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  1. Article ; Online: Regulation of the intestinal Na

    Han, Yiran / Bagchi, Pritha / Yun, C Chris

    American journal of physiology. Cell physiology

    2023  Volume 326, Issue 1, Page(s) C50–C59

    Abstract: Electroneutral NaCl transport by ... ...

    Abstract Electroneutral NaCl transport by Na
    MeSH term(s) Humans ; AMP-Activated Protein Kinases/metabolism ; Sodium-Hydrogen Exchanger 3/metabolism ; Phosphorylation ; Diabetes Mellitus, Type 2/drug therapy ; Metformin/pharmacology ; Intestines ; Diarrhea ; Aminoimidazole Carboxamide/pharmacology
    Chemical Substances AMP-Activated Protein Kinases (EC 2.7.11.31) ; Sodium-Hydrogen Exchanger 3 ; Metformin (9100L32L2N) ; Aminoimidazole Carboxamide (360-97-4)
    Language English
    Publishing date 2023-12-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392098-7
    ISSN 1522-1563 ; 0363-6143
    ISSN (online) 1522-1563
    ISSN 0363-6143
    DOI 10.1152/ajpcell.00540.2023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Proteomic Signaling of Dual-Specificity Phosphatase 4 (DUSP4) in Alzheimer's Disease.

    Wang, Erming / Pan, Allen L / Bagchi, Pritha / Rangaraju, Srikant / Seyfried, Nicholas T / Ehrlich, Michelle E / Salton, Stephen R / Zhang, Bin

    Biomolecules

    2024  Volume 14, Issue 1

    Abstract: DUSP4 is a member of the DUSP (dual-specificity phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, ... ...

    Abstract DUSP4 is a member of the DUSP (dual-specificity phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, we utilized the stereotactic delivery of adeno-associated virus (AAV)-DUSP4 to overexpress DUSP4 in the dorsal hippocampus of 5xFAD and wildtype (WT) mice, then used mass spectrometry (MS)-based proteomics along with the label-free quantification to profile the proteome and phosphoproteome in the hippocampus. We identified protein expression and phosphorylation patterns modulated in 5xFAD mice and examined the sex-specific impact of DUSP4 overexpression on the 5xFAD proteome/phosphoproteome. In 5xFAD mice, a substantial number of proteins were up- or down-regulated in both male and female mice in comparison to age and sex-matched WT mice, many of which are involved in AD-related biological processes, such as activated immune response or suppressed synaptic activities. Many proteins in pathways, such as immune response were found to be suppressed in response to DUSP4 overexpression in male 5xFAD mice. In contrast, such a shift was absent in female mice. For the phosphoproteome, we detected an array of phosphorylation sites regulated in 5xFAD compared to WT and modulated via DUSP4 overexpression in each sex. Interestingly, 5xFAD- and DUSP4-associated phosphorylation changes occurred in opposite directions. Strikingly, both the 5xFAD- and DUSP4-associated phosphorylation changes were found to be mostly in neurons and play key roles in neuronal processes and synaptic functions. Site-centric pathway analysis revealed that both the 5xFAD- and DUSP4-associated phosphorylation sites were enriched for a number of kinase sets in females but only a limited number of sets of kinases in male mice. Taken together, our results suggest that male and female 5xFAD mice responded to DUSP4 overexpression via shared and sex-specific molecular mechanisms, which might underly similar reductions in amyloid pathology in both sexes while learning deficits were reduced in only females with DUSP4 overexpression. Finally, we validated our findings with the sex-specific AD-associated proteomes in human cohorts and further developed DUSP4-centric proteomic network models and signaling maps for each sex.
    MeSH term(s) Animals ; Female ; Humans ; Male ; Mice ; Alzheimer Disease/genetics ; Dependovirus ; Dual-Specificity Phosphatases/genetics ; Mitogen-Activated Protein Kinase Phosphatases/genetics ; Proteome ; Proteomics ; Signal Transduction
    Chemical Substances Dual-Specificity Phosphatases (EC 3.1.3.48) ; DUSP4 protein, human (EC 3.1.3.48) ; Mitogen-Activated Protein Kinase Phosphatases (EC 3.1.3.16) ; Proteome ; MKP2 protein, mouse (EC 3.1.3.48)
    Language English
    Publishing date 2024-01-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom14010066
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  3. Article: Proteomic signaling of dual specificity phosphatase 4 (DUSP4) in Alzheimer's disease.

