Arc: mRNA & protein from one neuron to another

EDIT 1 [Jan 17, 2018]: I promised four days ago that I will post this, while it was still hot, but my Internet was down, thanks to the only behemoth provider in USA. And rated the worst company in the Nation, too. You definitely know by now about whom I’m talking about. Grrrr…  Anyway, here is the paper:

As promised, today’s paper talks about mRNA transfer between neurons.

Pastuzyn et al. (2018) looked at the gene Arc in neurons because they thought its Gag sequence looks suspiciously similar to some retroviruses. Could it be possible that it also behaves like a virus?

Arc is heavily involved in the immune system, is essential for the formation of long-term memories, and is involved in all sorts of diseases, like schizophrenia and Alzheimer’s, among other things.

Pastuzyn et al. (2018) is a relatively long and dense paper, albeit well written. So, I thought that this time, instead of giving you a summary of their research it would be better to give you the authors’ story directly in their own words written as subtitles in the Results section (bold letters – the authors words, normal font – mine). Warning: this is a much more jargon-dense blog post than my previous one on the same topic and, because it is so much material, I will not explain every term.

  • Fly and Tetrapod (us) Arc Genes Independently Originated from Distinct Lineages of Ty3/gypsy Retrotransposons, the phylogenomic analyses tell us, meaning the authors have done a lot of computer-assisted comparisons of similar forms of the gene in hundreds of species.
  • Arc Proteins Self-Assemble into Virus-like Capsids. Arc likes to oligomerize spontaneously (dimers and trimers). The oligomers resemble virus-like capsids, similar to HIV.
  • Arc Binds and Encapsulates RNA. Although it loves its own RNA about 10 times more than other RNAs, it’s a promiscuous protein (doesn’t care which RNA as long as it follows the rules of stoichiometry). Arc capsids encapsulate both the Arc protein (maybe other proteins too?), its mRNA, and whatever mRNA happened to be in the vicinity at the time of encapsulation. Arc capsids are able to protect the mRNA from RNAases.
  • Arc Capsid Assembly Requires RNA. If there is no RNA around, the capsids are few and poorly formed.
  • Arc Protein and Arc mRNA Are Released by Neurons in Extracellular Vesicles. Arc capsid packages Arc protein & Arc mRNA into extracellular vesicles (EV). The size of these EVs is < 100nm, putting them in the exosome category. This exosome, which the authors gave the unfortunate name of ACBAR (Arc Capsid Bearing Any RNA), is being expelled from cortical neurons in an activity-dependent manner. In other words, when neurons are stimulated, they release ACBARs.
  • Arc Mediates Intercellular Transfer of mRNA in Extracellular Vesicles. ACBARs dock to the host cell and then undergo clathrin-dependent endocytosis, meaning they expel their cargo in the host cell. The levels of Arc protein and Arc mRNA peaks in a host hippocampal cell in four hours from incubation. The ACBARs tend to congregate around donor cell’s dendrites.
  • Transferred Arc mRNA Can Undergo Activity-Dependent Translation. Activating the group 1 metabotropic glutamate receptor (mGluR1/5) by application of the agonist DHPG induces a significant increase of the amount of Arc protein in the host neurons.

This is a veritable tour de force paper. The Results section has 7 sub-sections, each with multiple experiments to dot every i and cross every t. I’m eyeballing about 40 experiments. It is true that there are 13 authors on the paper from different institutions – yeay for collaboration! – but c’mon! Is this what you need to get in Cell these days? Apparently so. Don’t get me wrong, this is an outstanding paper. But in the end it is still only one paper, which means only one first author. The rest are there for the ride because for a tenure track application nobody cares about your papers in CNS (Cell, Nature, Science = The Central Nervous System of the scientific community, har, har) if you’re not the first author. It looks like the increasing amount of work you need to be published in top tier journals these days is becoming a pet peeve of mine as I keep mentioning it (for example, here).

My pet peeves aside, Pastuzyn et al. (2018) is an excellent paper that opens interesting practical (drug delivery) and theoretical (biological repurpose of ancient invaders) gates. Kudos!

128-1 - Copy

REFERENCE: Pastuzyn ED, Day CE, Kearns RB, Kyrke-Smith M, Taibi AV, McCormick J, Yoder N, Belnap DM, Erlendsson S, Morado DR, Briggs JAG, Feschotte C, & Shepherd JD. (11 Jan 2018). The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell, 172(1-2):275-288.e18. PMID: 29328916. doi: 10.1016/j.cell.2017.12.024. ARTICLE | FULLTEXT PDF via ResearchGate

P.S. I said that ACBAR is an unfortunate acronym because I don’t know about you but I for one wouldn’t want my discovery to be linked either with a religion or with terrorist cries, even if that link is done only by a small fraction of the population. Although I can totally see the naming-by-committee going: “ACBAR! Our exosome is the greatest! Yeay!” or “Arc Acbar! Our Arc is the greatest. Double yeay!”. On a second thought, it’s kindda nerdy geeky neat. I still wouldn’t have done it though…

