Now, for repeat readers, you probably know I have a professional interest in the topic of transposable elements. So it should come as no surprise that a recent article published this month in the journal, Neuron, involving LINE1 (L1) retrotransposons and schizophrenia, has peaked my interest. As a recap, L1 retrotransposons are a type of mobile element within the human genome which are or were once capable of making copies of themselves which would then reinsert elsewhere in the DNA. The vast majority of such elements are transpositionally extinct, having mutated enough that the genes they house which produce products that help them reinsert are eventually rendered useless.
To summarize the recent study, the researchers found that neurons taken from schizophrenic patients postmortem showed higher numbers of L1 retrotransposons within their genomes as compared to glial cells within the same brains, liver tissue from the same people, and control brain and liver tissues. In short, the genomes of individual neurons from schizophrenics showed higher levels of L1-induced somatic mosaicism. (“Somatic mosaicism” means that the cells of the body exhibit differences in genotype.) They also found that these L1 insertions tended to preference central nervous system-related genes in schizophrenics, such as synaptic, cytoskeletal, and cell adhesion genes. In addition, the team collected fibroblast cells from two schizophrenic patients who were diagnosed with a 22q11 deletion syndrome, the most common type of mutation associated with schizophrenia accounting for 1-2% of that population; they induced pluripotent stem cells (iPSC) from the fibroblasts from these two patients, derived mature neurons from this cell population, and finally performed whole-genome sequencing on the neurons to determine total copy numbers of L1 elements which still had an intact second open reading frame (ORF2) vital for retrotransposition. As with the previous experiment, they found increased L1 copy numbers. And finally, they performed some minimal animal experimentation to illustrate that prenatal insult, such as poly-I:C or EGF which have been used to create animal models for schizophrenia, may increase rates of L1 retrotransposition (although these latter experiments were few in number and don’t appear to have had any statistical analyses performed on them).
Hey, what’s the big idea???
The reason that this article has gotten some notoriety already is its spin. We all love a good story and scientists are not immune to attempting to explain the etiological entirety of a condition in one fell swoop. (I don’t so much blame the authors, it’s a short-coming of this “business” which preferences pushing every article as a Holy Grail of breakthroughs. And I don’t decry them either because, though I may have my critique handy, I do find this a fascinatingly informative study.) In short, the authors state it thus:
“These findings suggest that hyperactive retrotransposition of L1 in neurons triggered by environmental and/or genetic risk factors may contribute to the susceptibility and pathophysiology of schizophrenia.”
You might not know what I’m going to say here, but you may be under the impression I’m winding up for a “Yes, but” argument. And you’d be right. So what’s the problem with the above hypothesis?
For one, retrotransposition events like those mentioned in the above study are comparatively rare compared to other types of recombination events. By “recombination”, I mean the deletion (like with 22q11 deletion syndrome), expansion, inversion, etc., of segments of DNA. Recombination is especially rife in loci that house highly repetitive sequences, like transposable elements (mostly extinct) and shorter repeat sequences, e.g., CACACACACA. These highly repetitive loci also seem to invite more instances of mobile element insertion, further perpetuating the instability.
The thing is that if there is an environmental or genetic insult that’s promoting this kind of instability, it will be creating occurrences of both recombination and the occasional transposition of elements like L1s. The problem with the study is that the authors are only acknowledging a tiny piece of this very large puzzle. If we’re talking genetic risk factors for schizophrenia, recombination events are much more likely to be at the root of a larger range of cases than the retrotransposition of L1s. So it’s not that I think the authors are completely wrong, I just don’t think they’re entirely correct.
Case in point: this study uses iPSC from two 22q11 deletion-related schizophrenic patients. Now, yes, the neurons derived from the iPSCs from these patients have higher L1 copy numbers. However, the authors fail to mention or realize that most causes of deletion in 22q11 lie at breakpoints formed by remnants of Alu elements, promoting recombination and loss of larger segments of DNA at that locus . Ultimately, this type of mutation seems to have little to do with L1 retrotransposition. Instead it suggests that there may have been multiple points of destabilization which created the condition-causing deletion at 22q11 and also increased rates of retrotransposition elsewhere. And as far as the preference for insertion into CNS-related genes, neuronal genes on average display characteristics indicative of greater instability (unpublished data), making them an easier target should a time window of vulnerability be expanded.
I also have some criticisms that such small sample numbers were used. For instance, the iPSCs were taken from only two patients. Who’s to say that the fibroblasts of these two patients haven’t developed an unusual level of somatic mosaicism and would not necessarily be representative of a larger sample of 22q11-deletion patients?
In any case, the study is a highly interesting one and promotes some excellent ideas, even though as I become more familiar with the work I get the impression that certain parts of the project, especially the iPSC and animal studies, were thrown together somewhat slapdash. I would rather see these redone with greater diligence, better descriptions of procedure, and much larger sample numbers. I have to remind myself (and the reader) that the results presented in those sections of the study aren’t necessary reliable and should be taken with a grain of salt. I would have also like to have seen the authors pair schizophrenics with the parental genomes for comparison. Even though each sample had its own internal control via use of the liver for comparison, parental genomes may have shown related trends in L1 insertion that could have leant a whole other layer to the understanding of schizophrenic etiology.
Anyways, some excellent food for thought which I hope you’ve found informative. And it’s always wonderful to see more genetics research focus on transposable elements (i.e., “The Other Half of the Genome“). It’s always baffled me how so many people consider 50% of our DNA just “junk”…