{"entity": "researcher", "timestamp": "2026-10-05T21:19:17.888Z", "family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "affiliations": ["Division of Oncology, Department of Clinical Sciences, Lund University, Sk\u00e5ne University Hospital, Lund, Sweden.", "Department of Surgery and Gastroenterology, Sk\u00e5ne University Hospital, Lund, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56"}}, "publications": [{"entity": "publication", "iuid": "0f4c992adb014d0c962a7a62313aed71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f4c992adb014d0c962a7a62313aed71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f4c992adb014d0c962a7a62313aed71"}}, "title": "Choice of High-Throughput Proteomics Method Affects Data Integration with Transcriptomics and the Potential Use in Biomarker Discovery.", "authors": [{"family": "Mosquim Junior", "given": "Sergio", "initials": "S", "orcid": "0000-0002-1537-7252", "researcher": {"href": "https://publications.scilifelab.se/researcher/1354a13a0b2f4a35865224291239e730.json"}}, {"family": "Siino", "given": "Valentina", "initials": "V", "orcid": "0000-0002-0489-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/04ca620e18e14085be456f76eb429902.json"}}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56.json"}}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}], "type": "journal article", "published": "2022-11-23", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "23", "issn-l": "2072-6694"}, "abstract": "In recent years, several advances have been achieved in breast cancer (BC) classification and treatment. However, overdiagnosis, overtreatment, and recurrent disease are still significant causes of complication and death. Here, we present the development of a protocol aimed at parallel transcriptome and proteome analysis of BC tissue samples using mass spectrometry, via Data Dependent and Independent Acquisitions (DDA and DIA). Protein digestion was semi-automated and performed on flowthroughs after RNA extraction. Data for 116 samples were acquired in DDA and DIA modes and processed using MaxQuant, EncyclopeDIA, or DIA-NN. DIA-NN showed an increased number of identified proteins, reproducibility, and correlation with matching RNA-seq data, therefore representing the best alternative for this setup. Gene Set Enrichment Analysis pointed towards complementary information being found between transcriptomic and proteomic data. A decision tree model, designed to predict the intrinsic subtypes based on differentially abundant proteins across different conditions, selected protein groups that recapitulate important clinical features, such as estrogen receptor status, HER2 status, proliferation, and aggressiveness. Taken together, our results indicate that the proposed protocol performed well for the application. Additionally, the relevance of the selected proteins points to the possibility of using such data as a biomarker discovery tool for personalized medicine.", "doi": "10.3390/cancers14235761", "pmid": "36497242", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9736226"}, {"db": "pii", "key": "cancers14235761"}], "notes": [], "created": "2023-09-27T07:00:02.527Z", "modified": "2023-09-27T07:00:02.646Z"}, {"entity": "publication", "iuid": "f3ea7ecc69e24f00b6d9979e061dd885", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3ea7ecc69e24f00b6d9979e061dd885.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3ea7ecc69e24f00b6d9979e061dd885"}}, "title": "Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer", "authors": [{"family": "Mehmeti-Ajradini", "given": "Meliha", "initials": "M"}, {"family": "Bergenfelz", "given": "Caroline", "initials": "C"}, {"family": "Larsson", "given": "Anna Maria", "initials": "AM"}, {"family": "Carlsson", "given": "Robert", "initials": "R"}, {"family": "Riesbeck", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6274-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/d757ccad30b043748c8fe48a7308210c.json"}}, {"family": "Ahl", "given": "Jonas", "initials": "J"}, {"family": "Janols", "given": "Helena", "initials": "H"}, {"family": "Wullt", "given": "Marlene", "initials": "M"}, {"family": "Bredberg", "given": "Anders", "initials": "A"}, {"family": "K\u00e4llberg", "given": "Eva", "initials": "E"}, {"family": "Bj\u00f6rk Gunnarsdottir", "given": "Frida", "initials": "F"}, {"family": "Rydberg Millrud", "given": "Camilla", "initials": "C"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L", "orcid": "0000-0001-7515-3130", "researcher": {"href": "https://publications.scilifelab.se/researcher/424bace557344431a47ffe5cdccbeb56.json"}}, {"family": "Paul", "given": "Gesine", "initials": "G"}, {"family": "Loman", "given": "Niklas", "initials": "N"}, {"family": "Adolfsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Carneiro", "given": "Ana", "initials": "A", "orcid": "0000-0002-1818-7008", "researcher": {"href": "https://publications.scilifelab.se/researcher/12ef95bff08743398bf3a374195e043e.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Killander", "given": "Fredrika", "initials": "F"}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Leandersson", "given": "Karin", "initials": "K", "orcid": "0000-0001-8254-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/4736923f382845c2990efb251340bfb4.json"}}], "type": "journal-article", "published": "2020-11-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "3", "issue": "11", "pages": "e202000893"}, "abstract": "Myeloid-derived suppressor cells (MDSCs) are known to contribute to immune evasion in cancer. However, the function of the human granulocytic (G)-MDSC subset during tumor progression is largely unknown, and there are no established markers for their identification in human tumor specimens. Using gene expression profiling, mass cytometry, and tumor microarrays, we here demonstrate that human G-MDSCs occur as neutrophils at distinct maturation stages, with a disease-specific profile. G-MDSCs derived from patients with metastatic breast cancer and malignant melanoma display a unique immature neutrophil profile, that is more similar to healthy donor neutrophils than to G-MDSCs from sepsis patients. Finally, we show that primary G-MDSCs from metastatic breast cancer patients co-transplanted with breast cancer cells, promote tumor growth, and affect vessel formation, leading to myeloid immune cell exclusion. Our findings reveal a role for human G-MDSC in tumor progression and have clinical implications also for targeted immunotherapy.", "doi": "10.26508/lsa.202000893", "pmid": "32958605", "labels": {"Cellular Immunomonitoring": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7536824"}, {"db": "pii", "key": "3/11/e202000893"}], "notes": [], "created": "2020-09-24T15:35:44.836Z", "modified": "2024-11-15T09:54:18.581Z"}]}