Epigenetics of BDNF in depression

Depression is the leading cause of disability worldwide, says the World Health Organization. The. The. I knew it was bad, but… ‘the’? More than 300 million people suffer from it worldwide and in many places fewer than 10% of these receive treatment. Lack of treatment is due to many things, from lack of access to healthcare to lack of proper diagnosis; and not in the least due to social stigma.

To complicate matters, the etiology of depression is still not fully elucidated, despite hundreds of thousand of experimental articles published out-there. Perhaps millions. But, because hundreds of thousands of experimental articles perhaps millions have been published, we know a helluva a lot about it than, say, 50 years ago. The enormous puzzle is being painstakingly assembled as we speak by scientists all over the world. I daresay we have a lot of pieces already, if not all at least 3 out of 4 corners, so we managed to build a not so foggy view of the general picture on the box lid. Here is one of the hottest pieces of the puzzle, one of those central pieces that bring the rabbit into focus.

Before I get to the rabbit, let me tell you about the corners. In the fifties people thought that depression is due to having too little neurotransmitters from the monoamine class in the brain. This thought did not arise willy-nilly, but from the observation that drugs that increase monoamine levels in the brain alleviate depression symptoms, and, correspondingly, drugs which deplete monoamines induce depression symptoms. A bit later on, the monoamine most culpable was found to be serotonin. All well and good, plenty of evidence, observational, correlational, causational, and mechanistic supporting the monoamine hypothesis of depression. But two more pieces of evidence kept nagging the researchers. The first one was that the monoamine enhancing drugs take days to weeks to start working. So, if low on serotonin is the case, then a selective serotonin reuptake inhibitor (SSRI) should elevate serotonin levels within maximum an hour of ingestion and lower symptom severity, so how come it takes weeks? The second was even more eyebrow raising: these monoamine-enhancing drugs work in about 50 % of the cases. Why not all? Or, more pragmatically put, why not most of all if the underlying cause is the same?

It took decades to address these problems. The problem of having to wait weeks until some beneficial effects of antidepressants show up has been explained away, at least partly, by issues in the serotonin regulation in the brain (e.g. autoreceptors senzitization, serotonin transporter abnormalities). As for the second problem, the most parsimonious answer is that that archeological site called DSM (Diagnostic and Statistical Manual of Mental Disorders), which psychologists, psychiatrists, and scientists all over the world have to use to make a diagnosis is nothing but a garbage bag of last century relics with little to no resemblance of this century’s understanding of the brain and its disorders. In other words, what DSM calls major depressive disorder (MDD) may as well be more than one disorder and then no wonder the antidepressants work only in half of the people diagnosed with it. As Goldberg put it in 2011, “the DSM diagnosis of major depression is made when a patient has any 5 out of 9 symptoms, several of which are opposites [emphasis added]”! He was referring to DSM-4, not that the 5 is much different. I mean, paraphrasing Goldberg, you really don’t need much of a degree other than some basic intro class in the physiology of whatever, anything really, to suspect that someone who’s sleeping a lot, gains weight, has increased appetite, appears tired or slow to others, and feels worthless might have a different cause for these symptoms than someone who has daily insomnias, lost weight recently, has decreased appetite, is hyperagitated, irritable, and feels excessive guilt. Imagine how much more understanding we would have about depression if scientists didn’t use the DSM for research. No wonder that there’s a lot of head scratching when your hypothesis, which is logically correct, paradigmatically coherent, internally consistent, flawlessly tested, turns out to be true only sometimes because your ‘depressed’ subjects are as a homogeneous group as a pack of Trail Mix.

I got sidetracked again. This time ranting against DSM. No matter, I’m back on track. So. The good thing about the work done trying to figure out how antidepressants work and psychiatrists’ minds work (DSM is written overwhelmingly by psychiatrists), scientists uncovered other things about depression. Some of the findings became clumped under the name ‘the neurotrophic hypothesis of depression’ in the early naughts. It stems from the finding that some chemicals needed by neurons for their cellular happiness are in low amount in depression. Almost two decades later, the hypothesis became mainstream theory as it explains away some other findings in depression, and is not incompatible with the monoamines’ behavior. Another piece of the puzzle found.

