Rice, Potatoes, Wheat, and Other Plants Interfere with Human Gene Expression

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miRNA-serum-comparison

Context of questionable relevance

It was exactly one year ago today that I first uttered the phrase, “paleo is a logical framework applied to modern humans, not a historical reenactment.” That idea seemed pretty straightforward to me, and it was well-received to the point of being quoted in a real life book (you should buy it, but not just for that reason). And sure, Robb and Andy misattributed it to somebody else in a podcast in the distant past, but I already forgave them for that. So here I am, still beating the drum of the paleo framework despite internal and external attempts to refute it, supersede it, minimize it, water it down, or exact (Exacto?) its death by a thousand cuts. Well folks, it still works. But really, this should come as no surprise…

“This guy is irritatingly correct, time and time again, even when he has limited evidence.” – E. O. Wilson on Charles Darwin

Maybe the blogs I read and the people I talk and listen to aren’t representative of the paleo community, and maybe I’m just imagining things, but the paleo zeitgeist has seemed rather buddy buddy with the white devils of late. Of course, I refer here to rice and the [non-sweet] potato. Support seems to come along the lines of, “potatoes/rice are starches. starch is good for you. therefore potatoes/rice are good for you”; “sure, raw potatoes/rice might have saponins or glycoalkaloids or lectins or phytates, but those compounds aren’t always bad, and they’re destroyed by cooking anyway”‘; “sure, rice is a grain, but what about population X and population Y who eat rice and don’t drop dead from these supposedly ‘toxic’ substances”; and commonly included with one of the first two, “I love potatoes/rice” or “potatoes/rice are good”. Even setting aside the restless and ubiquitous specter of The Self-Justification Diet™, there are significant problems with these arguments. I’m not going to deconstruct them at length here, but suffice it to say that they’re all logical fallacies of one stripe or another.

Even if I convince you that the individual arguments are flawed, the endeavor still wouldn’t tell you the paleo framework was correct or useful. So rather than that, I’ll introduce recent research that those looking at things from a microscopic perspective have been missing all along. Not surprisingly, the research demonstrates proximate effects that were effectively predictable with the paleo framework.

The two relevant components of the basic paleo framework are:

  1. Humans are probabilistically less likely to be adapted to foods introduced more recently into the human diet. This applies to the potato, which is indigenous to South America, and was not available to humans in Africa, Asia, Europe, Australia, or myriad island populations, until the Spanish brought them back to Europe in the late 16th century. All of those populations have been consuming potatoes for only 300-400 (I’m being generous with that second number) years.
  2. Because they can’t run away or fight back like animals, many plants have evolved chemical defense mechanisms. Because the ultimate goal of evolution is reproduction, and not survival, we can predict that chemical defense mechanisms are likely to be concentrated in the reproductive parts of plants. In many cases, this is the seed. Rice is a seed of a plant, and is therefore probabilistically likely to have chemical defense mechanisms.
Let the post-lectin, post-saponin, post-glycoalkaloid, post-metabolic syndrome, post-phytate era of paleo begin…

The Meat

Why miRNAs are important

As a wise man once said, “Reprogram your genes for effortless weight loss, vibrant health, and boundless energy.” Without delving into genetics, let’s just agree that gene expression is a proven concept. Roughly, your genome consists of a lot of conditional statements that result in the production of proteins which have wildly varied effects. Our genetic code is shaped by the environment in which we evolved. By matching the inputs of our environment to the conditions ‘expected’ by our genes, we may optimize the expression of our genes. Please know that this is a vast oversimplification, but is useful for thinking about our individual health and well-being.

For now, let’s just say that RNA relates to gene expression, and miRNA is short for “micro RNA”, which is just a subset of RNA.

