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  1. Article ; Online: Maintaining Golgi Homeostasis: A Balancing Act of Two Proteolytic Pathways.

    Benyair, Ron / Eisenberg-Lerner, Avital / Merbl, Yifat

    Cells

    2022  Volume 11, Issue 5

    Abstract: The Golgi apparatus is a central hub for cellular protein trafficking and signaling. Golgi structure and function is tightly coupled and undergoes dynamic changes in health and disease. A crucial requirement for maintaining Golgi homeostasis is the ... ...

    Abstract The Golgi apparatus is a central hub for cellular protein trafficking and signaling. Golgi structure and function is tightly coupled and undergoes dynamic changes in health and disease. A crucial requirement for maintaining Golgi homeostasis is the ability of the Golgi to target aberrant, misfolded, or otherwise unwanted proteins to degradation. Recent studies have revealed that the Golgi apparatus may degrade such proteins through autophagy, retrograde trafficking to the ER for ER-associated degradation (ERAD), and locally, through Golgi apparatus-related degradation (GARD). Here, we review recent discoveries in these mechanisms, highlighting the role of the Golgi in maintaining cellular homeostasis.
    MeSH term(s) Golgi Apparatus/metabolism ; Homeostasis ; Membrane Proteins/metabolism ; Protein Transport ; Proteolysis
    Chemical Substances Membrane Proteins
    Language English
    Publishing date 2022-02-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11050780
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Gatekeepers of the Gut: The Roles of Proteasomes at the Gastrointestinal Barrier.

    Mohapatra, Gayatree / Eisenberg-Lerner, Avital / Merbl, Yifat

    Biomolecules

    2021  Volume 11, Issue 7

    Abstract: The gut epithelial barrier provides the first line of defense protecting the internal milieu from the environment. To circumvent the exposure to constant challenges such as pathogenic infections and commensal bacteria, epithelial and immune cells at the ... ...

    Abstract The gut epithelial barrier provides the first line of defense protecting the internal milieu from the environment. To circumvent the exposure to constant challenges such as pathogenic infections and commensal bacteria, epithelial and immune cells at the gut barrier require rapid and efficient means to dynamically sense and respond to stimuli. Numerous studies have highlighted the importance of proteolysis in maintaining homeostasis and adapting to the dynamic changes of the conditions in the gut environment. Primarily, proteolytic activities that are involved in immune regulation and inflammation have been examined in the context of the lysosome and inflammasome activation. Yet, the key to cellular and tissue proteostasis is the ubiquitin-proteasome system, which tightly regulates fundamental aspects of inflammatory signaling and protein quality control to provide rapid responses and protect from the accumulation of proteotoxic damage. In this review, we discuss proteasome-dependent regulation of the gut and highlight the pathophysiological consequences of the disarray of proteasomal control in the gut, in the context of aberrant inflammatory disorders and tumorigenesis.
    Language English
    Publishing date 2021-07-05
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom11070989
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  3. Article ; Online: Histone degradation by the proteasome regulates chromatin and cellular plasticity.

    Shmueli, Merav D / Sheban, Daoud / Eisenberg-Lerner, Avital / Merbl, Yifat

    The FEBS journal

    2021  Volume 289, Issue 12, Page(s) 3304–3316

    Abstract: Histones constitute the primary protein building blocks of the chromatin and play key roles in the dynamic control of chromatin compaction and epigenetic regulation. Histones are regulated by intricate mechanisms that alter their functionality and ... ...

    Abstract Histones constitute the primary protein building blocks of the chromatin and play key roles in the dynamic control of chromatin compaction and epigenetic regulation. Histones are regulated by intricate mechanisms that alter their functionality and stability, thereby expanding the regulation of chromatin-transacting processes. As such, histone degradation is tightly regulated to provide spatiotemporal control of cellular histone abundance. While several mechanisms have been implicated in controlling histone stability, here, we discuss proteasome-dependent degradation of histones and the protein modifications that are associated with it. We then highlight specific cellular and physiological states that are associated with altered histone degradation by cellular proteasomes.
    MeSH term(s) Cell Plasticity ; Chromatin/genetics ; Epigenesis, Genetic ; Histones/genetics ; Histones/metabolism ; Proteasome Endopeptidase Complex/metabolism
    Chemical Substances Chromatin ; Histones ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2021-05-13
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15903
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 260: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  4. Article ; Online: Metabolic alterations in the tumor microenvironment and their role in oncogenesis.

