Affiliations : VCU, Virginia, USA
Journal reference: https://doi.org/10.1038/s41398-018-0267-7
Summary: What if we could explain the genetics behind suicide? Gaining a deeper understanding of the genes involved in placing an individual at higher risk of dying by suicide is a big step towards novel advanced treatment and prevention strategies. Read this article to find out more.
Depression is a complicated disease. Disruptions in brain chemistry and certain experiences or traumatic events can be major contributors to depression and suicide. We must also consider the interaction between the environment and our biological predispositions and ask how is it that some environmental exposures/traumas, that have lasting effects on our psyche and our minds, lead to biological changes in our brain chemistry and function? Such questions are the essence of the study of genetic and environmental interactions.
It turns out that certain genes can be turned on and off in response to certain environmental exposures or triggers. This type of gene regulation is known as “epigenetics”. The mechanisms that control when and how much of a certain gene is “expressed”, or turned on, vary greatly but some well established ones include DNA methylation, histone modifications, and non-coding RNAs. In this project, we investigate a specific type of RNA called long non-coding RNAs. Briefly, a cell’s DNA produces, or is transcribed into, RNA, which then usually goes on to produce, or become translated into, the proteins that carry out the important functions of a cell. However, non-coding RNAs (of varying sizes) do not get translated into proteins and have been shown to have other regulatory functions. Long non-coding RNAs (lncRNAs) are named as such, well because they are long and do not code for any proteins. It is not very creative, but at least it isn’t something unpronounceable.
Many lncRNAs have been discovered. However, the vast majority have no known function. The major aim of this project was to investigate whether there were differences in the amounts of lncRNAs in the brains of those who had depression and died by suicide compared to others who died naturally and did not have depression. Furthermore, we introduce strategies to hypothesize about the function of certain lncRNAs by identifying potential target genes it may be turning on or off.
In this project, we took brain samples from 26 depressed suicide completers and 24 controls, specifically from an area called the anterior cingulate cortex which is thought to be involved in emotional regulation and emotional pain. Whole brains were kept frozen or fixed in what’s called a “brain bank” located at the Douglas Bell-Canada Brain Bank in Montreal, Canada. Dissected chunks of brains were then broken up with reagents and RNA were extracted. Afterwards, a special technique called RNA-sequencing was done to look at and quantify the amount of distinct types of RNA there were in each brain sample. The amount of RNA there is can be thought of as how much a gene is activated or turned on. The greater the activity, the higher the expression of RNA.
When we looked at the expression of lncRNAs, we found around 350 that showed differences between depressed suicide completers and normal controls. We then focused on the top 23 showing the biggest and most statistically significant differences in expression.
One hypothesis for the mechanism by which some of them work is that a lncRNA gene may exert its effects on other genes that are close by. For example, a lncRNA gene may be transcribed into long non-coding RNAs which then fold into all sorts of wiggly and wonky shapes that act as “landing pads” for certain types of proteins. These special proteins may then be able to turn nearby protein coding genes on or off. To see if any of the top lncRNA genes associated with depression/suicide could potentially work this way, we looked to see if there were any nearby genes around them. We found 6 such protein coding genes and interestingly, several of them (IRF2, LY6E, and HMBOX1) were associated with the immune system. The immune system has been shown to be dysregulated in those with depression (Dantzer, O’Connor, Freund, Johnson, & Kelley, 2008) and is likely a significant component of a dysfunctional stress response system.
Another major way that lncRNAs are hypothesized to work is that DNA itself may be folded and looped such that genes separated by large stretches of DNA, may actually be fairly close in 3D space. Thus, “distant” genes could also be a target of lncRNAs in this way. The approach we took to identify these faraway gene targets was to use network analysis where networks of RNAs (both protein coding and non-coding) were constructed based on how similar the differences in their expression levels were, between depressed suicide completers and controls. This was done using a statistical tool that allowed us to identify 10 large networks of co-expressed genes then to look at ones that contained the significant lncRNAs we identified earlier. We looked to see which protein coding genes showed the highest level of co-expression, or similarity in expression levels, with the lncRNAs of interest. The protein coding genes we identified were associated with several important biological functions most of which may be disrupted in depression and suicide and lncRNAs may play a role in regulating them.
The findings from this project have confirmed that there are indeed differences in the expression of many lncRNAs in the brains of depressed individuals who have died by suicide.
However, several major questions remain to be addressed. The next step would include confirming whether the lncRNAs we have found actually do regulate their hypothetical gene targets and the mechanisms by which they carry out this regulation. Taking a step back, what caused these lncRNA genes to be turned on or off in the first place? If we zoom out from our focus at the molecular level, we can also ask how the differences we are detecting affect the neural circuitry, brain function, and behaviors underlying depression and suicide? Clearly, there is a lot more to be discovered and a lot more work to be done!