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  • 1
    In: Cell, Elsevier BV, Vol. 185, No. 12 ( 2022-06), p. 2184-2199.e16
    Materialart: Online-Ressource
    ISSN: 0092-8674
    RVK:
    RVK:
    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2022
    ZDB Id: 187009-9
    ZDB Id: 2001951-8
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 2
    In: Nature, Springer Science and Business Media LLC, Vol. 576, No. 7785 ( 2019-12-05), p. 112-120
    Materialart: Online-Ressource
    ISSN: 0028-0836 , 1476-4687
    RVK:
    RVK:
    RVK:
    Sprache: Englisch
    Verlag: Springer Science and Business Media LLC
    Publikationsdatum: 2019
    ZDB Id: 120714-3
    ZDB Id: 1413423-8
    SSG: 11
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 3
    Online-Ressource
    Online-Ressource
    Public Library of Science (PLoS) ; 2015
    In:  PLOS Computational Biology Vol. 11, No. 5 ( 2015-5-21), p. e1004269-
    In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 11, No. 5 ( 2015-5-21), p. e1004269-
    Materialart: Online-Ressource
    ISSN: 1553-7358
    Sprache: Englisch
    Verlag: Public Library of Science (PLoS)
    Publikationsdatum: 2015
    ZDB Id: 2193340-6
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 4
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2016
    In:  Molecular Cancer Research Vol. 14, No. 4 ( 2016-04-01), p. 332-343
    In: Molecular Cancer Research, American Association for Cancer Research (AACR), Vol. 14, No. 4 ( 2016-04-01), p. 332-343
    Kurzfassung: Liposarcoma is the second most common form of sarcoma, which has been categorized into four molecular subtypes, which are associated with differential prognosis of patients. However, the transcriptional regulatory programs associated with distinct histologic and molecular subtypes of liposarcoma have not been investigated. This study uses integrative analyses to systematically define the transcriptional regulatory programs associated with liposarcoma. Likewise, computational methods are used to identify regulatory programs associated with different liposarcoma subtypes, as well as programs that are predictive of prognosis. Further analysis of curated gene sets was used to identify prognostic gene signatures. The integration of data from a variety of sources, including gene expression profiles, transcription factor–binding data from ChIP-Seq experiments, curated gene sets, and clinical information of patients, indicated discrete regulatory programs (e.g., controlled by E2F1 and E2F4), with significantly different regulatory activity in one or multiple subtypes of liposarcoma with respect to normal adipose tissue. These programs were also shown to be prognostic, wherein liposarcoma patients with higher E2F4 or E2F1 activity associated with unfavorable prognosis. A total of 259 gene sets were significantly associated with patient survival in liposarcoma, among which & gt;50% are involved in cell cycle and proliferation. Implications: These integrative analyses provide a general framework that can be applied to investigate the mechanism and predict prognosis of different cancer types. Mol Cancer Res; 14(4); 332–43. ©2016 AACR.
    Materialart: Online-Ressource
    ISSN: 1541-7786 , 1557-3125
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2016
    ZDB Id: 2097884-4
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 2548-2548
    Kurzfassung: Introduction: Deconstructive immune cell profiling of central nervous system (CNS) tumors has focused on the tumor, excluding interrogation of the tumor microenvironment (TME). Integrated spatial analysis can ascertain the cell interactome and may be a key biomarker for effective anti-tumor immune responses. Methods: En bloc resections of glioma (n=10) and lung metastasis (n=10) to preserve the tissue architecture, underwent tissue segmentation and high dimension opal 7-color multiplex imaging. Bioinformatic analysis of scRNA was used to infer immune cell functionality. Results: CD3+ T cell frequency was equivalent between CNS cancer lineages. Within gliomas T cells were confined to the perivascular space and the infiltrating edge. In lung metastasis, T cells are confined to the tumor stroma. CD163+ macrophages predominate in brain metastasis throughout the TME (p & lt;0.05), while CD68+ monocytes (CD68+, CD11c+CD68+, and CD11+CD68+CD163+) are more common in gliomas (p & lt;0.05). T cell dyad and cluster immune interactions were more common in the absence of nuclear STAT3 expression. T cells usually interact with CD163+ macrophages as dyads in metastasis at the brain interface (p=0.031) and within tumor (p=0.0009); in clusters throughout the TME (interface: p=0.024; tumor: p=0.01; necrosis: p=0.045), and as STAT3+ dyads and cluster interactions in the tumor (p & lt;0.05). Immune suppressed CD11c+CD163+ dendritic cells (tumor: p=0.036; and necrosis p=0.020) predominate in metastasis. In contrast, gliomas typically lacked dyad and cluster interactions except for T cell and CD68+ dyads in the tumor (p=0.023). Bioinformatic analysis of CD45+ scRNA seq data revealed that the majority of innate immune populations express both pro-inflammatory and immune suppressive genes and that subsets of CD68+ and CD11c+CD68+ cells expressed markers such as TMEM119, P2YR13 and CX3CR1 that identify microglia. Conclusion: Current therapies are targeted to cell populations and singular pathways. Immunosuppressive macrophages dominate within