{"entity": "journal", "iuid": "1df211b098534b50b8bd27cd35b5d418", "timestamp": "2026-08-08T15:49:09.781Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Clin%20Transl%20Med.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Clin%20Transl%20Med"}}, "title": "Clin Transl Med", "issn": "2001-1326", "issn-l": null, "publications_count": 3, "publications": [{"entity": "publication", "iuid": "cb4b4d435f4947219be906a67e904ed5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb4b4d435f4947219be906a67e904ed5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb4b4d435f4947219be906a67e904ed5"}}, "title": "Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity.", "authors": [{"family": "Szeitz", "given": "Beata", "initials": "B", "orcid": "0000-0001-6414-0537", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7d73d277254472da3770838dddaac19.json"}}, {"family": "Hagemeijer", "given": "Yanick Paco", "initials": "YP"}, {"family": "Pahi", "given": "Zoltan Gabor", "initials": "ZG"}, {"family": "Ujfaludi", "given": "Zsuzsanna", "initials": "Z"}, {"family": "Kuras", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-9479-423X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a160035cccbb42b5a7164ad9cef6ac12.json"}}, {"family": "Rodriguez", "given": "Jimmy", "initials": "J"}, {"family": "Doma", "given": "Viktoria", "initials": "V"}, {"family": "Mohacsi", "given": "Reka", "initials": "R"}, {"family": "Herold", "given": "Magdolna", "initials": "M"}, {"family": "Herold", "given": "Zoltan", "initials": "Z"}, {"family": "Horvath", "given": "Zsolt", "initials": "Z"}, {"family": "Pla", "given": "Indira", "initials": "I"}, {"family": "Sugihara", "given": "Yutaka", "initials": "Y", "orcid": "0000-0002-4406-3017", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dcf4589722645699f04a66113fbbd1a.json"}}, {"family": "Baldetorp", "given": "Bo", "initials": "B"}, {"family": "Lindberg", "given": "Henrik", "initials": "H"}, {"family": "Oskolas", "given": "Henriett", "initials": "H"}, {"family": "Rezeli", "given": "Melinda", "initials": "M", "orcid": "0000-0003-4373-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/586ea8903ead4d6a974b6583aba07580.json"}}, {"family": "Gil", "given": "Jeovanis", "initials": "J", "orcid": "0000-0003-3601-3893", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aeb67da0d81436eaf7a008fcb298eec.json"}}, {"family": "Appelqvist", "given": "Roger", "initials": "R"}, {"family": "Kemeny", "given": "Lajos V", "initials": "LV"}, {"family": "Guedes", "given": "Jessica", "initials": "J"}, {"family": "Malm", "given": "Johan", "initials": "J"}, {"family": "Sanchez", "given": "Aniel", "initials": "A"}, {"family": "Boros", "given": "Imre Miklos", "initials": "IM"}, {"family": "Nemeth", "given": "Istvan Balazs", "initials": "IB"}, {"family": "Guryev", "given": "Victor", "initials": "V"}, {"family": "Pankotai", "given": "Tibor", "initials": "T", "orcid": "0000-0001-9810-5465", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390e4f386c6481a9022d45bab78f404.json"}}, {"family": "Paw\u0142owski", "given": "Krzysztof", "initials": "K"}, {"family": "Wieslander", "given": "Elisabet", "initials": "E"}, {"family": "Szasz", "given": "Attila Marcell", "initials": "AM"}, {"family": "Feny\u00f6", "given": "David", "initials": "D"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Timar", "given": "Jozsef", "initials": "J"}, {"family": "Marko-Varga", "given": "Gy\u00f6rgy", "initials": "G"}, {"family": "Betancourt", "given": "Lazaro Hiram", "initials": "LH", "orcid": "0000-0001-8207-7041", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba3e440ea6234811b5677126d7e24726.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Clin Transl Med", "issn": "2001-1326", "volume": "15", "issue": "10", "pages": "e70477", "issn-l": null}, "abstract": "Metastatic melanoma is a highly aggressive disease with poor survival rates despite recent therapeutic advancements with immunotherapy. The proteomic landscape of advanced melanoma remains poorly understood, especially regarding proteomic heterogeneity across metastases within patients.