{"entity": "journal", "iuid": "0905cb3c75ed4352959b8b22ae29a10f", "timestamp": "2026-07-20T13:30:47.551Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Lung%20Cancer.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Lung%20Cancer"}}, "title": "Lung Cancer", "issn": "1872-8332", "issn-l": "0169-5002", "publications_count": 5, "publications": [{"entity": "publication", "iuid": "1cc908774e03417da24ecc6add68739f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1cc908774e03417da24ecc6add68739f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1cc908774e03417da24ecc6add68739f"}}, "title": "Evaluation of NTRK immunohistochemistry as a screening method for NTRK gene fusion detection in non-small cell lung cancer.", "authors": [{"family": "Elfving", "given": "Hedvig", "initials": "H"}, {"family": "Brostr\u00f6m", "given": "Erika", "initials": "E"}, {"family": "Moens", "given": "Lotte N J", "initials": "LNJ"}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Cerjan", "given": "Dijana", "initials": "D"}, {"family": "Lauter", "given": "Gilbert", "initials": "G"}, {"family": "Nord", "given": "Helena", "initials": "H"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM"}, {"family": "Ullenhag", "given": "Gustav J", "initials": "GJ"}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "Backman", "given": "Max", "initials": "M"}, {"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Lung Cancer", "issn": "1872-8332", "volume": "151", "pages": "53-59", "issn-l": "0169-5002"}, "abstract": "The small molecule inhibitors larotrectinib and entrectinib have recently been approved as cancer agnostic drugs in patients with tumours harbouring a rearrangement of the neurotrophic tropomyosin receptor kinase (NTRK). These oncogenic fusions are estimated to occur in 0.1-3 % of non-small cell lung cancers (NSCLC). Although molecular techniques are most reliable for fusion detection, immunohistochemical analysis is considered valuable for screening. Therefore, we evaluated the newly introduced diagnostic immunohistochemical assay (clone EPR17341) on a representative NSCLC cohort.\n\nCancer tissue from 688 clinically and molecularly extensively annotated NSCLC patients were comprised on tissue microarrays and stained with the pan-TRK antibody clone EPR17341. Positive cases were further analysed with the TruSight Tumor 170 RNA assay (Illumina). Selected cases were also tested with a NanoString NTRK fusion assay. For 199 cases, NTRK RNA expression data were available from previous RNA sequencing analysis.\n\nAltogether, staining patterns for 617 NSCLC cases were evaluable. Of these, four cases (0.6 %) demonstrated a strong diffuse cytoplasmic and membranous staining, and seven cases a moderate staining (1.1 %). NanoString or TST170-analysis could not confirm an NTRK fusion in any of the IHC positive cases, or any of the cases with high mRNA levels. In the four cases with strong staining intensity in the tissue microarray, whole section staining revealed marked heterogeneity of NTRK protein expression.\n\nThe presence of NTRK fusion genes in non-small cell lung cancer is exceedingly rare. The use of the immunohistochemical NTRK assay will result in a small number of false positive cases. This should be considered when the assay is applied as a screening tool in clinical diagnostics.", "doi": "10.1016/j.lungcan.2020.11.023", "pmid": "33310622", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0169-5002(20)30697-8"}], "notes": [], "created": "2021-12-06T08:29:21.900Z", "modified": "2021-12-06T08:29:21.913Z"}, {"entity": "publication", "iuid": "28b02c11dee94c2dac39ef643d0f95e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28b02c11dee94c2dac39ef643d0f95e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28b02c11dee94c2dac39ef643d0f95e9"}}, "title": "Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.", "authors": [{"family": "Svedberg", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N"}, {"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Apell\u00e1niz-Ruiz", "given": "Mar\u00eda", "initials": "M"}, {"family": "Rodr\u00edguez-Antona", "given": "Cristina", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Lung Cancer", "issn": "1872-8332", "volume": "147", "issue": null, "pages": "106-114", "issn-l": "0169-5002"}, "abstract": "Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients.\n\nWhole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia.\n\nAssociation analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients.\n\nWe have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity.", "doi": "10.1016/j.lungcan.2020.07.005", "pmid": "32683206", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0169-5002(20)30516-X"}], "notes": [], "created": "2020-12-07T16:27:05.896Z", "modified": "2021-11-10T12:47:43.408Z"}, {"entity": "publication", "iuid": "b9b71a4c6139494dbeedba7da68e5c49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9b71a4c6139494dbeedba7da68e5c49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9b71a4c6139494dbeedba7da68e5c49"}}, "title": "Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11.", "authors": [{"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Falk-S\u00f6rqvist", "given": "Elin", "initials": "E"}, {"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Mattsson", "given": "Johanna Sm", "initials": "JS"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0002-4960-1232", "researcher": {"href": "https://publications.scilifelab.se/researcher/952a87a3216c44baa33286c842c10d22.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Moens", "given": "Lotte", "initials": "L"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "130", "issn": "1872-8332", "issue": null, "pages": "50-58", "title": "Lung Cancer", "issn-l": "0169-5002"}, "abstract": "Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.\n\nUsing targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.\n\nWe obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.