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  • 1
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2023
    In:  Microscopy and Microanalysis Vol. 29, No. Supplement_1 ( 2023-07-22), p. 2099-2099
    In: Microscopy and Microanalysis, Oxford University Press (OUP), Vol. 29, No. Supplement_1 ( 2023-07-22), p. 2099-2099
    Type of Medium: Online Resource
    ISSN: 1431-9276 , 1435-8115
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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    SSG: 11
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  • 2
    In: Journal of Visualized Experiments, MyJove Corporation, , No. 147 ( 2019-05-21)
    Type of Medium: Online Resource
    ISSN: 1940-087X
    Language: English
    Publisher: MyJove Corporation
    Publication Date: 2019
    detail.hit.zdb_id: 2259946-0
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  • 3
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2019
    In:  BMC Bioinformatics Vol. 20, No. 1 ( 2019-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2019-12)
    Abstract: In biological experiments, comprehensive experimental metadata tracking – which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies – remains a challenge, especially when the experiment involves multiple laboratory scientists who execute different steps of the protocol. Here we describe Annot, a novel web application designed to provide a flexible solution for this task. Results Annot enforces the use of controlled vocabulary for sample and reagent annotation while enabling robust investigation, study, and protocol tracking. The cornerstone of Annot’s implementation is a json syntax-compatible file format, which can capture detailed metadata for all aspects of complex biological experiments. Data stored in this json file format can easily be ported into spreadsheet or data frame files that can be loaded into R ( https://www.r-project.org/ ) or Pandas, Python’s data analysis library ( https://pandas.pydata.org/ ). Annot is implemented in Python3 and utilizes the Django web framework, Postgresql, Nginx, and Debian. It is deployed via Docker and supports all major browsers. Conclusions Annot offers a robust solution to annotate samples, reagents, and experimental protocols for established assays where multiple laboratory scientists are involved. Further, it provides a framework to store and retrieve metadata for data analysis and integration, and therefore ensures that data generated in different experiments can be integrated and jointly analyzed. This type of solution to metadata tracking can enhance the utility of large-scale datasets, which we demonstrate here with a large-scale microenvironment microarray study.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2041484-5
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  • 4
    In: Human Molecular Genetics, Oxford University Press (OUP), Vol. 32, No. 9 ( 2023-04-20), p. 1483-1496
    Abstract: Astrocytes and brain endothelial cells are components of the neurovascular unit that comprises the blood–brain barrier (BBB) and their dysfunction contributes to pathogenesis in Huntington’s disease (HD). Defining the contribution of these cells to disease can inform cell-type-specific effects and uncover new disease-modifying therapeutic targets. These cells express integrin (ITG) adhesion receptors that anchor the cells to the extracellular matrix (ECM) to maintain the integrity of the BBB. We used HD patient-derived induced pluripotent stem cell (iPSC) modeling to study the ECM–ITG interface in astrocytes and brain microvascular endothelial cells and found ECM–ITG dysregulation in human iPSC-derived cells that may contribute to the dysfunction of the BBB in HD. This disruption has functional consequences since reducing ITG expression in glia in an HD Drosophila model suppressed disease-associated CNS dysfunction. Since ITGs can be targeted therapeutically and manipulating ITG signaling prevents neurodegeneration in other diseases, defining the role of ITGs in HD may provide a novel strategy of intervention to slow CNS pathophysiology to treat HD.
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 5
    In: Diabetes, American Diabetes Association, Vol. 64, No. 5 ( 2015-05-01), p. 1632-1642
    Abstract: Metformin treatment is associated with a decreased risk and better prognosis of pancreatic cancer (PC) in patients with type 2 diabetes, but the mechanism of metformin’s PC growth inhibition in the context of a prediabetic state is unknown. We used a Panc02 pancreatic tumor cell transplant model in diet-induced obese (DIO) C57BL/6 mice to compare the effects of metformin and the direct mammalian target of rapamycin (mTOR) inhibitor rapamycin on PC growth, glucose regulation, mTOR pathway signaling, and candidate microRNA (miR) expression. In DIO/prediabetic mice, metformin and rapamycin significantly reduced pancreatic tumor growth and mTOR-related signaling. The rapamycin effects centered on decreased mTOR-regulated growth and survival signaling, including increased expression of let-7b and cell cycle–regulating miRs. Metformin (but not rapamycin) reduced glucose and insulin levels and expression of miR-34a and its direct targets Notch, Slug, and Snail. Metformin also reduced the number and size of Panc02 tumor spheres in vitro and inhibited the expression of Notch in spheroids. Our results suggest that metformin and rapamycin can both inhibit pancreatic tumor growth in obese, prediabetic mice through shared and distinct mechanisms. Metformin and direct mTOR inhibitors, alone or possibly in combination, represent promising intervention strategies for breaking the diabetes-PC link.