the TME and targeting this population may create an environment that favors T cell activation and effective immune responses. Furthermore, the immune interactome, an important event for anti-tumor immune response, is a function of cancer lineage, TME, and STAT3 expression, which will gain relevance for future therapeutics directed to modulating these interactions. Citation Format: Hinda Najem, Martina Ott, Cynthia Kassab, Arvind Rao, Ganesh Rao, Anantha Marisetty, Adam M. Sonabend, Craig Horbinski, Roel Verhaak, Anand Shakar, Santhoshi Krishnan, Frederick S. Varn, Victor A. Arietta, Pravesh Gupta, Sherise D. Ferguson, Jason Huse, Gregory N. Fuller, James Long, Dan Winskowski, Ben Freiberg, C. David James, Leonidas C. Platanias, Maciej S. Lesniak, Jared K. Burks, Amy B. Heimberger. The central nervous system immune cell interactome is a function of cancer lineage, tumor microenvironment and STAT3 expression [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 2548.
    Materialart: Online-Ressource
    ISSN: 1538-7445
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2022
    ZDB Id: 2036785-5
    ZDB Id: 1432-1
    ZDB Id: 410466-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 6
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 6 ( 2017-03-15), p. 1271-1282
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 6 ( 2017-03-15), p. 1271-1282
    Kurzfassung: With the recent advent of immunotherapy, there is a critical need to understand immune cell interactions in the tumor microenvironment in both pan-cancer and tissue-specific contexts. Multidimensional datasets have enabled systematic approaches to dissect these interactions in large numbers of patients, furthering our understanding of the patient immune response to solid tumors. Using an integrated approach, we inferred the infiltration levels of distinct immune cell subsets in 23 tumor types from The Cancer Genome Atlas. From these quantities, we constructed a coinfiltration network, revealing interactions between cytolytic cells and myeloid cells in the tumor microenvironment. By integrating patient mutation data, we found that while mutation burden was associated with immune infiltration differences between distinct tumor types, additional factors likely explained differences between tumors originating from the same tissue. We concluded this analysis by examining the prognostic value of individual immune cell subsets as well as how coinfiltration of functionally discordant cell types associated with patient survival. In multiple tumor types, we found that the protective effect of CD8+ T cell infiltration was heavily modulated by coinfiltration of macrophages and other myeloid cell types, suggesting the involvement of myeloid-derived suppressor cells in tumor development. Our findings illustrate complex interactions between different immune cell types in the tumor microenvironment and indicate these interactions play meaningful roles in patient survival. These results demonstrate the importance of personalized immune response profiles when studying the factors underlying tumor immunogenicity and immunotherapy response. Cancer Res; 77(6); 1271–82. ©2017 AACR.
    Materialart: Online-Ressource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2017
    ZDB Id: 2036785-5
    ZDB Id: 1432-1
    ZDB Id: 410466-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 7
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Epidemiology, Biomarkers & Prevention Vol. 27, No. 1 ( 2018-01-01), p. 86-95
    In: Cancer Epidemiology, Biomarkers & Prevention, American Association for Cancer Research (AACR), Vol. 27, No. 1 ( 2018-01-01), p. 86-95
    Kurzfassung: Background: Lung cancer is associated with the highest mortality rate of all cancer types, and the most common histologic subtype of lung cancer is adenocarcinoma. To apply more effective therapeutic treatment, molecular markers that are able to predict the recurrence risk of patients with adenocarcinoma are critically needed. Mutations in TP53 tumor suppressor gene have been found in approximately 50% of lung adenocarcinoma cases, but the presence of a TP53 mutation does not always associate with increased mortality. Methods: The Cancer Genome Atlas RNA sequencing data of lung adenocarcinoma were used to define a novel gene signature for P53 deficiency. This signature was then used to calculate a sample-specific P53 deficiency score based on a patient's transcriptomic profile and tested in four independent lung adenocarcinoma microarray datasets. Results: In all datasets, P53 deficiency score was a significant predictor for recurrence-free survival where high P53 deficiency score was associated with poor survival. The score was prognostic even after adjusting for several key clinical variables including age, tumor stage, smoking status, and P53 mutation status. Furthermore, the score was able to predict recurrence-free survival in patients with stage I adenocarcinoma and was also associated with smoking status. Conclusions: The P53 deficiency score was a better predictor of recurrence-free survival compared with P53 mutation status and provided additional prognostic values to established clinical factors. Impact: The P53 deficiency score can be used to stratify early-stage patients into subgroups based on their risk of recurrence for aiding physicians to decide personalized therapeutic treatment. Cancer Epidemiol Biomarkers Prev; 27(1); 86–95. ©2017 AACR.
