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  • 1
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-01-21)
    Kurzfassung: Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications.
    Materialart: Online-Ressource
    ISSN: 2041-1723
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2021
    ZDB Id: 2553671-0
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 2
    In: BMC Medicine, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2023-07-14)
    Kurzfassung: The feasibility of DNA methylation-based assays in detecting minimal residual disease (MRD) and postoperative monitoring remains unestablished. We aim to investigate the dynamic characteristics of cancer-related methylation signals and the feasibility of methylation-based MRD detection in surgical lung cancer patients. Methods Matched tumor, tumor-adjacent tissues, and longitudinal blood samples from a cohort (MEDAL) were analyzed by ultra-deep targeted sequencing and bisulfite sequencing. A tumor-informed methylation-based MRD (timMRD) was employed to evaluate the methylation status of each blood sample. Survival analysis was performed in the MEDAL cohort ( n  = 195) and validated in an independent cohort (DYNAMIC, n  = 36). Results Tumor-informed methylation status enabled an accurate recurrence risk assessment better than the tumor-naïve methylation approach. Baseline timMRD-scores were positively correlated with tumor burden, invasiveness, and the existence and abundance of somatic mutations. Patients with higher timMRD-scores at postoperative time-points demonstrated significantly shorter disease-free survival in the MEDAL cohort (HR: 3.08, 95% CI: 1.48–6.42; P  = 0.002) and the independent DYNAMIC cohort (HR: 2.80, 95% CI: 0.96–8.20; P  = 0.041). Multivariable regression analysis identified postoperative timMRD-score as an independent prognostic factor for lung cancer. Compared to tumor-informed somatic mutation status, timMRD-scores yielded better performance in identifying the relapsed patients during postoperative follow-up, including subgroups with lower tumor burden like stage I, and was more accurate among relapsed patients with baseline ctDNA-negative status. Comparing to the average lead time of ctDNA mutation, timMRD-score yielded a negative predictive value of 97.2% at 120 days prior to relapse. Conclusions The dynamic methylation-based analysis of peripheral blood provides a promising strategy for postoperative cancer surveillance. Trial registration This study (MEDAL, ME thylation based D ynamic A nalysis for L ung cancer) was registered on ClinicalTrials.gov on 08/05/2018 (NCT03634826). https://clinicaltrials.gov/ct2/show/NCT03634826 .
    Materialart: Online-Ressource
    ISSN: 1741-7015
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2023
    ZDB Id: 2131669-7
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 3
    In: European Journal of Cancer, Elsevier BV, Vol. 168 ( 2022-06), p. 1-11
    Materialart: Online-Ressource
    ISSN: 0959-8049
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    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2022
    ZDB Id: 1120460-6
    ZDB Id: 1468190-0
    ZDB Id: 82061-1
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 4
    In: Molecular Oncology, Wiley, Vol. 15, No. 12 ( 2021-12), p. 3679-3690
    Kurzfassung: Chondrosarcoma (CS) is a rare tumour type and the most common primary malignant bone cancer in adults. The prognosis, currently based on tumour grade, imaging and anatomical location, is not reliable, and more objective biomarkers are required. We aimed to determine whether the level of circulating tumour DNA (ctDNA) in the blood of CS patients could be used to predict outcome. In this multi‐institutional study, we recruited 145 patients with cartilaginous tumours, of which 41 were excluded. ctDNA levels were assessed in 83 of the remaining 104 patients, whose tumours harboured a hotspot mutation in IDH1 / 2 or GNAS . ctDNA was detected pre‐operatively in 31/83 (37%) and in 12/31 (39%) patients postoperatively. We found that detection of ctDNA was more accurate than pathology for identification of high‐grade tumours and was associated with a poor prognosis; ctDNA was never associated with CS grade 1/atypical cartilaginous tumours (ACT) in the long bones, in neoplasms sited in the small bones of the hands and feet or in tumours measuring less than 80 mm. Although the results are promising, they are based on a small number of patients, and therefore, introduction of this blood test into clinical practice as a complementary assay to current standard‐of‐care protocols would allow the assay to be assessed more stringently and developed for a more personalised approach for the treatment of patients with CS.
    Materialart: Online-Ressource
    ISSN: 1574-7891 , 1878-0261
    URL: Issue
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2021
    ZDB Id: 2322586-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 5
    Online-Ressource
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    Frontiers Media SA ; 2024
    In:  Frontiers in Genetics Vol. 15 ( 2024-5-8)
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 15 ( 2024-5-8)
    Materialart: Online-Ressource
    ISSN: 1664-8021
    Sprache: Unbekannt
    Verlag: Frontiers Media SA
    Publikationsdatum: 2024
    ZDB Id: 2606823-0
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 6
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2016-08-16)
    Kurzfassung: Oxaliplatin resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Herein, we show that miR-625-3p functionally induces oxaliplatin resistance in CRC cells, and identify the signalling networks affected by miR-625-3p . We show that the p38 MAPK activator MAP2K6 is a direct target of miR-625-3p , and, accordingly, is downregulated in non-responder patients of oxaliplatin therapy. miR-625-3p -mediated resistance is reversed by anti-miR-625-3p treatment and ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, reduction of p38 signalling by using siRNAs, chemical inhibitors or expression of a dominant-negative MAP2K6 protein induces resistance to oxaliplatin. Transcriptome, proteome and phosphoproteome profiles confirm inactivation of MAP2K6-p38 signalling as one likely mechanism of oxaliplatin resistance. Our study shows that miR-625-3p induces oxaliplatin resistance by abrogating MAP2K6-p38-regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p.