    Type of Medium: Online Resource
    ISSN: 0012-1797 , 1939-327X
    Language: English
    Publisher: American Diabetes Association
    Publication Date: 2015
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  • 6
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 7 ( 2016-7-19), p. e0159686-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2016
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  • 7
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2016
    In:  Molecular Cancer Research Vol. 14, No. 1_Supplement ( 2016-01-01), p. B68-B68
    In: Molecular Cancer Research, American Association for Cancer Research (AACR), Vol. 14, No. 1_Supplement ( 2016-01-01), p. B68-B68
    Abstract: MicroRNA (miRNAs) are small, post-transcriptional regulators that play an integral role in maintenance of cellular functions and whose dysregulation has been shown to promote many types of cancer, including breast cancer. Global downregulation of miRNAs has emerged as a common theme in human breast tumors and has been shown to contribute to oncogenesis. One of the primary mechanisms through which miRNAs are globally dysregulated is downregulation of enzymes involved in miRNA biogenesis. We aim to establish how calorie restriction (CR), which potently inhibits breast cancer progression, regulates global miRNA expression and the expression of miRNA biogenesis enzymes in mammary tumors. To address these questions, 100 female Sprague Dawley rats were administered either dimethylbenz(a)anthracene (DMBA) or vehicle control at 50 days of age, then randomized to receive either control (AIN-76A) diet ad-libitum (n=40) or a 30% CR diet regiment (n=60). Resultant mammary tumors were allowed to develop for 12 weeks. Calorie restriction significantly increased survival to study endpoint relative to control diet (75% vs 35%, respectively) (p=0.0047). Furthermore, of the animals that developed tumors, CR significantly decreased median tumor area by 56% compared to control diet (109.4 mm2 vs 250.9 mm2, respectively) (p=0.0286). Global miRNA expression was analyzed by miRNA-specific sequencing. Calorie restriction had a broad effect on miRNA expression, illustrated by the fact that of all the miRNAs with a greater than two-fold expression difference between CR and control, 80% are overexpressed in CR tumors compared to control tumors. These results can be explained by the additional finding that CR was able to prevent the loss of Dicer expression, a key miRNA biogenesis enzyme, observed in control-fed mammary tumor tissue compared to normal tissue. This important finding suggests that global miRNA normalization through the retention of Dicer expression during cancer progression could be a contributing mechanism to CR's anticancer effects. We are further investigating these findings by exogenously overexpressing Dicer in Rama25 cells (derived from a DMBA-induced mammary tumor in a Sprague Dawley rat) and MCF7 cells, and analyzing the resultant tumorigenic potential in vitro and in vivo. The results obtained will provide insights into the mechanisms of breast cancer progression and how CR inhibits progression through microRNA modulation. Citation Format: Kaylyn L. Devlin, Tiffany Sanford, Elizabeth Mambo, Stephen D. Hursting. Calorie restriction normalizes global microRNA expression by preventing the loss of Dicer expression during mammary tumorigenesis. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B68.
    Type of Medium: Online Resource
    ISSN: 1541-7786 , 1557-3125
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
    detail.hit.zdb_id: 2097884-4
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2015
    In:  Cancer Research Vol. 75, No. 9_Supplement ( 2015-05-01), p. P4-07-01-P4-07-01
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 9_Supplement ( 2015-05-01), p. P4-07-01-P4-07-01
    Abstract: MicroRNA (miRNAs) are small, post-transcriptional regulators that play an integral role in maintenance of cellular functions and whose dyregulation has been shown to promote many types of cancer, including breast cancer. Global downregulation of miRNAs has emerged as a common theme in human breast tumors and has been shown to contribute to oncogenesis. One of the primary mechanisms through which miRNAs are globally dysregulated is downregulation of enzymes involved in miRNA biogenesis. We aim to establish how calorie restriction (CR), which potently inhibits breast cancer progression, regulates global miRNA expression and miRNA biogenesis enzyme functionality in mammary tumors. To address these questions, 100 female Sprague Dawley rats were administered either dimethylbenz(a)anthracene (DMBA) or vehicle control at 50 days of age, then randomized to receive either control (AIN-76A) diet ad-libitum (n=40) or a 30% CR diet regiment (n=60). Resultant mammary tumors were allowed to develop for 12 weeks. Calorie restriction significantly increased survival to study endpoint relative to control diet (75% vs 35%, respectively) (p=0.0047). Furthermore, of the animals that developed tumors, CR significantly decreased median tumor area by 56% compared to control diet (109.4 mm2 vs 250.9 mm2, respectively) (p=0.0286). Global miRNA expression was analyzed through miRNA-specific sequencing. Calorie restriction had a broad effect on miRNA expression, illustrated by the fact that of all the miRNAs with a greater than two-fold expression difference between CR and control, 80% are overexpressed in CR tumors compared to control tumors. These results can be explained by the additional finding that CR was able to prevent the loss of Dicer expression, a key miRNA biogenesis enzyme, observed in control-fed mammary tumor tissue compared to normal tissue. This important finding suggests that global miRNA normalization through the retention of Dicer expression during cancer progression could be a contributing mechanism to CR’s anticancer effects. We plan to further these investigations by exogenously manipulating Dicer expression in Rama25 cells, which were originally derived from a DMBA-induced mammary tumor from a Sprague Dawley rat, and analyzing the resultant tumorigenic potential in vitro and in vivo. The results obtained will provide insights into the mechanisms of breast cancer progression and how CR inhibits progression through microRNA modulation. Citation Format: Kaylyn L Devlin, Tiffany Sanford, Elizabeth Mambo, Stephen D Hursting. Calorie restriction normalizes global microRNA expression by preventing the loss of dicer expression during mammary tumorigenesis [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-07-01.