One of these neurotrophins is called brain-derived neurotrophic factor (BDNF), which promotes cell survival and growth. Crucially, it also regulates synaptic plasticity, without which there would be no learning and no memory. The idea is that exposure to adverse events generates stress. Stress is differently managed by different people, largely due to genetic factors. In those not so lucky at the genetic lottery (how hard they take a stressor, how they deal with it), and in those lucky enough at genetics but not so lucky in life (intense and/or many stressors hit the organism hard regardless how well you take it or how good you are at it), stress kills a lot of neurons, literally, prevents new ones from being born, and prevents the remaining ones from learning well. Including learning on how to deal with the stressors, present and future, so the next time an adverse event happens, even if it is a minor stressor, the person is way more drastically affected. in other words, stress makes you more vulnerable to stressors. One of the ways stress is doing all these is by suppressing BDNF synthesis. Without BDNF, the individual exposed to stress that is exacerbated either by genes or environment ends up unable to self-regulate mood successfully. The more that mood is not regulated, the worse the brain becomes at self-regulating because the elements required for self-regulation, which include learning from experience, are busted. And so the vicious circle continues.

Maintaining this vicious circle is the ability of stressors to change the patterns of DNA expression and, not surprisingly, one of the most common findings is that the BDNF gene is hypermethylated in depression. Hypermethylation is an epigenetic change (a change around the DNA, not in the DNA itself), meaning that the gene in question is less expressed. This means lower amounts of BDNF are produced in depression.

After this long introduction, the today’s paper is a systematic review of one of epigenetic changes in depression: methylation. The 67 articles that investigated the role of methylation in depression were too heterogeneous to make a meta-analysis out of them, so Li et al. (2019) made a systematic review.

The main finding was that, overall, depression is associated with DNA methylation modifications. Two genes stood out as being hypermethylated: our friend BDNF and SLC6A4, a gene involved in the serotonin cycle. Now the question is who causes who: is stress methylating your DNA or does your methylated DNA make you more vulnerable to stress? There’s evidence both ways. Vicious circle, as I said. I doubt that for the sufferer it matters who started it first, but for the researchers it does.

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A little disclaimer: the picture I painted above offers a non-exclusive view on the causes of depression(s). There’s more. There’s always more. Gut microbes are in the picture too. And circulatory problems. And more. But the picture is more than half done, I daresay. Continuing my puzzle metaphor, we got the rabbit by the ears. Now what to do with it…

Well, one thing we can do with it, even with only half-rabbit done, is shout loud and clear that depression is a physical disease. And those who claim it can be cured by a positive attitude and blame the sufferers for not ‘trying hard enough’ or not ‘smiling more’ or not ‘being more positive’ can bloody well shut up and crawl back in the medieval cave they came from.

REFERENCES:

1. Li M, D’Arcy C, Li X, Zhang T, Joober R, & Meng X (4 Feb 2019). What do DNA methylation studies tell us about depression? A systematic review. Translational Psychiatry, 9(1):68. PMID: 30718449, PMCID: PMC6362194, DOI: 10.1038/s41398-019-0412-y. ARTICLE | FREE FULLTEXT PDF

2. Goldberg D (Oct 2011). The heterogeneity of “major depression”. World Psychiatry, 10(3):226-8. PMID: 21991283, PMCID: PMC3188778. ARTICLE | FREE FULLTEXT PDF

3. World Health Organization Depression Fact Sheet

By Neuronicus, 23 April 2019

NASA, not media, is to blame for the Twin Study 7% DNA change misunderstanding

In case the title threw you out of the loop, let me pull you back in. In 2015, NASA sent Scott Kelly to the International Space Station while his twin brother, Mark, stayed on the ground. When Scott came back, NASA ran a bunch of tests on them to see how space affects human body. Some of the findings were published a few weeks ago. Among the findings, one caught the eyes of media who ran stories like:  Astronaut Scott Kelly now has different DNA to his identical twin brother after spending just a year in space (Daily Mail), Astronaut’s DNA no longer matches identical twin’s after time in space, NASA finds (Channel 3), Astronaut Scott Kelly’s genes show long-term changes after a year in space (NBC), Astronaut Scott Kelly is no longer an identical twin: How a year in space altered his DNA (Fox News), Scott Kelly Spent a Year in Space and Now His DNA Is Different From His Identical Twin’s (Time),  Nasa astronaut twins Scott and Mark Kelly no longer genetically identical after space trip (Telegraph), Astronaut’s DNA changes after spending year in space when compared to identical twin bother (The Independent), Astronaut Scott Kelly’s DNA No Longer Matches Identical Twin’s After a Year in Space (People), NASA study: Astronaut’s DNA no longer identical to his identical twin’s after year in space (The Hill), NASA astronaut who spent a year in space now has different DNA from his twin (Yahoo News), Scott Kelly: NASA Twins Study Confirms Astronaut’s DNA Actually Changed in Space (Newsweek), If you go into space for a long time, you come back a genetically different person (Quartz), Space can change your DNA, we just learned (Salon), NASA Confirms Scott Kelly’s Genes Have Been Altered By Space Travel (Tech Times), even ScienceAlert 😦 ran Scott Kelly’s DNA Is No Longer Identical to His Twin’s After a Year in Space.  And dozens and dozens more….

