{"entity": "researcher", "timestamp": "2026-06-11T22:04:23.245Z", "family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "affiliations": ["Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195"}}, "publications": [{"entity": "publication", "iuid": "a13b9b2a120741f2af40dbd525b2c748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748"}}, "title": "Exploration of immune phenotypes in self-sampling citizens", "authors": [{"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Naluai", "given": "\u00c5sa Torinsson", "initials": "\u00c5T"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Bauer", "given": "Stefan", "initials": "S"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2026-02-00", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "2", "pages": "114611", "issn-l": "2589-0042"}, "abstract": "Blood proteins have provided essential insights into how humans responded to the recent pandemic. To expand our understanding beyond patients seeking medical care, we conducted a citizen-centric survey with 2,000 random residents (age: 18-69 years) from Sweden's two largest cities in 2021. With self-sampled dried blood spots (DBS) and health information from 437 (22%) volunteers, we performed multi-analyte COVID-19 serology, measured autoantibodies (AAbs) against 22 interferons, and quantified 502 circulating low-abundant immune-related blood proteins. Antibody assays confirmed self-reported infections (26%) and vaccinations (40%), showed timing-dependent discrepancies in the immune response, and revealed anti-type I interferon AAbs co-occurring frequently alongside natural infections. Proteomics data added plausible mechanistic insights into cell-mediated processes: data-driven analyses revealed 24% of participants presented deviating immune phenotypes linked to infections, immunity, respiratory effects, and age. Multi-molecular DBS analysis of random layperson samples captured the broader spectrum of immune system states, adding relevant insights for clinical and public health investigations.", "doi": "10.1016/j.isci.2025.114611", "pmid": "41630906", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12860695"}, {"db": "pii", "key": "S2589-0042(25)02872-X"}], "notes": [], "created": "2026-02-26T13:37:49.302Z", "modified": "2026-03-24T09:13:34.204Z"}, {"entity": "publication", "iuid": "638e3981672c479bb5ffcd2ac87dc4d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/638e3981672c479bb5ffcd2ac87dc4d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/638e3981672c479bb5ffcd2ac87dc4d5"}}, "title": "Blood biomarkers of Alzheimer's disease and progression across different stages of cognitive decline in the community.", "authors": [{"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}, {"family": "Gregorio", "given": "Caterina", "initials": "C", "orcid": "0000-0002-8163-1634", "researcher": {"href": "https://publications.scilifelab.se/researcher/21265a4e63634efba72a5ee676156baa.json"}}, {"family": "Rizzuto", "given": "Debora", "initials": "D"}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Canevelli", "given": "Marco", "initials": "M"}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}], "type": "journal article", "published": "2025-11-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Blood biomarkers of Alzheimer's disease (AD) are promising for dementia prediction, but their association with progression across intermediate stages of cognitive decline in the general population remains unclear. We followed 2148 dementia-free individuals from a Swedish population-based cohort for up to 16 years. Associations between baseline AD blood biomarkers and transitions between normal cognition, mild cognitive impairment (MCI), and dementia were examined. Lower amyloid-\u03b242/40 ratio and higher phosphorylated-tau181 (p-tau181), p-tau217, total-tau, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were associated with faster progression from MCI to all-cause and AD dementia, with the strongest associations for NfL and p-tau217. Elevated NfL and GFAP were linked to reduced MCI reversion to normal cognition, whereas no biomarker was associated with MCI development from normal cognition. These findings show robust group-level associations and indicate that AD blood biomarkers may help stratify dementia risk at the MCI stage in the community.", "doi": "10.1038/s41467-025-66728-2", "pmid": "41276530", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66728-2"}], "notes": [], "created": "2025-11-24T16:43:44.175Z", "modified": "2025-11-24T16:43:44.720Z"}, {"entity": "publication", "iuid": "f3a1b1396edb4101b0575fbc43ec7415", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415"}}, "title": "Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics.", "authors": [{"family": "Sissala", "given": "Noora", "initials": "N", "orcid": "0009-0000-0758-8140", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a96666a6a2e478fbdd3cf33d7db1e74.json"}}, {"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Leo", "given": "Isabelle R", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/21185d9c6a2343f189397cbbb95c6e71.json"}}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Eriksson", "given": "Lars E", "initials": "LE", "orcid": "0000-0001-5121-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebb717a9972245a5b2427a4b8421fe6f.