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  1. Article ; Online: The World of Protein Interactions: Defining the Caveolin 3 Cardiac Interactome.

    Van Eyk, Jennifer E

    Circulation research

    2021  Volume 128, Issue 6, Page(s) 720–722

    MeSH term(s) Caveolae ; Caveolin 3 ; Heart
    Chemical Substances Caveolin 3
    Language English
    Publishing date 2021-03-18
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 80100-8
    ISSN 1524-4571 ; 0009-7330 ; 0931-6876
    ISSN (online) 1524-4571
    ISSN 0009-7330 ; 0931-6876
    DOI 10.1161/CIRCRESAHA.121.318922
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  2. Article ; Online: Proteomics of the heart.

    Karpov, Oleg A / Stotland, Aleksandr / Raedschelders, Koen / Chazarin, Blandine / Ai, Lizhuo / Murray, Christopher I / Van Eyk, Jennifer E

    Physiological reviews

    2024  Volume 104, Issue 3, Page(s) 931–982

    Abstract: Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural ... ...

    Abstract Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
    MeSH term(s) Animals ; Humans ; Proteomics/methods ; Cardiovascular Diseases ; Heart ; Protein Processing, Post-Translational ; Mass Spectrometry/methods
    Language English
    Publishing date 2024-02-01
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 209902-0
    ISSN 1522-1210 ; 0031-9333
    ISSN (online) 1522-1210
    ISSN 0031-9333
    DOI 10.1152/physrev.00026.2023
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  3. Article ; Online: High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing.

    Ai, Lizhuo / Binek, Aleksandra / Kreimer, Simion / Ayres, Matthew / Stotland, Aleksandr / Van Eyk, Jennifer E

    Journal of proteome research

    2023  Volume 22, Issue 6, Page(s) 2124–2130

    Abstract: Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) ... ...

    Abstract Heart tissue sample preparation for mass spectrometry (MS) analysis that includes prefractionation reduces the cellular protein dynamic range and increases the relative abundance of nonsarcomeric proteins. We previously described "IN-Sequence" (IN-Seq) where heart tissue lysate is sequentially partitioned into three subcellular fractions to increase the proteome coverage more than a single direct tissue analysis by mass spectrometry. Here, we report an adaptation of the high-field asymmetric ion mobility spectrometry (FAIMS) coupled to mass spectrometry, and the establishment of a simple one step sample preparation coupled with gas-phase fractionation. The FAIMS approach substantially reduces manual sample handling, significantly shortens the MS instrument processing time, and produces unique protein identification and quantification approximating the commonly used IN-Seq method in less time.
    MeSH term(s) Proteome ; Ion Mobility Spectrometry/methods ; Tandem Mass Spectrometry/methods ; Proteomics/methods ; Specimen Handling
    Chemical Substances Proteome
    Language English
    Publishing date 2023-04-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00027
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  4. Article ; Online: Influence of FTDP-17 mutants on circular tau RNAs.

    Margvelani, Giorgi / Welden, Justin R / Maquera, Andrea Arizaca / Van Eyk, Jennifer E / Murray, Christopher / Miranda Sardon, Sandra C / Stamm, Stefan

    Biochimica et biophysica acta. Molecular basis of disease

    2024  Volume 1870, Issue 4, Page(s) 167036

    Abstract: At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs ( ... ...

    Abstract At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occurs through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations.
    MeSH term(s) Humans ; Frontotemporal Dementia/genetics ; Mutation ; RNA/genetics ; RNA, Circular/genetics ; tau Proteins/genetics
    Chemical Substances RNA (63231-63-0) ; RNA, Circular ; tau Proteins ; MAPT protein, human
    Language English
    Publishing date 2024-01-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 60-7
    ISSN 1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbadis.2024.167036
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  5. Article ; Online: The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics?

    Jiang, Yuming / DeBord, Daniel / Vitrac, Heidi / Stewart, Jordan / Haghani, Ali / Van Eyk, Jennifer E / Fert-Bober, Justyna / Meyer, Jesse G

    Journal of proteome research

    2024  

    Abstract: The coevolution of liquid chromatography (LC) with mass spectrometry (MS) has shaped contemporary proteomics. LC hyphenated to MS now enables quantification of more than 10,000 proteins in a single injection, a number that likely represents most proteins ...

    Abstract The coevolution of liquid chromatography (LC) with mass spectrometry (MS) has shaped contemporary proteomics. LC hyphenated to MS now enables quantification of more than 10,000 proteins in a single injection, a number that likely represents most proteins in specific human cells or tissues. Separations by ion mobility spectrometry (IMS) have recently emerged to complement LC and further improve the depth of proteomics. Given the theoretical advantages in speed and robustness of IMS in comparison to LC, we envision that ongoing improvements to IMS paired with MS may eventually make LC obsolete, especially when combined with targeted or simplified analyses, such as rapid clinical proteomics analysis of defined biomarker panels. In this perspective, we describe the need for faster analysis that might drive this transition, the current state of direct infusion proteomics, and discuss some technical challenges that must be overcome to fully complete the transition to entirely gas phase proteomics.
    Language English
    Publishing date 2024-05-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.4c00248
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  6. Book: Clinical proteomics

    Van Eyk, Jennifer E.

    from diagnosis to therapy

    2008  

    Author's details ed. by Jennifer E. van Eyk
    Keywords Proteomanalyse
    Subject Proteomics ; Proteomik ; Proteom-Analyse
    Language English
    Dates of publication 2008-9999
    Size XXXIII, 659 S. : Ill., graph. Darst., 240 mm x 170 mm
    Publisher Wiley VCH
    Publishing place Weinheim u.a.
    Publishing country Germany
    Document type Book
    HBZ-ID HT015343917
    ISBN 978-3-527-31637-3 ; 3-527-31637-X
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2008 A 424 order for loan Magazin

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  7. Article ; Online: Universal therapeutic targeting of age-related protein quality control system dysfunction in chronic diseases?