\n\nHere we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.", "doi": "10.1016/j.lungcan.2019.01.003", "pmid": "30885352", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0169-5002(19)30005-4"}], "notes": [], "created": "2019-11-29T13:21:46.345Z", "modified": "2024-01-16T13:48:44.581Z"}, {"entity": "publication", "iuid": "2da1046f242b46f1b8d0c059c2531df1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2da1046f242b46f1b8d0c059c2531df1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2da1046f242b46f1b8d0c059c2531df1"}}, "title": "Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer.", "authors": [{"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Holgersson", "given": "Georg", "initials": "G"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "St\u00e5hle", "given": "Elisabeth", "initials": "E"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "125", "issn": "1872-8332", "issue": null, "pages": "157-163", "title": "Lung Cancer", "issn-l": "0169-5002"}, "abstract": "Cancer-testis antigens (CTAs) are defined as proteins that are specifically expressed in testis or placenta and their expression is frequently activated in cancer. Due to their ability to induce an immune response, CTAs may serve as suitable targets for immunotherapy. The aim of this study was to evaluate if there is reactivity against CTAs in the plasma of non-small cell lung cancer (NSCLC) patients through the detection of circulating antibodies.\n\nTo comprehensively analyze autoantibodies against CTAs the multiplexing capacities of suspension bead array technology was used. Bead arrays were created with 120 protein fragments, representing 112 CTAs. Reactivity profiles were measured in plasma samples from 133 NSCLC patients and 57 cases with benign lung diseases.\n\nAltogether reactivity against 69 antigens, representing 81 CTAs, was demonstrated in at least one of the analyzed samples. Twenty-nine of the antigens (45 CTAs) demonstrated exclusive reactivity in NSCLC samples. Reactivity against cancer-testis antigen family 47; member A (CT47A) genes, P antigen family member 3 (PAGE3), variable charge X-linked (VCX), melanoma antigen family B1 (MAGEB1), lin-28 homolog B (LIN28B) and chromosome 12 open reading frame 54 (C12orf54) were only found in NSCLC patients at a frequency of 1%-4%. The presence of autoantibodies towards these six antigens was confirmed in an independent group of 34 NSCLC patients.\n\nWe identified autoantibodies against CTAs in the plasma of lung cancer patients. The reactivity pattern of autoantibodies was higher in cancer patients compared to the benign group, stable over time, but low in frequency of occurrence. The findings suggest that some CTAs are immunogenic and that these properties can be utilized as immune targets.", "doi": "10.1016/j.lungcan.2018.09.012", "pmid": "30429015", "labels": {"Autoimmunity and Serology Profiling": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0169-5002(18)30571-3"}], "notes": [], "created": "2018-09-27T10:09:23.485Z", "modified": "2024-01-16T13:48:45.262Z"}, {"entity": "publication", "iuid": "6ee4530a265845b59c37b9824ea78d7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ee4530a265845b59c37b9824ea78d7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ee4530a265845b59c37b9824ea78d7f"}}, "title": "LMO7 and LIMCH1 interact with LRIG proteins in lung cancer, with prognostic implications for early-stage disease.", "authors": [{"family": "Karlsson", "given": "Terese", "initials": "T"}, {"family": "Kvarnbrink", "given": "Samuel", "initials": "S"}, {"family": "Holmlund", "given": "Camilla", "initials": "C"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Johansson", "given": "Mikael", "initials": "M"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2018-11-00", "journal": {"title": "Lung Cancer", "issn": "0169-5002", "volume": "125", "issue": null, "pages": "174-184", "issn-l": null}, "abstract": "The human leucine-rich repeats and immunoglobulin-like domains (LRIG) protein family comprises the integral membrane proteins LRIG1, LRIG2 and LRIG3. LRIG1 is frequently down-regulated in human cancer, and high levels of LRIG1 in tumor tissue are associated with favorable clinical outcomes in several tumor types including non-small cell lung cancer (NSCLC). Mechanistically, LRIG1 negatively regulates receptor tyrosine kinases and functions as a tumor suppressor. However, the details of the molecular mechanisms involved are poorly understood, and even less is known about the functions of LRIG2 and LRIG3. The aim of this study was to further elucidate the functions and molecular interactions of the LRIG proteins.\n\nA yeast two-hybrid screen was performed using a cytosolic LRIG3 peptide as bait. In transfected human cells, co-immunoprecipitation and co-localization experiments were performed. Proximity ligation assay was performed to investigate interactions between endogenously expressed proteins. Expression levels of LMO7 and LIMCH1 in normal and malignant lung tissue were investigated using qRT-PCR and through in silico analyses of public data sets. Finally, a clinical cohort comprising 355 surgically treated NSCLC cases was immunostained for LMO7.\n\nIn the yeast two-hybrid screen, the two paralogous proteins LMO7 and LIMCH1 were identified as interaction partners to LRIG3. LMO7 and LIMCH1 co-localized and co-immunoprecipitated with both LRIG1 and LRIG3. Endogenously expressed LMO7 was in close proximity of both LRIG1 and LRIG3. LMO7 and LIMCH1 were highly expressed in normal lung tissue and down-regulated in malignant lung tissue. LMO7 immunoreactivity was shown to be a negative prognostic factor in LRIG1 positive tumors, predicting poor patient survival.\n\nThese findings suggest that LMO7 and LIMCH1 physically interact with LRIG proteins and that expression of LMO7 is of clinical importance in NSCLC.", "doi": "10.1016/j.lungcan.2018.09.017", "pmid": "30429017", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0169-5002(18)30576-2"}], "notes": [], "created": "2019-12-20T07:50:19.867Z", "modified": "2019-12-20T07:50:19.883Z"}], "created": "2018-09-27T10:09:23.492Z", "modified": "2020-11-27T13:14:07.434Z"}