    Wang, Erming / Pan, Allen L / Bagchi, Pritha / Ranjaraju, Srikant / Seyfried, Nicholas T / Ehrlich, Michelle E / Salton, Stephen R / Zhang, Bin

    bioRxiv : the preprint server for biology

    2023  

    Abstract: DUSP4 is a member of the DUSP (Dual-Specificity Phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, ... ...

    Abstract DUSP4 is a member of the DUSP (Dual-Specificity Phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, we utilized stereotactic delivery of adeno-associated virus (AAV)-DUSP4 to overexpress DUSP4 in the dorsal hippocampus of 5×FAD and wildtype (WT) mice, then used mass spectrometry (MS)-based proteomics along with label-free quantification to profile the proteome and phosphoproteome in the hippocampus. We identified patterns of protein expression and phosphorylation that are modulated in 5×FAD mice and examined the sex-specific impact of DUSP4 overexpression on the 5×FAD proteome/phosphoproteome. In 5×FAD mice, a substantial number of proteins were up- or down-regulated in both male and female mice in comparison to age and sex-matched WT mice, many of which are involved in AD-related biological processes, such as the activated immune response or suppression of synaptic activities. Upon DUSP4 overexpression, significantly regulated proteins were found in pathways that were suppressed, such as the immune response, in male 5×FAD mice. In contrast, such a shift was absent in female mice. For the phosphoproteome, we detected an array of phosphorylation sites that are regulated in 5×FAD compared to WT, and are modulated by DUSP4 overexpression in each sex. Interestingly, the changes in 5×FAD- and DUSP4-associated phosphorylation occurred in opposite directions. Strikingly, both the 5×FAD- and DUSP4-associated phosphorylation changes were found for the most part in neurons, and play key roles in neuronal processes and synaptic function. Site-centric pathway analysis revealed that both the 5×FAD- and DUSP4-associated phosphorylation sites were enriched for a number of kinase sets in female, but only a limited number of sets of kinases in male mice. Taken together, our results suggest that male and female 5×FAD mice respond to DUSP4 overexpression via shared and sex-specific molecular mechanisms, which might underly similar reductions in amyloid pathology in both sexes, while learning deficits were reduced in only females with DUSP4 overexpression. Finally, we validated our findings with the sex-specific AD-associated proteomes in human cohorts and further developed DUSP4-centric proteomic network models and signaling maps for each sex.
    Language English
    Publishing date 2023-09-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.13.557390
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Proteomic signaling of dual specificity phosphatase 4 (DUSP4) in Alzheimer's disease.

    Wang, Erming / Pan, Allen L / Bagchi, Pritha / Ranjaraju, Srikant / Seyfried, Nicholas T / Ehrlich, Michelle E / Salton, Stephen R / Zhang, Bin

    Research square

    2023  

    Abstract: DUSP4 is a member of the DUSP (Dual-Specificity Phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, ... ...

