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APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

Laßek M, Weingarten J, Wegner M, Mueller BF, Rohmer M, Baeumlisberger D, Arrey TN, Hick M, Ackermann J, Acker-Palmer A, Koch I, Müller U, Karas M, Volknandt W - PLoS Comput. Biol. (2016)

Bottom Line: Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry.The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis.The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell Biology and Neuroscience, Biologicum, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

ABSTRACT
The hallmarks of Alzheimer's disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

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The interactome of the native hippocampal PAZ core proteome.A Proteins grouped according to their localization (localization layout). B Community structure layout (function) of the network. The size of the rings corresponds to the respective number of proteins. The color code corresponds to the pie chart diagram (cf. Fig 1E). C Impact of APP deletion on relative protein abundance mapped according to their localizations. D Impact of the APP-KO on relative protein abundance mapped according to the community structure. E Impact of the NexCre-cDKO on relative protein abundance mapped according to their localizations. F Impact of the NexCre-cDKO on relative protein abundance mapped according to the community structure. Change in abundance of more than ±10% is reflected by increasing sizes of nodes. The color code corresponds to the degree of up- (magenta) and downregulation (green). Nodes in yellow represent proteins with changes in abundance of less than ±10%. Each node (dot in the rings) within this network represents a protein and each edge (connection) represents a reported physical interaction between two proteins. Edges are bundled for clarity.
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pcbi.1004832.g003: The interactome of the native hippocampal PAZ core proteome.A Proteins grouped according to their localization (localization layout). B Community structure layout (function) of the network. The size of the rings corresponds to the respective number of proteins. The color code corresponds to the pie chart diagram (cf. Fig 1E). C Impact of APP deletion on relative protein abundance mapped according to their localizations. D Impact of the APP-KO on relative protein abundance mapped according to the community structure. E Impact of the NexCre-cDKO on relative protein abundance mapped according to their localizations. F Impact of the NexCre-cDKO on relative protein abundance mapped according to the community structure. Change in abundance of more than ±10% is reflected by increasing sizes of nodes. The color code corresponds to the degree of up- (magenta) and downregulation (green). Nodes in yellow represent proteins with changes in abundance of less than ±10%. Each node (dot in the rings) within this network represents a protein and each edge (connection) represents a reported physical interaction between two proteins. Edges are bundled for clarity.

Mentions: To further characterize the impact of APP deletion the abundance of hippocampal constituents was visualized according to both their subcellular localization (Fig 3A, left) and their functional allocation (Fig 3B, right). The final network layout illustrates proteins as nodes and interactions (experimentally validated physical interactions) between proteins as edges (Figs 3–8). The resulting 615 proteins revealed a high degree of networking, confirming their direct association with the hippocampal PAZ core proteome.


APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

Laßek M, Weingarten J, Wegner M, Mueller BF, Rohmer M, Baeumlisberger D, Arrey TN, Hick M, Ackermann J, Acker-Palmer A, Koch I, Müller U, Karas M, Volknandt W - PLoS Comput. Biol. (2016)

The interactome of the native hippocampal PAZ core proteome.A Proteins grouped according to their localization (localization layout). B Community structure layout (function) of the network. The size of the rings corresponds to the respective number of proteins. The color code corresponds to the pie chart diagram (cf. Fig 1E). C Impact of APP deletion on relative protein abundance mapped according to their localizations. D Impact of the APP-KO on relative protein abundance mapped according to the community structure. E Impact of the NexCre-cDKO on relative protein abundance mapped according to their localizations. F Impact of the NexCre-cDKO on relative protein abundance mapped according to the community structure. Change in abundance of more than ±10% is reflected by increasing sizes of nodes. The color code corresponds to the degree of up- (magenta) and downregulation (green). Nodes in yellow represent proteins with changes in abundance of less than ±10%. Each node (dot in the rings) within this network represents a protein and each edge (connection) represents a reported physical interaction between two proteins. Edges are bundled for clarity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836664&req=5

pcbi.1004832.g003: The interactome of the native hippocampal PAZ core proteome.A Proteins grouped according to their localization (localization layout). B Community structure layout (function) of the network. The size of the rings corresponds to the respective number of proteins. The color code corresponds to the pie chart diagram (cf. Fig 1E). C Impact of APP deletion on relative protein abundance mapped according to their localizations. D Impact of the APP-KO on relative protein abundance mapped according to the community structure. E Impact of the NexCre-cDKO on relative protein abundance mapped according to their localizations. F Impact of the NexCre-cDKO on relative protein abundance mapped according to the community structure. Change in abundance of more than ±10% is reflected by increasing sizes of nodes. The color code corresponds to the degree of up- (magenta) and downregulation (green). Nodes in yellow represent proteins with changes in abundance of less than ±10%. Each node (dot in the rings) within this network represents a protein and each edge (connection) represents a reported physical interaction between two proteins. Edges are bundled for clarity.
Mentions: To further characterize the impact of APP deletion the abundance of hippocampal constituents was visualized according to both their subcellular localization (Fig 3A, left) and their functional allocation (Fig 3B, right). The final network layout illustrates proteins as nodes and interactions (experimentally validated physical interactions) between proteins as edges (Figs 3–8). The resulting 615 proteins revealed a high degree of networking, confirming their direct association with the hippocampal PAZ core proteome.

Bottom Line: Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry.The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis.The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell Biology and Neuroscience, Biologicum, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

ABSTRACT
The hallmarks of Alzheimer's disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

Show MeSH
Related in: MedlinePlus