    Eisenberg, Lihie / Eisenberg-Bord, Michal / Eisenberg-Lerner, Avital / Sagi-Eisenberg, Ronit

    Cancer letters

    2020  Volume 484, Page(s) 65–71

    Abstract: Metabolic reprogramming is a characteristic feature of both cancer cells and their neighbouring cells in the tumor microenvironment (TME). The latter include stroma fibroblasts and adipocytes, that respectively differentiate to become cancer associated ... ...

    Abstract Metabolic reprogramming is a characteristic feature of both cancer cells and their neighbouring cells in the tumor microenvironment (TME). The latter include stroma fibroblasts and adipocytes, that respectively differentiate to become cancer associated fibroblasts (CAFs) and cancer associated adipocytes (CAAs), and infiltrated immune cells, that collaborate with the stromal cells to provide the tumor a pro-tumorigenic niche. Here we discuss the association between the reprogramming of glucose metabolism in the TME and oncogenic signaling and its reflection in the non-canonical functions of metabolic enzymes. We also discuss the non-canonical actions of oncometabolites and the contribution to oncogenesis of external metabolites that accumulate in the TME as result of crosstalk between the tumor and the TME. Special emphasis is given in this regard to lysophosphatidic acid (LPA) and adenosine, two powerful metabolites, the concentrations of which rise in the TME due to altered metabolism of the tumor and its surrounding cells, allowing their action as external signals.
    MeSH term(s) Adenosine/metabolism ; Adipocytes/metabolism ; Cancer-Associated Fibroblasts/metabolism ; Carcinogenesis/metabolism ; Glycolysis ; Humans ; Lysophospholipids/metabolism ; Neoplasms/metabolism ; Neoplasms/pathology ; Signal Transduction ; Tumor Microenvironment
    Chemical Substances Lysophospholipids ; Adenosine (K72T3FS567) ; lysophosphatidic acid (PG6M3969SG)
    Language English
    Publishing date 2020-05-06
    Publishing country Ireland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 195674-7
    ISSN 1872-7980 ; 0304-3835
    ISSN (online) 1872-7980
    ISSN 0304-3835
    DOI 10.1016/j.canlet.2020.04.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1177: Show issues Location:
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  5. Article ; Online: From sensing interactions to controlling the interactions: a novel approach to obtain biological transistors for specific and label-free immunosensing.

    Samanta, Soumadri / Tiwari, Vinay S / Sadhujan, Sumesh / Harilal, Sherina / Eisenberg-Lerner, Avital / Rotfogel, Ziv / Pikhay, Evgeny / Shima-Edelstein, Ruth / Greental, Doron / Bashouti, Muhammad Y / Akabayov, Barak / Ron, Izhar / Roizin, Yakov / Erez, Offer / Shalev, Gil

    Nanoscale

    2024  Volume 16, Issue 13, Page(s) 6648–6661

    Abstract: Antibody-antigen interactions are shaped by the solution pH level, ionic strength, and electric fields, if present. In biological field-effect transistors (BioFETs), the interactions take place at the sensing area in which the pH level, ionic strength ... ...

    Abstract Antibody-antigen interactions are shaped by the solution pH level, ionic strength, and electric fields, if present. In biological field-effect transistors (BioFETs), the interactions take place at the sensing area in which the pH level, ionic strength and electric fields are determined by the Poisson-Boltzmann equation and the boundary conditions at the solid-solution interface and the potential applied at the solution electrode. The present study demonstrates how a BioFET solution electrode potential affects the sensing area double layer pH level, ionic strength, and electric fields and in this way shapes the biological interactions at the sensing area. We refer to this as 'active sensing'. To this end, we employed the
    MeSH term(s) alpha-Fetoproteins ; Biosensing Techniques/methods ; Electrodes
    Chemical Substances alpha-Fetoproteins
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/d3nr05974j
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  6. Article ; Online: Post-Translational Modification Profiling-Functional Proteomics for the Analysis of Immune Regulation.

    Eisenberg-Lerner, Avital / Regev, Ifat / Merbl, Yifat

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1647, Page(s) 139–152

    Abstract: Posttranslational modifications (PTMs) of proteins are an integral part of major cellular regulatory mechanisms dictating protein function, localization, and stability. The capacity to screen PTMs using protein microarrays has advanced our ability to ... ...