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "journal article", "published": "2025-11-04", "journal": {"title": "Commun Chem", "issn": "2399-3669", "issn-l": null, "volume": "8", "issue": "1", "pages": "327"}, "abstract": "Plasma proteomics technologies are advancing rapidly, offering new opportunities for biomarker discovery and precision medicine. Direct comparisons of available technologies are needed to understand how platform selection affects downstream findings. We compared the performance of a peptide fractionation-based mass spectrometry method (HiRIEF LC-MS/MS) and the Olink Explore 3072 proximity extension assays on 88 plasma samples, analyzing 1129 proteins with both methods. The platforms exhibited complementary proteome coverage, high precision, and concordance in estimating sex differences in protein levels. Quantitative agreement between platforms was moderate (median correlation 0.59, interquartile range 0.33-0.75), mainly influenced by technical factors. Finally, we present a publicly available tool for peptide-level analysis of platform agreement and demonstrate its utility in clarifying cross-platform discrepancies in protein and proteoform measurements. Our findings provide insights for platform selection and study design, and highlight the value of combining mass spectrometry and affinity-based approaches for more comprehensive and reliable plasma proteome profiling.", "doi": "10.1038/s42004-025-01753-2", "pmid": "41188494", "labels": {"National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Stockholm": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12586489"}, {"db": "pii", "key": "10.1038/s42004-025-01753-2"}], "notes": [], "created": "2025-11-07T07:35:27.214Z", "modified": "2025-11-27T13:03:30.885Z"}, {"entity": "publication", "iuid": "2ae5cc4ff3d946528ecb78f961464277", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ae5cc4ff3d946528ecb78f961464277.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ae5cc4ff3d946528ecb78f961464277"}}, "title": "Blood-based biomarkers of Alzheimer's disease and incident dementia in the community.", "authors": [{"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}, {"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Rizzuto", "given": "Debora", "initials": "D"}, {"family": "Xia", "given": "Xin", "initials": "X"}, {"family": "Qiu", "given": "Chengxuan", "initials": "C", "orcid": "0000-0003-1922-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/15238dd19bda48fcbf04b299a8368929.json"}}, {"family": "Orsini", "given": "Nicola", "initials": "N"}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Vetrano", "given": "Davide L", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}], "type": "journal article", "published": "2025-03-26", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "issn-l": "1078-8956"}, "abstract": "Evidence regarding the clinical validity of blood biomarkers of Alzheimer's disease (AD) in the general population is limited. We estimated the hazard and predictive performance of six AD blood biomarkers for incident all-cause and AD dementia-the ratio of amyloid-\u03b2 42 to amyloid-\u03b2 40 and levels of tau phosphorylated at T217 (p-tau217), tau phosphorylated at T181 (p-tau181), total tau, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP)-in a cohort of 2,148 dementia-free older adults from Sweden, who were followed for up to 16 years. In multi-adjusted Cox regression models, elevated baseline levels of p-tau181, p-tau217, NfL, and GFAP were associated with a significantly increased hazard for all-cause and AD dementia, displaying a non-linear dose-response relationship. Elevated concentrations of p-tau181, p-tau217, NfL, and GFAP demonstrated strong predictive performance (area under the curve ranging from 70.9% to 82.6%) for 10-year all-cause and AD dementia, with negative predictive values exceeding 90% but low positive predictive values (PPVs). Combining p-tau217 with NfL or GFAP further improved prediction, with PPVs reaching 43%. Our findings suggest that these biomarkers have the potential to rule out impending dementia in community settings, but they might need to be combined with other biological or clinical markers to be used as screening tools.", "doi": "10.1038/s41591-025-03605-x", "pmid": "40140622", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-025-03605-x"}], "notes": [], "created": "2025-04-02T14:34:39.959Z", "modified": "2025-04-02T14:34:40.970Z"}, {"entity": "publication", "iuid": "7352c8aca5214ed1878a95ee46d195ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7352c8aca5214ed1878a95ee46d195ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7352c8aca5214ed1878a95ee46d195ab"}}, "title": "Dietary patterns and blood-based biomarkers of Alzheimer's disease in cognitively intact older adults: Findings from a population-based study.", "authors": [{"family": "Mrhar", "given": "Anja", "initials": "A"}, {"family": "Carballo-Casla", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Grande", "given": "Giulia", "initials": "G", "orcid": "0000-0001-6312-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6fc0b0bad8243059965a2b828321c14.json"}}, {"family": "Valletta", "given": "Martina", "initials": "M", "orcid": "0000-0003-0139-8287", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa01849f48049c78eef04747ab1797a.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Gregori\u010d Kramberger", "given": "Milica", "initials": "M"}, {"family": "Kuhar", "given": "Ale\u0161", "initials": "A"}, {"family": "Winblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-0011-1179", "researcher": {"href": "https://publications.scilifelab.se/researcher/73185a13ca474153b66415e6a2dfff0f.json"}}, {"family": "Calder\u00f3n-Larra\u00f1aga", "given": "Amaia", "initials": "A"}, {"family": "Vetrano", "given": "Davide Liborio", "initials": "DL", "orcid": "0000-0002-3099-4830", "researcher": {"href": "https://publications.scilifelab.se/researcher/06867644d5f14eef958737353517f53d.json"}}], "type": "journal article", "published": "2025-03-14", "journal": {"title": "J Prev Alzheimers Dis", "issn": "2426-0266", "pages": "100124", "issn-l": null}, "abstract": "Diet can impact cognitive aging, but comprehensive data from human studies is lacking and the underlying biological mechanisms are still not fully understood.\n\nTo investigate the associations between two dietary patterns consistently linked to inflammation and brain health [the Mediterranean diet (MDS) and inflammatory potential of diet (EDII)] and five blood-based biomarkers of Alzheimer\u00b4s disease (AD) in a sample of dementia-free community-dwelling older adults.\n\nWe used cross-sectional data from the Swedish National Study on Aging and Care in Kungsholmen (SNAC-K).