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  • American Association for Cancer Research (AACR)  (5)
  • Kool, Marcel  (5)
  • 2020-2024  (5)
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  • American Association for Cancer Research (AACR)  (5)
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  • 2020-2024  (5)
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Subjects(RVK)
  • 1
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 11, No. 9 ( 2021-09-01), p. 2230-2247
    Abstract: Molecular groups of supratentorial ependymomas comprise tumors with ZFTA–RELA or YAP1-involving fusions and fusion-negative subependymoma. However, occasionally supratentorial ependymomas cannot be readily assigned to any of these groups due to lack of detection of a typical fusion and/or ambiguous DNA methylation–based classification. An unbiased approach with a cohort of unprecedented size revealed distinct methylation clusters composed of tumors with ependymal but also various other histologic features containing alternative translocations that shared ZFTA as a partner gene. Somatic overexpression of ZFTA-associated fusion genes in the developing cerebral cortex is capable of inducing tumor formation in vivo, and cross-species comparative analyses identified GLI2 as a key downstream regulator of tumorigenesis in all tumors. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating a potential therapeutic vulnerability in ZFTA fusion–positive tumors. Significance: ZFTA–RELA fusions are a hallmark feature of supratentorial ependymoma. We find that ZFTA acts as a partner for alternative transcriptional activators in oncogenic fusions of supratentorial tumors with various histologic characteristics. Establishing representative mouse models, we identify potential therapeutic targets shared by ZFTA fusion–positive tumors, such as GLI2. This article is highlighted in the In This Issue feature, p. 2113
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
    detail.hit.zdb_id: 2607892-2
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  • 2
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 28, No. 1 ( 2022-01-01), p. 116-128
    Abstract: International consensus and the 2021 WHO classification recognize eight molecular subgroups among non-WNT/non-SHH (Group 3/4) medulloblastoma, representing approximately 60% of tumors. However, very few clinical centers worldwide possess the technical capabilities to determine DNA methylation profiles or other molecular parameters of high risk for group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an IHC marker as a clinically tractable method for improved medulloblastoma risk stratification. Experimental Design: We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Results: TPD52 IHC positivity represented a significant independent predictor of early relapse and death for group 3/4 medulloblastoma [HRs between 3.67 and 26.7; 95% confidence interval (CI) between 1.00 and 706.23; P = 0.05, 0.017, and 0.0058]. Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing state-of-the-art risk stratification schemes, and reclassified approximately 50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity was a predictive indicator of poor response to chemotherapy [HR, 12.66; 95% CI, 3.53–45.40; P & lt; 0.0001], suggesting important implication for therapeutic choices. Conclusions: This study redefines the approach to risk stratification in group 3/4 medulloblastoma in global practice. Because integration of TPD52 IHC in classification algorithms significantly improved outcome prediction, this test could be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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    detail.hit.zdb_id: 2036787-9
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 14_Supplement ( 2020-07-15), p. B73-B73
    Abstract: In 2012, an international consensus paper reported that medulloblastoma comprises four molecular subgroups (WNT, SHH, Group 3, Group 4), each associated with distinct genomic features and clinical behavior. Independently, multiple recent reports have defined further intra-subgroup heterogeneity in the form of biologically and clinically relevant subtypes. However, owing to differences in patient cohorts and analytical methods, estimates of subtype number and definition have been inconsistent, especially within Group 3 and Group 4. Herein, we aimed to reconcile the definition of Group 3/Group 4 MB subtypes through the analysis of a series of 1,501 medulloblastomas with DNA methylation profiling data, including 852 with matched transcriptome data. Using multiple complementary bioinformatic approaches, we compared the concordance of subtype calls between published cohorts and analytical methods, including assessments of class definition confidence and reproducibility. While lowest-complexity solutions continued to support the original consensus subgroups of Group 3 and Group 4, our analysis most strongly supported a definition comprising eight robust Group 3/Group 4 subtypes (Types I-VIII). Subtype II was consistently identified across all component studies, while all others were supported by multiple class-definition methods. Regardless of analytical technique, increasing cohort size did not further increase the number of identified Group 3/Group 4 subtypes. Summarizing the molecular and clinicopathologic features of these eight subtypes indicated enrichment of specific driver gene alterations and cytogenetic events among subtypes and identified highly disparate survival outcomes, further supporting their biologic and clinical relevance. Collectively, this study provides continued support for consensus groups 3 and 4, while enabling robust derivation of, and categorical accounting for, the extensive intertumoral heterogeneity within Groups 3 and 4, revealed by recent high-resolution subclassification approaches. Further, these findings provide a basis for application of emerging methods (e.g., proteomics/single-cell approaches) that may additionally inform medulloblastoma subclassification. Outputs from this study will help shape definition of the next generation of medulloblastoma clinical protocols and facilitate the application of enhanced molecularly guided risk stratification to improve outcomes and quality of life for patients and their families. Citation Format: Tanvi Sharma, Edward C. Schwalbe, Daniel W. Williamson, Martin Sill, Volker Hovestadt, Martin Mynarek, Stefan Rutkowski, Giles W. Robinson, Amar Gajjar, Florence Cavalli, Vijay Ramaswamy, Michael D. Taylor, Janet C. Lindsey, Rebecca M. Hill, Natalie Jäger, Andrey Korshunov, Debbie Hicks, Simon Bailey, Marcel Kool, Lukas Chavez, Paul A. Northcott, Stefan M. Pfister, Steven C. Clifford. Second-generation molecular subgrouping of medulloblastoma: An international meta-analysis of Group 3 and Group 4 subtypes [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B73.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 2491-2491