    Abstract DUSP4 is a member of the DUSP (Dual-Specificity Phosphatase) subfamily that is selective to the mitogen-activated protein kinases (MAPK) and has been implicated in a range of biological processes and functions in Alzheimer's disease (AD). In this study, we utilized stereotactic delivery of adeno-associated virus (AAV)-DUSP4 to overexpress DUSP4 in the dorsal hippocampus of 5xFAD and wildtype (WT) mice, then used mass spectrometry (MS)-based proteomics along with label-free quantification to profile the proteome and phosphoproteome in the hippocampus. We identified patterns of protein expression and phosphorylation that are modulated in 5xFAD mice and examined the sex-specific impact of DUSP4 overexpression on the 5xFAD proteome/phosphoproteome. In 5xFAD mice, a substantial number of proteins were up- or down-regulated in both male and female mice in comparison to age and sex-matched WT mice, many of which are involved in AD-related biological processes, such as the activated immune response or suppression of synaptic activities. Upon DUSP4 overexpression, significantly regulated proteins were found in pathways that were suppressed, such as the immune response, in male 5xFAD mice. In contrast, such a shift was absent in female mice. For the phosphoproteome, we detected an array of phosphorylation sites that are regulated in 5xFAD compared to WT, and are modulated by DUSP4 overexpression in each sex. Interestingly, the changes in 5xFAD- and DUSP4-associated phosphorylation occurred in opposite directions. Strikingly, both the 5xFAD- and DUSP4-associated phosphorylation changes were found for the most part in neurons, and play key roles in neuronal processes and synaptic function. Site-centric pathway analysis revealed that both the 5xFAD- and DUSP4-associated phosphorylation sites were enriched for a number of kinase sets in female, but only a limited number of sets of kinases in male mice. Taken together, our results suggest that male and female 5xFAD mice respond to DUSP4 overexpression via shared and sex-specific molecular mechanisms, which might underly similar reductions in amyloid pathology in both sexes, while learning deficits were reduced in only females with DUSP4 overexpression. Finally, we validated our findings with the sex-specific AD-associated proteomes in human cohorts and further developed DUSP4-centric proteomic network models and signaling maps for each sex.
    Language English
    Publishing date 2023-10-19
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3453503/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A Conserved Switch Controls Virulence, Sporulation, and Motility in

    DiCandia, Michael A / Edwards, Adrianne N / Lee, Cheyenne D / Monteiro, Marcos P / Cuebas, Germ N Vargas / Bagchi, Pritha / McBride, Shonna M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Spore formation is required for environmental survival and transmission of the human ... ...

    Abstract Spore formation is required for environmental survival and transmission of the human enteropathogenic
    Language English
    Publishing date 2023-03-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.28.534590
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  6. Article ; Online: A conserved switch controls virulence, sporulation, and motility in C. difficile.

    DiCandia, Michael A / Edwards, Adrianne N / Alcaraz, Ysabella B / Monteiro, Marcos P / Lee, Cheyenne D / Vargas Cuebas, Germán / Bagchi, Pritha / McBride, Shonna M

    PLoS pathogens

    2024  Volume 20, Issue 5, Page(s) e1012224

    Abstract: Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile. In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, ... ...

    Abstract Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile. In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, the factors and mechanisms that directly regulate C. difficile Spo0A activity are not defined. In the well-studied Bacillus species, Spo0A is directly inactivated by Spo0E, a small phosphatase. To understand Spo0E function in C. difficile, we created a null mutation of the spo0E ortholog and assessed sporulation and physiology. The spo0E mutant produced significantly more spores, demonstrating Spo0E represses C. difficile sporulation. Unexpectedly, the spo0E mutant also exhibited increased motility and toxin production, and enhanced virulence in animal infections. We uncovered that Spo0E interacts with both Spo0A and the toxin and motility regulator, RstA. Direct interactions between Spo0A, Spo0E, and RstA constitute a previously unknown molecular switch that coordinates sporulation with motility and toxin production. Reinvestigation of Spo0E function in B. subtilis revealed that Spo0E induced motility, demonstrating Spo0E regulation of motility and sporulation among divergent species. Further, 3D structural analyses of Spo0E revealed specific and exclusive interactions between Spo0E and binding partners in C. difficile and B. subtilis that provide insight into the conservation of this regulatory mechanism among different species.
    Language English
    Publishing date 2024-05-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1012224
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  7. Article ; Online: Proximity-based labeling reveals DNA damage-induced phosphorylation of fused in sarcoma (FUS) causes distinct changes in the FUS protein interactome.