Even the astronauts themselves said their DNA is different and they are no longer twins:

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Alas, dear Scott & Mark Kelly, rest assured that despite these titles and their afferent stories, you two share the same DNA, still & forever. You are still identical twins until one of you changes species. Because that is what 7% alteration in human DNA means: you’re not human anymore.

So what gives?

Here is the root of all this misunderstanding:

“Another interesting finding concerned what some call the “space gene”, which was alluded to in 2017. Researchers now know that 93% of Scott’s genes returned to normal after landing. However, the remaining 7% point to possible longer term changes in genes related to his immune system, DNA repair, bone formation networks, hypoxia, and hypercapnia” (excerpt from NASA’s press release on the Twin Study on Jan 31, 2018, see reference).

If I wouldn’t know any better I too would think that yes, the genes were the ones who have changed, such is NASA’s verbiage. As a matter of actual fact, it is the gene expression which changed. Remember that DNA makes RNA and RNA makes protein? That’s the central dogma of molecular biology. A sequence of DNA that codes for a protein is called a gene. Those sequences do not change. But when to make a protein, how much protein, in what way, where to make this protein, which subtly different kinds of protein to make (alternative splicing), when not to make that protein, etc. is called the expression of that gene. And any of these aspects of gene expression are controlled or influenced by a whole variety of factors, some of these factors being environmental and as drastic as going to space or as insignificant as going to bed.

Some more scientifically inclined writers understood that the word “expression” was conspicuously missing from the above-mentioned paragraph and either ran clarification titles like After A Year In Space, NASA Astronaut’s Gene Expression Has Changed. Possibly Forever. (Huffington Post) or up-front rebukes like No, space did not permanently alter 7 percent of Scott Kelly’s DNA (The Verge) or No, Scott Kelly’s Year in Space Didn’t Mutate His DNA (National Geographic).

Now, I’d love, LOVE, I tell you, to jump to the throat of the media on this one so I can smugly show how superior my meager blog is when it comes to accuracy. But, I have to admit, this time is NASA’s fault. Although it is not NASA’s job to teach the central dogma of molecular biology to the media, they are, nonetheless, responsible for their own press releases. In this case, Monica Edwards and Laurie Abadie from NASA Human Research Strategic Communications did a booboo, in the words of the Sit-Com character Sheldon Cooper. Luckily for these two employees, the editor Timothy Gushanas published this little treat yesterday, right at the top of the press release:

“Editor’s note: NASA issued the following statement updating this article on March 15, 2018:

Mark and Scott Kelly are still identical twins; Scott’s DNA did not fundamentally change. What researchers did observe are changes in gene expression, which is how your body reacts to your environment. This likely is within the range for humans under stress, such as mountain climbing or SCUBA diving.

The change related to only 7 percent of the gene expression that changed during spaceflight that had not returned to preflight after six months on Earth. This change of gene expression is very minimal.  We are at the beginning of our understanding of how spaceflight affects the molecular level of the human body. NASA and the other researchers collaborating on these studies expect to announce more comprehensive results on the twins studies this summer.”

Good for you for rectifying your mistake, NASA! And good for you too the few media outlets that corrected their story like CNN who changed their title from Astronaut’s DNA no longer same as his identical twin, NASA finds to Astronaut’s gene expression no longer same as his identical twin, NASA finds.

But, seriously, NASA, what’s up with you guys keep screwing up molecular biology stuff?! Remember the arsenic-loving bacteria debacle? That paper is still not retracted  and that press release is still up on your website! Ntz, ntz, for shame… NASA, you need better understanding of basic science and/or better #Scicomm in your press releases. Hiring? I’m offering!

