{"entity": "journal", "iuid": "5a41ffa15592432bacc8cd13fdc6c057", "timestamp": "2026-06-10T00:41:28.789Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Mol%20Oncol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Mol%20Oncol"}}, "title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891", "publications_count": 19, "publications": [{"entity": "publication", "iuid": "fe4fbf54443842c687e997679feba32e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe4fbf54443842c687e997679feba32e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe4fbf54443842c687e997679feba32e"}}, "title": "Cytomegalovirus infection is common in prostate cancer and antiviral therapies inhibit progression in disease models.", "authors": [{"family": "Classon", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0392-7605", "researcher": {"href": "https://publications.scilifelab.se/researcher/641cf9db52e64f9fb8eee60a977a88be.json"}}, {"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Zamboni", "given": "Margherita", "initials": "M"}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Eriksson", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Pedersen", "given": "Lars", "initials": "L"}, {"family": "Sch\u00f6rling", "given": "Alrik", "initials": "A"}, {"family": "Thoss", "given": "Anna", "initials": "A"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P", "orcid": "0000-0002-6347-1999", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1e640e83948a4a3f8a1ddd49bd953.json"}}, {"family": "Adami", "given": "Hans-Olov", "initials": "HO"}, {"family": "S\u00f8rensen", "given": "Henrik Toft", "initials": "HT"}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "11", "pages": "3035-3059", "issn-l": "1574-7891"}, "abstract": "Metastatic prostate cancer is incurable, and new therapeutic targets and drugs are urgently needed. Viral infections are associated with several cancer types, but a link between viruses and prostate oncogenesis has not been established. Only recently, an association between human cytomegalovirus (CMV) seropositivity and increased risk of prostate cancer mortality was demonstrated. Here, we show that CMV infection is common in the normal prostate epithelium and in prostate tumor tissue, with 70-92% of tumors being infected. Additionally, we report that commonly studied prostate cancer cell lines are CMV infected. Loss-of-function experiments demonstrate that CMV promotes cell survival, proliferation, and androgen receptor signaling, identifying it as a therapeutic target in castration-sensitive and castration-resistant prostate cancer. Several anti-CMV pharmaceutical compounds in clinical use inhibited cell expansion in prostate cancer models both in vitro and in vivo. We conclude that CMV is common in prostate cancer, promotes core prostate cancer cell programs, and can be inhibited by well-tolerated drugs. These findings motivate investigation into potential clinical benefits of CMV inhibition in the treatment of prostate cancer.", "doi": "10.1002/1878-0261.70073", "pmid": "40493023", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12591316"}], "notes": [], "created": "2025-11-28T10:39:38.461Z", "modified": "2025-11-28T10:39:38.586Z"}, {"entity": "publication", "iuid": "3026cc0df25b4c178a58bdb7ba158810", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810"}}, "title": "Reduced vascular leakage correlates with breast carcinoma T regulatory cell infiltration but not with metastatic propensity.", "authors": [{"family": "He", "given": "Liqun", "initials": "L", "orcid": "0000-0002-4743-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6e2e4c7f88845bb895842e56a7622ae.json"}}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Hekmati", "given": "Neda", "initials": "N", "orcid": "0009-0009-4814-869X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e525846f61401ab94732e578190274.json"}}, {"family": "Bonello", "given": "Altea", "initials": "A"}, {"family": "Schiza", "given": "Aglaia", "initials": "A"}, {"family": "Nwadozi", "given": "Emmanuel", "initials": "E"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Welsh", "given": "Michael", "initials": "M", "orcid": "0000-0002-5467-9755", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01673aeb9be429c80da30d5407b2725.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891"}, "abstract": "The vasculature and the immune system both play roles in breast cancer progression and metastasis. In an experimental mouse model of Shb-gene deficiency in endothelial cells, breast cancer lung metastasis correlated with immune suppression rather than with vascular leakage. The present study aimed to assess underlying gene expression changes in endothelial and immune cells responsible for this phenotype and to explore their relationship to human disease. Mouse endothelial cell Shb-gene deficiency, leading to 'vessel normalization', resulted in altered expression of chemo/cytokine genes and upregulation of immune checkpoint genes in immune cells. Endothelial cells under these conditions exhibited gene expression patterns compatible with reduced angiogenesis and vascular leakage. Additionally, genes whose products relate to immune cell vascular transmigration and function were affected. In a human triple-negative breast cancer cohort, tumors with reduced vascular leakage exhibited a higher relative proportion of regulatory T cells and larger tumor size. However, these changes were not associated with increased metastasis. In conclusion, a low leakage vascular phenotype reduces tumor cell intravasation/metastasis and modifies the immune response, which in the current context becomes pro-tumoral.", "doi": "10.1002/1878-0261.70144", "pmid": "41102920", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:23:33.643Z", "modified": "2025-11-13T17:36:03.258Z"}, {"entity": "publication", "iuid": "a3100db488e742d697ed58d6ab55c467", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3100db488e742d697ed58d6ab55c467.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3100db488e742d697ed58d6ab55c467"}}, "title": "Systematic profiling of cancer-fibroblast interactions reveals drug combinations in ovarian cancer.", "authors": [{"family": "Gudoityte", "given": "Greta", "initials": "G", "orcid": "0000-0003-1963-7856", "researcher": {"href": "https://publications.scilifelab.se/researcher/a853b5ae2279410aab1b89ad437e4d82.json"}}, {"family": "Sharma", "given": "Osheen", "initials": "O"}, {"family": "Leuenberger", "given": "Laura", "initials": "L"}, {"family": "Wallin", "given": "Emelie", "initials": "E"}, {"family": "Fernebro", "given": "Josefin", "initials": "J"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bergstr\u00f6m", "given": "Rebecka", "initials": "R", "orcid": "0000-0001-7609-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c52bb8b2ae249049f0da222bcdfe932.