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  1. Article ; Online: More on Co-Occurrence of COMT and BRCA1/2 Variants in a Population.

    Horvath, Anelia

    The New England journal of medicine

    2017  Volume 377, Issue 8, Page(s) 795–796

    MeSH term(s) Breast Neoplasms ; Humans
    Language English
    Publishing date 2017--24
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc1708425
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.34: Show issues Location:
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  2. Article: Sex-dependent transcription of cardiac electrophysiology and links to acetylation modifiers based on the GTEx database.

    Pressler, Michael P / Horvath, Anelia / Entcheva, Emilia

    Frontiers in cardiovascular medicine

    2022  Volume 9, Page(s) 941890

    Abstract: Development of safer drugs based on epigenetic modifiers, e.g., histone deacetylase inhibitors (HDACi), requires better understanding of their effects on cardiac electrophysiology. Using RNAseq data from the genotype-tissue-expression database (GTEx), we ...

    Abstract Development of safer drugs based on epigenetic modifiers, e.g., histone deacetylase inhibitors (HDACi), requires better understanding of their effects on cardiac electrophysiology. Using RNAseq data from the genotype-tissue-expression database (GTEx), we created models that link the abundance of acetylation enzymes (HDAC/SIRT/HATs), and the gene expression of ion channels (IC)
    Language English
    Publishing date 2022-07-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2022.941890
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: TRIM28 promotes luminal cell plasticity in a mouse model of prostate cancer.

    Yende, Ashutosh S / Williams, Emily C / Pletcher, Andrew / Helfand, Alexandra / Ibeawuchi, Helen / North, Tanya M / Latham, Patricia S / Horvath, Anelia / Shibata, Maho

    Oncogene

    2023  Volume 42, Issue 17, Page(s) 1347–1359

    Abstract: The Tripartite motif-containing 28 (TRIM28) transcriptional cofactor is significantly upregulated in high-grade and metastatic prostate cancers. To study the role of TRIM28 in prostate cancer progression in vivo, we generated a genetically-engineered ... ...

    Abstract The Tripartite motif-containing 28 (TRIM28) transcriptional cofactor is significantly upregulated in high-grade and metastatic prostate cancers. To study the role of TRIM28 in prostate cancer progression in vivo, we generated a genetically-engineered mouse model, combining prostate-specific inactivation of Trp53, Pten and Trim28. Trim28 inactivated NPp53T mice developed an inflammatory response and necrosis in prostate lumens. By conducting single-cell RNA sequencing, we found that NPp53T prostates had fewer luminal cells resembling proximal luminal lineage cells, which are cells with progenitor activity enriched in proximal prostates and prostate invagination tips in wild-type mice with analogous populations in human prostates. However, despite increased apoptosis and reduction of cells expressing proximal luminal cell markers, we found that NPp53T mouse prostates evolved and progressed to invasive prostate carcinoma with a shortened overall survival. Altogether, our findings suggest that TRIM28 promotes expression of proximal luminal cell markers in prostate tumor cells and provides insights into TRIM28 function in prostate tumor plasticity.
    MeSH term(s) Humans ; Male ; Mice ; Animals ; Cell Plasticity ; Prostatic Neoplasms/pathology ; Tripartite Motif-Containing Protein 28/genetics ; Tripartite Motif-Containing Protein 28/metabolism ; Prostate/pathology ; Disease Models, Animal ; Neoplastic Stem Cells/pathology
    Chemical Substances Tripartite Motif-Containing Protein 28 (EC 2.3.2.27) ; TRIM28 protein, human (EC 2.3.2.27) ; Trim28 protein, mouse (EC 2.3.2.27)
    Language English
    Publishing date 2023-03-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 639046-8
    ISSN 1476-5594 ; 0950-9232
    ISSN (online) 1476-5594
    ISSN 0950-9232
    DOI 10.1038/s41388-023-02655-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2218: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: BRCA1 deficiency in mature CD8

    Wu, Bogang / Qi, Leilei / Chiang, Huai-Chin / Pan, Haihui / Zhang, Xiaowen / Greenbaum, Alexandra / Stark, Elizabeth / Wang, Li-Ju / Chen, Yidong / Haddad, Bassem R / Clagett, Dionyssia / Isaacs, Claudine / Elledge, Richard / Horvath, Anelia / Hu, Yanfen / Li, Rong

    Journal for immunotherapy of cancer

    2023  Volume 11, Issue 2

    Abstract: ... Women ... ...

