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  • 1
    In: Studies on Ethno-Medicine, Kamla Raj Enterprises, Vol. 11, No. 4 ( 2017-10-02), p. 297-301
    Type of Medium: Online Resource
    ISSN: 0973-5070
    Language: English
    Publisher: Kamla Raj Enterprises
    Publication Date: 2017
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  • 2
    Online Resource
    Online Resource
    Diva Enterprises Private Limited ; 2023
    In:  Indian Journal of Small Ruminants (The) Vol. 29, No. 2 ( 2023), p. 273-278
    In: Indian Journal of Small Ruminants (The), Diva Enterprises Private Limited, Vol. 29, No. 2 ( 2023), p. 273-278
    Type of Medium: Online Resource
    ISSN: 0971-9857 , 0973-9718
    Language: English
    Publisher: Diva Enterprises Private Limited
    Publication Date: 2023
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  • 3
    In: Cancer Cell, Elsevier BV, Vol. 42, No. 3 ( 2024-03), p. 413-428.e7
    Type of Medium: Online Resource
    ISSN: 1535-6108
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
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    SSG: 12
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  • 4
    In: American Journal of Respiratory and Critical Care Medicine, American Thoracic Society, Vol. 206, No. 12 ( 2022-12-15), p. 1480-1494
    Type of Medium: Online Resource
    ISSN: 1073-449X , 1535-4970
    RVK:
    Language: English
    Publisher: American Thoracic Society
    Publication Date: 2022
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  • 5
    In: Cancer Cell, Elsevier BV, Vol. 41, No. 1 ( 2023-01), p. 88-105.e8
    Type of Medium: Online Resource
    ISSN: 1535-6108
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
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    SSG: 12
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  • 6
    In: Science Advances, American Association for the Advancement of Science (AAAS), Vol. 7, No. 5 ( 2021-01-29)
    Abstract: Comprehensive genomic analyses of small cell lung cancer (SCLC) have revealed frequent mutually exclusive genomic amplification of MYC family members. Hence, it has been long suggested that they are functionally equivalent; however, more recently, their expression has been associated with specific neuroendocrine markers and distinct histopathology. Here, we explored a previously undescribed role of L-Myc and c-Myc as lineage-determining factors contributing to SCLC molecular subtypes and histology. Integrated transcriptomic and epigenomic analyses showed that L-Myc and c-Myc impart neuronal and non-neuroendocrine–associated transcriptional programs, respectively, both associated with distinct SCLC lineage. Genetic replacement of c-Myc with L-Myc in c-Myc–SCLC induced a neuronal state but was insufficient to induce ASCL1-SCLC. In contrast, c-Myc induced transition from ASCL1-SCLC to NEUROD1–SCLC characterized by distinct large-cell neuroendocrine carcinoma–like histopathology. Collectively, we characterize a role of historically defined general oncogenes, c-Myc and L-Myc, for regulating lineage plasticity across molecular and histological subtypes.
