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  1. Article ; Online: Mass spectrometry-based protein-protein interaction networks for the study of human diseases.

    Richards, Alicia L / Eckhardt, Manon / Krogan, Nevan J

    Molecular systems biology

    2021  Volume 17, Issue 1, Page(s) e8792

    Abstract: A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of ...

    Abstract A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
    MeSH term(s) Disease/genetics ; Gene Regulatory Networks ; Humans ; Mass Spectrometry ; Protein Interaction Mapping/methods
    Language English
    Publishing date 2021-01-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.20188792
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A proximity proteomics pipeline with improved reproducibility and throughput.

    Zhong, Xiaofang / Li, Qiongyu / Polacco, Benjamin J / Patil, Trupti / Marley, Aaron / Foussard, Helene / Khare, Prachi / Vartak, Rasika / Xu, Jiewei / DiBerto, Jeffrey F / Roth, Bryan L / Eckhardt, Manon / Zastrow, Mark Von / Krogan, Nevan J / Hüttenhain, Ruth

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Proximity labeling (PL) through biotinylation coupled with mass spectrometry (MS) has emerged as a powerful technique for capturing spatial proteomes within living cells. Large-scale sample processing for proximity proteomics requires a workflow that ... ...

    Abstract Proximity labeling (PL) through biotinylation coupled with mass spectrometry (MS) has emerged as a powerful technique for capturing spatial proteomes within living cells. Large-scale sample processing for proximity proteomics requires a workflow that minimizes hands-on time while enhancing quantitative reproducibility. Here, we present a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. By combining this pipeline with an optimized quantitative MS acquisition method based on data-independent acquisition (DIA), we not only significantly increased sample throughput but also improved the reproducibility of protein identification and quantification. We applied this pipeline to delineate subcellular proteomes across various cellular compartments, including endosomes, late endosomes/lysosomes, the Golgi apparatus, and the plasma membrane. Moreover, employing 5HT
    Language English
    Publishing date 2024-04-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.11.536358
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A systems approach to infectious disease.

    Eckhardt, Manon / Hultquist, Judd F / Kaake, Robyn M / Hüttenhain, Ruth / Krogan, Nevan J

    Nature reviews. Genetics

    2020  Volume 21, Issue 6, Page(s) 339–354

    Abstract: Ongoing social, political and ecological changes in the 21st century have placed more people at risk of life-threatening acute and chronic infections than ever before. The development of new diagnostic, prophylactic, therapeutic and curative strategies ... ...

    Abstract Ongoing social, political and ecological changes in the 21st century have placed more people at risk of life-threatening acute and chronic infections than ever before. The development of new diagnostic, prophylactic, therapeutic and curative strategies is critical to address this burden but is predicated on a detailed understanding of the immensely complex relationship between pathogens and their hosts. Traditional, reductionist approaches to investigate this dynamic often lack the scale and/or scope to faithfully model the dual and co-dependent nature of this relationship, limiting the success of translational efforts. With recent advances in large-scale, quantitative omics methods as well as in integrative analytical strategies, systems biology approaches for the study of infectious disease are quickly forming a new paradigm for how we understand and model host-pathogen relationships for translational applications. Here, we delineate a framework for a systems biology approach to infectious disease in three parts: discovery - the design, collection and analysis of omics data; representation - the iterative modelling, integration and visualization of complex data sets; and application - the interpretation and hypothesis-based inquiry towards translational outcomes.
    MeSH term(s) Communicable Diseases/therapy ; Data Analysis ; Host-Pathogen Interactions/physiology ; Humans ; Models, Biological ; Systems Analysis ; Systems Biology/methods
    Language English
    Publishing date 2020-02-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-020-0212-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer.

    Olwal, Charles Ochieng' / Fabius, Jacqueline M / Zuliani-Alvarez, Lorena / Eckhardt, Manon / Kyei, George Boateng / Quashie, Peter Kojo / Krogan, Nevan J / Bouhaddou, Mehdi / Bediako, Yaw

    Molecular omics

    2023  Volume 19, Issue 7, Page(s) 538–551

    Abstract: Women coinfected with human immunodeficiency virus type 1 (HIV-1) and human papillomavirus (HPV) are six times as likely to develop invasive cervical carcinoma compared to those without HIV. Unlike other HIV-associated cancers, the risk of cervical ... ...