\n\nParticipants who were institutionalized, had dementia or Parkinson's disease, or had missing data on diet and/or biomarkers were excluded. Our study sample consisted of 1907 adults \u226560 years old.\n\nAdherence to the MDS and EDII was assessed using a validated food frequency questionnaire. T-tau, p-tau181, A\u03b2 42/40, NfL, and GFAP were measured in serum. Associations were estimated through quantile regression models at the 25th, 50th, and 75th percentiles of the biomarkers' levels, and were adjusted for potential confounders and stratified by sex, age, and APOE-e4 genotype.\n\nIn the whole sample, higher adherence to the MDS was associated with lower levels of p-tau181 at the 50th and 75th percentiles [\u03b2 (95% CI) per 1-SD increment = -0.028 (-0.053, -0.002) and -0.036 (-0.072, -0.001), respectively], while higher adherence to the EDII was associated with higher levels of NfL at the 75th percentile [\u03b2 (95% CI) per 1-SD increment =0.031 (0.008, 0.053)]. Associations with other biomarkers were only apparent at lower levels of their distribution. Subgroup analyses showed: 1) a stronger inverse association between the MDS and p-tau181 in APOE-e4 carriers than non-carriers, and 2) an inverse association of the MDS with GFAP only in participants \u226578 years.\n\nDiet seems to be associated with biomarkers of AD pathology in cognitively intact older adults. Some associations were more apparent in the presence of genetic predisposition for AD or advanced age.", "doi": "10.1016/j.tjpad.2025.100124", "pmid": "40089420", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2274-5807(25)00068-8"}], "notes": [], "created": "2025-04-02T14:35:17.246Z", "modified": "2025-04-03T08:26:38.025Z"}, {"entity": "publication", "iuid": "cda91e0491824923836ba06fc6eea878", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cda91e0491824923836ba06fc6eea878.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cda91e0491824923836ba06fc6eea878"}}, "title": "Candidate serum protein biomarkers for active pulmonary tuberculosis diagnosis in tuberculosis endemic settings.", "authors": [{"family": "Ayalew", "given": "Sosina", "initials": "S"}, {"family": "Wegayehu", "given": "Teklu", "initials": "T"}, {"family": "Wondale", "given": "Biniam", "initials": "B"}, {"family": "Tarekegn", "given": "Azeb", "initials": "A"}, {"family": "Tessema", "given": "Bamlak", "initials": "B"}, {"family": "Admasu", "given": "Filippos", "initials": "F"}, {"family": "Piantadosi", "given": "Anne", "initials": "A"}, {"family": "Sahi", "given": "Maryam", "initials": "M"}, {"family": "Gebresilase", "given": "Tewodros Tariku", "initials": "TT"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Mihret", "given": "Adane", "initials": "A"}], "type": "journal article", "published": "2024-11-21", "journal": {"title": "BMC Infect. Dis.", "issn": "1471-2334", "volume": "24", "issue": "1", "pages": "1329", "issn-l": "1471-2334"}, "abstract": "Identification of non-sputum diagnostic markers for tuberculosis (TB) is urgently needed. This exploratory study aimed to discover potential serum protein biomarkers for the diagnosis of active pulmonary TB (PTB).\n\nWe employed Proximity Extension Assay (PEA) to measure levels of 92 protein biomarkers related to inflammation in serum samples from three patient groups: 30 patients with active PTB, 29 patients with other respiratory diseases with latent TB (ORD with LTBI+), and 29 patients with other respiratory diseases without latent TB (ORD with LTBI-). To understand the functional mechanisms associated with differentially expressed proteins, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Least absolute shrinkage and selection operator (LASSO) regression was employed to identify potential TB diagnostic protein biomarkers. Network interactions among the identified candidate diagnostic markers were then analyzed, and their diagnostic performance was evaluated using logistic regression and receiver operating characteristic (ROC) analysis.\n\nThe analysis revealed 37 differentially expressed proteins (DEPs) in the active PTB group compared to both ORD with LTBI + and ORD with LTBI- groups. Gene Ontology analysis indicated that these DEPs were primarily involved in the inflammatory response, while KEGG enrichment analysis highlighted the cytokine-cytokine receptor interaction pathway as the top significant hit. LASSO regression identified eight promising candidate protein biomarkers: IFN-gamma, LIF, uPA, CSF-1, SCF, SIRT2, 4E-BP1, and GDNF. The combined set of these eight proteins yielded an AUC of 0.943 for differentiating active PTB from ORD with LTBI+, and an AUC of 0.927 for distinguishing PTB from ORD with LTBI-.\n\nWe have identified eight protein markers that reliably differentiate active PTB from ORD irrespective of LTBI presence. Further large-scale validation and translation of these protein markers into a user-friendly and affordable point-of-care test hold the potential to significantly enhance TB control in high-burden regions.", "doi": "10.1186/s12879-024-10224-3", "pmid": "39573991", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11583743"}, {"db": "pii", "key": "10.1186/s12879-024-10224-3"}], "notes": [], "created": "2024-11-26T15:05:22.254Z", "modified": "2025-04-07T09:24:43.364Z"}, {"entity": "publication", "iuid": "111154cd228d47fabf63f871f677a0d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/111154cd228d47fabf63f871f677a0d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/111154cd228d47fabf63f871f677a0d7"}}, "title": "Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Gisslen", "given": "Magnus", "initials": "M"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "issn-l": null, "volume": "4", "issue": "1", "pages": "55"}, "abstract": "Self-sampling of dried blood spots (DBS) offers new routes to gather valuable health-related information from the general population. Yet, the utility of using deep proteome profiling from home-sampled DBS to obtain clinically relevant insights about SARS-CoV-2 infections remains largely unexplored.