“…the rapidly developing new field of miRNA, which plays an important role in modulating virtually all biological processes (e.g., cell proliferation, development, differentiation, adhesion, migration, interaction, and apoptosis) through its fine tuning of gene regulation.” (Sun, et al. 2010)

miRNAs have been widely shown to modulate various critical biological processes, including differentiation, apoptosis, proliferation, the immune response, and the maintenance of cell and tissue identity. Dysregulation of miRNAs has been linked to cancer and other diseases.” (Zhang, et al. 2011)

 The study

This study was recently published in the journal Nature (September 2011). It contains novel findings that miRNA from plants remains stable after cooking and digestion by humans. This plant miRNA has been found in significant quantities in human blood and tissue. Further, it has been demonstrated to interfere with human miRNA by mimicking it and binding to the receptors, then influencing gene expression in ways different from the miRNA produced naturally by our bodies.

Unless otherwise noted, all following quotations refer to Zhang, et al. 2011. Emphasis has been added by me.

 Abstract
Our previous studies have demonstrated that stable microRNAs (miRNAs) in mammalian serum and plasma are actively secreted from tissues and cells and can serve as a novel class of biomarkers for diseases, and act as signaling molecules in intercellular communication. Here, we report the surprising finding that exogenous plant miRNAs are present in the sera and tissues of various animals and that these exogenous plant miRNAs are primarily acquired orally, through food intake. MIR168a is abundant in rice and is one of the most highly enriched exogenous plant miRNAs in the sera of Chinese subjects. Functional studies in vitro and in vivo demonstrated that MIR168a could bind to the human/mouse low-density lipoprotein receptor adapter protein 1 (LDLRAP1) mRNA, inhibit LDLRAP1 expression in liver, and consequently decrease LDL removal from mouse plasma. These findings demonstrate that exogenous plant miRNAs in food can regulate the expression of target genes in mammals.

This wasn’t a gender thing:

” Upon investigation of the global miRNA expression profile in human serum, we found that exogenous plant miRNAs were consistently present in the serum of healthy… men and women.”

This effect was not tiny. Significant amounts of plant miRNA were found in humans:

the tested plant miRNAs were clearly present in sera from humans, mice, and calves… when compared to the endogenous mammalian miRNAs known to be stably present in animal serum, these plant miRNAs were relatively lower, but in a similar concentration range.”

The following quote demonstrates that not all plant miRNA is digested. Some is digested more than others, and some is not digested at all:

“the levels of MIR168a and MIR156a, the two plant miRNAs with the highest levels in the sera of [human] subjects, and MIR166a, a plant miRNA with modest level, were assessed… MIR161, whose expression level was undetectable, served as a negative control.”

The three plant miRNAs found were present in different levels in different plants. Note that cooking influenced the miRNA content differently by specific miRNA and by plant. While levels in rice decreased dramatically with cooking, levels in wheat increased with cooking. After cooking, all MIR156a levels remained significantly high.

It is worth noting that these three plant miRNAs, MIR168a, MIR156a, and MIR166a, were detected in [rice and] other foods, including Chinese cabbage (Brassica rapa pekinensis), wheat (Triticum aestivum), and potato (Solanum tuberosum).

“Interestingly, plant miRNAs were stable in cooked foods.”

It is important to note the following context. Much of the study was centered around MIR168a in rice. This was not because rice or MIR168a have better or worse effects in humans, but because the effect of each miRNA across each gene locus is unknown at this time. The effects of MIR156a are unknown, so we cannot draw the same conclusions about wheat or potatoes as we can about rice. It is known that plant miRNAs have a tendency to interfere with gene expression, but that precise expression remains a question as large as the numbers of gene expressions that can be interfered with against the number or miRNAs we might ingest from all over the plant kingdom.

“most plant miRNAs can act like RNA interference… [W]e performed bioinformatic analysis to identify any sequences in the human, mouse, or rat genome with perfect or near-perfect match to MIR168a. Approximately 50 putative target genes were identified as the target genes of MIR168a”

This known mechanism is why this study focused on MIR168a and rice:

“LDL is the major cholesterol-carrying lipoprotein of human plasma and plays an essential role in the pathogenesis of atherosclerosis. Downregulation of LDLRAP1 in the liver causes decreased endocytosis of LDL by liver cells and impairs the removal of LDL from plasma… Concomitant with a significant elevation in MIR168a levels in the livers of mice after 1 day of fresh rice feeding , LDLRAP1 expression dramatically decreased in the group of fresh rice-fed mice. In these experiments… LDL levels in mouse plasma were significantly elevated on days 3 and 7 after fresh rice feeding… the level of liver LDLRAP1 was not related to the levels of plasma cholesterol or triglycerides… the elevation of fresh rice-derived MIR168a… specifically decreased liver LDLRAP1 expression and thus caused an elevated LDL level in… plasma.”