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Joneborg", "given": "Ulrika", "initials": "U"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "9", "pages": "2574-2593", "issn-l": "1574-7891"}, "abstract": "Ovarian cancer (OC) is a leading cause of death of gynecological cancers in women. Poor patient response to treatment highlights the need to better understand how the tumor microenvironment affects OC progression. Growing evidence indicates the crucial role of non-cancerous components, such as cancer-associated fibroblasts, in establishing a complex network of cellular and molecular interactions, influencing cancer progression and response to treatment. Therefore, in this study, we sought to characterize the impact of fibroblasts on OC cell behavior and drug response. Using both direct and indirect cell co-culture systems, we observed distinct changes in cancer cell proliferation, morphology, and secretome in the presence of fibroblasts. Furthermore, an imaging-based high-throughput drug screen of 528 oncology compounds revealed multiple drugs that showed altered efficacy in the co-culture conditions, demonstrating the role of fibroblasts in driving cancer cell resistance to treatment. Most importantly, our data identified the two drug combinations of Birinapant or Vorinostat with Carboplatin as promising treatments, exploiting the altered cancer cell phenotype in co-cultures. These findings were supported by the increased sensitivity of ex vivo cultures to these combinations.", "doi": "10.1002/1878-0261.70051", "pmid": "40411295", "labels": {"Affinity Proteomics Stockholm": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420376"}], "notes": [], "created": "2025-11-07T13:36:45.741Z", "modified": "2025-11-18T20:45:51.242Z"}, {"entity": "publication", "iuid": "b5df9eacc566429a92e2fec363fc008e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5df9eacc566429a92e2fec363fc008e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5df9eacc566429a92e2fec363fc008e"}}, "title": "Pericytes change function depending on glioblastoma vicinity: emphasis on immune regulation.", "authors": [{"family": "Buizza", "given": "Carolina", "initials": "C"}, {"family": "Carlsson", "given": "Robert", "initials": "R"}, {"family": "Gamper", "given": "Coralie", "initials": "C"}, {"family": "Chitale", "given": "Gayatri", "initials": "G"}, {"family": "Bengzon", "given": "Johan", "initials": "J"}, {"family": "Paul", "given": "Gesine", "initials": "G", "orcid": "0000-0002-6806-2254", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbbb29ff13af4e28afddbf78764cad29.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "19", "issue": "9", "pages": "2491-2514", "issn-l": "1574-7891"}, "abstract": "Glioblastoma (GBM), the most aggressive brain tumor in adults, is characterized by its infiltrative growth along the perivascular space. Mural cells (MCs), encompassing pericytes and smooth muscle cells, are multifunctional perivascular cells implicated in GBM progression. MCs not only facilitate vascular co-option but have also been suggested to contribute to the immunosuppressive tumor microenvironment, promoting tumor growth and migration. However, whether MC interactions with immune cells differ based on their proximity to the tumor remains unclear. Using single-cell RNA sequencing, we analyzed MC transcriptome profiles across distinct regions relative to the tumor mass in mouse and human GBM samples. Tumor-residing MCs exhibited profound phenotypic changes, showing upregulated gene expression and enhanced signaling activity toward immune cells, with region-specific ligand-receptor interactions. Conversely, border-residing MCs, despite their abundance, showed reduced activation and lacked distinct transcriptional profiles. These findings reveal spatially defined transcriptional heterogeneity in MCs within the GBM microenvironment, underscoring their dynamic role in the GBM microenvironment. This study provides novel insights into MC responses in GBM, identifying potential avenues for targeting MC-immune-cell interactions in therapeutic interventions.", "doi": "10.1002/1878-0261.70095", "pmid": "40674254", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420362"}], "notes": [], "created": "2025-11-28T10:39:43.920Z", "modified": "2025-11-28T10:39:44.007Z"}, {"entity": "publication", "iuid": "f5829319dbfb49ad8137f41b82951481", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5829319dbfb49ad8137f41b82951481.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5829319dbfb49ad8137f41b82951481"}}, "title": "Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.", "authors": [{"family": "Classon", "given": "Johanna", "initials": "J", "orcid": "0000-0003-0392-7605", "researcher": {"href": "https://publications.scilifelab.se/researcher/641cf9db52e64f9fb8eee60a977a88be.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f196173b40b4819a5fcd11bf76a4e6e.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f8e781842747bb91bdb07e9d5c0cd8.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6015314c4c04ee08d7e4358cfb55b9f.json"}}, {"family": "Nkulikiyimfura", "given": "Dieudonn\u00e9", "initials": "D", "orcid": "0000-0002-6981-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/6af6961b78de4d0b96b011009cccc14c.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Druid", "given": "Henrik", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba167f912244d879746ed60a3c19568.