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  1. Article ; Online: Parkin promotes cell survival via linear ubiquitination.

    Fiškin, Evgenij / Dikic, Ivan

    The EMBO journal

    2013  Volume 32, Issue 8, Page(s) 1072–1074

    MeSH term(s) Cell Survival ; I-kappa B Kinase/metabolism ; Mitochondria/physiology ; Models, Biological ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances IKBKG protein, human ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; parkin protein (EC 2.3.2.27) ; I-kappa B Kinase (EC 2.7.11.10)
    Language English
    Publishing date 2013-03-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.1038/emboj.2013.70
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  2. Article ; Online: Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.

    Fiskin, Evgenij / Lareau, Caleb A / Ludwig, Leif S / Eraslan, Gökcen / Liu, Feimei / Ring, Aaron M / Xavier, Ramnik J / Regev, Aviv

    Nature biotechnology

    2021  Volume 40, Issue 3, Page(s) 374–381

    Abstract: Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel ... ...

    Abstract Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel droplet-based method that uses phage displaying, engineered, camelid single-domain antibodies ('nanobodies') for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, and mitochondrial DNA-based clonal tracing. We use PHAGE-ATAC for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis and the detection of SARS-CoV-2 spike protein in human cell populations. Finally, we construct a synthetic high-complexity phage library for selection of antigen-specific nanobodies that bind cells of particular molecular profiles, opening an avenue for protein detection, cell characterization and screening with single-cell genomics.
    MeSH term(s) Bacteriophages/genetics ; COVID-19 ; Chromatin/genetics ; Humans ; SARS-CoV-2 ; Single-Cell Analysis/methods ; Spike Glycoprotein, Coronavirus
    Chemical Substances Chromatin ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2021-10-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-021-01065-5
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  3. Article ; Online: Bacteria-host relationship: ubiquitin ligases as weapons of invasion.

    Maculins, Timurs / Fiskin, Evgenij / Bhogaraju, Sagar / Dikic, Ivan

    Cell research

    2016  Volume 26, Issue 4, Page(s) 499–510

    Abstract: Eukaryotic cells utilize the ubiquitin (Ub) system for maintaining a balanced functioning of cellular pathways. Although the Ub system is exclusive to eukaryotes, prokaryotic bacteria have developed an armory of Ub ligase enzymes that are capable of ... ...

    Abstract Eukaryotic cells utilize the ubiquitin (Ub) system for maintaining a balanced functioning of cellular pathways. Although the Ub system is exclusive to eukaryotes, prokaryotic bacteria have developed an armory of Ub ligase enzymes that are capable of employing the Ub systems of various hosts, ranging from plant to animal cells. These enzymes have been acquired through the evolution and can be classified into three main classes, RING (really interesting new gene), HECT (homologous to the E6-AP carboxyl terminus) and NEL (novel E3 ligases). In this review we describe the roles played by different classes of bacterial Ub ligases in infection and pathogenicity. We also provide an overview of the different mechanisms by which bacteria mimic specific components of the host Ub system and outline the gaps in our current understanding of their functions. Additionally, we discuss approaches and experimental tools for validating this class of enzymes as potential novel antibacterial therapy targets.
    MeSH term(s) Animals ; Bacteria/enzymology ; Bacteria/pathogenicity ; Bacterial Infections/drug therapy ; Bacterial Infections/microbiology ; Humans ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2016-04
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/cr.2016.30
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  4. Article ; Online: Global Analysis of Host and Bacterial Ubiquitinome in Response to Salmonella Typhimurium Infection.

    Fiskin, Evgenij / Bionda, Tihana / Dikic, Ivan / Behrends, Christian

    Molecular cell

    2016  Volume 62, Issue 6, Page(s) 967–981

    Abstract: Ubiquitination serves as a critical signal in the host immune response to infection. Many pathogens have evolved strategies to exploit the ubiquitin (Ub) system to promote their own survival through a complex interplay between host defense machinery and ... ...