    Abstract Women with
    MeSH term(s) Female ; Mice ; Animals ; CD8-Positive T-Lymphocytes ; Antineoplastic Agents ; Neoplasms ; Immunity ; Mice, Knockout ; Carcinogenesis
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2023-01-31
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2719863-7
    ISSN 2051-1426 ; 2051-1426
    ISSN (online) 2051-1426
    ISSN 2051-1426
    DOI 10.1136/jitc-2022-005852
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: SCExecute: custom cell barcode-stratified analyses of scRNA-seq data.

    Edwards, Nathan / Dillard, Christian / Prashant, N M / Hongyu, Liu / Yang, Mia / Ulianova, Evgenia / Horvath, Anelia

    Bioinformatics (Oxford, England)

    2022  Volume 39, Issue 1

    Abstract: Motivation: In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not ... ...

    Abstract Motivation: In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not sufficiently supported by available tools designed for high-throughput sequencing data.
    Results: We introduce SCExecute, which executes a user-provided command on barcode-stratified, extracted on-the-fly, single-cell binary alignment map (scBAM) files. SCExecute extracts the alignments with each cell barcode from aligned, pooled single-cell sequencing data. Simple commands, monolithic programs, multi-command shell scripts or complex shell-based pipelines are then executed on each scBAM file. scBAM files can be restricted to specific barcodes and/or genomic regions of interest. We demonstrate SCExecute with two popular variant callers-GATK and Strelka2-executed in shell-scripts together with commands for BAM file manipulation and variant filtering, to detect single-cell-specific expressed single nucleotide variants from droplet scRNA-seq data (10X Genomics Chromium System).In conclusion, SCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features.
    Availability and implementation: SCExecute is implemented in Python3 using the Pysam package and distributed for Linux, MacOS and Python environments from https://horvathlab.github.io/NGS/SCExecute.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Sequence Analysis, RNA ; Single-Cell Gene Expression Analysis ; Single-Cell Analysis ; Genomics ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2022-11-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac768
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Co-Occurrence of COMT and BRCA1/2 Variants in a Population.

    Movassagh, Mercedeh / Mudvari, Prakriti / Horvath, Anelia

    The New England journal of medicine

    2017  Volume 376, Issue 21, Page(s) 2090–2091

    MeSH term(s) Breast Neoplasms/genetics ; Catechol O-Methyltransferase/genetics ; Codon, Nonsense ; Female ; Frameshift Mutation ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Variation ; Heterozygote ; Humans
    Chemical Substances Codon, Nonsense ; COMT protein, human (EC 2.1.1.6) ; Catechol O-Methyltransferase (EC 2.1.1.6)
    Language English
    Publishing date 2017--25
    Publishing country United States
    Document type Letter
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc1701592
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.34: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Prostate cancer cell-platelet bidirectional signaling promotes calcium mobilization, invasion and apoptotic resistance via distinct receptor-ligand pairs.

    Garofano, Kaitlin / Rashid, Kameron / Smith, Michael / Brantner, Christine / Suwunnakorn, Sumanun / Diemert, David / Gordon, Olivia / Horvath, Anelia / Khan, Sikandar / Popratiloff, Anastas / Rhim, Johng / Sidahmed, Alfateh / Maggirwar, Sanjay B / O'Brien, Travis J / Perera, Minoli A / Lee, Norman H

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 2864

    Abstract: Platelets play a crucial role in cancer and thrombosis. However, the receptor-ligand repertoire mediating prostate cancer (PCa) cell-platelet interactions and ensuing consequences have not been fully elucidated. Microvilli emanating from the plasma ... ...

    Abstract Platelets play a crucial role in cancer and thrombosis. However, the receptor-ligand repertoire mediating prostate cancer (PCa) cell-platelet interactions and ensuing consequences have not been fully elucidated. Microvilli emanating from the plasma membrane of PCa cell lines (RC77 T/E, MDA PCa 2b) directly contacted individual platelets and platelet aggregates. PCa cell-platelet interactions were associated with calcium mobilization in platelets, and translocation of P-selectin and integrin α
    MeSH term(s) Male ; Humans ; Calcium ; Ligands ; Receptor, EphA1 ; Prostatic Neoplasms ; Integrins
    Chemical Substances Calcium (SY7Q814VUP) ; Ligands ; Receptor, EphA1 (EC 2.7.10.1) ; Integrins
    Language English
    Publishing date 2023-02-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-29450-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Evaluation of an angiotensin Type 1 receptor blocker on the reconsolidation of fear memory.

    Swiercz, Adam P / Iyer, Laxmi / Yu, Zhe / Edwards, Allison / Prashant, N M / Nguyen, Bryan N / Horvath, Anelia / Marvar, Paul J

    Translational psychiatry

    2020  Volume 10, Issue 1, Page(s) 363

    Abstract: Inhibition of the angiotensin type 1 receptor ( ... ...

