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  1. Article ; Online: Comparative Hippocampal Proteome and Phosphoproteome in a Niemann-Pick, Type C1 Mouse Model Reveal Insights into Disease Mechanisms.

    Nguyen, Thu T A / Mohanty, Varshasnata / Yan, Ying / Francis, Kevin R / Cologna, Stephanie M

    Journal of proteome research

    2023  Volume 23, Issue 1, Page(s) 84–94

    Abstract: Niemann-Pick disease, type C (NPC) is a neurodegenerative, lysosomal storage disorder in individuals carrying two mutated copies of either ... ...

    Abstract Niemann-Pick disease, type C (NPC) is a neurodegenerative, lysosomal storage disorder in individuals carrying two mutated copies of either the
    MeSH term(s) Animals ; Mice ; Proteome/genetics ; Proteome/metabolism ; Disease Models, Animal ; Intracellular Signaling Peptides and Proteins/metabolism ; Niemann-Pick Disease, Type C/genetics ; Hippocampus/metabolism
    Chemical Substances Proteome ; Intracellular Signaling Peptides and Proteins
    Language English
    Publishing date 2023-11-24
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00375
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Mass spectrometry-based lipid analysis and imaging.

    Pathmasiri, Koralege C / Nguyen, Thu T A / Khamidova, Nigina / Cologna, Stephanie M

    Current topics in membranes

    2021  Volume 88, Page(s) 315–357

    Abstract: Mass spectrometry imaging (MSI) is a powerful tool for in situ mapping of analytes across a sample. With growing interest in lipid biochemistry, the ability to perform such mapping without antibodies has opened many opportunities for MSI and lipid ... ...

    Abstract Mass spectrometry imaging (MSI) is a powerful tool for in situ mapping of analytes across a sample. With growing interest in lipid biochemistry, the ability to perform such mapping without antibodies has opened many opportunities for MSI and lipid analysis. Herein, we discuss the basics of MSI with particular emphasis on MALDI mass spectrometry and lipid analysis. A discussion of critical advancements as well as protocol details are provided to the reader. In addition, strategies for improving the detection of lipids, as well as applications in biomedical research, are presented.
    MeSH term(s) Lipids ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    Chemical Substances Lipids
    Language English
    Publishing date 2021-11-09
    Publishing country United States
    Document type Journal Article
    ISSN 1063-5823
    ISSN 1063-5823
    DOI 10.1016/bs.ctm.2021.10.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Endogenous Protein-Protein Interaction Network of the NPC Cholesterol Transporter 1 in the Cerebral Cortex.

    Javanshad, Roshan / Nguyen, Thu T A / Azaria, Ruth D / Li, Wenping / Edmison, Daisy / Gong, Liang-Wei / Gowrishankar, Swetha / Lieberman, Andrew P / Schultz, Mark L / Cologna, Stephanie M

    Journal of proteome research

    2024  

    Abstract: NPC intracellular cholesterol transporter 1 (NPC1) is a multipass, transmembrane glycoprotein mostly recognized for its key role in facilitating cholesterol efflux. Mutations in ... ...

    Abstract NPC intracellular cholesterol transporter 1 (NPC1) is a multipass, transmembrane glycoprotein mostly recognized for its key role in facilitating cholesterol efflux. Mutations in the
    Language English
    Publishing date 2024-04-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00788
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Discovery of a Small-Molecule Modulator of the Autophagy-Lysosome Pathway That Targets Lamin A/C and LAMP1, Induces Autophagic Flux, and Affects Lysosome Positioning in Neurons.

    Hippman, Ryan S / Snead, Amanda M / Petros, Zoe A / Korkmaz-Vaisys, Melissa A / Patel, Sruchi / Sotelo, Daniel / Dobria, Andrew / Salkovski, Maryna / Nguyen, Thu T A / Linares, Ricardo / Cologna, Stephanie M / Gowrishankar, Swetha / Aldrich, Leslie N

    ACS chemical neuroscience

    2023  Volume 14, Issue 24, Page(s) 4363–4382

    Abstract: Autophagy is a major catabolic degradation and recycling process that maintains homeostasis in cells and is especially important in postmitotic neurons. We implemented a high-content phenotypic assay to discover small molecules that promote autophagic ... ...

