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Chrupek et al CMJ 2012

  • MUSE - Science museum, Trento, Italy
Małgorzata Chrupek1, Helena Siipi2, Lucia
1University of Rzeszów, Faculty of Biotechnology,
Kolbuszowa, Poland
2University of Turku, Department of
Behavioural Sciences and Philosophy, Turku, Finland
3Museo delle scienze, Trento, Italy
Bio-objects as “boundary
crawlers:” the case of
Abstract microRNAs (miRNAs), short RNAs of 21-25 nu-
cleotides, are implied in gene expression and regulation,
in biological processes and in human pathologies includ-
ing cancer. Since miRNAs of plant origin can survive diges-
tion and cooking and enter in animal (including human)
sera and tissues, their intervention in mammalian gene
expression and regulation might be expected. Mouse ex-
perimental feeding, in fact, showed that a miRNA class (MI-
R168a) is involved in accumulation of the low-density li-
poprotein (LDL), the major cholesterol-carrying lipoprotein
of human plasma. Considering LDL’s role in atherosclerosis,
a negative inuence of miRNAs from food origin on our
health may be expected. Here we concentrate on the miR-
NAs’ capability to cross inter-kingdom boundaries through
the diet and acting as a “boundary crawler. The boundary
between plant and human is presented under a new per-
spective, where a new intimate relationship between two
genomes – mammalian and plant – belonging to quite dif-
ferent kingdoms is proposed. The food’s role as molecule
carrier in our health is also discussed. miRNAs, nally, are
presented as an example of “bio-objects” with impact on
both medical and cultural issues.
In this essay in a series of articles from “Bio-Objects” re-
search network supported by the Cooperation in Science
and Technology (COST) program (1), we present an ex-
ample of a bio-object: microRNAs (miRNAs). They belong
to a nucleic acid category, ie, organic molecules, objects
conventionally considered as non-living material, which
nevertheless we would here regard as extraordinary candi-
dates to t into the bio-objects’ group according to some
key features we attribute to bio-objects.
miRNAs have been recently detected in eukaryotic cells.
They raised the attention of the scientic community and
media, following the discovery that miRNAs of plant ori-
gin, introduced with the diet, have been found in the sera
and tissues of various animals, including humans. Experi-
ments of mouse feeding and an in vitro test that mimics
the gastrointestinal tract environment proved that the
food-derived plant miRNAs can pass through gastrointes-
tinal tract and enter the circulation and organs. Moreover,
food-derived mature plant miRNAs proved to be resistant
to cooking and digestion and quite stable in the mamma-
lian serum, blood, and tissues (2).
In this text, the meaning of this discovery will be discussed
in the framework of the concept of “bio-object character
and the feature of “boundary crawlers.
miRNAs are a family of short RNA organic molecules com-
posed of a number of nucleotides ranging from 21 to 25.
First discovered around 20 years ago in the nematode
Caenorhabditis elegans, many short RNAs were thereafter
isolated and nowadays thousands have been identied by
random cloning and computational prediction (3). In the
early 2000, miRNAs were shown to modulate gene ex-
pression at post-transcriptional level by binding to mes-
senger RNA (4). Since then, multiple roles in negative
as well as positive regulation of genes have been
doi: 10.3325/cmj.2012.53.285
286 Croat Med J. 2012;53:285-8
shown, proving miRNAs’ function in most biological pro-
cesses such as cell growth, development, and dierentia-
In plants, miRNAs have been found to play key functions
in organ development, such as leaf morphogenesis, oral
organ identity, and root development. They seem to be
involved in various stress responses, such as dehydration,
mineral-nutrient, and even mechanical stress (5). Recently,
miRNA-based methods of gene silencing have been devel-
oped as an important tool for the study of gene function in
plants and crop genetic improvement.
In humans, aberrant miRNAs’ expression is related to vari-
ous diseases such as heart disease, primary muscular disor-
ders, chronic hepatitis, AIDS, polycythemia vera, psoriasis,
diabetes, obesity, schizophrenia, fragile-X mental retarda-
tion, and Tourette’s syndrome, as reported in the Human
MicroRNA Disease Database (6). In oncology, miRNAs
proved to be down-regulated in breast, lung, and colon
cancer, and up-regulated in Burkitt’s and other human B-
cell lymphomas (7).