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "16", "issue": "19", "pages": "3452-3464", "issn-l": "1574-7891"}, "abstract": "Prostate cancer is a heterogeneous disease with a need for new prognostic biomarkers. Human leukocyte antigen (HLA) genes are highly polymorphic genes central to antigen presentation to T-cells. Two alleles, HLA-A*02:01 and HLA-A*24:02, have been associated with prognosis in patients diagnosed with de novo metastatic prostate cancer. We leveraged the next-generation sequenced cohorts CPC-GENE and TCGA-PRAD to examine HLA alleles, antiviral T-cell receptors and prostate cancer disease recurrence after prostatectomy. Carrying HLA-A*02:01 (111/229; 48% of patients) was independently associated with disease recurrence in patients with low-intermediate risk prostate cancer. HLA-A*11 (carried by 42/441; 10% of patients) was independently associated with rapid disease recurrence in patients with high-risk prostate cancer. Moreover, HLA-A*02:01 carriers in which anti-cytomegalovirus T-cell receptors (CMV-TCR) were identified in tumors (13/144; 10% of all patients in the cohort) had a higher risk of disease recurrence than CMV-TCR-negative patients. These findings suggest that HLA-type and CMV immunity may be valuable biomarkers for prostate cancer progression.", "doi": "10.1002/1878-0261.13273", "pmid": "35712787", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9533687"}, {"db": "RefSeq", "key": "NC_006273.2"}], "notes": [], "created": "2022-11-09T15:51:53.564Z", "modified": "2024-01-16T13:48:34.865Z"}, {"entity": "publication", "iuid": "34ae3216e2364627b19b470684323d89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34ae3216e2364627b19b470684323d89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34ae3216e2364627b19b470684323d89"}}, "title": "TGF\u03b2 selects for pro-stemness over pro-invasive phenotypes during cancer cell epithelial-mesenchymal transition.", "authors": [{"family": "Tsubakihara", "given": "Yutaro", "initials": "Y"}, {"family": "Ohata", "given": "Yae", "initials": "Y", "orcid": "0000-0002-5518-835X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca5c2da2b3d84f5ea796361868ddbe5f.json"}}, {"family": "Okita", "given": "Yukari", "initials": "Y", "orcid": "0000-0002-7279-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ffe4fba4894ee1aebb444b41046c35.json"}}, {"family": "Younis", "given": "Shady", "initials": "S", "orcid": "0000-0002-4319-1738", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b77c6e3ed14b9ba2e10132f89ef781.json"}}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}, {"family": "Ren", "given": "Jiang", "initials": "J"}, {"family": "Ten Dijke", "given": "Peter", "initials": "P", "orcid": "0000-0002-7234-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/299812073080446a91fc6228efbdc1c5.json"}}, {"family": "Miyazono", "given": "Kohei", "initials": "K", "orcid": "0000-0001-7341-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a14a58f628d435a94ad9540478117cb.json"}}, {"family": "Hikita", "given": "Atsuhiko", "initials": "A", "orcid": "0000-0001-9552-2976", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a91722cadc4a7facd16457ed23d901.json"}}, {"family": "Imamura", "given": "Takeshi", "initials": "T", "orcid": "0000-0001-5101-4304", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae63b202e284486eb903f18f78a8a024.json"}}, {"family": "Kato", "given": "Mitsuyasu", "initials": "M", "orcid": "0000-0001-9905-2473", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2badf9539854c4381da91f37aa0c867.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "16", "issue": "12", "pages": "2330-2354", "issn-l": "1574-7891"}, "abstract": "Transforming growth factor \u03b2 (TGF\u03b2) induces epithelial-mesenchymal transition (EMT), which correlates with stemness and invasiveness. Mesenchymal-epithelial transition (MET) is induced by TGF\u03b2 withdrawal and correlates with metastatic colonization. Whether TGF\u03b2 promotes stemness and invasiveness simultaneously via EMT remains unclear. We established a breast cancer cell model expressing red fluorescent protein (RFP) under the E-cadherin promoter. In 2D cultures, TGF\u03b2 induced EMT, generating RFPlow cells with a mesenchymal transcriptome, and regained RFP, with an epithelial transcriptome, after MET induced by TGF\u03b2 withdrawal. RFPlow cells generated robust mammospheres, with epithelio-mesenchymal cell surface features. Mammospheres that were forced to adhere generated migratory cells, devoid of RFP, a phenotype which was inhibited by a TGF\u03b2 receptor kinase inhibitor. Further stimulation of RFPlow mammospheres with TGF\u03b2 suppressed the generation of motile cells, but enhanced mammosphere growth. Accordingly, mammary fat-pad-transplanted mammospheres, in the absence of exogenous TGF\u03b2 treatment, established lung metastases with evident MET (RFPhigh cells). In contrast, TGF\u03b2-treated mammospheres revealed high tumour-initiating capacity, but limited metastatic potential. Thus, the biological context of partial EMT and MET allows TGF\u03b2 to differentiate between pro-stemness and pro-invasive phenotypes.", "doi": "10.1002/1878-0261.13215", "pmid": "35348275", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9208077"}, {"db": "RefSeq", "key": "E-MTAB-97509"}], "notes": [], "created": "2022-11-09T15:57:22.355Z", "modified": "2024-01-16T13:48:36.266Z"}, {"entity": "publication", "iuid": "d5c0c16b13b14f5e88c23efe7344bee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5c0c16b13b14f5e88c23efe7344bee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5c0c16b13b14f5e88c23efe7344bee1"}}, "title": "Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.", "authors": [{"family": "Thysell", "given": "Elin", "initials": "E"}, {"family": "K\u00f6hn", "given": "Linda", "initials": "L"}, {"family": "Semenas", "given": "Julius", "initials": "J", "orcid": "0000-0001-5394-7239", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0402a104066426dbeb5108ac120a46f.json"}}, {"family": "J\u00e4remo", "given": "Helena", "initials": "H"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Lundholm", "given": "Marie", "initials": "M"}, {"family": "Thellenberg Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Damber", "given": "Jan-Erik", "initials": "JE"}, {"family": "Widmark", "given": "Anders", "initials": "A"}, {"family": "Crnalic", "given": "Sead", "initials": "S"}, {"family": "Josefsson", "given": "Andreas", "initials": "A"}, {"family": "Wel\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Nilsson", "given": "Rolf J A", "initials": "RJA"}, {"family": "Bergh", "given": "Anders", "initials": "A"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P", "orcid": "0000-0002-6347-1999", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1e640e83948a4a3f8a1ddd49bd953.