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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 5107-5107
    Abstract: Background: The Aryl hydrocarbon receptor (AhR) is one of the most predominant regulators of cancer metabolism. The AhR exerts important immunosuppressive functions by activating Treg cells and myeloid-derived suppressor cells and repressing CD8+ effector T cells. Here, we propose that a best-in-class AhR inhibitor, DA-4505, improves anti-tumor efficacy via modulation of tumor immune surveillance compared to BAY2416964, an AHR antagonist drug candidate being studied in the clinical phase. Methods: To evaluate anti-tumor effects of DA-4505 and BAY2416964, the two AhR inhibitors were dosed at 10 mg/kg once daily alone or in combination with aPD-1 (10 mg/kg) in surgical and chemotherapy models, and a PDX model (YHIM2004). Tumor volume, relapse, and survival were evaluated, and immune profiles were analyzed with IHC, flow cytometry, and scRNAseq. Results: A significant tumor reduction appeared in the CT26 and 4T1 tumor models after the DA-4505 treatment compared to vehicle group (P & lt;0.05). In contrast, DA-4505 treatment did not induce significant tumor regression compared to vehicle group in tumor-bearing NOG mice, suggesting that anti-tumor effects of DA-4505 were driven by immunologic mechanisms. To evaluate the role of DA-4505 in conjunction with surgery, DA-4505 alone or in combination with anti-PD-1 was given prior to and following resection of the tumors in 4T1 tumor-bearing mice. Survival of mice treated with DA-4505 alone or DA-4505 combined with anti-PD-1 was significantly prolonged after resection compared to aPD-1 treatment group (P & lt;0.05). In addition, there were four mice that did not have a relapse by treating DA-4505 with or without aPD-1 after surgery (4/5). A tumor regression also appeared in the YHIM2004-engrafted humanized mouse study. A tumor reduction was shown by treating DA-4505 alone or in combination with pembrolizumab compared to vehicle group (P & lt;0.05). Next, we co-administered an AhR inhibitor and aPD-1 as a partner to improve the antitumor effects of chemotherapy. The DA-4505 add-on group showed tumor regression when compared with the combination therapy group treated with aPD-1 and chemotherapy (P & lt;0.0001). In addition, a significant increase in survival rate was shown in the group treated with a DA-4505 add-on compared to vehicle group (P & lt;0.001). Analysis of scRNAseq showed that M1 macrophage expressing CCL7 and CCL8 were increased in DA-4505 treated group compared to the vehicle and aPD-1 groups. This suggests that immune modulatory effect of DA-4505 may be due to enhanced recruitment of immune cells into the tumor site by macrophages with high chemotactic activity. Conclusion: The AhR inhibitor DA-4505 demonstrated an improvement in anti-tumor efficacy. In addition, it has shown a synergistic effect when combined with aPD-1. Discoveries from this study provide a preclinical rationale for future clinical implications in solid tumor. Citation Format: DongKwon Kim, Sujeong Baek, Seung Min Yang, Yu Jin Han, Seong-san Kang, Chun-Bong Synn, Mi Hyun Kim, Heekyung Han, Kwangmin Na, Young Taek Kim, Sungwoo Lee, Taedong Han, Hyounmie Doh, Jongho Cho, Dajeong Kim, Daewon Cha, Jae Hwan Kim, Youngseon Byeon, Young Seob Kim, Mi Ran Yun, Ji Yun Lee, Jii Bum Lee, Chang Gon Kim, Min Hee Hong, Sun Min Lim, Byoung Chul Cho, Kyoung-Ho Pyo. A novel AhR inhibitor ‘DA-4505’ improved the anti-cancer efficacy of surgical and chemotherapy via synergistic anti-tumor effects of aPD-1. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5107.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 2
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 4, No. 1 ( 2021-11-05)
    Abstract: There is currently a dearth of accessible whole genome sequencing (WGS) data for individuals residing in the Americas with Sub-Saharan African ancestry. We generated whole genome sequencing data at intermediate (15×) coverage for 2,294 individuals with large amounts of Sub-Saharan African ancestry, predominantly Atlantic African admixed with varying amounts of European and American ancestry. We performed extensive comparisons of variant callers, phasing algorithms, and variant filtration on these data to construct a high quality imputation panel containing data from 2,269 unrelated individuals. With the exception of the TOPMed imputation server (which notably cannot be downloaded), our panel substantially outperformed other available panels when imputing African American individuals. The raw sequencing data, variant calls and imputation panel for this cohort are all freely available via dbGaP and should prove an invaluable resource for further study of admixed African genetics.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2919698-X
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  • 3
    In: Nature Biotechnology, Springer Science and Business Media LLC
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Centre pour la Communication Scientifique Directe (CCSD) ; 2013
    In:  Discrete Mathematics & Theoretical Computer Science Vol. DMTCS Proceedings vol. AS,..., No. Proceedings ( 2013-01-01)
    In: Discrete Mathematics & Theoretical Computer Science, Centre pour la Communication Scientifique Directe (CCSD), Vol. DMTCS Proceedings vol. AS,..., No. Proceedings ( 2013-01-01)
    Abstract: We study the $\textit{diagrams}$ of affine permutations and their $\textit{balanced}$ labellings. As in the finite case, which was investigated by Fomin, Greene, Reiner, and Shimozono, the balanced labellings give a natural encoding of reduced decompositions of affine permutations. In fact, we show that the sum of weight monomials of the $\textit{column strict}$ balanced labellings is the affine Stanley symmetric function defined by Lam and we give a simple algorithm to recover reduced words from balanced labellings. Applying this theory, we give a necessary and sufficient condition for a diagram to be an affine permutation diagram. Finally, we conjecture that if two affine permutations are $\textit{diagram equivalent}$ then their affine Stanley symmetric functions coincide.