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REFERENCE: NASA. Edwards, M.  & Abadie, L. (Jan. 31, 2018). NASA Twins Study Confirms Preliminary Findings, Ed. Timothy Gushanas, retrieved on March 14,15, & 16, 2018. Address: https://www.nasa.gov/feature/nasa-twins-study-confirms-preliminary-findings

By Neuronicus, 16 March 2018

P.S. Sometimes is a pain to be obsessed with accuracy (cue in smallest violins). For example, I cannot stop myself from adding something just to be scrupulously correct. Since the day they were conceived, identical twins’ DNAs are starting to diverge. There are all sorts of things that do change the actual sequence of DNA. DNA can be damaged by radiation (which you can get a lot of in space) or exposure to some chemicals. Other changes are simply due to random mutations. So no twins are exactly identical, but the changes are so minuscule, nowhere near 1%, let alone 7%, that it is safe to say that their DNA is identical.

P.P.S. With all this hullabaloo about the 7% DNA change everybody glossed over and even I forgot to mention the one finding that is truly weird: the elongation of telomeres for Scott, the one that was in space. Telomeres are interesting things, they are repetitive sequences of DNA (TTAGGG/AATCCC) at the end of the chromosomes that are repeated thousands of times. The telomere’s job is to protect the end of the chromosomes. You see, every time a cell divides the DNA copying machinery cannot copy the last bits of the chromosome (blame it on physics or chemistry, one of them things) and so some of it is lost. So evolution came up with a solution: telomeres, which are bits of unusable DNA that can be safely ignored and left behind. Or so we think at the moment. The length of telomeres has been implicated in some curious things, like cancer and life-span (immortality thoughts, anyone?). The most common finding is the shortening of telomeres associated with stress, but Scott’s were elongated, so that’s the first weird thing. I didn’t even know the telomeres can get elongated in living healthy adult humans. But wait, there is more: NASA said that “the majority of those telomeres shortened within two days of Scott’s return to Earth”. Now that is the second oddest thing! If I would be NASA that’s where I would put my money on, not on the gene expression patterns. And I would really, really like to see which types of cells show those longer telomeres, because I have a hunch is some type of dermal cell, which may be ontogenetically related to a neuronal cell.

Tomato transcriptome

As most children, growing up I showed little appreciation for what I had, coveting instead what I did not. Now I realize how fortunate I have been to have grown up half the time in a metropolis and the other half at the countryside. At the farm. A subsistence farm, although I truly loathe the term because we were not just subsisting but thriving off the land, as we planted and harvested a bit of everything and we had a specimen or four of almost all the farm animals, from bipeds to quadrupeds.

I got on this memory lane after reading the paper of Shinozaki et al. (2018) on tomatoes. It was a difficult read for me as it was punctured by many term definition lookups since botany evolved quite steeply since the last time I checked, about 25 years or so.

Briefly, the scientists grew tomato plants in a greenhouse at Cornell, NY. They harvested the fruit from 60 plants about 5 to 50 days after the flower was at its peak (DPA, days post anthesis) following this chart:

  • Expanding [fruit] stage (harvested at 5, 10, 20, or 30 DPA)
  • Mature Green stage (full-size green fruit, ≈ 39 DPA),
  • Breaker stage (definite break in color from green to tannish-yellow with less than 10% of the surface, ≈ 42 DPA),
  • Pink stage (50% pink or red color, ≈ 44 DPA),
  • Light red stage (100% light red, ≈ 46 DPA),
  • Red ripe stage (full red for 8 days, ≈ 50 DPA).

(simplified from the Methods section, p. 10, see pic)

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Fig. 1 (partial from Shinozaki et al., 2018). A tissue/cell-based transcript profiling of developing tomato fruit. a Traced image of six targeted fruit tissues. Shaded areas of the total pericarp and the placenta were not harvested. b Traced image of five pericarp cells. c Representative pictures of harvested fruit spanning ten developmental stages. d Representative pictures of the stylar end of MG and Br stage fruit. DPA, days post anthesis; MG, mature green; Br, breaker; Pk, pink; LR, light red; RR, red ripe. Credit: DOI: 10.1038/s41467-017-02782-9. License: CC BY 4.0 IL.