    Materialart: Online-Ressource
    ISSN: 2041-1723
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2016
    ZDB Id: 2553671-0
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 3617-3617
    Kurzfassung: Background: Chemotherapy resistance in metastatic colorectal cancer (mCRC) is a major challenge, and development of biomarkers for determining therapy efficacy is vital to ensure optimal palliative treatment. Recently, quantification of changes in circulating tumor DNA (ctDNA) levels has attracted substantial attention as a predictive marker. Here, we provide evidence that ctDNA has the potential to be used as an early marker of therapeutic efficacy of irinotecan and fluorouracil (FOLFIRI). Experimental Procedures: Patients diagnosed with mCRC, and with indication for first-line combination chemotherapy, were prospectively enrolled in this phase II study. Blood was drawn at baseline, day 7, 14, 21, 40 and then monthly until progression. Response evaluation was done at eight-week intervals by CT scanning using RECIST criteria. Chemotherapy was administered at day one and two every two weeks. The levels of cell-free DNA (cfDNA) and ctDNA were determined using sensitive digital droplet PCR assays. ctDNA assays were designed either to mutations identified by targeted sequencing or on basis of known tumor mutations detected in primary or metastatic lesions using a panel of mutation-specific qPCR based assays (KRAS, NRAS, BRAF). Results: Twenty-four patients were enrolled. A KRAS, NRAS or BRAF mutation was observed in tumor tissue of 16 patients. In 12 of these the mutations were confirmed in baseline samples and used for assessing ctDNA. For the remaining 12 patients, a mutation for ctDNA quantification was identified by targeted tumor sequencing. Patients with high baseline ctDNA levels (75th centile) had significantly shorter progression-free survival (PFS) than patients with low baseline ctDNA levels. After first treatment cycle all patients experienced a decline in ctDNA levels demonstrating initial response to treatment; however, the reduction in ctDNA was not associated with prolonged PFS or overall survival (OS). Conversely, change in ctDNA levels from first to second cycle of treatment (three weeks after treatment start) predicted FOLFIRI efficacy. Patients with increasing ctDNA levels at this time point had a significantly shorter PFS and a shorter OS than patients with stable or decreasing ctDNA levels. Conclusion: In agreement with the literature, we show that baseline tumor DNA levels predicted PFS. The initial observed decline in ctDNA levels upon administration of FOLFIRI indicates that all tumors had cancer cells sensitive to treatment; however, after elimination of these, resistant clones expanded, leading to treatment resistance. Importantly, our study demonstrates that FOLFIRI efficacy can be evaluated as early as three weeks after treatment initiation by measurement of ctDNA levels. This enables early detection of treatment failure and allows for rapid adaptation of the treatment strategy. Citation Format: Iben Lyskjær, Camilla J. Kronborg, Mads H. Rasmussen, Boe S. Sørensen, Mona Rosenkilde, Michael Knudsen, Søren R. Krag, Karen-Lise G. Spindler, Claus L. Andersen. Prediction of irinotecan and flurouracil efficacy in metastatic colorectal cancer by early measurement of circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3617.