    Abstract: Using DNA methylation profiling, already in 2016 we had identified novel molecularly defined CNS tumor entities, including CNS high grade neuroepithelial tumors with MN1 alteration (HGNET-MN1), which have in the recently updated WHO classification of CNS tumors been renamed into Astroblastoma, MN1 altered. However, little is still known about the molecular and clinical characteristics of these tumors. To further molecularly and clinically characterize this unique entity, we collected patient material, clinical information and molecular data from 176 Astroblastoma, MN1 altered tumors, which were all identified based on their characteristic DNA methylation pattern. T-SNE clustering analyses of the DNA methylation data together with our large database of almost 100,000 reference cases showed that this entity forms one main cluster defined by interchromosomal gene fusions of mainly MN1 and BEND2 and a smaller, distinct, but adjacent cluster that mainly showed tumors with MN1:CXXC5 fusions. Comparing molecular data of the BEND2- and CXXC5-fused groups we found that chromosomal copy numbers show distinct patterns, such as 16q loss in one third of cases from the BEND2-fused group, and a gain of chromosome 5 in one third of CXXC5-fused cases. Patients of the BEND2-fused group showed a strong enrichment of female patients (85%), whereas the CXXC5-fused group showed the contrary trend and consisted of 75% male patients. Original histological diagnoses of 110 BEND2-fused cases revealed that most tumors were diagnosed as an Astroblastoma (39%), followed by Ependymoma (20%) and PNET histologies (15%), which is in line with previous findings on Astroblasotma, MN1 altered cases. The CXXC5-fused subset, however, showed a distinct histological distribution and only 1 out of 13 cases (8%) had an Astroblastoma histology in the original report, whereas the other cases were diagnosed as PNET (38%), Ependymoma (23%), HGG (23%), or unknown (8%). Investigations of clinical data revealed that BEND2-fused cases (n=65) show a 5/10 year OS of 97% and 89% and a 5/10 year PFS of 48% and 35%, respectively, which is in line with previous studies in smaller series indicating a favorable overall but unfavorable progression-free survival. The smaller subset of CXXC5-fused patients (n=8) indicated a 5/10 year OS of 83% and a 5/10 year PFS of 60% each. First analyses of BEND2-fused cases indicate that an Astroblastoma histology might be associated with a favorable OS, however further analyses, including a central pathology review, are needed to validate this observation. Citation Format: Felix Schmitt-Hoffner, Johannes Gojo, Monika Mauermann, Katja von Hoff, Martin Sill, Andrey Korshunov, Damian Stichel, Felix Sahm, Natalie Jäger, Stefan Pfister, Marcel Kool. Molecular and clinical characterization of the new WHO entity ‘Astroblastoma, MN1 altered’ and its molecular subgroups [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2491.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 14_Supplement ( 2020-07-15), p. A39-A39
    Abstract: Introduction: Embryonal tumors with multilayered rosettes (ETMRs) are aggressive brain tumors that occur mainly in infants. Patients face a very poor prognosis with a median overall survival of ~12 months after diagnosis. The tumors harbor in ~90% of all cases amplification of a miRNA cluster on chromosome 19 (C19MC) that is thought to be the driver of the disease. However, current treatment options are lacking as (a) the mechanisms downstream of C19MC are poorly understood and (b) the drivers in cases lacking the C19MC aberration are unknown. To develop better treatment protocols for ETMR patients, more insight is needed in what is driving these tumors and how that can be targeted. Materials and Methods: To investigate the genomic and epigenomic landscape of ETMR in depth, we collected 193 ETMR samples and 23 matched relapses and performed DNA methylation profiling on all and DNA (whole genome, whole exome, and panel) sequencing and mRNA and miRNA transcriptome analysis on a subset of them. The BT183 ETMR cell line was used for drug treatments. Results: Among the 22 tumors without C19MC amplification, we identified 8 cases with truncating DICER1 germline mutations in one allele and somatic missense mutations in the RNASE III domain in the other allele. No DICER1 mutations were identified in C19MC amplified cases. In addition, structural variations (SVs) affecting C19MC were found in 3 other C19MC nonamplified cases and amplification of another miRNA cluster, miR-17-92, in 2 other cases. However, despite the presence of different genetic aberrations, based on DNA methylation and transcriptome profiling no molecular subgrouping was observed within our cohort. Whole-genome sequencing revealed an overall low recurrence and conservation of SNVs but strong conservation of SVs from primary tumors to relapses, especially surrounding C19MC. Moreover, many newly acquired SNVs in the relapses are associated to a new cisplatin treatment-related mutational signature. SVs detected in ETMRs significantly colocalized with R-loops, structures that form upon a collision of replication and transcription and are associated to increased levels of chromosomal instability, which is frequently observed in ETMRs. Using a DICER1 KO model, we found that global deregulation of miRNAs led to increased levels of R-loops and R-loop associated chromosomal instability. Finally, we show that a combination of topoisomerase and PARP inhibitors is highly synergistic and strongly increased the levels of both R-loops and DNA damage in ETMR cells and effectively killed the cells. Conclusions: Our results show that genomically instable ETMR cells are vulnerable to further increases in chromosomal instability, knowledge that may lead to new treatment strategies for ETMR patients and possibly other cancers with high levels of R-loops. Citation Format: Sander Lambo, Susanne Grübner, Tobias Rausch, Sebastian Waszak, Christin Schmidt, Sonja Krausert, Loreen Weichert, Aparna Gorthi, Carolina Romero, Annie Huang, Julia Schueler, Jan Korbel, Alexander Bishop, Stefan Pfister, Andrey Korshunov, Marcel Kool. Molecular characterization of ETMRs reveals role for R-loop mediated genomic instability and new treatment options [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A39.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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