LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 1644

Search options

  1. Article: The Dearth of Representation in FDA Approved Drug Trials.

    Ibilibor, Christine / Armbruster, Shannon / Parker, Rell / Yu, Jia-Ray / Barros, Andrew

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: The generalizability of data derived from randomized controlled trials is of paramount importance given their utility in the Food & Drug Administration (FDA) drug approval process. An essential part of this process is the inclusion of reliably reported ... ...

    Abstract The generalizability of data derived from randomized controlled trials is of paramount importance given their utility in the Food & Drug Administration (FDA) drug approval process. An essential part of this process is the inclusion of reliably reported gender, race and ethnicity data in trials that lead to FDA drug approval. Despite previous mandates by the FDA and Clinicaltrials.gov, gender and race-specific data remains under reported. We reviewed 100 most recently approved FDA medications, and abstracted the clinical trial data from Clinicaltrials.gov that supported their approval. We then compared these FDA approved trials to non-FDA approved trials from the same year and of similar size. We found that 40% of the FDA trials were missing race/ethnicity information, while 24% of these trials did not include gender information. We demonstrate that there remains a significant amount of missing gender and racial/ethnic data in trials that lead to FDA-approved medications.
    Language English
    Publishing date 2024-01-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.16.24301376
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1.

    Escobar, Thelma M / Yu, Jia-Ray / Liu, Sanxiong / Lucero, Kimberly / Vasilyev, Nikita / Nudler, Evgeny / Reinberg, Danny

    Science advances

    2022  Volume 8, Issue 17, Page(s) eabm3945

    Abstract: The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication ... ...

    Abstract The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin, and MCM2, an integral component of the DNA replication machinery; moreover, NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in the G
    Language English
    Publishing date 2022-04-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abm3945
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: PRC2 is high maintenance.

    Yu, Jia-Ray / Lee, Chul-Hwan / Oksuz, Ozgur / Stafford, James M / Reinberg, Danny

    Genes & development

    2019  Volume 33, Issue 15-16, Page(s) 903–935

    Abstract: As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification ( ...

    Abstract As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification (hPTM) that fosters chromatin compaction. PRC2 also facilitates the inheritance of this hPTM through its self-contained "write and read" activities, key to preserving cellular identity during cell division. As these changes in gene expression occur without changes in DNA sequence and are inherited, the process is epigenetic in scope. Mutants of mammalian PRC2 or of its histone substrate contribute to the cancer process and other diseases, and research into these aberrant pathways is yielding viable candidates for therapeutic targeting. The effectiveness of PRC2 hinges on its being recruited to the proper chromatin sites; however, resolving the determinants to this process in the mammalian case was not straightforward and thus piqued the interest of many in the field. Here, we chronicle the latest advances toward exposing mammalian PRC2 and its high maintenance.
    MeSH term(s) Animals ; Chromatin/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; Humans ; Mutation ; Neoplasms/genetics ; Neoplasms/physiopathology ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; Protein Transport ; Research/trends
    Chemical Substances Chromatin ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
    Language English
    Publishing date 2019-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.325050.119
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Axo-axonic Innervation of Neocortical Pyramidal Neurons by GABAergic Chandelier Cells Requires AnkyrinG-Associated L1CAM.

    Tai, Yilin / Gallo, Nicholas B / Wang, Minghui / Yu, Jia-Ray / Van Aelst, Linda

    Neuron

    2019  Volume 102, Issue 2, Page(s) 358–372.e9

    Abstract: Among the diverse interneuron subtypes in the neocortex, chandelier cells (ChCs) are the only population that selectively innervate pyramidal neurons (PyNs) at their axon initial segment (AIS), the site of action potential initiation, allowing them to ... ...