    Abstract Posttranslational modifications (PTMs) of proteins are an integral part of major cellular regulatory mechanisms dictating protein function, localization, and stability. The capacity to screen PTMs using protein microarrays has advanced our ability to identify their targets and regulatory role. This chapter discusses a unique procedure that combines functional extract-based activity assay with large-scale screening utilities of protein microarrays. This "PTM-profiling" system offers advantages in quantitatively identifying modifications in an unbiased manner in the context of specific cellular conditions. While the possibilities of studying PTMs in different settings are enormous, the immune system presents an attractive model for studying the effects of perturbations in PTMs, and specifically the ubiquitin system, as these were already implicated in both immune function and dysfunction. This chapter discusses the significance of PTM profiling in addressing basic questions in immunology. We describe detailed protocols for the preparation of functional cell extracts from immune cell cultures, following differentiation or induced signals, and screening PTMs on protein arrays, as well as basic guidelines for data analysis and interpretation.
    MeSH term(s) Autoimmunity/immunology ; Cell Extracts/isolation & purification ; Humans ; Immune System/metabolism ; Immunity/immunology ; Protein Array Analysis/methods ; Protein Processing, Post-Translational ; Proteins/analysis ; U937 Cells ; Ubiquitin/chemistry ; Ubiquitin/metabolism
    Chemical Substances Cell Extracts ; Proteins ; Ubiquitin
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7201-2_9
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  7. Article ; Online: Post-translational modification profiling - A novel tool for mapping the protein modification landscape in cancer.

    Eisenberg-Lerner, Avital / Ciechanover, Aaron / Merbl, Yifat

    Experimental biology and medicine (Maywood, N.J.)

    2016  Volume 241, Issue 14, Page(s) 1475–1482

    Abstract: The ubiquitin system plays an important role in essentially every cellular process, regulating numerous pathways ranging from development, transcription, DNA damage response, cell cycle, and signal transduction. Its best studied role involves removal of ... ...

    Abstract The ubiquitin system plays an important role in essentially every cellular process, regulating numerous pathways ranging from development, transcription, DNA damage response, cell cycle, and signal transduction. Its best studied role involves removal of faulty proteins or those that are not necessary anymore. Aberrations in the ubiquitin system have been implicated in various pathologies including cancer, where specific mutations in E3 ligases such as Mdm2, pVHL, and BRCA1 have been linked to disease progression, prognosis, and resistance to drugs. Yet, there are hundreds of E3 ligases in the human genome and our knowledge of their target proteins and their dynamic regulation in the cellular environment is largely limited. In addition, fundamental questions related to recognition and specificity in ubiquitin conjugation remain unanswered. It is thus of major importance to characterize the ubiquitin landscape under various cellular conditions, and study how the regulatory network is altered in health and disease. To do so, analytical tools that allow identification of ubiquitin substrates, the conjugation and removal of ubiquitin, and the nature of specific ubiquitin linkages that are formed are needed. In this mini-review, we discuss common proteomic methodologies applied to studying the ubiquitome, and specifically focus on our recently developed post-translational modification (PTM) profiling approach. PTM profiling is a functional assay, amenable to biochemical manipulation, which allows the detection of protein modifications in a high-throughput manner. We discuss in detail the advantages and limitations of this system, focusing primarily on examples for analyzing the ubiquitin system in cancer. Uncovering the intricate signaling dynamics governed by and regulating ubiquitin modifications should clearly evolve into a new paradigm in understanding the molecular basis of malignant transformation and the development of novel therapeutic modalities.
    MeSH term(s) Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Processing, Post-Translational ; Proteomics/methods ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin-Protein Ligases/physiology ; Ubiquitination
    Chemical Substances Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2016-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 4015-0
    ISSN 1535-3699 ; 1525-1373 ; 0037-9727
    ISSN (online) 1535-3699 ; 1525-1373
    ISSN 0037-9727
    DOI 10.1177/1535370216651732
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    Ua VI Zs.111: Show issues Location:
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  8. Article ; Online: Phenotypic Screen Identifies JAK2 as a Major Regulator of FAT10 Expression.

    Reznik, Nava / Kozer, Noga / Eisenberg-Lerner, Avital / Barr, Haim / Merbl, Yifat / London, Nir

    ACS chemical biology

    2019  Volume 14, Issue 12, Page(s) 2538–2545

    Abstract: FAT10 is a ubiquitin-like protein suggested to target proteins for proteasomal degradation. It is highly upregulated upon pro-inflammatory cytokines, namely, TNFα, IFNγ, and IL6, and was found to be highly expressed in various epithelial cancers. ... ...