    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: 2015
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 2357-2357
    Abstract: Calorie restriction (CR) has an antitumorigenic effect against triple-negative breast cancer (TNBC). A key mitogenic pathway modulated by CR involves insulin-like growth factor (IGF)-1, which plays a central role in local and systemic growth and cell survival by activating the PI3K/AKT/mTOR pathway downstream of the IGF-1 receptor (IGF-1R). Although multiple miRNAs that target components of the IGF-1 signaling pathway have been identified, the impact of CR on IGF-1-related miRNA expression has not been addressed. We hypothesize that CR-induced decreases in TNBC development and progression involve miRNA's regulating IGF-1 signaling, we used C3(1)/SV40 T-antigen (C3-TAg) mice (a TNBC model), a C3-Tag progression series of cell lines (M28, M6, and M6C), and human TNBC cell line (MDA-MB-231). The expression of miRNAs previously reported to target components of the IGF-1 and/or mTOR pathways was evaluated by real-time PCR. Hormone levels were measured using the mouse Luminex Screening Assay. To mimic CR in vitro, and to test the effects of miRNA manipulation, the C3-Tag series of TNBC cell lines were treated (separately and in combination) with serum restriction, BMS754807 (inhibitor of IGF1-R), and various levels of recombinant IGF-1 as well as manipulated levels of miRNA's associated with IGF-1/mTOR signaling. We also conducted in silico analysis using Metabric, TCGA, TargetScan, and miRTarBase data sets to identify genes and pathways associated with specific miRNAs expression related to the PI3K/Akt/mTOR pathway. Our results confirm that CR maintains lower body weight, reduces circulating levels of IGF-1, and slows spontaneous TNBC development and progression in mice. CR also significantly increased the expression of miR-15b and miR-486. In vitro studies showed miR-15b and miR-486 expression decreased with increasing tumorigenicity of the C3-tag series of TNBC progression. Treatment of mouse and human TNBC cells with low IGF-1 induced miR-15b expression and inhibited proliferation. Moreover, miR-15b overexpression inhibited cell proliferation and decreased IGF-1R expression (mRNA and protein). Consistent with these results, the in silico analysis shows that the amplification of miR-15b correlates with downregulation of pathways involved in tumor growth and IGF1-R signaling. Together these findings suggest that reduced circulating IGF-1 levels in response to CR leads to the upregulation of miR-15b, which correspondingly targets and downregulates IGF-1R, both at the mRNA and protein levels. This combination of reduced IGF-1 ligand and miR-15b-induced IGF-1R downregulation contributes to the potent anticancer effects of CR and reveals potential targets for pharmacologically mimicking those effects. This research is supported by R35CA197627. Citation Format: Ximena Minerva Bustamante-Marin, Kaylyn L. Devlin, Om Dave, Jenna L. Merlino, Shannon B. McDonell, Michael F. Coleman, Stephen D. Hursting. Anticancer effects of calorie restriction in a murine C3-TAg model of triple-negative breast cancer: the role of miR-15b [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 2357.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 10
    In: Cell Systems, Elsevier BV, Vol. 9, No. 1 ( 2019-07), p. 35-48.e5
    Type of Medium: Online Resource
    ISSN: 2405-4712
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 2854138-8
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