    Type of Medium: Online Resource
    ISSN: 1365-8050
    Language: English
    Publisher: Centre pour la Communication Scientifique Directe (CCSD)
    Publication Date: 2013
    detail.hit.zdb_id: 1412155-4
    SSG: 17,1
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  • 5
    Online Resource
    Online Resource
    Society for Industrial & Applied Mathematics (SIAM) ; 2013
    In:  SIAM Journal on Discrete Mathematics Vol. 27, No. 2 ( 2013-01), p. 1106-1111
    In: SIAM Journal on Discrete Mathematics, Society for Industrial & Applied Mathematics (SIAM), Vol. 27, No. 2 ( 2013-01), p. 1106-1111
    Type of Medium: Online Resource
    ISSN: 0895-4801 , 1095-7146
    RVK:
    Language: English
    Publisher: Society for Industrial & Applied Mathematics (SIAM)
    Publication Date: 2013
    detail.hit.zdb_id: 1468404-4
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  • 6
    Online Resource
    Online Resource
    Korean Neurocritical Care Society ; 2018
    In:  Journal of Neurocritical Care Vol. 11, No. 2 ( 2018-08-31), p. 124-128
    In: Journal of Neurocritical Care, Korean Neurocritical Care Society, Vol. 11, No. 2 ( 2018-08-31), p. 124-128
    Type of Medium: Online Resource
    ISSN: 2508-1349
    Language: English
    Publisher: Korean Neurocritical Care Society
    Publication Date: 2018
    detail.hit.zdb_id: 3001572-8
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  • 7
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Bioinformatics Vol. 36, No. 24 ( 2021-04-05), p. 5582-5589
    In: Bioinformatics, Oxford University Press (OUP), Vol. 36, No. 24 ( 2021-04-05), p. 5582-5589
    Abstract: Population-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready cohort-level variants remains challenging. Results We introduce an open-source cohort-calling method that uses the highly accurate caller DeepVariant and scalable merging tool GLnexus. Using callset quality metrics based on variant recall and precision in benchmark samples and Mendelian consistency in father-mother-child trios, we optimize the method across a range of cohort sizes, sequencing methods and sequencing depths. The resulting callsets show consistent quality improvements over those generated using existing best practices with reduced cost. We further evaluate our pipeline in the deeply sequenced 1000 Genomes Project (1KGP) samples and show superior callset quality metrics and imputation reference panel performance compared to an independently generated GATK Best Practices pipeline. Availability and implementation We publicly release the 1KGP individual-level variant calls and cohort callset (https://console.cloud.google.com/storage/browser/brain-genomics-public/research/cohort/1KGP) to foster additional development and evaluation of cohort merging methods as well as broad studies of genetic variation. Both DeepVariant (https://github.com/google/deepvariant) and GLnexus (https://github.com/dnanexus-rnd/GLnexus) are open-source, and the optimized GLnexus setup discovered in this study is also integrated into GLnexus public releases v1.2.2 and later. Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2023
    In:  BMC Bioinformatics Vol. 24, No. 1 ( 2023-05-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 24, No. 1 ( 2023-05-12)
    Abstract: Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of variant calling, and are often limited to filtering which trades recall for precision. In this study, we develop population-aware DeepVariant models with a new channel encoding allele frequencies from the 1000 Genomes Project. This model reduces variant calling errors, improving both precision and recall in single samples, and reduces rare homozygous and pathogenic clinvar calls cohort-wide. We assess the use of population-specific or diverse reference panels, finding the greatest accuracy with diverse panels, suggesting that large, diverse panels are preferable to individual populations, even when the population matches sample ancestry. Finally, we show that this benefit generalizes to samples with different ancestry from the training data even when the ancestry is also excluded from the reference panel.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 9
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-01-11)
    Abstract: Genome-wide association studies (GWASs) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank ( n = 370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average).
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
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  • 10
    Online Resource
    Online Resource
    Institute of East and West Studies ; 2020
    In:  East and West Studies Vol. 32, No. 3 ( 2020-09-30), p. 159-184
    In: East and West Studies, Institute of East and West Studies, Vol. 32, No. 3 ( 2020-09-30), p. 159-184
    Type of Medium: Online Resource
    ISSN: 1225-8814
    URL: Issue
    Language: Unknown
    Publisher: Institute of East and West Studies
    Publication Date: 2020
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