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Artikel ; Online: Regulation of the intestinal Na

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

American journal of physiology. Cell physiology

2023 Band 326, Heft 1, Seite(n) C50–C59

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

Abstract	Electroneutral NaCl transport by Na
Mesh-Begriff(e)	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
Chemische Substanzen	AMP-Activated Protein Kinases (EC 2.7.11.31) ; Sodium-Hydrogen Exchanger 3 ; Metformin (9100L32L2N) ; Aminoimidazole Carboxamide (360-97-4)
Sprache	Englisch
Erscheinungsdatum	2023-12-04
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	392098-7
ISSN	1522-1563 ; 0363-6143
ISSN (online)	1522-1563
ISSN	0363-6143
DOI	10.1152/ajpcell.00540.2023
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Copper(I)-nitrene platform for chemoproteomic profiling of methionine.

Sahu, Samrat / Emenike, Benjamin / Beusch, Christian Michel / Bagchi, Pritha / Gordon, David Ezra / Raj, Monika

Nature communications

2024 Band 15, Heft 1, Seite(n) 4243

Abstract: Methionine plays a critical role in various biological and cell regulatory processes, making its chemoproteomic profiling indispensable for exploring its functions and potential in protein therapeutics. Building on the principle of rapid oxidation of ... ...

Abstract	Methionine plays a critical role in various biological and cell regulatory processes, making its chemoproteomic profiling indispensable for exploring its functions and potential in protein therapeutics. Building on the principle of rapid oxidation of methionine, we report Copper(I)-Nitrene Platform for robust, and selective labeling of methionine to generate stable sulfonyl sulfimide conjugates under physiological conditions. We demonstrate the versatility of this platform to label methionine in bioactive peptides, intact proteins (6.5-79.5 kDa), and proteins in complex cell lysate mixtures with varying payloads. We discover ligandable proteins and sites harboring hyperreactive methionine within the human proteome. Furthermore, this has been utilized to profile oxidation-sensitive methionine residues, which might increase our understanding of the protective role of methionine in diseases associated with elevated levels of reactive oxygen species. The Copper(I)-Nitrene Platform allows labeling methionine residues in live cancer cells, observing minimal cytotoxic effects and achieving dose-dependent labeling. Confocal imaging further reveals the spatial distribution of modified proteins within the cell membrane, cytoplasm, and nucleus, underscoring the platform's potential in profiling the cellular interactome.
Mesh-Begriff(e)	Humans ; Methionine/metabolism ; Methionine/chemistry ; Copper/metabolism ; Copper/chemistry ; Proteomics/methods ; Oxidation-Reduction ; Proteome/metabolism ; Cell Line, Tumor ; Peptides/metabolism ; Peptides/chemistry ; Imines
Chemische Substanzen	phenylnitrene
Sprache	Englisch
Erscheinungsdatum	2024-05-18
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-48403-0
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; 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 Band 14, Heft 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-Begriff(e)	Animals ; Female ; Humans ; Male ; Mice ; Alzheimer Disease/genetics ; Dependovirus ; Dual-Specificity Phosphatases/genetics ; Mitogen-Activated Protein Kinase Phosphatases/genetics ; Proteome ; Proteomics ; Signal Transduction
Chemische Substanzen	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)
Sprache	Englisch
Erscheinungsdatum	2024-01-03
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom14010066
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: 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.
Sprache	Englisch
Erscheinungsdatum	2023-09-14
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2023.09.13.557390
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: 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, 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.
Sprache	Englisch
Erscheinungsdatum	2023-10-19
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.21203/rs.3.rs-3453503/v1
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: 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
Sprache	Englisch
Erscheinungsdatum	2023-03-28
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2023.03.28.534590
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; 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 Band 20, Heft 5, Seite(n) 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.
Mesh-Begriff(e)	Clostridioides difficile/pathogenicity ; Clostridioides difficile/genetics ; Clostridioides difficile/metabolism ; Spores, Bacterial/genetics ; Virulence ; Bacterial Proteins/metabolism ; Bacterial Proteins/genetics ; Animals ; Mice ; Gene Expression Regulation, Bacterial ; Clostridium Infections/microbiology
Chemische Substanzen	Bacterial Proteins
Sprache	Englisch
Erscheinungsdatum	2024-05-13
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1012224
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; 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 Band 298, Heft 8, Seite(n) 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-Begriff(e)	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
Chemische Substanzen	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)
Sprache	Englisch
Erscheinungsdatum	2022-06-14
Erscheinungsland	United States
Dokumenttyp	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
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; 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 Band 122, Seite(n) 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 DRB115:03, 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-Begriff(e)	Humans ; Torticollis/immunology ; Torticollis/genetics ; Male ; Female ; Middle Aged ; Proteomics ; Adult ; Aged ; HLA-DQ beta-Chains/genetics ; HLA-DRB1 Chains/genetics ; Autoantibodies/blood
Chemische Substanzen	HLA-DQ beta-Chains ; HLA-DRB1 Chains ; Autoantibodies ; HLA-DQB1 antigen
Sprache	Englisch
Erscheinungsdatum	2024-02-17
Erscheinungsland	England
Dokumenttyp	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
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; 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 Band 34, Heft 1

Abstract: audio element]. ...

Abstract	[audio element].
Sprache	Englisch
Erscheinungsdatum	2023-02-21
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2116011-9
ISSN	1943-4731 ; 1943-4731
ISSN (online)	1943-4731
ISSN	1943-4731
DOI	10.7171/3fc1f5fe.283433d3
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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