{"entity": "researcher", "timestamp": "2026-08-14T12:52:20.139Z", "family": "Chen", "given": "Qiao Sen", "initials": "QS", "orcid": "0000-0002-5864-7574", "affiliations": ["Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Solnav\u00e4gen 30, 171 64 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a"}}, "publications": [{"entity": "publication", "iuid": "49398b063f5d4500a3dd373382da546a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a"}}, "title": "A genome-wide association study of imaging-defined atherosclerosis.", "authors": [{"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Chen", "given": "Qiao Sen", "initials": "QS", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y", "orcid": "0000-0003-1165-3595", "researcher": {"href": "https://publications.scilifelab.se/researcher/2869602ee77944d2b1a736638a76bb3a.json"}}, {"family": "Andersson", "given": "Therese", "initials": "T"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Jernberg", "given": "Tomas", "initials": "T"}, {"family": "Landfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-5695-2276", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85f85dce6c548fd9f36ac1540c9aff3.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Mannila", "given": "Maria", "initials": "M", "orcid": "0000-0001-6189-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/786397ffc6a54d3e8c54f5493fbb7aa2.json"}}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Pirazzi", "given": "Carlo", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0003-1617-3179", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4b5d952d50c4801aa88c0c9ae0d5813.json"}}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9474-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1a42fede5f4f6d87c20d6bb9f694de.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13944767ad9446e885ce32ca88afebd.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}], "type": "journal article", "published": "2025-03-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2266", "issn-l": "2041-1723"}, "abstract": "Imaging-defined atherosclerosis represents an intermediate phenotype of atherosclerotic cardiovascular disease (ASCVD). Genome-wide association studies (GWAS) on directly measured coronary plaques using coronary computed tomography angiography (CCTA) are scarce. In the so far largest population-based cohort with CCTA data, we performed a GWAS on coronary plaque burden as determined by the segment involvement score (SIS) in 24,811 European individuals. We identified 20 significant independent genetic markers for SIS, three of which were found in loci not implicated in ASCVD before. Further GWAS on coronary artery calcification showed similar results to that of SIS, whereas a GWAS on ultrasound-assessed carotid plaques identified both shared and non-shared loci with SIS. In two-sample Mendelian randomization studies using SIS-associated markers in UK Biobank and CARDIoGRAMplusC4D, one extra coronary segment with atherosclerosis corresponded to 1.8-fold increased odds of myocardial infarction. This GWAS data can aid future studies of causal pathways in ASCVD.", "doi": "10.1038/s41467-025-57457-7", "pmid": "40164586", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11958696"}, {"db": "pii", "key": "10.1038/s41467-025-57457-7"}], "notes": [], "created": "2025-05-12T05:48:37.162Z", "modified": "2025-11-14T11:06:44.446Z"}, {"entity": "publication", "iuid": "53004388459e465ab3c59b47d352f040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040"}}, "title": "Systems-level immunomonitoring in children with solid tumors to enable precision medicine.", "authors": [{"family": "Chen", "given": "Qi", "initials": "Q", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Zhao", "given": "Binbin", "initials": "B", "orcid": "0000-0002-5560-6750", "researcher": {"href": "https://publications.scilifelab.se/researcher/22329dc812fc4684acce02c18ae6fa18.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0001-5958-2584", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd87015d70fb4f71a9c5c40a22b84d4e.json"}}, {"family": "Hedberg", "given": "Gustav", "initials": "G"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Negrini", "given": "Erika", "initials": "E"}, {"family": "P\u00e1ez", "given": "Laura Pi\u00f1ero", "initials": "LP"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Reitzner", "given": "Stefan Markus", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}, {"family": "O'Neill", "given": "Olivia", "initials": "O"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0d6085e774a0fbdc1ad8d6eea3c23.json"}}, {"family": "Wang", "given": "Chunlin", "initials": "C"}, {"family": "Davis", "given": "Mark M", "initials": "MM"}, {"family": "Carlson", "given": "Lena-Maria", "initials": "LM"}, {"family": "Pal", "given": "Niklas", "initials": "N"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Herold", "given": "Nikolas", "initials": "N", "orcid": "0000-0001-9468-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2af6f17f76457680908c36693f2de5.