\r\n\r\nOur study involved 228 individuals from the general Swedish population who used a volumetric DBS sampling device and completed questionnaires at home during spring 2020 and summer 2021. Using multi-analyte COVID-19 serology, we stratified the donors by their response phenotypes, divided them into three study sets, and analyzed 276 proteins by proximity extension assays (PEA). After normalizing the data to account for variances in layman-collected samples, we investigated the association of DBS proteomes with serology and self-reported information.\r\n\r\nOur three studies display highly consistent variance of protein levels and share associations of proteins with sex (e.g., MMP3) and age (e.g., GDF-15). Studying seropositive (IgG+) and seronegative (IgG-) donors from the first pandemic wave reveals a network of proteins reflecting immunity, inflammation, coagulation, and stress response. A comparison of the early-infection phase (IgM+IgG-) with the post-infection phase (IgM-IgG+) indicates several proteins from the respiratory system. In DBS from the later pandemic wave, we find that levels of a virus receptor on B-cells differ between seropositive (IgG+) and seronegative (IgG-) donors.\r\n\r\nProteome analysis of volumetric self-sampled DBS facilitates precise analysis of clinically relevant proteins, including those secreted into the circulation or found on blood cells, augmenting previous COVID-19 reports with clinical blood collections. Our population surveys support the usefulness of DBS, underscoring the role of timing the sample collection to complement clinical and precision health monitoring initiatives.", "doi": "10.1038/s43856-024-00480-4", "pmid": "38565620", "labels": {"Affinity Proteomics Stockholm": "Technology development", "Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10987641"}, {"db": "pii", "key": "10.1038/s43856-024-00480-4"}], "notes": [], "created": "2024-04-18T09:27:59.211Z", "modified": "2024-08-28T11:04:43.993Z"}, {"entity": "publication", "iuid": "aef805d3eb8e440b931373450cc616f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aef805d3eb8e440b931373450cc616f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aef805d3eb8e440b931373450cc616f9"}}, "title": "Profiling of Surface Protein Epitopes on Viral Particles by Multiplex Dual-Reporter Strategy", "authors": [{"family": "Sahi", "given": "Maryam", "initials": "M"}, {"family": "Andersson", "given": "Sarah", "initials": "S"}, {"family": "Mattson", "given": "Cecilia", "initials": "C"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Kagiolglou", "given": "Sofia", "initials": "S"}, {"family": "Hofstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Chiodi", "given": "Francesca", "initials": "F", "orcid": "0000-0002-1385-8343", "researcher": {"href": "https://publications.scilifelab.se/researcher/c83e956e7a5840939e80840c40bdc636.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}], "type": "journal-article", "published": "2024-01-12", "journal": {"title": "J Vis Exp", "issn": "1940-087X", "issn-l": "1940-087X", "volume": null, "issue": "203", "pages": null}, "abstract": "Membrane proteins on enveloped viruses play an important role in many biological functions involving virus attachment to target cell receptors, fusion of viral particles to host cells, host-virus interactions, and disease pathogenesis. Furthermore, viral membrane proteins on virus particles and presented on host cell surfaces have proven to be excellent targets for antivirals and vaccines. Here, we describe a protocol to investigate surface proteins on intact severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles using the dual-reporter flow cytometric system. The assay exploits multiplex technology to obtain a triple detection of viral particles by three independent affinity reactions. Magnetic beads conjugated to recombinant human angiotensin-converting enzyme-2 (ACE2) were used to capture viral particles from the supernatant of cells infected with SARS-CoV-2. Then, two detection reagents labeled with R-phycoerythrin (PE) or Brilliant Violet 421 (BV421) were applied simultaneously. As a proof-of-concept, antibody fragments targeting different epitopes of the SARS-CoV-2 surface protein Spike (S1) were used. The detection of viral particles by three independent affinity reactions provides strong specificity and confirms the capture of intact virus particles. Dose-dependency curves of SARS-CoV-2 infected cell supernatant were generated with replicate coefficient variances (mean/SD) \u02c214%. Good assay performance in both channels confirmed that two virus surface target protein epitopes are detectable in parallel. The protocol described here could be applied for (i) high-multiplex, high-throughput profiling of surface proteins expressed on enveloped viruses; ii) detection of active intact viral particles; and (iii) assessment of specificity and affinity of antibodies and antiviral drugs for surface epitopes of viral antigens.The application can be potentially extended to any type of extracellular vesicles and bioparticles, exposing surface antigens in body fluids or other liquid matrices.", "doi": "10.3791/66230", "pmid": "38284526", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2024-01-15T15:17:17.666Z", "modified": "2025-12-04T19:27:45.324Z"}, {"entity": "publication", "iuid": "48993691f2c64543b650f3b600450b73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48993691f2c64543b650f3b600450b73"}}, "title": "Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.", "authors": [{"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Christian", "given": "Murray", "initials": "M"}, {"family": "Meineke", "given": "Birthe", "initials": "B"}, {"family": "Els\u00e4sser", "given": "Simon", "initials": "S", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Andr\u00e9ll", "given": "Juni", "initials": "J"}, {"family": "Havervall", "given": "Sebastian", "initials": "S"}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-1345-6491", "researcher": {"href": "https://publications.scilifelab.se/researcher/130fb6ef6b774613a767e98f9f9b2eb4.