    Abstract Ubiquitination serves as a critical signal in the host immune response to infection. Many pathogens have evolved strategies to exploit the ubiquitin (Ub) system to promote their own survival through a complex interplay between host defense machinery and bacterial virulence factors. Here we report dynamic changes in the global ubiquitinome of host epithelial cells and invading pathogen in response to Salmonella Typhimurium infection. The most significant alterations in the host ubiquitinome concern components of the actin cytoskeleton, NF-κB and autophagy pathways, and the Ub and RHO GTPase systems. Specifically, infection-induced ubiquitination promotes CDC42 activity and linear ubiquitin chain formation, both being required for NF-κB activation. Conversely, the bacterial ubiquitinome exhibited extensive ubiquitination of various effectors and several outer membrane proteins. Moreover, we reveal that bacterial Ub-modifying enzymes modulate a unique subset of host targets, affecting different stages of Salmonella infection.
    MeSH term(s) Bacterial Proteins/metabolism ; Epithelial Cells/metabolism ; Epithelial Cells/microbiology ; HCT116 Cells ; HeLa Cells ; Host-Pathogen Interactions ; Humans ; I-kappa B Kinase/genetics ; I-kappa B Kinase/metabolism ; NF-kappa B/genetics ; NF-kappa B/metabolism ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Proteomics/methods ; Salmonella Infections/genetics ; Salmonella Infections/metabolism ; Salmonella typhimurium/metabolism ; Salmonella typhimurium/pathogenicity ; Time Factors ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination ; cdc42 GTP-Binding Protein/metabolism
    Chemical Substances Bacterial Proteins ; NF-kappa B ; Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; TBK1 protein, human (EC 2.7.11.1) ; I-kappa B Kinase (EC 2.7.11.10) ; cdc42 GTP-Binding Protein (EC 3.6.5.2)
    Language English
    Publishing date 2016-06-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.04.015
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  5. Article: Global Analysis of Host and Bacterial Ubiquitinome in Response to Salmonella Typhimurium Infection

    Fiskin, Evgenij / Christian Behrends / Ivan Dikic / Tihana Bionda

    Molecular cell. 2016 June 16, v. 62, no. 6

    2016  

    Abstract: Ubiquitination serves as a critical signal in the host immune response to infection. Many pathogens have evolved strategies to exploit the ubiquitin (Ub) system to promote their own survival through a complex interplay between host defense machinery and ... ...

    Abstract Ubiquitination serves as a critical signal in the host immune response to infection. Many pathogens have evolved strategies to exploit the ubiquitin (Ub) system to promote their own survival through a complex interplay between host defense machinery and bacterial virulence factors. Here we report dynamic changes in the global ubiquitinome of host epithelial cells and invading pathogen in response to Salmonella Typhimurium infection. The most significant alterations in the host ubiquitinome concern components of the actin cytoskeleton, NF-κB and autophagy pathways, and the Ub and RHO GTPase systems. Specifically, infection-induced ubiquitination promotes CDC42 activity and linear ubiquitin chain formation, both being required for NF-κB activation. Conversely, the bacterial ubiquitinome exhibited extensive ubiquitination of various effectors and several outer membrane proteins. Moreover, we reveal that bacterial Ub-modifying enzymes modulate a unique subset of host targets, affecting different stages of Salmonella infection.
    Keywords autophagy ; epithelial cells ; guanosinetriphosphatase ; immune response ; microfilaments ; outer membrane proteins ; pathogens ; Salmonella Typhimurium ; salmonellosis ; transcription factor NF-kappa B ; ubiquitin ; ubiquitination ; virulence
    Language English
    Dates of publication 2016-0616
    Size p. 967-981.
    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.2016.04.015
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  6. Article ; Online: Selective monitoring of ubiquitin signals with genetically encoded ubiquitin chain-specific sensors.

    van Wijk, Sjoerd J L / Fiškin, Evgenij / Dikic, Ivan

    Nature protocols

    2013  Volume 8, Issue 7, Page(s) 1449–1458

    Abstract: Despite intensive research, there is a distinct lack of methodology for visualizing endogenous ubiquitination in living cells. In this protocol, we describe how unique properties of ubiquitin (Ub)-binding domains (UBDs) can be used to selectively detect, ...

    Abstract Despite intensive research, there is a distinct lack of methodology for visualizing endogenous ubiquitination in living cells. In this protocol, we describe how unique properties of ubiquitin (Ub)-binding domains (UBDs) can be used to selectively detect, visualize and inhibit Ub-dependent processes in mammalian cells. The procedure deals with designing and validating the binding selectivity of GFP-tagged K63- and linear-linked sensors (TAB2 NZF and NEMO UBAN, respectively) in vitro. We describe how these moieties can be used to inhibit tumor necrosis factor (TNF)-mediated NF-κB signaling and to detect ubiquitinated cytosolic Salmonella in living cells, emphasizing a more flexible use compared with chain-specific antibodies. These chain-specific sensors can be used to detect Ub-like or autophagy-related modifiers and, in combination with mass spectrometry, to identify new Ub targets. These Ub (-like) sensors can be designed, constructed and tested in ~2-3 weeks.
    MeSH term(s) Animals ; Binding Sites ; Biosensing Techniques/methods ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Humans ; NF-kappa B/metabolism ; Protein Structure, Tertiary ; Reproducibility of Results ; Signal Transduction ; Ubiquitin/analysis ; Ubiquitin/metabolism
    Chemical Substances NF-kappa B ; Ubiquitin ; Green Fluorescent Proteins (147336-22-9)
    Language English
    Publishing date 2013-06-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/nprot.2013.089
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  7. Article ; Online: Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA

    Evgenij Fiskin / Sagar Bhogaraju / Lina Herhaus / Sissy Kalayil / Marcel Hahn / Ivan Dikic

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 14

    Abstract: The HECT-like E3 ligase SopA inSalmonellahas been suggested to activate host RING ligases TRIM56 and TRIM65. Here, the authors use mass spectrometry, crystal structures and biochemistry to examine the interactions between these proteins in detail. ...

