A dummies guide to researching how AAG induces Endoplasmic Reticulum stress

Welcome back to my last blog post. Apologies for the title I couldn’t come up with any alliteration or film references for this one, however, to paraphrase the words of Thomas Dolby that I am currently listening to hopefully I can blind you with science.

As it has been almost a good 2 months since I started the blog about my dissertation, it’s probably best that I give you a brief recap on the Who? What? When? Where? and most importantly for this post the How?

The Five Ws

I’m Thomas Cox a final year MSci Biochemistry student at the University of Surrey and under the supervision of Dr Lisiane Meira, a researcher and lecturer in DNA Damage and Ageing, I shall be undertaking a dissertation for the next 4-5 months. The goal of the dissertation is to identify at least partially how the DNA repair molecule “AAG” can induce endoplasmic reticulum stress (ER stress) in cancer cells in response to alkylation-based DNA damage. If you have been following my blog this should now make sense, but if you are one of those that skips to the last chapter of the book to get a peek at the ending, I’ll simplify it. We are trying to understand how the activity of the protein AAG, that normally helps repair DNA after harmful carbon-based molecules called Alkyl groups are added to the DNA, can actually lead to the area of the cell that produces and folds proteins becoming stressed which if excessive or chronic can lead to cell death.

The reason we are trying to understand this is because if we know how AAG leads to the ER becoming stressed then we can design drugs to either avoid or induce this stress using the same pathway. By why would we design a drug to cause stress I hear you ask? Don’t we have enough stress in our lives? Well, that’s because it could be applied to chemotherapy. This is because cancer cells already have low to moderate levels of ER stress that are lacking in the body’s healthy cells, therefore by giving a drug that further increases the ERs stress of the body we can cause the healthy cells to feel a little ill but the cancer cells will be tipped into high levels of ER stress which should cause their deaths. Thus, killing the cancer cells and leaving most healthy cells unharmed (Hetz, 2012; Sano and Reed, 2013; Yadav et al., 2014).

The How

Figure 1
Possibly pathways for how AAG causes ER stress and the unfolded protein response (UPR).
The canonical pathway is highlighted in blue and suggests that the cause of the ER stress is from AAG undertaking its activity in base excision repair in order to repair DNA damage.
The non-canonical pathway in red suggests that the cause of the ER stress is from an unknown alternative AAG activity that is not associated with DNA repair. Theoretically this alternative activity could be induced through the detection of alkylation damaged proteins.  
Diagram provided by Dr Lisiane Meira

Now it’s time for the aforementioned blinding you with science. So, there are two theories as to how AAG causes ER stress, through its canonical activity of repairing DNA damage or through a hitherto unknown activity (non-canonical activity) that is possibly activated by alkylation damaged proteins (See figure 1).

To identify which theory is correct 2 AAG genes were developed, one is the completely normal AAG whilst the other codes for an AAG which has had its structure slightly altered so it has no canonical DNA repair activity. Therefore, this altered AAG shouldn’t be able to repair alkylation damaged, but it should be able to undertake any other activities that AAG has.

The experiment we will undertake is like an odd inventor, who for reasons totally unrelated to my Christmas binging of Aardman and cheese shall be called Wallace, that is trying to work out whether the front or rear brake on his bike is more important to slow down. First, he will go down a hill on a normal bike, with both front and rear brakes, and see how quickly he slows down when the brakes are applied. The normal bike is like the normal AAG where the rear brake is akin to the canonical DNA repair activity of AAG and the front break is akin to the non-canonical activity of AAG, whilst the rate of him slowing down is akin to the level of ER stress following alkylation damage. After measuring how fast a normal bike slows down, he then disables his rear brake so only the front brake works, this is like the altered AAG with no canonical activity but active non-canonical activity. He will then go down the hill on this altered bike/AAG, record how quickly he slows down once the brakes are applied and then compare this with the normal bike/AAG.

If the rate of slowing down is equal between both bikes, then the rear brake has no effect on slowing the bike thus the front brake does all the work. In term of our experiment if the level of ER stress is equal between the AAG’s with and without canonical activity then the loss of canonical activity has no effect in reducing ER stress, thus non-canonical activity must be the sole route for AAG mediated ER stress.

If the rate of slowing down is reduced but he still comes to a stop on the altered bike, then both the rear and front brakes have a role in how quickly the bike slows. In our terms if the ER stress is reduced but still present in the AAG without canonical activity then both canonical and non-canonical activity could be playing a role in causing the ER stress.

Finally, if the altered bike doesn’t slow down at all, leading poor Wallace to crash into a knitting shop, then the front brake has no effect on slowing down the bike and therefore slowing down the bike relies entirely on the rear brake. In our terms if the ER stress is virtually absent in the AAG lacking canonical activity then the remaining non-canonical activity has no effect in causing ER stress and thus the canonical activity is the sole route for AAG mediated ER stress

Whilst this doesn’t immediately identify how to utilise the pathway for chemotherapy it will identify the right direction for further research and as Sir Isaac Newton once said “If I have seen further it is by standing on the shoulders of Giants”, therefore these results we produce here may point ourselves or others in the correct direction so even greater and more impactful discoveries can be made.

It has been a joy to write this blog and I hope that you have come away with some understanding of how the endoplasmic reticulum, chemotherapy or DNA repair works, or at the very least have a newfound appreciation for how the smallest discovery could lead to great implications and applications if only it is studied and used in the right perspective (Either that or pity us long suffering students with all our deadlines 😉).

Bibliography

Hetz, C. (2012). The unfolded protein response: controlling cell fate decisions under ER stress and beyond. Nature Reviews Molecular Cell Biology, 13(2), pp.89-102.

Sano, R., & Reed, J. C. (2013). ER stress-induced cell death mechanisms. Biochimica et biophysica acta1833(12), pp.3460–3470.

Yadav, R. K., Chae, S. W., Kim, H. R., & Chae, H. J. (2014). Endoplasmic reticulum stress and cancer. Journal of cancer prevention, 19(2), pp.75–88.