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Dillner", "given": "Joakim", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Thomas", "given": "Cecilia E", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "McInerney", "given": "Gerald", "initials": "G", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2021-06-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3695"}, "abstract": "Serological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%-14.7%). This includes 5.4% of the samples being IgG+IgM+ against several SARS-CoV-2 proteins, as well as 2.1% being IgG-IgM+ and 5.0% being IgG+IgM- for the virus' S protein. Subjects classified as IgG+ for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG+ for only the S protein (OR = 6.1; p < 0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus.", "doi": "10.1038/s41467-021-23893-4", "pmid": "34140485", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23893-4"}, {"db": "pmc", "key": "PMC8211676"}], "notes": [], "created": "2021-10-05T16:26:34.397Z", "modified": "2021-12-06T07:43:55.459Z"}, {"entity": "publication", "iuid": "bd65c32eb20649e7aaa56f3c22ff33e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd65c32eb20649e7aaa56f3c22ff33e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd65c32eb20649e7aaa56f3c22ff33e1"}}, "title": "CSF levels of apolipoprotein C1 and autotaxin found to associate with neuropathic pain and fibromyalgia.", "authors": [{"family": "Lind", "given": "Anne-Li", "initials": "AL"}, {"family": "Just", "given": "David", "initials": "D", "orcid": "0000-0001-6126-2256", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f687d3a9cf4400932c75510807c764.json"}}, {"family": "Mikus", "given": "Maria", "initials": "M", "orcid": "0000-0001-6560-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/f569884286e147a18003426c423ec63c.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Ioannou", "given": "Marina", "initials": "M"}, {"family": "Gerdle", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4316-1264", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d3d1896af4848e2bb6054dc1c2da715.json"}}, {"family": "Ghafouri", "given": "Bijar", "initials": "B", "orcid": "0000-0002-6396-5104", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44d0ed628b54a7883f3e7eff1e0a2e7.json"}}, {"family": "B\u00e4ckryd", "given": "Emmanuel", "initials": "E"}, {"family": "Tanum", "given": "Lars", "initials": "L", "orcid": "0000-0003-4001-6325", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd48b6df768d4337b78b4c1a257b1382.json"}}, {"family": "Gordh", "given": "Torsten", "initials": "T"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}], "type": "journal article", "published": "2019-10-15", "journal": {"title": "J Pain Res", "issn": "1178-7090", "volume": "12", "issue": null, "pages": "2875-2889", "issn-l": "1178-7090"}, "abstract": "Neuropathic pain and fibromyalgia are two common and poorly understood chronic pain conditions that lack satisfactory treatments, cause substantial suffering and societal costs. Today, there are no biological markers on which to base chronic pain diagnoses, treatment choices or to understand the pathophysiology of pain for the individual patient. This study aimed to investigate cerebrospinal fluid (CSF) protein profiles potentially associated with fibromyalgia and neuropathic pain.\n\nCSF samples were collected from 25 patients with neuropathic pain (two independent sets, n=14 patients for discovery, and n=11 for verification), 40 patients with fibromyalgia and 134 controls without neurological disease from two different populations. CSF protein profiling of 55 proteins was performed using antibody suspension bead array technology.\n\nWe found increased levels of apolipoprotein C1 (APOC1) in CSF of neuropathic pain patients compared to controls and there was a trend for increased levels also in fibromyalgia patients. In addition, levels of ectonucleotide pyrophosphatase family member 2 (ENPP2, also referred to as autotaxin) were increased in the CSF of fibromyalgia patients compared to all other groups including patients with neuropathic pain.\n\nThe increased levels of APOC1 and ENPP2 found in neuropathic pain and fibromyalgia patients may shed light on the underlying mechanisms of these conditions. Further investigation is required to elucidate their role in maintaining pain and other main symptoms of these disorders.", "doi": "10.2147/JPR.S215348", "pmid": "31686904", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "215348"}, {"db": "pmc", "key": "PMC6800548"}], "notes": [], "created": "2020-01-08T13:20:56.475Z", "modified": "2021-07-08T12:12:51.607Z"}, {"entity": "publication", "iuid": "258308396bfd46d4a0e8e2cb27558cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1"}}, "title": "Systematic Development of Sandwich Immunoassays for the Plasma Secretome.", "authors": [{"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca04d9b9132747efb7db0efb6e34756a.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Iglesias", "given": "MariaJesus", "initials": "M"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "19", "issue": "15", "pages": "e1900008", "issn-l": "1615-9853"}, "abstract": "The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, \u22481800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.", "doi": "10.1002/pmic.201900008", "pmid": "31278833", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T10:38:13.224Z", "modified": "2021-07-08T13:44:33.106Z"}, {"entity": "publication", "iuid": "9dbe3bf19fd34984889399769e724b95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95"}}, "title": "Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2019-07-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "7", "pages": "2706-2718", "issn-l": "1535-3893"}, "abstract": "The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (\u226460 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.", "doi": "10.1021/acs.jproteome.8b00924", "pmid": "31094526", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T14:57:52.618Z", "modified": "2021-07-08T13:44:33.481Z"}, {"entity": "publication", "iuid": "cca3260cc4224306b9f2b254e6b95349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349"}}, "title": "Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.", "authors": [{"family": "Andersson", "given": "Annika", "initials": "A"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ilag", "given": "Leopold