Immediately after harvesting, the tomato was scanned with a micro-computed tomograph (micro-CT) to generate a 3D image of the fruit, including its internal structures. Then, the fruit was dissected by hand or laser, depending of its size, divided into various tissue types and then preserved either via snap-freezing in liquid nitrogen or standard tissue fixation for light or transmission electron microscopy. Finally, the researchers used kits to extract and analyze the RNA from their samples. And, last but not least, a lot of math & stats.

This is what I got out of it:

  1. A total of 24,660 genes were uniquely expressed in various tomato cell types and at various stages of development.
  2. The tomato ripens from within, meaning from the interior to the exterior and not the other way around.
  3. The ripening seems to be a continuous process, starting before the ‘Breaker’ stage.
  4. The ripening signals originate in the locular tissues (the goo around the seeds; it’s possible that the seeds themselves send the signals to the locular tissue to start the ripening process).
  5. The flesh of the fruit is only one part of the tomato and the most investigated, but the other types of tissue are also important. For example, some genes responsible for aroma and flavor (CTOMT1, TOMLOXC) are predominantly or even exclusively expressed in the flesh, but some genes that improve the nutritional value (SlGAD3) are expressed mostly in the placenta.
  6. The fruit can do photosynthesis, probably for the benefit of its seeds.
  7. Each developmental stage is characterized by a distinct transcriptome profile (by inference, also a distinct proteomic profile, although not necessarily in exact correspondence)
  8. Botany, like any serious science, is complicated.

Ah, I have been vindicated. By science, nonetheless! You see, in my pursuit to recapture the tomato taste of my childhood I sample various homegrown exemplars of Solanum lycopersicum derived both from more or less failed personal attempts with pots on the balcony and from various farmer’s market vendors. While I can understand – though not approve of – the industrial scale agro-growers’ practice to pick the tomatoes green, unripe and then artificially injecting them with ethylene to prolong shelf life, I completely fail to understand the picking them up when green by the sellers in the farmer’s markets. I had many surreal conversations with such vendors (I cannot call them farmers for the life of me) who more than once attempted to reassure me that 1) Everybody’s picking tomatoes green off the vine because that’s how it’s done and 2) Ripening happens on the window sill. In vain have I tried to explain the difference between ripen and rotten; in vain have I pointed out that color is only one indicator of ripening; in vain did I explain that during ripening on the vine the plant delivers certain substances to the fruit that lead to changes in the flesh composition to make it more nutritious for the future seedling, process that the aforesaid window sill does nor partake in. Alas, ultimately, my arguments (and my family’s last 400 years of farming experience) hit the wall of “I am growing tomatoes for three years now and I know what I’m doing. Are you buying or not?” As you might imagine, I end up going home frustrated and yet staring at some exorbitantly expensive and looking as sad as I feel greenish tomatoes.

For me, this is what Shinozaki et al. (2018) validated: Ripening is a complex process that involves a lot of physiological changes in the fruit, not merely some extra production of ethylene that can be conveniently supplied externally by a syringe or rotting on the window sill. Of course, there is nowhere in the paper that Shinozaki et al. (2018) say that. What they do say is this: “The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients” (Abstract). Tomayto, tomahto…

Now we know that… simply put, I’m right. Sometimes is good to be right. I am old enough to prefer happiness and tranquility over rightness & righteousness, but still young enough that sometimes, just sometimes, it feels good to be right. Yes, the Shinozaki et al. (2018) paper exists only for my vindication in my farmer’s market squabbles and not for providing a huge comprehensive atlas on the tomato transcriptome, along with an awesome spatiotemporal map showing the place and time of the expression of genes responsible for fruit ripening, quality traits and so on.

Good job, Shinozaki et al. (2018)!

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REFERENCE: Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich DJ, Shi Y, Xu Y, Zheng Y, Snyder SI, Martin LBB, Ruiz-May E, Thannhauser TW, Chen K, Domozych DS, Catalá C, Fei Z, Mueller LA, Giovannoni JJ, & Rose JKC (25 Jan 2018). High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nature Communications, 9(1):364. PMID: 29371663, PMCID: PMC5785480, DOI: 10.1038/s41467-017-02782-9. ARTICLE | FREE FULLTEXT PDF | The Tomato Expression Atlas database

By Neuronicus, 7 February 2018

How do you remember?

Memory processes like formation, maintenance and consolidation have been the subjects of extensive research and, as a result, we know quite a bit about them. And just when we thought that we are getting a pretty clear picture of the memory tableau and all that is left is a little bit of dusting around the edges and getting rid of the pink elephant in the middle of the room, here comes a new player that muddies the waters again.