    Abstract Women coinfected with human immunodeficiency virus type 1 (HIV-1) and human papillomavirus (HPV) are six times as likely to develop invasive cervical carcinoma compared to those without HIV. Unlike other HIV-associated cancers, the risk of cervical cancer development does not change when HPV/HIV coinfected women begin antiretroviral therapy, suggesting HIV-associated immune suppression is not a key driver of cervical cancer development in coinfected women. Here, we investigated whether the persistent secretion of inflammatory factors in HIV-positive patients on antiretroviral therapy could enhance cancer signaling in HPV-infected cervical cells
    MeSH term(s) Humans ; Female ; Uterine Cervical Neoplasms/genetics ; Human Papillomavirus Viruses ; Phosphatidylinositol 3-Kinases/genetics ; Proto-Oncogene Proteins c-akt ; Papillomavirus Infections/complications ; Papillomavirus Infections/genetics ; HIV Infections/complications ; HIV Infections/genetics ; Mutation
    Chemical Substances Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1)
    Language English
    Publishing date 2023-08-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2515-4184
    ISSN (online) 2515-4184
    DOI 10.1039/d3mo00025g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online ; Thesis: Quantitative analysis of the early steps of virus host cell interaction of human immunodeficiency virus type 1 and hepatitis C virus

    Eckhardt, Manon

    2010  

    Title variant Quantitative Analyse der frühen Schritte der Virus-Wirtszell-Interaktion des Humanen Immundefizienvirus und Hepatitis C Virus
    Author's details Manon Eckhardt
    Language English
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Heidelberg, 2010
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  6. Article ; Online: Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

    Bouhaddou, Mehdi / Eckhardt, Manon / Chi Naing, Zun Zar / Kim, Minkyu / Ideker, Trey / Krogan, Nevan J

    Current opinion in genetics & development

    2019  Volume 54, Page(s) 110–117

    Abstract: Massive efforts to sequence cancer genomes have compiled an impressive catalogue of cancer mutations, revealing the recurrent exploitation of a handful of 'hallmark cancer pathways'. However, unraveling how sets of mutated proteins in these and other ... ...

    Abstract Massive efforts to sequence cancer genomes have compiled an impressive catalogue of cancer mutations, revealing the recurrent exploitation of a handful of 'hallmark cancer pathways'. However, unraveling how sets of mutated proteins in these and other pathways hijack pro-proliferative signaling networks and dictate therapeutic responsiveness remains challenging. Here, we show that cancer driver protein-protein interactions are enriched for additional cancer drivers, highlighting the power of physical interaction maps to explain known, as well as uncover new, disease-promoting pathway interrelationships. We hypothesize that by systematically mapping the protein-protein and genetic interactions in cancer-thereby creating Cancer Cell Maps-we will create resources against which to contextualize a patient's mutations into perturbed pathways/complexes and thereby specify a matching targeted therapeutic cocktail.
    MeSH term(s) Computational Biology ; Databases, Genetic ; Epistasis, Genetic/genetics ; Gene Regulatory Networks ; Humans ; Mutation/genetics ; Neoplasms/genetics ; Precision Medicine ; Protein Interaction Maps/genetics ; Signal Transduction/genetics
    Language English
    Publishing date 2019-07-06
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2019.04.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.

    Rathore, Ujjwal / Haas, Paige / Easwar Kumar, Vigneshwari / Hiatt, Joseph / Haas, Kelsey M / Bouhaddou, Mehdi / Swaney, Danielle L / Stevenson, Erica / Zuliani-Alvarez, Lorena / McGregor, Michael J / Turner-Groth, Autumn / Ochieng' Olwal, Charles / Bediako, Yaw / Braberg, Hannes / Soucheray, Margaret / Ott, Melanie / Eckhardt, Manon / Hultquist, Judd F / Marson, Alexander /
    Kaake, Robyn M / Krogan, Nevan J

    mBio

    2024  Volume 15, Issue 4, Page(s) e0222223

    Abstract: During HIV infection of CD4+ T cells, ubiquitin pathways are essential to viral replication and host innate immune response; however, the role of specific E3 ubiquitin ligases is not well understood. Proteomics analyses identified 116 single-subunit E3 ... ...

