippocampus.\n\nOur findings reveal both overlapping and distinct p-tau patterns in retina and hippocampus, with a notable link for p-tau S396 + T403/S404. This enhances our understanding of tauopathies in both tissues and supports retinal tau as a promising biomarker for AD diagnosis and monitoring.", "doi": "10.1016/j.nbd.2025.107057", "pmid": "40835172", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pii", "key": "S0969-9961(25)00273-6"}], "notes": [], "created": "2026-07-01T10:56:04.516Z", "modified": "2026-07-01T10:56:04.523Z"}, {"entity": "publication", "iuid": "cb4b4d435f4947219be906a67e904ed5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb4b4d435f4947219be906a67e904ed5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb4b4d435f4947219be906a67e904ed5"}}, "title": "Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity.", "authors": [{"family": "Szeitz", "given": "Beata", "initials": "B", "orcid": "0000-0001-6414-0537", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7d73d277254472da3770838dddaac19.json"}}, {"family": "Hagemeijer", "given": "Yanick Paco", "initials": "YP"}, {"family": "Pahi", "given": "Zoltan Gabor", "initials": "ZG"}, {"family": "Ujfaludi", "given": "Zsuzsanna", "initials": "Z"}, {"family": "Kuras", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-9479-423X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a160035cccbb42b5a7164ad9cef6ac12.json"}}, {"family": "Rodriguez", "given": "Jimmy", "initials": "J"}, {"family": "Doma", "given": "Viktoria", "initials": "V"}, {"family": "Mohacsi", "given": "Reka", "initials": "R"}, {"family": "Herold", "given": "Magdolna", "initials": "M"}, {"family": "Herold", "given": "Zoltan", "initials": "Z"}, {"family": "Horvath", "given": "Zsolt", "initials": "Z"}, {"family": "Pla", "given": "Indira", "initials": "I"}, {"family": "Sugihara", "given": "Yutaka", "initials": "Y", "orcid": "0000-0002-4406-3017", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dcf4589722645699f04a66113fbbd1a.json"}}, {"family": "Baldetorp", "given": "Bo", "initials": "B"}, {"family": "Lindberg", "given": "Henrik", "initials": "H"}, {"family": "Oskolas", "given": "Henriett", "initials": "H"}, {"family": "Rezeli", "given": "Melinda", "initials": "M", "orcid": "0000-0003-4373-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/586ea8903ead4d6a974b6583aba07580.json"}}, {"family": "Gil", "given": "Jeovanis", "initials": "J", "orcid": "0000-0003-3601-3893", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aeb67da0d81436eaf7a008fcb298eec.json"}}, {"family": "Appelqvist", "given": "Roger", "initials": "R"}, {"family": "Kemeny", "given": "Lajos V", "initials": "LV"}, {"family": "Guedes", "given": "Jessica", "initials": "J"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "Sanchez", "given": "Aniel", "initials": "A"}, {"family": "Boros", "given": "Imre Miklos", "initials": "IM"}, {"family": "Nemeth", "given": "Istvan Balazs", "initials": "IB"}, {"family": "Guryev", "given": "Victor", "initials": "V"}, {"family": "Pankotai", "given": "Tibor", "initials": "T", "orcid": "0000-0001-9810-5465", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390e4f386c6481a9022d45bab78f404.json"}}, {"family": "Paw\u0142owski", "given": "Krzysztof", "initials": "K"}, {"family": "Wieslander", "given": "Elisabet", "initials": "E"}, {"family": "Szasz", "given": "Attila Marcell", "initials": "AM"}, {"family": "Feny\u00f6", "given": "David", "initials": "D"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Timar", "given": "Jozsef", "initials": "J"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}, {"family": "Betancourt", "given": "Lazaro Hiram", "initials": "LH", "orcid": "0000-0001-8207-7041", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba3e440ea6234811b5677126d7e24726.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Clin Transl Med", "issn": "2001-1326", "volume": "15", "issue": "10", "pages": "e70477", "issn-l": null}, "abstract": "Metastatic melanoma is a highly aggressive disease with poor survival rates despite recent therapeutic advancements with immunotherapy. The proteomic landscape of advanced melanoma remains poorly understood, especially regarding proteomic heterogeneity across metastases within patients.\n\nWe collected 83 melanoma metastases from 19 different metastatic sites in 24 patients with advanced metastatic melanoma almost exclusively from the pre-immunotherapy era, using semi-rapid autopsies. The metastases were subjected to histopathological evaluation, RNA-sequencing and mass spectrometry-based proteomics for protein quantitation and non-reference peptide (NRP) sequence detection using a proteogenomic data integration approach.