By Neuronicus, 14 January 2018

EDIT 2 [Jan 22, 2018]: There is another paper that discovered that Arc forms capsids that encapsulate RNA and then shuttles it across the neuromuscular junction in Drosophila (fly). To their credit, Cell published both these papers back-to-back so no researcher gets scooped of their discovery. From what I can see, the discovery really happened simultaneously, so I modified my infopic to reflect that (both papers were submitted in January 2017, received in revised version on August 15, 2017 and published in the same issue on January 11, 2018). Here is the reference to the other article:

Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, & Thomson T (11 Jan 2018). Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons, Cell. 172(1-2): 262-274.e11. PMID: 29328915. doi: 10.1016/j.cell.2017.12.022. ARTICLE

EDIT 3 [Jan 29, 2018]: Dr. Shepherd, the last author of the paper I featured, was kind enough to answer a few of my questions about the implications of his and his team’s findings, answers which you will find here.

By Neuronicus, 22 January 2018

Can you tickle yourself?

As I said before, with so many science outlets out there, it’s hard to find something new and interesting to cover that hasn’t been covered already. Admittedly, sometimes some new paper comes out that is so funny or interesting that I too fall in line with the rest of them and cover it. But, most of the time, I try to bring you something that you won’t find it reported by other science journalists. So, I’m sacrificing the novelty for originality by choosing something from my absolutely huge article folder (about 20 000 papers).

And here is the gem for today, titled enticingly “Why can’t you tickle yourself?”. Blakemore, Wolpert & Frith (2000) review several papers on the subject, including some of their own, and arrive to the conclusion that the reason you can’t tickle yourself is because you expect it. Let me explain: when you do a movement that results in a sensation, you have a pretty accurate expectation of how that’s going to feel. This expectation then dampens the sensation, a process probably evolved to let you focus on more relevant things in the environment that on what you’re doing o yourself (don’t let your mind go all dirty now, ok?).

Mechanistically speaking, it goes like this: when you move your arm to tickle your foot, a copy of the motor command you gave to the arm (the authors call this “efference copy”) goes to a ‘predictor’ region of the brain (the authors believe this is the cerebellum) that generates an expectation (See Fig. 1). Once the movement has been completed, the actual sensation is compared to the expected one. If there is a discrepancy, you get tickled, if not, not so much. But, you might say, even when someone else is going to tickle me I have a pretty good idea what to expect, so where’s the discrepancy? Why do I still get tickled when I expect it? Because you can’t fool your brain that easily. The brain then says; “Alright, alright, we expect tickling. But do tell me this, where is that motor command? Hm? I didn’t get any!” So here is your discrepancy: when someone tickles you, there is the sensation, but no motor command, signals 1 and 2 from the diagram are missing.

93 - Copy
Fig. 1. My take on the tickling mechanism after Blakemore, Wolpert & Frith (2000). Credits. Picture: Sobotta 1909, Diagram: Neuronicus 2016. Data: Blakemore, Wolpert & Frith (2002). Overall: Public Domain

Likewise, when someone tickles you with your own hand, there is an attenuation of sensation, but is not completely disappeared, because there is some registration in the brain regarding the movement of your own arm, even if it was not a motor command initiated by you. So you get tickled just a little bit. The brain is no fool: is aware of who had done what and with whose hands (your dirty mind thought that, I didn’t say it!) .

This mechanism of comparing sensation with movement of self and others appears to be impaired in schizophrenia. So when these patients say that “I hear some voices and I can’t shut them up” or ” My hand moved of its own accord, I had no control over it”, it may be that they are not aware of initiating those movements, the self-monitoring mechanism is all wacky. Supporting this hypothesis, the authors conducted an fMRI experiment (Reference 2) where they showed that that the somatosensory and the anterior cingulate cortices show reduced activation when attempting to self-tickle as opposed to being tickled by the experimenter (please, stop that line of thinking…). Correspondingly, the behavioral portion of the experiment showed that the schizophrenics can tickle themselves. Go figure!

94 - Copy

Reference 1: Blakemore SJ, Wolpert D, & Frith C (3 Aug 2000). Why can’t you tickle yourself? Neuroreport, 11(11):R11-6. PMID: 10943682. ARTICLE FULLTEXT

Reference 2: Blakemore SJ, Smith J, Steel R, Johnstone CE, & Frith CD (Sep 2000, Epub 17 October 2000). The perception of self-produced sensory stimuli in patients with auditory hallucinations and passivity experiences: evidence for a breakdown in self-monitoring. Psychological Medicine, 30(5):1131-1139. PMID: 12027049. ARTICLE

By Neuronicus, 7 August 2016

The culprit in methamphetamine-induced psychosis is very likely BDNF

Psychoses. Credit: NIH (Publication Number 15-4209) & Neuronicus.
Psychoses. Credit: NIH (Publication Number 15-4209) & Neuronicus. License: PD.

Methamphetamine prolonged use may lead to psychotic episodes in the absence of the drug. These episodes are persistent and closely resemble schizophrenia. One of the (many) molecules involved in both schizophrenia and meth abuse is BDNF (brain derived neurotrophic factor), a protein mainly known for its role in neurogenesis and long-term memory.