    Abstract During HIV infection of CD4+ T cells, ubiquitin pathways are essential to viral replication and host innate immune response; however, the role of specific E3 ubiquitin ligases is not well understood. Proteomics analyses identified 116 single-subunit E3 ubiquitin ligases expressed in activated primary human CD4+ T cells. Using a CRISPR-based arrayed spreading infectivity assay, we systematically knocked out 116 E3s from activated primary CD4+ T cells and infected them with NL4-3 GFP reporter HIV-1. We found 10 E3s significantly positively or negatively affected HIV infection in activated primary CD4+ T cells, including UHRF1 (pro-viral) and TRAF2 (anti-viral). Furthermore, deletion of either TRAF2 or UHRF1 in three JLat models of latency spontaneously increased HIV transcription. To verify this effect, we developed a CRISPR-compatible resting primary human CD4+ T cell model of latency. Using this system, we found that deletion of TRAF2 or UHRF1 initiated latency reactivation and increased virus production from primary human resting CD4+ T cells, suggesting these two E3s represent promising targets for future HIV latency reversal strategies.
    Importance: HIV, the virus that causes AIDS, heavily relies on the machinery of human cells to infect and replicate. Our study focuses on the host cell's ubiquitination system which is crucial for numerous cellular processes. Many pathogens, including HIV, exploit this system to enhance their own replication and survival. E3 proteins are part of the ubiquitination pathway that are useful drug targets for host-directed therapies. We interrogated the 116 E3s found in human immune cells known as CD4+ T cells, since these are the target cells infected by HIV. Using CRISPR, a gene-editing tool, we individually removed each of these enzymes and observed the impact on HIV infection in human CD4+ T cells isolated from healthy donors. We discovered that 10 of the E3 enzymes had a significant effect on HIV infection. Two of them, TRAF2 and UHRF1, modulated HIV activity within the cells and triggered an increased release of HIV from previously dormant or "latent" cells in a new primary T cell assay. This finding could guide strategies to perturb hidden HIV reservoirs, a major hurdle to curing HIV. Our study offers insights into HIV-host interactions, identifies new factors that influence HIV infection in immune cells, and introduces a novel methodology for studying HIV infection and latency in human immune cells.
    MeSH term(s) Humans ; CCAAT-Enhancer-Binding Proteins/metabolism ; CD4-Positive T-Lymphocytes ; CRISPR-Cas Systems ; HIV Infections ; TNF Receptor-Associated Factor 2/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitins/metabolism ; Virus Latency ; Virus Replication ; HIV/physiology
    Chemical Substances CCAAT-Enhancer-Binding Proteins ; TNF Receptor-Associated Factor 2 ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitins ; UHRF1 protein, human (EC 2.3.2.27) ; PSMD2 protein, human
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02222-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.

    Cakir, Zeynep / Lord, Samuel J / Zhou, Yuan / Jang, Gwendolyn M / Polacco, Benjamin J / Eckhardt, Manon / Jimenez-Morales, David / Newton, Billy W / Orr, Adam L / Johnson, Jeffrey R / da Cruz, Alexandre / Mullins, R Dyche / Krogan, Nevan J / Mahley, Robert W / Swaney, Danielle L

    Molecular & cellular proteomics : MCP

    2023  Volume 22, Issue 5, Page(s) 100541

    Abstract: Apolipoprotein (apo) E4 is the major genetic risk factor for Alzheimer's disease. While neurons generally produce a minority of the apoE in the central nervous system, neuronal expression of apoE increases dramatically in response to stress and is ... ...