    Abstract FAT10 is a ubiquitin-like protein suggested to target proteins for proteasomal degradation. It is highly upregulated upon pro-inflammatory cytokines, namely, TNFα, IFNγ, and IL6, and was found to be highly expressed in various epithelial cancers. Evidence suggests that FAT10 is involved in cancer development and may have a pro-tumorigenic role. However, its biological role is still unclear, as well as its biochemical and cellular regulation. To identify pathways underlying FAT10 expression in the context of pro-inflammatory stimulation, which characterizes the cancerous environment, we implemented a phenotypic transcriptional reporter screen with a library of annotated compounds. We identified AZ960, a potent JAK2 inhibitor, which significantly downregulates FAT10 under pro-inflammatory cytokines induction, in an NFκB-independent manner. We validated JAK2 as a major regulator of FAT10 expression via knockdown, and we suggest that the transcriptional effects are mediated through pSTAT1/3/5. Overall, we have elucidated a pathway regulating FAT10 transcription and discovered a tool compound to chemically downregulate FAT10 expression, and to further study its biology.
    MeSH term(s) A549 Cells ; Aminopyridines/pharmacology ; HEK293 Cells ; Humans ; Janus Kinase 2/antagonists & inhibitors ; Janus Kinase 2/metabolism ; Phenotype ; Protein Kinase Inhibitors/pharmacology ; Pyrazoles/pharmacology ; Ubiquitins/metabolism
    Chemical Substances 5-fluoro-2-(1-(4-fluorophenyl)ethylamino)-6-(5-methyl-1H-pyrazol-3-ylamino)nicotinonitrile ; Aminopyridines ; Protein Kinase Inhibitors ; Pyrazoles ; UBD protein, human ; Ubiquitins ; JAK2 protein, human (EC 2.7.10.2) ; Janus Kinase 2 (EC 2.7.10.2)
    Language English
    Publishing date 2019-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.9b00667
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  9. Article ; Online: DAPk silencing by DNA methylation conveys resistance to anti EGFR drugs in lung cancer cells.

    Eisenberg-Lerner, Avital / Kimchi, Adi

    Cell cycle (Georgetown, Tex.)

    2012  Volume 11, Issue 11, Page(s) 2051

    MeSH term(s) Epigenesis, Genetic ; Histones/physiology ; Humans
    Chemical Substances Histones
    Language English
    Publishing date 2012-06-01
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2146183-1
    ISSN 1551-4005 ; 1538-4101 ; 1554-8627
    ISSN (online) 1551-4005
    ISSN 1538-4101 ; 1554-8627
    DOI 10.4161/cc.20538
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5881: Show issues Location:
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  10. Article ; Online: PKD at the crossroads of necrosis and autophagy.

    Eisenberg-Lerner, Avital / Kimchi, Adi

    Autophagy

    2012  Volume 8, Issue 3, Page(s) 433–434

    Abstract: Reactive oxygen species (ROS) that accumulate under oxidative pressure cause severe damage to cellular components, and induce various cellular responses, including apoptosis, programmed necrosis and autophagy, depending on the cellular setting. Various ... ...

    Abstract Reactive oxygen species (ROS) that accumulate under oxidative pressure cause severe damage to cellular components, and induce various cellular responses, including apoptosis, programmed necrosis and autophagy, depending on the cellular setting. Various studies have described ROS-induced autophagy, but only a few direct factors that regulate autophagy under oxidative stress are known to date. We have identified DAPK and PKD as such regulators by demonstrating their role in the process of autophagy in general, and specifically during oxidative stress. PKD acts as a downstream effector of DAPk in the regulation of autophagy. Furthermore, PKD functions within the autophagic network as an activator of VPS34, by associating with and phosphorylating VPS34, leading to its activation. Significantly, PKD is recruited to the autophagosomal membranes, placing it within proximity of its autophagic target.
    MeSH term(s) Apoptosis ; Apoptosis Regulatory Proteins/metabolism ; Autophagy ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Cell Line ; Death-Associated Protein Kinases ; Endoplasmic Reticulum Stress ; Humans ; Necrosis ; Oxidative Stress ; Phagosomes/metabolism ; Protein Kinase C/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction
    Chemical Substances Apoptosis Regulatory Proteins ; Reactive Oxygen Species ; protein kinase D (EC 2.7.10.-) ; Death-Associated Protein Kinases (EC 2.7.11.1) ; Protein Kinase C (EC 2.7.11.13) ; Calcium-Calmodulin-Dependent Protein Kinases (EC 2.7.11.17)
    Language English
    Publishing date 2012-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.4161/auto.19288
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