About Autophagy

The Process of Autophagy ^

The part (or parts) of the cell that is to be degraded is first engulfed by a double membrane to separate it from the rest of the cell; the resulting membrane-enclosed bubble of cytosol (along with all the proteins the bubble contains) becomes what is called the autophagosome. The autophagosome eventually fuses with a cellular organelle called a lysosome, a much larger membrane-enclosed bubble that contains a variety of enzymes that can break down many types of cellular components (which is why lysosomes are sometimes referred to as the “garbage disposals” of the cell). These enzymes only work in a very acidic environment, so the pH inside lysosomes is much lower than the neutral pH in the rest of the cell. This pH barrier, as well as the physical barrier of the organelle membrane, protects the rest of the cell from being degraded should the enzymes somehow leak out. Once the contents of the autophagosome are delivered to the lysosome, the lysosomal enzymes break down the new contents, which can then be recycled and reused within the cell.

Until a couple of years ago, it was believed that the main mechanism by which the nerve cell got rid of huntingtin aggregates involved what is called the ubiquitin-proteasome system, which is responsible for tagging and degrading improperly formed proteins. However, recent research shows that proteins with abnormally expanded stretches of the amino acid glutamine, like the altered huntingtin protein (which is associated with HD), are also disposed of by the process of autophagy. In this process, the aggregated proteins are gathered up and transported to the lysosome, where they are broken down and their component amino acids are recycled. Studies of nerve cells have shown that the mutant huntingtin protein can often be found in autophagosomes, the membrane-bound sacs that carry cell parts to the lysosome for degradation.

Researchers have investigated whether proteins with expanded sections of the amino acids glutamine and alanine could be degraded by cells using the process of autophagy. They compared autophagy with the ubiquitin-proteasome process, which was originally thought to be the only process by which these harmful proteins are degraded. The researchers used cells that expressed these proteins and tagged them with green fluorescent protein (GFP) in order to visualize their fate within the cells. GFP allows researchers to see the amount and the location of a specific protein present in the cell because it fluoresces, or glows, when viewed under a special microscope. To study how huntingtin aggregates are broken down by the cell, they used cells that produced, or expressed, part of the HD allele that contained either 55 or 74 CAG repeats. (To read more about the huntingtin protein, click here.)

To determine whether autophagy is indeed a key process in the clearance of huntingtin aggregates, the researchers first used two different compounds to inhibit autophagy at different points of the process and observed the effect on aggregate formation. The first compound they used inhibits autophagy by preventing a membrane from surrounding the cell contents that are about to be degraded; if the autophagosome cannot form, the contents cannot be delivered to the lysosome to be broken down. The second compound they used prevents the autophagosome from fusing with the lysosome and releasing its contents, which also prevents autophagy from occurring. Treatment with these compounds resulted in visibly higher levels of huntingtin aggregates in cell cultures, which showed that autophagy does play a role in the breakdown of aggregates. Along with the increase in aggregates, the researchers also saw increased cell death when the cells were treated with autophagy-inhibiting compounds.

The researchers also tested the role of the ubiquitin-proteasome system in reducing protein aggregation in the same cell cultures. Most previous experiments have used a certain compound to inhibit the proteasome that is thought to inhibit the function of the lysosome as well. Because they wanted to test the role of the proteasome only, the researchers used a different compound that inhibits the proteasome and has no effect on lysosomes. They found that inhibiting the proteasome increased aggregate formation in one cell line but not in another. While these results are somewhat inconclusive, they may suggest that the ubiquitin-proteasome process is not the main mechanism by which cells get rid of the disease-state huntingtin protein. More research about the role of autophagy in degrading mutant huntingtin needs to be done.

Several drugs are known to modulate the process of autophagy in different ways. The hope is that drugs which promote autophagy will aid nerve cells in breaking down huntingtin aggregates and help to protect the cells. Research is being done to identify the effectiveness of different types of drugs.

For further reading^

• Raught, et al. “The target of rapamycin (TOR) proteins.” Proceedings of the National Academy of Sciences of the United States of America. 2001 Jun 19;98(13):7037-44.
  Short paper which describes various functions of target of rapamycin (TOR) proteins in fairly technical writing.
• Ravikumar, et al. “Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy.” Human Molecular Genetics. 2002 May 1;11(9):1107-17.
  2001 Jun 19;98(13):7037-44.
  Fairly technical article which describes experiments aimed to discover whether or not proteins with multiple amino acid repeats could be controlled through the process of autophagy.
• Ravikumar, et al. “Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease.” Nature Genetics 2004 Jun 36(6):585-95.
  This technical paper describing the effects of mTOR inhibition was cited in the “mTOR and HD” section.
• Sarkar S., et al. “Rapamycin and mTOR-independent autophagy inducers ameliorate toxicity of polyglutamine-expanded huntingtin and related proteinopathies.” Cell Death and Differentiation advance online publication, 18 July 2008; doi:10.1038/cdd.2008.110.
  Very technical paper which describes the effects of autophagy inducers in controlling HD and other diseases caused by malformed proteins.
• Thoreen, et al. “Huntingtin aggregates ask to be eaten.” Nature Genetics. 2002 Jun;36(6):553-4.
  Less technical article that describes the role of autophagy in controlling mutant huntingtin aggregates.
• Williams et al. “Novel targets for Huntington’s Disease in an mTOR-independent autophagy pathway.” 2008 May;5(4):295-305
  Less technical article which reviewed the role of calpains in HD and different autophagy-inducing therapies was cited in the “Calpains and HD” and the “Combination Therapies” sections.