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Ljungblad", "given": "Linda", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "5", "pages": "1425-1440.e11", "issn-l": "0092-8674"}, "abstract": "Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic T cell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded T cell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded T cells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.", "doi": "10.1016/j.cell.2024.12.014", "pmid": "39837329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)01427-2"}], "notes": [], "created": "2025-01-30T10:50:10.864Z", "modified": "2025-11-28T10:42:05.786Z"}, {"entity": "publication", "iuid": "a008d0a0c0f14c8bb8ffab0497dc6037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a008d0a0c0f14c8bb8ffab0497dc6037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a008d0a0c0f14c8bb8ffab0497dc6037"}}, "title": "A machine learning based approach to identify carotid subclinical atherosclerosis endotypes.", "authors": [{"family": "Chen", "given": "Qiao Sen", "initials": "QS", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Bergman", "given": "Otto", "initials": "O"}, {"family": "Ziegler", "given": "Louise", "initials": "L"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D", "orcid": "0000-0002-2766-8882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c131cad5784434eb16cf720f7964ecb.json"}}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Gallo", "given": "Antonio", "initials": "A"}, {"family": "Pirro", "given": "Matteo", "initials": "M"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Lind", "given": "Lars", "initials": "L", "orcid": "0000-0003-2335-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c517dacca7c4ec58a3e03b59ffb4044.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": "IMPROVE study group\n", "given": "", "initials": ""}], "type": "journal article", "published": "2023-07-21", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "issn-l": "0008-6363"}, "abstract": "To define endotypes of carotid subclinical atherosclerosis.\n\nWe integrated demographic, clinical, and molecular data (n = 124) with ultrasonographic carotid measurements from study participants in the IMPROVE cohort (n = 3340). We applied a neural network algorithm and hierarchical clustering to identify carotid atherosclerosis endotypes. A measure of carotid subclinical atherosclerosis, the c-IMTmean-max, was used to extract atherosclerosis-related features and SHapley Additive exPlanations (SHAP) to reveal endotypes. The association of endotypes with carotid ultrasonographic measurements at baseline, after 30 months, and with the 3-year atherosclerotic cardiovascular disease (ASCVD) risk was estimated by linear (\u03b2, SE) and Cox [hazard ratio (HR), 95% confidence interval (CI)] regression models. Crude estimates were adjusted by common cardiovascular risk factors, and baseline ultrasonographic measures. Improvement in ASCVD risk prediction was evaluated by C-statistic and by net reclassification improvement with reference to SCORE2, c-IMTmean-max, and presence of carotid plaques. An ensemble stacking model was used to predict endotypes in an independent validation cohort, the PIVUS (n = 1061). We identified four endotypes able to differentiate carotid atherosclerosis risk profiles from mild (endotype 1) to severe (endotype 4). SHAP identified endotype-shared variables (age, biological sex, and systolic blood pressure) and endotype-specific biomarkers. In the IMPROVE, as compared to endotype 1, endotype 4 associated with the thickest c-IMT at baseline (\u03b2, SE) 0.36 (0.014), the highest number of plaques 1.65 (0.075), the fastest c-IMT progression 0.06 (0.013), and the highest ASCVD risk (HR, 95% CI) (1.95, 1.18-3.23). Baseline and progression measures of carotid subclinical atherosclerosis and ASCVD risk were associated with the predicted endotypes in the PIVUS. Endotypes consistently improved measures of ASCVD risk discrimination and reclassification in both study populations.\n\nWe report four replicable subclinical carotid atherosclerosis-endotypes associated with progression of atherosclerosis and ASCVD risk in two independent populations. Our approach based on endotypes can be applied for precision medicine in ASCVD prevention.", "doi": "10.1093/cvr/cvad106", "pmid": "37475157", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "7226279"}], "notes": [], "created": "2023-11-29T19:27:08.131Z", "modified": "2023-11-29T19:27:08.184Z"}]}