\n\nWe collected 83 melanoma metastases from 19 different metastatic sites in 24 patients with advanced metastatic melanoma almost exclusively from the pre-immunotherapy era, using semi-rapid autopsies. The metastases were subjected to histopathological evaluation, RNA-sequencing and mass spectrometry-based proteomics for protein quantitation and non-reference peptide (NRP) sequence detection using a proteogenomic data integration approach.\n\nNRPs associated with mutations frequently occurred in proteins related to focal adhesion, vesicle-mediated transport, MAPK signalling and immune response pathways across the cohort. Intrapatient heterogeneity was negligible when considering morphology and driver gene mutation status but was substantial at the proteogenomic level. This heterogeneity was not driven by metastasis location, albeit liver metastases exhibited distinct proteogenomic patterns, including upregulation of metabolic pathways. Cluster analysis outlined four proteomic clusters (C1-4) of the metastases, characterised by the upregulation of cell cycle and RNA-splicing (C1), mitochondrial processes (C3), extracellular matrix (ECM) and immune pathways (C2) and ECM and vesicle-mediated transport pathways (C4). Around two-thirds of patients had metastases that had strongly distinct phenotypes. Patients in our cohort whose metastases were primarily assigned to clusters C1 and C3 exhibited shorter overall survival than patients whose metastases were categorised mainly into the C2 and C4 clusters.\n\nOur unique multi-metastasis cohort captured the proteogenomic heterogeneity of immunotherapy-na\u00efve melanoma distant metastases, establishing a foundation for future studies aimed at identifying novel therapeutic targets to complement current immunotherapies.\n\nComprehensive proteogenomic profiling of post-mortem melanoma metastases, collected primarily before the immunotherapy era. Description of 1177 protein sequence variants predicted by RNA-Seq and validated via mass spectrometry-based proteomics. Empirical evidence of prominent intrapatient heterogeneity, driven by heterogeneous protein expression related to cell cycle- and mitochondrial processes, immune system and extracellular matrix organization.", "doi": "10.1002/ctm2.70477", "pmid": "41017066", "labels": {"Clinical Proteomics Lund": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12477065"}], "notes": [], "created": "2026-07-01T10:54:20.521Z", "modified": "2026-07-01T10:54:20.903Z"}, {"entity": "publication", "iuid": "1e1b2164ef184a55b6c748ff0a49d7e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e1b2164ef184a55b6c748ff0a49d7e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e1b2164ef184a55b6c748ff0a49d7e8"}}, "title": "Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery.", "authors": [{"family": "Wikstr\u00f6m", "given": "Tove", "initials": "T", "orcid": "0000-0002-4208-8667", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a4bdff199a4630b9ce97733eb0e20f.json"}}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Ek", "given": "Joakim", "initials": "J"}, {"family": "Kuusela", "given": "Pihla", "initials": "P"}, {"family": "Rekabdar", "given": "Elham", "initials": "E"}, {"family": "Lindgren", "given": "Peter", "initials": "P"}, {"family": "Wennerholm", "given": "Ulla-Britt", "initials": "UB"}, {"family": "Jacobsson", "given": "Bo", "initials": "B"}, {"family": "Valentin", "given": "Lil", "initials": "L"}, {"family": "Hagberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Clin Transl Med", "issn": "2001-1326", "issn-l": null, "volume": "12", "issue": "9", "pages": "e1023"}, "abstract": "Intrauterine infection and inflammation caused by microbial transfer from the vagina are believed to be important factors causing spontaneous preterm delivery (PTD). Multiple studies have examined the relationship between the cervicovaginal microbiome and spontaneous PTD with divergent results. Most studies have applied a DNA-based assessment, providing information on the microbial composition but not transcriptional activity. A transcriptomic approach was applied to investigate differences in the active vaginal microbiome and human transcriptome at midgestation between women delivering spontaneously preterm versus those delivering at term.