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  • 1
    In: Langmuir, American Chemical Society (ACS), Vol. 23, No. 26 ( 2007-12-01), p. 12864-12874
    Type of Medium: Online Resource
    ISSN: 0743-7463 , 1520-5827
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    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2007
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  • 2
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 3630-3630
    Abstract: Introduction Hox gene expression is high in hematopoietic stem/progenitor cells (HSPCs), decreases during normal differentiation but remains elevated in leukemia subtypes. Polycomb repressor complexes and histone modifiers, e.g. Mixed Lineage Leukemia (MLL), are key regulators of Hox expression. MLL rearrangements, frequent in acute leukemia, are associated high HOXA expression. However, necessity for the HoxA cluster in MLL-leukemia maintenance is not fully elucidated. Methodology Ectopic overexpression of MLL-AF9 (MA9) in HSPCs in conditional compound transgenic mouse backgrounds MxCre+/HoxAflox/flox (MAFF) or HoxAflox/flox (AFlox) models resulted in increased colony formation and growth in liquid culture. Transformed colonies, serially re-plated (n=5) in methylcellulose and transplanted into sub-lethally irradiated recipient mice, resulted in primary leukemia. Initially, MAFF-MA9 leukemias were used to examine in vivo deletion of the HoxA cluster using intraperitoneal injections of Poly(I:C) to initiate an interferon response. To further examine the necessity for the HoxA cluster in disease maintenance, AFlox-MA9 leukemias were treated ex vivo with Cre-recombinase (MSCV-Cre-GFP) or vector control (MSCV-GFP), sorted based on GFP expression and used for gDNA-PCR, gene expression (Illumina BeadArray) and transplantation into sub-lethally irradiated recipient mice (500 cGy). Results Generation of MLL-AF9 leukemias in the MAFF background (MAFF-MA9) resulted in deletion of one HoxA cluster allele (HoxA+/-), validated by genomic PCR and gDNA sequencing from expanded single colonies (Figure 1) presumably due to viral-induced activation of the Mx1 promoter. PolyI:C treatment of these mice resulted in a modest extension in survival (1-2 days) compared to controls. Luciferase labelling and transplantation of MAFF-MA9 leukemias into NSG mice, followed by PolyI:C treatment, showed a measurable decrease in disease burden compared to control, however this did not correlate with overall survival. Direct treatment of MAFF-MA9 cells with interferon-α (in vitro) resulted in further deletion of the HoxA cluster (HoxA-/hypo) and significant reduction in colony formation compared to controls. Although non-leukemic MAFF HSPCs retained colony forming ability after complete HoxA cluster deletion (HoxA-/-) no HoxA-/- colonies were recovered from the interferon-α treated MAFF-MA9 cultures. Cre-recombinase-induced deletion of the Hoxa cluster from AFlox-MA9 leukemia cells was confirmed by gDNA-PCR and sequencing (Figure 1). Transplantation of Cre-treated AFlox-MA9 cells resulted in significant increased survival (P 〈 0.002) by up to 74 days in recipient mice, compared to controls (Figure 2). Further examination of the leukemias that developed from these Cre-treated AFlox-MA9 cells demonstrated retention of one allele of the HoxA cluster, as a result of escapees. To gain insight into the molecular mechanisms underlying the HoxA requirement for MLL-AF9 maintenance, matched Cre- or control treated AFlox-MA9 samples used for the transplantation were further examined for differential gene expression by Illumina BeadArray analysis. Preliminary analysis of the data has confirmed significant reduction in the expression of HoxA cluster genes (a2, a4, a5, a7, a9) and increased expression of several genes involved in adhesion, differentiation or immune response (e.g. Itgb3bp, Mpo, Cxcl2). Further analysis including submission of gene signatures to the LINCS database (https://www.broadinstitute.org/software/cprg/?q=node/40) will be done to identify candidate small molecules that mimic HoxA deletion in MLL-AF9. Conclusion Together these data support a fundamental role for the HoxA cluster in MLL-AF9 maintenance indicating dependency for this leukemia subtype which may be exploited for therapeutic benefit. Figure 1. Deletion of Hoxa cluster validated by Sanger sequencing. The chromatograph (A) and sequence obtained (B) from PCR products generated from primers used to detect Hoxa cluster deletion with retention of the 5' UTR and 3' UTR regions of the Hoxa13 and Hoxa1 genes respectively. Figure 1. Deletion of Hoxa cluster validated by Sanger sequencing. The chromatograph (A) and sequence obtained (B) from PCR products generated from primers used to detect Hoxa cluster deletion with retention of the 5' UTR and 3' UTR regions of the Hoxa13 and Hoxa1 genes respectively. Figure 2. Deletion of the Hoxa cluster results in significant increase in survival of Cre-GFPHi AFlox-MA9 mice compared to GFPhi control mice (n=10). Significance as calculated by Log-rank (Mantel-Cox) Test is denoted *** = p 〈 0.001. Figure 2. Deletion of the Hoxa cluster results in significant increase in survival of Cre-GFPHi AFlox-MA9 mice compared to GFPhi control mice (n=10). Significance as calculated by Log-rank (Mantel-Cox) Test is denoted *** = p 〈 0.001. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 3