    Materialart: Online-Ressource
    ISSN: 1055-9965 , 1538-7755
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2018
    ZDB Id: 2036781-8
    ZDB Id: 1153420-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 8
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2021
    In:  Cancer Research Vol. 81, No. 13_Supplement ( 2021-07-01), p. 2068-2068
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 2068-2068
    Kurzfassung: Diffuse gliomas are highly aggressive brain tumors that invariably relapse despite treatment with chemo- and radiotherapy. Treatment with alkylating chemotherapy can drive tumors to develop a hypermutator phenotype. In contrast, the genomic effects of radiation therapy (RT) remain unknown. We analyzed the mutational spectra following treatment with ionizing radiation in sequencing data from 190 paired primary-recurrent gliomas from the Glioma Longitudinal Analysis (GLASS) dataset and 2116 post-treatment metastatic tumors from the Hartwig Medical Foundation. We identified a significant increase in the burden of small deletions following radiation therapy that was independent of other factors and was significantly associated with the clinically applied RT-dosage in Gy (P = 1e-02, multivariable log-linear regression). These novel deletions demonstrated distinct characteristics when compared to pre-existing deletions present prior to RT-treatment and deletions in RT-untreated tumors. Radiation therapy-acquired deletions were characterized by a larger deletion size (GLASS and metastatic cohort, P = 1.2e-02 and P = 8e-11, respectively; Mann-Whitney U test), an increased distance to repetitive DNA elements (P & lt; 2.2e-16, Kolmogorov-Smirnov test) and a reduction in microhomology at breakpoints (P = 3.2e-02, paired Wilcoxon signed-rank test). These observations suggested that canonical non-homologous end joining (c-NHEJ) was the preferred pathway for DNA double strand break repair of RT-induced DNA damage. Furthermore, radiotherapy resulted in frequent chromosomal deletions and significantly increased frequencies of CDKN2A homozygous deletions. Finally, a high burden of RT-associated deletions was associated with worse clinical outcomes (GLASS and metastatic cohort, P & lt; 1e-04 and P = 2.6e-02, respectively; Wald test). Our results collectively suggest that effective repair of RT-induced DNA damage is detrimental to patient survival and that inhibiting c-NHEJ may be a viable strategy for improving the cancer-killing effect of radiotherapy. Taken together, the identified genomic scars as a result of radiation therapy reflect a more aggressive tumor with increased levels of resistance to follow up treatments. Citation Format: Emre Kocakavuk, Kevin J. Anderson, Kevin C. Johnson, Frederick S. Varn, Samirkumar B. Amin, Erik P. Sulman, Floris P. Barthel, Roel G. Verhaak. Radiotherapy is associated with a deletion signature that contributes to poor cancer patient outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2068.