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891", "volume": "16", "issue": "4", "pages": "846-859"}, "abstract": "To improve treatment of metastatic prostate cancer, the biology of metastases needs to be understood. We recently described three subtypes of prostate cancer bone metastases (MetA-C), based on differential gene expression. The aim of this study was to verify the clinical relevance of these subtypes and to explore their biology and relations to genetic drivers. Freshly-frozen metastasis samples were obtained as hormone-naive (n = 17), short-term castrated (n = 21), or castration-resistant (n = 65) from a total of 67 patients. Previously published sequencing data from 573 metastasis samples were also analyzed. Through transcriptome profiling and sample classification based on a set of predefined MetA-C-differentiating genes, we found that most metastases were heterogeneous for the MetA-C subtypes. Overall, MetA was the most common subtype, while MetB was significantly enriched in castration-resistant samples and in liver metastases, and consistently associated with poor prognosis. By gene set enrichment analysis, the phenotype of MetA was described by high androgen response, protein secretion and adipogenesis, MetB by high cell cycle activity and DNA repair, and MetC by epithelial-to-mesenchymal transition and inflammation. The MetB subtype demonstrated single nucleotide variants of RB transcriptional corepressor 1 (RB1) and loss of 21 genes at chromosome 13, including RB1, but provided independent prognostic value to those genetic aberrations. In conclusion, a distinct set of gene transcripts can be used to classify prostate cancer metastases into the subtypes MetA-C. The MetA-C subtypes show diverse biology, organ tropism, and prognosis. The MetA-C classification may be used independently, or in combination with genetic markers, primarily to identify MetB patients in need of complementary therapy to conventional androgen receptor-targeting treatments.", "doi": "10.1002/1878-0261.13158", "pmid": "34889043", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8847984"}], "notes": [], "created": "2022-01-11T07:51:15.811Z", "modified": "2022-12-05T11:19:52.667Z"}, {"entity": "publication", "iuid": "b2805e31dce94755af4fde64db297814", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2805e31dce94755af4fde64db297814.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2805e31dce94755af4fde64db297814"}}, "title": "Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells", "authors": [{"family": "H\u00fchn", "given": "Daniela", "initials": "D"}, {"family": "Mart\u00ed\u2010Rodrigo", "given": "Pablo", "initials": "P", "orcid": "0000-0002-1049-0918", "researcher": {"href": "https://publications.scilifelab.se/researcher/e63e9b1775f046ed8c8feb106f8cebca.json"}}, {"family": "Mouron", "given": "Silvana", "initials": "S"}, {"family": "Hansel", "given": "Catherine", "initials": "C"}, {"family": "Tschapalda", "given": "Kirsten", "initials": "K"}, {"family": "Porebski", "given": "Bartlomiej", "initials": "B"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Lidemalm", "given": "Louise", "initials": "L"}, {"family": "Quintela\u2010Fandino", "given": "Miguel", "initials": "M"}, {"family": "Carreras\u2010Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Fernandez\u2010Capetillo", "given": "Oscar", "initials": "O", "orcid": "0000-0002-2690-6885", "researcher": {"href": "https://publications.scilifelab.se/researcher/7134c59abca24f96903fc50914311b40.json"}}], "type": "journal-article", "published": "2022-01-00", "journal": {"title": "Mol Oncol", "issn": "1574-7891", "issn-l": null, "volume": "16", "issue": "1", "pages": "148-165"}, "abstract": null, "doi": "10.1002/1878-0261.13083", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-28T13:54:09.398Z", "modified": "2025-10-17T13:04:27.970Z"}, {"entity": "publication", "iuid": "99bbc9211a014ec2a9ee1106611e757c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99bbc9211a014ec2a9ee1106611e757c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99bbc9211a014ec2a9ee1106611e757c"}}, "title": "Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells.", "authors": [{"family": "H\u00fchn", "given": "Daniela", "initials": "D"}, {"family": "Mart\u00ed-Rodrigo", "given": "Pablo", "initials": "P", "orcid": "0000-0002-1049-0918", "researcher": {"href": "https://publications.scilifelab.se/researcher/e63e9b1775f046ed8c8feb106f8cebca.json"}}, {"family": "Mouron", "given": "Silvana", "initials": "S"}, {"family": "Hansel", "given": "Catherine", "initials": "C"}, {"family": "Tschapalda", "given": "Kirsten", "initials": "K"}, {"family": "Porebski", "given": "Bartlomiej", "initials": "B"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Lidemalm", "given": "Louise", "initials": "L"}, {"family": "Quintela-Fandino", "given": "Miguel", "initials": "M"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Fernandez-Capetillo", "given": "Oscar", "initials": "O", "orcid": "0000-0002-2690-6885", "researcher": {"href": "https://publications.scilifelab.se/researcher/7134c59abca24f96903fc50914311b40.json"}}], "type": "journal article", "published": "2021-08-15", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891", "volume": null, "issue": null, "pages": null}, "abstract": "Among others, expression levels of programmed cell death 1 ligand 1 (PD-L1) have been explored as biomarkers of the response to immune checkpoint inhibitors in cancer therapy. Here, we present the results of a chemical screen that interrogated how medically approved drugs influence PD-L1 expression. As expected, corticosteroids and inhibitors of Janus kinases were among the top PD-L1 downregulators. In addition, we identified that PD-L1 expression is induced by antiestrogenic compounds. Transcriptomic analyses indicate that chronic estrogen receptor alpha (ER\u03b1) inhibition triggers a broad immunosuppressive program in ER-positive breast cancer cells, which is subsequent to their growth arrest and involves the activation of multiple immune checkpoints together with the silencing of the antigen-presenting machinery. Accordingly, estrogen-deprived MCF7 cells are resistant to T-cell-mediated cell killing, in a manner that is independent of PD-L1, but which is reverted by estradiol. Our study reveals that while antiestrogen therapies efficiently limit the growth of ER-positive breast cancer cells, they concomitantly trigger a transcriptional program that favors their immune evasion.", "doi": "10.1002/1878-0261.13083", "pmid": "34392603", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2021-11-18T11:57:22.385Z", "modified": "2025-10-17T13:04:28.053Z"}, {"entity": "publication", "iuid": "08c0640fd0ba40e3b8b64e721c6d1135", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08c0640fd0ba40e3b8b64e721c6d1135.