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Signaling Networks That Control Neuron Function Mapped For The First Time

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In the first large-scale proteomics study of its kind, researchers at the University of California, San Diego (UCSD) School of Medicine have mapped thousands of neuronal proteins to discover how they connect into complex signaling networks that guide neuron function. Their research — using quantitative mass spectrometry, computational software and bioinformatics to match the proteins to their cellular functions — may lead to a better understanding of brain development, neurodegenerative diseases, and spinal cord regeneration.
Mouse neuron showing multiple neurites with fan-shaped growth cones. (Credit: UCSD School of Medicine)

Led by Richard Klemke, Ph.D., professor of pathology at UCSD School of Medicine and the Moores UCSD Cancer Center, the research team designed a new technology enabling them to, for the first time, isolate and purify neurites — long membrane extensions from the neuron that give rise to axons or dendrites. This technological breakthrough opens the door to understanding how neurites form and differentiate to regenerate neuronal connections and give rise to a functioning network. It also led to the discovery of how two key signaling molecules are regulated by a complex protein network that controls neurite outgrowth.

The formation of neurites, a process called neuritogenesis, is the first step in the differentiation of neurons, the basic information cells of the central nervous system.

“Understanding how neurites form is crucial, as these structures give rise to the specialized axons and dendrites which relay sensory input and enable us to see, hear, taste, reason and dream,” said Klemke.

Neurons regenerate by sending out one or several long, thin neurites that will ultimately differentiate into axons, which primarily receive signals, or dendrites, primarily involved in sending out signals. These long, branch-like protrusions have a specialized sensory structure called a growth cone that probes the extracellular environment to find its way and determine which direction the neurite should move in order to hook up with other neurites that will also differentiate into axons and dendrites.

The neural signaling network of dendrites and axons forms a huge information grid, which the UCSD team is studying in order to discover how neurons connect properly and regenerate to maintain proper wiring of the brain. Understanding the role that neuritogenesis plays in the regeneration of nerve connections damaged by diseases such as Alzheimer’s, Parkinson’s or other neurogenerative diseases is an important component of mapping the signaling network.

“Our primary goal is to identify unique proteins that cause the neurite to sprout and differentiate,” said Klemke. “We also want to understand the underlying signals that guide neurite formation and migration in response to directional cues.”

Klemke’s postdoctoral associates Olivier Pertz and Yingchun Wang identified a complex network of enriched proteins called GEFs and GAPs that control neuritogenesis by modulating signaling.

“This signaling provides external guidance cues to mechanical mechanisms inside the cell that make the neurite go forward, turn, or reverse direction,” Klemke said. “Understanding how the thousands of neurite proteins work in concert may someday help us guide neurites to the right place in the body to regenerate and reverse the impact of neural degenerative diseases or help facilitate spinal cord healing after injury.”

The researchers developed a unique microporous filter technology to separate the neurite from the cell body of the neuron, called the soma. The ability to slice millions of neurons into their soma and neurite components opened the door to using mass spectrometry, a tool able to identify the thousands of proteins that uniquely compose the two structures. Using information gleaned from published work, the researchers were then able to predict the function of most of the neurite proteins. This allowed them to construct a blueprint of how the thousands of proteins work together to facilitate neurite formation.

PNAS 2007 104: 8328-8333; published online before print as 10.1073/pnas.0701103104

Profiling signaling polarity in chemotactic cells

Yingchun Wang, Shi-Jian Ding, Wei Wang, Jon M. Jacobs, Wei-Jun Qian, Ronald J. Moore, Feng Yang, David G. Camp, II, Richard D. Smith, and Richard L. Klemke

Cell movement requires morphological polarization characterized by formation of a leading pseudopodium (PD) at the front and a trailing rear at the back. However, little is known about how protein networks are spatially integrated to regulate this process at the system level. Here, we apply global proteome profiling in combination with newly developed quantitative phosphoproteomics approaches for comparative analysis of the cell body (CB) and PD proteome of chemotactic cells. The spatial relationship of 3,509 proteins and 228 distinct sites of phosphorylation were mapped revealing networks of signaling proteins that partition to the PD and/or the CB compartments. The major network represented in the PD includes integrin signaling, actin regulatory, and axon guidance proteins, whereas the CB consists of DNA/RNA metabolism, cell cycle regulation, and structural maintenance. Our findings provide insight into the spatial organization of signaling networks that control cell movement and provide a comprehensive system-wide profile of proteins and phosphorylation sites that control cell polarization.

Written by huehueteotl

February 5, 2008 at 1:09 pm

One Response

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  1. If you want to see a reader’s feedback🙂 , I rate this article for 4/5. Detailed info, but I have to go to that damn yahoo to find the missed pieces. Thank you, anyway!

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    April 15, 2009 at 2:12 pm


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