    Johnson, Michelle A / Nuckols, Thomas A / Merino, Paola / Bagchi, Pritha / Nandy, Srijita / Root, Jessica / Taylor, Georgia / Seyfried, Nicholas T / Kukar, Thomas

    The Journal of biological chemistry

    2022  Volume 298, Issue 8, Page(s) 102135

    Abstract: Accumulation of cytoplasmic inclusions containing fused in sarcoma (FUS), an RNA/DNA-binding protein, is a common hallmark of frontotemporal lobar degeneration and amyotrophic lateral sclerosis neuropathology. We have previously shown that DNA damage can ...

    Abstract Accumulation of cytoplasmic inclusions containing fused in sarcoma (FUS), an RNA/DNA-binding protein, is a common hallmark of frontotemporal lobar degeneration and amyotrophic lateral sclerosis neuropathology. We have previously shown that DNA damage can trigger the cytoplasmic accumulation of N-terminally phosphorylated FUS. However, the functional consequences of N-terminal FUS phosphorylation are unknown. To gain insight into this question, we utilized proximity-dependent biotin labeling via ascorbate peroxidase 2 aired with mass spectrometry to investigate whether N-terminal phosphorylation alters the FUS protein-protein interaction network (interactome), and subsequently, FUS function. We report the first analysis comparing the interactomes of three FUS variants: homeostatic wildtype FUS (FUS WT), phosphomimetic FUS (FUS PM; a proxy for N-terminally phosphorylated FUS), and the toxic FUS proline 525 to leucine mutant (FUS P525L) that causes juvenile amyotrophic lateral sclerosis. We found that the phosphomimetic FUS interactome is uniquely enriched for a group of cytoplasmic proteins that mediate mRNA metabolism and translation, as well as nuclear proteins involved in the spliceosome and DNA repair functions. Furthermore, we identified and validated the RNA-induced silencing complex RNA helicase MOV10 as a novel interacting partner of FUS. Finally, we provide functional evidence that N-terminally phosphorylated FUS may disrupt homeostatic translation and steady-state levels of specific mRNA transcripts. Taken together, these results highlight phosphorylation as a unique modulator of the interactome and function of FUS.
    MeSH term(s) Amyotrophic Lateral Sclerosis/metabolism ; DNA Damage ; Humans ; Mutation ; Phosphorylation ; RNA Helicases/metabolism ; RNA, Messenger/metabolism ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; RNA-Binding Proteins/metabolism
    Chemical Substances FUS protein, human ; RNA, Messenger ; RNA-Binding Protein FUS ; RNA-Binding Proteins ; Mov10 protein, human (EC 2.7.7.-) ; RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102135
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  8. Article ; Online: Exploration of potential immune mechanisms in cervical dystonia.

    Scorr, Laura M / Kilic-Berkmen, Gamze / Sutcliffe, Diane J / Dinasarapu, Ashok R / McKay, J Lucas / Bagchi, Pritha / Powell, Michael D / Boss, Jeremy M / Cereb, Nezih / Little, Marian / Gragert, Loren / Hanfelt, John / McKeon, Andrew / Tyor, William / Jinnah, H A

    Parkinsonism & related disorders

    2024  Volume 122, Page(s) 106036

    Abstract: Background: Although there are many possible causes for cervical dystonia (CD), a specific etiology cannot be identified in most cases. Prior studies have suggested a relationship between autoimmune disease and some cases of CD, pointing to possible ... ...