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08c0640fd0ba40e3b8b64e721c6d1135"}}, "title": "Cancer diagnostics based on plasma protein biomarkers: hard times but great expectations.", "authors": [{"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Hammond", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "15", "issue": "6", "pages": "1715-1726", "issn-l": "1574-7891"}, "abstract": "Cancer diagnostics based on the detection of protein biomarkers in blood has promising potential for early detection and continuous monitoring of disease. However, the currently available protein biomarkers and assay formats largely fail to live up to expectations, mainly due to insufficient diagnostic specificity. Here, we discuss what kinds of plasma proteins might prove useful as biomarkers of malignant processes in specific organs. We consider the need to search for biomarkers deep down in the lowest reaches of the proteome, below current detection levels. In this regard, we comment on the poor molecular detection sensitivity of current protein assays compared to nucleic acid detection reactions, and we discuss requirements for achieving detection of vanishingly small amounts of proteins, to ensure detection of early stages of malignant growth through liquid biopsy.", "doi": "10.1002/1878-0261.12809", "pmid": "33012111", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8169444"}], "notes": [], "created": "2021-12-10T09:29:53.647Z", "modified": "2021-12-10T09:29:53.660Z"}, {"entity": "publication", "iuid": "1db10b1c89f44f58a9844ca95744ecf0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1db10b1c89f44f58a9844ca95744ecf0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1db10b1c89f44f58a9844ca95744ecf0"}}, "title": "Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.", "authors": [{"family": "Chen", "given": "Yi", "initials": "Y", "orcid": "0000-0002-4891-8289", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ae866ca9a3244aba9678dc66a1e69e1.json"}}, {"family": "Hesla", "given": "Asle C", "initials": "AC"}, {"family": "Lin", "given": "Yingbo", "initials": "Y"}, {"family": "Ghaderi", "given": "Mehran", "initials": "M"}, {"family": "Liu", "given": "Mingzhi", "initials": "M"}, {"family": "Yang", "given": "Chen", "initials": "C"}, {"family": "Zhang", "given": "Yifan", "initials": "Y"}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Haglund", "given": "Felix", "initials": "F", "orcid": "0000-0002-7015-3841", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cbee146fa4e27bc8d26111283b854.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "14", "issue": "5", "pages": "1101-1117", "issn-l": "1574-7891"}, "abstract": "Ewing sarcomas (ESs) are aggressive sarcomas driven by EWS fusion genes. We sought to investigate whether whole-transcriptome sequencing (RNA-seq) could be used to detect patterns associated with chemotherapy response or tumor progression after first-line treatment. Transcriptome sequencing (RNA-seq) of 13 ES cases was performed. Among the differentially expressed pathways, we identified IGF2 expression as a potential driver of chemotherapy response and progression. We investigated the effect of IGF2 on proliferation, radioresistance, apoptosis, and the transcriptome pattern in four ES cell lines and the effect of IGF2 expression in a validation series of 14 patients. Transcriptome analysis identified differentially expressed genes (adj. P < 0.005) and pathways associated with chemotherapy response (285 genes), short overall survival (662 genes), and progression after treatment (447 genes). Imprinting independent promoter P3-mediated IGF2 expression was identified in a subset of cases with aggressive clinical course. In ES cell lines, IGF2 induced proliferation, but promoted radioresistance only in CADO cells. High IGF2 expression was also significantly associated with shorter overall survival in patients with ES. Transcriptome analysis of the clinical samples and the cell lines revealed an IGF-dependent signature, potentially related to a stem cell-like phenotype. Transcriptome analysis is a potentially powerful complementary tool to predict the clinical behavior of ES and may be utilized for clinical trial stratification strategies and personalized oncology. Certain gene signatures, for example, IGF-related pathways, are coupled to biological functions that could be of clinical importance. Finally, our results indicate that IGF inhibition may be successful as a first-line therapy in conjunction with conventional radiochemotherapy for a subset of patients.", "doi": "10.1002/1878-0261.12655", "pmid": "32115849", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7191197"}], "notes": [], "created": "2020-07-08T13:04:54.124Z", "modified": "2024-01-16T13:48:42.546Z"}, {"entity": "publication", "iuid": "3512e2bf962741998ecc07bef378e14b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3512e2bf962741998ecc07bef378e14b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3512e2bf962741998ecc07bef378e14b"}}, "title": "Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.", "authors": [{"family": "Mitra", "given": "Shamik", "initials": "S", "orcid": "0000-0001-6995-0600", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3b10a7bd10941d58ee17b74795931fd.json"}}, {"family": "Lauss", "given": "Martin", "initials": "M"}, {"family": "Cabrita", "given": "Rita", "initials": "R"}, {"family": "Choi", "given": "Jiyeon", "initials": "J"}, {"family": "Zhang", "given": "Tongwu", "initials": "T"}, {"family": "Isaksson", "given": "Karolin", "initials": "K"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Carneiro", "given": "Ana", "initials": "A"}, {"family": "Staaf", "given": "Johan", "initials": "J"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nielsen", "given": "Kari", "initials": "K"}, {"family": "Brown", "given": "Kevin M", "initials": "KM"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-6865-0147", "researcher": {"href": "https://publications.scilifelab.se/researcher/0099af8e34f64a37a35392d32a0d357e.