    Materialart: Online-Ressource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2021
    ZDB Id: 2036785-5
    ZDB Id: 1432-1
    ZDB Id: 410466-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 9
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5786-5786
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5786-5786
    Kurzfassung: Gliomas are the most common malignant brain tumors and characterized by high recurrence rate and therapeutic resistance. Gliomas are clinically separated by mutations in isocitrate dehydrogenase (IDH) genes, but all subtypes have an altered energy metabolism. Mitochondria are essential cellular organelles that mediate many biological processes associated with tumorigenesis, such as energy metabolism and cell death, that can be impacted by mitochondrial mutations and copy number. As part of the Glioma Longitudinal AnalyiSiS consortium, we characterized mitochondrial genome evolution in response to treatment, using whole-genome sequencing data and associated RNA sequencing data from 152 paired tumor samples from 76 patients. Mitochondrial mutations are unequally distributed across the mitochondrial glioma genome, with only 4 of 13 mtDNA genes harboring a mutation across the cohort. Previous consortium analyses have investigated nuclear DNA hypermutation and changes in aneuploidy in response to chemotherapy and radiation treatment. Previous findings have identified hypermutation and copy number alterations as mechanisms of therapeutic resistance in glioma, but did not include analyses on mitochondrial DNA. Our analysis identified key differences between mitochondrial genome evolution and nuclear genome evolution. The mitochondrial mutational burden was not correlated with an increase in nuclear mutational burden. Unlike the nuclear DNA, we did not observe any samples with treatment-associated hypermutation. Mitochondrial copy number varied greatly but was increased at recurrence in IDH wild-type tumors. In tumors with a mutation in the IDH1 gene, mitochondrial copy number decreases were associated with an increase in aneuploidy score in samples that received radiation therapy. Expression analyses highlighted key differences in the active repair mechanisms between mtDNA and nuclear DNA. Our findings shed light on the variations in DNA repair mechanisms between the nucleus and the cytoplasm in glioma and lay the foundation for further analyses on the co-evolution of the mitochondrial and nuclear genomes in treatment-resistant tumors. Citation Format: Taylor E. Wade, Frederick S. Varn, Kevin C. Johnson, Roel G. Verhaak. Mitochondrial genome evolution in gliomas under therapy [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 5786.
    Materialart: Online-Ressource
    ISSN: 1538-7445
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2022
    ZDB Id: 2036785-5
    ZDB Id: 1432-1
    ZDB Id: 410466-3
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 10
    Online-Ressource
    Online-Ressource
    American Association for Cancer Research (AACR) ; 2021
    In:  Clinical Cancer Research Vol. 27, No. 8_Supplement ( 2021-04-15), p. PO-019-PO-019
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 27, No. 8_Supplement ( 2021-04-15), p. PO-019-PO-019
    Kurzfassung: Diffuse gliomas are highly aggressive brain tumors that invariably relapse despite treatment with chemo- and radiotherapy. Treatment with alkylating chemotherapy can drive tumors to develop a hypermutator phenotype. In contrast, the genomic effects of radiation therapy (RT) remain unknown. We analyzed the mutational spectra following treatment with ionizing radiation in sequencing data from 190 paired primary-recurrent gliomas from the Glioma Longitudinal Analysis (GLASS) dataset and 3693 post-treatment metastatic tumors from the Hartwig Medical Foundation (HMF). We identified a significant increase in the burden of small deletions following radiation therapy that was independent of other factors. These novel deletions demonstrated distinct characteristics when compared to pre-existing deletions present prior to RT-treatment and deletions in RT-untreated tumors. Radiation therapy-acquired deletions were characterized by a larger deletion size (GLASS and metastatic cohort, P=1.2e-02 and P=8e-11, respectively; Mann-Whitney U test), an increased distance to repetitive DNA elements (P & lt;2.2e-16, Kolmogorov-Smirnov test) and a reduction in microhomology at breakpoints (P=3.2e-02, paired Wilcoxon signed-rank test). These observations suggested that canonical non-homologous end joining (c-NHEJ) was the preferred pathway for DNA double strand break repair of RT-induced DNA damage. Furthermore, radiotherapy resulted in frequent chromosomal deletions and significantly increased frequencies of CDKN2A homozygous deletions. Finally, a high burden of RT-associated deletions was associated with worse clinical outcomes (GLASS and metastatic cohort, P & lt; 1e-04 and P = 2.6e-02, respectively; Wald test). Our results suggest that effective repair of RT-induced DNA damage is detrimental to patient survival and that inhibiting c-NHEJ may be a viable strategy for improving the cancer-killing effect of radiotherapy. Taken together, the identified genomic scars as a result of radiation therapy reflect a more aggressive tumor with increased levels of resistance to follow up treatments. Citation Format: Emre Kocakavuk, Kevin J. Anderson, Frederick S. Varn, Kevin C. Johnson, Samirkumar B. Amin, Erik. P. Sulman, Martijn Lolkema, Floris P. Barthel, Roel G.W. Verhaak. Radiotherapy in cancer is associated with a deletion signature that contributes to poor patient outcomes [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-019.
    Materialart: Online-Ressource
    ISSN: 1078-0432 , 1557-3265
    RVK:
    Sprache: Englisch
    Verlag: American Association for Cancer Research (AACR)
    Publikationsdatum: 2021
    ZDB Id: 1225457-5
    ZDB Id: 2036787-9
    Standort Signatur Einschränkungen Verfügbarkeit
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