DNA methylation. The attaching of a methyl group (CH3) to the DNA’s cytosine by a DNA methyltransferase (Dnmt) was considered until very recently a process reserved for the immature cells in helping them meet their final fate. In other words, DNA methylation plays a role in cell differentiation by suppressing gene expression. It has other roles in X-chromosome inactivation and cancer, but it was not suspected to play a role in memory until this decade.

Oliveira (2016) gives us a nice review of the role(s) of DNA methylation in memory formation and maintenance. First, we encounter the pharmacological studies that found that injecting Dnmt inhibitors in various parts of the brain in various species disrupted memory formation or maintenance. Next, we see the genetic studies, where mice Dnmt knock-downs and knock-outs also show impaired memory formation and maintenance. Finally, knowing which genes’ transcription is essential for memory, the researcher takes us through several papers that examine the DNA de novo methylation and demethylation of these genes in response to learning events and its role in alternative splicing.

Based on these here available data, the author proposes that activity induced DNA methylation serves two roles in memory: to “on the one hand, generate a primed and more permissive epigenome state that could facilitate future transcriptional responses and on the other hand, directly regulate the expression of genes that set the strength of the neuronal network connectivity, this way altering the probability of reactivation of the same network” (p. 590).

Here you go; another morsel of actual science brought to your fingertips by yours truly.

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Reference: Oliveira AM (Oct 2016, Epub 15 Sep 2016). DNA methylation: a permissive mark in memory formation and maintenance. Learning & Memory,  23(10): 587-593. PMID: 27634149, DOI: 10.1101/lm.042739.116. ARTICLE

By Neuronicus, 22 September 2016

One parent’s gene better than the other’s

Not all people with the same bad genetic makeup that predisposes them to a particular disease go and develop that disease or, at any rate, not with the same severity and prognosis. The question is why? After all, they have the same genes…

Here comes a study that answers that very important question. Eloy et al. (2016) looked at the most common pediatric eye cancer (1 in 15,000) called retinoblastoma (Rb). In the hereditary form of this cancer, the disease occurs if the child carries mutant (i.e. bad) copies of the RB1 tumour suppressor gene located on chromosome 13 (13q14). These copies, called alleles, are inherited by the child from the mother or from the father. But some children with this genetic disadvantage do not develop Rb. They should, so why not?

The authors studied 57 families with Rb history. They took blood and tumour samples from the participants and then did a bunch of genetic tests: DNA, RNA, and methylation analyses.

They found out that when the RB1 gene is inherited from the mother, the child has only 9.7% chances of developing Rb, but when the gene is inherited from the father the child has only 67.5% chances of developing Rb.

The mechanism for this different outcomes may reside in the differential methylation of the gene. Methylation is a chemical process that suppresses the expression of a gene, meaning that less protein is produced from that gene. The maternal gene had less methylation, meaning that more protein was produced, which was able to offer some protection against the cancer. Seems counter-intuitive, you’d think less bad protein is a good thing, but there is a long and complicated explanation for that, which, in a very simplified form, posits that other events influence the function of the resultant protein.

Again, epigenetics seem to offer explanations for pesky genetic inheritance questions. Epigenetic processes, like DNA methylation, are modalities through which traits can be inherited that are not coded in the DNA itself.

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Reference: Eloy P, Dehainault C, Sefta M, Aerts I, Doz F, Cassoux N, Lumbroso le Rouic L, Stoppa-Lyonnet D, Radvanyi F, Millot GA, Gauthier-Villars M, & Houdayer C (29 Feb 2016). A Parent-of-Origin Effect Impacts the Phenotype in Low Penetrance Retinoblastoma Families Segregating the c.1981C>T/p.Arg661Trp Mutation of RB1. PLoS Genetics, 12(2):e1005888. eCollection 2016. PMID: 26925970, PMCID: PMC4771840, DOI: 10.1371/journal.pgen.1005888. ARTICLE | FREE FULLTEXT PDF

By Neuronicus, 24 July 2016

Fructose bad effects reversed by DHA, an omega-3 fatty acid

Despite alarm signals raised by various groups and organizations regarding the dangers of the presence of sugars – particularly fructose derived from corn syrup – in almost every food in the markets, only in the past decade there has been some serious evidence against high consumption of fructose.