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "14", "issue": "5", "pages": "933-950", "issn-l": "1574-7891"}, "abstract": "The presence of immune cells in the tumor microenvironment has been associated with response to immunotherapies across several cancer types, including melanoma. Despite its therapeutic relevance, characterization of the melanoma immune microenvironments remains insufficiently explored. To distinguish the immune microenvironment in a cohort of 180 metastatic melanoma clinical specimens, we developed a method using promoter CpG methylation of immune cell type-specific genes extracted from genome-wide methylation arrays. Unsupervised clustering identified three immune methylation clusters with varying levels of immune CpG methylation that are related to patient survival. Matching protein and gene expression data further corroborated the identified epigenetic characterization. Exploration of the possible immune exclusion mechanisms at play revealed likely dependency on MITF protein level and PTEN loss-of-function events for melanomas unresponsive to immunotherapies (immune-low). To understand whether melanoma tumors resemble other solid tumors in terms of immune methylation characteristics, we explored 15 different solid tumor cohorts from TCGA. Low-dimensional projection based on immune cell type-specific methylation revealed grouping of the solid tumors in line with melanoma immune methylation clusters rather than tumor types. Association of survival outcome with immune cell type-specific methylation differed across tumor and cell types. However, in melanomas immune cell type-specific methylation was associated with inferior patient survival. Exploration of the immune methylation patterns in a pan-cancer context suggested that specific immune microenvironments might occur across the cancer spectrum. Together, our findings underscore the existence of diverse immune microenvironments, which may be informative for future immunotherapeutic applications.", "doi": "10.1002/1878-0261.12663", "pmid": "32147909", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7191190"}], "notes": [], "created": "2020-05-07T10:58:12.836Z", "modified": "2024-01-16T13:48:42.568Z"}, {"entity": "publication", "iuid": "ef763beb1ed645cfaf970e9cf6a6afae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef763beb1ed645cfaf970e9cf6a6afae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef763beb1ed645cfaf970e9cf6a6afae"}}, "title": "Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.", "authors": [{"family": "Franz\u00e9n", "given": "Bo", "initials": "B"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Ramqvist", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Kierkegaard", "given": "Jonas", "initials": "J"}, {"family": "Masucci", "given": "Giuseppe", "initials": "G"}, {"family": "Auer", "given": "Gert", "initials": "G"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "13", "issn": "1878-0261", "issue": "2", "pages": "376-391", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and for follow-up of personalized cancer therapy, including immunotherapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissue samples; however, the minute amounts of sample require sensitive multiplex molecular analysis to be of clinical biomarker utility. We have applied proximity extension assays (PEA) to analyze 167 proteins in FNA samples from patients with breast cancer (BC; n = 25) and benign lesions (n = 32). We demonstrate that the FNA BC samples could be divided into two main clusters, characterized by differences in expression levels of the estrogen receptor (ER) and the proliferation marker Ki67. This clustering corresponded to some extent to established BC subtypes. Our analysis also revealed several proteins whose expression levels differed between BC and benign lesions (e.g., CA9, GZMB, IL-6, VEGFA, CXCL11, PDL1, and PCD1), as well as several chemokines correlating with ER and Ki67 status (e.g., CCL4, CCL8, CCL20, CXCL8, CXCL9, and CXCL17). Finally, we also identified three signatures that could predict Ki67 status, ER status, and tumor grade, respectively, based on a small subset of proteins, which was dominated by chemokines. To our knowledge, expression profiles of CCL13 in benign lesions and BC have not previously been described but were shown herein to correlate with proliferation (P = 0.00095), suggesting a role in advanced BC. Given the broad functional range of the proteins analyzed, immune-related proteins were overrepresented among the observed alterations. Our pilot study supports the emerging role of chemokines in BC progression. Due to the minimally traumatic sampling and clinically important molecular information for therapeutic decisions, this methodology is promising for future immunoscoring and monitoring of treatment efficacy in BC.", "doi": "10.1002/1878-0261.12410", "pmid": "30451357", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6360506"}], "notes": [], "created": "2019-01-14T19:31:57.036Z", "modified": "2023-04-14T13:55:59.371Z"}, {"entity": "publication", "iuid": "f4879bb970374d7290430fcb284ab42c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4879bb970374d7290430fcb284ab42c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4879bb970374d7290430fcb284ab42c"}}, "title": "A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions", "authors": [{"family": "Franz\u00e9n", "given": "Bo", "initials": "B"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Becker", "given": "Susanne", "initials": "S"}, {"family": "Wik", "given": "Lotta", "initials": "L"}, {"family": "Kierkegaard", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Annika", "initials": "A"}, {"family": "Muppani", "given": "Naveen R", "initials": "NR"}, {"family": "Auer", "given": "Gert", "initials": "G"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}], "type": "journal-article", "published": "2018-09-00", "journal": {"volume": "12", "issn": "1878-0261", "issue": "9", "pages": "1415-1428", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and to follow-up personalized cancer therapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissues; however, the minute sample amounts require sensitive multiplex molecular analysis to achieve clinical utility. We have applied proximity extension assays (PEA) and NanoString (NS) technology for analyses of proteins and of RNA, respectively, in FNA samples. Using samples from patients with breast cancer (BC, n\u00a0=\u00a025) or benign lesions (n\u00a0=\u00a033), we demonstrate that these FNA-based molecular analyses (a) can offer high sensitivity and reproducibility, (b) may provide correct diagnosis in shorter time and at a lower cost than current practice, (c) correlate with results from routine analysis (i.e., benchmarking against immunohistochemistry tests for ER, PR, HER2, and Ki67), and (d) may also help identify new markers related to immunotherapy. A specific 11-protein signature, including FGF binding protein 1, decorin, and furin, distinguished all cancer patient samples from all benign lesions in our main cohort and in smaller replication cohort. Due to the minimally traumatic sampling and rich molecular information, this combined proteomics and transcriptomic methodology is promising for diagnostics and evaluation of treatment efficacy in BC.", "doi": "10.1002/1878-0261.12350", "pmid": "30019538", "labels": {"Clinical Biomarkers": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-10-30T08:20:05.244Z", "modified": "2024-01-16T13:48:45.690Z"}, {"entity": "publication", "iuid": "112517057913461ea2691f4a8a12a961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/112517057913461ea2691f4a8a12a961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/112517057913461ea2691f4a8a12a961"}}, "title": "Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells", "authors": [{"family": "Maturi", "given": "Varun", "initials": "V"}, {"family": "Mor\u00e9n", "given": "Anita", "initials": "A"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Heldin", "given": "Carl Henrik", "initials": "CH"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}], "type": "journal-article", "published": "2018-06-00", "journal": {"volume": "12", "issn": "1878-0261", "issue": "7", "pages": "1153-1174", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": null, "doi": "10.1002/1878-0261.12317", "pmid": "29729076", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-15T09:51:04.648Z", "modified": "2024-01-16T13:48:46.219Z"}, {"entity": "publication", "iuid": "6b579fa6a62344afa63ce461a7ce0be5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b579fa6a62344afa63ce461a7ce0be5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b579fa6a62344afa63ce461a7ce0be5"}}, "title": "Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.", "authors": [{"family": "Malgerud", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-1691-0880", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c4ba0afe85a4328b373dc0ebd862c1a.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Gustafsson-Liljefors", "given": "Maria", "initials": "M"}, {"family": "Karimi", "given": "Masoud", "initials": "M"}, {"family": "Moro", "given": "Carlos Fern\u00e1ndez", "initials": "CF"}, {"family": "Stecker", "given": "Katrin", "initials": "K"}, {"family": "Picker", "given": "Alexander", "initials": "A"}, {"family": "Huelsewig", "given": "Carolin", "initials": "C"}, {"family": "Stein", "given": "Martin", "initials": "M"}, {"family": "Bohnert", "given": "Regina", "initials": "R"}, {"family": "Del Chiaro", "given": "Marco", "initials": "M"}, {"family": "Haas", "given": "Stephan L", "initials": "SL"}, {"family": "Heuchel", "given": "Rainer L", "initials": "RL"}, {"family": "Permert", "given": "Johan", "initials": "J"}, {"family": "Maeurer", "given": "Markus J", "initials": "MJ"}, {"family": "Brock", "given": "Stephan", "initials": "S"}, {"family": "Verbeke", "given": "Caroline S", "initials": "CS"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Jackson", "given": "David B", "initials": "DB"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "L\u00f6hr", "given": "Johannes Matthias", "initials": "JM"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "11", "issn": "1878-0261", "issue": "10", "pages": "1413-1429", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is a tumor with an extremely poor prognosis, predominantly as a result of chemotherapy resistance and numerous somatic mutations. Consequently, PDAC is a prime candidate for the use of sequencing to identify causative mutations, facilitating subsequent administration of targeted therapy. In a feasibility study, we retrospectively assessed the therapeutic recommendations of a novel, evidence-based software that analyzes next-generation sequencing (NGS) data using a large panel of pharmacogenomic biomarkers for efficacy and toxicity. Tissue from 14 patients with PDAC was sequenced using NGS with a 620 gene panel. FASTQ files were fed into treatmentmap. The results were compared with chemotherapy in the patients, including all side effects. No changes in therapy were made. Known driver mutations for PDAC were confirmed (e.g. KRAS, TP53). Software analysis revealed positive biomarkers for predicted effective and ineffective treatments in all patients. At least one biomarker associated with increased toxicity could be detected in all patients. Patients had been receiving one of the currently approved chemotherapy agents. In two patients, toxicity could have been correctly predicted by the software analysis. The results suggest that NGS, in combination with an evidence-based software, could be conducted within a 2-week period, thus being feasible for clinical routine. Therapy recommendations were principally off-label use. Based on the predominant KRAS mutations, other drugs were predicted to be ineffective. The pharmacogenomic biomarkers indicative of increased toxicity could be retrospectively linked to reported negative side effects in the respective patients. Finally, the occurrence of somatic and germline mutations in cancer syndrome-associated genes is noteworthy, despite a high frequency of these particular variants in the background population. These results suggest software-analysis of NGS data provides evidence-based information on effective, ineffective and toxic drugs, potentially forming the basis for precision cancer medicine in PDAC.", "doi": "10.1002/1878-0261.12108", "pmid": "28675654", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5623817"}, {"db": "figshare", "key": "10.6084/m9.figshare.5311114"}], "notes": [], "created": "2017-11-03T12:53:31.739Z", "modified": "2023-06-19T07:51:37.793Z"}, {"entity": "publication", "iuid": "2eb04d257d6a465eae2a1bd2c14653b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2eb04d257d6a465eae2a1bd2c14653b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2eb04d257d6a465eae2a1bd2c14653b5"}}, "title": "A ribonucleotide reductase inhibitor with deoxyribonucleoside-reversible cytotoxicity.", "authors": [{"family": "Crona", "given": "Mikael", "initials": "M"}, {"family": "Cod\u00f3", "given": "Paula", "initials": "P"}, {"family": "Jonna", "given": "Venkateswara