\n\nVaginal swabs were collected in women with a singleton pregnancy at 18 + 0 to 20 + 6 gestational weeks. For each case of spontaneous PTD (delivery <37 + 0 weeks) two term controls were randomized (39 + 0 to 40 + 6 weeks). Vaginal specimens were subject to sequencing of both human and microbial RNA. Microbial reads were taxonomically classified using Kraken2 and RefSeq as a reference. Statistical analyses were performed using DESeq2. GSEA and HUMAnN3 were used for pathway analyses.\n\nWe found 17 human genes to be differentially expressed (false discovery rate, FDR < 0.05) in the preterm group (n = 48) compared to the term group (n = 96). Gene expression of kallikrein-2 (KLK2), KLK3 and four isoforms of metallothioneins 1 (MT1s) was higher in the preterm group (FDR < 0.05). We found 11 individual bacterial species to be differentially expressed (FDR < 0.05), most with a low occurrence. No statistically significant differences in bacterial load, diversity or microbial community state types were found between the groups.\n\nIn our mainly white population, primarily bacterial species of low occurrence were differentially expressed at midgestation in women who delivered preterm versus at term. However, the expression of specific human transcripts including KLK2, KLK3 and several isoforms of MT1s was higher in preterm cases. This is of interest, because these genes may be involved in critical inflammatory pathways associated with spontaneous PTD.", "doi": "10.1002/ctm2.1023", "pmid": "36103557", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9473488"}], "notes": [], "created": "2022-12-02T12:22:31.415Z", "modified": "2023-06-19T11:57:13.449Z"}, {"entity": "publication", "iuid": "7c53a49ec172487fb74db4ca20599e14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c53a49ec172487fb74db4ca20599e14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c53a49ec172487fb74db4ca20599e14"}}, "title": "Immunomodulation by intravenous omega-3 fatty acid treatment in older subjects hospitalized for COVID-19: A single-blind randomized controlled trial.", "authors": [{"family": "Arnardottir", "given": "Hildur", "initials": "H", "orcid": "0000-0002-5163-3946", "researcher": {"href": "https://publications.scilifelab.se/researcher/3be3f07b7bfd432a9574cc290e8d1b0f.json"}}, {"family": "Pawelzik", "given": "Sven-Christian", "initials": "SC"}, {"family": "Sarajlic", "given": "Philip", "initials": "P", "orcid": "0000-0002-8690-7994", "researcher": {"href": "https://publications.scilifelab.se/researcher/95f012af81d844ca978c1e55b3c6eea7.json"}}, {"family": "Quaranta", "given": "Alessandro", "initials": "A", "orcid": "0000-0002-3167-3772", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1dedd4f8de4178919597abbedaead3.json"}}, {"family": "Kolmert", "given": "Johan", "initials": "J"}, {"family": "Religa", "given": "Dorota", "initials": "D", "orcid": "0000-0003-4583-4570", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ed462862983451881f8de6f1e905fef.json"}}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3cd2b99e3e9486ba41030c809a48c51.json"}}, {"family": "B\u00e4ck", "given": "Magnus", "initials": "M", "orcid": "0000-0003-0853-5141", "researcher": {"href": "https://publications.scilifelab.se/researcher/2208efeca524405f8162841b2d2e5910.json"}}], "type": "letter", "published": "2022-09-00", "journal": {"title": "Clin Transl Med", "issn": "2001-1326", "volume": "12", "issue": "9", "pages": "e895", "issn-l": null}, "abstract": null, "doi": "10.1002/ctm2.895", "pmid": "36121173", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9484265"}], "notes": [], "created": "2022-11-11T07:13:22.451Z", "modified": "2022-11-17T20:36:40.565Z"}], "created": "2022-11-11T07:13:22.591Z", "modified": "2022-11-11T07:13:22.591Z"}