A bitter-sweet (sic!) paper comes from Meng et al. (2016) who, in addition to showing some bad things that fructose does to brain and body, it also shows some rescue from its deleterious effects by DHA (docosahexaenoic acid), an omega-3 fatty acid.

The authors had 3 groups of rodents: one group got fructose in their water for 6 weeks, another group got fructose and DHA, and another group got their normal chow. The amount of fructose was calculated to be ecologically valid, meaning that they fed the animals the equivalent of 1 litre soda bottle per day (130 g of sugar for a 60 Kg human).

The rats that got fructose had worse learning and memory performance at a maze test compared to the other two groups.

The rats that got fructose had altered gene expression in two brain areas: hypothalamus (involved in metabolism) and hippocampus (involved in learning and memory) compared to the other two groups.

The rats that got fructose had bad metabolic changes that are precursors for Type 2 diabetes, obesity and other metabolic disorders (high blood glucose, triglycerides, insulin, and insulin resistance index) compared to the other two groups.

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The genetic analyses that the researchers did (sequencing the RNA and analyzing the DNA methylation) revealed a whole slew of the genes that had been affected by the fructose treatment. So, they did some computer work that involved Bayesian modeling  and gene library searching and they selected two genes (Bgn and Fmod) out of almost a thousand possible candidates who seemed to be the drivers of these changes. Then, they engineered mice that lacked these genes. The resultant mice had the same metabolic changes as the rats that got fructose, but… their learning and memory was even better than that of the normals? I must have missed something here. EDIT: Well… yes and no. Please read the comment below from the Principal Investigator of the study.

It is an ok paper, done by the collaboration of 7 laboratories from 3 countries. But there are a few things that bother me, as a neuroscientist, about it. First is the behavior of the genetic knock-outs. Do they really learn faster? The behavioral results are not addressed in the discussion. Granted, a genetic knockout deletes that gene everywhere in the brain and in the body, whereas the genetic alterations induced by fructose are almost certainly location-specific.

Which brings me to the second bother: nowhere in the paper (including the supplemental materials, yeas, I went through those) are any brain pictures or diagrams or anything that can tell us which nuclei of the hypothalamus the samples came from. Hypothalamus is a relatively small structure with drastically different functional nuclei very close to one another. For example, the medial preoptic nucleus that deals with sexual hormones is just above the suprachiasmatic nucleus that deals with circadian rhythms and near the preoptic is the anterior nucleus that deals mainly with thermoregulation. The nuclei that deal with hunger and satiety (the lateral and the ventromedial nucleus, respectively) are located in different parts of the hypothalamus. In short, it would matter very much where they got their samples from because the transcriptome and methylome would differ substantially from nucleus to nucleus. Hippocampus is not so complicated as that, but it also has areas with specialized functions. So maybe they messed up the identification of the two genes Bgn and Fmod as drivers of the changes; after all, they found almost 1 000 genes altered by fructose. And that mess-up might have been derived by their blind hypothalamic and hippocampal sampling. EDIT: They didn’t mess up,  per se. Turns out there were technical difficulties of extracting enough nucleic acids from specific parts of hypothalamus for analyses. I told you them nuclei are small…

Anyway, the good news comes from the first experiment, where DHA reverses the bad effects of fructose. Yeay! As a side note, the fructose from corn syrup is metabolized differently than the fructose from fruits. So you are far better off consuming the equivalent amount on fructose from a litre of soda in fruits. And DHA comes either manufactured from algae or extracted from cold-water oceanic fish oils (but not farmed fish, apparently).

If anybody that read the paper has some info that can help clarify my “bothers”, please do so in the Comment section below. The other media outlets covering this paper do not mention anything about the knockouts. Thanks! EDIT: The last author of the paper, Dr. Yang, was very kind and clarified a bit of my “bothers” in the Comments section. Thanks again!

Reference: Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee J-H, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X (2016). Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine, doi: 10.1016/j.ebiom.2016.04.008. Article | FREE fulltext PDF | Supplementals | Science Daily cover | NeuroscienceNews cover

By Neuronicus, 24 April 2016

Mechanisms of stress resilience

71 stress - CopyLast year a new peer-reviewed journal called Neurobiology of Stress made its debut. The journal is published by Elsevier, who, in an uncharacteristic move, has provided Open Access for its first three issues. So hurry up and download the papers.

The very first issue is centered around the idea of resilience. That is, exposed to the same stressors, some people are more likely to develop stress-induced diseases, whereas others seem to be immune to the serious effects of stress.