L", "initials": "LL"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "Clin. Chim. Acta", "issn": "1873-3492", "volume": "494", "issue": null, "pages": "79-93", "issn-l": "0009-8981"}, "abstract": "Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.", "doi": "10.1016/j.cca.2019.03.243", "pmid": "30858094", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0009-8981(19)30348-1"}], "notes": [], "created": "2020-01-08T10:40:27.440Z", "modified": "2021-07-08T13:44:33.634Z"}, {"entity": "publication", "iuid": "d81332752ac544d4a3f4e26a9be1bf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d81332752ac544d4a3f4e26a9be1bf56"}}, "title": "Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Ioannou", "given": "Marina", "initials": "M"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Branca", "given": "Rui M", "initials": "RM"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-06-06", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "8324", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score \u2265 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.", "doi": "10.1038/s41598-019-43552-5", "pmid": "31171813", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-43552-5"}, {"db": "pmc", "key": "PMC6554399"}], "notes": [], "created": "2019-11-06T15:11:37.992Z", "modified": "2024-01-16T13:48:44.259Z"}, {"entity": "publication", "iuid": "1db8dc97446746fb82180569ebc97fac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1db8dc97446746fb82180569ebc97fac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1db8dc97446746fb82180569ebc97fac"}}, "title": "Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci.", "authors": [{"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Assadi", "given": "Ghazaleh", "initials": "G"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Reznichenko", "given": "Anna", "initials": "A"}, {"family": "Akhter", "given": "Tahmina", "initials": "T"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Bonfiglio", "given": "Ferdinando", "initials": "F"}, {"family": "Hansen", "given": "Mark Berner", "initials": "MB"}, {"family": "Sandberg", "given": "Kristian", "initials": "K", "orcid": "0000-0002-6395-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/2747d3fe7810406fafc429d9e66225ef.json"}}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2019-01-10", "journal": {"volume": "25", "issn": "1536-4844", "issue": "2", "pages": "306-316", "title": "Inflamm Bowel Dis", "issn-l": null}, "abstract": "Few studies have investigated the blood proteome of inflammatory bowel disease (IBD). We characterized the serum abundance of proteins encoded at 163 known IBD risk loci and tested these proteins for their biomarker discovery potential.\n\nBased on the Human Protein Atlas (HPA) antibody availability, 218 proteins from genes mapping at 163 IBD risk loci were selected. Targeted serum protein profiles from 49 Crohn's disease (CD) patients, 51 ulcerative colitis (UC) patients, and 50 sex- and age-matched healthy individuals were obtained using multiplexed antibody suspension bead array assays. Differences in relative serum abundance levels between disease groups and controls were examined. Replication was attempted for CD-UC comparisons (including disease subtypes) by including 64 additional patients (33 CD and 31 UC). Antibodies targeting a potentially novel risk protein were validated by paired antibodies, Western blot, immuno-capture mass spectrometry, and epitope mapping.\n\nBy univariate analysis, 13 proteins mostly related to neutrophil, T-cell, and B-cell activation and function were differentially expressed in IBD patients vs healthy controls, 3 in CD patients vs healthy controls and 2 in UC patients vs healthy controls (q < 0.01). Multivariate analyses further differentiated disease groups from healthy controls and CD subtypes from UC (P < 0.05). Extended characterization of an antibody targeting a novel, discriminative serum marker, the laccase (multicopper oxidoreductase) domain containing 1 (LACC1) protein, provided evidence for antibody on-target specificity.\n\nUsing affinity proteomics, we identified a set of IBD-associated serum proteins encoded at IBD risk loci. These candidate proteins hold the potential to be exploited as diagnostic biomarkers of IBD.", "doi": "10.1093/ibd/izy326", "pmid": "30358838", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5144272"}, {"db": "pmc", "key": "PMC6327232"}], "notes": [], "created": "2018-10-26T06:07:49.951Z", "modified": "2025-10-17T13:05:08.266Z"}, {"entity": "publication", "iuid": "6ad7359492824600bfadb8deddc0e1c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ad7359492824600bfadb8deddc0e1c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ad7359492824600bfadb8deddc0e1c5"}}, "title": "Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Eklund", "given": "Martin", "initials": "M"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Eriksson", "given": "Mikael", "initials": "M"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Gabrielson", "given": "Marike", "initials": "M"}], "type": "journal article", "published": "2018-02-14", "journal": {"volume": "20", "issn": "1465-542X", "issue": "1", "pages": "14", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "Mammographic breast density is one of the strongest risk factors for breast cancer, but molecular understanding of how breast density relates to cancer risk is less complete. Studies of proteins in blood plasma, possibly associated with mammographic density, are well-suited as these allow large-scale analyses and might shed light on the association between breast cancer and breast density.