\n\nNRPs associated with mutations frequently occurred in proteins related to focal adhesion, vesicle-mediated transport, MAPK signalling and immune response pathways across the cohort. Intrapatient heterogeneity was negligible when considering morphology and driver gene mutation status but was substantial at the proteogenomic level. This heterogeneity was not driven by metastasis location, albeit liver metastases exhibited distinct proteogenomic patterns, including upregulation of metabolic pathways. Cluster analysis outlined four proteomic clusters (C1-4) of the metastases, characterised by the upregulation of cell cycle and RNA-splicing (C1), mitochondrial processes (C3), extracellular matrix (ECM) and immune pathways (C2) and ECM and vesicle-mediated transport pathways (C4). Around two-thirds of patients had metastases that had strongly distinct phenotypes. Patients in our cohort whose metastases were primarily assigned to clusters C1 and C3 exhibited shorter overall survival than patients whose metastases were categorised mainly into the C2 and C4 clusters.\n\nOur unique multi-metastasis cohort captured the proteogenomic heterogeneity of immunotherapy-na\u00efve melanoma distant metastases, establishing a foundation for future studies aimed at identifying novel therapeutic targets to complement current immunotherapies.\n\nComprehensive proteogenomic profiling of post-mortem melanoma metastases, collected primarily before the immunotherapy era. Description of 1177 protein sequence variants predicted by RNA-Seq and validated via mass spectrometry-based proteomics. Empirical evidence of prominent intrapatient heterogeneity, driven by heterogeneous protein expression related to cell cycle- and mitochondrial processes, immune system and extracellular matrix organization.", "doi": "10.1002/ctm2.70477", "pmid": "41017066", "labels": {"Clinical Proteomics Lund": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12477065"}], "notes": [], "created": "2026-07-01T10:54:20.521Z", "modified": "2026-07-01T10:54:20.903Z"}, {"entity": "publication", "iuid": "ddbca7e5d1ca41958583253b3f6832ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddbca7e5d1ca41958583253b3f6832ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddbca7e5d1ca41958583253b3f6832ff"}}, "title": "Mass spectrometry peptidomics data from infected and uninfected porcine wounds.", "authors": [{"family": "Forsberg", "given": "Fredrik", "initials": "F", "orcid": "0009-0000-6464-2676", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa3e86a7b284ca8be485deaba255c8a.json"}}, {"family": "Kjellstr\u00f6m", "given": "Sven", "initials": "S", "orcid": "0000-0003-4646-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfae5f64ec9d45e282cdfd038539fe25.json"}}, {"family": "Petrlova", "given": "Jitka", "initials": "J"}, {"family": "Puthia", "given": "Manoj", "initials": "M", "orcid": "0000-0001-6048-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/f794b8d0d66a4bab964e915ff71a7023.json"}}, {"family": "Schmidtchen", "given": "Artur", "initials": "A", "orcid": "0000-0001-9209-3141", "researcher": {"href": "https://publications.scilifelab.se/researcher/406510dc3844487e9c45f713ea173b8e.json"}}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad3c999da10c41e4a3afda2718815083.json"}}, {"family": "Hartman", "given": "Erik", "initials": "E", "orcid": "0000-0001-9997-2405", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd725d94e9941ea835537ba503fb309.json"}}], "type": "journal article", "published": "2025-09-02", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "1533", "issn-l": "2052-4463"}, "abstract": "Recently, mass spectrometry based peptidomics studies have proven useful in the identification of biomarkers and bioactive peptide-based therapeutics. Here, we present a dataset comprised of temporal wound fluid peptidomics data from highly defined porcine models. Wound fluids from porcine wounds infected with Staphylococcus aureus and Pseudomonas aeruginosa, and uninfected controls, were sampled at different timepoints of the infection. Peptides were extracted from the samples, followed by liquid chromatography tandem mass spectrometry analysis in data dependent acquisition mode. The resulting spectra and searched files have been deposited to online repositories and made easily accessible to enable further investigations of the infected and uninfected wound fluid peptidome.", "doi": "10.1038/s41597-025-05842-8", "pmid": "40897740", "labels": {"Clinical Proteomics Lund": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12405536"}, {"db": "pii", "key": "10.1038/s41597-025-05842-8"}], "notes": [], "created": "2026-07-01T10:49:51.860Z", "modified": "2026-07-01T10:49:52.391Z"}, {"entity": "publication", "iuid": "9d21fed99d724073b273c4111d795658", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d21fed99d724073b273c4111d795658.