Lower BDNF levels have been observed in schizophrenia, therefore Manning et al. (2015) wondered if it’s also involved in meth-induced psychosis. So they got normal mice and mice that were genetically engineered to express lower levels of BDNF. They gave them meth for 3 weeks, with escalating doses form one week to the next. Interestingly, no meth on weekends, which made me rapidly scroll to the beginning of the paper and confirm my suspicion that the experiments were not done in USA; if they were, the grad students would not have had the weekends off and mice would have received meth every day, including weekends. Look how social customs can influence research! Anyway, social commentary aside, after the meth injections, the researchers let the mice untroubled for 2 more weeks. And then they tested them on a psychosis test.

How do you measure psychosis in rodents? By inference, since the mouse will not grab your coat and tell you about the newly appeared hypnotizing wall pattern and the like. Basically, it was observed that psychotic people have a tendency to walk in a disorganized manner when given the opportunity to explore, a behavior that was also observed in rodents on amphetamines. This disorganized walk can be quantifies into an entropic index, which is thought to reflect occurrence of psychosis (I know, a lot of inferring. But you come up with a better model of psychosis in rodent!).

Manning et al. (2015) gave their mice amphetamine to mimic psychosis and then observed their behavior. And the results were that the genetically engineered mice to express less BDNF showed reduced psychosis (i.e. had a lower entropic index). In conclusion, the alteration of the BDNF pathway may be responsible for the development of psychosis in methamphetamine users.

Reference: Manning EE, Halberstadt AL, & van den Buuse M. (Epub 9 Oct 2015). BDNF-Deficient Mice Show Reduced Psychosis-Related Behaviors Following Chronic Methamphetamine. International Journal of Neuropsychopharmacology, 1–5. doi: 10.1093/ijnp/pyv116. Article | FREE FULLTEXT PDF

By Neuronicus, 9 November 2015

As nutty as Dali, as crazy as van Gogh

Left: Portrait of Salvador Dali (taken in Hôtel Meurice, Paris, by Allen Warren, 1972). Right: Self-portrait with bandaged ear and pipe (van Gogh, 1889). Courtesy of Wikipedia.
Left: Portrait of Salvador Dali (taken in Hôtel Meurice, Paris, by Allen Warren, 1972). Right: Self-portrait with bandaged ear and pipe (van Gogh, 1889). Courtesy of Wikipedia.

Having a brain disease means to have different scores on emotion, cognition, and behavior inventories than the population mean. Also different from the population mean is the ability of an artist to create evocative things. Whether is a piece of music or a painting (or in my case a simple straight line), whether we like it or not, most of us agree that we couldn’t have done it. Also, artists show a decrease in practical reasoning, just like the schizophrenics.

Power et al. (2015) sought to find out if there is a link between being creative and having schizophrenia or bipolar disorder. Lucky for them, the north-European countries keep detailed medical and genetic databases of their population: they had access to 5 databases from Iceland, Sweden, and Netherlands, featuring tens to hundreds of thousands of people.

The authors analyzed hundreds of thousands of individual genetic differences (i.e. SNPs = single nucleotide polymorphisms) that had been previously linked with schizophrenia or bipolar disorder. As a side note, some of this data was obtained by inviting citizens to voluntarily fill out a detailed medical questionnaire and donate blood for DNA analysis. A staggering amount of people agreed. I wonder how many would have done so in U.S.A….

Anyway, the authors defined creative individuals (artists) as “those having (or ever having had) positions in the fields of dance, film, music, theater, visual arts or writing” (online supplemental methods), including those teaching these subjects. And they found out that the same genetic makeup that increases the risk of developing schizophrenia or bipolar disorder also underlies creativity. This link was not explained by education, age, sex, or shared environment.

The study also knocked down an evolutionary explanation for the persistence of schizophrenia and bipolar disorders in the genetic pool. The hypothesis posits that we still have these devastating brain disorders because they come with the side effect of creativity that offsets their negative fitness; but that does not hold, as the artists in this study had less children than the average population. Authors did not offer an alternative speculation.

Reference: Power, R. A., Steinberg, S., Bjornsdottir, G., Rietveld, C. A., Abdellaoui, A., Nivard, M. M., Johannesson, M., Galesloot, T.E., Hottenga, J. J., Willemsen, G., Cesarini, D., Benjamin, D. J., Magnusson, P. K., Ullén, F., Tiemeier, H., Hofman, A., van Rooij, F. J., Walters, G. B., Sigurdsson, E., Thorgeirsson, T. E., Ingason, A., Helgason, A., Kong, A., Kiemeney, L. A., Koellinger, P., Boomsma, D. I., Gudbjartsson, D., Stefansson, H., & Stefansson K. (July 2015, Epub 8 June 2015). Polygenic risk scores for schizophrenia and bipolar disorder predict creativity. Nature Neuroscience, 8(7):953-5. doi: 10.1038/nn.4040. Article + Nature comment

By Neuronicus, 7 October 2015