    Abstract Autophagy is a major catabolic degradation and recycling process that maintains homeostasis in cells and is especially important in postmitotic neurons. We implemented a high-content phenotypic assay to discover small molecules that promote autophagic flux and completed target identification and validation studies to identify protein targets that modulate the autophagy pathway and promote neuronal health and survival. Efficient syntheses of the prioritized compounds were developed to readily access analogues of the initial hits, enabling initial structure-activity relationship studies to improve potency and preparation of a biotin-tagged pulldown probe that retains activity. This probe facilitated target identification and validation studies through pulldown and competition experiments using both an unbiased proteomics approach and western blotting to reveal Lamin A/C and LAMP1 as the protein targets of compound
    MeSH term(s) Humans ; Lamin Type A/metabolism ; Autophagy/physiology ; Neurons/metabolism ; Lysosomes/metabolism ; Alzheimer Disease/metabolism ; Lysosomal-Associated Membrane Protein 1/metabolism
    Chemical Substances Lamin Type A ; LAMP1 protein, human ; Lysosomal-Associated Membrane Protein 1
    Language English
    Publishing date 2023-12-09
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7193
    ISSN (online) 1948-7193
    DOI 10.1021/acschemneuro.3c00573
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: PPARα and PPARγ Signaling Is Enhanced in the Brain of the Naked Mole-Rat, a Mammal that Shows Intrinsic Neuroprotection from Oxygen Deprivation.

    Pergande, Melissa R / Amoroso, Vince G / Nguyen, Thu T A / Li, Wenping / Vice, Emily / Park, Thomas J / Cologna, Stephanie M

    Journal of proteome research

    2021  Volume 20, Issue 9, Page(s) 4258–4271

    Abstract: Naked mole-rats (NMRs) are a long-lived animal that do not develop age-related diseases including neurodegeneration and cancer. Additionally, NMRs have a profound ability to consume reactive oxygen species (ROS) and survive long periods of oxygen ... ...

    Abstract Naked mole-rats (NMRs) are a long-lived animal that do not develop age-related diseases including neurodegeneration and cancer. Additionally, NMRs have a profound ability to consume reactive oxygen species (ROS) and survive long periods of oxygen deprivation. Here, we evaluated the unique proteome across selected brain regions of NMRs at different ages. Compared to mice, we observed numerous differentially expressed proteins related to altered mitochondrial function in all brain regions, suggesting that the mitochondria in NMRs may have adapted to compensate for energy demands associated with living in a harsh, underground environment. Keeping in mind that ROS can induce polyunsaturated fatty acid peroxidation under periods of neuronal stress, we investigated docosahexaenoic acid (DHA) and arachidonic acid (AA) peroxidation under oxygen-deprived conditions and observed that NMRs undergo DHA and AA peroxidation to a far less extent compared to mice. Further, our proteomic analysis also suggested enhanced peroxisome proliferator-activated receptor (PPAR)-retinoid X receptor (RXR) activation in NMRs via the PPARα-RXR and PPARγ-RXR complexes. Correspondingly, we present several lines of evidence supporting PPAR activation, including increased eicosapetenoic and omega-3 docosapentaenoic acid, as well as an upregulation of fatty acid-binding protein 3 and 4, known transporters of omega-3 fatty acids and PPAR activators. These results suggest enhanced PPARα and PPARγ signaling as a potential, innate neuroprotective mechanism in NMRs.
    MeSH term(s) Animals ; Brain ; Mice ; Mole Rats ; Neuroprotection ; Oxygen ; PPAR alpha/genetics ; PPAR gamma/genetics ; Proteomics
    Chemical Substances PPAR alpha ; PPAR gamma ; Oxygen (S88TT14065)
    Language English
    Publishing date 2021-08-05
    Publishing country United States
    Document type Journal Article ; 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.1c00131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Characterization of the Cerebrospinal Fluid Proteome in Patients with Fragile X-Associated Tremor/Ataxia Syndrome.

    Abbasi, Diana A / Nguyen, Thu T A / Hall, Deborah A / Robertson-Dick, Erin / Berry-Kravis, Elizabeth / Cologna, Stephanie M

    Cerebellum (London, England)

    2021  Volume 21, Issue 1, Page(s) 86–98

    Abstract: Fragile X-associated tremor/ataxia syndrome (FXTAS), first described in 2001, is a neurodegenerative and movement disorder, caused by a premutation in the fragile X mental retardation 1 (FMR1) gene. To date, the biological mechanisms causing this ... ...