    Materialart: Online-Ressource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2018
    ZDB Id: 2036785-5
    ZDB Id: 1432-1
    ZDB Id: 410466-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 8
    In: The Journal of Pathology, Wiley, Vol. 252, No. 2 ( 2020-10), p. 151-164
    Kurzfassung: Diagnosing MPNST can be challenging, but genetic alterations recently identified in polycomb repressive complex 2 (PRC2) core component genes, EED and SUZ12 , resulting in global loss of the histone 3 lysine 27 trimethylation (H3K27me3) epigenetic mark, represent drivers of malignancy and a valuable diagnostic tool. However, the reported loss of H3K27me3 expression ranges from 35% to 84%. We show that advances in molecular pathology now allow many MPNST mimics to be classified confidently. We confirm that MPNSTs harbouring mutations in PRC2 core components are associated with loss of H3K27me3 expression; whole‐genome doubling was detected in 68%, and SSTR2 was amplified in 32% of MPNSTs. We demonstrate that loss of H3K27me3 expression occurs overall in 38% of MPNSTs, but is lost in 76% of histologically classical cases, whereas loss was detected in only 23% cases with heterologous elements and 14% where the diagnosis could not be provided on morphology alone. H3K27me3 loss is rarely seen in other high‐grade sarcomas and was not found to be associated with an inferior outcome in MPNST. We show that DNA methylation profiling distinguishes MPNST from its histological mimics, was unrelated to anatomical site, and formed two main clusters, MeGroups 4 and 5. MeGroup 4 represents classical MPNSTs lacking H3K27me3 expression in the majority of cases, whereas MeGroup 5 comprises MPNSTs exhibiting non‐classical histology and expressing H3K27me3 and cluster with undifferentiated sarcomas. The two MeGroups are distinguished by differentially methylated PRC2‐associated genes, the majority of which are hypermethylated in the promoter regions in MeGroup 4, indicating that the PRC2 target genes are not expressed in these tumours. The methylation profiles of MPNSTs with retention of H3K27me3 in MeGroups 4 and 5 are independent of mutations in PRC2 core components and the driver(s) in these groups remain to be identified. Our results open new avenues of investigation. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
    Materialart: Online-Ressource
    ISSN: 0022-3417 , 1096-9896
    URL: Issue
    RVK:
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 1475280-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 9
    In: Genome Medicine, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2022-08-30)
    Kurzfassung: Central conventional chondrosarcoma (CS) is the most common subtype of primary malignant bone tumour in adults. Treatment options are usually limited to surgery, and prognosis is challenging. These tumours are characterised by the presence and absence of IDH1 and IDH2 mutations, and recently, TERT promoter alterations have been reported in around 20% of cases. The effect of these mutations on clinical outcome remains unclear. The purpose of this study was to determine if prognostic accuracy can be improved by the addition of genomic data, and specifically by examination of IDH1, IDH2 , and TERT mutations. Methods In this study, we combined both archival samples and data sourced from the Genomics England 100,000 Genomes Project ( n = 356). Mutations in IDH1 , IDH2 , and TERT were profiled using digital droplet PCR ( n = 346), whole genome sequencing ( n =68), or both ( n = 64). Complex events and other genetic features were also examined, along with methylation array data ( n = 84). We correlated clinical features and patient outcomes with our genetic findings. Results IDH2 -mutant tumours occur in older patients and commonly present with high-grade or dedifferentiated disease. Notably, TERT mutations occur most frequently in IDH2 -mutant tumours, although have no effect on survival in this group. In contrast, TERT mutations are rarer in IDH1 -mutant tumours, yet they are associated with a less favourable outcome in this group. We also found that methylation profiles distinguish IDH1- from IDH2 -mutant tumours. IDH wild-type tumours rarely exhibit TERT mutations and tend to be diagnosed in a younger population than those with tumours harbouring IDH1 and IDH2 mutations. A major genetic feature of this group is haploidisation and subsequent genome doubling. These tumours evolve less frequently to dedifferentiated disease and therefore constitute a lower risk group. Conclusions Tumours with IDH1 or IDH2 mutations or those that are IDHwt have significantly different genetic pathways and outcomes in relation to TERT mutation. Diagnostic testing for IDH1 , IDH2 , and TERT mutations could therefore help to guide clinical monitoring and prognostication.
    Materialart: Online-Ressource
    ISSN: 1756-994X
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2022
    ZDB Id: 2484394-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 10
    In: The Journal of Pathology, Wiley, Vol. 252, No. 4 ( 2020-12), p. 433-440
    Kurzfassung: The rare benign giant cell tumour of bone (GCTB) is defined by an almost unique mutation in the H3.3 family of histone genes H3‐3A or H3‐3B ; however, the same mutation is occasionally found in primary malignant bone tumours which share many features with the benign variant. Moreover, lung metastases can occur despite the absence of malignant histological features in either the primary or metastatic lesions. Herein we investigated the genetic events of 17 GCTBs including benign and malignant variants and the methylation profiles of 122 bone tumour samples including GCTBs. Benign GCTBs possessed few somatic alterations and no other known drivers besides the H3.3 mutation, whereas all malignant tumours harboured at least one additional driver mutation and exhibited genomic features resembling osteosarcomas, including high mutational burden, additional driver event(s), and a high degree of aneuploidy. The H3.3 mutation was found to predate the development of aneuploidy. In contrast to osteosarcomas, malignant H3.3‐mutated tumours were enriched for a variety of alterations involving TERT , other than amplification, suggesting telomere dysfunction in the transformation of benign to malignant GCTB. DNA sequencing of the benign metastasising GCTB revealed no additional driver alterations; polyclonal seeding in the lung was identified, implying that the metastatic lesions represent an embolic event. Unsupervised clustering of DNA methylation profiles revealed that malignant H3.3‐mutated tumours are distinct from their benign counterpart, and other bone tumours. Differential methylation analysis identified CCND1 , encoding cyclin D1, as a plausible cancer driver gene in these tumours because hypermethylation of the CCND1 promoter was specific for GCTBs. We report here the genomic and methylation patterns underlying the rare clinical phenomena of benign metastasising and malignant transformation of GCTB and show how the combination of genomic and epigenomic findings could potentially distinguish benign from malignant GCTBs, thereby predicting aggressive behaviour in challenging diagnostic cases. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
    Materialart: Online-Ressource
    ISSN: 0022-3417 , 1096-9896
    URL: Issue
    RVK:
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2020
    ZDB Id: 1475280-3
    Standort Signatur Einschränkungen Verfügbarkeit
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