Plant miRNAs mimic endogenous mammalian miRNA, bind to their receptors, and inhibit protein expression:

“Plant miRNAs execute their function in mammalian cells… in a fashion of mammalian miRNA…the results that MIR168a was also able to target the artificially expressed LDLRAP1 protein in 293T cells (Figure 3I-3K) strongly demonstrate that plant MIR168a could bind to its binding site located in exon 4 of mammalian LDLRAP1 gene, and then inhibit LDLRAP1 protein expression.”

Why the focus on disruptive plant foods, and not animal foods?

This was one of the biggest questions I had before and after reading the study. Unless I missed it, no specific mention is made of what happens when humans or other mammals ingest mammalian miRNA. This leaves the question open as to the scope of miRNA influence we may obtain through food. Upon closer examination, I did find one point of entry into further inquiry on this question. It seems that there is a difference across the board between mammalian miRNA and plant miRNA. This does not mean that all plants are bad to eat or that all mammals are good to eat. Nor does it mean that all plants are good to eat or that all mammals are bad to eat. It’s likely still true that there is no such thing as food and that everything we might ingest simply exists on a multi-dimensional spectrum of healthful to toxic.

“Plant miRNAs are 2′-O-methyl modified on their terminal nucleotide, which renders them resistant to periodate. In contrast, mammalian miRNAs with free 2′ and 3′ hydroxyls are sensitive to periodate… Indeed, as shown in Figure 1E, most mammalian miRNAs in human serum, such as miR-423-5p, miR-320a, miR-483-5p, miR-16, and miR-221, had an unmodified 2′, 3′ hydroxyls and were therefore oxidized… In contrast, MIR156a, MIR168a, and MIR166a in human serum remained unchanged…”

Whether mammalian miRNAs found in human serum were exogenous or endogenous is not specified. If we knew that they were exogenous, and they were oxidized, we would have a significant difference in mechanism between plant and mammal miRNA. If we assume that the mammalian miRNAs mentioned are all endogenous, we can still see a significant difference, but the question remains open as to whether ingested mammalian miRNAs remain stable after ingestion, are oxidized in the digestion process, or are metabolized via another mechanism.

Still a lot of unknowns

At this point, we can’t definitively say a lot about the effects of plant miRNAs (or mammalian for that matter). Is it possible that the cooking-stable, digestion-stable MIR168a found in rice is the only plant miRNA that interferes with human gene expression? Sure. But is that probable? Nope.

Is it possible that there is an unknown benefit to gene expressions altered by miRNA? Sure. From an evolutionary standpoint, it’s possible that humans have adapted to use plant miRNAs as a cellular signaling mechanism to activate conditional clauses wherein different genes are expressed in order to optimize phenotypic adaptation to a plant-rich environment. What is the probability of this? It is not improbable that an organism would adapt to such a signaling mechanism given sufficient evolutionary pressure, genetic variance, and time. However, there are issues with this line of reasoning. First, in non-agricultural phases of human evolution, the plants would be engaged in an evolutionary arms race to continue to evolve their chemical defense mechanisms as humans adapted to them. Second, it currently appears that this effect does not exert acute deleterious effects on individual humans that would effect survival and reproduction enough to provide significantly strong selection pressure. Third, while time is less important than selection pressure in evolution, it remains true that a few hundred years is indeed very short in evolutionary time, and this period of time is not unknown to history. Had this sort of selection taken place, we wouldn’t have stories of the Irish potato famine (too few calories), we’d have stories of the Irish potato poisoning, in which thousands upon thousands would have died from eating potatoes (too many toxins).

There are many other unknowns. Perhaps you’ll share some in the comments.

Commonly questioned practices this study got right

 

There are often complaints that studies on mice cannot be extrapolated to humans. This can be a fair criticism, but is not likely to be used to mount a successful challenge to this study. Wherever ethically acceptable, humans were tested.