    Abstract Fragile X-associated tremor/ataxia syndrome (FXTAS), first described in 2001, is a neurodegenerative and movement disorder, caused by a premutation in the fragile X mental retardation 1 (FMR1) gene. To date, the biological mechanisms causing this condition are still not well understood, as not all premutation carriers develop FXTAS. To further understand this syndrome, we quantitatively compared the cerebrospinal fluid (CSF) proteome of FXTAS patients with age-matched controls using mass spectrometry. We identified 415 proteins of which 97 were altered in FXTAS patients. These proteins suggest changes in acute phase response signaling, liver X receptor/ retinoid X receptor (LXR/RXR) activation, and farnesoid X receptor (FXR)/RXR activation, which are the main pathways found to be affected. Additionally, we detected changes in many other proteins including amyloid-like protein 2, contactin-1, afamin, cell adhesion molecule 4, NPC intracellular cholesterol transporter 2, and cathepsin B, that had been previously noted to hold important roles in other movement disorders. Specific to RXR pathways, several apolipoproteins (APOA1, APOA2, APOA4, APOC2, and APOD) showed significant changes in the CSF of FXTAS patients. Lastly, CSF parameters were analyzed to investigate abnormalities in blood brain barrier function. Correlations were observed between patient albumin quotient values, a measure of permeability, and CGG repeat length as well as FXTAS rating scale scores.
    MeSH term(s) Ataxia/genetics ; Fragile X Mental Retardation Protein/genetics ; Fragile X Syndrome ; Humans ; Proteome/genetics ; Proteome/metabolism ; Tremor ; Trinucleotide Repeat Expansion
    Chemical Substances FMR1 protein, human ; Proteome ; Fragile X Mental Retardation Protein (139135-51-6)
    Language English
    Publishing date 2021-05-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2112586-7
    ISSN 1473-4230 ; 1473-4222
    ISSN (online) 1473-4230
    ISSN 1473-4222
    DOI 10.1007/s12311-021-01262-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Correction to: Characterization of the Cerebrospinal Fluid Proteome in Patients with Fragile X-Associated Tremor/Ataxia Syndrome.

    Abbasi, Diana A / Nguyen, Thu T A / Hall, Deborah A / Robertson-Dick, Erin / Berry-Kravis, Elizabeth / Cologna, Stephanie M

    Cerebellum (London, England)

    2021  Volume 21, Issue 1, Page(s) 99–100

    Language English
    Publishing date 2021-09-10
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2112586-7
    ISSN 1473-4230 ; 1473-4222
    ISSN (online) 1473-4230
    ISSN 1473-4222
    DOI 10.1007/s12311-021-01321-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: PPARα and PPARγ Signaling Is Enhanced in the Brain of the Naked Mole-Rat, a Mammal that Shows Intrinsic Neuroprotection from Oxygen Deprivation

    Pergande, Melissa R. / Amoroso, Vince G. / Nguyen, Thu T. A. / Li, Wenping / Vice, Emily / Park, Thomas J. / Cologna, Stephanie M.

    Journal of proteome research. 2021 Aug. 05, v. 20, no. 9

    2021  

    Abstract: Naked mole-rats (NMRs) are a long-lived animal that do not develop age-related diseases including neurodegeneration and cancer. Additionally, NMRs have a profound ability to consume reactive oxygen species (ROS) and survive long periods of oxygen ... ...

    Abstract Naked mole-rats (NMRs) are a long-lived animal that do not develop age-related diseases including neurodegeneration and cancer. Additionally, NMRs have a profound ability to consume reactive oxygen species (ROS) and survive long periods of oxygen deprivation. Here, we evaluated the unique proteome across selected brain regions of NMRs at different ages. Compared to mice, we observed numerous differentially expressed proteins related to altered mitochondrial function in all brain regions, suggesting that the mitochondria in NMRs may have adapted to compensate for energy demands associated with living in a harsh, underground environment. Keeping in mind that ROS can induce polyunsaturated fatty acid peroxidation under periods of neuronal stress, we investigated docosahexaenoic acid (DHA) and arachidonic acid (AA) peroxidation under oxygen-deprived conditions and observed that NMRs undergo DHA and AA peroxidation to a far less extent compared to mice. Further, our proteomic analysis also suggested enhanced peroxisome proliferator-activated receptor (PPAR)-retinoid X receptor (RXR) activation in NMRs via the PPARα-RXR and PPARγ-RXR complexes. Correspondingly, we present several lines of evidence supporting PPAR activation, including increased eicosapetenoic and omega-3 docosapentaenoic acid, as well as an upregulation of fatty acid-binding protein 3 and 4, known transporters of omega-3 fatty acids and PPAR activators. These results suggest enhanced PPARα and PPARγ signaling as a potential, innate neuroprotective mechanism in NMRs.
    Keywords Heterocephalus glaber ; arachidonic acid ; brain ; docosahexaenoic acid ; docosapentaenoic acid ; energy ; fatty acid-binding proteins ; gene expression regulation ; hypoxia ; mitochondria ; mole rats ; neurodegenerative diseases ; neurons ; neuroprotective effect ; peroxidation ; proteome ; proteomics ; reactive oxygen species ; research
    Language English
    Dates of publication 2021-0805
    Size p. 4258-4271.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00131
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Investigating Phosphorylation Patterns of the Ion Channel TRPM7 Using Multiple Extraction and Enrichment Techniques Reveals New Phosphosites.