    In: Journal of Chemical Information and Modeling, American Chemical Society (ACS), Vol. 62, No. 3 ( 2022-02-14), p. 718-729
    Type of Medium: Online Resource
    ISSN: 1549-9596 , 1549-960X
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2022
    detail.hit.zdb_id: 1491237-5
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  • 4
    In: Cancers, MDPI AG, Vol. 11, No. 12 ( 2019-12-17), p. 2036-
    Abstract: High expression of the HOXA cluster correlates with poor clinical outcome in acute myeloid leukemias, particularly those harboring rearrangements of the mixed-lineage-leukemia gene (MLLr). Whilst decreased HOXA expression acts as a readout for candidate experimental therapies, the necessity of the HOXA cluster for leukemia maintenance has not been fully explored. Primary leukemias were generated in hematopoietic stem/progenitor cells from Cre responsive transgenic mice for conditional deletion of the Hoxa locus. Hoxa deletion resulted in reduced proliferation and colony formation in which surviving leukemic cells retained at least one copy of the Hoxa cluster, indicating dependency. Comparative transcriptome analysis of Hoxa wild type and deleted leukemic cells identified a unique gene signature associated with key pathways including transcriptional mis-regulation in cancer, the Fanconi anemia pathway and cell cycle progression. Further bioinformatics analysis of the gene signature identified a number of candidate FDA-approved drugs for potential repurposing in high HOXA expressing cancers including MLLr leukemias. Together these findings support dependency for an MLLr leukemia on Hoxa expression and identified candidate drugs for further therapeutic evaluation.
    Type of Medium: Online Resource
    ISSN: 2072-6694
    Language: English
    Publisher: MDPI AG
    Publication Date: 2019
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  • 5
    In: Oncotarget, Impact Journals, LLC, Vol. 7, No. 45 ( 2016-11-08), p. 73448-73461
    Type of Medium: Online Resource
    ISSN: 1949-2553
    URL: Issue
    Language: English
    Publisher: Impact Journals, LLC
    Publication Date: 2016
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  • 6
    Online Resource
    Online Resource
    MDPI AG ; 2021
    In:  Pharmaceuticals Vol. 14, No. 8 ( 2021-08-17), p. 807-
    In: Pharmaceuticals, MDPI AG, Vol. 14, No. 8 ( 2021-08-17), p. 807-
    Abstract: At the end of 2019, a highly contagious infection began its ominous conquest of the world. It was soon discovered that the disease was caused by a novel coronavirus designated as SARS-CoV-2, and the disease was thus abbreviated to COVID-19 (COVID). The global medical community has directed its efforts not only to find effective therapies against the deadly pathogen but also to combat the concomitant complications. Two of the most common respiratory manifestations of COVID are a significant reduction in the diffusing capacity of the lungs (DLCO) and the associated pulmonary interstitial damage. One year after moderate COVID, the incidence rate of impaired DLCO and persistent lung damage still exceeds 30%, and one-third of the patients have severe DLCO impairment and fibrotic lung damage. The persistent respiratory complications may cause substantial population morbidity, long-term disability, and even death due to the lung fibrosis progression. The incidence of COVID-induced pulmonary fibrosis caused by COVID can be estimated based on a 15-year observational study of lung pathology after SARS. Most SARS patients with fibrotic lung damage recovered within the first year and then remained healthy; however, in 20% of the cases, significant fibrosis progression was found in 5–10 years. Based on these data, the incidence rate of post-COVID lung fibrosis can be estimated at 2–6% after moderate illness. What is worse, there are reasons to believe that fibrosis may become one of the major long-term complications of COVID, even in asymptomatic individuals. Currently, despite the best efforts of the global medical community, there are no treatments for COVID-induced pulmonary fibrosis. In this review, we analyze the latest data from ongoing clinical trials aimed at treating post-COVID lung fibrosis and analyze the rationale for the current drug candidates. We discuss the use of antifibrotic therapy for idiopathic pulmonary fibrosis, the IN01 vaccine, glucocorticosteroids as well as the stromal vascular fraction for the treatment and rehabilitation of patients with COVID-associated pulmonary damage.