In particular, actual human blood and tissue samples were taken. These samples convincingly demonstrated the presence of plant miRNA in human blood and tissue in levels relatively equal to miRNA produced naturally by humans.

Further, these levels were compared against mice and calves. An example of the data is shown to the left. Note that the mice tended to demonstrate the lowest relative levels of miRNA. Humans represent the highest levels for the most relevant miRNA. Therefore, it is more reasonable to expect the effects measured in mice would be more pronounced in humans if we could control humans’ diets enough to conduct this experiment.

What conventional medicine should be saying about this study

It seems pretty simple: Rice elevates MIR168a in humans. Elevated MIR168a impairs the liver’s removal of LDL, or “bad cholesterol”. Increased LDL cholesterol causes atherosclerosis which leads to cardiovascular disease. Rice increases LDL cholesterol, and therefore, eating rice causes cardiovascular disease.
Now, I don’t completely buy into this narrative — particularly because there’s no mention of LDL particle size in this study. However, this article was published in Nature, one of the most prestigious journals on the planet, and there’s no uproar. If this study had concluded that eating red meat interferes with the liver in a way that raises “bad cholesterol”, would it not be the cover story everywhere?

How this study might fit with a paleo diet framework.

It’s hard to say anything definitive about this study beyond the convincing proof that rice miRNAs interfere with human gene expression. That said, we can use the paleo framework to make some predictions. We can predict that miRNAs that are evolutionarily novel are more likely to be deleterious to human health than beneficial. We can also suppose that even if the bulk of miRNAs are deleterious to humans, there may be a minority that are beneficial to most humans, and a few might be beneficial to humans with particular alleles.

The view that known individual components are not always harmful, and therefore shouldn’t be totally avoided, still leaves big gaps in our knowledge, and makes our daily decisions about what to eat susceptible to the undiscovered.
Paleo is bigger than lectins and phytates and saponins.

We’ve been presented with many past arguments about rice and potatoes being fine, but too high in carbohydrates to recommend for everyone.
The paleo framework is bigger than metabolic syndrome.

The more we learn about wheat, the more nefarious compounds we find.
Paleo is bigger than gluten free.

Although I personally think bok choy sucks based on taste, I never had a health reason for disliking it…
Paleo doesn’t know everything.

Potatoes and rice, still not paleo.

What I’m doing differently in light of this study

  • Less likely to deviate from sashimi at sushi restaurants.
  • Downgrading potatoes and rice from “neutral nutrient-poor waste of time” to “sneaky untrustworthy bastards”.
  • Downgrading wheat from “probably a bad idea for everyone” to “all the shitty stuff about wheat plus the shitty stuff about soy”.
  • Downgrading bok choy from “Hey, I’m not going to eat this, would you like it?” to “I’m not making out with you if you eat that”.

What I’m doing the same in light of this study

  • Preferentially consuming animal foods.
  • Scaling carbohydrate/starches daily in relation to activity levels
  • Eating carrots and sweet potatoes when I want to ingest subterranean plant storage organs (because orange is sexier than white).
  • Remaining skeptical of the applicability of populations isolated by geography like islands (Kitavans) and other extremes (Inuit) to humans in general.
  • Aping Darwin while recognizing that Science™ provides us with limited evidence for us to use in our everyday lives, yet trying to be irritatingly correct anyway.

<sarcasm>Eat your vegetables folks, particularly if you want your gene expression impaired by the plant kingdom.</sarcasm>
Final thought: Think like a geek. Eat like a hunter. Train like a fighter. Look like a model. (Play and live like you don’t live in a zoo is always implied)

References
Sun, W., Julie Li, Y.-S., Huang, H.-D., Shyy, J. Y.-J., & Chien, S. (2010). microRNA: A Master Regulator of Cellular Processes for Bioengineering Systems. Annual review of biomedical engineering, 12, 1-27. [full-text PDF]

Zhang, L., Hou, D., Chen, X., Li, D., Zhu, L., Zhang, Y., Li, J., et al. (2011). Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research, 1-20