\n\nPlasma samples from 1329 women in the Swedish KARMA project, without prior history of breast cancer, were profiled with antibody suspension bead array (SBA) assays. Two sample sets comprising 729 and 600 women were screened by two different SBAs targeting a total number of 357 proteins. Protein targets were selected through searching the literature, for either being related to breast cancer or for being linked to the extracellular matrix. Association between proteins and absolute area-based breast density (AD) was assessed by quantile regression, adjusting for age and body mass index (BMI).\n\nPlasma profiling revealed linear association between 20 proteins and AD, concordant in the two sets of samples (p < 0.05). Plasma levels of seven proteins were positively associated and 13 proteins negatively associated with AD. For eleven of these proteins evidence for gene expression in breast tissue existed. Among these, ABCC11, TNFRSF10D, F11R and ERRF were positively associated with AD, and SHC1, CFLAR, ACOX2, ITGB6, RASSF1, FANCD2 and IRX5 were negatively associated with AD.\n\nScreening proteins in plasma indicates associations between breast density and processes of tissue homeostasis, DNA repair, cancer development and/or progression in breast cancer. Further validation and follow-up studies of the shortlisted protein candidates in independent cohorts will be needed to infer their role in breast density and its progression in premenopausal and postmenopausal women.", "doi": "10.1186/s13058-018-0940-z", "pmid": "29444691", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13058-018-0940-z"}, {"db": "pmc", "key": "PMC5813412"}], "notes": [], "created": "2018-10-31T09:21:59.155Z", "modified": "2024-01-16T13:48:46.936Z"}, {"entity": "publication", "iuid": "feb578c0af8f44d999e4cdc360c28358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358"}}, "title": "Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Nyaiesh", "given": "Etienne-Nicholas", "initials": "EN"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "10", "issn": "1936-5233", "issue": "3", "pages": "385-395", "title": "Transl Oncol", "issn-l": null}, "abstract": "Blood-based proteomic profiling may aid and expand our understanding of diseases and their different phenotypes. The aim of the presented study was to profile serum samples from patients with malignant melanoma using affinity proteomic assays to describe proteins in the blood stream that are associated to stage or recurrence of melanoma.\n\nMultiplexed protein analysis was conducted using antibody suspension bead arrays. A total of 232 antibodies against 132 proteins were selected from (i) a screening with 4595 antibodies and 32 serum samples from melanoma patients and controls, (ii) antibodies used for immunohistochemistry, (iii) protein targets previously related with melanoma. The analysis was performed with 149 serum samples from patients with malignant melanoma. Antibody selectivity was then assessed by Western blot, immunocapture mass spectrometry, and epitope mapping. Lastly, indicative antibodies were applied for IHC analysis of melanoma tissues.\n\nSerum levels of regucalcin (RGN) and syntaxin 7 (STX7) were found to be lower in patients with both recurring tumors and a high Breslow's thickness (T-stage 3/4) compared to low thickness (T-stage 1/2) without disease recurrence. Serum levels of methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) were instead elevated in sera of T3/4 patients with recurrence. The analysis of tissue sections with S100A6 and MTHFD1L showed positive staining in a majority of patients with melanoma, and S100A6 was significantly associated to T-stage.\n\nOur findings provide a starting point to further study RGN, STX7, MTHFD1L and S100A6 in serum to elucidate their involvement in melanoma progression and to assess a possible contribution to support clinical indications.", "doi": "10.1016/j.tranon.2017.03.002", "pmid": "28433799", "labels": {"Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1936-5233(17)30031-1"}, {"db": "pmc", "key": "PMC5403766"}], "notes": [], "created": "2017-08-30T14:34:48.682Z", "modified": "2021-07-08T13:44:33.779Z"}, {"entity": "publication", "iuid": "aaaf64893fe54c5196aaf8f4943829e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aaaf64893fe54c5196aaf8f4943829e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aaaf64893fe54c5196aaf8f4943829e6"}}, "title": "PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study.", "authors": [{"family": "Bruzelius", "given": "Maria", "initials": "M"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ", "orcid": "0000-0003-4122-1945", "researcher": {"href": "https://publications.scilifelab.se/researcher/adccb07f0a744e648516bd7b672d70be.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8808-7128", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ca6e46c2f1486199d08bc9f9b702be.json"}}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Gyorgy", "given": "Beata", "initials": "B"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Holmstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A", "orcid": "0000-0002-0618-0538", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb944b0f90b64afc8162f15874069946.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd1197769804dd48b9de86f11340ef2.json"}}, {"family": "Soria", "given": "Jose Manuel", "initials": "JM"}, {"family": "Smadja", "given": "David M", "initials": "DM", "orcid": "0000-0001-7731-9202", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc861e04da204cc9a00a047a026c8b7a.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE", "orcid": "0000-0002-9065-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a85b080902c04dacb81456efa67374db.