Rao", "initials": "VR"}, {"family": "Hofer", "given": "Anders", "initials": "A"}, {"family": "Fernandes", "given": "Aristi P", "initials": "AP"}, {"family": "Tholander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2016-11-00", "journal": {"volume": "10", "issn": "1878-0261", "issue": "9", "pages": "1375-1386", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "Ribonucleotide Reductase (RNR) is the sole enzyme that catalyzes the reduction of ribonucleotides into deoxyribonucleotides. Even though RNR is a recognized target for antiproliferative molecules, and the main target of the approved drug hydroxyurea, few new leads targeted to this enzyme have been developed. We have evaluated a recently identified set of RNR inhibitors with respect to inhibition of the human enzyme and cellular toxicity. One compound, NSC73735, is particularly interesting; it is specific for leukemia cells and is the first identified compound that hinders oligomerization of the mammalian large RNR subunit. Similar to hydroxyurea, it caused a disruption of the cell cycle distribution of cultured HL-60 cells. In contrast to hydroxyurea, the disruption was reversible, indicating higher specificity. NSC73735 thus defines a potential lead candidate for RNR-targeted anticancer drugs, as well as a chemical probe with better selectivity for RNR inhibition than hydroxyurea.", "doi": "10.1016/j.molonc.2016.07.008", "pmid": "27511871", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "S1574-7891(16)30068-0"}], "notes": [], "created": "2017-05-03T13:02:40.112Z", "modified": "2017-09-06T11:42:09.026Z"}, {"entity": "publication", "iuid": "f39d3a704227439cb7d71960369fb3e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f39d3a704227439cb7d71960369fb3e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f39d3a704227439cb7d71960369fb3e6"}}, "title": "Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.", "authors": [{"family": "O'Hurley", "given": "Gillian", "initials": "G"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Rahman", "given": "Arman", "initials": "A"}, {"family": "Li", "given": "Bo", "initials": "B"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}], "type": "evaluation studies", "published": "2014-06-00", "journal": {"volume": "8", "issn": "1878-0261", "issue": "4", "pages": "783-798", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "The use of immunohistochemistry (IHC) in clinical cohorts is of paramount importance in determining the utility of a biomarker in clinical practice. A major bottleneck in translating a biomarker from bench-to-bedside is the lack of well characterized, specific antibodies suitable for IHC. Despite the widespread use of IHC as a biomarker validation tool, no universally accepted standardization guidelines have been developed to determine the applicability of particular antibodies for IHC prior to its use. In this review, we discuss the technical challenges faced by the use of immunohistochemical biomarkers and rigorously explore classical and emerging antibody validation technologies. Based on our review of these technologies, we provide strict criteria for the pragmatic validation of antibodies for use in immunohistochemical assays.", "doi": "10.1016/j.molonc.2014.03.008", "pmid": "24725481", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S1574-7891(14)00056-8"}], "notes": [], "created": "2017-05-04T14:56:08.513Z", "modified": "2017-05-30T12:58:08.312Z"}, {"entity": "publication", "iuid": "6244cbe772234367ad54dc7e754d85a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6244cbe772234367ad54dc7e754d85a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6244cbe772234367ad54dc7e754d85a5"}}, "title": "Glioma-derived macrophage migration inhibitory factor (MIF) promotes mast cell recruitment in a STAT5-dependent manner.", "authors": [{"family": "P\u00f5lajeva", "given": "Jelena", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Lundequist", "given": "Anders", "initials": "A"}, {"family": "Sj\u00f6sten", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Smits", "given": "Anja", "initials": "A"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Westermark", "given": "Bengt", "initials": "B"}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "Forsberg Nilsson", "given": "Karin", "initials": "K"}, {"family": "Tchougounova", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2014-02-00", "journal": {"volume": "8", "issn": "1878-0261", "issue": "1", "pages": "50-58", "title": "Mol Oncol", "issn-l": "1574-7891"}, "abstract": "Recently, glioma research has increased its focus on the diverse types of cells present in brain tumors. We observed previously that gliomas are associated with a profound accumulation of mast cells (MCs) and here we investigate the underlying mechanism. Gliomas express a plethora of chemoattractants. First, we demonstrated pronounced migration of human MCs toward conditioned medium from cultures of glioma cell lines. Subsequent cytokine array analyses of media from cells, cultured in either serum-containing or -free conditions, revealed a number of candidates which were secreted in high amounts in both cell lines. Among these, we then focused on macrophage migration inhibitory factor (MIF), which has been reported to be pro-inflammatory and -tumorigenic. Infiltration of MCs was attenuated by antibodies that neutralized MIF. Moreover, a positive correlation between the number of MCs and the level of MIF in a large cohort of human glioma tissue samples was observed. Further, both glioma-conditioned media and purified MIF promoted differential phosphorylation of a number of signaling molecules, including signal transducer and activator of transcription 5 (STAT5), in MCs. Inhibition of pSTAT5 signaling significantly attenuated the migration of MCs toward glioma cell-conditioned medium shown to contain MIF. In addition, analysis of tissue microarrays (TMAs) of high-grade gliomas revealed a direct correlation between the level of pSTAT5 in MCs and the level of MIF in the medium. In conclusion, these findings indicate the important influence of signaling cascades involving MIF and STAT5 on the recruitment of MCs to gliomas.", "doi": "10.1016/j.molonc.2013.09.002", "pmid": "24091309", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S1574-7891(13)00137-3"}], "notes": [], "created": "2017-05-04T14:56:01.482Z", "modified": "2017-05-30T12:54:33.517Z"}], "created": "2017-05-09T09:12:35.133Z", "modified": "2020-11-27T13:14:07.730Z"}