    Van Eyk, Jennifer E

    Trends in cardiovascular medicine

    2015  Volume 25, Issue 3, Page(s) 248–249

    MeSH term(s) Heart Diseases/therapy ; Humans ; Proteostasis Deficiencies/therapy
    Language English
    Publishing date 2015-04
    Publishing country United States
    Document type Comment ; Editorial
    ZDB-ID 1097434-9
    ISSN 1873-2615 ; 1050-1738
    ISSN (online) 1873-2615
    ISSN 1050-1738
    DOI 10.1016/j.tcm.2015.01.012
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  8. Article ; Online: Assessment of a 60-Biomarker Health Surveillance Panel (HSP) on Whole Blood from Remote Sampling Devices by Targeted LC/MRM-MS and Discovery DIA-MS Analysis.

    Whelan, Stephen A / Hendricks, Nathan / Dwight, Zachary L / Fu, Qin / Moradian, Annie / Van Eyk, Jennifer E / Mockus, Susan M

    Analytical chemistry

    2023  Volume 95, Issue 29, Page(s) 11007–11018

    Abstract: Telehealth, accessing healthcare and wellness remotely, should be a cost-effective and efficient way for individuals to receive care. The convenience of having a reliable remote collection device for blood tests will facilitate access to precision ... ...

    Abstract Telehealth, accessing healthcare and wellness remotely, should be a cost-effective and efficient way for individuals to receive care. The convenience of having a reliable remote collection device for blood tests will facilitate access to precision medicine and healthcare. Herein, we tested a 60-biomarker health surveillance panel (HSP), containing 35 FDA/LDT assays and covering at least 14 pathological states, on 8 healthy individuals' ability to collect their own capillary blood from a lancet finger prick and directly compared it to the traditional phlebotomist venous blood and plasma collection methods. All samples were spiked with 114 stable-isotope-labeled (SIL) HSP peptides and quantitatively analyzed by liquid chromatography-multiple reaction monitoring-mass spectrometry (LC/MRM-MS) scheduled method targeting 466 transitions from 114 HSP peptides and by a discovery data-independent acquisition mass spectrometry (DIA-MS) method. The average peak area ratio (PAR) of the HSP quantifier peptide transitions from all 8 volunteers' capillary blood (
    MeSH term(s) Humans ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Peptides/chemistry ; Biomarkers ; Blood Specimen Collection
    Chemical Substances Peptides ; Biomarkers
    Language English
    Publishing date 2023-06-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c01189
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  9. Article: Influence of FTDP-17 mutants on circular Tau RNAs.

    Margvelani, Giorgi / Welden, Justin R / Maquera, Andrea Arizaca / Van Eyk, Jennifer E / Murray, Christopher / Miranda Sardon, Sandra C / Stamm, Stefan

    bioRxiv : the preprint server for biology

    2023  

    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.08.556913
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  10. Article ; Online: The Molecular Twin artificial-intelligence platform integrates multi-omic data to predict outcomes for pancreatic adenocarcinoma patients.

    Osipov, Arsen / Nikolic, Ognjen / Gertych, Arkadiusz / Parker, Sarah / Hendifar, Andrew / Singh, Pranav / Filippova, Darya / Dagliyan, Grant / Ferrone, Cristina R / Zheng, Lei / Moore, Jason H / Tourtellotte, Warren / Van Eyk, Jennifer E / Theodorescu, Dan

    Nature cancer

    2024  Volume 5, Issue 2, Page(s) 299–314

    Abstract: Contemporary analyses focused on a limited number of clinical and molecular biomarkers have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma. Here we describe a precision medicine platform known as the Molecular ... ...

    Abstract Contemporary analyses focused on a limited number of clinical and molecular biomarkers have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma. Here we describe a precision medicine platform known as the Molecular Twin consisting of advanced machine-learning models and use it to analyze a dataset of 6,363 clinical and multi-omic molecular features from patients with resected pancreatic ductal adenocarcinoma to accurately predict disease survival (DS). We show that a full multi-omic model predicts DS with the highest accuracy and that plasma protein is the top single-omic predictor of DS. A parsimonious model learning only 589 multi-omic features demonstrated similar predictive performance as the full multi-omic model. Our platform enables discovery of parsimonious biomarker panels and performance assessment of outcome prediction models learning from resource-intensive panels. This approach has considerable potential to impact clinical care and democratize precision cancer medicine worldwide.
    MeSH term(s) Humans ; Adenocarcinoma/genetics ; Adenocarcinoma/surgery ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms/surgery ; Multiomics ; Artificial Intelligence ; Carcinoma, Pancreatic Ductal/genetics ; Carcinoma, Pancreatic Ductal/surgery ; Intelligence
    Language English
    Publishing date 2024-01-22
    Publishing country England
    Document type Journal Article
    ISSN 2662-1347
    ISSN (online) 2662-1347
    DOI 10.1038/s43018-023-00697-7
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