    Abstract Background: Although there are many possible causes for cervical dystonia (CD), a specific etiology cannot be identified in most cases. Prior studies have suggested a relationship between autoimmune disease and some cases of CD, pointing to possible immunological mechanisms.
    Objective: The goal was to explore the potential role of multiple different immunological mechanisms in CD.
    Methods: First, a broad screening test compared neuronal antibodies in controls and CD. Second, unbiased blood plasma proteomics provided a broad screen for potential biologic differences between controls and CD. Third, a multiplex immunoassay compared 37 markers associated with immunological processes in controls and CD. Fourth, relative immune cell frequencies were investigated in blood samples of controls and CD. Finally, sequencing studies investigated the association of HLA DQB1 and DRB1 alleles in controls versus CD.
    Results: Screens for anti-neuronal antibodies did not reveal any obvious abnormalities. Plasma proteomics pointed towards certain abnormalities of immune mechanisms, and the multiplex assay pointed more specifically towards abnormalities in T lymphocytes. Abnormal immune cell frequencies were identified for some CD cases, and these cases clustered together as a potential subgroup. Studies of HLA alleles indicated a possible association between CD and DRB1*15:03, which is reported to mediate the penetrance of autoimmune disorders.
    Conclusions: Altogether, the association of CD with multiple different blood-based immune measures point to abnormalities in cell-mediated immunity that may play a pathogenic role for a subgroup of individuals with CD.
    MeSH term(s) Humans ; Torticollis/immunology ; Torticollis/genetics ; Male ; Female ; Middle Aged ; Proteomics ; Adult ; Aged ; HLA-DQ beta-Chains/genetics ; HLA-DRB1 Chains/genetics ; Autoantibodies/blood
    Chemical Substances HLA-DQ beta-Chains ; HLA-DRB1 Chains ; Autoantibodies ; HLA-DQB1 antigen
    Language English
    Publishing date 2024-02-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1311489-x
    ISSN 1873-5126 ; 1353-8020
    ISSN (online) 1873-5126
    ISSN 1353-8020
    DOI 10.1016/j.parkreldis.2024.106036
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  9. Article ; Online: Connect, Collaborate, and Succeed: The Ninth Annual Meeting of the Southeastern Association of Shared Resources (SEASR) Nashville, TN, USA, June 8-10, 2022.

    Bagchi, Pritha / Boukli, Nawal M / Browner, Natasha / Daria, Deidre / Griffiths, Lyra / Mesa, Tania E / Phipps, John / Pitre, Aaron / Schafer, Jenny / Somasundaram, Thayumanasamy / Seagroves, Tiffany N

    Journal of biomolecular techniques : JBT

    2023  Volume 34, Issue 1

    Abstract: audio element]. ...

    Abstract [audio element].
    Language English
    Publishing date 2023-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2116011-9
    ISSN 1943-4731 ; 1943-4731
    ISSN (online) 1943-4731
    ISSN 1943-4731
    DOI 10.7171/3fc1f5fe.283433d3
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  10. Article: Defining the ligand-dependent proximatome of the sigma 1 receptor.

    Zhao, Jing / Veeranan-Karmegam, Rajalakshmi / Baker, Frederick C / Mysona, Barbara A / Bagchi, Pritha / Liu, Yutao / Smith, Sylvia B / Gonsalvez, Graydon B / Bollinger, Kathryn E

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1045759

    Abstract: Sigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular ...

    Abstract Sigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular systems. It is proposed to function as a ligand-dependent molecular chaperone that modulates multiple intracellular signaling pathways. The purpose of this study was to define the S1R proximatome under native conditions and upon binding to well-characterized ligands. This was accomplished by fusing the biotin ligase, Apex2, to the C terminus of S1R. Cells stably expressing S1R-Apex or a GFP-Apex control were used to map proximal proteins. Biotinylated proteins were labeled under native conditions and in a ligand dependent manner, then purified and identified using quantitative mass spectrometry. Under native conditions, S1R biotinylates over 200 novel proteins, many of which localize within the endomembrane system (endoplasmic reticulum, Golgi, secretory vesicles) and function within the secretory pathway. Under conditions of cellular exposure to either S1R agonist or antagonist, results show enrichment of proteins integral to secretion, extracellular matrix formation, and cholesterol biosynthesis. Notably, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) displays increased binding to S1R under conditions of treatment with Haloperidol, a well-known S1R antagonist; whereas Low density lipoprotein receptor (LDLR) binds more efficiently to S1R upon treatment with (+)-Pentazocine ((+)-PTZ), a classical S1R agonist. Furthermore, we demonstrate that the ligand bound state of S1R correlates with specific changes to the cellular secretome. Our results are consistent with the postulated role of S1R as an intracellular chaperone and further suggest important and novel functionalities related to secretion and cholesterol metabolism.
    Language English
    Publishing date 2023-06-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1045759
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