Human miRNAs can be used as highly useful biomark-
ers, especially for future cancer diagnostics. They rapidly
emerge as attractive targets for disease intervention, and
miRNA-based therapies are under investigation. Con-
straints of these therapies seem to be, however, low miR-
NAs’ in vivo stability since they can be degraded by endog-
enous RNases, and quick elimination via kidney ltration
due to their small molecular mass. Therefore, enhance-
ment of stability and eective delivery strategies are im-
portant goals for successful miRNA-mediated gene silenc-
ing in medicine. An important step further was a recent
discovery that microvesicles can be carriers of circulating
miRNAs, which improves miRNA’s stability (2).
Immune-related miRNAs were found in human breast milk
and proved to be stable. Accordingly, they might be trans-
ferred from the mother’s milk to the infant via the digestive
tract, thus playing a critical role in the development of the
infant immune system (8).
During research aiming at studying the function of cir-
culating miRNAs in pathology, miRNAs of rice have been
surprisingly detected in the serum and plasma of human
and animals and the majority of these have been found in
microvesicles. miRNA’s origin was easily conrmed with
specics tests (2). Because of their property to act as
gene regulators, further research was conducted to
clarify whether exogenous diet-derived miRNAs of plant
origin accumulated in mammalian blood and tissues were
capable to regulate gene expression of mammalians.
It was observed that in mouse, during experimental feed-
ing, the concentration of a specic miRNAclass, MIR168a,
varied depending on the quantity of rice dispensed. More-
over, in 31 healthy humans, the presence of nearly 30
types of miRNAs of plant origin was found (2). Finally, se-
quence database analysis showed the complementarity of
MIR168a with nearly 50 mammalian genes, of which the
most highly conserved sequence of a putative binding site
is located in exon 4 of the “low-density lipoprotein recep-
tor adapter protein 1” (LDLRAP1). It has been found that
MIR168a binds to LDLRAP1 and in the liver causes a de-
creased endocytosis of the low-density lipoprotein (LDL),
which subsequently remains in the plasma. LDL is the ma-
jor cholesterol-carrying lipoprotein of human plasma and
it has the crucial role in the pathogenesis of atherosclero-
sis. Therefore, this result indicates possible negative inu-
ence of miRNA from the food on our health (2).
This is just an example of miRNAs’ gene modulation. As
dierent miRNAs can act with dierent genes it could be
possible that they have positive or/and negative eects
on our health. So, it might be expected that other miR-
NAs with possible benecial eects would be further de-
Concerning human health, agro-food innovation, and
possible application in nutrition, we believe that miRNAs
may be attributed to the bio-object class. They have, in
fact, crucial features of the bio-objects, ie, they are biologi-
cal products potentially useful for enhancing human life
quality and because of their ability to move across dier-
ent domains they are not stable entities (“boundary crawl-
ers”) (9). They are balancing on the ne line between “natu-
ral” and “non-natural”/”articial.” If evidence of transferring
from mother to infant via breast milk would be provided,
their capability of crossing individual/individual boundary
would also be shown. Moreover their very special feature
is the ability to cross plant-mammalian boundaries as here
Plant-mammalian boundary
The capability of plant miRNAs to regulate mammalian
genes, thus to cross inter-kingdom boundaries, allows to
Chrupek et al: Bio-objects as “boundary crawlers:” the case of microRNAs
give to these nucleic acids the attribution of “boundary
crawlers. The term “boundary” has normative and non-
normative senses. In its non-normative sense the term just
refers to something that separates two entities from each
other. However, in many contexts, boundary is also some-
thing that should not be crossed or crossing of which is
somehow extraordinary.
According to our understanding, in academic discussions
it is sensible to distinguish between these two senses of
the term, and in the context of miRNAs merely to use it in
its non-normative sense. The boundary crossings of miR-
NAs may seem extraordinary for us, but it is not because
they are unacceptable or highly uncommon, but because
we have just until recently lacked knowledge of them.
miRNAs question the reality of species barrier and exis-
tence of species and kingdom boundaries as natural kinds.
The concept of natural kinds can be better expressed with
the words by Bird and Tobin (10): To say that a kind is natu-
ral is to say that it corresponds to a grouping or ordering
that does not depend on humans. We tend to assume that
science is successful in revealing these kinds; it is a corol-
lary of scientic realism that when all goes well the classi-
cations and taxonomies employed by science correspond
to the real kinds in nature.
