Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Metabolism models may explain why Alzheimer's disease kills some neuron types first

07.12.2010
Bioengineers from the University of California, San Diego developed an explanation for why some types of neurons die sooner than others in the brains of people with Alzheimer’s disease. These insights, published in the journal Nature Biotechnology on November 21, come from detailed models of brain energy metabolism developed in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

The Alzheimer’s insights demonstrate how fundamental insights on human metabolism can be gleaned from computer models that incorporate large genomic and proteomic data sets with information from biochemical studies. UC San Diego bioengineering professor Bernhard Palsson and his students and collaborators first developed this “in silico” modeling approach for E. coli and other prokaryotes, and later extended it to human tissues.

The Nature Biotechnology paper describes the first time this modeling approach has been used to capture how the metabolism of specific human cell types affect the metabolism of other cell types.

“In human tissues, different cells have different roles. We’re trying to predict how the behavior of one cell type will affect the behavior of other cell types,” said Nathan Lewis, a Ph.D. candidate in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering and the first author on the Nature Biotechnology paper, which also includes authors from the University of Heidelberg, Massachusetts Institute of Technology, and the German Cancer Research Center (DKFZ).

Similar approaches can be used to identify potential off-target effects of drugs, provide insights on disease progression, and offer new tools for uncovering the underlying biological mechanisms in a wide range of human tissues and cell types.

Why Some Neurons Die First in the Alzheimer’s Brain

In the brains of people with Alzheimer’s disease, certain cells, such as glutamatergic and cholinergic neurons, tend to die in much larger numbers in moderate stages of Alzheimer’s disease, while GABAergic neurons are relatively unaffected until later stages of the disease.

“There is a big question as to what is causing this cell-type specificity,” said Lewis.

The researchers builtPalsson Lab: Systems Biology Research Group computational models that captured the metabolic interactions between each of the three neuron types and their associated astrocyte cells. Next, the bioengineersknocked down α-ketoglutarate, a gene known to be damaged in patients with Alzheimer’s disease, and let their models of brain metabolism run to see what happens.

The results from the models agreed with clinical data. When the bioengineers disrupted the α-ketoglutarate enzyme in the models for cholinergic and glutamatergic neurons, the metabolic rate of these neurons dropped, leading to cell death. “But then you have the GABAergic neurons that show no effect. So the cell types that are known to be lost early on in Alzheimer’s show slowed metabolic rates,” explained Lewis.

Analysis of their models then led the bioengineers to the biochemical pathways that allowed the GABAergic neurons to be relatively unaffected despite the disrupted gene.

“We looked at what upstream is allowing this and found a GABA-specific enzyme called glutamate decarboxylase,” said Lewis.

When the researchers added this enzyme to the models of the other neuron types, the metabolic rates of these neurons improved as well. Thus the model allowed the researchers to identify a gene and how it contributes to the whole cell to potentially prolong the life of certain cells in Alzheimer’s disease.

Large Scale Modeling of Metabolic Interactions

The new Nature Biotechnology paper uses the Alzheimer’s brain study as an example of how to build models of metabolism that go one level deeper than previous work by taking into account the tissue microenvironment and metabolic interactions between specific cell types.

The models for each cell can be represented like a circuit, with certain inputs and outputs. For example, sugars, like glucose, are inputs, and the models detail how these inputs are used to build cell parts and secrete byproducts as outputs. The metabolic models the bioengineers built provide a means to study these networks.

For example, each cell type has different biochemical pathways that can take the sugars from point A to B. If you knock out a gene in between, the network might find a different route, produce different products, or predict cell death. When models for multiple cells are combined, additional insight can be gained since the inputs and outputs of each model begin to affect the other cells.

“There are many potential applications for these models. For example, this modeling approach could be useful for predicting off target side effects of drugs. You could theoretically take a cell line, throw a drug at it and see which metabolic pathways are significantly affected. Thus, you could decrease the amount of resources spent on drug development if the model suggests negative side effects that may cause it to fail,” said Lewis.

“Large-scale in silico modeling of metabolic interactions between cell types in the human brain,” by Nathan E Lewis (1), Gunnar Schramm (2,5), Aarash Bordbar (1), Jan Schellenberger (3), Michael P Andersen (1), Jeffrey K Cheng (1), Nilam Patel (1), Alex Yee (1), Randall A Lewis (4), Roland Eils (2,5), Rainer König (2,5) & Bernhard Ø Palsson (1); published online on November 21, 2010 in Nature Biotechnology.

(1) Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
(2) Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany.
(3) Bioinformatics Program, University of California, San Diego, La Jolla, California, USA.
(4) Department of Economics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

(5) Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

This work was funded in part by a Fulbright fellowship, a National Science Foundation IGERT Plant Systems Biology training grant (no. DGE-0504645), a US National Institutes of Health grant 2R01GM068837_05A1 and the Helmholtz Alliance on Systems Biology and the BMBF by the NGFN+ neuroblastoma project ENGINE.

Daniel Kane | EurekAlert!
Further information:
http://www.ucsd.edu

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>