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d21fed99d724073b273c4111d795658"}}, "title": "Data-Driven Cluster Analysis of Cerebrospinal Fluid Proteome and Associations with Clinical Phenotypes in Systemic Lupus Erythematosus.", "authors": [{"family": "Grenmyr", "given": "Elsa", "initials": "E", "orcid": "0009-0001-2638-401X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a444ccb93e41482b89fc5701e9d1f112.json"}}, {"family": "Zervides", "given": "Kristoffer", "initials": "K", "orcid": "0000-0003-4311-1635", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3d97e5524f4b96b9c1eec6a3046ad4.json"}}, {"family": "Najibi", "given": "Seyed Morteza", "initials": "SM", "orcid": "0000-0001-6756-508X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57edb80d12c241ac81cee27e914bcc31.json"}}, {"family": "Gullstrand", "given": "Birgitta", "initials": "B", "orcid": "0000-0002-9172-990X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a3099cf6d14f9e8a9cec8e6f305761.json"}}, {"family": "Welinder", "given": "Charlotte", "initials": "C", "orcid": "0000-0001-9626-0576", "researcher": {"href": "https://publications.scilifelab.se/researcher/924dc427398e4ba7b31eb5b4b47a89ca.json"}}, {"family": "Nystedt", "given": "Jessika", "initials": "J", "orcid": "0000-0002-7193-1828", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ca2947d930a471eb7fa23c622b7a5bb.json"}}, {"family": "Nilsson", "given": "Petra C", "initials": "PC"}, {"family": "Sundgren", "given": "Pia C", "initials": "PC", "orcid": "0000-0001-9237-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c755205abb4ecfabb3d5f021b7a1f6.json"}}, {"family": "Kahn", "given": "Robin", "initials": "R", "orcid": "0000-0002-3167-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f81ea4fa0314830a81ceec70ec188da.json"}}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A", "orcid": "0000-0002-4418-5786", "researcher": {"href": "https://publications.scilifelab.se/researcher/894f8618182f401dafa8071e75ca57fa.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "ACR Open Rheumatol", "issn": "2578-5745", "volume": "7", "issue": "9", "pages": "e70089", "issn-l": null}, "abstract": "To explore the cerebrospinal fluid (CSF) proteome in systemic lupus erythematosus (SLE) and the associations between the CSF proteomic patterns and clinical manifestations.\n\nCSF samples from 29 female outpatients with SLE were analyzed with label-free liquid chromatography tandem mass spectrometry. Inclusion and CSF collection were conducted irrespective of clinical manifestations and disease duration. Proteomic data were used for sample clustering and analyzed for clinical variance. Proteins were clustered using Weighted Gene Co-expression Correlation Network Analysis. Modules were biologically characterized and analyzed for correlation to the clinical dataset.\n\nThree patient clusters were identified. Cluster 1 was characterized by the highest frequency of nephritis, depression, and cognitive dysfunction. Cluster 2 showed the highest frequency of alopecia and Sjogren disease antigen A-antibodies (anti-SSA) and a low frequency of cognitive impairment. Cluster 3 had a higher frequency of autonomic neuropathy and headache. Six protein modules were identified (module 1 [M1]-M6). Modules were characterized by nervous tissue proteins (M1), central nervous system (CNS) lipoproteins (M2), macrophage proteins (M3), plasma proteins (M4), Ig (M5), and intracellular metabolic proteins (M6). M1 and M2 proteins were most abundant in cluster 1 and correlated with nephritis, depression, and cognitive impairment. Increased abundance of M4 and M5 proteins were most distinct in cluster 2 and inversely correlated to cognitive impairment and brain atrophy.\n\nPatients clustered by their CSF proteomic pattern had different disease phenotypes. Nephritis and neuronal damage defined the group with higher levels of neuronal proteins in CSF, which may suggest shared pathogenetic pathways in SLE affecting the kidney and CNS.", "doi": "10.1002/acr2.70089", "pmid": "40874685", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12392285"}], "notes": [], "created": "2025-11-28T10:11:22.816Z", "modified": "2025-11-28T10:11:23.769Z"}, {"entity": "publication", "iuid": "8a5e42afead043b98d5731408ed7ba25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a5e42afead043b98d5731408ed7ba25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a5e42afead043b98d5731408ed7ba25"}}, "title": "The DNA repair factor ku80 binds and activates the adhesion receptor ELTD1/ADGRL4.", "authors": [{"family": "Amisten", "given": "Stefan", "initials": "S"}, {"family": "Rezeli", "given": "Melinda", "initials": "M"}, {"family": "Grossi", "given": "Mario", "initials": "M"}, {"family": "Bryl-Gorecka", "given": "Paulina", "initials": "P"}, {"family": "H\u00e5kansson", "given": "Anton", "initials": "A"}, {"family": "Torngren", "given": "Kristina", "initials": "K"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Olde", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2025-06-01", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "volume": "764", "pages": "151785", "issn-l": "0006-291X"}, "abstract": "We