Much research has been carried out to uncover the effects of chronic stress or of an exposure to a single severe stressor, which vary from cardiovascular disorders, obesity, irritable bowel syndrome, immune system dysfunctions to posttraumatic stress disorder, generalized anxiety, specific phobias, or depression. By comparison, there is little, but significant data on resilience: the ability to NOT develop those nasty stress-induced disorders. Without doubt, one reason for this scarcity is the difficulty in finding such rare subjects in our extremely stressful society. Therefore most of the papers in this issue focus on animal models.

Nevertheless, there is enough data on resilience to lead to no less that twenty reviews on the subject. It was difficult to choose one as most are very interesting, tackling various aspects of resilience, from sex differences to prenatal exposure to stress, from epigenetic to neurochemical modifications, from social inequalities to neurogenesis and so on.

So I chose for today a more general review of Pfau & Russo (2015), entitled “Peripheral and central mechanisms of stress resilience”. After it introduces the reader to four animal models of resilience, the paper looks at the neruoendocrine responses to stress and identifies some possible chemical mediators of resilience (like certain hormones), then at the immune responses to stress (bad, bad cytokines), and finally at the brain responses to stress (surprisingly, not focusing on amygdala, hypothalamus or hippocampus, but on the dopamine system originating from ventral tegmental area).

I catalogue the review as a medium difficulty read because it requires a certain amount of knowledge of the stress field beforehand. But do check out the other ones in the issue, too!

Reference: Pfau ML & Russo SJ (1 Jan 2015). Peripheral and central mechanisms of stress resilience. Neurobiology of Stress, 1:66-79. PMID: 25506605, PMCID: PMC4260357, DOI: 10.1016/j.ynstr.2014.09.004. Article | FREE FULLTEXT PDF

By Neuronicus, 24 January 2016

Golf & Grapes OR Grandkids (but not both!)

Pesticides may be bad for you, but they are devastating for your great grandchildren, because there will be no great great grandchildren. Photo Credit: JetsandZeppelins from Flickr under CC BY 2.0 license
Pesticides may be bad for you, but they are devastating for your great grandchildren, because there will be no great great grandchildren. Photo Credit: JetsandZeppelins from Flickr under CC BY 2.0 license

Transgenerational epigenetic inheritance (TGI) refers to the inheritance of a trait from one generation to another without altering the DNA code (normally, evolution is driven by changes in the DNA itself). Instead, it happens by modifying the proteins that wrap around the DNA, the histones; these histones, in turn, control what genes will be expressed and when. Until a decade ago, TGI was considered impossible, nay, a scientific heresy since it had too close of a resemblance to Lamarckian evolution. But, true to its guiding principles, the scientific endeavor had to bite the bullet in front of amassing evidence and accept the fact that it may have been a kernel of truth to the so called ‘soft inheritance’.

Anway et al.’s paper was one of the first to promote the concept, ten years ago. They exposed pregnant rats to the pesticides vinclozolin or methoxychlor (only vinclozolin is still used widely in U.S.A. and several EU countries, particularly in agriculture, wine production, and turf maintenance; methoxychlor was banned in the early noughts). The authors found out that more than 90% of the male offspring had “increased incidence of male infertility”. These effects were transferred through the male germ line to nearly all males of all subsequent generations examined” up to great great grandsons, inclusively (Anway et al., 2005). (I don’t want to speculate how they managed to breed the low fertility males…). That doesn’t mean that the F5 generation was OK (the great great great gransons); it means that they stopped investigating after the F4 generation (or they couldn’t breed the F4s). Moreover, the mechanism of inheritance seems to be altered methylation of the DNA histones of the male germline, and not alteration of the DNA itself. Females were affected too, but they didn’t have enough data on that experiment (the Ph.D. student that did the work had to graduate sometime…).

Although the authors used higher amounts of pesticides than they suspected back then, in 2005, to be found in the environment, the study still gives pause for thought. After all, it has been 10 years since this paper plus the previous 20 years of use of the stuff. And no, you cannot get rid of it by washing your grapes and vegetables really thoroughly.

Reference: Anway, M. D., Cupp, A. S., Uzumcu, M., & Skinner, M. K. (3 June 2005). Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 308(5727): 1466-1469. DOI:10.1126/science.1108190. Article + Science Cover + FREE PDF

by Neuronicus, 25 September 2015