    Type of Medium: Online Resource
    ISSN: 2375-2548
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5709-5709
    Abstract: Introduction: The current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors, SCLC-A (ASCL1), SCLC-N (NEUROD1), SCLC-P (POU2F3), and SCLC-Y (YAP1) still leaves its major subtype SCLC-A as a large heterogeneous group, necessitating more precise characterization of lineage subclasses. Experimental procedure: To refine the current SCLC classification and to identify specific lineage features of the SCLC subtypes, we performed unsupervised hierarchical clustering of H3K27ac profiles on transcriptional regulators from 25 SCLC cell lines and determined the epigenomic features for each cluster. Functional significance of the transcriptional lineage regulators for the identified cluster was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. The specific cistromic profiles by ChIP-seq and its functional transcriptional partners using co-immunoprecipitation followed by mass spectrometry were determined to reveal their functional output in the identified subtype. Rb1fl/flTrp53fl/fl and Rb1fl/flTrp53fl/flNkx2-1fl/fl genetic engineered mouse model were generated to explore the function of Nkx2-1 in tumor initiation and differentiation. H3K27ac profiles were further analyzed to reveal 6 human SCLC specimen and 20 mice tumors epigenomic landscapes. Summary: We identified previously uncharacterized epigenomic sub-clusters of the major SCLC-A subtype, named SCLC-A1 and SCLC-A2. SCLC-A1 was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-A1, where it maintains neural lineage rather than pulmonary epithelial identity. We further found maintenance of this neural identity in SCLC-A1 is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1. ? Conclusions: We comprehensively describe an additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-A1 subtype by the core regulatory circuitry representing NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain a neuronal linage state. Citation Format: ranran kong, Ayushi S. Patel, Takashi Sato, Seungyeul Yoo, Abhilasha Sinha, Yang Tian, Feng Jiang, Charles A. Powell, Eric Snyder, Jiantao Jiang, Shaomin Li, Hideo Watanabe. Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer [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 5709.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 12_Supplement ( 2022-06-15), p. 1696-1696
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 1696-1696
    Abstract: Tumor evolution is dictated by the genetic, epigenetic and transcriptional landscape of the ‘cell-of-origin’ or the tumor initiating cell. While the genomic landscape of cancers has been extensively profiled, efforts to identify the cell-of-origin in individual tumors have been largely restricted to cell type specific activation of oncogenes in genetically engineered mouse models and correlative studies on gene expression patterns between normal tissue and tumor. Prior work from our lab has shown that highly expressed genes within a cell exhibit an overall increase in mutation rates as a consequence of transcription-coupled damage (TCD) which overwhelms transcription-coupled repair (TCR) relative to genes with low or medium level expressions. We therefore hypothesized that tumor cells retain a TCD-mutational signature representative of their cell-of-origin, enabling us to identify the cell-of-origin from the mutational landscape of human tumors.To test this hypothesis, we explored tumors originating from the lung which comprise comprise of distinct histological subtypes: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) that is further categorized into lung adenocarcinoma (LUAD), squamous cell lung cancer (LUSC) and large cell carcinoma (LCC). To identify lung epithelial cell type signatures, we first analyzed a publicly available single cell transcriptomic atlas of the normal human lung of 9,407 cells. For each of the 14 epithelial cell types defined in the lung atlas, we curated a gene signature of its respective unique and highly expressed genes. We next studied the somatic genetic variants in a dataset of 488 samples, which consisted of 230 LUAD tumors and 178 LUSC tumors from TCGA as well as 80 SCLC tumors from a previously published dataset. For each of the 488 tumors, we generated TCD-scores as a function of mutation frequency for each cell-type specific gene signature.Unsupervised hierarchical clustering on the 14 TCD-scores corresponding to the 14 epithelial cell types for each tumor, revealed heterogeneous patterns of cell-type specific mutational signatures. More specifically, LUAD samples were heterogeneously enriched for high AT2-specific, club-specific, ciliated-specific TCD-scores, while LUSC tumors were enriched for basal-specific and ciliated-specific TCD-scores. Together these data suggest that a tumor’s mutational profile can serve as a metric for the identification of the cell-of-origin. Further work will test the extension in different cancer types in other organs or a pan-cancer analysis. The identification of cell-of-origin for cancer subtypes would enable a better understanding of the tumor biology, and ultimately may lead to preventive therapies for individuals at high risk of developing cancer. Citation Format: Ayushi S. Patel, Itai Yanai. Cell-type specific mutational signatures as a proxy for cell-of-origin identification in lung cancer histological subtypes [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 1696.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2020