investigated the mRNA expression of G protein-coupled receptors (GPCRs) in cells from four human vascular beds: umbilical vein (HUVEC), microvasculature (MVEC), aorta (HAEC), and coronary artery (CAEC). Our study revealed that the orphan receptor ELTD1 (ADGRL4) was the most abundantly expressed GPCR mRNA in all four EC types. When recombinantly expressed in U87 cells, ELTD1 receptors activated canonical GPCR pathways, particularly the Gq pathway. Conditioned medium from U87 cells also activated ELTD1 in HEK293 cells, supporting the existence of an autocrine ELTD1-activating factor. Using affinity capture and mass spectrometry in combination with the label free xCelligence system, we identified the proteins ku80 and erythrocyte beta spectrin (SPTB) as ligands to ELTD1. Ku80 demonstrated higher potency in activating ELTD1 than SPTB, thus leading us to focus on this protein. INCA-X, a functional antibody targeting the ku80/ku70 complex, and ELTD1 siRNA impaired endothelial tube formation in a similar manner, suggesting a common pathway. In a study cohort of myocardial infarction patients, high plasma levels of the extracellular domain of ELTD1 correlated (P < 0.05) with high (>2.9) cardiovascular flow reserve, thus indicating an association between ELTD1 and active angiogenesis and revascularization.", "doi": "10.1016/j.bbrc.2025.151785", "pmid": "40245572", "labels": {"Clinical Proteomics Lund": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-291X(25)00499-1"}], "notes": [], "created": "2026-07-01T10:54:42.557Z", "modified": "2026-07-01T10:54:42.561Z"}, {"entity": "publication", "iuid": "7550315fbef140b8a65cc116f93087de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7550315fbef140b8a65cc116f93087de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7550315fbef140b8a65cc116f93087de"}}, "title": "Human proteome distribution atlas for tissue-specific plasma proteome dynamics.", "authors": [{"family": "Malmstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Hauri", "given": "Simon", "initials": "S"}, {"family": "Mohanty", "given": "Tirthankar", "initials": "T"}, {"family": "Scott", "given": "Aaron", "initials": "A"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Gueto-Tettay", "given": "Carlos", "initials": "C"}, {"family": "\u00c5hrman", "given": "Emma", "initials": "E"}, {"family": "Nozohoor", "given": "Shahab", "initials": "S"}, {"family": "Tingstedt", "given": "Bobby", "initials": "B"}, {"family": "Regner", "given": "Sara", "initials": "S"}, {"family": "Elfving", "given": "Peter", "initials": "P"}, {"family": "Bjermer", "given": "Leif", "initials": "L"}, {"family": "Forsvall", "given": "Andreas", "initials": "A"}, {"family": "Doyle", "given": "Alexander", "initials": "A"}, {"family": "Magnusson", "given": "Mattias", "initials": "M"}, {"family": "Hedenfalk", "given": "Ingrid", "initials": "I"}, {"family": "Kannisto", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Brandt", "given": "Christian", "initials": "C"}, {"family": "Nilsson", "given": "Emma", "initials": "E"}, {"family": "Dahlin", "given": "Lars B", "initials": "LB"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "Linder", "given": "Adam", "initials": "A"}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-05-15", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "10", "pages": "2810-2822.e16", "issn-l": "0092-8674"}, "abstract": "The plasma proteome is maintained by the influx and efflux of proteins from surrounding organs and cells. To quantify the extent to which different organs and cells impact the plasma proteome in healthy and diseased conditions, we developed a mass-spectrometry-based proteomics strategy to infer the tissue origin of proteins detected in human plasma. We first constructed an extensive human proteome atlas from 18 vascularized organs and the 8 most abundant cell types in blood. The atlas was interfaced with previous RNA and protein atlases to objectively define proteome-wide protein-organ associations to infer the origin and enable the reproducible quantification of organ-specific proteins in plasma. We demonstrate that the resource can determine disease-specific quantitative changes of organ-enriched protein panels in six separate patient cohorts, including sepsis, pancreatitis, and myocardial injury. The strategy can be extended to other diseases to advance our understanding of the processes contributing to plasma proteome dynamics.", "doi": "10.1016/j.cell.2025.03.013", "pmid": "40203824", "labels": {"Clinical Proteomics Lund": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00286-7"}], "notes": [], "created": "2025-11-28T10:08:51.977Z", "modified": "2025-11-28T10:08:51.981Z"}, {"entity": "publication", "iuid": "16c0e800a96140579c32a12c1db7eebd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16c0e800a96140579c32a12c1db7eebd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16c0e800a96140579c32a12c1db7eebd"}}, "title": "Angiotensinogen