    Abstract Among the diverse interneuron subtypes in the neocortex, chandelier cells (ChCs) are the only population that selectively innervate pyramidal neurons (PyNs) at their axon initial segment (AIS), the site of action potential initiation, allowing them to exert powerful control over PyN output. Yet, mechanisms underlying their subcellular innervation of PyN AISs are unknown. To identify molecular determinants of ChC/PyN AIS innervation, we performed an in vivo RNAi screen of PyN-expressed axonal cell adhesion molecules (CAMs) and select Ephs/ephrins. Strikingly, we found the L1 family member L1CAM to be the only molecule required for ChC/PyN AIS innervation. Further, we show that L1CAM is required during both the establishment and maintenance of innervation, and that selective innervation of PyN AISs by ChCs requires AIS anchoring of L1CAM by the cytoskeletal ankyrin-G/βIV-spectrin complex. Thus, our findings identify PyN-expressed L1CAM as a critical CAM required for innervation of neocortical PyN AISs by ChCs. VIDEO ABSTRACT.
    MeSH term(s) Animals ; Ankyrins/metabolism ; Axons/metabolism ; Cell Adhesion ; Cell Adhesion Molecules/metabolism ; Ephrins/metabolism ; GABAergic Neurons/metabolism ; Interneurons/metabolism ; Mice ; Neocortex/cytology ; Neocortex/metabolism ; Nerve Tissue Proteins/metabolism ; Neural Cell Adhesion Molecule L1/metabolism ; Pyramidal Cells/metabolism ; Receptor, EphA1/metabolism ; Spectrin/metabolism ; Synapses
    Chemical Substances Ank3 protein, mouse ; Ankyrins ; Cell Adhesion Molecules ; Ephrins ; Nerve Tissue Proteins ; Neural Cell Adhesion Molecule L1 ; betaIV spectrin ; Spectrin (12634-43-4) ; Receptor, EphA1 (EC 2.7.10.1)
    Language English
    Publishing date 2019-03-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 808167-0
    ISSN 1097-4199 ; 0896-6273
    ISSN (online) 1097-4199
    ISSN 0896-6273
    DOI 10.1016/j.neuron.2019.02.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: The H3K36me2 writer-reader dependency in H3K27M-DIPG.

    Yu, Jia-Ray / LeRoy, Gary / Bready, Devin / Frenster, Joshua D / Saldaña-Meyer, Ricardo / Jin, Ying / Descostes, Nicolas / Stafford, James M / Placantonakis, Dimitris G / Reinberg, Danny

    Science advances

    2021  Volume 7, Issue 29

    Abstract: Histone H3K27M is a driving mutation in diffuse intrinsic pontine glioma (DIPG), a deadly pediatric brain tumor. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity and displacement of H3K27me2/3, promoting oncogenesis of ...

    Abstract Histone H3K27M is a driving mutation in diffuse intrinsic pontine glioma (DIPG), a deadly pediatric brain tumor. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity and displacement of H3K27me2/3, promoting oncogenesis of DIPG. As a consequence, a histone modification H3K36me2, antagonistic to H3K27me2/3, is aberrantly elevated. Here, we investigate the role of H3K36me2 in H3K27M-DIPG by tackling its upstream catalyzing enzymes (writers) and downstream binding factors (readers). We determine that NSD1 and NSD2 are the key writers for H3K36me2. Loss of NSD1/2 in H3K27M-DIPG impedes cellular proliferation and tumorigenesis by disrupting tumor-promoting transcriptional programs. Further, we demonstrate that LEDGF and HDGF2 are the main readers mediating the protumorigenic effects downstream of NSD1/2-H3K36me2. Treatment with a chemically modified peptide mimicking endogenous H3K36me2 dislodges LEDGF/HDGF2 from chromatin and specifically inhibits the proliferation of H3K27M-DIPG. Our results indicate a functional pathway of NSD1/2-H3K36me2-LEDGF/HDGF2 as an acquired dependency in H3K27M-DIPG.
    Language English
    Publishing date 2021-07-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abg7444
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Cloud-Based Machine Learning Methods for Parameter Prediction in Textile Manufacturing.

    Chang, Ray-I / Lin, Jia-Ying / Hung, Yu-Hsin

    Sensors (Basel, Switzerland)

    2024  Volume 24, Issue 4

    Abstract: In traditional textile manufacturing, downstream manufacturers use raw materials, such as Nylon and cotton yarns, to produce textile products. The manufacturing process involves warping, sizing, beaming, weaving, and inspection. Staff members typically ... ...

    Abstract In traditional textile manufacturing, downstream manufacturers use raw materials, such as Nylon and cotton yarns, to produce textile products. The manufacturing process involves warping, sizing, beaming, weaving, and inspection. Staff members typically use a trial-and-error approach to adjust the appropriate production parameters in the manufacturing process, which can be time consuming and a waste of resources. To enhance the efficiency and effectiveness of textile manufacturing economically, this study proposes a query-based learning method in regression analytics using existing manufacturing data. Query-based learning allows the model training to evolve its decision-making process through dynamic interactions with its solution space. In this study, predefined target parameters of quality factors were first used to validate the training results and create new training patterns. These new patterns were then imported into the solution space of the training model. In predicting product quality, the results show that the proposed query-based regression algorithm has a mean squared error of 0.0153, which is better than those of the original regression-related methods (Avg. mean squared error = 0.020). The trained model was deployed as an application programing interface (API) for cloud-based analytics and an extensive auto-notification service.
    Language English
    Publishing date 2024-02-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s24041304
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article: Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin

    Lee, Chul-Hwan / Yu, Jia-Ray / Kumar, Sunil / Jin, Ying / LeRoy, Gary / Bhanu, Natarajan / Kaneko, Syuzo / Garcia, Benjamin A / Hamilton, Andrew D / Reinberg, Danny

    Molecular cell. 2018 May 03, v. 70, no. 3

    2018  

    Abstract: PRC2 is a therapeutic target for several types of cancers currently undergoing clinical trials. Its activity is regulated by a positive feedback loop whereby its terminal enzymatic product, H3K27me3, is specifically recognized and bound by an aromatic ... ...

    Abstract PRC2 is a therapeutic target for several types of cancers currently undergoing clinical trials. Its activity is regulated by a positive feedback loop whereby its terminal enzymatic product, H3K27me3, is specifically recognized and bound by an aromatic cage present in its EED subunit. The ensuing allosteric activation of the complex stimulates H3K27me3 deposition on chromatin. Here we report a stepwise feedback mechanism entailing key residues within distinctive interfacing motifs of EZH2 or EED that are found to be mutated in cancers and/or Weaver syndrome. PRC2 harboring these EZH2 or EED mutants manifested little activity in vivo but, unexpectedly, exhibited similar chromatin association as wild-type PRC2, indicating an uncoupling of PRC2 activity and recruitment. With genetic and chemical tools, we demonstrated that targeting allosteric activation overrode the gain-of-function effect of EZH2Y646X oncogenic mutations. These results revealed critical implications for the regulation and biology of PRC2 and a vulnerability in tackling PRC2-addicted cancers.
    Keywords chromatin ; clinical trials ; gain-of-function mutation ; mutants ; neoplasms ; therapeutics
    Language English
    Dates of publication 2018-0503
    Size p. 422-434.e6.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2018.03.020
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  8. Article ; Online: Dual role for DOCK7 in tangential migration of interneuron precursors in the postnatal forebrain.

    Nakamuta, Shinichi / Yang, Yu-Ting / Wang, Chia-Lin / Gallo, Nicholas B / Yu, Jia-Ray / Tai, Yilin / Van Aelst, Linda

    The Journal of cell biology

    2017  Volume 216, Issue 12, Page(s) 4313–4330

    Abstract: Throughout life, stem cells in the ventricular-subventricular zone generate neuroblasts that migrate via the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into local interneurons. Although progress has been made toward ... ...

    Abstract Throughout life, stem cells in the ventricular-subventricular zone generate neuroblasts that migrate via the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into local interneurons. Although progress has been made toward identifying extracellular factors that guide the migration of these cells, little is known about the intracellular mechanisms that govern the dynamic reshaping of the neuroblasts' morphology required for their migration along the RMS. In this study, we identify DOCK7, a member of the DOCK180-family, as a molecule essential for tangential neuroblast migration in the postnatal mouse forebrain. DOCK7 regulates the migration of these cells by controlling both leading process (LP) extension and somal translocation via distinct pathways. It controls LP stability/growth via a Rac-dependent pathway, likely by modulating microtubule networks while also regulating F-actin remodeling at the cell rear to promote somal translocation via a previously unrecognized myosin phosphatase-RhoA-interacting protein-dependent pathway. The coordinated action of both pathways is required to ensure efficient neuroblast migration along the RMS.
    MeSH term(s) Actins/genetics ; Actins/metabolism ; Animals ; Animals, Newborn ; Cell Differentiation ; Cell Line, Tumor ; Cell Movement ; Embryo, Mammalian ; Gene Expression Regulation, Developmental ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; Mice ; Microtubules/metabolism ; Microtubules/ultrastructure ; Myosin-Light-Chain Phosphatase/genetics ; Myosin-Light-Chain Phosphatase/metabolism ; Neurons/metabolism ; Neurons/ultrastructure ; Primary Cell Culture ; Prosencephalon/cytology ; Prosencephalon/growth & development ; Prosencephalon/metabolism ; Proto-Oncogene Proteins c-akt/genetics ; Proto-Oncogene Proteins c-akt/metabolism ; Signal Transduction ; rho GTP-Binding Proteins/genetics ; rho GTP-Binding Proteins/metabolism
    Chemical Substances Actins ; Dock7 protein, mouse ; Guanine Nucleotide Exchange Factors ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Myosin-Light-Chain Phosphatase (EC 3.1.3.53) ; RhoA protein, mouse (EC 3.6.5.2) ; rho GTP-Binding Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2017-10-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.201704157
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma.