    In:  Cancer Research Vol. 80, No. 16_Supplement ( 2020-08-15), p. 1295-1295
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 1295-1295
    Abstract: Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer with a dismal prognosis. The standard-of-care remains to be uniform treatment with chemotherapy and radiotherapy, while emerging evidence suggests its molecular heterogeneity that has been previously under-appreciated. In primary SCLC, the gene loci for Myc family members are amplified mutually exclusively, their expression is correlated with unique neuroendocrine markers and distinct histopathology of xenografts from SCLC cell lines and murine SCLC. In this study, we use integrative genomic and epigenomic analyses to explore a novel role for c-Myc and L-Myc as lineage determining factors to bridge the gap between SCLC molecular subtypes and histological classification. First, we built a novel network using the Bayesian estimation from combined mRNA expression profile datasets for a total of 135 primary SCLC tumors. This revealed distinct transcriptional networks for c-Myc and L-Myc; wherein L-Myc was enriched for neuronal pathways and c-Myc for Notch signaling and epithelial-to-mesenchymal transition. The assay for transposase accessible-chromatin profiling of 3 representative cell lines for each c-Myc and L-Myc, revealed enrichment of biological processes involved in neuronal development for L-Myc expressing cell lines and active Notch signaling in c-Myc expressing cell lines. Together, these analyses implied that c-Myc and L-Myc govern distinct transcriptional programs to impart respective transcriptional networks associated with features unique to SCLC molecular subtypes. Next, we genetically engineered c-Myc amplified SCLC to exchange c-Myc with L-Myc and found L-Myc regulates neuronal associated pathways but was insufficient to induce lineage switch, however; c-Myc was required for the maintenance of NeuroD1-driven lineage state. In contrast, exogenous expression of c-Myc in classical-ASCL1-positive SCLC revealed incompatibility of c-Myc expression in this subtype, and led to suppression of neuronal associated pathways, trans-differentiation to NeuroD1-SCLC accompanied by variant histopathological features. Pharmacological inhibition of neuroendocrine-low associated Notch signaling and its target RE-1 silencing transcription factor (REST), revealed c-Myc-induced suppression of ASCL1 is not mediated by Notch signaling but rather by direct activation of REST expression. Collectively, our findings reveal a previously undescribed role for historically defined general oncogenes, c-Myc and L-Myc, in regulating lineage plasticity across SCLC molecular subtypes as well as histological classes. Citation Format: Ayushi S. Patel, Seungyeul Yoo, Ranran Kong, Takashi Sato, Maya Fridrikh, German Nudelman, Charles A. Powell, Jun Zhu, Hideo Watanabe. Myc family members differentially regulate lineage plasticity in small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1295.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 10
    In: Cancers, MDPI AG, Vol. 14, No. 3 ( 2022-01-29), p. 708-
    Abstract: Lung cancer is the most common cause of cancer-related deaths in both men and women, accounting for one-quarter of total cancer-related mortality globally. Lung adenocarcinoma is the major subtype of non-small cell lung cancer (NSCLC) and accounts for around 40% of lung cancer cases. Lung adenocarcinoma is a highly heterogeneous disease and patients often display variable histopathological morphology, genetic alterations, and genomic aberrations. Recent advances in transcriptomic and genetic profiling of lung adenocarcinoma by investigators, including our group, has provided better stratification of this heterogeneous disease, which can facilitate devising better treatment strategies suitable for targeted patient cohorts. In a recent study we have shown gene expression profiling identified novel clustering of early stage LUAD patients and correlated with tumor invasiveness and patient survival. In this study, we focused on copy number alterations in LUAD patients. SNP array data identified amplification at chromosome 12q15 on MDM2 locus and protein overexpression in a subclass of LUAD patients with an invasive subtype of the disease. High copy number amplification and protein expression in this subclass correlated with poor overall survival. We hypothesized that MDM2 copy number and overexpression predict response to MDM2-targeted therapy. In vitro functional data on a panel of LUAD cells showed that MDM2-targeted therapy effectively suppresses cell proliferation, migration, and invasion in cells with MDM2 amplification/overexpression but not in cells without MDM2 amplification, independent of p53 status. To determine the key signaling mechanisms, we used RNA sequencing (RNA seq) to examine the response to therapy in MDM2-amplified/overexpressing p53 mutant and wild-type LUAD cells. RNA seq data shows that in MDM2-amplified/overexpression with p53 wild-type condition, the E2F → PEG10 → MMPs pathway is operative, while in p53 mutant genetic background, MDM2-targeted therapy abrogates tumor progression in LUAD cells by suppressing epithelial to mesenchymal transition (EMT) signaling. Our study provides a potentially clinically relevant strategy of selecting LUAD patients for MDM2-targeted therapy that may provide for increased response rates and, thus, better survival.
    Type of Medium: Online Resource
    ISSN: 2072-6694
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2527080-1
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