and C3 compete for renin-induced complement activation.", "authors": [{"family": "Kristoffersson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Sk\u00f6ld", "given": "Albin", "initials": "A"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Wendler", "given": "Markus", "initials": "M"}, {"family": "Kalliokoski", "given": "Gabriella", "initials": "G"}, {"family": "Bekassy", "given": "Zivile", "initials": "Z"}, {"family": "Karpman", "given": "Diana", "initials": "D"}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1563868", "issn-l": "1664-3224"}, "abstract": "Renin from plasma, kidney, and recombinant sources was previously demonstrated to cleave C3 to C3a and C3b. C3a was generated at a similar rate to that by C3 convertase, and C3 cleavage was inhibited by the renin inhibitor aliskiren. Renin endogenously produced by Calu6 cells also led to C3 deposition on cells. These results have been challenged by another group suggesting that recombinant renin does not cleave C3 or that renin was contaminated by trypsin, which also cleaves C3. Here, we investigated C3 cleavage by recombinant renin and competitive inhibition in the presence of angiotensinogen. Recombinant renin was analyzed by mass spectrometry using endopeptidase LysC digestion and did not contain trypsin. C3 cleavage, using our protocol and that of the other group, showed cleavage to C3b by immunoblotting. Cleavage was inhibited by aliskiren, which inhibits renin but not trypsin. Cleavage to C3a occurred within 1 min as detected by enzyme-linked immunosorbent assay (ELISA). Angiotensinogen competed for renin-mediated C3 cleavage and inhibited C3a generation, but C3 did not inhibit cleavage of angiotensinogen to angiotensin I (detected by ELISA). The results suggest that renin cleaves C3 but angiotensinogen is its preferred substrate. The interaction between renin and C3 may gain importance in the kidney where renin concentrations are considerably higher than in the circulation and when the primary substrate, angiotensinogen, is cleaved and thereby depleted.", "doi": "10.3389/fimmu.2025.1563868", "pmid": "40242769", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11999838"}], "notes": [], "created": "2026-07-01T10:47:35.391Z", "modified": "2026-07-01T10:47:35.399Z"}, {"entity": "publication", "iuid": "133cc9ada6a74cdaa7c6a273df1a804c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/133cc9ada6a74cdaa7c6a273df1a804c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/133cc9ada6a74cdaa7c6a273df1a804c"}}, "title": "Refinement of Protein Extraction Protocols for Human Peripheral Nerve Tissue.", "authors": [{"family": "Frostadottir", "given": "Drifa", "initials": "D", "orcid": "0000-0001-6955-8932", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7f3353130574c9197429d3b2412a9a1.json"}}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Perez", "given": "Raquel", "initials": "R"}, {"family": "Dahlin", "given": "Lars B", "initials": "LB"}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "ACS Omega", "issn": "2470-1343", "volume": "10", "issue": "5", "pages": "5111-5118", "issn-l": "2470-1343"}, "abstract": "Our aim was to establish an effective method for protein extraction from freshly frozen human peripheral nerves, determine the minimum amount required for consistent protein extraction outcomes, and assess which method produced the highest number of protein identities. Five extraction methods were compared using 8 M urea and Ripa buffer using either the Bullet Blender or Bioruptor. Out of the total 2619 identified proteins, protein extraction using the Ripa buffer combined with either Bioruptor or Bullet Blender resulted in the identification of 1582 (60%) and 1615 (62%) proteins, respectively. In contrast, using 8 M urea and Bioruptor for protein extraction resulted in 1022 proteins (39%), whereas employing Bullet Blender yielded 1446 proteins (55%). Sample amounts, ranging from 0.6 to 10 mg, were prepared with consistent protein extraction outcome obtained for samples \u22651.2 mg. Combining Ripa and 8 M urea with Bullet Blender increased protein identification to 2126 (81%). Proteins were classified by their cell components, molecular functions, and biological processes. Furthermore, a subclassification of proteins involved in the extracellular matrix (ECM) was introduced. We recommend the use of Ripa buffer, in combination with 8 M urea and Bullet Blender for extracting proteins from fresh-frozen human nerves weighing \u22651.2 mg.", "doi": "10.1021/acsomega.4c11373", "pmid": "39959086", "labels": {"Clinical Proteomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11822717"}], "notes": [], "created": "2026-07-01T10:48:25.925Z", "modified": "2026-07-01T10:48:26.068Z"}]}