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}], "type": "clinical trial", "published": "2016-12-08", "journal": {"volume": "128", "issn": "1528-0020", "issue": "23", "pages": "e59-e66", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "There is a clear clinical need for high-specificity plasma biomarkers for predicting risk of venous thromboembolism (VTE), but thus far, such markers have remained elusive. Utilizing affinity reagents from the Human Protein Atlas project and multiplexed immuoassays, we extensively analyzed plasma samples from 2 individual studies to identify candidate protein markers associated with VTE risk. We screened plasma samples from 88 VTE cases and 85 matched controls, collected as part of the Swedish \"Venous Thromboembolism Biomarker Study,\" using suspension bead arrays composed of 755 antibodies targeting 408 candidate proteins. We identified significant associations between VTE occurrence and plasma levels of human immunodeficiency virus type I enhancer binding protein 1 (HIVEP1), von Willebrand factor (VWF), glutathione peroxidase 3 (GPX3), and platelet-derived growth factor \u03b2 (PDGFB). For replication, we profiled plasma samples of 580 cases and 589 controls from the French FARIVE study. These results confirmed the association of VWF and PDGFB with VTE after correction for multiple testing, whereas only weak trends were observed for HIVEP1 and GPX3. Although plasma levels of VWF and PDGFB correlated modestly (\u03c1 \u223c 0.30) with each other, they were independently associated with VTE risk in a joint model in FARIVE (VWF P < .001; PDGFB P = .002). PDGF\u0392 was verified as the target of the capture antibody by immunocapture mass spectrometry and sandwich enzyme-linked immunosorbent assay. In conclusion, we demonstrate that high-throughput affinity plasma proteomic profiling is a valuable research strategy to identify potential candidate biomarkers for thrombosis-related disorders, and our study suggests a novel association of PDGFB plasma levels with VTE.", "doi": "10.1182/blood-2016-05-711846", "pmid": "27742707", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)33937-9"}], "notes": [], "created": "2017-05-03T12:59:07.466Z", "modified": "2023-06-19T13:11:23.382Z"}, {"entity": "publication", "iuid": "7362064a1f044c14a2e50a26392e171a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a"}}, "title": "CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "12", "pages": "1242-1253", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "This study is part of a larger effort aiming to expand the knowledge of brain-enriched proteins in human cerebrospinal fluid (CSF) and to provide novel insight into the relation between such proteins and different neurodegenerative diseases.\n\nHere 280 brain-enriched proteins in CSF from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are profiled. In total, 441 human samples of ventricular CSF collected post mortem and lumbar CSF collected ante mortem are analyzed using 376 antibodies in a suspension bead array setup, utilizing a direct labelling approach.\n\nAmong several proteins displaying differentiated profiles between sample groups, we focus here on two synaptic proteins, neuromodulin (GAP43) and neurogranin (NRGN). They are both found at elevated levels in CSF from AD patients in two independent cohorts, providing disease-associated profiles in addition to verifying and strengthening previously observed patterns. Increased levels are also observed for patients for whom the AD diagnosis was not established at the time of sampling.\n\nThese findings indicate that analyzing the brain-enriched proteins in CSF is of particular interest to increase the understanding of the CSF proteome and its relation to neurodegenerative disorders. In addition, this study lends support to the notion that measurements of these synaptic proteins could potentially be of great relevance in future diagnostic tests for AD.", "doi": "10.1002/prca.201500150", "pmid": "27604409", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5157753"}], "notes": [], "created": "2017-05-03T12:59:05.983Z", "modified": "2021-07-08T13:44:33.352Z"}, {"entity": "publication", "iuid": "042bd68daa014d59b178e63954eac1ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad"}}, "title": "Immunocapture strategies in translational proteomics.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2015-11-11", "journal": {"volume": "13", "issn": "1744-8387", "issue": "1", "pages": "83-98", "title": "Expert Rev Proteomics", "issn-l": "1478-9450"}, "abstract": "Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.", "doi": "10.1586/14789450.2016.1111141", "pmid": "26558424", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4732419"}], "notes": [], "created": "2017-05-02T12:56:45.584Z", "modified": "2021-07-08T13:44:32.996Z"}, {"entity": "publication", "iuid": "d25e8eeba2b9401a99f09ce2238e2a9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f"}}, "title": "Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Amor", "given": "Sandra", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "4607-4619", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.", "doi": "10.1021/pr500609e", "pmid": "25231264", "labels": {"Fluorescence Tissue Profiling": null, "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:19.857Z", "modified": "2021-07-08T13:44:33.645Z"}, {"entity": "publication", "iuid": "ef02a7c09ee04259ad9d5d188407e72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e"}}, "title": "Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "O\u2019Hurley", "given": "Gillian", "initials": "G"}, {"family": "Branca", "given": "Rui", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2014-03-00", "journal": {"volume": "2", "issn": "2212-9626", "issue": null, "pages": "14-24", "title": "Translational Proteomics", "issn-l": null}, "abstract": null, "doi": "10.1016/j.trprot.2013.12.001", "pmid": null, "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:41.613Z", "modified": "2021-07-08T12:12:51.627Z"}, {"entity": "publication", "iuid": "87e3d2bb0d5442fe9c4911cc26f86f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f"}}, "title": "Selectivity analysis of single binder assays used in plasma protein profiling.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "23-24", "pages": "3406-3410", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.", "doi": "10.1002/pmic.201300030", "pmid": "24151238", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4265267"}], "notes": [], "created": "2017-05-04T14:55:38.987Z", "modified": "2021-07-08T13:44:33.385Z"}]}