    Abstract Inhibition of the angiotensin type 1 receptor (AT
    MeSH term(s) Amygdala ; Animals ; Conditioning, Classical ; Extinction, Psychological ; Fear ; Memory ; Receptor, Angiotensin, Type 1
    Chemical Substances Receptor, Angiotensin, Type 1
    Language English
    Publishing date 2020-10-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2609311-X
    ISSN 2158-3188 ; 2158-3188
    ISSN (online) 2158-3188
    ISSN 2158-3188
    DOI 10.1038/s41398-020-01043-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Selective disruption of trigeminal sensory neurogenesis and differentiation in a mouse model of 22q11.2 deletion syndrome.

    Karpinski, Beverly A / Maynard, Thomas M / Bryan, Corey A / Yitsege, Gelila / Horvath, Anelia / Lee, Norman H / Moody, Sally A / LaMantia, Anthony-Samuel

    Disease models & mechanisms

    2021  Volume 15, Issue 2

    Abstract: 22q11.2 Deletion Syndrome (22q11DS) is a neurodevelopmental disorder associated with cranial nerve anomalies and disordered oropharyngeal function, including pediatric dysphagia. Using the LgDel 22q11DS mouse model, we investigated whether sensory neuron ...

    Abstract 22q11.2 Deletion Syndrome (22q11DS) is a neurodevelopmental disorder associated with cranial nerve anomalies and disordered oropharyngeal function, including pediatric dysphagia. Using the LgDel 22q11DS mouse model, we investigated whether sensory neuron differentiation in the trigeminal ganglion (CNgV), which is essential for normal orofacial function, is disrupted. We did not detect changes in cranial placode cell translocation or neural crest migration at early stages of LgDel CNgV development. However, as the ganglion coalesces, proportions of placode-derived LgDel CNgV cells increase relative to neural crest cells. In addition, local aggregation of placode-derived cells increases and aggregation of neural crest-derived cells decreases in LgDel CNgV. This change in cell-cell relationships was accompanied by altered proliferation of placode-derived cells at embryonic day (E)9.5, and premature neurogenesis from neural crest-derived precursors, reflected by an increased frequency of asymmetric neurogenic divisions for neural crest-derived precursors by E10.5. These early differences in LgDel CNgV genesis prefigure changes in sensory neuron differentiation and gene expression by postnatal day 8, when early signs of cranial nerve dysfunction associated with pediatric dysphagia are observed in LgDel mice. Apparently, 22q11 deletion destabilizes CNgV sensory neuron genesis and differentiation by increasing variability in cell-cell interaction, proliferation and sensory neuron differentiation. This early developmental divergence and its consequences may contribute to oropharyngeal dysfunction, including suckling, feeding and swallowing disruptions at birth, and additional orofacial sensory/motor deficits throughout life.
    MeSH term(s) Animals ; Cell Differentiation ; DiGeorge Syndrome ; Humans ; Mice ; Neural Crest ; Neurogenesis ; Sensory Receptor Cells
    Language English
    Publishing date 2021-05-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2451104-3
    ISSN 1754-8411 ; 1754-8403
    ISSN (online) 1754-8411
    ISSN 1754-8403
    DOI 10.1242/dmm.047357
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments.

    N M, Prashant / Liu, Hongyu / Dillard, Christian / Ibeawuchi, Helen / Alsaeedy, Turkey / Chan, Hang / Horvath, Anelia Dafinova

    Genes

    2021  Volume 12, Issue 10

    Abstract: Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information ... ...

    Abstract Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell scRNA-seq data, wherein the alignments are split by cellular barcode prior to the variant call. We also reanalyze publicly available data on the MCF7 cell line during anticancer treatment. We assessed SNV calls by three variant callers-GATK, Strelka2, and Mutect2, in combination with a method for the cell-level tabulation of the sequencing read counts bearing variant alleles-SCReadCounts (single-cell read counts). Our analysis shows that variant calls on individual cell alignments identify at least a two-fold higher number of SNVs as compared to the pooled scRNA-seq; these SNVs are enriched in novel variants and in stop-codon and missense substitutions. Our study indicates an immense potential of SNV calls from individual cell scRNA-seq data and emphasizes the need for cell-level variant detection approaches and tools, which can contribute to the understanding of the cellular heterogeneity and the relationships to phenotypes, and help elucidate somatic mutation evolution and functionality.
    MeSH term(s) Humans ; MCF-7 Cells ; Polymorphism, Single Nucleotide ; RNA-Seq/methods ; Sequence Alignment/methods ; Single-Cell Analysis/methods
    Language English
    Publishing date 2021-09-30
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12101558
    Database MEDical Literature Analysis and Retrieval System OnLINE

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