Plant miRNA may enter into our body by food intake, may
resist digestion, and may regulate genes. As a result, just
through a “natural action” like eating (thus dierently from
technical interventions such as for instance gene therapy
which needs sophisticated equipment), a piece of genetic
information from plant origin is delivered into the animal/
human organism and is able to regulate our gene expres-
sion with the nal result to inuence our health. According-
ly, we may see the boundary/relationship between plant
and human/animal from a new perspective, by perceiving a
new intimate relationship between two genomes – mam-
malian and plant – belonging to quite dierent kingdoms.
It has been already accepted, in fact, that diet may change
our health, but it has never been shown in a “direct route.
Another nucleic acid group, the xeno-nucleic acids (XNA)
are the polymers constructed in laboratory and not found
in nature. They are able to store and process genetic infor-
mation like their “natural” DNA and RNA counterparts (11).
We believe it is intuitive perceiving their bio-object quality
on the basis of their human technological origin as well as
on their ability to balance on the boundary between “natu-
ral” and “articial.
This is also the case for articial miRNAs (amiRNAs), which
are designed to target one or several genes of interest and
provide a new and highly specic approach for eective
gene silencing in plants. The miRNAs are a sort of pecu-
liar bio-objects which could be considered as “natural,” as
they were discovered in living organisms, but also “arti-
cial” since they have a synthetic counterpart (amiRNA).
Thus, miRNAs seem to be natural when they come from
food, but non-natural when they are managed via articial
vectors. Additionally, when constructed miRNA (amiRNA)
shares all of the properties with another miRNA that has
come into being through natural processes, should we not
consider the rst one as “natural” with respect to its proper-
ties and “non-natural” with respect to its origin?
If one accepts the view that naturalness is not merely a
question of origin, but may also refer to properties and re-
lations (12), amiRNAs might also be considered “natural”
and parts of the living beings.
If further research conrms a role of dierent quali-quan-
titative content of miRNAs in the various foodstus in our
“health-and/or-disease-status,” a new rationale for recog-
nizing the relevance of the diet in our lives will be provid-
ed. This fact should enrich these molecules with one of the
most relevant features we recognize to bio-objects, ie, the
bio-social implication.
Besides availability and control of food resources, in fact,
quality and style of diet are relevant topics in our sated soci-
ety. Incorrect diet habits and food disorders are recognized
as notable social problems. Accordingly, nutrition research
shifted from epidemiology and physiology to molecular bi-
ology and genetics as exemplied by the recent progress of
nutrigenomics (13). This latter discipline aims at providing
people with methods and tools for disease prevention and
health promotion by foods that match the lifestyles, cul-
tures, and genetics, on the basis of personalized dietary rec-
ommendation. In addition to nutriogeneomics, so-called
functional food (which might in future also contain miR-
NAs) blurs a distinction between food and medicine.
On the other hand, the notion that to be t and healthy
we need to eat “good” food is a very ancient argument
of physicians of both Occidental and Far Eastern
288 Croat Med J. 2012;53:285-8
medical cultures. Among them, worth remembering are
the dictum, “Our food should be our medicine” by Hip-
pokrates of Kos four centuries BCE and the relevance of
diet in the classical texts of Chinese traditional medicine
starting with Huang Di Nei Jing, two centuries BCE. Cultur-
al, ethical, social, subjective, and psychic implications have
also been recognized to food by Herodotus, ve centuries
BCE, who in The Histories characterized peoples through
their food behavior, and by other luminaries, among them
Ludwig Andreas Feuerbach (1850) with his famous expres-
sion, “der Mensch ist was er isst” (in English “Man is what he
eats”). Food that one eats is today often an integral part
of one’s identity and lifestyle. Religions and cultures set
certain limits to diets of their members, but people also
build their identity on lifestyle choices regarding food. One
may consider himself as a vegan, member of the slow food
movement etc. As already pointed out (14), food choice is
a basic form of self-creating, self-expression, and self-de-
nition. With ndings regarding miRNAs, this view may be
further strengthened to concern not only mental but also
the physical self.
In conclusion, being a bio-object on the borders between
natural/non-natural and plant/animal, crossing dierent
domains, and carrying bio-social implications, miRNAs can
be considered as another example of the impact of life sci-
ence innovation with potential in both medical and cul-
tural issues.
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ResearchGate has not been able to resolve any citations for this publication.