    Abstract Apolipoprotein (apo) E4 is the major genetic risk factor for Alzheimer's disease. While neurons generally produce a minority of the apoE in the central nervous system, neuronal expression of apoE increases dramatically in response to stress and is sufficient to drive pathology. Currently, the molecular mechanisms of how apoE4 expression may regulate pathology are not fully understood. Here, we expand upon our previous studies measuring the impact of apoE4 on protein abundance to include the analysis of protein phosphorylation and ubiquitylation signaling in isogenic Neuro-2a cells expressing apoE3 or apoE4. ApoE4 expression resulted in a dramatic increase in vasodilator-stimulated phosphoprotein (VASP) S235 phosphorylation in a protein kinase A (PKA)-dependent manner. This phosphorylation disrupted VASP interactions with numerous actin cytoskeletal and microtubular proteins. Reduction of VASP S235 phosphorylation via PKA inhibition resulted in a significant increase in filopodia formation and neurite outgrowth in apoE4-expressing cells, exceeding levels observed in apoE3-expressing cells. Our results highlight the pronounced and diverse impact of apoE4 on multiple modes of protein regulation and identify protein targets to restore apoE4-related cytoskeletal defects.
    MeSH term(s) Actins/metabolism ; Alzheimer Disease/metabolism ; Apolipoprotein E3/genetics ; Apolipoprotein E3/metabolism ; Apolipoprotein E4/genetics ; Apolipoprotein E4/metabolism ; Apolipoproteins E/genetics ; Apolipoproteins E/metabolism ; Phosphorylation ; Proteomics ; Animals ; Mice
    Chemical Substances Actins ; Apolipoprotein E3 ; Apolipoprotein E4 ; Apolipoproteins E ; vasodilator-stimulated phosphoprotein
    Language English
    Publishing date 2023-04-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2075924-1
    ISSN 1535-9484 ; 1535-9476
    ISSN (online) 1535-9484
    ISSN 1535-9476
    DOI 10.1016/j.mcpro.2023.100541
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online ; Thesis: Quantitative analysis of the early steps of virus host cell interaction of human immunodeficiency virus type 1 and hepatitis C virus

    Eckhardt, Manon [Verfasser]

    2010  

    Author's details presented by Manon Eckhardt
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  10. Article ; Online: The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.

    Tutuncuoglu, Beril / Cakir, Merve / Batra, Jyoti / Bouhaddou, Mehdi / Eckhardt, Manon / Gordon, David E / Krogan, Nevan J

    Cancer discovery

    2020  Volume 10, Issue 7, Page(s) 916–921

    Abstract: The mapping of SARS-CoV-2 human protein-protein interactions by Gordon and colleagues revealed druggable targets that are hijacked by the virus. Here, we highlight several oncogenic pathways identified at the host-virus interface of SARS-CoV-2 to enable ... ...

    Abstract The mapping of SARS-CoV-2 human protein-protein interactions by Gordon and colleagues revealed druggable targets that are hijacked by the virus. Here, we highlight several oncogenic pathways identified at the host-virus interface of SARS-CoV-2 to enable cancer biologists to apply their knowledge for rapid drug repurposing to treat COVID-19, and help inform the response to potential long-term complications of the disease.
    MeSH term(s) Betacoronavirus ; COVID-19 ; Cell Cycle ; Coronavirus Infections/drug therapy ; Coronavirus Infections/genetics ; Coronavirus Infections/metabolism ; Coronavirus Infections/physiopathology ; DNA Damage ; Drug Repositioning ; Epigenomics ; Humans ; Neoplasm Proteins/antagonists & inhibitors ; Neoplasm Proteins/drug effects ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/physiopathology ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/genetics ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/physiopathology ; Protein Biosynthesis ; SARS-CoV-2
    Chemical Substances Neoplasm Proteins
    Keywords covid19
    Language English
    Publishing date 2020-05-22
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2625242-9
    ISSN 2159-8290 ; 2159-8274
    ISSN (online) 2159-8290
    ISSN 2159-8274
    DOI 10.1158/2159-8290.CD-20-0559
    Database MEDical Literature Analysis and Retrieval System OnLINE

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