    Lee, Chul-Hwan / Yu, Jia-Ray / Granat, Jeffrey / Saldaña-Meyer, Ricardo / Andrade, Joshua / LeRoy, Gary / Jin, Ying / Lund, Peder / Stafford, James M / Garcia, Benjamin A / Ueberheide, Beatrix / Reinberg, Danny

    Genes & development

    2019  Volume 33, Issue 19-20, Page(s) 1428–1440

    Abstract: The histone methyltransferase activity of PRC2 is central to the formation of H3K27me3-decorated facultative heterochromatin and gene silencing. In addition, PRC2 has been shown to automethylate its core subunits, EZH1/EZH2 and SUZ12. Here, we identify ... ...

    Abstract The histone methyltransferase activity of PRC2 is central to the formation of H3K27me3-decorated facultative heterochromatin and gene silencing. In addition, PRC2 has been shown to automethylate its core subunits, EZH1/EZH2 and SUZ12. Here, we identify the lysine residues at which EZH1/EZH2 are automethylated with EZH2-K510 and EZH2-K514 being the major such sites in vivo. Automethylated EZH2/PRC2 exhibits a higher level of histone methyltransferase activity and is required for attaining proper cellular levels of H3K27me3. While occurring independently of PRC2 recruitment to chromatin, automethylation promotes PRC2 accessibility to the histone H3 tail. Intriguingly, EZH2 automethylation is significantly reduced in diffuse intrinsic pontine glioma (DIPG) cells that carry a lysine-to-methionine substitution in histone H3 (H3K27M), but not in cells that carry either EZH2 or EED mutants that abrogate PRC2 allosteric activation, indicating that H3K27M impairs the intrinsic activity of PRC2. Our study demonstrates a PRC2 self-regulatory mechanism through its EZH1/2-mediated automethylation activity.
    MeSH term(s) Child ; Enzyme Activation ; Gene Silencing ; Glioma/enzymology ; Glioma/genetics ; Histones/genetics ; Histones/metabolism ; Humans ; Lysine/metabolism ; Methylation ; Polycomb Repressive Complex 2/metabolism ; Protein Subunits/genetics ; Protein Subunits/metabolism
    Chemical Substances Histones ; Protein Subunits ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2019-09-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.328773.119
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells.

    LeRoy, Gary / Oksuz, Ozgur / Descostes, Nicolas / Aoi, Yuki / Ganai, Rais A / Kara, Havva Ortabozkoyun / Yu, Jia-Ray / Lee, Chul-Hwan / Stafford, James / Shilatifard, Ali / Reinberg, Danny

    Science advances

    2019  Volume 5, Issue 10, Page(s) eaay3068

    Abstract: FACT (facilitates chromatin transcription) is a protein complex that allows RNA polymerase II (RNAPII) to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is ... ...

    Abstract FACT (facilitates chromatin transcription) is a protein complex that allows RNA polymerase II (RNAPII) to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is absent in most tissues. Therefore, we screened for additional proteins that might replace FACT upon differentiation. We identified two proteins, lens epithelium-derived growth factor (LEDGF) and hepatoma-derived growth factor 2 (HDGF2), each containing two high mobility group A (HMGA)-like AT-hooks and a methyl-lysine reading Pro-Trp-Trp-Pro (PWWP) domain that binds to H3K36me2 and H3K36me3.LEDGF and HDGF2 colocalize with H3K36me2/3 at genomic regions containing active genes. In myoblasts, LEDGF and HDGF2 are enriched on most active genes. Upon differentiation to myotubes, LEDGF levels decrease, while HDGF2 levels are maintained. Moreover, HDGF2 is required for their proper expression. HDGF2 knockout myoblasts exhibit an accumulation of paused RNAPII within the transcribed region of many HDGF2 target genes, indicating a defect in early elongation.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Gene Expression Regulation ; HeLa Cells ; Humans ; Intercellular Signaling Peptides and Proteins/metabolism ; Mice ; Nucleosomes/metabolism ; Protein Binding ; Stem Cells/metabolism ; Transcription, Genetic
    Chemical Substances Intercellular Signaling Peptides and Proteins ; Nucleosomes ; hepatoma-derived growth factor ; lens epithelium-derived growth factor
    Language English
    Publishing date 2019-10-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.aay3068
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top