Full-text available
Thus far, the moral debateconcerning genetically modified foods (GMF) hasfocused on extrinsic consequentialist questionsabout the health effects, environmental impacts,and economic benefits of such foods. Thisextrinsic approach to the morality of GMF isdependent on unsubstantiated empirical claimsand fails to account for the intrinsic moralvalue of food and food choice and theirconnection to the agent's concept of the goodlife. I develop a set of objections to GMFgrounded in the concept of integrity andmaintain that food and food choice can beintimately connected to the agent's personalintegrity. I argue that due to the constitutionof GMF and the manner in which they areproduced, such foods are incompatible with thefundamental values and integrity of certainindividual moral agents or groups. I identifythree types of integrity that are threatened byGMF: religious, consumer, and integrity basedon certain other moral or metaphysical grounds.I maintain that these types of integrity aresufficiently important to provide justificationfor political and societal actions to protectthe interests of those affected. I conclude byproposing specific steps for handling GMFconsistent with the moral principles ofinformed consent, non-maleficence, and respectfor the integrity of all members of society.They include mandatory labeling of GMF, theimplementation of a system for control andregulations concerning such foods, andguaranteed provision of conventional foods.
Full-text available
Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.
Full-text available
Breast milk is a complex liquid rich in immunological components that affect the development of the infant's immune system. Exosomes are membranous vesicles of endocytic origin that are found in various body fluids and that can mediate intercellular communication. MicroRNAs (miRNAs), a well-defined group of non-coding small RNAs, are packaged inside exosomes in human breast milk. Here, we identified 602 unique miRNAs originating from 452 miRNA precursors (pre-miRNAs) in human breast milk exosomes using deep sequencing technology. We found that, out of 87 well-characterized immune-related pre-miRNAs, 59 (67.82%) are presented and enriched in breast milk exosomes (P < 10(-16), χ(2) test). In addition, compared with exogenous synthetic miRNAs, these endogenous immune-related miRNAs are more resistant to relatively harsh conditions. It is, therefore, tempting to speculate that these exosomal miRNAs are transferred from the mother's milk to the infant via the digestive tract, and that they play a critical role in the development of the infant immune system.
Full-text available
This short text is the second in a series of articles from the recently established “Bio-Objects” research network supported by the European Commission’s Cooperation in Science and Technology (COST) program (1). Here we explore in more detail the ways in which we understand the boundaries of bio-objects determined through a “bio-objectification” process wherein life-forms or living entities are first made into objects, become possible, through scientific labor and its associated technologies, and then come to be attributed with specific identities. This move from living entity, through bio-objectification to what we can call “bio-identification” helps us to understand the contested, often controversial process seen in the biological sciences (and not merely in biomedicine, but elsewhere, such as in agriculture and food research) where we see a new mixture of relations to life or to which “life” is attributed, such as animal-human hybrids, chimera, genetically modified organisms, or transgenics. As a consequence of these novel relations, the boundaries between human and animal, organic and nonorganic, living and the suspension of living (and the meaning of death itself), are often questioned and destabilized, and their identities have to be negotiated and (temporarily) stabilized, and so given an identity. What is common to what we call bio-objects, is that they all in various ways challenge conventional cultural, scientific, and institutional orderings and classifications.
Full-text available
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.
Nature Reviews Genetics 5, 522–531 (2004)In figure 2, the orientation of some RNA structures was incorrect. The corrected version is shown below.
MicroRNAs (miRNAs) are endogenous approximate 22 nucleotide small RNAs that play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Past few years have witnessed an explosive increase in research reports on plant miRNAs. To date, more than 700 miRNAs have been identified with cloning methods or computational approaches from a variety of plants. Large numbers of miRNA targets were predicted, some of which were validated or confirmed experimentally. In addition to their important functions in organ development such as leaf morphogenesis, floral organ identity and root development, plant miRNAs also function in feedback regulation in small RNA pathway and in directing some siRNAs biogenesis. Moreover, they are involved in various stress responses, such as oxidative, mineral-nutrient, dehydration stress and even mechanical stress. However, the unexpected new data about miRNAs imply that we just make the first step in the small RNA world.
We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice. Of the 49 predicted targets, 34 are members of transcription factor gene families involved in developmental patterning or cell differentiation. The near-perfect complementarity between plant miRNAs and their targets suggests that many plant miRNAs act similarly to small interfering RNAs and direct mRNA cleavage. The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages.
Nutrigenomics: goals and perspectives
  • M Muller
  • S Kersten
Muller M, Kersten S. Nutrigenomics: goals and perspectives. Nat Rev Genet. 2003;4:315-22. Medline:12671662