    Abstract The HECT-like E3 ligase SopA inSalmonellahas been suggested to activate host RING ligases TRIM56 and TRIM65. Here, the authors use mass spectrometry, crystal structures and biochemistry to examine the interactions between these proteins in detail.
    Keywords Science ; Q
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA.

    Fiskin, Evgenij / Bhogaraju, Sagar / Herhaus, Lina / Kalayil, Sissy / Hahn, Marcel / Dikic, Ivan

    Nature communications

    2017  Volume 8, Page(s) 14004

    Abstract: The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was ...

    Abstract The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was previously proposed to activate host RING ligases TRIM56 and TRIM65. Here we elucidate an inhibitory mechanism of TRIM56 and TRIM65 targeting by SopA. We present the crystal structure of SopA in complex with the RING domain of human TRIM56, revealing the atomic details of their interaction and the basis for SopA selectivity towards TRIM56 and TRIM65. Structure-guided biochemical analysis shows that SopA inhibits TRIM56 E3 ligase activity by occluding the E2-interacting surface of TRIM56. We further demonstrate that SopA ubiquitinates TRIM56 and TRIM65, resulting in their proteasomal degradation during infection. Our results provide the basis for how a bacterial HECT ligase blocks host RING ligases and exemplifies the multivalent power of bacterial effectors during infection.
    MeSH term(s) Amino Acid Motifs ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Host-Pathogen Interactions ; Humans ; Proteolysis ; Salmonella Infections/enzymology ; Salmonella Infections/genetics ; Salmonella Infections/microbiology ; Salmonella typhimurium/chemistry ; Salmonella typhimurium/enzymology ; Salmonella typhimurium/genetics ; Tripartite Motif Proteins/chemistry ; Tripartite Motif Proteins/genetics ; Tripartite Motif Proteins/metabolism ; Ubiquitin-Protein Ligases/chemistry ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Bacterial Proteins ; Tripartite Motif Proteins ; TRIM56 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; SopA protein, Bacteria (EC 3.4.-) ; TRIM65 protein, human (EC 6.3.2.-)
    Language English
    Publishing date 2017-01-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms14004
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  9. Article: Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis.

    Fiskin, Evgenij / Eraslan, Gökcen / Alora-Palli, Maria B / Leyva-Castillo, Juan Manuel / Kim, Sean / Choe, Heather / Lareau, Caleb A / Lau, Helena / Finan, Emily P / Teixeira-Soldano, Isabella / LaBere, Brenna / Chu, Anne / Woods, Brian / Chou, Janet / Slyper, Michal / Waldman, Julia / Islam, Sabina / Schneider, Lynda / Phipatanakul, Wanda /
    Platt, Craig / Rozenblatt-Rosen, Orit / Delorey, Toni M / Deguine, Jacques / Smith, Gideon P / Geha, Raif / Regev, Aviv / Xavier, Ramnik

    bioRxiv : the preprint server for biology

    2023  

    Abstract: In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic ... ...

    Abstract In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete with regard to the hallmarks of pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells spanning 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from four studies into a comprehensive human skin cell atlas in health and disease. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD. This disrupted epithelial differentiation was associated with signals from a unique immune and stromal multicellular community comprised of
    Language English
    Publishing date 2023-10-31
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.29.563503
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  10. Article ; Online: Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.

    Lareau, Caleb A / Dubois, Sonia M / Buquicchio, Frank A / Hsieh, Yu-Hsin / Garg, Kopal / Kautz, Pauline / Nitsch, Lena / Praktiknjo, Samantha D / Maschmeyer, Patrick / Verboon, Jeffrey M / Gutierrez, Jacob C / Yin, Yajie / Fiskin, Evgenij / Luo, Wendy / Mimitou, Eleni P / Muus, Christoph / Malhotra, Rhea / Parikh, Sumit / Fleming, Mark D /
    Oevermann, Lena / Schulte, Johannes / Eckert, Cornelia / Kundaje, Anshul / Smibert, Peter / Vardhana, Santosha A / Satpathy, Ansuman T / Regev, Aviv / Sankaran, Vijay G / Agarwal, Suneet / Ludwig, Leif S

    Nature genetics

    2023  Volume 55, Issue 7, Page(s) 1198–1209

    Abstract: Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific ... ...

    Abstract Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.
    MeSH term(s) Humans ; DNA, Mitochondrial/genetics ; Multiomics ; Mitochondrial Diseases/genetics ; Mitochondria/genetics ; Mutation
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2023-06-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-023-01433-8
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