    Nguyen, Thu T A / Li, Wenping / Park, Thomas J / Gong, Liang-Wei / Cologna, Stephanie M

    Journal of the American Society for Mass Spectrometry

    2019  Volume 30, Issue 8, Page(s) 1359–1367

    Abstract: The study of membrane proteins, and in particular ion channels, is crucial to understanding cellular function. Mass spectrometry-based approaches including bottom-up strategies to study membrane proteins have been successful yet still can remain ... ...

    Abstract The study of membrane proteins, and in particular ion channels, is crucial to understanding cellular function. Mass spectrometry-based approaches including bottom-up strategies to study membrane proteins have been successful yet still can remain challenging. In this study, we sought to evaluate the phosphorylation patterns of the ion channel TRPM7 which is involved in a range of critical physiological functions. To overcome extraction obstacles associated with analyzing membrane proteins, we incorporated the use of 5% SDS solubilization coupled with SCAD and S-Trap digestion methods to eliminate detergent interference in downstream LC-MS/MS analysis. We found that the SCAD method was more efficient, yielding 84% of the overall identified proteins; however, the variability was greater than the S-Trap method. Using both methods together with TiO
    MeSH term(s) Amino Acid Sequence ; Chromatography, Liquid ; HEK293 Cells ; Humans ; Phosphopeptides/analysis ; Phosphorylation ; Protein Serine-Threonine Kinases/chemistry ; TRPM Cation Channels/chemistry ; Tandem Mass Spectrometry
    Chemical Substances Phosphopeptides ; TRPM Cation Channels ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; TRPM7 protein, human (EC 2.7.11.1)
    Language English
    Publishing date 2019-05-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1073671-2
    ISSN 1879-1123 ; 1044-0305
    ISSN (online) 1879-1123
    ISSN 1044-0305
    DOI 10.1007/s13361-019-02223-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Quantitative, Label-Free Proteomics in the Symptomatic Niemann-Pick, Type C1 Mouse Model Using Standard Flow Liquid Chromatography and Thermal Focusing Electrospray Ionization.

    Pergande, Melissa R / Nguyen, Thu T A / Haney-Ball, Carol / Davidson, Cristin D / Cologna, Stephanie M

    Proteomics

    2019  Volume 19, Issue 9, Page(s) e1800432

    Abstract: Niemann-Pick disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system. ...

    Abstract Niemann-Pick disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system. This abnormal accumulation results in a cascade of pathophysiological events including progressive, cerebellar neurodegeneration, among others. While significant progress has been made to better understand NPC1, the downstream effects of cholesterol storage and the major mechanisms that drive neurodegeneration remain unclear. In the current study, a) the use of a commercial, highly efficient standard flow-ESI platform for protein biomarker identification is implemented and b) protein biomarkers are identified and evaluated at a terminal time point in the NPC1 null mouse model. In this study, alterations are observed in proteins related to fatty acid homeostasis, calcium binding and regulation, lysosomal regulation, and inositol biosynthesis and metabolism, as well as signaling by Rho family GTPases. New observations from this study include altered expression of Pcp2 and Limp2 in Npc1 mutant mice relative to control, with Pcp2 exhibiting multiple isoforms and specific to the cerebella. This study provides valuable insight into pathways altered in the late-stage pathophysiology of NPC1.
    MeSH term(s) Animals ; CD36 Antigens/genetics ; Cholesterol/genetics ; Chromatography, Liquid ; Disease Models, Animal ; Guanine Nucleotide Exchange Factors/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Liver/metabolism ; Lysosomal Membrane Proteins/genetics ; Lysosomes/genetics ; Mice ; Mutation ; Neuropeptides/genetics ; Niemann-Pick C1 Protein ; Niemann-Pick Disease, Type C/genetics ; Proteomics/methods ; Signal Transduction/genetics ; Spectrometry, Mass, Electrospray Ionization
    Chemical Substances CD36 Antigens ; Guanine Nucleotide Exchange Factors ; Intracellular Signaling Peptides and Proteins ; Lysosomal Membrane Proteins ; Neuropeptides ; Niemann-Pick C1 Protein ; Npc1 protein, mouse ; Pcp2 protein, mouse ; Scarb2 protein, mouse ; Cholesterol (97C5T2UQ7J)
    Language English
    Publishing date 2019-04-18
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201800432
    Database MEDical Literature Analysis and Retrieval System OnLINE

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