    Type of Medium: Online Resource
    ISSN: 1424-8247
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
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    SSG: 15,3
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 52 ( 2014-12-30), p. 18448-18453
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 52 ( 2014-12-30), p. 18448-18453
    Abstract: The development of novel antitumor agents that have high efficacy in suppressing tumor growth, have low toxicity to nontumor tissues, and exhibit rapid localization in the targeted tumor sites is an ongoing avenue of research at the interface of chemistry, cancer biology, and pharmacology. Supramolecular metal-based coordination complexes (SCCs) have well-defined shapes and geometries, and upon their internalization, SCCs could affect multiple oncogenic signaling pathways in cells and tissues. We investigated the uptake, intracellular localization, and antitumor activity of two rhomboidal Pt(II)-based SCCs. Laser-scanning confocal microscopy in A549 and HeLa cells was used to determine the uptake and localization of the assemblies within cells and their effect on tumor growth was investigated in mouse s.c. tumor xenograft models. The SCCs are soluble in cell culture media within the entire range of studied concentrations (1 nM–5 µM), are nontoxic, and showed efficacy in reducing the rate of tumor growth in s.c. mouse tumor xenografts. These properties reveal the potential of Pt(II)-based SCCs for future biomedical applications as therapeutic agents.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
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    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 8
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. D1 ( 2022-01-07), p. D1307-D1316
    Abstract: The United States has a complex regulatory scheme for marketing drugs. Understanding drug regulatory status is a daunting task that requires integrating data from many sources from the United States Food and Drug Administration (FDA), US government publications, and other processes related to drug development. At NCATS, we created Inxight Drugs (https://drugs.ncats.io), a web resource that attempts to address this challenge in a systematic manner. NCATS Inxight Drugs incorporates and unifies a wealth of data, including those supplied by the FDA and from independent public sources. The database offers a substantial amount of manually curated literature data unavailable from other sources. Currently, the database contains 125 036 product ingredients, including 2566 US approved drugs, 6242 marketed drugs, and 9684 investigational drugs. All substances are rigorously defined according to the ISO 11238 standard to comply with existing regulatory standards for unique drug substance identification. A special emphasis was placed on capturing manually curated and referenced data on treatment modalities and semantic relationships between substances. A supplementary resource ‘Novel FDA Drug Approvals’ features regulatory details of newly approved FDA drugs. The database is regularly updated using NCATS Stitcher data integration tool that automates data aggregation and supports full data access through a RESTful API.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 9
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 40, No. 16_suppl ( 2022-06-01), p. e20540-e20540
    Abstract: e20540 Background: Tailoring the best treatments to cancer patients is an important open challenge. Here, we build a precision oncology data science and software framework for PERsonalized single-Cell Expression-based Planning for Treatments In Oncology (PERCEPTION). Methods: Our approach capitalizes on recently published matched bulk and single-cell transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients’ single-cell (SC) tumor transcriptomics. Our approach is a two-step process: first, the prediction models are trained on large-scale bulk-expression profiles of cancer cell lines and then, in a second step, the models’ performance is further optimized by training on SC-expression profiles of cancer cell lines. Results: First, we show that PERCEPTION successfully predicts the response to monotherapy and combination treatments in screens performed in cancer and patient-tumor-derived primary cells based on SC-expression profiles. Second, it successfully stratifies responders to combination therapy based on the patients’ tumor’s SC-expression in two very recent multiple myeloma and breast cancer clinical trials. Thirdly, it captures the development of clinical resistance to five standard tyrosine kinase inhibitors using tumor SC-expression profiles obtained during treatment in a lung cancer patients’ cohort. Notably, PERCEPTION outperforms state-of-the-art bulk expression-based predictors in all three clinical cohorts. Conclusions: In sum, this study provides a first-of-its-kind conceptual and computational method that is predictive of response to therapy in patients, based on the clonal SC gene expression of their tumors.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2022
    detail.hit.zdb_id: 2005181-5
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  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2020
    In:  Journal of Biomedical Semantics Vol. 11, No. 1 ( 2020-12)
    In: Journal of Biomedical Semantics, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-12)
    Abstract: The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare diseases. As the cumulative scientific understanding and underlying evidence for these diseases have expanded over time, existing practices to generate knowledge from these publications and resources have not been able to keep pace. Through determining the applicability of computational approaches to enhance or replace manual curation tasks, we aim to both improve the sustainability and relevance of consumer health information, but also to develop a foundational database, from which translational science researchers may start to unravel disease characteristics that are vital to the research process. Results We developed a meta-ontology based integrative knowledge graph for rare diseases in Neo4j. This integrative knowledge graph includes a total of 3,819,623 nodes and 84,223,681 relations from 34 different biomedical data resources, including curated drug and rare disease associations. Semi-automatic mappings were generated for 2154 unique FDA orphan designations to 776 unique GARD diseases, and 3322 unique FDA designated drugs to UNII, as well as 180,363 associations between drug and indication from Inxight Drugs, which were integrated into the knowledge graph. We conducted four case studies to demonstrate the capabilities of this integrative knowledge graph in accelerating the curation of scientific understanding on rare diseases through the generation of disease mappings/profiles and pathogenesis associations. Conclusions By integrating well-established database resources, we developed an integrative knowledge graph containing a large volume of biomedical and research data. Demonstration of several immediate use cases and limitations of this process reveal both the potential feasibility and barriers of utilizing graph-based resources and approaches to support their use by providers of consumer health information, such as GARD, that may struggle with the needs of maintaining knowledge reliant on an evolving and growing evidence-base. Finally, the successful integration of these datasets into a freely accessible knowledge graph highlights an opportunity to take a translational science view on the field of rare diseases by enabling researchers to identify disease characteristics, which may play a role in the translation of discover across different research domains.
    Type of Medium: Online Resource
    ISSN: 2041-1480
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2548651-2
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